_3dmet:
  biocontext:
    prefix: 3DMET
  comment: Website has been down since 2023/2024
  deprecated: true
  edam:
    description: Identifier of a metabolite from the 3DMET database.
    name: Compound ID (3DMET)
    obsolete: false
    prefix: '2635'
  fairsharing:
    abbreviation: 3DMET
    description: 3DMET is a database of three-dimensional structures of natural metabolites.
    homepage: http://www.3dmet.dna.affrc.go.jp/
    name: Three-Dimensional Structure Database of Natural Metabolites
    prefix: FAIRsharing.5ab0n7
    publications:
    - doi: 10.1021/ci300309k
      pubmed_id: 23293959
      title: 'Three-Dimensional Structure Database of Natural Metabolites (3DMET):
        A Novel Database of Curated 3D Structures.'
    subjects:
    - Life Science
    - Metabolomics
  integbio:
    alt_name: A three-dimensional-structure database of natural metabolites
    description: This database is composed of three-dimensional structures and physical
      properties of natural metabolites, mainly those useful in agriculture (design
      of chemicals used in agriculture, compositional analysis of food). Compounds
      with similar structures and physical properties can be searched through an easy
      interface.
    fairsharing: biodbcore-000465
    homepage: http://www.3dmet.dna.affrc.go.jp/
    information_keywords:
    - 3D structure
    maintainer: NARO (National Agriculture and Food Research Organization)
    name: 3DMET
    prefix: nbdc00351
    status: Inactive
    target_keywords:
    - Metabolite
    - Chemical compound
  mappings:
    biocontext: 3DMET
    edam: '2635'
    fairsharing: FAIRsharing.5ab0n7
    integbio: nbdc00351
    miriam: 3dmet
    n2t: 3dmet
    prefixcommons: 3dmet
    wikidata: P2796
  miriam:
    deprecated: true
    description: 3DMET is a database collecting three-dimensional structures of natural
      metabolites.
    homepage: http://www.3dmet.dna.affrc.go.jp/
    id: '00000066'
    name: 3DMET
    namespaceEmbeddedInLui: false
    pattern: ^B\d{5}$
    prefix: 3dmet
    sampleId: B00162
    uri_format: http://www.3dmet.dna.affrc.go.jp/cgi/show_data.php?acc=$1
  n2t:
    description: 3DMET is a database collecting three-dimensional structures of natural
      metabolites.
    example: B00162
    homepage: http://www.3dmet.dna.affrc.go.jp/
    name: 3DMET database
    namespaceEmbeddedInLui: false
    pattern: ^B\d{5}$
    prefix: 3dmet
    uri_format: http://www.3dmet.dna.affrc.go.jp/cgi/show_data.php?acc=$1
  name: 3D Metabolites
  prefix: _3dmet
  prefixcommons:
    description: 3DMET is a database of three-dimensional structures of natural metabolites.
    example: B00162
    homepage: http://www.3dmet.dna.affrc.go.jp
    keywords:
    - chemical
    - metabolite
    - structure
    miriam: 3dmet
    name: Three-Dimensional Structure Database of Natural Metabolites
    pattern: ^B\d{5}$
    prefix: 3dmet
    pubmed_ids:
    - '23293959'
    - '29892514'
  publications:
  - doi: 10.2142/biophysico.15.0_87
    pmc: PMC5992871
    pubmed: '29892514'
    title: 'Chemical curation to improve data accuracy: recent development of the
      3DMET database'
    year: 2018
  - doi: 10.1021/ci300309k
    pmc: null
    pubmed: '23293959'
    title: 'Three-dimensional structure database of natural metabolites (3DMET): a
      novel database of curated 3D structures'
    year: 2013
  synonyms:
  - 3dmet
  wikidata:
    description: identifier of chemical compounds in 3DMet database
    example:
    - B01253
    - B01305
    name: 3DMet ID
    pattern: ^B\d{5}$
    prefix: P2796
    uri_format: http://www.3dmet.dna.affrc.go.jp/cgi/show_data.php?acc=$1
_4dn.biosource:
  cellosaurus:
    category: Biological sample resources
    homepage: https://data.4dnucleome.org/
    name: 4D Nucleome Data Portal
    prefix: 4DN
    uri_format: https://data.4dnucleome.org/biosources/$1
  contact:
    email: Job.Dekker@umassmed.edu
    github: null
    name: Job Dekker
    orcid: 0000-0001-5631-0698
  example: 4DNSR73BT2A2
  fairsharing:
    abbreviation: 4DN
    description: The 4D Nucleome Data Portal (4DN) hosts data generated by the 4DN
      Network and other reference nucleomics data sets, and an expanding tool set
      for open data processing and visualization. It is a platform to search, visualize,
      and download nucleomics data.
    homepage: https://data.4dnucleome.org/
    name: 4DNucleome Data Portal
    prefix: FAIRsharing.CugtbQ
    publications:
    - doi: 10.1038/nature23884
      pubmed_id: 28905911
      title: The 4D nucleome project.
    subjects:
    - Life Science
    twitter: 4dn_dcic
  homepage: https://data.4dnucleome.org/biosources
  mappings:
    cellosaurus: 4DN
    fairsharing: FAIRsharing.CugtbQ
    miriam: 4dn
    prefixcommons: 4dn
    wikidata.entity: Q110613621
  miriam:
    deprecated: false
    description: The 4D Nucleome Data Portal hosts data generated by the 4DN Network
      and other reference nucleomics data sets. The 4D Nucleome Network aims to understand
      the principles underlying nuclear organization in space and time, the role nuclear
      organization plays in gene expression and cellular function, and how changes
      in nuclear organization affect normal development as well as various diseases.
    homepage: https://data.4dnucleome.org/
    id: 00000833
    name: 4D Nucleome
    namespaceEmbeddedInLui: false
    pattern: ^4DN[A-Z]{2}[A-Z0-9]{7}$
    prefix: 4dn
    sampleId: 4DNES265ETYQ
    uri_format: https://data.4dnucleome.org/$1
  name: 4D Nucleome Data Portal Biosource
  prefix: _4dn.biosource
  prefixcommons:
    description: The 4D Nucleome Data Portal hosts data generated by the 4DN Network
      and other reference nucleomics data sets. The 4D Nucleome Network aims to understand
      the principles underlying nuclear organization in space and time, the role nuclear
      organization plays in gene expression and cellular function, and how changes
      in nuclear organization affect normal development as well as various diseases.
    example: 4DNESBOY2QLJ
    homepage: https://data.4dnucleome.org/
    keywords:
    - DNA
    - protein
    miriam: 4dn
    name: 4D Nucleome
    pattern: ^4DN[A-Z]{2}[A-Z0-9]{7}$
    prefix: 4dn
    pubmed_ids:
    - '28905911'
    uri_format: https://data.4dnucleome.org/$1
  publications:
  - doi: 10.1038/nature23884
    pmc: PMC5617335
    pubmed: '28905911'
    title: The 4D nucleome project
    year: 2017
  synonyms:
  - 4DN
  - 4dn.biosource
  uri_format: https://data.4dnucleome.org/biosources/$1
  wikidata:
    database: Q110613621
_4dn.replicate:
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  contributor_extras:
  - email: laylamichan@ciencias.unam.mx
    github: lmichan
    name: Layla Michán Aguirre
    orcid: 0000-0002-5798-662X
  - email: mineromero2901@ciencias.unam.mx
    github: MinRo60
    name: Minerva María Romero Pérez
    orcid: 0000-0002-6240-9325
  - email: victorinolavida@ciencias.unam.mx
    github: Victorinolavida
    name: José Victorino Ruiz Lavida
    orcid: 0000-0001-5130-7705
  description: Database portal containing replicate experiments of different assays
    and samples
  example: 4DNESWX1J3QU
  homepage: https://data.4dnucleome.org/experiment-set-replicates/
  mappings:
    wikidata.entity: Q110613797
  name: 4D Nucleome Data Portal Experiment Replicate
  prefix: _4dn.replicate
  synonyms:
  - 4dn.replicate
  uri_format: https://data.4dnucleome.org/experiment-set-replicates/$1
  wikidata:
    database: Q110613797
aacdb:
  contact:
    email: hj@uestc.edu.cn
    github: null
    name: Jian Huang
    orcid: 0000-0003-3282-8892
  contributor:
    email: ji.kang@northeastern.edu
    github: kanghosaeyo
    name: Kangho Ji
    orcid: 0009-0009-3402-8013
  description: Identifiers represent antibody-antigen complexes in the Antigen-Antibody
    Complex Database (AACDB), which provides comprehensive structural and functional
    annotations including paratope and epitope information, antibody developability
    data, and antigen-drug target relationships to support immunoinformatics research
    and therapeutic antibody development.
  example: '61'
  github_request_issue: 1727
  homepage: https://i.uestc.edu.cn/AACDB
  keywords:
  - antibody
  - antigen
  - molecular biophysics
  - structural biology
  logo: https://i.uestc.edu.cn/AACDB/images/logo.png
  name: Antibody-Antigen Complex Database
  pattern: ^\d+$
  prefix: aacdb
  publications:
  - doi: 10.7554/elife.104934
    pmc: PMC12097784
    pubmed: '40402563'
    title: A comprehensive antigen-antibody complex database unlocking insights into
      interaction interface
    year: 2025
  reviewer:
    email: b.gyori@northeastern.edu
    github: bgyori
    name: Benjamin M. Gyori
    orcid: 0000-0001-9439-5346
  uri_format: https://i.uestc.edu.cn/AACDB/details.php?id=$1
aaindex:
  contact:
    email: shuichi@hgc.jp
    github: skwsm
    name: Shuichi Kawashima
    orcid: 0000-0001-7883-3756
  contributor_extras:
  - email: sumirp77@gmail.com
    github: sumirp
    name: Sumir H Pandit
    orcid: 0000-0002-1216-4761
  edam:
    description: Identifier of an entry from the AAindex database.
    name: AAindex
    obsolete: false
    prefix: '1128'
  integbio:
    alt_name: Amino acid indices, substitution matrices and pair-wise contact potentials
    description: "The AAindex database collects and organizes amino acid properties.\
      \ Users can search from dozens of studies summarizing multiple biophysical parameters\
      \ for three types of information:\n- AAindex1: Biophysical properties of individual\
      \ amino acids. All indexed studies have been compared to other studies in the\
      \ database and pairwise correlation coefficients between related studies are\
      \ provided. \n- AAindex2: Substitution indices indicating amino acid similarity.\n\
      - AAindex3: Pairwise contact potentials between amino acids in various contexts.\n\
      All three databases can be searched either by study or keyword using DBGET."
    homepage: http://www.genome.jp/aaindex/
    information_keywords:
    - Sequence
    maintainer: Kyoto University Institute for Chemical Research Bioinformatics Center
    name: AAindex
    prefix: nbdc00004
    pubmeds:
    - '17998252'
    - '9847231'
    - '10592278'
    - '3244698'
    - '9053899'
    status: Active
    target_keywords:
    - Protein
  mappings:
    edam: '1128'
    integbio: nbdc00004
    prefixcommons: aaindex
    wikidata.entity: Q85738825
  prefix: aaindex
  prefixcommons:
    description: 'AAindex is a database of numerical indices representing various
      physicochemical and biochemical properties of amino acids and pairs of amino
      acids. AAindex consists of three sections now: AAindex1 for the amino acid index
      of 20 numerical values, AAindex2 for the amino acid mutation matrix and AAindex3
      for the statistical protein contact potentials.'
    example: BUNA790102
    homepage: http://www.genome.ad.jp/aaindex/
    keywords:
    - protein
    name: Amino acid indices, substitution matrices and pair-wise contact potentials
    pattern: ^[A-Z]+\d+$
    prefix: aaindex
    pubmed_ids:
    - '17998252'
    uri_format: http://www.genome.jp/dbget-bin/www_bget?aaindex:$1
  publications:
  - doi: 10.1093/nar/gkm998
    pmc: PMC2238890
    pubmed: '17998252'
    title: 'AAindex: amino acid index database, progress report 2008'
    year: 2007
  references:
  - https://github.com/biopragmatics/bioregistry/pull/1098
  reviewer:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  wikidata:
    database: Q85738825
aao:
  agroportal:
    contact:
      email: cavoc@ml.affrc.go.jp
      name: Akane Takezaki
    description: Agriculture Activity ontology (AAO) is an ontology that describes
      agricultural work using attributes such as purpose, behavior, objective, and
      its attribute values.
    name: Agriculture Activity Ontology
    prefix: AAO
  biocontext:
    prefix: AAO
  description: A structured controlled vocabulary of the anatomy of Amphibians. Note
    that AAO is currently being integrated into Uberon.
  example: 0000138
  fairsharing:
    abbreviation: AAO
    contact:
      email: david.c.blackburn@gmail.com
      name: David Blackburn
      orcid: 0000-0002-1810-9886
    description: A structured controlled vocabulary of the anatomy of Amphibians.
      Note that AAO has been integrated into Uberon.
    homepage: http://bioportal.bioontology.org/ontologies/AAO
    name: Amphibian gross Anatomy Ontology
    prefix: FAIRsharing.mxx5rp
    publications:
    - doi: 10.1186/2041-1480-5-21
      pubmed: '25009735'
      title: Unification of multi-species vertebrate anatomy ontologies for comparative
        biology in Uberon
      year: 2014
    - doi: 10.1142/9789812772435_0035
      title: AN ANATOMICAL ONTOLOGY FOR AMPHIBIANS
      year: 2006
    subjects:
    - Anatomy
  mappings:
    agroportal: AAO
    biocontext: AAO
    fairsharing: FAIRsharing.mxx5rp
    obofoundry: aao
    prefixcommons: aao
    wikidata.entity: Q114677701
  obofoundry:
    contact: david.c.blackburn@gmail.com
    contact.label: David Blackburn
    contact.orcid: 0000-0002-1810-9886
    deprecated: true
    domain: anatomy and development
    homepage: http://github.com/seger/aao
    name: Amphibian gross anatomy
    prefix: aao
  pattern: ^\d{7}$
  prefix: aao
  prefixcommons:
    bioportal: '1090'
    description: The Amphibian Anatomical Ontology (AmphibAnat) is an NSF-sponsored
      project dedicated to constructing semi-automatically a draft ontology of amphibian
      anatomy. In this project, small, subset ontologies are constructed manually,
      and data-mining software (that we develop) is used to mine electronic media
      for instances of concepts and properties to be added to the ontologies.
    example: ASD:0000138
    homepage: http://www.amphibanat.org
    keywords:
    - obo
    - anatomy
    name: Amphibian Anatomical Ontology
    pattern: ^[A-Z]+:\d+$
    prefix: aao
    pubmed_ids:
    - '17992749'
  publications:
  - doi: 10.1186/2041-1480-5-21
    pmc: PMC4089931
    pubmed: '25009735'
    title: Unification of multi-species vertebrate anatomy ontologies for comparative
      biology in Uberon
    year: 2014
  - doi: 10.1142/9789812772435_0035
    pmc: null
    pubmed: '17992749'
    title: An anatomical ontology for amphibians
    year: 2007
  - doi: 10.1186/2041-1480-5-21
    pmc: null
    pubmed: '25009735'
    title: Unification of multi-species vertebrate anatomy ontologies for comparative
      biology in Uberon
    year: 2014
  - doi: 10.1142/9789812772435_0035
    pmc: null
    pubmed: null
    title: AN ANATOMICAL ONTOLOGY FOR AMPHIBIANS
    year: 2006
  - doi: null
    pmc: null
    pubmed: '17992749'
    title: null
    year: null
abcam:
  cellosaurus:
    category: Cell line collections (Providers)
    homepage: https://www.abcam.com/nav/cell-lines-and-lysates
    name: Abcam cell line products
    prefix: Abcam
    uri_format: https://www.abcam.com/$1.html
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  contributor_extras:
  - email: sumirp77@gmail.com
    github: sumirp
    name: Sumir H Pandit
    orcid: 0000-0002-1216-4761
  description: Vendor for assays, cells, and antibodies
  example: ab275461
  homepage: https://www.abcam.com
  mappings:
    cellosaurus: Abcam
    wikidata.entity: Q29123382
  name: Abcam
  prefix: abcam
  references:
  - https://github.com/biopragmatics/bioregistry/pull/1098
  uri_format: https://www.abcam.com/$1.html
  wikidata:
    database: Q29123382
abcd:
  cellosaurus:
    category: Biological sample resources
    homepage: https://web.expasy.org/abcd/
    name: AntiBodies Chemically Defined database
    prefix: ABCD
    uri_format: https://web.expasy.org/abcd/$1
  contact:
    email: Pierre.Cosson@unige.ch
    github: null
    name: Pierre Cosson
    orcid: 0000-0002-4881-0358
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  contributor_extras:
  - email: sumirp77@gmail.com
    github: sumirp
    name: Sumir H Pandit
    orcid: 0000-0002-1216-4761
  description: The ABCD (AntiBodies Chemically Defined) database is a manually curated
    depository of sequenced antibodies
  example: AD834
  fairsharing:
    abbreviation: ABCD
    description: The ABCD (AntiBodies Chemically Defined) database is a manually curated
      depository of sequenced antibodies.
    homepage: https://web.expasy.org/abcd/
    name: ABCD database
    prefix: FAIRsharing.Z8OKi5
    publications:
    - doi: 10.1093/nar/gkz714
      pubmed_id: 31410491
      title: 'The ABCD database: a repository for chemically defined antibodies.'
    subjects:
    - Molecular biology
    - Immunology
  homepage: https://web.expasy.org/abcd/
  mappings:
    cellosaurus: ABCD
    fairsharing: FAIRsharing.Z8OKi5
    uniprot: DB-0236
    wikidata.entity: Q110998933
  name: AntiBodies Chemically Defined database
  prefix: abcd
  publications:
  - doi: 10.1093/nar/gkz714
    pmc: PMC6943046
    pubmed: '31410491'
    title: 'The ABCD database: a repository for chemically defined antibodies'
    year: 2020
  - doi: 10.1093/nar/gkz714
    pmc: null
    pubmed: null
    title: 'The ABCD database: a repository for chemically defined antibodies.'
    year: null
  references:
  - https://github.com/biopragmatics/bioregistry/pull/1098
  uniprot:
    abbreviation: ABCD
    category: Protocols and materials databases
    homepage: https://web.expasy.org/abcd
    name: ABCD curated depository of sequenced antibodies
    prefix: DB-0236
    uri_format: https://web.expasy.org/cgi-bin/abcd/search_abcd.pl?input=$1
  uri_format: https://web.expasy.org/abcd/ABCD_$1
  wikidata:
    database: Q110998933
abm:
  cellosaurus:
    category: Cell line collections (Providers)
    homepage: https://www.abmgood.com/Cell-Biology.html
    name: Applied Biological Materials cell line products
    prefix: ABM
    uri_format: https://www.abmgood.com/search?query=$1&filter_by=cat_no
  contributor_extras:
  - email: benjamin_gyori@hms.harvard.edu
    github: bgyori
    name: Benjamin M. Gyori
    orcid: 0000-0001-9439-5346
  example: T0599
  mappings:
    cellosaurus: ABM
  prefix: abm
  uri_format: https://www.abmgood.com/search?query=$1
abs:
  biocontext:
    prefix: ABS
  edam:
    description: Identifier of an entry (promoter) from the ABS database.
    name: ABS
    obsolete: false
    prefix: '2741'
  fairsharing:
    abbreviation: ABS
    contact:
      email: enrique.blanco@crg.eu
      name: Enrique Blanco
      orcid: 0000-0001-6261-7370
    description: ABS is a database of Annotated regulatory Binding Sites from known
      binding sites identified in promoters of orthologous vertebrate genes.
    homepage: https://genome.crg.es/datasets/abs2005/
    name: Annotated regulatory Binding Sites from Orthologous Promoters
    prefix: FAIRsharing.7mnebr
    publications:
    - doi: 10.1093/nar/gkj116
      pubmed_id: 16381947
      title: 'ABS: a database of Annotated regulatory Binding Sites from orthologous
        promoters.'
    subjects:
    - Biology
  mappings:
    biocontext: ABS
    edam: '2741'
    fairsharing: FAIRsharing.7mnebr
    miriam: abs
    n2t: abs
    pathguide: '217'
    prefixcommons: abs
    wikidata.entity: Q111134507
  miriam:
    deprecated: false
    description: The database of Annotated regulatory Binding Sites (from orthologous
      promoters), ABS, is a public database of known binding sites identified in promoters
      of orthologous vertebrate genes that have been manually curated from bibliography.
    homepage: http://genome.crg.es/datasets/abs2005/
    id: '00000277'
    name: ABS
    namespaceEmbeddedInLui: false
    pattern: ^A\d+$
    prefix: abs
    sampleId: A0014
    uri_format: http://genome.crg.es/datasets/abs2005/entries/$1.html
  n2t:
    description: The database of Annotated regulatory Binding Sites (from orthologous
      promoters), ABS, is a public database of known binding sites identified in promoters
      of orthologous vertebrate genes that have been manually curated from bibliography.
    example: A0014
    homepage: http://genome.crg.es/datasets/abs2005/
    name: ABS at IMIM
    namespaceEmbeddedInLui: false
    pattern: ^A\d+$
    prefix: abs
    uri_format: http://genome.crg.es/datasets/abs2005/entries/$1.html
  name: Annotated Regulatory Binding Sites
  pathguide:
    abbreviation: ABS
    homepage: http://genome.crg.es/datasets/abs2005/
    name: Annotated regulatory Binding Sites
    prefix: '217'
  prefix: abs
  prefixcommons:
    description: 'ABS: A database of Annotated regulatory Binding Sites from known
      binding sites identified in promoters of orthologous vertebrate genes.'
    example: A0014
    homepage: http://genome.imim.es/datasets/abs2005/
    keywords:
    - interaction
    - gene
    - regulation
    miriam: abs
    name: 'ABS: a database of Annotated regulatory Binding Sites from Orthologous
      Promoters'
    pattern: ^A\d+$
    prefix: abs
    pubmed_ids:
    - '16381947'
    uri_format: http://genome.crg.es/datasets/abs2005/entries/$1.html
  publications:
  - doi: 10.1093/nar/gkj116
    pmc: PMC1347478
    pubmed: '16381947'
    title: 'ABS: a database of Annotated regulatory Binding Sites from orthologous
      promoters'
    year: 2006
  - doi: 10.1093/nar/gkj116
    pmc: null
    pubmed: null
    title: 'ABS: a database of Annotated regulatory Binding Sites from orthologous
      promoters.'
    year: null
  - doi: null
    pmc: null
    pubmed: '16381947'
    title: null
    year: null
  wikidata:
    database: Q111134507
absd:
  contact:
    email: nicolas.maillet@pasteur.fr
    github: null
    name: Nicolas Maillet
    orcid: 0000-0003-1611-5243
  contributor:
    email: palayoor.n@northeastern.edu
    github: nalikapalayoor
    name: Nalika Palayoor
    orcid: 0009-0008-8406-631X
  description: The AntiBody Sequence Database is a public dataset for antibody sequence
    data. It provides unique identifiers for antibody sequences, including both immunoglobulin
    and single-chain variable fragment sequences. These are are critical for immunological
    studies, and  allows users to search and retrieve antibody sequences based on
    sequence similarity and specificity, and other biological properties.
  example: 81d0ea69a9ab134f6ba68314e982171a367d3ab739c85c5ba49701dd02170ed3
  github_request_issue: 1362
  homepage: https://absd.pasteur.cloud
  name: AntiBody Sequence Database
  pattern: ^[a-f0-9]{64}$
  prefix: absd
  publications:
  - doi: 10.1093/nargab/lqae171
    pmc: PMC11655285
    pubmed: '39703430'
    title: AntiBody Sequence Database
    year: 2024
  reviewer:
    email: b.gyori@northeastern.edu
    github: bgyori
    name: Benjamin M. Gyori
    orcid: 0000-0001-9439-5346
  uri_format: https://absd.pasteur.cloud/antibody/$1
ac:
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  contributor_extras:
  - email: sumirp77@gmail.com
    github: sumirp
    name: Sumir H Pandit
    orcid: 0000-0002-1216-4761
  description: Activity Streams is an open format specification for activity stream
    protocols, which are used to syndicate activities taken in social web applications
    and services, similar to those in Facebook's, Instagram's, and Twitter's. The
    standard provides a general way to represent activities.
  example: Add
  homepage: http://www.w3.org/ns/activitystreams
  keywords:
  - semantic web
  - social media
  mappings:
    wikidata.entity: Q4677626
    zazuko: as
  name: Activity Streams
  preferred_prefix: ac
  prefix: ac
  references:
  - https://github.com/biopragmatics/bioregistry/pull/1098
  synonyms:
  - as
  uri_format: http://www.w3.org/ns/activitystreams#$1
  wikidata:
    database: Q4677626
  zazuko:
    prefix: as
    uri_format: https://www.w3.org/ns/activitystreams#$1
ac.subtype:
  ecoportal:
    contact:
      email: steve.baskauf@vanderbilt.edu
      name: Steve Baskauf
    description: Audubon Core uses the terms ac:subtype and ac:subtypeLiteral to refine
      the type of a media item to a level more specific than the Dublin Core Type
      Vocabulary, http://purl.org/dc/dcmitype/. This controlled vocabulary provides
      values for ac:subtype and ac:subtypeLiteral.
    homepage: http://rs.tdwg.org/ac/doc/subtype/
    license: CC-BY-4.0
    name: Audubon Core subtype Controlled Vocabulary
    prefix: ACSUBTYPE
    publications:
    - http://rs.tdwg.org/ac/doc/subtype/
    version: '2020-10-13'
  example: Animation
  mappings:
    ecoportal: ACSUBTYPE
    tib: acsubtype
  name: Audubon Core Subtype Controlled Vocabulary
  part_of_database: ac
  prefix: ac.subtype
  tib:
    description: Controlled vocabulary for the Audubon Core term subtype
    download_rdf: http://rs.tdwg.org/acsubtype.ttl
    homepage: http://rs.tdwg.org/acsubtype.htm
    keywords:
    - FAIR Data Spaces
    - life sciences, biology
    name: subtype controlled vocabulary
    prefix: acsubtype
    uri_format: http://rs.tdwg.org/acsubtype/$1
ac.variant:
  ecoportal:
    contact:
      email: steve.baskauf@vanderbilt.edu
      name: Steve Baskauf
    description: Audubon Core uses the terms ac:variant and ac:variantLiteral to provide
      information about the size, extent, and availability of the Service Access Point
      of a media item. This controlled vocabulary provides values for those terms.
    license: CC-BY-4.0
    name: Audubon Core variant Controlled Vocabulary
    prefix: ACVARIANT
    publications:
    - http://rs.tdwg.org/ac/doc/variant/
    version: '2020-10-13'
  example: v001
  mappings:
    ecoportal: ACVARIANT
    tib: acvariant
  name: Audubon Core Variant Controlled Vocabulary
  part_of_database: ac
  prefix: ac.variant
  tib:
    description: Controlled vocabulary for the Audubon Core term variant
    download_rdf: http://rs.tdwg.org/acvariant.ttl
    homepage: http://rs.tdwg.org/acvariant.htm
    keywords:
    - FAIR Data Spaces
    - life sciences, biology
    name: variant controlled vocabulary
    prefix: acvariant
aceview.worm:
  biocontext:
    prefix: ACEVIEW.WORM
  contact:
    email: mieg@ncbi.nlm.nih.gov
    github: null
    name: Danielle Thierry-Mieg
    orcid: 0000-0001-9568-4211
  mappings:
    biocontext: ACEVIEW.WORM
    miriam: aceview.worm
    n2t: aceview.worm
    prefixcommons: aceview.worm
  miriam:
    deprecated: false
    description: AceView provides a curated sequence representation of all public
      mRNA sequences (mRNAs from GenBank or RefSeq, and single pass cDNA sequences
      from dbEST and Trace). These are aligned on the genome and clustered into a
      minimal number of alternative transcript variants and grouped into genes. In
      addition, alternative features such as promoters, and expression in tissues
      is recorded. This collection references C. elegans genes and expression.
    homepage: https://www.ncbi.nlm.nih.gov/IEB/Research/Acembly/index.html?worm
    id: 00000282
    name: Aceview Worm
    namespaceEmbeddedInLui: false
    pattern: ^[a-z0-9-]+$
    prefix: aceview.worm
    sampleId: aap-1
    uri_format: https://www.ncbi.nlm.nih.gov/IEB/Research/Acembly/av.cgi?db=worm&c=Gene&l=$1
  n2t:
    description: AceView provides a curated sequence representation of all public
      mRNA sequences (mRNAs from GenBank or RefSeq, and single pass cDNA sequences
      from dbEST and Trace). These are aligned on the genome and clustered into a
      minimal number of alternative transcript variants and grouped into genes. In
      addition, alternative features such as promoters, and expression in tissues
      is recorded. This collection references C. elegans genes and expression.
    example: aap-1
    homepage: https://www.ncbi.nlm.nih.gov/IEB/Research/Acembly/index.html?worm
    name: AceView Worm at NCBI
    namespaceEmbeddedInLui: false
    pattern: ^[a-z0-9-]+$
    prefix: aceview.worm
    uri_format: https://www.ncbi.nlm.nih.gov/IEB/Research/Acembly/av.cgi?db=worm&c=Gene&l=$1
  prefix: aceview.worm
  prefixcommons:
    description: AceView provides a curated, comprehensive and non-redundant sequence
      representation of all public mRNA sequences (mRNAs from GenBank or RefSeq, and
      single pass cDNA sequences from dbEST and Trace). These experimental cDNA sequences
      are first co-aligned on the genome then clustered into a minimal number of alternative
      transcript variants and grouped into genes.
    example: AP2B1
    homepage: http://www.ncbi.nlm.nih.gov/IEB/Research/Acembly/
    keywords:
    - RNA
    - DNA
    - gene
    miriam: aceview.worm
    name: AceView Worm Genome
    pattern: ^[a-z0-9-]+$
    prefix: aceview.worm
    pubmed_ids:
    - '16925834'
    synonyms:
    - aceview_wormgenes
    uri_format: http://www.ncbi.nlm.nih.gov/IEB/Research/Acembly/av.cgi?db=[?species_database]&c=Gene&l=$1
  publications:
  - doi: 10.1186/gb-2006-7-s1-s12
    pmc: PMC1810549
    pubmed: '16925834'
    title: 'AceView: a comprehensive cDNA-supported gene and transcripts annotation'
    year: 2006
acl:
  bartoc:
    abbreviation: acl
    description: The Basic Access Control ontology describes how access rights (access
      control) are defined on the web.
    homepage: http://www.w3.org/wiki/WebAccessControl
    name: Basic Access Control ontology
    prefix: '17815'
  example: Access
  lov:
    description: Defines the element of Authorization and its essential properties,     and
      also some classes of access such as read and write.
    homepage: http://www.w3.org/wiki/WebAccessControl
    keywords:
    - API
    modified: '2012-12-18'
    name: Basic Access Control ontology
    prefix: acl
    uri_prefix: http://www.w3.org/ns/auth/acl#$1
  mappings:
    bartoc: '17815'
    lov: acl
    zazuko: acl
  prefix: acl
  zazuko:
    prefix: acl
    uri_format: http://www.w3.org/ns/auth/acl#$1
adcad:
  aberowl:
    description: Ontology to support disciplinary annotation of datasets housed at
      the Arctic Data Center (https://arcticdata.io)
    download_owl: http://aber-owl.net/media/ontologies/ADCAD/1/adcad.owl
    homepage: https://github.com/NCEAS/adc-disciplines
    name: Arctic Data Center Academic Disciplines Ontology
    prefix: ADCAD
    version: Version 1.0.0
  bioportal:
    contact:
      email: mecum@nceas.ucsb.edu
      name: Bryce Mecum
    description: Ontology to support disciplinary annotation of datasets housed at
      the Arctic Data Center (https://arcticdata.io)
    homepage: https://github.com/NCEAS/adc-disciplines
    name: Arctic Data Center Academic Disciplines Ontology
    prefix: ADCAD
    version: Version 1.0.0
  contact:
    email: brycemecum@gmail.com
    github: amoeba
    name: Bryce Mecum
    orcid: 0000-0002-0381-3766
  contributor:
    email: j.harry.caufield@gmail.com
    github: caufieldjh
    name: Harry Caufield
    orcid: 0000-0001-5705-7831
  description: An ontology to support disciplinary annotation of Arctic Data Center
    datasets.
  download_owl: https://github.com/NCEAS/adc-disciplines/raw/main/ADCAD.ttl
  example: '00000'
  github_request_issue: 827
  homepage: https://arcticdata.io/
  license: CC-BY-4.0
  mappings:
    aberowl: ADCAD
    bioportal: ADCAD
  name: Arctic Data Center Academic Disciplines Ontology
  pattern: ^\d{5}$
  prefix: adcad
  repository: https://github.com/NCEAS/adc-disciplines
  reviewer:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  uri_format: https://purl.dataone.org/odo/ADCAD_$1
addexbio:
  cellosaurus:
    category: Cell line collections (Providers)
    homepage: https://www.addexbio.com/productshow?id=4
    name: AddexBio cell line products
    prefix: AddexBio
    uri_format: https://www.addexbio.com/productdetail?pid=$1
  example: C0020004/4992
  mappings:
    cellosaurus: AddexBio
  prefix: addexbio
addgene:
  contact:
    email: joanne.kamens@addgene.org
    github: null
    name: Joanne Kamens
    orcid: 0000-0002-7000-1477
  fairsharing:
    abbreviation: Addgene
    description: Addgene is a non-profit plasmid repository dedicated to helping scientists
      around the world share high-quality plasmids. Addgene are working with thousands
      of laboratories to assemble a high-quality library of published plasmids for
      use in research and discovery. By linking plasmids with articles, scientists
      can always find data related to the materials they request.
    homepage: http://www.addgene.org/
    license: https://www.addgene.org/terms-of-use
    name: Addgene
    prefix: FAIRsharing.8hcczk
    publications:
    - doi: 10.1038/nbt.2177
      pubmed_id: 22491276
      title: Addgene provides an open forum for plasmid sharing.
    - doi: 10.1038/505272a
      pubmed_id: null
      title: Repositories share key research tools
    - doi: 10.1093/nar/gku893
      pubmed_id: 25392412
      title: 'The Addgene repository: an international nonprofit plasmid and data
        resource'
    subjects:
    - Life Science
    twitter: Addgene
  integbio:
    description: Addgene is a non-profit organization providing plasmids to researchers.
      It is a collaboration with several hundred research teams, creating a high quality
      plasmid library and repository used for publications. By linking the plasmid
      to its publications, researchers always have access to necessary plasmid and
      associated data. The site contains links to deposit plasmids, request plasmids,
      access sequence information on plasmids, as well as links to a vector database
      and associated protocols. They provide Viral service, CRISPR tools, Fluorescent
      proteins, Cancer resources as special colections.
    fairsharing: biodbcore-000196
    homepage: http://www.addgene.org/
    information_keywords:
    - Bioresource
    - Method
    - Sequence
    - Repository
    maintainer: Addgene
    name: addgene
    prefix: nbdc00356
    status: Active
    target_keywords:
    - DNA
  mappings:
    fairsharing: FAIRsharing.8hcczk
    integbio: nbdc00356
    miriam: addgene
    n2t: addgene
    prefixcommons: addgene
    re3data: r3d100010741
    rrid: Addgene
  miriam:
    deprecated: false
    description: Addgene is a non-profit plasmid repository. Addgene facilitates the
      exchange of genetic material between laboratories by offering plasmids and their
      associated cloning data to not-for-profit laboratories around the world.
    homepage: http://addgene.org/
    id: '00000675'
    name: Addgene Plasmid Repository
    namespaceEmbeddedInLui: false
    pattern: ^[0-9]{5}(-[a-zA-Z0-9-]{0,7})?$|^[0-9]{10}$
    prefix: addgene
    sampleId: '50943'
    uri_format: http://addgene.org/$1
  n2t:
    description: Addgene is a non-profit plasmid repository. Addgene facilitates the
      exchange of genetic material between laboratories by offering plasmids and their
      associated cloning data to not-for-profit laboratories around the world.
    example: '50943'
    homepage: http://addgene.org/
    name: Addgene Plasmid Repository
    namespaceEmbeddedInLui: false
    pattern: ^[0-9]{5}(-[a-zA-Z0-9-]{0,7})?$|^[0-9]{10}$
    prefix: addgene
    uri_format: http://addgene.org/$1
  prefix: addgene
  prefixcommons:
    description: Addgene is a global, nonprofit repository that was created to help
      scientists share plasmids.
    example: '41816'
    homepage: http://www.addgene.org
    keywords:
    - plasmid
    miriam: addgene
    name: Addgene
    pattern: ^\d+$
    prefix: addgene
    pubmed_ids:
    - '25392412'
    uri_format: http://www.addgene.org/$1
  publications:
  - doi: 10.1038/505272a
    pmc: null
    pubmed: '24429608'
    title: Repositories share key research tools
    year: 2014
  - doi: 10.1093/nar/gku893
    pmc: PMC4384007
    pubmed: '25392412'
    title: 'The Addgene repository: an international nonprofit plasmid and data resource'
    year: 2014
  - doi: 10.1038/nbt.2177
    pmc: null
    pubmed: '22491276'
    title: Addgene provides an open forum for plasmid sharing
    year: 2012
  - doi: 10.1038/nbt.2177
    pmc: null
    pubmed: null
    title: Addgene provides an open forum for plasmid sharing.
    year: null
  - doi: 10.1038/505272a
    pmc: null
    pubmed: null
    title: Repositories share key research tools
    year: null
  - doi: 10.1093/nar/gku893
    pmc: null
    pubmed: null
    title: 'The Addgene repository: an international nonprofit plasmid and data resource'
    year: null
  - doi: null
    pmc: null
    pubmed: '25392412'
    title: null
    year: null
  re3data:
    description: Addgene archives and distributes plasmids for researchers around
      the globe. They are working with thousands of laboratories to assemble a high-quality
      library of published plasmids for use in research and discovery. By linking
      plasmids with articles, scientists can always find data related to the materials
      they request.
    doi: 10.17616/R3X620
    homepage: https://www.addgene.org/
    name: Addgene
    prefix: r3d100010741
    xrefs:
      nif: 0000-11872
  rrid:
    homepage: http://www.addgene.org
    keywords:
    - FASEB list
    - bio.tools
    - molecular biology
    - plasmid
    - repository
    - sequence alignment
    name: Addgene
    prefix: Addgene
    scr: '002037'
    twitter: Addgene
addicto:
  contact:
    email: robertwest100@gmail.com
    github: robertjwest
    name: Robert J. West
    orcid: 0000-0001-6398-0921
  contact_group_email: contact@addictovocab.org
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  download_owl: https://addictovocab.org/addicto.owl
  example: '0000447'
  logo: https://addictovocab.org/images/logo.svg
  mappings:
    ols: addicto
  ols:
    description: The Addiction Ontology (AddictO) is an ontology being developed all
      aspects of addiction research.
    download_owl: http://addictovocab.org/addicto.owl
    homepage: https://addictovocab.org
    name: Addiction Ontology
    prefix: addicto
    uri_format: http://addictovocab.org/ADDICTO_$1
    version: '2025-09-24'
    version.iri: http://addictovocab.org/addicto.owl/2025-09-24
  prefix: addicto
  repository: https://github.com/addicto-org/addiction-ontology
  uri_format: http://addictovocab.org/ADDICTO_$1
adms:
  bartoc:
    abbreviation: adms
    description: ADMS is a profile of DCAT, used to describe semantic assets (or just
      'Assets'), defined as highly reusable metadata (e.g. xml schemata, generic data
      models) and reference data (e.g. code lists, taxonomies, dictionaries, vocabularies)
      that are used for eGovernment system development.
    homepage: https://www.w3.org/TR/vocab-adms
    name: Asset Description Metadata Schema
    prefix: '17818'
  contact:
    email: bert.van.nuffelen@tenforce.com
    github: bertvannuffelen
    name: Bert Van Nuffelen
    orcid: null
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: A vocabulary for describing semantic assets, defined as highly reusable
    metadata (e.g. XML1 schemata, generic data models) and reference data (e.g. code
    lists, taxonomies, dictionaries, vocabularies).
  example: Asset
  homepage: http://www.w3.org/ns/adms
  license: CC-BY-4.0
  lov:
    description: ADMS is a profile of DCAT, used to describe semantic assets (or just
      'Assets'), defined as highly reusable metadata (e.g. xml schemata, generic data
      models) and reference data (e.g. code lists, taxonomies, dictionaries, vocabularies)
      that are used for eGovernment system development.
    homepage: http://www.w3.org/TR/vocab-adms/
    keywords:
    - Metadata
    modified: '2015-07-22'
    name: Asset Description Metadata Schema
    prefix: adms
    uri_prefix: http://www.w3.org/ns/adms#$1
  mappings:
    bartoc: '17818'
    lov: adms
  name: Asset Description Metadata Schema Vocabulary
  prefix: adms
  repository: https://github.com/SEMICeu/ADMS
  uri_format: http://www.w3.org/ns/adms#$1
ado:
  aberowl:
    description: Alzheimer's Disease Ontology is a knowledge-based ontology that encompasses
      varieties of concepts related to Alzheimer'S Disease, structured by upper level
      Basic Formal Ontology(BFO). This Ontology is enriched by the interrelated entities
      that demonstrate the network of the understanding on Alzheimer's disease and
      can be readily applied for text mining.
    download_owl: http://aber-owl.net/media/ontologies/ADO/8/ado.owl
    homepage: https://github.com/Fraunhofer-SCAI-Applied-Semantics/ADO
    name: Alzheimer's Disease Ontology
    prefix: ADO
  bioportal:
    contact:
      email: alpha.tom.kodamullil@scai.fraunhofer.de
      name: Alpha Tom Kodamullil
    description: Alzheimer's Disease Ontology is a knowledge-based ontology that encompasses
      varieties of concepts related to Alzheimer's Disease, structured by upper level
      Basic Formal Ontology (BFO). This ontology is enriched by the interrelated entities
      that demonstrate the network of the understanding on Alzheimer's disease and
      can be readily applied for text mining.
    homepage: https://github.com/Fraunhofer-SCAI-Applied-Semantics/ADO
    name: Alzheimer's Disease Ontology
    prefix: ADO
    publications:
    - https://pubmed.ncbi.nlm.nih.gov/23830913/
    version: 2.0.1
  contributor_extras:
  - email: sumirp77@gmail.com
    github: sumirp
    name: Sumir H Pandit
    orcid: 0000-0002-1216-4761
  example: '0000001'
  fairsharing:
    abbreviation: ADO
    description: The Alzheimer's Disease Ontology (ADO) is an ontology representing
      relevant knowledge on Alzheimer’s disease. ADO was developed with the purpose
      of containing information relevant to four main biological views—preclinical,
      clinical, etiological, and molecular/cellular mechanisms—and contains synonyms
      and references.
    homepage: https://bioportal.bioontology.org/ontologies/ADO
    name: Alzheimer's Disease Ontology
    prefix: FAIRsharing.ckd4rf
    publications:
    - doi: 10.1016/j.jalz.2013.02.009
      pubmed: '23830913'
      title: 'ADO: a disease ontology representing the domain knowledge specific to
        Alzheimer''s disease'
      year: 2013
    subjects:
    - Health Science
    user_defined_tags:
    - Alzheimer’s disease
  mappings:
    aberowl: ADO
    bioportal: ADO
    fairsharing: FAIRsharing.ckd4rf
    obofoundry: ado
    ols: ado
    ontobee: ADO
    wikidata.entity: Q54887745
  obofoundry:
    contact: alpha.tom.kodamullil@scai.fraunhofer.de
    contact.github: akodamullil
    contact.label: Alpha Tom Kodamullil
    contact.orcid: 0000-0001-9896-3531
    depends_on:
    - bfo
    deprecated: false
    description: Alzheimer's Disease Ontology is a knowledge-based ontology that encompasses
      varieties of concepts related to Alzheimer'S Disease, structured by upper level
      Basic Formal Ontology(BFO). This Ontology is enriched by the interrelated entities
      that demonstrate the network of the understanding on Alzheimer's disease and
      can be readily applied for text mining.
    domain: health
    download.owl: http://purl.obolibrary.org/obo/ado.owl
    homepage: https://github.com/Fraunhofer-SCAI-Applied-Semantics/ADO
    license: CC BY 4.0
    license.url: https://creativecommons.org/licenses/by/4.0/
    name: Alzheimer's Disease Ontology
    preferredPrefix: ADO
    prefix: ado
    repository: https://github.com/Fraunhofer-SCAI-Applied-Semantics/ADO
  ols:
    description: Alzheimer's Disease Ontology is a knowledge-based ontology that encompasses
      varieties of concepts related to Alzheimer'S Disease, foundamentally structured
      by upper level Basic Formal Ontology(BFO). This Ontology is enriched by the
      interrelational entities that demonstrate the nextwork of the understanding
      on Alzheimer's disease and can be readily applied for text mining.
    download_owl: http://purl.obolibrary.org/obo/ado.owl
    homepage: https://github.com/Fraunhofer-SCAI-Applied-Semantics/ADO
    name: Alzheimer's Disease Ontology (ADO)
    prefix: ado
    tracker: https://github.com/Fraunhofer-SCAI-Applied-Semantics/ADO/issues
    version: '2023-09-20'
    version.iri: http://purl.obolibrary.org/obo/ado/releases/2023-09-20/ado.owl
  ontobee:
    library: Library
    name: Alzheimer's Disease Ontology
    prefix: ADO
  pattern: ^\d{7}$
  prefix: ado
  providers:
  - code: legacy
    description: Legacy URI used before switching to OBO PURLs
    example: null
    first_party: null
    homepage: http://scai.fraunhofer.de
    name: Legacy
    publications: null
    status: null
    uri_format: http://scai.fraunhofer.de/AlzheimerOntology#$1
  publications:
  - doi: 10.1016/j.jalz.2013.02.009
    pmc: null
    pubmed: '23830913'
    title: 'ADO: a disease ontology representing the domain knowledge specific to
      Alzheimer''s disease'
    year: 2013
  references:
  - https://github.com/biopragmatics/bioregistry/pull/1098
  uri_format: http://purl.obolibrary.org/obo/ADO_$1
  wikidata:
    database: Q54887745
adw:
  aberowl:
    description: An ontology for animal life history and natural history characteristics
      suitable for populations and higher taxonomic entities.
    download_owl: http://aber-owl.net/media/ontologies/ADW/2/adw.owl
    homepage: http://www.animaldiversity.org
    name: Animal Natural History and Life History Ontology
    prefix: ADW
    version: 10/11/04
  agroportal:
    contact:
      email: adw.staff@umich.edu
      name: Animal Diversity Web technical staff
    description: An ontology for animal life history and natural history characteristics
      suitable for populations and higher taxonomic entities.
    homepage: https://bioportal.bioontology.org/ontologies/ADW
    name: Animal Natural History and Life History Ontology
    prefix: ADW
  biocontext:
    prefix: ADW
  bioportal:
    contact:
      email: adw.staff@umich.edu
      name: Animal Diversity Web technical staff
    description: An ontology for animal life history and natural history characteristics
      suitable for populations and higher taxonomic entities.
    homepage: http://www.animaldiversity.org
    name: Animal Natural History and Life History Ontology
    prefix: ADW
    version: 10/11/04
  contributor_extras:
  - email: sumirp77@gmail.com
    github: sumirp
    name: Sumir H Pandit
    orcid: 0000-0002-1216-4761
  fairsharing:
    abbreviation: ADW
    description: An ontology for animal life history and natural history characteristics
      suitable for populations and higher taxonomic entities.
    domains:
    - Taxonomic classification
    homepage: http://bioportal.bioontology.org/ontologies/1530
    name: Animal natural history and life history
    prefix: FAIRsharing.t9fvdn
    subjects:
    - Life Science
    - Anatomy
  mappings:
    aberowl: ADW
    agroportal: ADW
    biocontext: ADW
    bioportal: ADW
    fairsharing: FAIRsharing.t9fvdn
    miriam: adw
    n2t: adw
    obofoundry: adw
    wikidata.entity: Q114677837
  miriam:
    deprecated: false
    description: Animal Diversity Web (ADW) is an online database of animal natural
      history, distribution, classification, and conservation biology.
    homepage: https://animaldiversity.org/
    id: 00000492
    name: Animal Diversity Web
    namespaceEmbeddedInLui: false
    pattern: ^[A-Z_a-z]+$
    prefix: adw
    sampleId: Lycalopex_vetulus
    uri_format: https://animaldiversity.org/accounts/$1/
  n2t:
    description: Animal Diversity Web (ADW) is an online database of animal natural
      history, distribution, classification, and conservation biology.
    example: Lycalopex_vetulus
    homepage: https://animaldiversity.org/
    name: Animal Diversity Web at University of Michigan
    namespaceEmbeddedInLui: false
    pattern: ^[A-Z_a-z]+$
    prefix: adw
    uri_format: https://animaldiversity.org/accounts/$1/
  obofoundry:
    contact: adw_geeks@umich.edu
    contact.label: Animal Diversity Web technical staff
    deprecated: true
    domain: organisms
    homepage: http://www.animaldiversity.org
    name: Animal natural history and life history
    prefix: adw
  prefix: adw
  references:
  - https://github.com/biopragmatics/bioregistry/pull/1098
  uri_format: https://animaldiversity.org/accounts/$1
  wikidata:
    database: Q114677837
aeo:
  aberowl:
    description: AEO is an ontology of anatomical structures that expands CARO, the
      Common Anatomy Reference Ontology
    download_owl: http://aber-owl.net/media/ontologies/AEO/8/aeo.owl
    homepage: https://github.com/obophenotype/human-developmental-anatomy-ontology/
    name: Anatomical Entity Ontology
    prefix: AEO
  bartoc:
    abbreviation: AEO
    description: 'This ontology is inactive."


      "The AEO is an ontology of anatomical structures that expands CARO, the Common
      Anatomy Reference Ontology, to about 160 classes using the is_a relationship;
      it thus provides a detailed type classification for tissues. The ~100 new classes
      were chosen for their use in categorizing the major vertebrate and invertebrate
      anatomy ontologies at a granularity adequate for tissues of a single cell type.


      The AEO is intended to be useful in increasing the amount of knowledge in anatomy
      ontologies, facilitating annotation and enabling interoperability across anatomy
      ontologies.


      An important subcategory of the AEO is simple tissue (a synonym of the CARO
      portion of tissue), a recognisable anatomical entity composed predominantly
      to a single cell type. CARO had a only few epithelial classes here and these
      are inadequate for capturing the richness of anatomical tissue knowledge. The
      AEO has ~70 simple tissues and these are linked to their cell types (~100) as
      detailed in the cell type ontology through a has_part relationship. The AEO
      thus includes a subset of the cell type ontology.


      The AEO has been refined through its use in annotating the ~2500 terms of the
      new version of the Ontology of Developing Human Anatomy and, while this has
      improved the ontology, it may have given it a mammalian bias.


      The ontology can be used to classify most organisms as its terms are appropriate
      for most plant and fungal tissues. I plan to improve the ontology to include
      more non-animal anatomical terms.'
    name: Ontology of Anatomical Entities
    prefix: '181'
  biocontext:
    prefix: AEO
  bioportal:
    contact:
      email: J.Bard@ed.ac.uk
      name: Jonathan Bard
    description: AEO is an ontology of anatomical structures that expands CARO, the
      Common Anatomy Reference Ontology, to about 200 classes using the is_a relationship;
      it thus provides a detailed type classification for tissues. The new classes
      were chosen for their use in categorizing the major vertebrate and invertebrate
      anatomy ontologies at a granularity adequate for tissues of a single cell type.
      The ontology should be useful in increasing the amount of knowledge in anatomy
      ontologies, facilitating annotation and enabling interoperability across anatomy
      ontologies
    homepage: https://github.com/obophenotype/human-developmental-anatomy-ontology/
    name: Anatomical Entity Ontology
    prefix: AEO
  contributor_extras:
  - email: sumirp77@gmail.com
    github: sumirp
    name: Sumir H Pandit
    orcid: 0000-0002-1216-4761
  download_obo: http://purl.obolibrary.org/obo/aeo.obo
  example: '0001017'
  fairsharing:
    abbreviation: AEO
    description: The AEO ontology of anatomical structures is a resource to facilitate
      the increase in knowledge in anatomy ontologies, supporting annotation and enabling
      compatibility with other anatomy ontologies. The ontology can be used to classify
      most organisms as its terms are appropriate for most plant and fungal tissues.
      It is envisaged that in future the ontology will include more non-animal anatomical
      terms. This ontology is available for use, and thus marked as Ready, although
      please note that the OBO Foundry has marked it as Inactive (a status not used
      within FAIRsharing), used when the project has a contact person who is responsive
      and a version of the ontology is available, but no edits are being made and
      requests for edits are either greatly delayed or not being addressed by the
      ontology’s editors.
    homepage: http://www.obofoundry.org/ontology/aeo.html
    name: Anatomical Entity Ontology
    prefix: FAIRsharing.93ee19
    publications:
    - doi: 10.3389/fgene.2012.00018
      pubmed: '22347883'
      title: The AEO, an Ontology of Anatomical Entities for Classifying Animal Tissues
        and Organs
      year: 2012
    subjects:
    - Anatomy
  mappings:
    aberowl: AEO
    bartoc: '181'
    biocontext: AEO
    bioportal: AEO
    fairsharing: FAIRsharing.93ee19
    obofoundry: aeo
    ols: aeo
    ontobee: AEO
    wikidata.entity: Q81661532
  obofoundry:
    appears_in:
    - ehdaa2
    contact: J.Bard@ed.ac.uk
    contact.label: Jonathan Bard
    deprecated: true
    description: AEO is an ontology of anatomical structures that expands CARO, the
      Common Anatomy Reference Ontology
    domain: anatomy and development
    download.owl: http://purl.obolibrary.org/obo/aeo.owl
    homepage: https://github.com/obophenotype/human-developmental-anatomy-ontology/
    license: CC BY 4.0
    license.url: https://creativecommons.org/licenses/by/4.0/
    name: Anatomical Entity Ontology
    preferredPrefix: AEO
    prefix: aeo
    repository: https://github.com/obophenotype/human-developmental-anatomy-ontology
  ols:
    description: AEO is an ontology of anatomical structures that expands CARO, the
      Common Anatomy Reference Ontology
    download_owl: http://purl.obolibrary.org/obo/aeo.owl
    homepage: https://github.com/obophenotype/human-developmental-anatomy-ontology/
    name: Anatomical Entity Ontology
    prefix: aeo
    tracker: https://github.com/obophenotype/human-developmental-anatomy-ontology/issues
  ontobee:
    library: Library
    name: Anatomical Entity Ontology
    prefix: AEO
  pattern: ^\d{7}$
  prefix: aeo
  publications:
  - doi: 10.3389/fgene.2012.00018
    pmc: PMC3278863
    pubmed: '22347883'
    title: The AEO, an Ontology of Anatomical Entities for Classifying Animal Tissues
      and Organs
    year: 2012
  references:
  - https://github.com/biopragmatics/bioregistry/pull/1098
  synonyms:
  - AEO_RETIRED
  wikidata:
    database: Q81661532
aeon:
  contact:
    email: philip.stroemert@tib.eu
    github: StroemPhi
    name: Philip Strömert
    orcid: 0000-0002-1595-3213
  contributor:
    email: philip.stroemert@tib.eu
    github: StroemPhi
    name: Philip Strömert
    orcid: 0000-0002-1595-3213
  description: The academic event ontology, currently still in development and thus
    unstable, is an OBO compliant reference ontology for describing academic events
    such as conferences, workshops or seminars and their series. It is being developed
    as part of the [ConfIDent project](https://projects.tib.eu/confident/) to allow
    RDF representations of the academic events and series stored and curated in the
    [ConfIDent platform](https://www.confident-conference.org/index.php/main_page).
  download_owl: https://raw.githubusercontent.com/tibonto/aeon/main/aeon.owl
  example: '0000001'
  github_request_issue: 617
  homepage: https://tibonto.github.io/aeon/
  license: CC-BY-4.0
  mappings:
    tib: aeon
  name: Academic Event Ontology
  pattern: ^\d{7}$
  prefix: aeon
  repository: https://github.com/tibonto/aeon
  reviewer:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  tib:
    description: NOT READY FOR PRODUCTION (PURLs not registered)- The Academic Event
      Ontology (AEON) is used to represent information regarding academic events.
    download_owl: https://raw.githubusercontent.com/tibonto/aeon/main/aeon.owl
    homepage: https://github.com/tibonto/aeon
    keywords:
    - TIB
    - history
    - social sciences
    - educational science
    name: Academic Event Ontology
    prefix: aeon
    tracker: https://github.com/tibonto/aeon/issues
    uri_format: https://github.com/tibonto/aeon$1
    version.iri: http://purl.obolibrary.org/obo/aeon/releases/2023-02-22/aeon.owl
  uri_format: http://purl.obolibrary.org/obo/AEON_$1
aero:
  aberowl:
    description: The Adverse Event Reporting Ontology (AERO) is an ontology aimed
      at supporting clinicians at the time of data entry, increasing quality and accuracy
      of reported adverse events.
    download_owl: http://aber-owl.net/media/ontologies/AERO/45/aero.owl
    homepage: http://purl.obolibrary.org/obo/aero
    name: Adverse Event Reporting Ontology
    prefix: AERO
    version: unknown
  biocontext:
    prefix: AERO
  bioportal:
    contact:
      email: mcourtot@gmail.com
      name: Melanie Courtot
    description: The Adverse Event Reporting Ontology (AERO) is an ontology aimed
      at supporting clinicians at the time of data entry, increasing quality and accuracy
      of reported adverse events.
    homepage: http://purl.obolibrary.org/obo/aero
    name: Adverse Event Reporting Ontology
    prefix: AERO
    version: unknown
  contributor_extras:
  - email: sumirp77@gmail.com
    github: sumirp
    name: Sumir H Pandit
    orcid: 0000-0002-1216-4761
  example: '0000125'
  fairsharing:
    abbreviation: AERO
    contact:
      email: mcourtot@gmail.com
      name: Melanie Courtot
      orcid: 0000-0002-9551-6370
    description: The Adverse Event Reporting Ontology (AERO) is an ontology aimed
      at supporting clinicians at the time of data entry, increasing quality and accuracy
      of reported adverse events.
    domains:
    - Electronic Health Record
    - Adverse Reaction
    homepage: http://purl.obolibrary.org/obo/aero
    license: CC-BY-3.0
    name: Adverse Event Reporting ontology
    prefix: FAIRsharing.rycy2x
    subjects:
    - Preclinical Studies
    - Biomedical Science
    - Health Science
    - Medicine
  mappings:
    aberowl: AERO
    biocontext: AERO
    bioportal: AERO
    fairsharing: FAIRsharing.rycy2x
    obofoundry: aero
    ols: aero
    wikidata.entity: Q55118235
  obofoundry:
    contact: mcourtot@gmail.com
    contact.label: Melanie Courtot
    contact.orcid: 0000-0002-9551-6370
    deprecated: true
    description: The Adverse Event Reporting Ontology (AERO) is an ontology aimed
      at supporting clinicians at the time of data entry, increasing quality and accuracy
      of reported adverse events
    domain: health
    download.owl: http://purl.obolibrary.org/obo/aero.owl
    homepage: http://purl.obolibrary.org/obo/aero
    license: CC BY 3.0
    license.url: http://creativecommons.org/licenses/by/3.0/
    name: Adverse Event Reporting Ontology
    prefix: aero
  ols:
    description: The Adverse Event Reporting Ontology (AERO) is an ontology aimed
      at supporting clinicians at the time of data entry, increasing quality and accuracy
      of reported adverse events
    homepage: http://purl.obolibrary.org/obo/aero
    name: Adverse Event Reporting Ontology
    prefix: aero
  pattern: ^\d{7}$
  prefix: aero
  references:
  - https://github.com/biopragmatics/bioregistry/pull/1098
  wikidata:
    database: Q55118235
affy.probeset:
  biocontext:
    prefix: AFFY.PROBESET
  mappings:
    biocontext: AFFY.PROBESET
    miriam: affy.probeset
    n2t: affy.probeset
    togoid: AffyProbeset
  miriam:
    deprecated: false
    description: An Affymetrix ProbeSet is a collection of up to 11 short (~22 nucleotide)
      microarray probes designed to measure a single gene or a family of genes as
      a unit. Multiple probe sets may be available for each gene under consideration.
    homepage: http://bio2rdf.org
    id: 00000394
    name: Affymetrix Probeset
    namespaceEmbeddedInLui: false
    pattern: ^\d{4,}((_[asx])?_at)?$
    prefix: affy.probeset
    sampleId: 243002_at
    uri_format: http://bio2rdf.org/affymetrix:$1
  n2t:
    description: An Affymetrix ProbeSet is a collection of up to 11 short (~22 nucleotide)
      microarray probes designed to measure a single gene or a family of genes as
      a unit. Multiple probe sets may be available for each gene under consideration.
    example: 243002_at
    homepage: http://www.affymetrix.com/
    name: Affymetrix ProbeSet in Santa Clara
    namespaceEmbeddedInLui: false
    pattern: \d{4,}((_[asx])?_at)?
    prefix: affy.probeset
    uri_format: https://www.affymetrix.com/LinkServlet?probeset=$1
  prefix: affy.probeset
  togoid:
    examples:
    - 1553582_a_at
    - 211531_x_at
    - 202573_at
    - 201640_x_at
    - 205117_at
    - 201017_at
    - 205099_s_at
    - 200614_at
    - 201895_at
    - 202666_s_at
    keywords:
    - Probe
    name: Affymetrix probeset
    pattern: ^(?\d{3,}(?:_[a-z])?_at)$
    prefix: AffyProbeset
    uri_format: http://identifiers.org/affy.probeset/$1
afo:
  aberowl:
    description: '<p><strong>Allotrope Merged Ontology Suite</strong></p> <p>The AFO
      is an ontology suite that provides a standard vocabulary and semantic model
      for the representation of laboratory analytical processes. The AFO suite is
      aligned at the upper layer to the Basic Formal Ontology (BFO). The core domains
      modeled include: Equipment, Material, Process, and Results.</p> <p>license:
      http://purl.allotrope.org/voc/creative-commons-attribution-license<br/> rights:
      http://purl.allotrope.org/voc/copyright<br/></p>'
    download_owl: http://aber-owl.net/media/ontologies/AFO/42/afo.owl
    name: Allotrope Merged Ontology Suite
    prefix: AFO
    version: REC/2025/06
  bioportal:
    contact:
      email: more.info@allotrope.org
      name: Allotrope Foundation
    description: '<p><strong>Allotrope Merged Ontology Suite</strong></p> <p>The AFO
      is an ontology suite that provides a standard vocabulary and semantic model
      for the representation of laboratory analytical processes. The AFO suite is
      aligned at the upper layer to the Basic Formal Ontology (BFO). The core domains
      modeled include: Equipment, Material, Process, and Results.</p> <p>license:
      http://purl.allotrope.org/voc/creative-commons-attribution-license<br/> rights:
      http://purl.allotrope.org/voc/copyright<br/></p>'
    homepage: http://purl.allotrope.org
    name: Allotrope Merged Ontology Suite
    prefix: AFO
    publications:
    - http://www.allotrope.org
    version: REC/2025/06
  fairsharing:
    abbreviation: AFO
    description: The Agriculture and Forestry Ontology (AFO), also known as the Agriforest
      Ontology, combines the concepts of the Agriforest Thesaurus with The Finnish
      General Upper Ontology (YSO). This combination of ontologies can be used for
      describing resources especially in domain of agriculture, forestry, veterinary
      medicine, food science, environmental science and biology.
    domains:
    - food
    homepage: https://seco.cs.aalto.fi/ontologies/afo/
    license: CC-BY-4.0
    name: Agriculture and Forestry Ontology
    prefix: FAIRsharing.595710
    subjects:
    - Forest Management
    - Agriculture
    - Environmental Science
    - Agricultural Engineering
    - Veterinary Medicine
    - Biology
    - Food Chemistry
  homepage: https://www.allotrope.org/
  mappings:
    aberowl: AFO
    bioportal: AFO
    fairsharing: FAIRsharing.595710
    ols: afo
    ontobee: AFO
    tib: afo
  no_own_terms: true
  ols:
    description: Allotrope Merged Ontology Suite
    name: Allotrope Merged Ontology Suite
    prefix: afo
    uri_format: http://purl.allotrope.org/ontologies$1
    version: '2025-12-01'
    version.iri: http://purl.allotrope.org/voc/afo/merged/REC/2025/12/merged-without-qudt-and-inferred
  ontobee:
    library: Not Specified/No
    name: Allotrope Foundation Ontology
    prefix: AFO
  prefix: afo
  tib:
    description: The AFO is an ontology suite that provides a standard vocabulary
      and semantic model for the representation of laboratory analytical processes.
      The AFO suite is aligned at the upper layer to the Basic Formal Ontology (BFO).
      The core domains modeled include, Equipment, Material, Process, and Results.
      This artifact contains all triples of Allotrope Foundation Merged Without QUDT
      Ontology Suite together with triples inferred with HermiT.
    download_rdf: https://purl.allotrope.org/voc/afo/merged/REC/2025/03/merged-without-qudt-and-inferred.ttl
    keywords:
    - NFDI4CAT
    - NFDI4CHEM
    - NFDI4ING
    - chemistry
    name: Allotrope Foundation Ontology Merged Without QUDT And Inferred (REC/2025/03)
    prefix: afo
    uri_format: https://purl.allotrope.org/voc/afo/merged/REC/2025/03/merged-without-qudt-and-inferred$1
    version.iri: http://purl.allotrope.org/voc/afo/merged/REC/2025/03/merged-without-qudt-and-inferred
afpo:
  aberowl:
    description: AfPO is a tool which enables to annotate the African individuals,
      and brings together knowledge accumulated about existing populations with their
      genetic fingerprint in a standardized format.
    download_owl: http://aber-owl.net/media/ontologies/AFPO/1/afpo.owl
    homepage: https://github.com/h3abionet/afpo
    name: African Population Ontology
    prefix: AFPO
  bioportal:
    contact:
      email: mcmelek@msn.com
      name: Melek Chaouch
    description: AfPO is a tool which enables to annotate the African individuals,
      and brings together knowledge accumulated about existing populations with their
      genetic fingerprint in a standardized format.
    homepage: https://github.com/h3abionet/afpo
    name: African Population Ontology
    prefix: AFPO
    version: '2024-03-21'
  example: '0000440'
  mappings:
    aberowl: AFPO
    bioportal: AFPO
    obofoundry: afpo
    ols: afpo
    ontobee: AfPO
  obofoundry:
    contact: mcmelek@msn.com
    contact.github: Melek-C
    contact.label: Melek Chaouch
    contact.orcid: 0000-0001-5868-4204
    deprecated: false
    description: AfPO is an ontology that can be used in the study of diverse populations
      across Africa. It brings together publicly available demographic, anthropological
      and genetic data relating to African people in a standardised and structured
      format. The AfPO can be employed to classify African study participants comprehensively
      in prospective research studies. It can also be used to classify past study
      participants by mapping them using a language or ethnicity identifier or synonyms.
    domain: organisms
    download.json: http://purl.obolibrary.org/obo/afpo.json
    download.obo: http://purl.obolibrary.org/obo/afpo.obo
    download.owl: http://purl.obolibrary.org/obo/afpo.owl
    homepage: https://github.com/h3abionet/afpo
    license: CC BY 4.0
    license.url: https://creativecommons.org/licenses/by/4.0/
    name: African Population Ontology
    preferredPrefix: AfPO
    prefix: afpo
    repository: https://github.com/h3abionet/afpo
  ols:
    description: AfPO is an ontology that can be used in the study of diverse populations
      across Africa. It brings together publicly available demographic, anthropological
      and genetic data relating to African people in a standardised and structured
      format. The AfPO can be employed to classify African study participants comprehensively
      in prospective research studies. It can also be used to classify past study
      participants by mapping them using a language or ethnicity identifier or synonyms.
    download_owl: http://purl.obolibrary.org/obo/afpo.owl
    homepage: https://github.com/h3abionet/afpo
    name: African Population Ontology
    prefix: afpo
    tracker: https://github.com/h3abionet/afpo/issues
    version: '2024-03-21'
    version.iri: http://purl.obolibrary.org/obo/afpo/releases/2024-03-21/afpo.owl
  ontobee:
    library: Library
    name: African Population Ontology
    prefix: AfPO
  prefix: afpo
aftol.category:
  contact:
    email: davem@umn.edu
    github: null
    name: David J. McLaughlin
    orcid: null
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: Categories in the AFTOL database
  example: '229'
  homepage: https://aftol.umn.edu
  name: Assembling the Fungal Tree of Life - Category
  prefix: aftol.category
  uri_format: https://aftol.umn.edu/glossary?category=$1
aftol.taxonomy:
  biocontext:
    prefix: AFTOL.TAXONOMY
  contact:
    email: davem@umn.edu
    github: null
    name: David J. McLaughlin
    orcid: null
  contributor_extras:
  - email: laylamichan@ciencias.unam.mx
    github: lmichan
    name: Layla Michán Aguirre
    orcid: 0000-0002-5798-662X
  homepage: https://aftol.umn.edu
  mappings:
    biocontext: AFTOL.TAXONOMY
    miriam: aftol.taxonomy
    n2t: aftol.taxonomy
  miriam:
    deprecated: true
    description: The Assembling the Fungal Tree of Life (AFTOL) project is dedicated
      to significantly enhancing our understanding of the evolution of the Kingdom
      Fungi, which represents one of the major clades of life. There are roughly 80,000
      described species of Fungi, but the actual diversity in the group has been estimated
      to be about 1.5 million species.
    homepage: http://aftol.org/data.php
    id: '00000411'
    name: AFTOL
    namespaceEmbeddedInLui: false
    pattern: ^\d+$
    prefix: aftol.taxonomy
    sampleId: '959'
    uri_format: http://wasabi.lutzonilab.net/pub/displayTaxonInfo?aftol_id=$1
  n2t:
    description: The Assembling the Fungal Tree of Life (AFTOL) project is dedicated
      to significantly enhancing our understanding of the evolution of the Kingdom
      Fungi, which represents one of the major clades of life. There are roughly 80,000
      described species of Fungi, but the actual diversity in the group has been estimated
      to be about 1.5 million species.
    example: '959'
    homepage: http://aftol.org/data.php
    name: AFTOL at University of Minnesota
    namespaceEmbeddedInLui: false
    pattern: ^\d+$
    prefix: aftol.taxonomy
    uri_format: http://wasabi.lutzonilab.net/pub/displayTaxonInfo?aftol_id=$1
  name: Assembling the Fungal Tree of Life - Taxonomy
  prefix: aftol.taxonomy
agilent.probe:
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: 'This is the Agilent SurePrint G3 Human GE v2 8x60k Microarray, Agilent
    design ID 039494, GridName 039494_D_F_20120628. Probe layout is 1 x 1 x 384 rows
    x 164 cols, which is different from a similar ADF A-GEOD-16699 (1 x 1 x 328 rows
    x 192 cols). Version 2 of this array  contains long intergenic non-coding RNA
    (lincRNA) probes designed to the human catalog of lincRNAs from the Broad Institute,
    along with an update of mRNA content when compared to version 1. Probes were designed
    using GRCh37 assembly of the human genome. Annotation of probes came from the
    following database: RefSeq Build 50, Ensembl Release 52, Unigene Build 216, GenBank
    (April 2009), Broad Institute Human lincRNA catalog (Nov 2011), Broad Institute
    TUCP transcripts catalog (Nov 2011).  Probe annotation was taken from A-GEOD-16699.'
  example: A_24_P98555
  homepage: https://www.ebi.ac.uk/arrayexpress/files/A-MEXP-2320/A-MEXP-2320.adf.txt
  keywords:
  - transcriptomics
  name: Agilent Probe
  pattern: ^A_\d+_.+$
  prefix: agilent.probe
  references:
  - http://www.cs.tau.ac.il/cgi-bin/cgiwrap/click/get.cgi/conversionFiles/conversion_human_14850_agilent2entrez.txt
agricola:
  appears_in:
  - chebi
  - pmc
  biocontext:
    prefix: AGRICOLA
  contact:
    email: judith.blake@jax.org
    github: judyblake
    name: Judith A Blake
    orcid: 0000-0001-8522-334X
  contributor_extras:
  - email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  - email: cjmungall@lbl.gov
    github: cmungall
    name: Chris Mungall
    orcid: 0000-0002-6601-2165
  - email: sumirp77@gmail.com
    github: sumirp
    name: Sumir H Pandit
    orcid: 0000-0002-1216-4761
  example: IND608186955
  example_extras:
  - GUA85008832
  go:
    homepage: http://agricola.nal.usda.gov/
    name: AGRICultural OnLine Access
    prefix: AGRICOLA_ID
  mappings:
    biocontext: AGRICOLA
    go: AGRICOLA_ID
    miriam: agricola
    n2t: agricola
    wikidata.entity: Q4651693
  miriam:
    deprecated: false
    description: AGRICOLA (AGRICultural OnLine Access) serves as the catalog and index
      to the collections of the National Agricultural Library, as well as a primary
      public source for world-wide access to agricultural information. The database
      covers materials in all formats and periods, including printed works from as
      far back as the 15th century.
    homepage: http://agricola.nal.usda.gov/
    id: 00000589
    name: AGRICOLA
    namespaceEmbeddedInLui: false
    pattern: ^\d+$
    prefix: agricola
    sampleId: '50018'
    uri_format: http://ddr.nal.usda.gov/dspace/handle/10113/$1
  n2t:
    description: AGRICOLA (AGRICultural OnLine Access) serves as the catalog and index
      to the collections of the National Agricultural Library, as well as a primary
      public source for world-wide access to agricultural information. The database
      covers materials in all formats and periods, including printed works from as
      far back as the 15th century.
    example: '50018'
    homepage: http://agricola.nal.usda.gov/
    name: AGRICOLA at National Agricultural Library
    namespaceEmbeddedInLui: false
    pattern: ^\d+$
    prefix: agricola
    uri_format: http://ddr.nal.usda.gov/dspace/handle/10113/$1
  name: Agricultural Online Access
  pattern: ^(IND|GUA)\d+$
  prefix: agricola
  providers:
  - code: usda
    description: This endpoint no longer works but is maintained for legacy purposes
    example: null
    first_party: null
    homepage: https://agricola.nal.usda.gov
    name: USDA Legacy Endpoint
    publications: null
    status: null
    uri_format: https://agricola.nal.usda.gov/vwebv/holdingsInfo?bibId=$1
  publications:
  - doi: 10.1093/nar/gkz813
    pmc: PMC6943066
    pubmed: '31552413'
    title: 'Alliance of Genome Resources Portal: unified model organism research platform'
    year: 2020
  references:
  - https://github.com/biopragmatics/bioregistry/pull/1098
  synonyms:
  - AGR
  - AGRICOLA_ID
  uri_format: https://europepmc.org/article/AGR/$1
  wikidata:
    database: Q4651693
agrkb:
  biolink:
    is_identifiers: false
    is_obo: false
    prefix: AGRKB
    uri_format: https://www.alliancegenome.org/$1
  contact:
    email: cjmungall@lbl.gov
    github: cmungall
    name: Chris Mungall
    orcid: 0000-0002-6601-2165
  contributor:
    email: smoxon@lbl.gov
    github: sierra-moxon
    name: Sierra Moxon
    orcid: 0000-0002-8719-7760
  description: 'The [Alliance of Genome Resources](https://www.alliancegenome.org/about-us)
    creates identifiers for several biological entity types including genes, other
    sequence features, constructs, morpholinos, TALENs, CRISPRs, variants, alleles,
    genotypes, strains, environments and experiments, phenotype annotations, expression
    annotations, disease annotations, interactions, and variant annotations.


    The Alliance of Genome Resources was founded by the following Model Organism databases
    and the Gene Ontology Consortium and distributes high-quality, curated knowledge
    about several model organisms in a single, unified location:


    - [ZFIN](https://zfin.org) - Zebrafish Information Network

    - [WormBase](https://wormbase.org)

    - [MGI](https://www.mgi.org) - Mouse Genome Informatics

    - [RGD](https://rgd.mcw.edu) - Rat Genome Database

    - [SGD](https://www.yeastgenome.org) - Saccharomyces Genome Database

    - [FlyBase](https://flybase.org)

    - [Xenbase](https://www.xenbase.org)'
  example: '100000000000001'
  github_request_issue: 359
  homepage: https://www.alliancegenome.org
  keywords:
  - model organism database
  mappings:
    biolink: AGRKB
    uniprot: DB-0266
  name: Alliance of Genome Resources Knowledge Base
  pattern: ^[1-9][0-9]{14}$
  prefix: agrkb
  reviewer:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  uniprot:
    abbreviation: AGR
    category: Organism-specific databases
    homepage: https://www.alliancegenome.org/
    name: The Alliance of Genome Resources
    prefix: DB-0266
    publications:
    - doi: 10.1093/nar/gkz813
      pubmed: '31552413'
    uri_format: https://www.alliancegenome.org/gene/$1
  uri_format: https://www.alliancegenome.org/accession/$1
agro:
  aberowl:
    description: Ontology of agronomic practices, agronomic techniques, and agronomic
      variables used in agronomic experiments
    download_owl: http://aber-owl.net/media/ontologies/AGRO/7/agro.owl
    homepage: https://github.com/AgriculturalSemantics/agro
    name: Agronomy Ontology
    prefix: AGRO
  agroportal:
    contact:
      email: m.a.laporte@cgiar.org
      name: Marie-Angélique Laporte
    description: AgrO is an ontlogy for representing agronomic practices, techniques,
      variables and related entities
    example_uri: http://purl.obolibrary.org/obo/AGRO_00000002
    homepage: https://bigdata.cgiar.org/resources/agronomy-ontology/
    license: CC-BY-4.0
    name: Agronomy Ontology
    prefix: AGRO
    publications:
    - http://ceur-ws.org/Vol-1747/IT205_ICBO2016.pdf
    repository: https://github.com/AgriculturalSemantics/agro
    version: '1.0'
  biocontext:
    prefix: AGRO
  bioportal:
    contact:
      email: m.a.laporte@cgiar.org
      name: Marie-Angélique Laporte
    description: AGRO, the AGRonomy Ontology, describes agronomic practices, agronomic
      techniques, and agronomic variables used in agronomic experiments. AGRO is being
      built using traits identified by agronomists, the ICASA variables, and other
      existing ontologies such as ENVO, UO, and PATO, IAO, and CHEBI. Further, AGRO
      will power an Agronomy Management System and fieldbook modeled on a CGIAR Breeding
      Management System to capture agronomic data.
    homepage: https://github.com/AgriculturalSemantics/agro
    name: AGRonomy Ontology
    prefix: AGRO
  contributor_extras:
  - email: sumirp77@gmail.com
    github: sumirp
    name: Sumir H Pandit
    orcid: 0000-0002-1216-4761
  download_obo: https://raw.githubusercontent.com/KrishnaTO/agro/master/agro.obo
  example: '00020007'
  fairsharing:
    abbreviation: AgrO
    description: AgrO, the Agronomy Ontology, describes agronomic practices, agronomic
      techniques, and agronomic variables used in agronomic experiments. AgrO is being
      built by CGIAR using traits identified by agronomists, the ICASA variables,
      and other existing ontologies such as ENVO, UO, and PATO. It will complement
      existing crop, livestock, and fish ontologies to enable harmonized approaches
      to data collection, facilitating easier data sharing and reuse. A key use case
      for AgrO is the Agronomy Field Information Management System (AgroFIMS). AgroFIMS
      enables digital collection of agronomic data that is semantically described
      a priori with agronomic terms from AgrO.
    domains:
    - Cropping systems
    homepage: https://bigdata.cgiar.org/resources/agronomy-ontology/
    license: CC-BY-4.0
    name: Agronomy Ontology
    prefix: FAIRsharing.m40bhw
    repository: https://github.com/AgriculturalSemantics/agro/issues/
    subjects:
    - Farming Systems Research
    - Agriculture
    - Agronomy
    - Plant Breeding
  mappings:
    aberowl: AGRO
    agroportal: AGRO
    biocontext: AGRO
    bioportal: AGRO
    fairsharing: FAIRsharing.m40bhw
    obofoundry: agro
    ols: agro
    ontobee: AGRO
    tib: agro
    wikidata.entity: Q81661533
  obofoundry:
    contact: m.a.laporte@cgiar.org
    contact.github: marieALaporte
    contact.label: Marie-Angélique Laporte
    contact.orcid: 0000-0002-8461-9745
    depends_on:
    - bfo
    - envo
    - foodon
    - go
    - iao
    - ncbitaxon
    - obi
    - pato
    - peco
    - po
    - ro
    - to
    - uo
    - xco
    deprecated: false
    description: Ontology of agronomic practices, agronomic techniques, and agronomic
      variables used in agronomic experiments
    domain: agriculture
    download.owl: http://purl.obolibrary.org/obo/agro.owl
    homepage: https://github.com/AgriculturalSemantics/agro
    license: CC BY 4.0
    license.url: https://creativecommons.org/licenses/by/4.0/
    name: Agronomy Ontology
    preferredPrefix: AGRO
    prefix: agro
    publications:
    - id: http://ceur-ws.org/Vol-1747/IT205_ICBO2016.pdf
      title: 'Data-driven Agricultural Research for Development: A Need for Data Harmonization
        Via Semantics.'
    repository: https://github.com/AgriculturalSemantics/agro
  ols:
    description: AgrO is an ontlogy for representing agronomic practices, techniques,
      variables and related entities
    download_owl: http://purl.obolibrary.org/obo/agro.owl
    homepage: https://github.com/AgriculturalSemantics/agro
    name: Agronomy Ontology
    prefix: agro
    tracker: https://github.com/AgriculturalSemantics/agro/issues/
    version: '2022-11-02'
    version.iri: http://purl.obolibrary.org/obo/agro/releases/2022-11-02/agro.owl
  ontobee:
    library: Library
    name: Agronomy Ontology
    prefix: AGRO
  pattern: ^\d{8}$
  prefix: agro
  references:
  - https://github.com/biopragmatics/bioregistry/pull/1098
  tib:
    description: AgrO is an ontlogy for representing agronomic practices, techniques,
      variables and related entities
    download_owl: http://purl.obolibrary.org/obo/agro.owl
    homepage: https://github.com/AgriculturalSemantics/agro
    keywords:
    - DataPLANT
    - agriculture
    name: Agronomy Ontology
    prefix: agro
    tracker: https://github.com/AgriculturalSemantics/agro/issues/
    version.iri: http://purl.obolibrary.org/obo/agro/releases/2022-11-02/agro.owl
  uri_format: http://purl.obolibrary.org/obo/AGRO_$1
  wikidata:
    database: Q81661533
agrovoc:
  aberowl:
    name: AGROVOC
    prefix: AGROVOC
  agroportal:
    contact:
      email: AGROVOC@fao.org
      name: AGROVOC
    description: AGROVOC is a multilingual and controlled vocabulary designed to cover
      concepts and terminology under FAO's areas of interest. It is a large Linked
      Open Data set about agriculture, available for public use, and its highest impact
      is through facilitating the access and visibility of data across domains and
      languages.
    example_uri: http://aims.fao.org/aos/agrovoc/c_38445
    homepage: http://www.fao.org/agrovoc/
    license: CC-BY-4.0
    name: AGROVOC
    prefix: AGROVOC
    publications:
    - https://www.fao.org/agrovoc/publications
  banana: c_
  bartoc:
    abbreviation: AGROVOC
    description: 'AGROVOC is a controlled vocabulary covering all areas of interest
      of the Food and Agriculture Organization (FAO) of the United Nations, including
      food, nutrition, agriculture, fisheries, forestry, environment etc. It is published
      by FAO and edited by a community of experts.


      AGROVOC consists of over 40,900 concepts available in up to 42 languages: Arabic,
      Belarusian, Chinese, Czech, English, Estonian, French, German, Hindi, Hungarian,
      Italian, Japanese, Korean, Lao, Malay, Norwegian Bokmål, Persian, Polish, Portuguese,
      Russian, Slovak, Spanish, Swahili, Telugu, Thai, Turkish, Ukrainian and others.


      You can use AGROVOC to look up the common name of a plant in a language that
      you do not master, or to find  relations between a commodity and the crop from
      which it is produced. Your library can use AGROVOC to index its documents, or
      you can use it from inside your content management system (e.g., Drupal) to
      organize your documents or web site. You can also use AGROVOC as an hub to access
      many other vocabularies available on the web.


      To date, AGROVOC is used by researchers, librarians and information managers
      for indexing, retrieving and organizing data in agricultural information systems
      and Web pages. Currently, AGROVOC is an SKOS-XL concept scheme and a Linked
      Open Data (LOD) set aligned with 16 other multilingual knowledge organization
      systems related to agriculture.


      You may download AGROVOC, access its Web Services or SPARQL endpoint.'
    homepage: http://www.fao.org/agrovoc/
    license: CC BY-SA 3.0
    name: AGROVOC
    prefix: '305'
    wikidata_database: Q292649
  bioportal:
    contact:
      email: alex.skrenchuk@stanford.edu
      name: Alex Skrenchuk
    description: AGROVOC is a multilingual and controlled vocabulary designed to cover
      concepts and terminology under FAO's areas of interest. It is a large Linked
      Open Data set about agriculture, available for public use, and its highest impact
      is through facilitating the access and visibility of data across domains and
      languages.
    name: AGROVOC
    prefix: AGROVOC
  comment: The download page for the [rdf](https://data.apps.fao.org/catalog/dataset/agrovoc-2025-07/resource/b5571fb6-7098-4866-b053-87b550e4624a)
    resource states it's available under CC-BY-4.0, though this information is not
    widely accesible on the website.
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: AGROVOC is a multilingual and controlled vocabulary designed to cover
    concepts and terminology under FAO's areas of interest. It is the largest Linked
    Open Data set about agriculture available for public use and its greatest impact
    is through providing the access and visibility of data across domains and languages.
  download_rdf: https://agrovoc.fao.org/latestAgrovoc/agrovoc_core.rdf.zip
  ecoportal:
    contact:
      email: agrovoc@fao.org
      name: AGROVOC Team
    description: AGROVOC is a multilingual, multidisciplinary thesaurus covering the
      activities of the Food and Agriculture Organization of the UN. AGROVOC covers
      all areas of interest to FAO, such as food, nutrition, agriculture, forestry,
      fisheries, names of animals and plants, environment, biological notions, techniques
      of plant cultivation, etc. It is coordinated by FAO, with a network of institutions
      responsible for the different language versions and domains. As of March 2024,
      AGROVOC consists of +41 000 concepts and +1 145 000 terms in up to 42 languages.
    example_uri: http://aims.fao.org/aos/agrovoc/c_38445
    homepage: https://agrovoc.fao.org/browse/agrovoc/en/
    license: CC-BY-4.0
    name: AGROVOC
    prefix: AGROVOC
    publications:
    - https://www.fao.org/agrovoc/publications
    version: 2024-04
  example: '2842'
  fairsharing:
    abbreviation: AGROVOC
    description: AGROVOC is a controlled vocabulary covering all areas of interest
      of the Food and Agriculture Organization (FAO) of the United Nations, including
      food, nutrition, agriculture, fisheries, forestry, environment etc. It is published
      by FAO and edited by a community of experts. AGROVOC consists of over 41,400
      concepts available in up to 42 languages. AGROVOC uses semantic web technologies,
      linking to other multilingual knowledge organization systems and building bridges
      between datasets. Your library can use AGROVOC to index its documents or datasets,
      or you can use it from inside your content management system (e.g., Drupal)
      to organize your documents or web site. You can also use AGROVOC as an hub to
      access many other vocabularies available on the web.  To date, AGROVOC is used
      by researchers, librarians and information managers for indexing, retrieving
      and organizing data in agricultural information systems and Web pages. Currently,
      AGROVOC is an SKOS-XL concept scheme and a Linked Open Data (LOD*) set aligned
      with over 20 other multilingual knowledge organization systems related to agriculture.
      You may browse AGROVOC, access its Web Services or SPARQL endpoint.
    domains:
    - Agricultural products
    - food
    - climate
    homepage: https://www.fao.org/agrovoc/
    license: CC-BY-4.0
    name: AGROVOC
    prefix: FAIRsharing.anpj91
    publications:
    - doi: 10.3390/engproc2021009017
      title: 'How Agricultural Digital Innovation Can Benefit from Semantics: The
        Case of the AGROVOC Multilingual Thesaurus'
      year: 2021
    - doi: 10.4060/cb2838en
      title: AGROVOC – Semantic data interoperability on food and agriculture
      year: 2021
    - doi: 10.1016/j.compag.2020.105965
      title: 'AGROVOC: The linked data concept hub for food and agriculture'
      year: 2022
    subjects:
    - Food Security
    - Forest Management
    - Agriculture
    - Agronomy
    - Fisheries Science
    - Environmental Science
    - Aquaculture
    - Water Management
    - Knowledge and Information Systems
    - Botany
    - Data Management
    - Nutritional Science
    twitter: FAOAIMS
  homepage: https://data.apps.fao.org/catalog/organization/agrovoc
  license: CC-BY-4.0
  mappings:
    aberowl: AGROVOC
    agroportal: AGROVOC
    bartoc: '305'
    bioportal: AGROVOC
    ecoportal: AGROVOC
    fairsharing: FAIRsharing.anpj91
    wikidata: P8061
    wikidata.entity: Q292649
  name: Agronomy Vocabulary
  pattern: ^[a-z0-9]+$
  prefix: agrovoc
  publications:
  - doi: 10.1016/j.compag.2020.105965
    pmc: null
    pubmed: null
    title: 'AGROVOC: The linked data concept hub for food and agriculture'
    year: 2022
  - doi: 10.4060/cb2838en
    pmc: null
    pubmed: null
    title: AGROVOC
    year: 2021
  - doi: 10.3390/engproc2021009017
    pmc: null
    pubmed: null
    title: 'How Agricultural Digital Innovation Can Benefit from Semantics: The Case
      of the AGROVOC Multilingual Thesaurus'
    year: 2021
  references:
  - http://agrovoc.uniroma2.it/latestAgrovoc/agrovoc_core.nt.zip
  - http://agrovoc.uniroma2.it/latestAgrovoc/agrovoc_lod.nt.zip
  - https://en.wikipedia.org/wiki/AGROVOC
  uri_format: http://aims.fao.org/aos/agrovoc/c_$1
  wikidata:
    database: Q292649
    description: identifier for a subject in AGROVOC thesaurus
    example:
    - c_00824893
    - c_10
    - c_33507
    name: AGROVOC ID
    prefix: P8061
    uri_format: https://aims.fao.org/aos/agrovoc/$1
    uri_format_rdf: http://aims.fao.org/aos/agrovoc/$1
agsc:
  contact:
    email: srvoss@uky.edu
    github: null
    name: Stephen Randal Voss
    orcid: 0000-0002-8332-3176
  description: The Ambystoma Genetic Stock Center (AGSC) maintains a breeding colony
    of Mexican axolotls (Ambystoma mexicanum) and distributes axolotl embryos, larvae,
    and adults to laboratories and classrooms throughout the United States and abroad.
    [from homepage]
  example: 100E
  mappings:
    rrid: AGSC
  prefix: agsc
  rrid:
    homepage: https://ambystoma.uky.edu/genetic-stock-center/
    keywords:
    - adult
    - ambystoma
    - embryo
    - k-12 teacher
    - larvae
    - salamander
    name: Ambystoma Genetic Stock Center
    prefix: AGSC
    pubmeds:
    - '16359543'
    scr: '006372'
  uri_format: https://scicrunch.org/resolver/RRID:AGSC_$1
agsd:
  contributor_extras:
  - email: sumirp77@gmail.com
    github: sumirp
    name: Sumir H Pandit
    orcid: 0000-0002-1216-4761
  fairsharing:
    abbreviation: AGSD
    description: A comprehensive catalogue of animal genome size data where haploid
      DNA contents (C-values, in picograms) are currently available for 4972 species
      (3231 vertebrates and 1741 non-vertebrates) based on 6518 records from 669 published
      sources.
    homepage: http://www.genomesize.com
    name: Animal Genome Size Database
    prefix: FAIRsharing.efp5v2
    publications: []
    subjects:
    - Life Science
  mappings:
    fairsharing: FAIRsharing.efp5v2
    prefixcommons: agsd
    re3data: r3d100012517
    wikidata.entity: Q4764809
  prefix: agsd
  prefixcommons:
    description: The Animal Genome Size Database (AGSD) is a comprehensive catalogue
      of animal genome size data where haploid DNA contents (C-values, in picograms)
      are currently available for 4972 species (3231 vertebrates and 1741 non-vertebrates)
      based on 6518 records from 669 published sources.
    example: '4779'
    homepage: http://www.genomesize.com
    keywords:
    - DNA
    - genome
    name: Animal Genome Size Database
    pattern: ^\d+$
    prefix: agsd
    uri_format: http://www.genomesize.com/result_species.php?id=$1
  re3data:
    description: Welcome to the Animal Genome Size Database, Release 2.0, a comprehensive
      catalogue of animal genome size data.
    doi: 10.17616/R3R782
    homepage: https://www.genomesize.com/
    name: Animal Genome Size Database
    prefix: r3d100012517
    xrefs:
      nif: 0000-02548
      omics: '16749'
  references:
  - https://github.com/biopragmatics/bioregistry/pull/1098
  reviewer:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  wikidata:
    database: Q4764809
aio:
  aberowl:
    description: This ontology models classes and relationships describing deep learning
      networks, their component layers and activation functions, as well as potential
      biases.
    download_owl: http://aber-owl.net/media/ontologies/AIO/23/aio.owl
    homepage: https://github.com/berkeleybop/artificial-intelligence-ontology
    name: Artificial Intelligence Ontology
    prefix: AIO
    version: '2024-11-11'
  bioportal:
    contact:
      email: MJoachimiak@lbl.gov
      name: marcin pawel joachimiak
    description: This ontology models classes and relationships describing deep learning
      networks, their component layers and activation functions, as well as potential
      biases.
    homepage: https://github.com/berkeleybop/artificial-intelligence-ontology
    name: Artificial Intelligence Ontology
    prefix: AIO
    publications:
    - https://arxiv.org/abs/2404.03044
    version: '2024-11-11'
  contact:
    email: MJoachimiak@lbl.gov
    github: realmarcin
    name: Marcin Pawel Joachimiak
    orcid: 0000-0001-8175-045X
  contributor:
    email: Lindsey.Anderson@pnnl.gov
    github: lnanderson
    name: Lindsey N. Anderson
    orcid: 0000-0002-8741-7823
  description: This ontology models classes and relationships describing deep learning
    networks, their component layers and activation functions, as well as potential
    biases.
  download_json: https://raw.githubusercontent.com/berkeleybop/artificial-intelligence-ontology/main/aio.json
  download_obo: https://raw.githubusercontent.com/berkeleybop/artificial-intelligence-ontology/main/aio.obo
  download_owl: https://raw.githubusercontent.com/berkeleybop/artificial-intelligence-ontology/main/aio.owl
  example: Causal_Graphical_Model
  fairsharing:
    abbreviation: AIO
    contact:
      email: MJoachimiak@lbl.gov
      name: Marcin P. Joachimiak
      orcid: 0000-0001-8175-045X
    description: The Artificial Intelligence Ontology (AIO) is a systematized collection
      of terms covering artificial intelligence (AI) concepts, methodologies, and
      interrelations aimed to address the rapidly evolving landscape of AI terminolgy
      by providing a comprehensive framework that encompasses both technical and ethical
      aspects of AI technologies. The primary audience for this collection includes
      AI researchers, developers, and educators seeking to standardize terminology
      and concepts within the AI domain.
    domains:
    - Machine Learning
    - Natural Language Processing
    - Knowledge representation
    homepage: https://github.com/berkeleybop/artificial-intelligence-ontology
    license: CC-BY-4.0
    name: Artificial Intelligence Ontology
    prefix: FAIRsharing.8d6247
    publications:
    - doi: 10.48550/arxiv.2404.03044
      title: 'The Artificial Intelligence Ontology: LLM-assisted construction of AI
        concept hierarchies'
      year: 2024
    repository: https://github.com/berkeleybop/artificial-intelligence-ontology
    subjects:
    - Computational Biology
    - Artificial Intelligence
  github_request_issue: 884
  homepage: https://github.com/berkeleybop/artificial-intelligence-ontology
  mappings:
    aberowl: AIO
    bioportal: AIO
    fairsharing: FAIRsharing.8d6247
  name: The Artificial Intelligence Ontology
  prefix: aio
  repository: https://github.com/berkeleybop/artificial-intelligence-ontology
  reviewer:
    email: benjamin_gyori@hms.harvard.edu
    github: bgyori
    name: Benjamin M. Gyori
    orcid: 0000-0001-9439-5346
  uri_format: https://w3id.org/aio/$1
aism:
  aberowl:
    description: The AISM contains terms used in insect biodiversity research for
      describing structures of the exoskeleton and the skeletomuscular system. It
      aims to serve as the basic backbone of generalized terms to be expanded with
      order-specific terminology.
    download_owl: http://aber-owl.net/media/ontologies/AISM/20/aism.owl
    homepage: https://github.com/insect-morphology/aism
    name: Ontology for the Anatomy of the Insect SkeletoMuscular system (AISM)
    prefix: AISM
  bioportal:
    contact:
      email: entiminae@gmail.com
      name: Jennifer C. Girón
    description: The AISM contains terms used in insect biodiversity research for
      describing structures of the exoskeleton and the skeletomuscular system. It
      aims to serve as the basic backbone of generalized terms to be expanded with
      order-specific terminology.
    homepage: https://github.com/insect-morphology/aism
    name: Ontology for the Anatomy of the Insect SkeletoMuscular system
    prefix: AISM
    publications:
    - http://www.example.com
    version: '2023-04-14'
  contributor_extras:
  - email: sumirp77@gmail.com
    github: sumirp
    name: Sumir H Pandit
    orcid: 0000-0002-1216-4761
  example: '0000027'
  mappings:
    aberowl: AISM
    bioportal: AISM
    obofoundry: aism
    ols: aism
    ontobee: AISM
    wikidata.entity: Q112972813
  name: Ontology for the Anatomy of the Insect SkeletoMuscular system
  obofoundry:
    appears_in:
    - colao
    - lepao
    contact: entiminae@gmail.com
    contact.github: JCGiron
    contact.label: Jennifer C. Girón
    contact.orcid: 0000-0002-0851-6883
    depends_on:
    - bfo
    - bspo
    - caro
    - pato
    - ro
    - uberon
    deprecated: false
    description: The AISM contains terms used in insect biodiversity research for
      describing structures of the exoskeleton and the skeletomuscular system. It
      aims to serve as the basic backbone of generalized terms to be expanded with
      order-specific terminology.
    domain: anatomy and development
    download.json: http://purl.obolibrary.org/obo/aism.json
    download.obo: http://purl.obolibrary.org/obo/aism.obo
    download.owl: http://purl.obolibrary.org/obo/aism.owl
    homepage: https://github.com/insect-morphology/aism
    license: CC BY 4.0
    license.url: https://creativecommons.org/licenses/by/4.0/
    name: Ontology for the Anatomy of the Insect SkeletoMuscular system (AISM)
    preferredPrefix: AISM
    prefix: aism
    repository: https://github.com/insect-morphology/aism
  ols:
    description: The ontology for the Anatomy of the Insect SkeletoMuscular system
      (AISM) contains terms used to describe the cuticle - as a single anatomical
      structure - and the skeletal muscle system, to be used in insect biodiversity
      research.
    download_owl: http://purl.obolibrary.org/obo/aism.owl
    homepage: https://github.com/insect-morphology/aism
    name: Ontology for the Anatomy of the Insect SkeletoMuscular system
    prefix: aism
    tracker: https://github.com/insect-morphology/aism/issues
    version: '2025-03-18'
    version.iri: http://purl.obolibrary.org/obo/aism/releases/2025-03-18/aism.owl
  ontobee:
    library: Library
    name: Ontology for the Anatomy of the Insect SkeletoMuscular system (AISM)
    prefix: AISM
  pattern: ^\d{7}$
  prefix: aism
  references:
  - https://github.com/biopragmatics/bioregistry/pull/1098
  uri_format: http://purl.obolibrary.org/obo/AISM_$1
  wikidata:
    database: Q112972813
alfred:
  comment: This resource doesn't exist on the web anymore
  contributor_extras:
  - email: sumirp77@gmail.com
    github: sumirp
    name: Sumir H Pandit
    orcid: 0000-0002-1216-4761
  deprecated: true
  mappings:
    prefixcommons: alfred
    wikidata.entity: Q294392
  prefix: alfred
  prefixcommons:
    description: ALFRED has been designed to make allele frequency data on anthropologically
      defined human population samples readily available to the scientific community
      and to link these polymorphism data to the molecular genetics-human genome databases.
    example: LO362836C
    homepage: http://alfred.med.yale.edu
    keywords:
    - classification
    - genome
    license: http://alfred.med.yale.edu/alfred/fullcopyrightpage.asp
    name: The ALlele FREquency Database
    pattern: ^[A-Z]+\d+$
    prefix: alfred
    pubmed_ids:
    - '12519999'
    uri_format: https://alfred.med.yale.edu/alfred/recordinfo.asp?UNID=$1
  publications:
  - doi: 10.1093/nar/gkg043
    pmc: PMC165490
    pubmed: '12519999'
    title: 'ALFRED: the ALelle FREquency Database. Update'
    year: 2003
  - doi: null
    pmc: null
    pubmed: '12519999'
    title: null
    year: null
  references:
  - https://github.com/biopragmatics/bioregistry/pull/1098
  reviewer:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  wikidata:
    database: Q294392
allergome:
  biocontext:
    prefix: ALLERGOME
  contact:
    email: adriano.mari@allergome.org
    github: null
    name: Adriano Mari
    orcid: 0000-0002-9137-1442
  contributor_extras:
  - email: sumirp77@gmail.com
    github: sumirp
    name: Sumir H Pandit
    orcid: 0000-0002-1216-4761
  fairsharing:
    abbreviation: Allergome
    description: Allergome aims to supply information on Allergenic Molecules (Allergens)
      causing an IgE-mediated (allergic, atopic) disease (anaphylaxis, asthma, atopic
      dermatitis, conjunctivitis, rhinitis, urticaria). The resource is funded through
      the Allergen Data Laboratories via unrestricted grants from companies and institutions.
    homepage: http://www.allergome.org/
    license: https://creativecommons.org/licenses/by-nc-sa/2.5
    name: Allergome
    prefix: FAIRsharing.w6cxgb
    publications:
    - doi: null
      pubmed_id: 17393720
      title: 'Allergome: a unifying platform.'
    - doi: 10.1016/j.cellimm.2007.02.012
      pubmed_id: 17434469
      title: 'Bioinformatics applied to allergy: allergen databases, from collecting
        sequence information to data integration. The Allergome platform as a model.'
    subjects:
    - Medicine
    - Health Science
    - Life Science
    - Biomedical Science
  integbio:
    description: Allergome aims to supply information on Allergenic Molecules (Allergens)
      causing an IgE-mediated (allergic, atopic) disease (anaphylaxis, asthma, atopic
      dermatitis, conjunctivitis, rhinitis, urticaria). The resource is funded through
      the Allergen Data Laboratories via unrestricted grants from companies and institutions.
    fairsharing: FAIRsharing.w6cxgb
    homepage: http://www.allergome.org/
    information_keywords:
    - Sequence
    - Taxonomy
    maintainer: Allergy Data Laboratories s.c.||IFARAI (International Fund for Advanced
      Research in Allergy and Immunology)
    name: Allergome
    prefix: nbdc01708
    pubmeds:
    - '17393720'
    - '17434469'
    status: Active
    target_keywords:
    - Metabolite
    - Health/Disease
  mappings:
    biocontext: ALLERGOME
    fairsharing: FAIRsharing.w6cxgb
    integbio: nbdc01708
    miriam: allergome
    n2t: allergome
    prefixcommons: allergome
    uniprot: DB-0160
    wikidata.entity: Q111136043
  miriam:
    deprecated: false
    description: Allergome is a repository of data related to all IgE-binding compounds.
      Its purpose is to collect a list of allergenic sources and molecules by using
      the widest selection criteria and sources.
    homepage: http://www.allergome.org/
    id: '00000334'
    name: Allergome
    namespaceEmbeddedInLui: false
    pattern: ^\d+$
    prefix: allergome
    sampleId: '1948'
    uri_format: http://www.allergome.org/script/dettaglio.php?id_molecule=$1
  n2t:
    description: Allergome is a repository of data related to all IgE-binding compounds.
      Its purpose is to collect a list of allergenic sources and molecules by using
      the widest selection criteria and sources.
    example: '1948'
    homepage: http://www.allergome.org/
    name: Allergome at Rome
    namespaceEmbeddedInLui: false
    pattern: ^\d+$
    prefix: allergome
    uri_format: http://www.allergome.org/script/dettaglio.php?id_molecule=$1
  prefix: allergome
  prefixcommons:
    description: Allergome aims to supply information on Allergenic Molecules (Allergens)
      causing an IgE-mediated (allergic, atopic) disease (anaphylaxis, asthma, atopic
      dermatitis, conjunctivitis, rhinitis, urticaria).
    example: '1948'
    homepage: http://www.allergome.org
    keywords:
    - allergen
    license: CC BY-NC-SA 2.5
    miriam: allergome
    name: 'Allergome: a platform for allergen knowledge'
    pattern: ^\d+$
    prefix: allergome
    pubmed_ids:
    - '17393720'
    - '17434469'
    uri_format: http://www.allergome.org/script/refArray_view.php?idMol=$1
  publications:
  - doi: 10.1007/s11882-009-0055-9
    pmc: null
    pubmed: '19671381'
    title: 'Allergen databases: current status and perspectives'
    year: 2009
  - doi: 10.1016/j.cellimm.2007.02.012
    pmc: null
    pubmed: '17434469'
    title: 'Bioinformatics applied to allergy: allergen databases, from collecting
      sequence information to data integration. The Allergome platform as a model'
    year: 2007
  - doi: null
    pmc: null
    pubmed: '17393720'
    title: 'Allergome: a unifying platform'
    year: 2006
  - doi: 10.1016/j.cellimm.2007.02.012
    pmc: null
    pubmed: null
    title: 'Bioinformatics applied to allergy: allergen databases, from collecting
      sequence information to data integration. The Allergome platform as a model.'
    year: null
  - doi: null
    pmc: null
    pubmed: '17393720'
    title: null
    year: null
  - doi: null
    pmc: null
    pubmed: '17434469'
    title: null
    year: null
  - doi: 10.1007/s11882-009-0055-9
    pmc: null
    pubmed: '19671381'
    title: null
    year: null
  - doi: 10.1016/j.cellimm.2007.02.012
    pmc: null
    pubmed: null
    title: 'Bioinformatics applied to allergy: allergen databases, from collecting
      sequence information to data integration. The Allergome platform as a model.'
    year: null
  - doi: null
    pmc: null
    pubmed: '17393720'
    title: null
    year: null
  - doi: null
    pmc: null
    pubmed: '17434469'
    title: null
    year: null
  - doi: 10.1007/s11882-009-0055-9
    pmc: null
    pubmed: '19671381'
    title: null
    year: null
  references:
  - https://github.com/biopragmatics/bioregistry/pull/1098
  uniprot:
    abbreviation: Allergome
    category: Protein family/group databases
    homepage: https://www.allergome.org/
    name: Allergome; a platform for allergen knowledge
    prefix: DB-0160
    publications:
    - doi: 10.1007/s11882-009-0055-9
      pubmed: '19671381'
    uri_format: https://www.allergome.org/script/dettaglio.php?id_molecule=$1
  wikidata:
    database: Q111136043
alzforum.mutation:
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  contributor_extras:
  - email: sumirp77@gmail.com
    github: sumirp
    name: Sumir H Pandit
    orcid: 0000-0002-1216-4761
  description: Alzforum mutations is a repository of genes and rare variants associated
    with Alzheimer's disease.
  example: app-d678n-tottori
  homepage: https://www.alzforum.org/mutations
  keywords:
  - alzheimer's disease
  - genes
  - variants
  mappings:
    wikidata.entity: Q111254799
  name: Alzforum Mutations
  prefix: alzforum.mutation
  references:
  - https://github.com/biopragmatics/bioregistry/pull/1098
  synonyms:
  - Alzforum_mut
  uri_format: https://www.alzforum.org/mutations/$1
  wikidata:
    database: Q111254799
alzgene:
  contact:
    email: bertram@helix.mgh.harvard.edu
    github: null
    name: Lars Bertram
    orcid: 0000-0002-0108-124X
  mappings:
    prefixcommons: alzgene
  prefix: alzgene
  prefixcommons:
    description: The AlzGene database provides a comprehensive, unbiased and regularly
      updated field synopsis of genetic association studies performed in Alzheimer’s
      disease. In addition, hundreds of up-to-date meta-analyses are available for
      all eligible polymorphisms with sufficient data.
    example: '88'
    homepage: http://www.alzgene.org
    keywords:
    - gene
    name: Alzheimer Gene Database
    pattern: ^\d+$
    prefix: alzgene
    pubmed_ids:
    - '17192785'
    uri_format: http://www.alzgene.org/geneoverview.asp?geneid=$1
  publications:
  - doi: 10.1038/ng1934
    pmc: null
    pubmed: '17192785'
    title: 'Systematic meta-analyses of Alzheimer disease genetic association studies:
      the AlzGene database'
    year: 2007
  reviewer:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
amoebadb:
  biocontext:
    prefix: AMOEBADB
  contact:
    email: oharb@upenn.edu
    github: ramobrah
    name: Omar S. Harb
    orcid: 0000-0003-4446-6200
  contributor_extras:
  - email: sumirp77@gmail.com
    github: sumirp
    name: Sumir H Pandit
    orcid: 0000-0002-1216-4761
  fairsharing:
    abbreviation: AmoebaDB
    description: AmoebaDB belongs to the EuPathDB family of databases and is an integrated
      genomic and functional genomic database for Entamoeba and Acanthamoeba parasites.
      In its first released, AmoebaDB contained the genomes of three Entamoeba species.
      AmoebaDB integrates whole genome sequence and annotation and will rapidly expand
      to include experimental data and environmental isolate sequences provided by
      community researchers . The database includes supplemental bioinformatics analyses
      and a web interface for data-mining.
    homepage: http://amoebadb.org
    name: AmoebaDB
    prefix: FAIRsharing.swbypy
    publications:
    - doi: 10.1093/nar/gkp941
      pubmed_id: 19914931
      title: 'EuPathDB: a portal to eukaryotic pathogen databases.'
    subjects:
    - Functional Genomics
    - Genomics
    twitter: eupathdb
  integbio:
    description: This is an database of genomes and results of functional genomic
      analysis of parasitic amoeba such as Entamoeba histolytica and Acanthamoeba,
      which is a family database of the EuPathDB. It includes the full genome sequence
      data and microarray expression data. A wide variety of search and download functions,
      as well as bioinformatics tools are supported for genes, genomes, motifs, SNPs,
      ESTs, and ORFs.
    fairsharing: biodbcore-000564
    homepage: http://amoebadb.org/amoeba/
    information_keywords:
    - Sequence
    - Expression
    - Repository
    maintainer: EuPathDB Bioinformatics Resource Center
    name: AmoebaDB
    prefix: nbdc01207
    pubmeds:
    - '20974635'
    - '19914931'
    status: Active
    target_keywords:
    - Genome/Gene
    - cDNA/EST
    - Genetic variation
    - Protein
  mappings:
    biocontext: AMOEBADB
    fairsharing: FAIRsharing.swbypy
    integbio: nbdc01207
    miriam: amoebadb
    n2t: amoebadb
    prefixcommons: amoebadb
    re3data: r3d100012457
    wikidata.entity: Q4747456
  miriam:
    deprecated: false
    description: AmoebaDB is one of the databases that can be accessed through the
      EuPathDB (http://EuPathDB.org; formerly ApiDB) portal, covering eukaryotic pathogens
      of the genera Cryptosporidium, Giardia, Leishmania, Neospora, Plasmodium, Toxoplasma,
      Trichomonas and Trypanosoma. While each of these groups is supported by a taxon-specific
      database built upon the same infrastructure, the EuPathDB portal offers an entry
      point to all these resources, and the opportunity to leverage orthology for
      searches across genera.
    homepage: http://amoebadb.org/amoeba/
    id: 00000148
    name: AmoebaDB
    namespaceEmbeddedInLui: false
    pattern: ^EDI_\d+$
    prefix: amoebadb
    sampleId: EDI_244000
    uri_format: https://amoebadb.org/amoeba/app/record/gene/$1
  n2t:
    description: AmoebaDB is one of the databases that can be accessed through the
      EuPathDB (http://EuPathDB.org; formerly ApiDB) portal, covering eukaryotic pathogens
      of the genera Cryptosporidium, Giardia, Leishmania, Neospora, Plasmodium, Toxoplasma,
      Trichomonas and Trypanosoma. While each of these groups is supported by a taxon-specific
      database built upon the same infrastructure, the EuPathDB portal offers an entry
      point to all these resources, and the opportunity to leverage orthology for
      searches across genera.
    example: EDI_244000
    homepage: http://amoebadb.org/amoeba/
    name: AmoebaDB at EuPathDB
    namespaceEmbeddedInLui: false
    pattern: ^EDI_\d+$
    prefix: amoebadb
    uri_format: https://amoebadb.org/amoeba/app/record/gene/$1
  prefix: amoebadb
  prefixcommons:
    description: AmoebaDB is one of the databases that can be accessed through the
      EuPathDB (http://EuPathDB.org; formerly ApiDB) portal, covering eukaryotic pathogens
      of the genera Cryptosporidium, Giardia, Leishmania, Neospora, Plasmodium, Toxoplasma,
      Trichomonas and Trypanosoma. While each of these groups is supported by a taxon-specific
      database built upon the same infrastructure, the EuPathDB portal offers an entry
      point to all these resources, and the opportunity to leverage orthology for
      searches across genera.
    example: EDI_244000
    homepage: http://amoebadb.org
    keywords:
    - model organism
    miriam: amoebadb
    name: AmoebaDB
    pattern: ^EDI_\d+$
    prefix: amoebadb
    pubmed_ids:
    - '19914931'
    uri_format: https://amoebadb.org/amoeba/app/record/gene/$1
  publications:
  - doi: 10.1093/nar/gkp941
    pmc: PMC2808945
    pubmed: '19914931'
    title: 'EuPathDB: a portal to eukaryotic pathogen databases'
    year: 2009
  re3data:
    description: AmoebaDB belongs to the EuPathDB family of databases and is an integrated
      genomic and functional genomic database for Entamoeba and Acanthamoeba parasites.
      In its first iteration (released in early 2010), AmoebaDB contains the genomes
      of three Entamoeba species (see below). AmoebaDB integrates whole genome sequence
      and annotation and will rapidly expand to include experimental data and environmental
      isolate sequences provided by community researchers . The database includes
      supplemental bioinformatics analyses and a web interface for data-mining.
    doi: 10.17616/R3PX9Q
    homepage: https://amoebadb.org/amoeba/app
    name: AmoebaDB
    prefix: r3d100012457
  references:
  - https://github.com/biopragmatics/bioregistry/pull/1098
  wikidata:
    database: Q4747456
amphibiaweb.species:
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  github_request_issue: 1552
  homepage: https://amphibiaweb.org
  mappings:
    wikidata: P5036
  prefix: amphibiaweb.species
  uri_format: https://amphibiaweb.org/species/$1
  wikidata:
    description: identifier for a species, in the AmphibiaWeb database
    example:
    - '149'
    - '165'
    - '8667'
    name: AmphibiaWeb Species ID
    pattern: ^[1-9]\d*$
    prefix: P5036
    uri_format: https://amphibiaweb.org/species/$1
amphx:
  aberowl:
    description: An ontology for the development and anatomy of Amphioxus (Branchiostoma
      lanceolatum).
    download_owl: http://aber-owl.net/media/ontologies/AMPHX/4/amphx.owl
    homepage: https://github.com/EBISPOT/amphx_ontology
    name: The Amphioxus Development and Anatomy Ontology
    prefix: AMPHX
  bioportal:
    contact:
      email: hescriva@obs-banyuls.fr
      name: Hector Escriva
    description: An ontology for the development and anatomy of Amphioxus (Branchiostoma
      lanceolatum).
    homepage: https://github.com/EBISPOT/amphx_ontology
    name: The Amphioxus Development and Anatomy Ontology
    prefix: AMPHX
  contributor_extras:
  - email: sumirp77@gmail.com
    github: sumirp
    name: Sumir H Pandit
    orcid: 0000-0002-1216-4761
  example: '1000160'
  mappings:
    aberowl: AMPHX
    bioportal: AMPHX
    obofoundry: amphx
    ols: amphx
    ontobee: AMPHX
    wikidata.entity: Q112972859
  obofoundry:
    contact: hescriva@obs-banyuls.fr
    contact.github: hescriva
    contact.label: Hector Escriva
    contact.orcid: 0000-0001-7577-5028
    depends_on:
    - uberon
    deprecated: false
    description: An ontology for the development and anatomy of Amphioxus (Branchiostoma
      lanceolatum).
    domain: anatomy and development
    download.obo: http://purl.obolibrary.org/obo/amphx.obo
    download.owl: http://purl.obolibrary.org/obo/amphx.owl
    homepage: https://github.com/EBISPOT/amphx_ontology
    license: CC BY 3.0
    license.url: http://creativecommons.org/licenses/by/3.0/
    name: The Amphioxus Development and Anatomy Ontology
    preferredPrefix: AMPHX
    prefix: amphx
    repository: https://github.com/EBISPOT/amphx_ontology
  ols:
    description: An ontology for the development and anatomy of Amphioxus (Branchiostoma
      lanceolatum).
    download_owl: http://purl.obolibrary.org/obo/amphx.owl
    homepage: https://github.com/EBISPOT/amphx_ontology
    name: Amphioxus Development and Anatomy Ontology (AMPHX)
    prefix: amphx
    tracker: https://github.com/EBISPOT/amphx_ontology/issues
    uri_format: http://purl.obolibrary.org/obo/AMPHX_$1
    version: '2020-12-18'
    version.iri: http://purl.obolibrary.org/obo/amphx/releases/2020-12-18/amphx.owl
  ontobee:
    library: Library
    name: The Amphioxus Development and Anatomy Ontology
    prefix: AMPHX
  pattern: ^\d+$
  prefix: amphx
  references:
  - https://github.com/biopragmatics/bioregistry/pull/1098
  uri_format: http://purl.obolibrary.org/obo/AMPHX_$1
  wikidata:
    database: Q112972859
ans.educationlevel:
  contact:
    email: sasutton@uw.edu
    github: stuartasutton
    name: Stuart A. Sutton
    orcid: 0000-0002-3511-2892
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: This vocabulary defines education levels for pre-kindergarten through
    grade 12 for the United States. It also defines general categories for post-secondary
    education (vocational, professional and life-long learning).
  download_skos:
    rdf_format: xml
    url: https://s3.amazonaws.com/jestaticd2l/purl/scheme/ASNEducationLevel
  example: Pre-K
  example_extras:
  - '1'
  - '2'
  - K
  homepage: http://purl.org/ASN/scheme/ASNEducationLevel/
  keywords:
  - education level
  - open educational resources
  name: U.S. Education Level Vocabulary
  prefix: ans.educationlevel
  uri_format: http://purl.org/ASN/scheme/ASNEducationLevel/$1
antibodyregistry:
  biocontext:
    prefix: ANTIBODYREGISTRY
  contact:
    email: abandrowski@ncmir.ucsd.edu
    github: bandrow
    name: Anita Bandrowski
    orcid: 0000-0002-5497-0243
  contact_group_email: rii-help@scicrunch.org
  contributor_extras:
  - email: sumirp77@gmail.com
    github: sumirp
    name: Sumir H Pandit
    orcid: 0000-0002-1216-4761
  domain: antibody
  integbio:
    description: 'The Antibody Registry exists to give researchers a way to universally
      identify antibodies used in publications. The registry lists many commercial
      antibodies from about 200 vendors which have each been assigned a unique identifier.
      If the antibody that you are using does not appear in the list, an entry can
      be made by filling in as little as 2 pieces of information: the catalog number
      and the url of the vendor where our curators can find information and material
      data sheets. Many optional fields can also be filled in that will help curators
      identify the reagent. After submitting an antibody, you are given a permanent
      identifier that can be used in publications. This identifier even if it is later
      found to be a duplicate, can be quickly traced back in the antibody registry.
      We never delete records, but we collapse duplicate entries on a regular basis
      (the old identifiers are kept to help with search).'
    fairsharing: FAIRsharing.3wdd17
    homepage: https://antibodyregistry.org/
    information_keywords:
    - Interaction/Pathway
    - Method
    maintainer: NIF (Neuroscience Information Framework)
    name: Antibody Registry
    prefix: nbdc01696
    pubmeds:
    - '24032093'
    status: Active
    target_keywords:
    - Protein
  logo: https://www.antibodyregistry.org/assets/logo.svg
  mappings:
    biocontext: ANTIBODYREGISTRY
    integbio: nbdc01696
    miriam: antibodyregistry
    n2t: antibodyregistry
    rrid: AB
    wikidata.entity: Q111182712
  miriam:
    deprecated: false
    description: The Antibody Registry provides identifiers for antibodies used in
      publications. It lists commercial antibodies from numerous vendors, each assigned
      with a unique identifier. Unlisted antibodies can be submitted by providing
      the catalog number and vendor information.
    homepage: http://antibodyregistry.org/
    id: '00000516'
    name: Antibody Registry
    namespaceEmbeddedInLui: false
    pattern: ^\d{6}$
    prefix: antibodyregistry
    sampleId: '493771'
    uri_format: http://antibodyregistry.org/AB_$1
  n2t:
    description: The Antibody Registry provides identifiers for antibodies used in
      publications. It lists commercial antibodies from numerous vendors, each assigned
      with a unique identifier. Unlisted antibodies can be submitted by providing
      the catalog number and vendor information.
    example: '493771'
    homepage: http://antibodyregistry.org/
    name: Antibody Registry at University of California
    namespaceEmbeddedInLui: false
    pattern: ^\d{6}$
    prefix: antibodyregistry
    uri_format: http://antibodyregistry.org/AB_$1
  prefix: antibodyregistry
  publications:
  - doi: 10.1093/nar/gkac927
    pmc: PMC9825422
    pubmed: '36370112'
    title: 'The Antibody Registry: ten years of registering antibodies'
    year: 2023
  references:
  - https://github.com/biopragmatics/bioregistry/pull/1098
  rrid:
    homepage: http://antibodyregistry.org/
    keywords:
    - antibody
    - reagent
    - unique identifiers
    name: Antibody Registry
    prefix: AB
    scr: 006397
  wikidata:
    database: Q111182712
antifam:
  contact:
    email: agb@ebi.ac.uk
    github: null
    name: Alex Bateman
    orcid: 0000-0002-6982-4660
  contributor:
    email: b.gyori@northeastern.edu
    github: bgyori
    name: Benjamin M. Gyori
    orcid: 0000-0001-9439-5346
  description: AntiFam is a database of spurious protein families that have been removed
    from Pfam due to incorrect hidden Markov model prediction.
  example: ANF00001
  github_request_issue: 1523
  homepage: https://www.ebi.ac.uk/interpro/entry/antifam
  mappings:
    uniprot: DB-0275
  name: AntiFam
  pattern: ^ANF\d{5}$
  prefix: antifam
  publications:
  - doi: 10.1093/database/bas003
    pmc: PMC3308159
    pubmed: '22434837'
    title: 'AntiFam: a tool to help identify spurious ORFs in protein annotation'
    year: 2012
  - doi: 10.1093/database/bas003
    pmc: null
    pubmed: '22434837'
    title: null
    year: null
  reviewer:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  uniprot:
    abbreviation: AntiFam
    category: Family and domain databases
    homepage: https://www.ebi.ac.uk/interpro/entry/antifam
    name: AntiFam resource to identify spurious protein predictions
    prefix: DB-0275
    publications:
    - doi: 10.1093/database/bas003
      pubmed: '22434837'
    uri_format: https://www.ebi.ac.uk/interpro/entry/antifam/$1
antweb:
  biocontext:
    prefix: ANTWEB
  fairsharing:
    abbreviation: AntWeb
    description: AntWeb is a website documenting the known species of ants, with records
      for each species linked to their geographical distribution, life history, and
      includes pictures.
    homepage: http://www.antweb.org
    license: CC-BY-4.0
    name: AntWeb
    prefix: FAIRsharing.yk38tw
    publications:
    - doi: 10.1038/424242b
      pubmed_id: 12867945
      title: Ants join online colony to boost conservation efforts.
    subjects:
    - Anatomy
    - Life Science
  integbio:
    description: AntWeb is a website documenting the known species of ants, with records
      for each species linked to their geographical distribution, life history, and
      includes pictures.
    fairsharing: FAIRsharing.yk38tw
    homepage: http://www.antweb.org
    information_keywords:
    - Classification
    - Image/Movie
    maintainer: California Academy of Sciences
    name: AntWeb
    prefix: nbdc01710
    pubmeds:
    - '12867945'
    status: Active
    target_keywords:
    - Organism
  mappings:
    biocontext: ANTWEB
    fairsharing: FAIRsharing.yk38tw
    integbio: nbdc01710
    miriam: antweb
    n2t: antweb
    ncbi: AntWeb
    prefixcommons: antweb
    wikidata: P5299
  miriam:
    deprecated: false
    description: AntWeb is a website documenting the known species of ants, with records
      for each species linked to their geographical distribution, life history, and
      includes pictures.
    homepage: http://www.antweb.org/
    id: '00000146'
    name: AntWeb
    namespaceEmbeddedInLui: false
    pattern: ^casent\d+(\-D\d+)?$
    prefix: antweb
    sampleId: casent0106247
    uri_format: http://www.antweb.org/specimen.do?name=$1
  n2t:
    description: AntWeb is a website documenting the known species of ants, with records
      for each species linked to their geographical distribution, life history, and
      includes pictures.
    example: casent0106247
    homepage: http://www.antweb.org/
    name: AntWeb at California Academy of Sciences
    namespaceEmbeddedInLui: false
    pattern: ^casent\d+(\-D\d+)?$
    prefix: antweb
    uri_format: http://www.antweb.org/specimen.do?name=$1
  name: AntWeb
  ncbi:
    example: CASENT0058943-D01
    homepage: http://www.antweb.org
    name: Ant Database
    prefix: AntWeb
  prefix: antweb
  prefixcommons:
    description: AntWeb is a website documenting the known species of ants, with records
      for each species linked to their geographical distribution, life history, and
      includes pictures.
    example: casent0106247
    homepage: https://www.antweb.org
    keywords:
    - classification
    - anatomy
    license: CC BY-SA 3.0
    miriam: antweb
    name: 'AntWeb: Ant of the World'
    pattern: ^casent\d+(\-\w+\d+)?$
    prefix: antweb
    pubmed_ids:
    - '12867945'
    uri_format: http://www.antweb.org/specimen.do?name=$1
  publications:
  - doi: 10.1038/424242b
    pmc: null
    pubmed: '12867945'
    title: Ants join online colony to boost conservation efforts
    year: 2003
  wikidata:
    description: identifier for a taxon in the AntWeb database
    example:
    - Haidomyrmex
    - Zatania electra
    homepage: https://www.antweb.org
    name: AntWeb ID
    pattern: ^[A-Z][a-z]+( [a-z]+){0,2}$
    prefix: P5299
    uri_format: https://www.antweb.org/description.do?taxonName=$1
anzctr:
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  contributor_extras:
  - email: sumirp77@gmail.com
    github: sumirp
    name: Sumir H Pandit
    orcid: 0000-0002-1216-4761
  description: 'The Australian New Zealand Clinical Trials Registry (ANZCTR) is an
    online register of clinical trials being undertaken in Australia, New Zealand
    and elsewhere. The ANZCTR includes trials from the full spectrum of therapeutic
    areas of pharmaceuticals, surgical procedures, preventive measures, lifestyle,
    devices, treatment and rehabilitation strategies and complementary therapies.


    In 2007 the ANZCTR was one of the first three trial registries to be recognised
    by the World Health Organization International Clinical Trials Registry Platform
    (WHO ICTRP) as a Primary Registry. WHO recognises registries as Primary Registries
    if they fulfil certain criteria with respect to data content, quality and validity,
    accessibility, unique identification, technical capacity and administration. The
    ANZCTR contributes data to the WHO ICTRP, which was developed in 2007. Trials
    from all ICTRP Primary Registries can be searched at: www.who.int/trialsearch.
    (from website)'
  example: ACTRN12623000498695
  homepage: https://anzctr.org.au
  mappings:
    wikidata.entity: Q65242932
  name: Australian New Zealand Clinical Trials Registry
  pattern: ^ACTRN\d+$
  prefix: anzctr
  providers:
  - code: redirect
    description: Australian New Zealand Clinical Trials Registry (redirect)
    example: null
    first_party: null
    homepage: https://anzctr.org.au
    name: Australian New Zealand Clinical Trials Registry (redirect)
    publications: null
    status: null
    uri_format: https://anzctr.org.au/ACTRN$1.aspx
  references:
  - https://github.com/biopragmatics/bioregistry/pull/1098
  synonyms:
  - ACTRN
  uri_format: https://anzctr.org.au/Trial/Registration/TrialReview.aspx?ACTRN=$1
  wikidata:
    database: Q65242932
    property: P7019
aop:
  biocontext:
    prefix: AOP
  contributor_extras:
  - email: sumirp77@gmail.com
    github: sumirp
    name: Sumir H Pandit
    orcid: 0000-0002-1216-4761
  mappings:
    biocontext: AOP
    miriam: aop
    n2t: aop
    wikidata.entity: Q111254792
  miriam:
    deprecated: false
    description: International repository of Adverse Outcome Pathways.
    homepage: https://aopwiki.org/
    id: '00000617'
    name: AOPWiki
    namespaceEmbeddedInLui: false
    pattern: ^\d+$
    prefix: aop
    sampleId: '98'
    uri_format: https://aopwiki.org/aops/$1
  n2t:
    description: International repository of Adverse Outcome Pathways.
    example: '98'
    homepage: https://aopwiki.org/
    name: AOPWiki
    namespaceEmbeddedInLui: false
    pattern: ^\d+$
    prefix: aop
    uri_format: https://aopwiki.org/aops/$1
  prefix: aop
  references:
  - https://github.com/biopragmatics/bioregistry/pull/1098
  wikidata:
    database: Q111254792
aop.events:
  biocontext:
    prefix: AOP.EVENTS
  mappings:
    biocontext: AOP.EVENTS
    miriam: aop.events
    n2t: aop.events
  miriam:
    deprecated: false
    description: International repository of Adverse Outcome Pathways.
    homepage: https://aopwiki.org/
    id: '00000652'
    name: AOPWiki (Key Event)
    namespaceEmbeddedInLui: false
    pattern: ^\d+$
    prefix: aop.events
    sampleId: '3'
    uri_format: https://aopwiki.org/events/$1
  n2t:
    description: International repository of Adverse Outcome Pathways.
    example: '3'
    homepage: https://aopwiki.org/
    name: AOPWiki (Key Event)
    namespaceEmbeddedInLui: false
    pattern: ^\d+$
    prefix: aop.events
    uri_format: https://aopwiki.org/events/$1
  part_of_database: aop
  prefix: aop.events
aop.relationships:
  biocontext:
    prefix: AOP.RELATIONSHIPS
  mappings:
    biocontext: AOP.RELATIONSHIPS
    miriam: aop.relationships
    n2t: aop.relationships
  miriam:
    deprecated: false
    description: International repository of Adverse Outcome Pathways.
    homepage: https://aopwiki.org/
    id: '00000653'
    name: AOPWiki (Key Event Relationship)
    namespaceEmbeddedInLui: false
    pattern: ^\d+$
    prefix: aop.relationships
    sampleId: '5'
    uri_format: https://aopwiki.org/relationships/$1
  n2t:
    description: International repository of Adverse Outcome Pathways.
    example: '5'
    homepage: https://aopwiki.org/
    name: AOPWiki (Key Event Relationship)
    namespaceEmbeddedInLui: false
    pattern: ^\d+$
    prefix: aop.relationships
    uri_format: https://aopwiki.org/relationships/$1
  part_of_database: aop
  prefix: aop.relationships
aop.stressor:
  biocontext:
    prefix: AOP.STRESSOR
  mappings:
    biocontext: AOP.STRESSOR
    miriam: aop.stressor
    n2t: aop.stressor
  miriam:
    deprecated: false
    description: International repository of Adverse Outcome Pathways.
    homepage: https://aopwiki.org/
    id: '00000654'
    name: AOPWiki (Stressor)
    namespaceEmbeddedInLui: false
    pattern: ^\d+$
    prefix: aop.stressor
    sampleId: '9'
    uri_format: https://aopwiki.org/stressors/$1
  n2t:
    description: International repository of Adverse Outcome Pathways.
    example: '9'
    homepage: https://aopwiki.org/
    name: AOPWiki (Stressor)
    namespaceEmbeddedInLui: false
    pattern: ^\d+$
    prefix: aop.stressor
    uri_format: https://aopwiki.org/stressors/$1
  part_of_database: aop
  prefix: aop.stressor
aopo:
  comment: There's no associated primary publication to my knowledge. The class and
    property CURIE format strings are somewhat inconsistent, but all conform to http://aopkb.org/aop_ontology#AdverseOutcomePathway,
    http://aopkb.org/aop_ontology#has_key_event or http://aopkb.org/aop_ontology#hasProcess.
    It is not indexed in the OLS but supports the AOP-WIKI RDF (see https://doi.org/10.1089/aivt.2021.0010
    or https://aopwiki.rdf.bigcat-bioinformatics.org/).
  contact:
    email: null
    github: DataSciBurgoon
    name: Lyle Burgoon
    orcid: 0000-0003-4977-5352
  contributor:
    email: javier.millanacosta@maastrichtuniversity.nl
    github: jmillanacosta
    name: Javier Millán Acosta
    orcid: 0000-0001-5608-781X
  description: The AOPO provides classes and relationships for the semantic representation
    of the Adverse Outcome Pathway framework.
  download_owl: https://github.com/DataSciBurgoon/aop-ontology/raw/refs/heads/master/aopo.owl
  example: AdverseOutcomePathway
  github_request_issue: 1744
  homepage: https://github.com/DataSciBurgoon/aop-ontology
  keywords:
  - adverse outcome pathway
  - ontology
  license: Apache-2.0
  name: Adverse Outcome Pathway Ontology
  pattern: ^[A-Za-z_]+$
  prefix: aopo
  publications:
  - doi: 10.1089/aivt.2017.0017
    pmc: PMC6060416
    pubmed: '30057931'
    title: Creating a Structured Adverse Outcome Pathway Knowledgebase via Ontology-Based
      Annotations
    year: 2017
  repository: https://github.com/DataSciBurgoon/aop-ontology
  reviewer:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  uri_format: http://aopkb.org/aop_ontology#$1
apaonto:
  aberowl:
    description: APA thesaurus . Flat ontology file
    download_owl: http://aber-owl.net/media/ontologies/APAONTO/4/apaonto.owl
    name: Psychology Ontology
    prefix: APAONTO
    version: '4'
  bioportal:
    contact:
      email: alexgarciac@gmail.com
      name: alexander garcia
    description: APA thesaurus . Flat ontology file
    name: Psychology Ontology
    prefix: APAONTO
    version: '4'
  contact:
    email: awalker@apa.org
    github: null
    name: Alvin Walker
    orcid: 0000-0003-1082-8760
  contributor_extras:
  - email: sumirp77@gmail.com
    github: sumirp
    name: Sumir H Pandit
    orcid: 0000-0002-1216-4761
  description: An ontology developed by the American Psychological Association (APA).
    Note that URIs in this ontology appear to have been generated with erroneous settings
    in Protege.
  example: Abdomen
  fairsharing:
    abbreviation: APAONTO
    description: 'Record does not exist anymore: Psychology Ontology. The record with
      identifier content 10.25504/FAIRsharing.gkw1w8 was invalid.'
    domains:
    - behavior
    homepage: http://bioportal.bioontology.org/ontologies/APAONTO
    name: Psychology Ontology
    prefix: FAIRsharing.gkw1w8
    subjects:
    - Psychology
  homepage: https://bioportal.bioontology.org/ontologies/APAONTO
  mappings:
    aberowl: APAONTO
    bioportal: APAONTO
    fairsharing: FAIRsharing.gkw1w8
    wikidata.entity: Q111194686
  prefix: apaonto
  references:
  - https://github.com/biopragmatics/bioregistry/issues/528
  - https://github.com/biopragmatics/bioregistry/pull/1098
  uri_format: http://ontology.apa.org/apaonto/termsonlyOUT%20(5).owl#$1
  wikidata:
    database: Q111194686
apd:
  biocontext:
    prefix: APD
  contact:
    email: gwang@unmc.edu
    github: null
    name: Guangshun Wang
    orcid: 0000-0002-4841-7927
  fairsharing:
    abbreviation: APD
    description: The Antimicrobial Peptide Database (APD) contains information on
      antimicrobial peptides from across a wide taxonomic range. It includes a glossary,
      nomenclature, classification, information search, prediction, design, and statistics
      of AMPs. The antimicrobial peptides in this database contain less than 100 amino
      acid residues, are in the mature and active form, and primarily from natural
      sources, ranging from bacteria, fungi, plants, to animals.
    homepage: https://wangapd3.com/main.php
    name: Antimicrobial Peptide Database
    prefix: FAIRsharing.ctwd7b
    publications:
    - doi: 10.1093/nar/gkn823
      pubmed_id: 18957441
      title: 'APD2: the updated antimicrobial peptide database and its application
        in peptide design.'
    - doi: 10.1093/nar/gkh025
      pubmed_id: 14681488
      title: 'APD: the Antimicrobial Peptide Database.'
    - doi: 10.1093/nar/gkv1278
      pubmed_id: 26602694
      title: 'APD3: the antimicrobial peptide database as a tool for research and
        education.'
    subjects:
    - Biology
  mappings:
    biocontext: APD
    fairsharing: FAIRsharing.ctwd7b
    miriam: apd
    n2t: apd
    prefixcommons: apd
    re3data: r3d100012901
  miriam:
    deprecated: true
    description: The antimicrobial peptide database (APD) provides information on
      anticancer, antiviral, antifungal and antibacterial peptides.
    homepage: http://aps.unmc.edu/AP/
    id: 00000278
    name: APD
    namespaceEmbeddedInLui: false
    pattern: ^\d{5}$
    prefix: apd
    sampleId: '01001'
    uri_format: http://aps.unmc.edu/AP/database/query_output.php?ID=$1
  n2t:
    description: The antimicrobial peptide database (APD) provides information on
      anticancer, antiviral, antifungal and antibacterial peptides.
    example: '01001'
    homepage: http://aps.unmc.edu/AP/
    name: APD at Nebraska
    namespaceEmbeddedInLui: false
    pattern: ^\d{5}$
    prefix: apd
    uri_format: http://aps.unmc.edu/AP/database/query_output.php?ID=$1
  name: Antimicrobial Peptide Database
  prefix: apd
  prefixcommons:
    description: The Antimicrobial Peptide Database (APD) contains data from the Protein
      Data Bank (PDB), Swiss-Prot Protein Knowledgebase and PubMed National Library
      of Medicine. The antimicrobial peptides in this database contain less than 100
      amino acid residues, are in the mature and active form, and primarily from natural
      sources, ranging from bacteria, fungi, plants, to animals.
    example: '1228'
    homepage: http://aps.unmc.edu/AP/
    keywords:
    - protein
    miriam: apd
    name: Antimicrobial Peptide Database
    pattern: ^\d+$
    prefix: apd
    pubmed_ids:
    - '26602694'
    uri_format: http://aps.unmc.edu/AP/database/query_output.php?ID=$1
  publications:
  - doi: 10.1093/nar/gkv1278
    pmc: PMC4702905
    pubmed: '26602694'
    title: 'APD3: the antimicrobial peptide database as a tool for research and education'
    year: 2015
  - doi: 10.1093/nar/gkn823
    pmc: PMC2686604
    pubmed: '18957441'
    title: 'APD2: the updated antimicrobial peptide database and its application in
      peptide design'
    year: 2008
  - doi: 10.1093/nar/gkh025
    pmc: PMC308759
    pubmed: '14681488'
    title: 'APD: the Antimicrobial Peptide Database'
    year: 2004
  - doi: 10.1093/nar/gkn823
    pmc: null
    pubmed: null
    title: 'APD2: the updated antimicrobial peptide database and its application in
      peptide design.'
    year: null
  - doi: 10.1093/nar/gkh025
    pmc: null
    pubmed: null
    title: 'APD: the Antimicrobial Peptide Database.'
    year: null
  - doi: 10.1093/nar/gkv1278
    pmc: null
    pubmed: null
    title: 'APD3: the antimicrobial peptide database as a tool for research and education.'
    year: null
  - doi: null
    pmc: null
    pubmed: '26602694'
    title: null
    year: null
  re3data:
    description: The Antimicrobial Peptide Database (APD) was originally created by
      a graduate student, Zhe Wang, as his master's thesis in the laboratory of Dr.
      Guangshun Wang. The project was initiated in 2002 and the first version of the
      database was open to the public in August 2003. It contained 525 peptide entries,
      which can be searched in multiple ways, including APD ID, peptide name, amino
      acid sequence, original location, PDB ID, structure, methods for structural
      determination, peptide length, charge, hydrophobic content, antibacterial, antifungal,
      antiviral, anticancer, and hemolytic activity. Some results of this bioinformatics
      tool were reported in the 2004 database paper. The peptide data stored in the
      APD were gleaned from the literature (PubMed, PDB, Google, and Swiss-Prot) manually
      in over a decade.
    doi: 10.17616/R3023M
    homepage: https://aps.unmc.edu/database
    license: Copyrights
    name: Antimicrobial Peptide Database
    prefix: r3d100012901
    synonyms:
    - AMP Database
    - APD
    xrefs:
      nif: 0000-02553
      omics: '05706'
aphidbase.transcript:
  biocontext:
    prefix: APHIDBASE.TRANSCRIPT
  contact:
    email: fabrice.legeai@rennes.inra.fr
    github: null
    name: Fabrice Legeai
    orcid: 0000-0002-6472-4839
  mappings:
    biocontext: APHIDBASE.TRANSCRIPT
    miriam: aphidbase.transcript
    n2t: aphidbase.transcript
    prefixcommons: aphidbase
  miriam:
    deprecated: false
    description: AphidBase is a centralized bioinformatic resource that was developed
      to facilitate community annotation of the pea aphid genome by the International
      Aphid Genomics Consortium (IAGC). The AphidBase Information System was designed
      to organize and distribute genomic data and annotations for a large international
      community. This collection references the transcript report, which describes
      genomic location, sequence and exon information.
    homepage: http://www.aphidbase.com/aphidbase
    id: 00000393
    name: AphidBase Transcript
    namespaceEmbeddedInLui: false
    pattern: ^ACYPI\d{6}(-RA)?$
    prefix: aphidbase.transcript
    sampleId: ACYPI000159
    uri_format: http://bipaa.genouest.org/apps/grs-2.3/grs?reportID=aphidbase_transcript_report&objectID=$1
  n2t:
    description: AphidBase is a centralized bioinformatic resource that was developed
      to facilitate community annotation of the pea aphid genome by the International
      Aphid Genomics Consortium (IAGC). The AphidBase Information System was designed
      to organize and distribute genomic data and annotations for a large international
      community. This collection references the transcript report, which describes
      genomic location, sequence and exon information.
    example: ACYPI000159
    homepage: http://www.aphidbase.com/aphidbase
    name: AphidBase at INRA
    namespaceEmbeddedInLui: false
    pattern: ^ACYPI\d{6}(-RA)?$
    prefix: aphidbase.transcript
    uri_format: http://bipaa.genouest.org/apps/grs-2.3/grs?reportID=aphidbase_transcript_report&objectID=$1
  prefix: aphidbase.transcript
  prefixcommons:
    description: The Aphid Genome Database's aim is to improve the current pea aphid
      genome assembly and annotation, and to provide new aphid genome sequences as
      well as tools for analysis of these genomes.
    example: ACYPI003698-RA
    homepage: http://www.aphidbase.com
    keywords:
    - genome
    miriam: aphidbase.transcript
    name: 'Aphidbase: an aphid genomics database'
    pattern: ^ACYPI\d+$
    prefix: aphidbase
    pubmed_ids:
    - '20482635'
  publications:
  - doi: 10.1111/j.1365-2583.2009.00930.x
    pmc: PMC4372297
    pubmed: '20482635'
    title: 'AphidBase: a centralized bioinformatic resource for annotation of the
      pea aphid genome'
    year: 2010
apid.interactions:
  biocontext:
    prefix: APID.INTERACTIONS
  contributor_extras:
  - email: sumirp77@gmail.com
    github: sumirp
    name: Sumir H Pandit
    orcid: 0000-0002-1216-4761
  mappings:
    biocontext: APID.INTERACTIONS
    miriam: apid.interactions
    n2t: apid.interactions
    wikidata.entity: Q111047825
  miriam:
    deprecated: false
    description: APID (Agile Protein Interactomes DataServer) provides information
      on the protein interactomes of numerous  organisms, based on the integration
      of known experimentally validated protein-protein physical interactions (PPIs).
      Interactome data includes a report on  quality levels and coverage over the
      proteomes for each organism included. APID integrates PPIs from primary databases
      of molecular interactions (BIND, BioGRID, DIP, HPRD, IntAct, MINT) and also
      from experimentally resolved 3D structures (PDB) where more than two distinct
      proteins have been identified. This collection references protein interactors,
      through a UniProt identifier.
    homepage: http://cicblade.dep.usal.es:8080/APID/
    id: '00000576'
    name: APID Interactomes
    namespaceEmbeddedInLui: false
    pattern: ^([A-N,R-Z][0-9]([A-Z][A-Z, 0-9][A-Z, 0-9][0-9]){1,2})|([O,P,Q][0-9][A-Z,
      0-9][A-Z, 0-9][A-Z, 0-9][0-9])(\.\d+)?$
    prefix: apid.interactions
    sampleId: P01116
    uri_format: http://cicblade.dep.usal.es:8080/APID/Interactions.action?protein=$1
  n2t:
    description: APID (Agile Protein Interactomes DataServer) provides information
      on the protein interactomes of numerous  organisms, based on the integration
      of known experimentally validated protein-protein physical interactions (PPIs).
      Interactome data includes a report on  quality levels and coverage over the
      proteomes for each organism included. APID integrates PPIs from primary databases
      of molecular interactions (BIND, BioGRID, DIP, HPRD, IntAct, MINT) and also
      from experimentally resolved 3D structures (PDB) where more than two distinct
      proteins have been identified. This collection references protein interactors,
      through a UniProt identifier.
    example: P01116
    homepage: http://cicblade.dep.usal.es:8080/APID/
    name: APID at Salamanca
    namespaceEmbeddedInLui: false
    pattern: ^([A-N,R-Z][0-9]([A-Z][A-Z, 0-9][A-Z, 0-9][0-9]){1,2})|([O,P,Q][0-9][A-Z,
      0-9][A-Z, 0-9][A-Z, 0-9][0-9])(\.\d+)?$
    prefix: apid.interactions
    uri_format: http://cicblade.dep.usal.es:8080/APID/Interactions.action?protein=$1
  prefix: apid.interactions
  provides: uniprot
  references:
  - https://github.com/biopragmatics/bioregistry/pull/1098
  wikidata:
    database: Q111047825
apo:
  aberowl:
    description: A structured controlled vocabulary for the phenotypes of Ascomycete
      fungi
    download_owl: http://aber-owl.net/media/ontologies/APO/64/apo.owl
    homepage: http://www.yeastgenome.org/
    name: Ascomycete phenotype ontology
    prefix: APO
  biocontext:
    prefix: APO
  bioportal:
    contact:
      email: sgd-helpdesk@lists.stanford.edu
      name: Saccharomyces Genome Database
    description: A structured controlled vocabulary for the phenotypes of Ascomycete
      fungi, A structured controlled vocabulary for the phenotypes of Ascomycete fungi.
    homepage: http://www.yeastgenome.org/
    license: CC-BY-4.0
    name: Ascomycete Phenotype Ontology
    prefix: APO
    version: '2025-11-10'
  contributor_extras:
  - email: sumirp77@gmail.com
    github: sumirp
    name: Sumir H Pandit
    orcid: 0000-0002-1216-4761
  example: 0000184
  fairsharing:
    abbreviation: APO
    contact:
      email: cherry@stanford.edu
      name: J. Michael Cherry
      orcid: 0000-0001-9163-5180
    description: Ascomycete Phenotype Ontology is a structured controlled vocabulary
      for the phenotypes of Ascomycete fungi.
    domains:
    - mutation
    - study design
    - phenotype
    - morphology
    - life cycle stage
    homepage: https://github.com/obophenotype/ascomycete-phenotype-ontology
    license: CC-BY-4.0
    name: Ascomycete Phenotype Ontology
    prefix: FAIRsharing.dyqz3y
    publications:
    - doi: 10.1093/database/bap001
      pubmed: '20157474'
      title: New mutant phenotype data curation system in the Saccharomyces Genome
        Database
      year: 2010
    repository: https://github.com/obophenotype/ascomycete-phenotype-ontology/issues
    subjects:
    - Life Science
    - Phenomics
    - Cell Biology
    - Genomics
    twitter: yeastgenome
  mappings:
    aberowl: APO
    biocontext: APO
    bioportal: APO
    fairsharing: FAIRsharing.dyqz3y
    obofoundry: apo
    ols: apo
    ontobee: APO
    wikidata.entity: Q81661535
  obofoundry:
    contact: stacia@stanford.edu
    contact.github: srengel
    contact.label: Stacia R Engel
    contact.orcid: 0000-0001-5472-917X
    deprecated: false
    description: A structured controlled vocabulary for the phenotypes of Ascomycete
      fungi
    domain: phenotype
    download.obo: http://purl.obolibrary.org/obo/apo.obo
    download.owl: http://purl.obolibrary.org/obo/apo.owl
    homepage: http://www.yeastgenome.org/
    license: CC BY 4.0
    license.url: https://creativecommons.org/licenses/by/4.0/
    name: Ascomycete phenotype ontology
    preferredPrefix: APO
    prefix: apo
    publications:
    - id: https://www.ncbi.nlm.nih.gov/pubmed/20157474
      title: New mutant phenotype data curation system in the Saccharomyces Genome
        Database
    repository: https://github.com/obophenotype/ascomycete-phenotype-ontology
  ols:
    description: A structured controlled vocabulary for the phenotypes of Ascomycete
      fungi.
    download_owl: http://purl.obolibrary.org/obo/apo.owl
    homepage: http://www.yeastgenome.org/
    name: Ascomycete Phenotype Ontology (APO)
    prefix: apo
    tracker: https://github.com/obophenotype/ascomycete-phenotype-ontology/issues
    version: '2025-11-10'
    version.iri: http://purl.obolibrary.org/obo/apo/releases/2025-11-10/apo.owl
  ontobee:
    library: Library
    name: Ascomycete phenotype ontology
    prefix: APO
  pattern: ^\d{7}$
  preferred_prefix: APO
  prefix: apo
  publications:
  - doi: 10.1093/database/bap001
    pmc: PMC2790299
    pubmed: '20157474'
    title: New mutant phenotype data curation system in the Saccharomyces Genome Database
    year: 2009
  references:
  - https://github.com/biopragmatics/bioregistry/pull/1098
  uri_format: http://purl.obolibrary.org/obo/APO_$1
  wikidata:
    database: Q81661535
apollosv:
  aberowl:
    description: An OWL2 ontology of phenomena in infectious disease epidemiology
      and population biology for use in epidemic simulation.
    download_owl: http://aber-owl.net/media/ontologies/APOLLO_SV/26/apollo_sv.owl
    homepage: https://github.com/ApolloDev/apollo-sv
    name: Apollo Structured Vocabulary
    prefix: APOLLO_SV
  bioportal:
    contact:
      email: hoganwr@gmail.com
      name: William Hogan
    description: Apollo-SV, developed as an OWL specification, defines the terms and
      relations necessary for interoperation between epidemic simulators and public
      health application software that interface with these simulators.
    homepage: https://github.com/ApolloDev/apollo-sv
    name: Apollo Structured Vocabulary
    prefix: APOLLO-SV
    version: '2024-12-24'
  download_obo: https://github.com/ApolloDev/apollo-sv/raw/refs/heads/main/apollo_sv.obo
  example: '00000443'
  fairsharing:
    abbreviation: Apollo-SV
    contact:
      email: hoganwr@gmail.com
      name: William Hogan
      orcid: 0000-0002-9881-1017
    description: Apollo-SV, developed as an OWL specification, defines the terms and
      relations necessary for interoperation between epidemic simulators and public
      health application software that interface with these simulators.
    domains:
    - infection process
    - pathogen
    homepage: https://github.com/ApolloDev/apollo-sv
    license: CC-BY-4.0
    name: Apollo-SV
    prefix: FAIRsharing.ngv2xx
    publications:
    - pubmed: '24551417'
      title: 'Apollo: giving application developers a single point of access to public
        health models using structured vocabularies and Web services'
      year: 2014
    - doi: 10.1186/s13326-016-0092-y
      pubmed: '27538448'
      title: 'The Apollo Structured Vocabulary: an OWL2 ontology of phenomena in infectious
        disease epidemiology and population biology for use in epidemic simulation'
      year: 2016
    repository: https://github.com/ApolloDev/apollo-sv
    subjects:
    - Population Genetics
    - Biomedical Science
    - Ecology
    - Epidemiology
  mappings:
    aberowl: APOLLO_SV
    bioportal: APOLLO-SV
    fairsharing: FAIRsharing.ngv2xx
    obofoundry: apollo_sv
    ols: apollo_sv
    ontobee: APOLLO_SV
  obofoundry:
    appears_in:
    - scdo
    contact: hoganwr@gmail.com
    contact.github: hoganwr
    contact.label: William Hogan
    contact.orcid: 0000-0002-9881-1017
    deprecated: false
    description: An OWL2 ontology of phenomena in infectious disease epidemiology
      and population biology for use in epidemic simulation.
    domain: health
    download.owl: http://purl.obolibrary.org/obo/apollo_sv.owl
    homepage: https://github.com/ApolloDev/apollo-sv
    license: CC BY 4.0
    license.url: https://creativecommons.org/licenses/by/4.0/
    name: Apollo Structured Vocabulary
    preferredPrefix: APOLLO_SV
    prefix: apollo_sv
    publications:
    - id: https://doi.org/10.1186/s13326-016-0092-y
      title: 'The Apollo Structured Vocabulary: an OWL2 ontology of phenomena in infectious
        disease epidemiology and population biology for use in epidemic simulation'
    repository: https://github.com/ApolloDev/apollo-sv
  ols:
    description: An OWL2 ontology of phenomena in infectious disease epidemiology
      and population biology for use in epidemic simulation.
    download_owl: http://purl.obolibrary.org/obo/apollo_sv.owl
    homepage: https://github.com/ApolloDev/apollo-sv
    name: Apollo Structured Vocabulary
    prefix: apollo_sv
    tracker: https://github.com/ApolloDev/apollo-sv/issues
    version: '2024-12-24'
    version.iri: http://purl.obolibrary.org/obo/apollo_sv/releases/2024-12-24/apollo_sv.owl
  ontobee:
    library: Library
    name: Apollo Structured Vocabulary
    prefix: APOLLO_SV
  pattern: ^\d{8}$
  prefix: apollosv
  providers:
  - code: conflated
    description: This might be resulting from properties in Apollo SV actually trying
      to use appropriate identifiers
    example: null
    first_party: null
    homepage: http://purl.obolibrary.org
    name: OBO PURL in Parts
    publications: null
    status: null
    uri_format: http://purl.obolibrary.org/obo/apollo_sv/dev/apollo_sv.owl#APOLLO_SV_$1
  publications:
  - doi: 10.1186/s13326-016-0092-y
    pmc: PMC4989460
    pubmed: '27538448'
    title: 'The Apollo Structured Vocabulary: an OWL2 ontology of phenomena in infectious
      disease epidemiology and population biology for use in epidemic simulation'
    year: 2016
  - doi: null
    pmc: PMC3900155
    pubmed: '24551417'
    title: 'Apollo: giving application developers a single point of access to public
      health models using structured vocabularies and Web services'
    year: 2013
  uri_format: http://purl.obolibrary.org/obo/APOLLO_SV_$1
arachnoserver:
  biocontext:
    prefix: ARACHNOSERVER
  contact:
    email: glenn.king@imb.uq.edu.au
    github: null
    name: Glenn King
    orcid: 0000-0002-2308-2200
  contributor_extras:
  - email: sumirp77@gmail.com
    github: sumirp
    name: Sumir H Pandit
    orcid: 0000-0002-1216-4761
  edam:
    description: Unique identifier of a toxin from the ArachnoServer database.
    name: ArachnoServer
    obsolete: false
    prefix: '2578'
  fairsharing:
    abbreviation: ArachnoServer
    description: ArachnoServer is a manually curated database containing information
      on the sequence, three-dimensional structure, and biological activity of protein
      toxins derived from spider venom.
    homepage: http://www.arachnoserver.org
    name: 'ArachnoServer: Spider toxin database'
    prefix: FAIRsharing.c54ywe
    publications:
    - doi: 10.1093/nar/gkq1058
      pubmed_id: 21036864
      title: ArachnoServer 2.0, an updated online resource for spider toxin sequences
        and structures.
    subjects:
    - Life Science
  integbio:
    description: 'ArachnoServer is a manually curated database which contains information
      on the sequence, three-dimensional structure, and biological activity of protein
      toxins derived from spider venom. All spider toxin entries are sourced from
      UniProtKB/Swiss-Prot, then manually curated using available literature and patent
      information. Spider taxonomy is based on the latest version of the authoritative
      World Spider Catalog. A key property of ArachnoServer is the use of a molecular
      target ontology based on the channel and receptor subtype definitions recommended
      by IUPHAR. Furthermore, in addition to any legacy synonyms, all peptide toxins
      in the database have been assigned names according to the recently described
      rational nomenclature for spider toxins (King et al., 2008).

      This database allows advanced searches of toxin information, browsing, as well
      as similarity searches using BLAST. Each toxin record is displayed in a single
      page and a toxin''s structure can be dynamically visualised.'
    fairsharing: biodbcore-000504
    homepage: https://arachnoserver.qfab.org/mainMenu.html
    information_keywords:
    - Sequence
    - 3D structure
    maintainer: QFAB (Queensland Facility for Advanced Bioinformatics)
    name: ArachnoServer
    prefix: nbdc01221
    pubmeds:
    - '19674480'
    - '19674480'
    status: Active
    target_keywords:
    - Protein
  mappings:
    biocontext: ARACHNOSERVER
    edam: '2578'
    fairsharing: FAIRsharing.c54ywe
    integbio: nbdc01221
    miriam: arachnoserver
    n2t: arachnoserver
    prefixcommons: arachnoserver
    re3data: r3d100012902
    uniprot: DB-0145
    wikidata.entity: Q4783563
  miriam:
    deprecated: false
    description: ArachnoServer (www.arachnoserver.org) is a manually curated database
      providing information on the sequence, structure and biological activity of
      protein toxins from spider venoms. It include a molecular target ontology designed
      specifically for venom toxins, as well as current and historic taxonomic information.
    homepage: http://www.arachnoserver.org/
    id: 00000193
    name: ArachnoServer
    namespaceEmbeddedInLui: false
    pattern: ^AS\d{6}$
    prefix: arachnoserver
    sampleId: AS000060
    uri_format: http://www.arachnoserver.org/toxincard.html?id=$1
  n2t:
    description: ArachnoServer (www.arachnoserver.org) is a manually curated database
      providing information on the sequence, structure and biological activity of
      protein toxins from spider venoms. It include a molecular target ontology designed
      specifically for venom toxins, as well as current and historic taxonomic information.
    example: AS000060
    homepage: http://www.arachnoserver.org/
    name: ArachnoServer at Brisbane
    namespaceEmbeddedInLui: false
    pattern: ^AS\d{6}$
    prefix: arachnoserver
    uri_format: http://www.arachnoserver.org/toxincard.html?id=$1
  prefix: arachnoserver
  prefixcommons:
    description: ArachnoServer is a manually curated database containing information
      on the sequence, three-dimensional structure, and biological activity of protein
      toxins derived from spider venom.
    example: AS000060
    homepage: http://www.arachnoserver.org
    keywords:
    - drug
    - protein
    miriam: arachnoserver
    name: 'ArachnoServer: Spider toxin database'
    pattern: ^AS\d{6}$
    prefix: arachnoserver
    pubmed_ids:
    - '21036864'
    - '29069336'
    uri_format: http://www.arachnoserver.org/toxincard.html?id=$1
  publications:
  - doi: 10.1093/bioinformatics/btx661
    pmc: null
    pubmed: '29069336'
    title: 'ArachnoServer 3.0: an online resource for automated discovery, analysis
      and annotation of spider toxins'
    year: 2018
  - doi: 10.1093/nar/gkq1058
    pmc: PMC3013666
    pubmed: '21036864'
    title: ArachnoServer 2.0, an updated online resource for spider toxin sequences
      and structures
    year: 2010
  - doi: 10.1093/nar/gkq1058
    pmc: null
    pubmed: null
    title: ArachnoServer 2.0, an updated online resource for spider toxin sequences
      and structures.
    year: null
  - doi: null
    pmc: null
    pubmed: '21036864'
    title: null
    year: null
  - doi: null
    pmc: null
    pubmed: '29069336'
    title: null
    year: null
  - doi: 10.1093/bioinformatics/btx661
    pmc: null
    pubmed: '29069336'
    title: null
    year: null
  - doi: 10.1093/nar/gkq1058
    pmc: null
    pubmed: null
    title: ArachnoServer 2.0, an updated online resource for spider toxin sequences
      and structures.
    year: null
  - doi: null
    pmc: null
    pubmed: '21036864'
    title: null
    year: null
  - doi: null
    pmc: null
    pubmed: '29069336'
    title: null
    year: null
  - doi: 10.1093/bioinformatics/btx661
    pmc: null
    pubmed: '29069336'
    title: null
    year: null
  re3data:
    description: ArachnoServer is a manually curated database containing information
      on the sequence, three-dimensional structure, and biological activity of protein
      toxins derived from spider venom. Spiders are the largest group of venomous
      animals and they are predicted to contain by far the largest number of pharmacologically
      active peptide toxins (Escoubas et al., 2006). ArachnoServer has been custom-built
      so that a wide range of biological scientists, including neuroscientists, pharmacologists,
      and toxinologists, can readily access key data relevant to their discipline
      without being overwhelmed by extraneous information.
    doi: 10.17616/R30Z3K
    homepage: https://arachnoserver.qfab.org/mainMenu.html
    name: ArachnoServer
    prefix: r3d100012902
    xrefs:
      omics: '03117'
  references:
  - https://github.com/biopragmatics/bioregistry/pull/1141
  uniprot:
    abbreviation: ArachnoServer
    category: Organism-specific databases
    homepage: http://www.arachnoserver.org
    name: ArachnoServer
    prefix: DB-0145
    publications:
    - doi: 10.1093/bioinformatics/btx661
      pubmed: '29069336'
  wikidata:
    database: Q4783563
araport:
  contact:
    email: hello@vivekkrish.com
    github: vivekkrish
    name: Vivek Krishnakuma
    orcid: 0000-0002-5227-0200
  description: Website with general information about Arabidopsis and functionalities
    such as a genomic viewer
  homepage: https://www.araport.org/
  integbio:
    alt_name: Arabidopsis Information Portal
    description: 'Araport is an open-access online community resource for Arabidopsis
      research. It hosts the Araport11, updated Arabidopsis genome annotation from
      TAIR10. Araport offers two core web applications: ThaleMine for data mining
      and JBrowse for genome browsing. The site also hosts ''science apps,'' that
      use dynamic web pages to present data obtained on-demand from third-party servers.
      The Araport11 data are also available by bulk download and web services.'
    fairsharing: biodbcore-001076/
    homepage: https://www.araport.org/
    information_keywords:
    - Sequence
    - Expression
    - Interaction/Pathway
    - Portal
    maintainer: JCVI (J. Craig Venter Institute)||Texas Advanced Computing Center,
      The University of Texas at Austin||University of Cambridge
    name: Araport
    prefix: nbdc02433
    pubmeds:
    - '28013278'
    - '27862469'
    - '25414324'
    status: Active
    target_keywords:
    - Genome/Gene
    - DNA
    - RNA
    - Protein
  mappings:
    integbio: nbdc02433
    miriam: tair.name
    ncbi: Araport
    pathguide: '768'
    uniprot: DB-0221
  miriam:
    deprecated: false
    description: The Arabidopsis Information Resource (TAIR) maintains a database
      of genetic and molecular biology data for the model higher plant Arabidopsis
      thaliana. The name of a Locus is unique and used by TAIR, TIGR, and MIPS.
    homepage: https://www.arabidopsis.org/
    id: 00000976
    name: TAIR gene name
    namespaceEmbeddedInLui: false
    pattern: ^AT.G[0-9]{5}$
    prefix: tair.name
    sampleId: AT5G05330
    uri_format: https://www.arabidopsis.org/locus?name=$1
  name: Arabidopsis Information Portal
  ncbi:
    example: AT1G01010
    homepage: https://www.araport.org/
    name: Arabidopsis Information Portal
    prefix: Araport
  pathguide:
    abbreviation: Araport
    homepage: https://www.araport.org/
    name: Arabidopsis Information Portal
    prefix: '768'
  prefix: araport
  publications:
  - doi: 10.1093/nar/gku1200
    pmc: PMC4383980
    pubmed: '25414324'
    title: 'Araport: the Arabidopsis information portal'
    year: 2014
  - doi: 10.1093/nar/gku1200
    pmc: null
    pubmed: '25414324'
    title: null
    year: null
  uniprot:
    abbreviation: Araport
    category: Organism-specific databases
    homepage: https://bar.utoronto.ca/thalemine/begin.do
    name: Arabidopsis Information Portal
    prefix: DB-0221
    publications:
    - doi: 10.1093/nar/gku1200
      pubmed: '25414324'
    uri_format: https://bar.utoronto.ca/thalemine/portal.do?externalids=$1
  uri_format: https://www.arabidopsis.org/servlets/TairObject?type=locus&name=$1
archdb:
  fairsharing:
    abbreviation: ArchDB
    contact:
      email: narcis.fernandez@gmail.com
      name: Narcis Fernandez-Fuentes
      orcid: 0000-0002-6421-1080
    contributor_extras:
    - email: sumirp77@gmail.com
      github: sumirp
      name: Sumir H Pandit
      orcid: 0000-0002-1216-4761
    description: ArchDB is a compilation of structural classifications of loops extracted
      from known protein structures. The structural classification is based on the
      geometry and conformation of the loop. The geometry is defined by four internal
      variables and the type of regular flanking secondary structures, resulting in
      10 different loop types. Loops in ArchDB have been classified using an improved
      version (Espadaler et al.) of the original ArchType program published in 1997
      by Oliva et al.
    homepage: http://sbi.imim.es/archdb
    name: ArchDB
    prefix: FAIRsharing.tp9z4q
    publications:
    - doi: 10.1093/nar/gkh002
      pubmed_id: 14681390
      title: 'ArchDB: automated protein loop classification as a tool for structural
        genomics.'
    - doi: 10.1093/nar/gkt1189
      pubmed_id: 24265221
      title: 'ArchDB 2014: structural classification of loops in proteins.'
    subjects:
    - Life Science
  integbio:
    description: ArchDB is a compilation of structural classifications of loops extracted
      from known protein structures. The structural classification is based on the
      geometry and conformation of the loop. The geometry is defined by four internal
      variables and the type of regular flanking secondary structures, resulting in
      10 different loop types. Loops in ArchDB have been classified using an improved
      version (Espadaler et al.) of the original ArchType program published in 1997
      by Oliva et al.
    fairsharing: FAIRsharing.tp9z4q
    homepage: http://sbi.imim.es/archdb
    information_keywords:
    - Classification
    - Sequence
    - 3D structure
    maintainer: LMGM (Laboratoire de Microbiologie et Genetique Moleculaires)||SBI
      (The Structural Bioinformatics Laboratory)||bioinsilico.org
    name: ArchDB
    prefix: nbdc01795
    pubmeds:
    - '14681390'
    - '24265221'
    status: Active
    target_keywords:
    - Protein
  mappings:
    fairsharing: FAIRsharing.tp9z4q
    integbio: nbdc01795
    prefixcommons: archdb
  prefix: archdb
  prefixcommons:
    description: ArchDB is a compilation of structural classifications of loops extracted
      from known protein structures. Loops in ArchDB have been classified using an
      improved version (Espadaler et al.) of the original ArchType program published
      in 1997 by Oliva et al..
    example: '39421'
    homepage: http://sbi.imim.es/archdb
    keywords:
    - classification
    - protein
    name: ArchDB
    pattern: ^\d+$
    prefix: archdb
    pubmed_ids:
    - '24265221'
    uri_format: http://sbi.imim.es/cgi-bin/archdb//loops.pl?loop=$1
  publications:
  - doi: 10.1093/nar/gkt1189
    pmc: PMC3964960
    pubmed: '24265221'
    title: 'ArchDB 2014: structural classification of loops in proteins'
    year: 2013
  - doi: 10.1093/nar/gkh002
    pmc: PMC308737
    pubmed: '14681390'
    title: 'ArchDB: automated protein loop classification as a tool for structural
      genomics'
    year: 2004
  reviewer:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
ardb:
  biocontext:
    prefix: ARDB
  mappings:
    biocontext: ARDB
    miriam: ardb
    n2t: ardb
    wikidata.entity: Q112205944
  miriam:
    deprecated: true
    description: The Antibiotic Resistance Genes Database (ARDB) is a manually curated
      database which characterises genes involved in antibiotic resistance. Each gene
      and resistance type is annotated with information, including resistance profile,
      mechanism of action, ontology, COG and CDD annotations, as well as external
      links to sequence and protein databases. This collection references resistance
      genes.
    homepage: http://ardb.cbcb.umd.edu/
    id: '00000522'
    name: Antibiotic Resistance Genes Database
    namespaceEmbeddedInLui: false
    pattern: ^[A-Z_]{3}[0-9]{4,}$
    prefix: ardb
    sampleId: CAE46076
    uri_format: http://ardb.cbcb.umd.edu/cgi/search.cgi?db=L&amp;field=ni&amp;term=$1
  n2t:
    description: The Antibiotic Resistance Genes Database (ARDB) is a manually curated
      database which characterises genes involved in antibiotic resistance. Each gene
      and resistance type is annotated with information, including resistance profile,
      mechanism of action, ontology, COG and CDD annotations, as well as external
      links to sequence and protein databases. This collection references resistance
      genes.
    example: CAE46076
    homepage: http://ardb.cbcb.umd.edu/
    name: ARDB at University of Maryland
    namespaceEmbeddedInLui: false
    pattern: ^[A-Z_]{3}[0-9]{4,}$
    prefix: ardb
    uri_format: http://ardb.cbcb.umd.edu/cgi/search.cgi?db=L&amp;field=ni&amp;term=$1
  prefix: ardb
  references:
  - https://github.com/biopragmatics/bioregistry/pull/1141
  wikidata:
    database: Q112205944
ark:
  banana: ark
  bartoc:
    abbreviation: ARK
    description: Archival Resource Keys (ARKs) serve as persistent identifiers, or
      stable, trusted references for information objects. Among other things, they
      aim to be web addresses (URLs) that don’t return 404 Page Not Found errors.
      The ARK Alliance is an open global community supporting the ARK infrastructure
      on behalf of research and scholarship.
    homepage: https://arks.org/
    license: CC BY-NC 4.0
    name: Archival Resource Key
    prefix: '20715'
  biocontext:
    prefix: ARK
  contact:
    email: jakkbl@gmail.com
    github: jkunze
    name: John Kunze
    orcid: 0000-0001-7604-8041
  contributor_extras:
  - email: jakkbl@gmail.com
    github: jkunze
    name: John Kunze
    orcid: 0000-0001-7604-8041
  - email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  - email: sumirp77@gmail.com
    github: sumirp
    name: Sumir H Pandit
    orcid: 0000-0002-1216-4761
  example: /53355/cl010066723
  fairsharing:
    abbreviation: ARK Identifier
    description: Archival Resource Keys (ARKs) serve as persistent identifiers, or
      stable, trusted references for information objects. Among other things, they
      aim to be web addresses (URLs) that don’t return 404 Page Not Found errors.
      The ARK Alliance is an open global community supporting the ARK infrastructure
      on behalf of research and scholarship. End users, especially researchers, rely
      on ARKs for long term access to the global scientific and cultural record. Since
      2001 some 12.3 billion ARKs have been created by over 1700 organizations — libraries,
      data centers, archives, museums, publishers, government agencies, and vendors.
      They identify anything digital, physical, or abstract. ARKs are open, mainstream,
      non-paywalled, decentralized persistent identifiers that can be created by an
      organization as soon as it is registered with a NAAN (Name Assigning Authority
      Number). Once registered, an ARK organization can create unlimited numbers of
      ARKs and publicize them via the n2t.net global resolver or via their own local
      resolver.
    domains:
    - Data retrieval
    homepage: https://arks.org/
    logo: https://api.fairsharing.org/rails/active_storage/blobs/redirect/eyJfcmFpbHMiOnsibWVzc2FnZSI6IkJBaHBBaThDIiwiZXhwIjpudWxsLCJwdXIiOiJibG9iX2lkIn19--c69281eac0647c6b7a664f0932bee0d5fd27781d/gold_boat_arka.png?disposition=inline
    name: Archival Resource Key Identifier
    prefix: FAIRsharing.f928f1
    repository: https://github.com/arks-org
    subjects:
    - Subject Agnostic
    twitter: arks_org
  homepage: https://arks.org
  mappings:
    bartoc: '20715'
    biocontext: ARK
    fairsharing: FAIRsharing.f928f1
    miriam: ark
    n2t: ark
    wikidata.entity: Q2860403
  mastodon: arks_org@fosstodon.org
  miriam:
    deprecated: false
    description: Archival Resource Keys (ARKs) serve as persistent identifiers, or
      stable, trusted references for information objects. Among other things, they
      aim to be web addresses (URLs) that don’t return 404 Page Not Found errors.
      The ARK Alliance is an open global community supporting the ARK infrastructure
      on behalf of research and scholarship. End users, especially researchers, rely
      on ARKs for long term access to the global scientific and cultural record. Since
      2001 some 8.2 billion ARKs have been created by over 1000 organizations — libraries,
      data centers, archives, museums, publishers, government agencies, and vendors.
      They identify anything digital, physical, or abstract. ARKs are open, mainstream,
      non-paywalled, decentralized persistent identifiers that can be created by an
      organization as soon as it is registered with a NAAN (Name Assigning Authority
      Number). Once registered, an ARK organization can create unlimited numbers of
      ARKs and publicize them via the n2t.net global resolver or via their own local
      resolver.
    homepage: https://arks.org
    id: 00000592
    name: Archival Resource Key (ARK)
    namespaceEmbeddedInLui: true
    pattern: ^(ark\:)/*[0-9A-Za-z]+(?:/[\w/.=*+@\$-]*)?(?:\?.*)?$
    prefix: ark
    sampleId: /53355/cl010066723
    uri_format: https://n2t.net/ark:$1
  n2t:
    example: /88435/hq37vq534
    homepage: https://wiki.ucop.edu/display/Curation/ARK
    name: Archival Resource Key
    namespaceEmbeddedInLui: false
    prefix: ark
    uri_format: n2t.net/ark:$1
  name: Archival Resource Key
  pattern: ^/*[0-9A-Za-z]+(?:/[\w/.=*+@\$-]*)?(?:\?.*)?$
  prefix: ark
  references:
  - https://n2t.net/e/about.html
  - https://github.com/biopragmatics/bioregistry/pull/1141
  twitter: ARKsInTheOpen
  uri_format: http://n2t.net/ark:$1
  wikidata:
    database: Q2860403
    property: P8091
aro:
  aberowl:
    description: Antibiotic resistance genes and mutations
    download_owl: http://aber-owl.net/media/ontologies/ARO/32/aro.owl
    homepage: https://github.com/arpcard/aro
    name: Antibiotic Resistance Ontology
    prefix: ARO
  biocontext:
    prefix: ARO
  bioportal:
    contact:
      email: mcarthua@mcmaster.ca
      name: Andrew G. McArthur
    description: The Antibiotic Resistance Ontology describes antibiotic resistance
      genes and mutations, their products, mechanisms, and associated phenotypes,
      as well as antibiotics and their molecular targets. It is integrated with the
      Comprehensive Antibiotic Resistance Database, a curated resource containing
      high quality reference data on the molecular basis of antimicrobial resistance.
    homepage: https://github.com/arpcard/aro
    name: Antibiotic Resistance Ontology
    prefix: ARO
  contributor_extras:
  - email: sumirp77@gmail.com
    github: sumirp
    name: Sumir H Pandit
    orcid: 0000-0002-1216-4761
  download_obo: http://purl.obolibrary.org/obo/aro.obo
  example: '1000001'
  fairsharing:
    abbreviation: ARO
    description: The Antibiotic Resistance Ontology describes antibiotic resistance
      genes and mutations, their products, mechanisms, and associated phenotypes,
      as well as antibiotics and their molecular targets. It is integrated with the
      Comprehensive Antibiotic Resistance Database (https://card.mcmaster.ca), a curated
      resource containing high quality reference data on the molecular basis of antimicrobial
      resistance.
    domains:
    - antimicrobial agent
    - mutation
    - gene
    homepage: https://github.com/arpcard/aro
    license: CC-BY-4.0
    name: Antibiotic Resistance Ontology
    prefix: FAIRsharing.d8fa2d
    publications:
    - doi: 10.1093/nar/gkz935
      title: 'CARD 2020: antibiotic resistome surveillance with the comprehensive
        antibiotic resistance database'
      year: 2019
    repository: https://github.com/arpcard/aro/blob/master/README.md
    subjects:
    - Genetics
    user_defined_tags:
    - antibiotic resistance
  mappings:
    aberowl: ARO
    biocontext: ARO
    bioportal: ARO
    fairsharing: FAIRsharing.d8fa2d
    obofoundry: aro
    ols: aro
    ontobee: ARO
    wikidata.entity: Q81661539
  obofoundry:
    appears_in:
    - scdo
    contact: mcarthua@mcmaster.ca
    contact.github: agmcarthur
    contact.label: Andrew G. McArthur
    contact.orcid: 0000-0002-1142-3063
    deprecated: false
    description: Antibiotic resistance genes and mutations
    domain: microbiology
    download.owl: http://purl.obolibrary.org/obo/aro.owl
    homepage: https://github.com/arpcard/aro
    license: CC BY 4.0
    license.url: https://creativecommons.org/licenses/by/4.0/
    name: Antibiotic Resistance Ontology
    preferredPrefix: ARO
    prefix: aro
    publications:
    - id: https://www.ncbi.nlm.nih.gov/pubmed/31665441
      title: 'CARD 2020: antibiotic resistome surveillance with the comprehensive
        antibiotic resistance database.'
    repository: https://github.com/arpcard/aro
  ols:
    description: Antibiotic resistance genes and mutations
    homepage: https://github.com/arpcard/aro
    name: Antibiotic Resistance Ontology
    prefix: aro
    tracker: https://github.com/arpcard/aro/issues
  ontobee:
    library: Library
    name: Antibiotic Resistance Ontology
    prefix: ARO
  pattern: ^\d{7}$
  prefix: aro
  publications:
  - doi: 10.1093/nar/gkz935
    pmc: PMC7145624
    pubmed: '31665441'
    title: 'CARD 2020: antibiotic resistome surveillance with the comprehensive antibiotic
      resistance database'
    year: 2020
  references:
  - https://github.com/biopragmatics/bioregistry/pull/1141
  uri_format: http://purl.obolibrary.org/obo/ARO_$1
  wikidata:
    database: Q81661539
arrayexpress:
  biocontext:
    prefix: ARRAYEXPRESS
  cellosaurus:
    category: Gene expression databases
    homepage: https://www.ebi.ac.uk/biostudies/arrayexpress
    name: ArrayExpress Archive of Functional Genomics
    prefix: ArrayExpress
    uri_format: https://www.ebi.ac.uk/biostudies/ArrayExpress/studies/$1
  contact:
    email: brazma@ebi.ac.uk
    github: null
    name: Alvis Brazma
    orcid: 0000-0001-5988-7409
  contributor_extras:
  - email: sumirp77@gmail.com
    github: sumirp
    name: Sumir H Pandit
    orcid: 0000-0002-1216-4761
  fairsharing:
    abbreviation: ArrayExpress
    description: ArrayExpress is a database of functional genomics experiments that
      can be queried and the data downloaded. It includes gene expression data from
      microarray and high throughput sequencing studies. Data is collected to MIAME
      and MINSEQE standards. Experiments are submitted directly to ArrayExpress or
      are imported from the NCBI GEO database.
    homepage: https://www.ebi.ac.uk/arrayexpress/
    name: ArrayExpress
    prefix: FAIRsharing.6k0kwd
    publications:
    - doi: 10.1093/nar/gkg091
      pubmed_id: 12519949
      title: ArrayExpress--a public repository for microarray gene expression data
        at the EBI.
    - doi: 10.1093/nar/gku1057
      pubmed_id: 25361974
      title: ArrayExpress update-simplifying data submissions.
    - doi: 10.1093/nar/gky964
      pubmed_id: 30357387
      title: ArrayExpress update – from bulk to single-cell expression data
    subjects:
    - Functional Genomics
    twitter: ArrayExpressEBI
  integbio:
    alt_name: ArrayExpress Archive
    description: 'ArrayExpress is a database of experiments related to the structure,
      function, evolution, and mapping of genomes.

      It contains information on gene expression obtained from microarray and sequencing
      studies.

      Altogether 36,292 experiments are listed. Each experiment is described and reported
      in detail.

      Altogether 13,748 arrays are listed and described.

      Keyword and advanced search options are available.

      The data may also be downloaded.'
    fairsharing: biodbcore-000305
    homepage: https://www.ebi.ac.uk/biostudies/arrayexpress
    information_keywords:
    - Expression
    - Repository
    maintainer: EMBL-EBI (European Bioinformatics Institute)
    name: ArrayExpress
    prefix: nbdc00009
    pubmeds:
    - '12519949'
    - '14744115'
    - '15608260'
    - '16939801'
    - '17132828'
    - '19015125'
    - '21071405'
    status: Active
    target_keywords:
    - Genome/Gene
    - cDNA/EST
    - RNA
    - Protein
  mappings:
    biocontext: ARRAYEXPRESS
    cellosaurus: ArrayExpress
    fairsharing: FAIRsharing.6k0kwd
    integbio: nbdc00009
    miriam: arrayexpress
    n2t: arrayexpress
    prefixcommons: arrayexpress
    re3data: r3d100010222
    wikidata.entity: Q106638376
  miriam:
    deprecated: false
    description: ArrayExpress is a public repository for microarray data, which is
      aimed at storing MIAME-compliant data in accordance with Microarray Gene Expression
      Data (MGED) recommendations.
    homepage: https://www.ebi.ac.uk/arrayexpress/
    id: '00000036'
    name: ArrayExpress
    namespaceEmbeddedInLui: false
    pattern: ^[AEP]-\w{4}-\d+$
    prefix: arrayexpress
    providers:
    - code: omicsdi
      description: ArrayExpress through OmicsDI
      homepage: https://www.omicsdi.org/
      name: ArrayExpress through OmicsDI
      uri_format: https://www.omicsdi.org/dataset/arrayexpress-repository/$1
    sampleId: E-MEXP-1712
    uri_format: https://www.ebi.ac.uk/arrayexpress/experiments/$1
  n2t:
    description: ArrayExpress is a public repository for microarray data, which is
      aimed at storing MIAME-compliant data in accordance with Microarray Gene Expression
      Data (MGED) recommendations.
    example: E-MEXP-1712
    homepage: https://www.ebi.ac.uk/arrayexpress/
    name: ArrayExpress
    namespaceEmbeddedInLui: false
    pattern: ^[AEP]-\w{4}-\d+$
    prefix: arrayexpress
    uri_format: https://www.ebi.ac.uk/arrayexpress/experiments/$1
  prefix: arrayexpress
  prefixcommons:
    description: ArrayExpress is a public repository for microarray data, which is
      aimed at storing MIAME-compliant data in accordance with Microarray Gene Expression
      Data (MGED) recommendations.
    example: E-MEXP-1712
    homepage: http://www.ebi.ac.uk/arrayexpress
    keywords:
    - expression
    - microarray
    - nucleotide
    license: http://www.ebi.ac.uk/Information/termsofuse.html
    miriam: arrayexpress
    name: ArrayExpress
    pattern: ^[AEP]-\w{4}-\d+$
    prefix: arrayexpress
    pubmed_ids:
    - '12519949'
    uri_format: http://www.ebi.ac.uk/arrayexpress/experiments/$1
  publications:
  - doi: 10.1093/nar/gky964
    pmc: PMC6323929
    pubmed: '30357387'
    title: ArrayExpress update - from bulk to single-cell expression data
    year: 2019
  - doi: 10.1093/nar/gku1057
    pmc: PMC4383899
    pubmed: '25361974'
    title: ArrayExpress update--simplifying data submissions
    year: 2014
  - doi: 10.1093/nar/gkg091
    pmc: PMC165538
    pubmed: '12519949'
    title: ArrayExpress--a public repository for microarray gene expression data at
      the EBI
    year: 2003
  - doi: 10.1093/nar/gkg091
    pmc: null
    pubmed: null
    title: ArrayExpress--a public repository for microarray gene expression data at
      the EBI.
    year: null
  - doi: 10.1093/nar/gku1057
    pmc: null
    pubmed: null
    title: ArrayExpress update-simplifying data submissions.
    year: null
  - doi: 10.1093/nar/gky964
    pmc: null
    pubmed: null
    title: ArrayExpress update – from bulk to single-cell expression data
    year: null
  - doi: null
    pmc: null
    pubmed: '12519949'
    title: null
    year: null
  re3data:
    description: ArrayExpress is one of the major international repositories for high-throughput
      functional genomics data from both microarray and high-throughput sequencing
      studies, many of which are supported by peer-reviewed publications. Data sets
      are submitted directly to ArrayExpress and curated by a team of specialist biological
      curators. In the past (until 2018) datasets from the NCBI Gene Expression Omnibus
      database were imported on a weekly basis. Data is collected to MIAME and MINSEQE
      standards.
    doi: 10.17616/R3302G
    homepage: https://www.ebi.ac.uk/biostudies/arrayexpress
    name: Array Express
    prefix: r3d100010222
    synonyms:
    - functional genomics data
    xrefs:
      nif: 0000-30123
      omics: '01023'
  references:
  - https://github.com/biopragmatics/bioregistry/pull/1141
  wikidata:
    database: Q106638376
arrayexpress.platform:
  biocontext:
    prefix: ARRAYEXPRESS.PLATFORM
  mappings:
    biocontext: ARRAYEXPRESS.PLATFORM
    miriam: arrayexpress.platform
    n2t: arrayexpress.platform
  miriam:
    deprecated: false
    description: ArrayExpress is a public repository for microarray data, which is
      aimed at storing MIAME-compliant data in accordance with Microarray Gene Expression
      Data (MGED) recommendations.This collection references the specific platforms
      used in the generation of experimental results.
    homepage: https://www.ebi.ac.uk/arrayexpress/
    id: 00000294
    name: ArrayExpress Platform
    namespaceEmbeddedInLui: false
    pattern: ^[AEP]-\w{4}-\d+$
    prefix: arrayexpress.platform
    sampleId: A-GEOD-50
    uri_format: https://www.ebi.ac.uk/arrayexpress/arrays/$1
  n2t:
    description: ArrayExpress is a public repository for microarray data, which is
      aimed at storing MIAME-compliant data in accordance with Microarray Gene Expression
      Data (MGED) recommendations.This collection references the specific platforms
      used in the generation of experimental results.
    example: A-GEOD-50
    homepage: https://www.ebi.ac.uk/arrayexpress/
    name: ArrayExpress Platform at EBI
    namespaceEmbeddedInLui: false
    pattern: ^[AEP]-\w{4}-\d+$
    prefix: arrayexpress.platform
    uri_format: https://www.ebi.ac.uk/arrayexpress/arrays/$1
  part_of_database: arrayexpress
  prefix: arrayexpress.platform
arraymap:
  biocontext:
    prefix: ARRAYMAP
  fairsharing:
    abbreviation: arrayMap
    contact:
      email: mbaudis@me.com
      name: Michael Baudis
      orcid: 0000-0002-9903-4248
    description: Part of the Progenetix project, the arrayMap database facilitates
      the study of the genetics of human cancer. The Progenetix project provides the
      data customisation and visualization tools to mine the available data. The arrayMap
      database is developed by the group "Theoretical Cytogenetics and Oncogenomics"
      at the Department of Molecular Life Sciences of the University of Zurich.
    homepage: http://arraymap.org
    license: https://creativecommons.org/licenses/by-nc-nd/2.5/ch
    name: arrayMap - Genomic Array Data for Cancer CNV Profiles
    prefix: FAIRsharing.1fbc5y
    publications:
    - doi: 10.1371/journal.pone.0036944
      pubmed_id: 22629346
      title: 'arrayMap: a reference resource for genomic copy number imbalances in
        human malignancies.'
    - doi: 10.1093/nar/gku1123
      pubmed_id: 25428357
      title: 'arrayMap 2014: an updated cancer genome resource.'
    - doi: 10.1186/1471-2164-15-82
      pubmed_id: 24476156
      title: Chromothripsis-like patterns are recurring but heterogeneously distributed
        features in a survey of 22,347 cancer genome screens.
    - doi: 10.1093/nar/gkv1310
      pubmed_id: 26615188
      title: 'The SIB Swiss Institute of Bioinformatics'' resources: focus on curated
        databases.'
    subjects:
    - Genomics
    - Bioinformatics
    - Life Science
    - Biomedical Science
    twitter: progenetix
  mappings:
    biocontext: ARRAYMAP
    fairsharing: FAIRsharing.1fbc5y
    miriam: arraymap
    n2t: arraymap
    re3data: r3d100012630
  miriam:
    deprecated: false
    description: arrayMap is a collection of pre-processed oncogenomic array data
      sets and CNA (somatic copy number aberrations) profiles. CNA are a type of mutation
      commonly found in cancer genomes. arrayMap data is assembled from public repositories
      and supplemented with additional sources, using custom curation pipelines. This
      information has been mapped to multiple editions of the reference human genome.
    homepage: https://www.arraymap.org
    id: '00000621'
    name: ArrayMap
    namespaceEmbeddedInLui: false
    pattern: ^[\w\-:,]{3,64}$
    prefix: arraymap
    sampleId: icdom:8500_3
    uri_format: https://www.arraymap.org/pgx:$1
  n2t:
    description: arrayMap is a collection of pre-processed oncogenomic array data
      sets and CNA (somatic copy number aberrations) profiles. CNA are a type of mutation
      commonly found in cancer genomes. arrayMap data is assembled from public repositories
      and supplemented with additional sources, using custom curation pipelines. This
      information has been mapped to multiple editions of the reference human genome.
    example: icdom:8500_3
    homepage: https://www.arraymap.org
    name: ArrayMap
    namespaceEmbeddedInLui: false
    pattern: ^[\w\-:,]{3,64}$
    prefix: arraymap
    uri_format: https://www.arraymap.org/pgx:$1
  prefix: arraymap
  publications:
  - doi: 10.1093/nar/gkv1310
    pmc: PMC4702916
    pubmed: '26615188'
    title: 'The SIB Swiss Institute of Bioinformatics'' resources: focus on curated
      databases'
    year: 2015
  - doi: 10.1093/nar/gku1123
    pmc: PMC4383937
    pubmed: '25428357'
    title: 'arrayMap 2014: an updated cancer genome resource'
    year: 2014
  - doi: 10.1186/1471-2164-15-82
    pmc: PMC3909908
    pubmed: '24476156'
    title: Chromothripsis-like patterns are recurring but heterogeneously distributed
      features in a survey of 22,347 cancer genome screens
    year: 2014
  - doi: 10.1371/journal.pone.0036944
    pmc: PMC3356349
    pubmed: '22629346'
    title: 'arrayMap: a reference resource for genomic copy number imbalances in human
      malignancies'
    year: 2012
  re3data:
    description: arrayMap is a repository of cancer genome profiling data. Original)
      from primary repositories (e.g. NCBI GEO, EBI ArrayExpress, TCGA) is re-processed
      and annotated for metadata. Unique visualization of the processed data allows
      critical evaluation of data quality and genome information. Structured metadata
      provides easy access to summary statistics, with a focus on copy number aberrations
      in cancer entities.
    doi: 10.17616/R3X78M
    homepage: https://progenetix.org/progenetix-cohorts/arraymap/
    name: arrayMap
    prefix: r3d100012630
arxiv:
  bartoc:
    abbreviation: arXiv
    description: Subject categories of arXiv.org repository.
    homepage: https://arxiv.org/category_taxonomy
    name: arXiv categories
    prefix: '20434'
  biocontext:
    prefix: ARXIV
  contributor_extras:
  - email: sumirp77@gmail.com
    github: sumirp
    name: Sumir H Pandit
    orcid: 0000-0002-1216-4761
  keywords:
  - preprints
  - publishing
  mappings:
    bartoc: '20434'
    biocontext: ARXIV
    miriam: arxiv
    n2t: arxiv
    prefixcommons: arxiv
    wikidata: P818
    wikidata.entity: Q118398
  miriam:
    deprecated: false
    description: arXiv is an e-print service in the fields of physics, mathematics,
      non-linear science, computer science, and quantitative biology.
    homepage: https://arxiv.org/
    id: '00000035'
    name: arXiv
    namespaceEmbeddedInLui: false
    pattern: ^(\w+(\-\w+)?(\.\w+)?\/?)?\d{4,7}(\.\d+(v\d+)?)?$
    prefix: arxiv
    sampleId: 0807.4956v1
    uri_format: https://arxiv.org/abs/$1
  n2t:
    description: arXiv is an e-print service in the fields of physics, mathematics,
      non-linear science, computer science, and quantitative biology.
    example: 0807.4956v1
    homepage: https://arxiv.org/
    name: Cornell University arXiv
    namespaceEmbeddedInLui: false
    pattern: ^(\w+(\-\w+)?(\.\w+)?)?\d{4,7}(\.\d+(v\d+)?)?$
    prefix: arxiv
    uri_format: https://arxiv.org/abs/$1
  name: arXiv
  prefix: arxiv
  prefixcommons:
    description: arXiv is an e-print service in the fields of physics, mathematics,
      non-linear science, computer science, and quantitative biology.
    example: 0807.4956v1
    homepage: http://arxiv.org
    keywords:
    - bibliography
    name: arXiv
    pattern: ^(\w+(\-\w+)?(\.\w+)?/)?\d{4,7}(\.\d{4}(v\d+)?)?$
    prefix: arxiv
    uri_format: http://arxiv.org/abs/$1
  providers:
  - code: scholia
    description: Scholia is a service that creates visual scholarly profiles for topic,
      people, organizations, species, chemicals, etc using bibliographic and other
      information in Wikidata.
    example: null
    first_party: null
    homepage: https://scholia.toolforge.org/
    name: Scholia
    publications: null
    status: null
    uri_format: https://scholia.toolforge.org/arxiv/$1
  - code: ar5iv
    description: Articles from arXiv.org as responsive HTML5 web pages.
    example: null
    first_party: null
    homepage: https://ar5iv.labs.arxiv.org/
    name: ar5iv
    publications: null
    status: null
    uri_format: https://ar5iv.org/abs/$1
  references:
  - https://github.com/biopragmatics/bioregistry/pull/1141
  wikidata:
    database: Q18920853
    description: identifier of a document in arXiv pre-print archive
    example:
    - '0806.2878'
    - '1109.1746'
    homepage: http://arxiv.org/abs/
    name: arXiv ID
    pattern: ^(\d{4}.\d{4,5}|[a-z\-]+(\.[A-Z]{2})?\/\d{7})(v\d+)?$
    prefix: P818
    uri_format: http://arxiv.org/abs/$1
asap:
  biocontext:
    prefix: ASAP
  contact:
    email: glasner@svm.vetmed.wisc.edu
    github: null
    name: Jeremy D. Glasner
    orcid: 0000-0003-1848-4464
  fairsharing:
    abbreviation: ASAP
    description: ASAP is a relational database and web interface developed to store,
      update and distribute genome sequence data and gene expression data. It was
      designed to facilitate ongoing community annotation of genomes and to grow with
      genome projects as they move from the preliminary data stage through post-sequencing
      functional analysis.
    homepage: https://asap.ahabs.wisc.edu/asap/home.php
    name: A Systematic Annotation Package
    prefix: FAIRsharing.anpa6
    publications:
    - doi: 10.1093/nar/gkg125
      pubmed_id: 12519969
      title: ASAP, a systematic annotation package for community analysis of genomes.
    subjects:
    - Developmental Biology
    - Life Science
    - Comparative Genomics
  go:
    homepage: https://asap.genetics.wisc.edu/asap/ASAP1.htm
    name: A Systematic Annotation Package for Community Analysis of Genomes
    prefix: ASAP
    uri_format: https://asap.genetics.wisc.edu/asap/feature_info.php?FeatureID=$1
  mappings:
    biocontext: ASAP
    fairsharing: FAIRsharing.anpa6
    go: ASAP
    miriam: asap
    n2t: asap
    ncbi: ASAP
    prefixcommons: asap
    re3data: r3d100010666
  miriam:
    deprecated: true
    description: ASAP (a systematic annotation package for community analysis of genomes)
      stores bacterial genome sequence and functional characterization data. It includes
      multiple genome sequences at various stages of analysis, corresponding experimental
      data and access to collections of related genome resources.
    homepage: https://www.genome.wisc.edu/tools/asap.htm
    id: 00000283
    name: ASAP
    namespaceEmbeddedInLui: false
    pattern: ^[A-Za-z0-9-]+$
    prefix: asap
    sampleId: ABE-0009634
    uri_format: http://asap.ahabs.wisc.edu/asap/feature_info.php?LocationID=WIS&FeatureID=$1
  n2t:
    description: ASAP (a systematic annotation package for community analysis of genomes)
      stores bacterial genome sequence and functional characterization data. It includes
      multiple genome sequences at various stages of analysis, corresponding experimental
      data and access to collections of related genome resources.
    example: ABE-0009634
    homepage: http://asap.ahabs.wisc.edu/asap/home.php
    name: ASAP at University of Wisconsin
    namespaceEmbeddedInLui: false
    pattern: ^[A-Za-z0-9-]+$
    prefix: asap
    uri_format: http://asap.ahabs.wisc.edu/asap/feature_info.php?LocationID=WIS&FeatureID=$1
  name: A Systematic Annotation Package for Community Analysis of Genomes
  ncbi:
    example: ABE-0000006
    homepage: https://asap.genetics.wisc.edu/asap/logon.php
    name: A Systematic Annotation Package for Community Analysis of Genomes
    prefix: ASAP
  prefix: asap
  prefixcommons:
    description: ASAP is a relational database and web interface developed to store,
      update and distribute genome sequence data and gene expression data.  It was
      designed to facilitate ongoing community annotation of genomes and to grow with
      genome projects as they move from the preliminary data stage through post-sequencing
      functional analysis.
    example: ABZ-0129277
    homepage: https://asap.ahabs.wisc.edu/annotation/php/ASAP1.htm
    keywords:
    - genome
    - gene expression
    name: A Systematic Annotation Package
    pattern: ^ABZ-\d+$
    prefix: asap
    pubmed_ids:
    - '12519969'
    - '16381899'
    uri_format: https://asap.ahabs.wisc.edu/asap/feature_info.php?FeatureID=$1
  publications:
  - doi: 10.1093/nar/gkj164
    pmc: PMC1347526
    pubmed: '16381899'
    title: 'ASAP: a resource for annotating, curating, comparing, and disseminating
      genomic data'
    year: 2006
  - doi: 10.1093/nar/gkg125
    pmc: PMC165572
    pubmed: '12519969'
    title: ASAP, a systematic annotation package for community analysis of genomes
    year: 2003
  re3data:
    description: 'ASAP (a systematic annotation package for community analysis of
      genomes) is a relational database and web interface developed to store, update
      and distribute genome sequence data and gene expression data collected by or
      in collaboration with researchers at the University of Wisconsin - Madison.

      ASAP was designed to facilitate ongoing community annotation of genomes and
      to grow with genome projects as they move from the preliminary data stage through
      post-sequencing functional analysis. The ASAP database includes multiple genome
      sequences at various stages of analysis, and gene expression data from preliminary
      experiments.'
    doi: 10.17616/R3CG7P
    homepage: https://asap.ahabs.wisc.edu/asap/home.php
    name: ASAP
    prefix: r3d100010666
    synonyms:
    - A systematic annotation package for community analysis of genomes
    xrefs:
      nif: 0000-02571
ascl:
  biocontext:
    prefix: ASCL
  contact:
    email: aallen@ascl.net
    github: null
    name: Alice Allen
    orcid: 0000-0003-3477-2845
  contributor_extras:
  - email: sumirp77@gmail.com
    github: sumirp
    name: Sumir H Pandit
    orcid: 0000-0002-1216-4761
  fairsharing:
    abbreviation: ASCL
    description: The Astrophysics Source Code Library (ASCL) is a free online registry
      for source code of interest to astronomers and astrophysicists. It provides
      code that has been used in research that has appeared in, or been submitted
      to, peer-reviewed publications.Peer-reviewed papers that describe methods or
      experiments involving the development or use of source code are added by the
      ASCL team.
    homepage: http://ascl.net/
    name: Astrophysics Source Code Library
    prefix: FAIRsharing.wb0txg
    publications:
    - doi: 10.5334/jors.bv
      pubmed_id: null
      title: 'Looking before Leaping: Creating a Software Registry'
    subjects:
    - Astrophysics and Astronomy
    twitter: asclnet
  mappings:
    biocontext: ASCL
    fairsharing: FAIRsharing.wb0txg
    miriam: ascl
    n2t: ascl
    re3data: r3d100011865
    wikidata.entity: Q17013974
  miriam:
    deprecated: false
    description: The Astrophysics Source Code Library (ASCL) is a free online registry
      for software that have been used in research that has appeared in, or been submitted
      to, peer-reviewed publications. The ASCL is indexed by the SAO/NASA Astrophysics
      Data System (ADS) and Web of Science's Data Citation Index (WoS DCI), and is
      citable by using the unique ascl ID assigned to each code. The ascl ID can be
      used to link to the code entry by prefacing the number with ascl.net (i.e.,
      ascl.net/1201.001).
    homepage: http://ascl.net/
    id: '00000641'
    name: Astrophysics Source Code Library
    namespaceEmbeddedInLui: false
    pattern: ^[0-9\.]+$
    prefix: ascl
    sampleId: '1801.012'
    uri_format: http://ascl.net/$1
  n2t:
    description: The Astrophysics Source Code Library (ASCL) is a free online registry
      for software that have been used in research that has appeared in, or been submitted
      to, peer-reviewed publications. The ASCL is indexed by the SAO/NASA Astrophysics
      Data System (ADS) and Web of Science's Data Citation Index (WoS DCI), and is
      citable by using the unique ascl ID assigned to each code. The ascl ID can be
      used to link to the code entry by prefacing the number with ascl.net (i.e.,
      ascl.net/1201.001).
    example: '1801.012'
    homepage: http://ascl.net/
    name: Astrophysics Source Code Library
    namespaceEmbeddedInLui: false
    pattern: ^[0-9\.]+$
    prefix: ascl
    uri_format: http://ascl.net/$1
  prefix: ascl
  publications:
  - doi: 10.5334/jors.bv
    pmc: null
    pubmed: null
    title: 'Looking before Leaping: Creating a Software Registry'
    year: 2015
  - doi: 10.5334/jors.bv
    pmc: null
    pubmed: null
    title: 'Looking before Leaping: Creating a Software Registry'
    year: null
  - doi: 10.5334/jors.bv
    pmc: null
    pubmed: null
    title: 'Looking before Leaping: Creating a Software Registry'
    year: null
  re3data:
    description: The Astrophysics Source Code Library (ASCL) is a free online registry
      for source codes of interest to astronomers and astrophysicists and lists codes
      that have been used in research that has appeared in, or been submitted to,
      peer-reviewed publications. The ASCL is citable by using the unique ascl ID
      assigned to each code. The ascl ID can be used to link to the code entry by
      prefacing the number with ascl.net (i.e., ascl.net/1201.001).
    doi: 10.17616/R3NW6X
    homepage: https://ascl.net/
    name: Astrophysics Source Code Library
    prefix: r3d100011865
    synonyms:
    - ASCL
    - ASCL.net Astrophysics Source Code Library
  wikidata:
    database: Q17013974
asin:
  biocontext:
    prefix: ASIN
  contributor_extras:
  - email: sumirp77@gmail.com
    github: sumirp
    name: Sumir H Pandit
    orcid: 0000-0002-1216-4761
  mappings:
    biocontext: ASIN
    miriam: asin
    n2t: asin
    wikidata.entity: Q1753278
  miriam:
    deprecated: false
    description: Almost every product on our site has its own ASIN, a unique code
      we use to identify it. For books, the ASIN is the same as the ISBN number, but
      for all other products a new ASIN is created when the item is uploaded to our
      catalogue.
    homepage: https://www.amazon.co.uk/gp/help/customer/display.html/277-3416785-8259466?ie=UTF8&nodeId=898182
    id: '00000670'
    name: Amazon Standard Identification Number (ASIN)
    namespaceEmbeddedInLui: false
    pattern: ^[0-9]{10}$
    prefix: asin
    sampleId: 0471491039
    uri_format: https://amzn.com/$1
  n2t:
    description: Almost every product on our site has its own ASIN, a unique code
      we use to identify it. For books, the ASIN is the same as the ISBN number, but
      for all other products a new ASIN is created when the item is uploaded to our
      catalogue.
    example: 0471491039
    homepage: https://www.amazon.co.uk/gp/help/customer/display.html/277-3416785-8259466?ie=UTF8&nodeId=898182
    name: Amazon Standard Identification Number (ASIN)
    namespaceEmbeddedInLui: false
    pattern: ^[0-9]{10}$
    prefix: asin
    uri_format: https://amzn.com/$1
  name: Amazon Standard Identification Number
  prefix: asin
  references:
  - https://github.com/biopragmatics/bioregistry/pull/1141
  wikidata:
    database: Q1753278
    property: P5749
aspgd.locus:
  biocontext:
    prefix: ASPGD.LOCUS
  biolink:
    is_identifiers: false
    is_obo: false
    prefix: AspGD
    uri_format: http://www.aspergillusgenome.org/cgi-bin/locus.pl?dbid=$1
  go:
    homepage: http://www.aspergillusgenome.org/
    name: Aspergillus Genome Database
    prefix: AspGD_LOCUS
    uri_format: http://www.aspergillusgenome.org/cgi-bin/locus.pl?locus=$1
  mappings:
    biocontext: ASPGD.LOCUS
    biolink: AspGD
    go: AspGD_LOCUS
    miriam: aspgd.locus
    n2t: aspgd.locus
  miriam:
    deprecated: true
    description: The Aspergillus Genome Database (AspGD) is a repository for information
      relating to fungi of the genus Aspergillus, which includes organisms of clinical,
      agricultural and industrial importance. AspGD facilitates comparative genomics
      by providing a full-featured genomics viewer, as well as matched and standardized
      sets of genomic information for the sequenced aspergilli. This collection references
      gene information.
    homepage: http://www.aspgd.org/
    id: '00000412'
    name: AspGD Locus
    namespaceEmbeddedInLui: false
    pattern: ^[A-Za-z_0-9]+$
    prefix: aspgd.locus
    sampleId: ASPL0000349247
    uri_format: http://www.aspergillusgenome.org/cgi-bin/locus.pl?dbid=$1
  n2t:
    description: The Aspergillus Genome Database (AspGD) is a repository for information
      relating to fungi of the genus Aspergillus, which includes organisms of clinical,
      agricultural and industrial importance. AspGD facilitates comparative genomics
      by providing a full-featured genomics viewer, as well as matched and standardized
      sets of genomic information for the sequenced aspergilli. This collection references
      gene information.
    example: ASPL0000349247
    homepage: http://www.aspgd.org/
    name: AspGD at Stanford Medical School
    namespaceEmbeddedInLui: false
    pattern: ^[A-Za-z_0-9]+$
    prefix: aspgd.locus
    uri_format: http://www.aspergillusgenome.org/cgi-bin/locus.pl?dbid=$1
  prefix: aspgd.locus
aspgd.protein:
  biocontext:
    prefix: ASPGD.PROTEIN
  mappings:
    biocontext: ASPGD.PROTEIN
    miriam: aspgd.protein
    n2t: aspgd.protein
  miriam:
    deprecated: true
    description: The Aspergillus Genome Database (AspGD) is a repository for information
      relating to fungi of the genus Aspergillus, which includes organisms of clinical,
      agricultural and industrial importance. AspGD facilitates comparative genomics
      by providing a full-featured genomics viewer, as well as matched and standardized
      sets of genomic information for the sequenced aspergilli. This collection references
      protein information.
    homepage: http://www.aspgd.org/
    id: '00000413'
    name: AspGD Protein
    namespaceEmbeddedInLui: false
    pattern: ^[A-Za-z_0-9]+$
    prefix: aspgd.protein
    sampleId: ASPL0000349247
    uri_format: http://www.aspergillusgenome.org/cgi-bin/protein/proteinPage.pl?dbid=$1
  n2t:
    description: The Aspergillus Genome Database (AspGD) is a repository for information
      relating to fungi of the genus Aspergillus, which includes organisms of clinical,
      agricultural and industrial importance. AspGD facilitates comparative genomics
      by providing a full-featured genomics viewer, as well as matched and standardized
      sets of genomic information for the sequenced aspergilli. This collection references
      protein information.
    example: ASPL0000349247
    homepage: http://www.aspgd.org/
    name: AspGD Protein at Stanford Medical School
    namespaceEmbeddedInLui: false
    pattern: ^[A-Za-z_0-9]+$
    prefix: aspgd.protein
    uri_format: http://www.aspergillusgenome.org/cgi-bin/protein/proteinPage.pl?dbid=$1
  prefix: aspgd.protein
asrp:
  contact:
    email: kasschau@cgrb.oregonstate.edu
    github: null
    name: Kristin D. Kasschau
    orcid: null
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: Arabidopsis Small RNA Project is a repository of data on Arabidopsis
    small RNA genes.
  example: ASRP1423
  homepage: https://asrp.danforthcenter.org/
  mappings:
    prefixcommons: asrp
  name: Arabidopsis Small RNA Project
  prefix: asrp
  prefixcommons:
    description: This project focuses on small RNAs. It involves function analysis,
      regulation, and the evolution of RNA silencing pathways at a genome-wide level.
      Technologies are being used in the sequence-based profiling of the genome of
      A. thaliana small RNAs and their classification associated with silencing effector
      proteins.
    example: '365115'
    homepage: http://asrp.cgrb.oregonstate.edu
    keywords:
    - RNA
    - genome
    - regulation
    name: Arabidopsis Small RNA Project
    pattern: ^\d+$
    prefix: asrp
    pubmed_ids:
    - '15608278'
    - '17999994'
    uri_format: http://asrp.cgrb.oregonstate.edu/db/sRNAdisplay.html?ASRP_id=$1
  publications:
  - doi: 10.1093/nar/gkm997
    pmc: PMC2238918
    pubmed: '17999994'
    title: 'Update of ASRP: the Arabidopsis Small RNA Project database'
    year: 2007
  - doi: 10.1093/nar/gki127
    pmc: PMC540081
    pubmed: '15608278'
    title: 'ASRP: the Arabidopsis Small RNA Project Database'
    year: 2005
  - doi: null
    pmc: null
    pubmed: '15608278'
    title: null
    year: null
  - doi: null
    pmc: null
    pubmed: '17999994'
    title: null
    year: null
astd:
  comment: This resource doesn't exist on the web anymore
  deprecated: true
  edam:
    description: Identifier of an object from the ASTD database.
    name: ASTD
    obsolete: false
    prefix: '2367'
  mappings:
    edam: '2367'
    prefixcommons: astd
  prefix: astd
  prefixcommons:
    description: The Alternative Splicing and Transcript Diversity (ASTD) database
      project is creating a database of alternative splice events and transcripts
      of genes from human, mouse and rat. Full length transcripts are generated with
      the aim of understanding the mechanism of alternative splicing on a genome-wide
      scale.
    example: ENSG00000136147
    homepage: http://www.ebi.ac.uk/astd/
    keywords:
    - gene
    - transcript
    - alternative splicing
    name: Alternative Splicing and Transcript Diversity
    pattern: ^ENSG\d+$
    prefix: astd
    pubmed_ids:
    - '19059335'
    uri_format: http://www.ebi.ac.uk/astd/geneview.html?acc=$1
  provides: ensembl
  publications:
  - doi: 10.1016/j.ygeno.2008.11.003
    pmc: null
    pubmed: '19059335'
    title: 'ASTD: The Alternative Splicing and Transcript Diversity database'
    year: 2008
  - doi: null
    pmc: null
    pubmed: '19059335'
    title: null
    year: null
  reviewer:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
asteraceaegd.genome:
  contact:
    email: greatchen@cdutcm.edu.cn
    github: null
    name: Wei Chen
    orcid: 0000-0002-6857-7696
  contributor:
    email: m.naguthana@hotmail.com
    github: nagutm
    name: Mufaddal Naguthanawala
    orcid: 0009-0009-5240-7463
  description: The AGD is an integrated database resource dedicated to collecting
    the genomic-related data of the Asteraceae family. This collection refers to the
    genomic data of Asteraceae species.
  example: '0002'
  github_request_issue: 1214
  homepage: https://cbcb.cdutcm.edu.cn/AGD/
  name: Asteraceae Genome Database - Genome
  pattern: ^\d{4}$
  prefix: asteraceaegd.genome
  publications:
  - doi: 10.3389/fpls.2024.1445365
    pmc: PMC11366637
    pubmed: '39224843'
    title: 'Asteraceae genome database: a comprehensive platform for Asteraceae genomics'
    year: 2024
  reviewer:
    email: b.gyori@northeastern.edu
    github: bgyori
    name: Benjamin M. Gyori
    orcid: 0000-0001-9439-5346
  uri_format: https://cbcb.cdutcm.edu.cn/AGD/genome/details/?id=$1
asteraceaegd.plant:
  contact:
    email: greatchen@cdutcm.edu.cn
    github: null
    name: Wei Chen
    orcid: 0000-0002-6857-7696
  contributor:
    email: m.naguthana@hotmail.com
    github: nagutm
    name: Mufaddal Naguthanawala
    orcid: 0009-0009-5240-7463
  description: The AGD is an integrated database resource dedicated to collecting
    the genomic-related data of the Asteraceae family. This collections refers to
    the broader phenotypic and genetic resources of Asteraceae plants.
  example: '0016'
  github_request_issue: 1214
  homepage: https://cbcb.cdutcm.edu.cn/AGD/
  name: Asteraceae Genome Database - Plant
  pattern: ^\d{4}$
  prefix: asteraceaegd.plant
  publications:
  - doi: 10.3389/fpls.2024.1445365
    pmc: PMC11366637
    pubmed: '39224843'
    title: 'Asteraceae genome database: a comprehensive platform for Asteraceae genomics'
    year: 2024
  reviewer:
    email: b.gyori@northeastern.edu
    github: bgyori
    name: Benjamin M. Gyori
    orcid: 0000-0001-9439-5346
  uri_format: https://cbcb.cdutcm.edu.cn/AGD/plant/details/?id=$1
atc:
  aberowl:
    description: The Anatomical Therapeutic Chemical (ATC) Classification System is
      used for the classification of active ingredients of drugs according to the
      organ or system on which they act and their therapeutic, pharmacological and
      chemical properties. It is controlled by the World Health Organization Collaborating
      Centre for Drug Statistics Methodology (WHOCC), and was first published in 1976.
    name: Anatomical Therapeutic Chemical Classification
    prefix: ATC
    version: 2016AB
  bartoc:
    abbreviation: ATC
    description: In the Anatomical Therapeutic Chemical (ATC) classification system,
      the active substances are divided into different groups according to the organ
      or system on which they act and their therapeutic, pharmacological and chemical
      properties. Drugs are classified in groups at five different levels. The drugs
      are divided into fourteen main groups (1st level), with pharmacological/therapeutic
      subgroups (2nd level).  The 3rd and 4th levels are chemical/pharmacological/therapeutic
      subgroups and the 5th level is the chemical substance. The 2nd, 3rd and 4th
      levels are often used to identify pharmacological subgroups when that is considered
      more appropriate than therapeutic or chemical subgroups.
    homepage: http://www.whocc.no/atc_ddd_index
    name: Anatomical Therapeutic Chemical Classification System
    prefix: '449'
    wikidata_database: Q192093
  biocontext:
    prefix: ATC
  bioportal:
    contact:
      email: whocc@fhi.no
      name: WHO Collaborating Centre for Drug Statistics Methodology
    description: The Anatomical Therapeutic Chemical (ATC) Classification System is
      used for the classification of active ingredients of drugs according to the
      organ or system on which they act and their therapeutic, pharmacological and
      chemical properties. It is controlled by the World Health Organization Collaborating
      Centre for Drug Statistics Methodology (WHOCC), and was first published in 1976.
    homepage: http://www.who.int/classifications/atcddd/en/
    name: Anatomical Therapeutic Chemical Classification
    prefix: ATC
    publications:
    - http://en.wikipedia.org/wiki/Anatomical_Therapeutic_Chemical_Classification_System
    version: ATC_2024_01_19_24_09_03
  edam:
    description: Unique identifier of a drug conforming to the Anatomical Therapeutic
      Chemical (ATC) Classification System, a drug classification system controlled
      by the WHO Collaborating Centre for Drug Statistics Methodology (WHOCC).
    name: ATC code
    obsolete: false
    prefix: '3103'
  fairsharing:
    abbreviation: ATC
    description: The Anatomical Therapeutic Chemical (ATC) Classification System is
      used for the classification of active ingredients of drugs according to the
      organ or system on which they act and their therapeutic, pharmacological and
      chemical properties. It is controlled by the World Health Organization Collaborating
      Centre for Drug Statistics Methodology (WHOCC), and was first published in 1976.
    domains:
    - ATC code
    - drug
    - Approved drug
    homepage: http://www.whocc.no/atc/structure_and_principles/
    name: Anatomical Therapeutic Chemical Classification
    prefix: FAIRsharing.1a27h8
    publications:
    - doi: 10.1007/s002280000200
      pubmed: '11214783'
      title: Different versions of the anatomical therapeutic chemical classification
        system and the defined daily dose--are drug utilisation data comparable?
      year: 2001
    - pubmed: '7368387'
      title: '[New classification of drugs. The Medical list and the Drug catalogue
        are introduced in Anatomical--Therapeutic--Chemical classification code (ACT-code)
        in 1981]'
      year: 1980
    subjects:
    - Chemical Biology
    - Biomedical Science
    - Pharmacology
    user_defined_tags:
    - Pharmacological family classification
  hl7:
    description: WHO ATC, Anatomical Therapeutic Chemical classification. The classification
      system divides drugs into different groups according to the organ or system
      on which they act and/or their therapeutic and chemical characteristics. It
      contains several subsets.
    homepage: http://www.who-umc.org/
    name: WHO Anatomical Therapeutic Chemical classification
    organization: World Health Organization
    preferred_prefix: whoATC
    prefix: 2.16.840.1.113883.6.73
    status: Complete
  mappings:
    aberowl: ATC
    bartoc: '449'
    biocontext: ATC
    bioportal: ATC
    edam: '3103'
    fairsharing: FAIRsharing.1a27h8
    hl7: 2.16.840.1.113883.6.73
    miriam: atc
    n2t: atc
    prefixcommons: atc
    togoid: Atc
    wikidata: P267
    wikidata.entity: Q192093
  miriam:
    deprecated: false
    description: The Anatomical Therapeutic Chemical (ATC) classification system,
      divides active substances into different groups according to the organ or system
      on which they act and their therapeutic, pharmacological and chemical properties.
      Drugs are classified in groups at five different levels;  Drugs are divided
      into fourteen main groups (1st level), with pharmacological/therapeutic subgroups
      (2nd level).  The 3rd and 4th levels are chemical/pharmacological/therapeutic
      subgroups and the 5th level is the chemical substance. The Anatomical Therapeutic
      Chemical (ATC) classification system and the Defined Daily Dose (DDD) is a tool
      for exchanging and comparing data on drug use at international, national or
      local levels.
    homepage: http://www.whocc.no/atc_ddd_index/
    id: 00000088
    name: Anatomical Therapeutic Chemical
    namespaceEmbeddedInLui: false
    pattern: ^[A-Z](\d+([A-Z]{1,2}(\d+)?)?)?$
    prefix: atc
    sampleId: A10BA02
    uri_format: http://www.whocc.no/atc_ddd_index/?code=$1
  n2t:
    description: The Anatomical Therapeutic Chemical (ATC) classification system,
      divides active substances into different groups according to the organ or system
      on which they act and their therapeutic, pharmacological and chemical properties.
      Drugs are classified in groups at five different levels;  Drugs are divided
      into fourteen main groups (1st level), with pharmacological/therapeutic subgroups
      (2nd level).  The 3rd and 4th levels are chemical/pharmacological/therapeutic
      subgroups and the 5th level is the chemical substance. The Anatomical Therapeutic
      Chemical (ATC) classification system and the Defined Daily Dose (DDD) is a tool
      for exchanging and comparing data on drug use at international, national or
      local levels.
    example: A10BA02
    homepage: http://www.whocc.no/atc_ddd_index/
    name: Anatomical Therapeutic Chemical Index at WHO
    namespaceEmbeddedInLui: false
    pattern: ^[A-Z](\d+([A-Z]{1,2}(\d+)?)?)?$
    prefix: atc
    uri_format: http://www.whocc.no/atc_ddd_index/?code=$1
  name: Anatomical Therapeutic Chemical Classification System
  prefix: atc
  prefixcommons:
    alt_uri_formats:
    - http://purl.bioontology.org/ontology/UATC/$1
    bioportal: '3021'
    description: The Anatomical Therapeutic Chemical (ATC) classification system,
      divides active substances into different groups according to the organ or system
      on which they act and their therapeutic, pharmacological and chemical properties.
      Drugs are classified in groups at five different levels; Drugs are divided into
      fourteen main groups (1st level), with pharmacological/therapeutic subgroups
      (2nd level). The 3rd and 4th levels are chemical/pharmacological/therapeutic
      subgroups and the 5th level is the chemical substance. The Anatomical Therapeutic
      Chemical (ATC) classification system and the Defined Daily Dose (DDD) is a tool
      for exchanging and comparing data on drug use at international, national or
      local levels.
    example: A10BA02
    homepage: http://www.whocc.no/atc_ddd_index/
    keywords:
    - chemical
    name: Anatomical Therapeutic Chemical
    pattern: ^\w(\d+)?(\w{1,2})?(\d+)?$
    prefix: atc
    synonyms:
    - uatc
    uri_format: http://www.whocc.no/atc_ddd_index/?code=$1
  providers:
  - code: bioportal.purl
    description: BioPortal assigned additional PURLs for ATC codes
    example: null
    first_party: null
    homepage: http://purl.bioontology.org/ontology/ATC
    name: BioPortal
    publications: null
    status: null
    uri_format: http://purl.bioontology.org/ontology/ATC/$1
  publications:
  - doi: 10.1007/s002280000200
    pmc: null
    pubmed: '11214783'
    title: Different versions of the anatomical therapeutic chemical classification
      system and the defined daily dose--are drug utilisation data comparable?
    year: 2000
  - doi: null
    pmc: null
    pubmed: '7368387'
    title: '[New classification of drugs. The Medical list and the Drug catalogue
      are introduced in Anatomical--Therapeutic--Chemical classification code (ACT-code)
      in 1981]'
    year: 1980
  - doi: 10.1007/s002280000200
    pmc: null
    pubmed: '11214783'
    title: Different versions of the anatomical therapeutic chemical classification
      system and the defined daily dose--are drug utilisation data comparable?
    year: 2001
  - doi: null
    pmc: null
    pubmed: '7368387'
    title: '[New classification of drugs. The Medical list and the Drug catalogue
      are introduced in Anatomical--Therapeutic--Chemical classification code (ACT-code)
      in 1981]'
    year: 1980
  - doi: 10.1007/s002280000200
    pmc: null
    pubmed: '11214783'
    title: Different versions of the anatomical therapeutic chemical classification
      system and the defined daily dose--are drug utilisation data comparable?
    year: 2001
  - doi: null
    pmc: null
    pubmed: '7368387'
    title: '[New classification of drugs. The Medical list and the Drug catalogue
      are introduced in Anatomical--Therapeutic--Chemical classification code (ACT-code)
      in 1981]'
    year: 1980
  synonyms:
  - ATC_code
  - ATTC
  togoid:
    examples:
    - J01DD11
    - B02BA02
    - A03AD30
    - R03AC17
    - J01CA05
    - D07AB07
    - D07XB03
    - G04CA01
    - S01BC11
    - G03DB05
    keywords:
    - Drug
    name: ATC classification
    pattern: ^(?[A-Z]\d{2}[A-Z]{2}\d{2})$
    prefix: Atc
    uri_format: http://identifiers.org/atc/$1
  wikidata:
    description: therapeutic chemical identification code per ATC
    example:
    - A02BC04
    - D08AX08
    homepage: https://www.whocc.no/
    name: ATC code
    pattern: ^[A-V]([0-9][0-9]([A-Z]([A-Z]([0-9][0-9])?)?)?)[0-9]$
    prefix: P267
    uri_format: https://www.whocc.no/atc_ddd_index/?code=$1
atcc:
  biocontext:
    prefix: ATCC
  cellosaurus:
    category: Cell line collections (Providers)
    homepage: https://www.atcc.org/
    name: American Type Culture Collection
    prefix: ATCC
    uri_format: https://www.atcc.org/products/$1
  example_extras:
  - ccl-1.4
  - ccl-1
  fairsharing:
    abbreviation: ATCC
    description: ATCC authenticates microorganisms and cell lines and manages logistics
      of long-term preservation and distribution of cultures for the scientific community.
      ATCC supports the cultures it acquires and authenticates with expert technical
      support, intellectual property management and characterization data.
    homepage: http://www.atcc.org/
    name: American Type Culture Collection database
    prefix: FAIRsharing.j0ezpm
    publications: []
    subjects:
    - Virology
    - Life Science
    - Epidemiology
  hl7:
    description: American Type Culture Collection
    name: ATC
    preferred_prefix: ATC
    prefix: 2.16.840.1.113883.6.77
    status: Pending
  homepage: https://www.lgcstandards-atcc.org
  mappings:
    biocontext: ATCC
    cellosaurus: ATCC
    fairsharing: FAIRsharing.j0ezpm
    hl7: 2.16.840.1.113883.6.77
    miriam: atcc
    n2t: atcc
    ncbi: ATCC
  miriam:
    deprecated: false
    description: The American Type Culture Collection (ATCC) is a private, nonprofit
      biological resource center whose mission focuses on the acquisition, authentication,
      production, preservation, development and distribution of standard reference
      microorganisms, cell lines and other materials for research in the life sciences.
    homepage: http://www.atcc.org/
    id: 00000284
    name: ATCC
    namespaceEmbeddedInLui: false
    pattern: ^\d+$
    prefix: atcc
    sampleId: '11303'
    uri_format: https://www.atcc.org/products/$1
  n2t:
    description: The American Type Culture Collection (ATCC) is a private, nonprofit
      biological resource center whose mission focuses on the acquisition, authentication,
      production, preservation, development and distribution of standard reference
      microorganisms, cell lines and other materials for research in the life sciences.
    example: '11303'
    homepage: http://www.atcc.org/
    name: ATCC in Virginia
    namespaceEmbeddedInLui: false
    pattern: ^\d+$
    prefix: atcc
    uri_format: http://www.lgcstandards-atcc.org/Products/All/$1.aspx
  name: American Type Culture Collection
  ncbi:
    example: '123456'
    homepage: http://www.atcc.org/
    name: American Type Culture Collection database
    prefix: ATCC
  pattern: ^([a-zA-Z]+-)?\d+(\.\d)?$
  prefix: atcc
  synonyms:
  - ATCC
  - ATCC number
  - ATCC(dna)
  - ATCC(in host)
  uri_format: https://www.atcc.org/products/$1
atcvet:
  biocontext:
    prefix: ATCVET
  mappings:
    biocontext: ATCVET
    miriam: atcvet
    n2t: atcvet
  miriam:
    deprecated: false
    description: The ATCvet system for the classification of veterinary medicines
      is based on the same overall principles as the ATC system for substances used
      in human medicine. In ATCvet systems, preparations are divided into groups,
      according to their therapeutic use. First, they are divided into 15 anatomical
      groups (1st level), classified as QA-QV in the ATCvet system, on the basis of
      their main therapeutic use.
    homepage: http://www.whocc.no/atcvet/atcvet_index/
    id: '00000267'
    name: Anatomical Therapeutic Chemical Vetinary
    namespaceEmbeddedInLui: false
    pattern: ^Q[A-Z0-9]+$
    prefix: atcvet
    sampleId: QJ51RV02
    uri_format: http://www.whocc.no/atcvet/atcvet_index/?code=$1
  n2t:
    description: The ATCvet system for the classification of veterinary medicines
      is based on the same overall principles as the ATC system for substances used
      in human medicine. In ATCvet systems, preparations are divided into groups,
      according to their therapeutic use. First, they are divided into 15 anatomical
      groups (1st level), classified as QA-QV in the ATCvet system, on the basis of
      their main therapeutic use.
    example: QJ51RV02
    homepage: http://www.whocc.no/atcvet/atcvet_index/
    name: Anatomical Therapeutic Chemical Vet Index at WHO
    namespaceEmbeddedInLui: false
    pattern: ^Q[A-Z0-9]+$
    prefix: atcvet
    uri_format: http://www.whocc.no/atcvet/atcvet_index/?code=$1
  prefix: atcvet
atfdb.family:
  biocontext:
    prefix: ATFDB.FAMILY
  mappings:
    biocontext: ATFDB.FAMILY
    miriam: atfdb.family
    n2t: atfdb.family
  miriam:
    deprecated: false
    description: The Animal Transcription Factor DataBase (AnimalTFDB) classifies
      TFs in sequenced animal genomes, as well as collecting the transcription co-factors
      and chromatin remodeling factors of those genomes. This collections refers to
      transcription factor families, and the species in which they are found.
    homepage: https://guolab.wchscu.cn/AnimalTFDB4
    id: '00000316'
    name: Animal TFDB Family
    namespaceEmbeddedInLui: false
    pattern: ^\w+$
    prefix: atfdb.family
    sampleId: CUT
    uri_format: https://guolab.wchscu.cn/AnimalTFDB4//#/family_summary/TF/$1
  n2t:
    description: The Animal Transcription Factor DataBase (AnimalTFDB) classifies
      TFs in sequenced animal genomes, as well as collecting the transcription co-factors
      and chromatin remodeling factors of those genomes. This collections refers to
      transcription factor families, and the species in which they are found.
    example: CUT
    homepage: http://www.bioguo.org/AnimalTFDB/family_index.php
    name: Animal TFDB at Hubei Bioinformatics & Molecular Imaging Key Laboratory
    namespaceEmbeddedInLui: false
    pattern: ^\w+$
    prefix: atfdb.family
    uri_format: http://www.bioguo.org/AnimalTFDB/family.php?fam=$1
  prefix: atfdb.family
ato:
  aberowl:
    description: A taxonomy of Amphibia
    download_obo: http://aber-owl.net/media/ontologies/ATO/2/ato.obo
    homepage: http://www.amphibanat.org
    name: Amphibian Taxonomy Ontology
    prefix: ATO
    version: See Remote Site
  biocontext:
    prefix: ATO
  bioportal:
    contact:
      email: sbhdbe@mst.edu
      name: AmphiAnat list
    description: A taxonomy of Amphibia
    homepage: http://www.amphibanat.org
    name: Amphibian Taxonomy Ontology
    prefix: ATO
    version: See Remote Site
  contact:
    email: david.c.blackburn@gmail.com
    github: null
    name: David Blackburn
    orcid: 0000-0002-1810-9886
  example: '0000000'
  fairsharing:
    abbreviation: ATO
    description: Amphibian Taxonomy Ontology is an ontology of Amphibian species and
      genres. It is being integrated into UBERON resource
    domains:
    - Taxonomic classification
    homepage: http://purl.bioontology.org/ontology/ATO
    name: Amphibian Taxonomy Ontology
    prefix: FAIRsharing.ayjdsm
    subjects:
    - Taxonomy
  mappings:
    aberowl: ATO
    biocontext: ATO
    bioportal: ATO
    fairsharing: FAIRsharing.ayjdsm
    obofoundry: ato
    wikidata.entity: Q114677879
  obofoundry:
    contact: david.c.blackburn@gmail.com
    contact.label: David Blackburn
    contact.orcid: 0000-0002-1810-9886
    deprecated: true
    domain: organisms
    homepage: http://www.amphibanat.org
    name: Amphibian taxonomy
    prefix: ato
  pattern: ^\d{7}$
  prefix: ato
atol:
  aberowl:
    description: 'ATOL (Animal Trait Ontology for Livestock) is an ontology of characteristics
      defining phenotypes of livestock in their environment (EOL). ATOL aims to: -
      provide a reference ontology of phenotypic traits of farm animals for the international
      scientific and educational - communities, farmers, etc.; - deliver this reference
      ontology in a language which can be used by computers in order to support database
      management, semantic analysis and modeling; - represent traits as generic as
      possible for livestock vertebrates; - make the ATOL ontology as operational
      as possible and closely related to measurement techniques; - structure the ontology
      in relation to animal production'
    download_owl: http://aber-owl.net/media/ontologies/ATOL/1/atol.owl
    homepage: www.atol-ontology.com
    name: Animal Trait Ontology for Livestock
    prefix: ATOL
  agroportal:
    contact:
      email: jerome.bugeon@inrae.fr
      name: Jerome Bugeon
    description: 'ATOL définit et organise les caractères phénotypiques des animaux
      d’élevage, en prenant en compte les préoccupations sociétales et les grands
      types de production (lait, œuf, viande, fertilité, alimentation)., ATOL (Animal
      Trait Ontology for Livestock) is an ontology of characteristics defining phenotypes
      of livestock in their environment (EOL). ATOL aims to: - provide a reference
      ontology of phenotypic traits of farm animals for the international scientific
      and educational - communities, farmers, etc.; - deliver this reference ontology
      in a language which can be used by computers in order to support database management,
      semantic analysis and modeling; - represent traits as generic as possible for
      livestock vertebrates; - make the ATOL ontology as operational as possible and
      closely related to measurement techniques; - structure the ontology in relation
      to animal production'
    example_uri: http://opendata.inra.fr/ATOL/ATOL_0000455
    homepage: http://www.atol-ontology.com/
    license: CC-BY-4.0
    name: Animal Trait Ontology for Livestock
    prefix: ATOL
    publications:
    - http://www.atol-ontology.com/rb/fr/6
  bioportal:
    contact:
      email: matthieu.reichstadt@clermont.inra.fr
      name: Reichstadt Matthieu
    description: 'ATOL (Animal Trait Ontology for Livestock) is an ontology of characteristics
      defining phenotypes of livestock in their environment (EOL). ATOL aims to: -
      provide a reference ontology of phenotypic traits of farm animals for the international
      scientific and educational - communities, farmers, etc.; - deliver this reference
      ontology in a language which can be used by computers in order to support database
      management, semantic analysis and modeling; - represent traits as generic as
      possible for livestock vertebrates; - make the ATOL ontology as operational
      as possible and closely related to measurement techniques; - structure the ontology
      in relation to animal production'
    homepage: http://www.atol-ontology.com
    name: Animal Trait Ontology for Livestock
    prefix: ATOL
    version: '6.0'
  contact:
    email: pylebail@rennes.inra.fr
    github: null
    name: Pierre-Yves LeBail
    orcid: 0000-0002-8310-5195
  download_owl: http://sicpa-web.cati.inrae.fr/ontologies/visualisation/ontologie/atol/creation_fichier_owl.php?filename=atol.owl
  example: '0002233'
  fairsharing:
    abbreviation: ATOL
    description: 'ATOL (Animal Trait Ontology for Livestock) is an ontology of characteristics
      defining phenotypes of livestock in their environment. ATOL aims to: provide
      a reference ontology of phenotypic traits of farm animals for the international
      scientific and educational - communities, farmers, etc.; deliver this reference
      ontology in a language which can be used by computers in order to support database
      management, semantic analysis and modeling; represent traits as generic as possible
      for livestock vertebrates; make the ATOL ontology as operational as possible
      and closely related to measurement techniques; and structure the ontology in
      relation to animal production.'
    domains:
    - phenotype
    homepage: http://www.atol-ontology.com/en/atol-2/
    license: CC-BY-4.0
    name: Animal Trait Ontology for Livestock
    prefix: FAIRsharing.wsfk5z
    subjects:
    - Agriculture
    - Life Science
    - Animal Husbandry
    user_defined_tags:
    - Livestock
  mappings:
    aberowl: ATOL
    agroportal: ATOL
    bioportal: ATOL
    fairsharing: FAIRsharing.wsfk5z
    ols: atol
  ols:
    contact: pylebail@rennes.inra.fr
    description: 'ATOL (Animal Trait Ontology for Livestock) is an ontology of characteristics
      defining phenotypes of livestock in their environment (EOL). ATOL aims to: -
      provide a reference ontology of phenotypic traits of farm animals for the international
      scientificand educational - communities, farmers, etc.; - deliver this reference
      ontology in a language which can be used by computers in order to support database
      management, semantic analysis and modeling; - represent traits as generic as
      possible for livestock vertebrates; - make the ATOL ontology as operational
      as possible and closely related to measurement techniques; - structure the ontology
      in relation to animal production.'
    download: http://www.atol-ontology.com/public/telechargement/atol.owl
    homepage: http://www.atol-ontology.com
    name: Animal Trait Ontology for Livestock
    prefix: atol
    version: '2018-09-13'
  pattern: ^\d{7}$
  prefix: atol
  uri_format: http://opendata.inra.fr/ATOL/ATOL_$1
atomistic:
  description: An EMMO-based domain ontology for atomistic and electronic modelling.
  example: 08fd7117-66ac-5b6d-b65e-34a826675877
  license: CC-BY-4.0
  mappings:
    tib: atomistic
  prefix: atomistic
  repository: https://github.com/emmo-repo/domain-atomistic
  tib:
    description: An EMMO-based domain ontology for atomistic and electronic modelling.Atomistic
      is released under the Creative Commons Attribution 4.0 International license
      (CC BY 4.0).
    download_rdf: https://raw.githubusercontent.com/emmo-repo/domain-atomistic/master/atomistic.ttl
    homepage: https://github.com/emmo-repo/domain-atomistic
    keywords:
    - NFDI4ING
    - engineering
    name: Atomistic
    prefix: atomistic
    uri_format: https://w3id.org/emmo/domain/atomistic#$1
    version.iri: https://w3id.org/emmo/domain/atomistic/0.0.2
autdb:
  biocontext:
    prefix: AUTDB
  mappings:
    biocontext: AUTDB
    miriam: autdb
    n2t: autdb
  miriam:
    deprecated: true
    description: AutDB is a curated database for autism research. It is built on information
      extracted from the studies on molecular genetics and biology of Autism Spectrum
      Disorders (ASD). The four modules of AutDB include information on Human Genes,
      Animal models, Protein Interactions (PIN) and Copy Number Variants (CNV) respectively.
      It provides an annotated list of ASD candidate genes in the form of reference
      dataset for interrogating molecular mechanisms underlying the disorder.
    homepage: http://autism.mindspec.org/autdb/
    id: '00000415'
    name: AutDB
    namespaceEmbeddedInLui: false
    pattern: ^[A-Z]+[A-Z-0-9]{2,}$
    prefix: autdb
    sampleId: ADA
    uri_format: http://autism.mindspec.org/GeneDetail/$1
  n2t:
    description: AutDB is a curated database for autism research. It is built on information
      extracted from the studies on molecular genetics and biology of Autism Spectrum
      Disorders (ASD). The four modules of AutDB include information on Human Genes,
      Animal models, Protein Interactions (PIN) and Copy Number Variants (CNV) respectively.
      It provides an annotated list of ASD candidate genes in the form of reference
      dataset for interrogating molecular mechanisms underlying the disorder.
    example: ADA
    homepage: http://autism.mindspec.org/autdb/
    name: AutDB at MindSpec
    namespaceEmbeddedInLui: false
    pattern: ^[A-Z]+[A-Z-0-9]{2,}$
    prefix: autdb
    uri_format: http://autism.mindspec.org/GeneDetail/$1
  prefix: autdb
authenticus:
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  homepage: https://www.authenticus.pt
  keywords:
  - person
  - researcher
  mappings:
    wikidata: P7834
  prefix: authenticus
  references:
  - https://github.com/biopragmatics/bioregistry/pull/1171
  wikidata:
    description: ID of a researcher in Authenticus website
    example:
    - P-008-GD6
    - P-00A-A83
    - P-00N-E5D
    - R-000-008
    - R-000-00F
    - R-001-0W1
    name: Authenticus ID
    pattern: ^[A-Z]-[0-9A-Z]{3}-[0-9A-Z]{3}$
    prefix: P7834
    uri_format: https://www.authenticus.pt/$1
authorea.author:
  example: '229233'
  mappings:
    wikidata: P5039
  prefix: authorea.author
  wikidata:
    description: identifier for an author on the Authorea writing service
    example:
    - '106'
    - '229233'
    homepage: https://www.authorea.com
    name: Authorea author ID
    pattern: ^[1-9]\d*$
    prefix: P5039
    uri_format: https://www.authorea.com/users/$1
babelon:
  contact:
    email: nicolas.matentzoglu@gmail.com
    github: matentzn
    name: Nicolas Matentzoglu
    orcid: 0000-0002-7356-1779
  contributor:
    email: nicolas.matentzoglu@gmail.com
    github: matentzn
    name: Nicolas Matentzoglu
    orcid: 0000-0002-7356-1779
  description: Babelon is a simple standard for managing ontology translations and
    language profiles. Profiles are managed as TSV files, see for example https://github.com/obophenotype/hpo-translations/tree/main/babelon.
    The goal of Babelon as a data model and vocabulary is to capture the minimum data
    required to capture important metadata such as confidence and precision of translation.
  example: translation_language
  github_request_issue: 903
  homepage: https://monarch-initiative.github.io/babelon/
  license: MIT
  name: Babelon
  pattern: ^[a-z][a-z0-9_]+[a-z0-9]$
  prefix: babelon
  repository: https://github.com/monarch-initiative/babelon
  reviewer:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  uri_format: https://w3id.org/babelon/$1
bacdive:
  contact:
    email: lorenz.reimer@dsmz.de
    github: null
    name: Lorenz Reimer
    orcid: 0000-0002-7805-0660
  contact_group_email: contact@bacdive.de
  fairsharing:
    abbreviation: BacDive
    contact:
      email: contact@bacdive.de
      name: Lorenz Reimer
      orcid: 0000-0002-7805-0660
    description: BacDive—the Bacterial Diversity Metadatabase merges detailed strain-linked
      information on the different aspects of bacterial and archaeal biodiversity.
      BacDive contains entries for over 63,000 strains and provides information on
      their taxonomy, morphology, physiology, sampling and concomitant environmental
      conditions as well as molecular biology.
    homepage: https://bacdive.dsmz.de/
    license: CC BY-NC 4.0
    name: Bacterial Diversity Metadatabase
    prefix: FAIRsharing.aSszvY
    publications:
    - doi: 10.1093/nar/gkv983
      pubmed_id: 26424852
      title: BacDive--The Bacterial Diversity Metadatabase in 2016.
    - doi: 10.1016/j.jbiotec.2017.05.004
      pubmed_id: 28487186
      title: Mobilization and integration of bacterial phenotypic data-Enabling next
        generation biodiversity analysis through the BacDive metadatabase.
    - doi: 10.1093/nar/gkt1058
      pubmed_id: 24214959
      title: BacDive--the Bacterial Diversity Metadatabase.
    - doi: 10.1093/nar/gky879
      pubmed_id: 30256983
      title: 'BacDive in 2019: bacterial phenotypic data for High-throughput biodiversity
        analysis.'
    subjects:
    - Biodiversity
    - Life Science
    - Microbiology
  mappings:
    fairsharing: FAIRsharing.aSszvY
    miriam: bacdive
    n2t: bacdive
    re3data: r3d100013060
    wikidata: P2946
  miriam:
    deprecated: false
    description: BacDive—the Bacterial Diversity Metadatabase merges detailed strain-linked
      information on the different aspects of bacterial and archaeal biodiversity.
    homepage: https://bacdive.dsmz.de/
    id: '00000676'
    name: Bacterial Diversity Metadatabase
    namespaceEmbeddedInLui: false
    pattern: ^[0-9]+$
    prefix: bacdive
    sampleId: '131392'
    uri_format: https://bacdive.dsmz.de/strain/$1
  n2t:
    description: BacDive&#x2014;the Bacterial Diversity Metadatabase merges detailed
      strain-linked information on the different aspects of bacterial and archaeal
      biodiversity.
    example: '131392'
    homepage: https://bacdive.dsmz.de/
    name: Bacterial Diversity Metadatabase
    namespaceEmbeddedInLui: false
    pattern: ^[0-9]+$
    prefix: bacdive
    uri_format: https://bacdive.dsmz.de/strain/$1
  name: BacDive
  prefix: bacdive
  publications:
  - doi: 10.1093/nar/gky879
    pmc: PMC6323973
    pubmed: '30256983'
    title: 'BacDive in 2019: bacterial phenotypic data for High-throughput biodiversity
      analysis'
    year: 2019
  - doi: 10.1016/j.jbiotec.2017.05.004
    pmc: null
    pubmed: '28487186'
    title: Mobilization and integration of bacterial phenotypic data-Enabling next
      generation biodiversity analysis through the BacDive metadatabase
    year: 2017
  - doi: 10.1093/nar/gkv983
    pmc: PMC4702946
    pubmed: '26424852'
    title: BacDive--The Bacterial Diversity Metadatabase in 2016
    year: 2015
  - doi: 10.1093/nar/gkt1058
    pmc: PMC3965005
    pubmed: '24214959'
    title: BacDive--the Bacterial Diversity Metadatabase
    year: 2013
  re3data:
    description: BacDive (The Bacterial Diversity Database) is the worldwide largest
      database for standardized bacterial and archaeal strain-level information. Its
      mission is to mobilize and integrate research data on strain level from diverse
      sources and make it freely accessible. BacDive is a comprehensive resource containing
      diverse data on bacterial and archaeal strains, including taxonomy, morphology,
      physiology, sampling and environmental data and sequence information.
    doi: 10.17616/R31NJMKK
    homepage: https://bacdive.dsmz.de/
    name: BacDive
    prefix: r3d100013060
    synonyms:
    - The Bacterial Diversity Database
    xrefs:
      omics: '10161'
  wikidata:
    description: identifier for a microorganism, in the BacDive database
    example:
    - '1419'
    - '2631'
    - '8607'
    name: BacDive ID
    pattern: ^\d{1,6}$
    prefix: P2946
    uri_format: https://bacdive.dsmz.de/strain/$1
bacmap.biog:
  biocontext:
    prefix: BACMAP.BIOG
  mappings:
    biocontext: BACMAP.BIOG
    miriam: bacmap.biog
    n2t: bacmap.biog
  miriam:
    deprecated: false
    description: BacMap is an electronic, interactive atlas of fully sequenced bacterial
      genomes. It contains labeled, zoomable and searchable chromosome maps for sequenced
      prokaryotic (archaebacterial and eubacterial) species. Each map can be zoomed
      to the level of individual genes and each gene is hyperlinked to a richly annotated
      gene card. All bacterial genome maps are supplemented with separate prophage
      genome maps as well as separate tRNA and rRNA maps. Each bacterial chromosome
      entry in BacMap contains graphs and tables on a variety of gene and protein
      statistics. Likewise, every bacterial species entry contains a bacterial 'biography'
      card, with taxonomic details, phenotypic details, textual descriptions and images.
      This collection references 'biography' information.
    homepage: http://bacmap.wishartlab.com/
    id: '00000361'
    name: BacMap Biography
    namespaceEmbeddedInLui: false
    pattern: ^\d+$
    prefix: bacmap.biog
    sampleId: '1050'
    uri_format: http://bacmap.wishartlab.com/organisms/$1
  n2t:
    description: BacMap is an electronic, interactive atlas of fully sequenced bacterial
      genomes. It contains labeled, zoomable and searchable chromosome maps for sequenced
      prokaryotic (archaebacterial and eubacterial) species. Each map can be zoomed
      to the level of individual genes and each gene is hyperlinked to a richly annotated
      gene card. All bacterial genome maps are supplemented with separate prophage
      genome maps as well as separate tRNA and rRNA maps. Each bacterial chromosome
      entry in BacMap contains graphs and tables on a variety of gene and protein
      statistics. Likewise, every bacterial species entry contains a bacterial 'biography'
      card, with taxonomic details, phenotypic details, textual descriptions and images.
      This collection references 'biography' information.
    example: '1050'
    homepage: http://bacmap.wishartlab.com/
    name: BacMap Biography at University of Alberta
    namespaceEmbeddedInLui: false
    pattern: ^\d+$
    prefix: bacmap.biog
    uri_format: http://bacmap.wishartlab.com/organisms/$1
  prefix: bacmap.biog
bacmap.map:
  biocontext:
    prefix: BACMAP.MAP
  mappings:
    biocontext: BACMAP.MAP
    miriam: bacmap.map
    n2t: bacmap.map
  miriam:
    deprecated: false
    description: BacMap is an electronic, interactive atlas of fully sequenced bacterial
      genomes. It contains labeled, zoomable and searchable chromosome maps for sequenced
      prokaryotic (archaebacterial and eubacterial) species. Each map can be zoomed
      to the level of individual genes and each gene is hyperlinked to a richly annotated
      gene card. All bacterial genome maps are supplemented with separate prophage
      genome maps as well as separate tRNA and rRNA maps. Each bacterial chromosome
      entry in BacMap contains graphs and tables on a variety of gene and protein
      statistics. Likewise, every bacterial species entry contains a bacterial 'biography'
      card, with taxonomic details, phenotypic details, textual descriptions and images.
      This collection references genome map information.
    homepage: http://bacmap.wishartlab.com/
    id: '00000416'
    name: BacMap Map
    namespaceEmbeddedInLui: false
    pattern: ^\w+(\_)?\d+(\.\d+)?$
    prefix: bacmap.map
    sampleId: AP011135
    uri_format: http://bacmap.wishartlab.com/maps/$1/index.html
  n2t:
    description: BacMap is an electronic, interactive atlas of fully sequenced bacterial
      genomes. It contains labeled, zoomable and searchable chromosome maps for sequenced
      prokaryotic (archaebacterial and eubacterial) species. Each map can be zoomed
      to the level of individual genes and each gene is hyperlinked to a richly annotated
      gene card. All bacterial genome maps are supplemented with separate prophage
      genome maps as well as separate tRNA and rRNA maps. Each bacterial chromosome
      entry in BacMap contains graphs and tables on a variety of gene and protein
      statistics. Likewise, every bacterial species entry contains a bacterial 'biography'
      card, with taxonomic details, phenotypic details, textual descriptions and images.
      This collection references genome map information.
    example: AP011135
    homepage: http://bacmap.wishartlab.com/
    name: BacMap Genome Map at University of Alberta
    namespaceEmbeddedInLui: false
    pattern: ^\w+(\_)?\d+(\.\d+)?$
    prefix: bacmap.map
    uri_format: http://bacmap.wishartlab.com/maps/$1/index.html
  prefix: bacmap.map
bactibase:
  contact:
    email: ismail.fliss@fsaa.ulaval.ca
    github: null
    name: Ismail Fliss
    orcid: 0000-0002-8467-9414
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: Bactibase is a database describing the physical and chemical properties
    of bacteriocins from gram-negative and gram-positive bacteria.
  example: BAC045
  fairsharing:
    abbreviation: BACTIBASE
    description: BACTIBASE contains calculated or predicted physicochemical properties
      of bacteriocins produced by both Gram-positive and Gram-negative bacteria. The
      information in this database is very easy to extract and allows rapid prediction
      of relationships structure/function and target organisms of these peptides and
      therefore better exploitation of their biological activity in both the medical
      and food sectors.
    homepage: http://bactibase.hammamilab.org/main.php
    license: http://opendatacommons.org/licenses/pddl/1.0
    name: 'Bactibase: database dedicated to bacteriocins'
    prefix: FAIRsharing.5f5mfm
    publications:
    - doi: 10.1186/1471-2180-10-22
      pubmed_id: 20105292
      title: 'BACTIBASE second release: a database and tool platform for bacteriocin
        characterization.'
    - doi: 10.1186/1471-2180-7-89
      pubmed_id: 17941971
      title: 'BACTIBASE: a new web-accessible database for bacteriocin characterization.'
    subjects:
    - Life Science
  homepage: http://bactibase.hammamilab.org
  mappings:
    fairsharing: FAIRsharing.5f5mfm
    prefixcommons: bactibase
    re3data: r3d100012755
  name: Bactibase
  prefix: bactibase
  prefixcommons:
    description: BACTIBASE contains calculated or predicted physicochemical properties
      of 177 bacteriocins produced by both Gram-positive and Gram-negative bacteria.
      The information in this database is very easy to extract and allows rapid prediction
      of relationships structure/function and target organisms of these peptides and
      therefore better exploitation of their biological activity in both the medical
      and food sectors.
    example: BAC152
    homepage: http://bactibase.pfba-lab-tun.org/main.php
    keywords:
    - protein
    name: 'Bactibase: database dedicated to bacteriocins'
    pattern: ^BA\d+$
    prefix: bactibase
    uri_format: http://bactibase.pfba-lab-tun.org/$1
  publications:
  - doi: 10.1186/1471-2180-10-22
    pmc: PMC2824694
    pubmed: '20105292'
    title: 'BACTIBASE second release: a database and tool platform for bacteriocin
      characterization'
    year: 2010
  - doi: 10.1186/1471-2180-7-89
    pmc: PMC2211298
    pubmed: '17941971'
    title: 'BACTIBASE: a new web-accessible database for bacteriocin characterization'
    year: 2007
  - doi: 10.1186/1471-2180-10-22
    pmc: null
    pubmed: null
    title: 'BACTIBASE second release: a database and tool platform for bacteriocin
      characterization.'
    year: null
  - doi: 10.1186/1471-2180-7-89
    pmc: null
    pubmed: null
    title: 'BACTIBASE: a new web-accessible database for bacteriocin characterization.'
    year: null
  - doi: 10.1186/1471-2180-10-22
    pmc: null
    pubmed: null
    title: 'BACTIBASE second release: a database and tool platform for bacteriocin
      characterization.'
    year: null
  - doi: 10.1186/1471-2180-7-89
    pmc: null
    pubmed: null
    title: 'BACTIBASE: a new web-accessible database for bacteriocin characterization.'
    year: null
  re3data:
    description: BACTIBASE contains calculated or predicted physicochemical properties
      of bacteriocins produced by both Gram-positive and Gram-negative bacteria. The
      information in this database is very easy to extract and allows rapid prediction
      of relationships structure/function and target organisms of these peptides and
      therefore better exploitation of their biological activity in both the medical
      and food sectors.
    doi: 10.17616/R30227
    homepage: http://bactibase.hammamilab.org/main.php
    name: BACTIBASE
    prefix: r3d100012755
    synonyms:
    - a database dedicated to bacteriocins
    xrefs:
      omics: '05726'
  uri_format: http://bactibase.hammamilab.org/$1
bams:
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  deprecated: true
  description: 'BAMS (Brain Architectural Management System) describes vertebrate
    neuroinformatics data at four levels of organization: expressed molecules, neuron
    types and classes, brain regions, and networks of brain regions.'
  homepage: https://bams1.org
  name: Brain Architecture Knowledge Management System Neuroanatomical Ontology
  prefix: bams
  references:
  - https://www.frontiersin.org/articles/10.3389/neuro.11.002.2008/full
bao:
  aberowl:
    description: The BioAssay Ontology (BAO) describes chemical biology screening
      assays and their results including high-throughput screening (HTS) data for
      the purpose of categorizing assays and data analysis. BAO is an extensible,
      knowledge-based, highly expressive (currently SHOIQ(D)) description of biological
      assays making use of descriptive logic based features of the Web Ontology Language
      (OWL). BAO currently has over 1000 classes and also makes use of several other
      ontologies. It describes several concepts related to biological screening, including
      Perturbagen, Format, Meta Target, Design, Detection Technology, and Endpoint.
      Perturbagens are perturbing agents that are screened in an assay; they are mostly
      small molecules. Assay Meta Target describes what is known about the biological
      system and / or its components interrogated in the assay (and influenced by
      the Perturbagen). Meta target can be directly described as a molecular entity
      (e.g. a purified protein or a protein complex), or indirectly by a biological
      process or event (e.g. phosphorylation). Format describes the biological or
      chemical features common to each test condition in the assay and includes biochemical,
      cell-based, organism-based, and variations thereof. The assay Design describes
      the assay methodology and implementation of how the perturbation of the biological
      system is translated into a detectable signal. Detection Technology relates
      to the physical method and technical details to detect and record a signal.
      Endpoints are the final HTS results as they are usually published (such as IC50,
      percent inhibition, etc.). BAO has been designed to accommodate multiplexed
      assays. All main BAO components include multiple levels of sub-categories and
      specification classes, which are linked via object property relationships forming
      an expressive knowledge-based representation.
    download_owl: http://aber-owl.net/media/ontologies/BAO/32/bao.owl
    homepage: http://www.bioassayontology.org/
    name: BioAssay Ontology
    prefix: BAO
    version: 2.3.3
  biocontext:
    prefix: BAO
  bioportal:
    contact:
      email: c.chung@miami.edu
      name: Caty Chung
    description: The BioAssay Ontology (BAO) describes chemical biology screening
      assays and their results including high-throughput screening (HTS) data for
      the purpose of categorizing assays and data analysis. BAO is an extensible,
      knowledge-based, highly expressive (currently SHOIQ(D)) description of biological
      assays making use of descriptive logic based features of the Web Ontology Language
      (OWL). BAO currently has over 1000 classes and also makes use of several other
      ontologies. It describes several concepts related to biological screening, including
      Perturbagen, Format, Meta Target, Design, Detection Technology, and Endpoint.
      Perturbagens are perturbing agents that are screened in an assay; they are mostly
      small molecules. Assay Meta Target describes what is known about the biological
      system and / or its components interrogated in the assay (and influenced by
      the Perturbagen). Meta target can be directly described as a molecular entity
      (e.g. a purified protein or a protein complex), or indirectly by a biological
      process or event (e.g. phosphorylation). Format describes the biological or
      chemical features common to each test condition in the assay and includes biochemical,
      cell-based, organism-based, and variations thereof. The assay Design describes
      the assay methodology and implementation of how the perturbation of the biological
      system is translated into a detectable signal. Detection Technology relates
      to the physical method and technical details to detect and record a signal.
      Endpoints are the final HTS results as they are usually published (such as IC50,
      percent inhibition, etc.). BAO has been designed to accommodate multiplexed
      assays. All main BAO components include multiple levels of sub-categories and
      specification classes, which are linked via object property relationships forming
      an expressive knowledge-based representation.
    name: BioAssay Ontology
    prefix: BAO
    publications:
    - http://www.bioassayontology.org/
    version: 2.8.18a
  download_owl: http://www.bioassayontology.org/bao/bao_complete.owl
  fairsharing:
    abbreviation: BAO
    description: The BioAssay Ontology (BAO) describes chemical biology screening
      assays and their results including high-throughput screening (HTS) data for
      the purpose of categorizing assays and data analysis.
    domains:
    - molecular entity
    - chemical entity
    - reagent
    - cell
    - biological_process
    - assay
    - protein
    - target
    homepage: http://bioassayontology.org
    license: CC-BY-4.0
    name: BioAssay Ontology
    prefix: FAIRsharing.mye76w
    publications:
    - doi: 10.1186/2041-1480-5-s1-s5
      pubmed: '25093074'
      title: 'Evolving BioAssay Ontology (BAO): modularization, integration and applications'
      year: 2014
    - doi: 10:1371/journal.pone.0049198
      pubmed: '10'
      title: Digitoxin metabolism by rat liver microsomes
      year: 1975
    - doi: 10.1371/journal.pone.0049198
      pubmed: '23155465'
      title: Formalization, annotation and analysis of diverse drug and probe screening
        assay datasets using the BioAssay Ontology (BAO)
      year: 2012
    - doi: 10.1186/1471-2105-12-257
      pubmed: '21702939'
      title: 'BioAssay Ontology (BAO): a semantic description of bioassays and high-throughput
        screening results'
      year: 2011
    repository: https://github.com/BioAssayOntology/BAO/wiki
    subjects:
    - Life Science
    - Biochemistry
    - Biomedical Science
  mappings:
    aberowl: BAO
    biocontext: BAO
    bioportal: BAO
    fairsharing: FAIRsharing.mye76w
    miriam: bao
    n2t: bao
    ols: bao
    ontobee: BAO
    tib: bao
  miriam:
    deprecated: false
    description: The BioAssay Ontology (BAO) describes chemical biology screening
      assays and their results including high-throughput screening (HTS) data for
      the purpose of categorizing assays and data analysis.
    homepage: http://bioportal.bioontology.org/ontologies/BAO/
    id: 00000597
    name: BioAssay Ontology
    namespaceEmbeddedInLui: false
    pattern: ^\d{7}$
    prefix: bao
    sampleId: 0002989
    uri_format: http://bioportal.bioontology.org/ontologies/BAO/bao:BAO_$1
  n2t:
    description: The BioAssay Ontology (BAO) describes chemical biology screening
      assays and their results including high-throughput screening (HTS) data for
      the purpose of categorizing assays and data analysis.
    example: 0002989
    homepage: http://bioportal.bioontology.org/ontologies/BAO/
    name: BioAssay Ontology through BioPortal
    namespaceEmbeddedInLui: false
    pattern: ^\d{7}$
    prefix: bao
    uri_format: http://bioportal.bioontology.org/ontologies/BAO/bao:BAO_$1
  ols:
    contact: bao@miamiedu.onmicrosoft.com
    description: The BioAssay Ontology (BAO) describes biological screening assays
      and their results including high-throughput screening (HTS) data for the purpose
      of categorizing assays and data analysis. BAO is an extensible, knowledge-based,
      highly expressive (currently SHOIQ(D)) description of biological assays making
      use of descriptive logic based features of the Web Ontology Language (OWL).
      BAO currently has over 700 classes and also makes use of several other ontologies.
      It describes several concepts related to biological screening, including Perturbagen,
      Format, Meta Target, Design, Detection Technology, and Endpoint. Perturbagens
      are perturbing agents that are screened in an assay; they are mostly small molecules.
      Assay Meta Target describes what is known about the biological system and /
      or its components interrogated in the assay (and influenced by the Perturbagen).
      Meta target can be directly described as a molecular entity (e.g. a purified
      protein or a protein complex), or indirectly by a biological process or event
      (e.g. phosphorylation). Format describes the biological or chemical features
      common to each test condition in the assay and includes biochemical, cell-based,
      organism-based, and variations thereof. The assay Design describes the assay
      methodology and implementation of how the perturbation of the biological system
      is translated into a detectable signal. Detection Technology relates to the
      physical method and technical details to detect and record a signal. Endpoints
      are the final HTS results as they are usually published (such as IC50, percent
      inhibition, etc). BAO has been designed to accommodate multiplexed assays. All
      main BAO components include multiple levels of sub-categories and specification
      classes, which are linked via object property relationships forming an expressive
      knowledge-based representation.
    homepage: http://bioassayontology.org
    name: BioAssay Ontology
    prefix: bao
    uri_format: http://www.bioassayontology.org/bao#BAO_$1
    version: 2.8.18a
    version.iri: http://www.bioassayontology.org/bao/bao_complete.owl
  ontobee:
    library: Not Specified/No
    name: BioAssay Ontology
    prefix: BAO
  prefix: bao
  publications:
  - doi: 10.1186/2041-1480-5-s1-s5
    pmc: PMC4108877
    pubmed: '25093074'
    title: 'Evolving BioAssay Ontology (BAO): modularization, integration and applications'
    year: 2014
  - doi: 10.1371/journal.pone.0049198
    pmc: PMC3498356
    pubmed: '23155465'
    title: Formalization, annotation and analysis of diverse drug and probe screening
      assay datasets using the BioAssay Ontology (BAO)
    year: 2012
  - doi: 10.1186/1471-2105-12-257
    pmc: PMC3149580
    pubmed: '21702939'
    title: 'BioAssay Ontology (BAO): a semantic description of bioassays and high-throughput
      screening results'
    year: 2011
  - doi: 10:1371/journal.pone.0049198
    pmc: null
    pubmed: '10'
    title: Digitoxin metabolism by rat liver microsomes
    year: 1975
  repository: https://github.com/BioAssayOntology/BAO
  synonyms:
  - BAO
  tib:
    description: BioAssay Ontology (BAO) is created to establish common reference
      metadata terms and definitions required for describing relevant information
      of low-and high-throughput drug and probe screening assays and results. The
      main objectives of BAO are to enable effective integration, aggregation, retrieval,
      and analyses of drug screening data. BAO is a formal OWL-DL ontology and captures
      deep knowledge about screening assays and their results enabling classifications
      that enable data analysis and facilitate meaningful retrieval of screening results.
    download_owl: https://raw.githubusercontent.com/BioAssayOntology/BAO/master/bao_complete_merged.owl
    keywords:
    - NFDI4CAT
    - DataPLANT
    - life sciences, biology
    - chemical and environmental engineering
    license: https://creativecommons.org/licenses/by-sa/4.0/
    name: BioAssay Ontology
    prefix: bao
    tracker: https://github.com/BioAssayOntology/BAO/issues
    uri_format: http://www.bioassayontology.org/bao#BAO_$1
  uri_format: http://www.bioassayontology.org/bao#BAO_$1
bartoc:
  contact:
    email: voss@gbv.de
    github: nichtich
    name: Jakob Voß
    orcid: 0000-0002-7613-4123
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  contributor_extras:
  - email: voss@gbv.de
    github: nichtich
    name: Jakob Voß
    orcid: 0000-0002-7613-4123
  description: 'The Basic Register of Thesauri, Ontologies & Classifications (BARTOC)
    is a database of Knowledge Organization Systems and KOS related registries.

    The main goal of BARTOC is to list as many Knowledge Organization Systems as possible
    at one place in order to achieve greater visibility, highlight their features,
    make them searchable and comparable, and foster knowledge sharing. BARTOC includes
    any kind of KOS from any subject area, in any language, any publication format,
    and any form of accessibility. BARTOC’s search interface is available in 20 European
    languages and provides two search options: Basic Search by keywords, and Advanced
    Search by taxonomy terms. A circle of editors has gathered around BARTOC from
    all across Europe and BARTOC has been approved by the International Society for
    Knowledge Organization (ISKO).'
  example: '241'
  fairsharing:
    abbreviation: BARTOC
    description: The Basel Register of Thesauri, Ontologies & Classifications (BARTOC)
      is a database of Knowledge Organization Systems (KOS) and KOS -related registries.
      Its main goal is to list as many KOS as possible in one place in order to achieve
      greater visibility, make them searchable and comparable, and foster knowledge
      sharing. BARTOC includes any kind of KOS from any subject area, in any language,
      any publication format, and any form of accessibility. BARTOC’s search interface
      is available in 20 European languages.
    homepage: https://bartoc.org/
    license: http://opendatacommons.org/licenses/pddl/1.0
    name: Basel Register of Thesauri, Ontologies and Classifications
    prefix: FAIRsharing.f1777e
    publications: []
    repository: https://github.com/gbv/bartoc.org
    subjects:
    - Knowledge and Information Systems
    - Ontology and Terminology
  homepage: https://bartoc.org
  license: PDDL 1.0
  mappings:
    bartoc: '2054'
    fairsharing: FAIRsharing.f1777e
    wikidata: P2689
  name: Basic Register of Thesauri, Ontologies & Classifications
  owners:
  - name: Verbundzentrale des GBV
    partnered: false
    ror: 048vdhs48
    wikidata: null
  pattern: ^[1-9][0-9]*$
  prefix: bartoc
  references:
  - https://github.com/biopragmatics/bioregistry/issues/783
  repository: https://github.com/gbv/bartoc.org
  uri_format: https://bartoc.org/en/node/$1
  wikidata:
    description: identifier in the BARTOC Terminology Registry
    example:
    - '18801'
    - '241'
    homepage: https://bartoc.org/
    name: BARTOC ID
    pattern: ^[1-9][0-9]*$
    prefix: P2689
    uri_format: https://bartoc.org/en/node/$1
    uri_format_rdf: http://bartoc.org/en/node/$1
battinfo:
  example: 74ed2670_657d_4f0b_b0a6_3f13bc2e9c17
  homepage: https://big-map.github.io/BattINFO/index.html
  mappings:
    tib: battinfo
  name: Battery Interface Ontology
  prefix: battinfo
  repository: https://github.com/BIG-MAP/BattINFO
  tib:
    description: A battery interface domain ontology based on EMMO.
    download_rdf: https://raw.githubusercontent.com/BIG-MAP/BattINFO/master/battinfo.ttl
    keywords:
    - NFDI4ING
    - engineering
    - electrical engineering
    name: Battery Interface Ontology (BattINFO)
    prefix: battinfo
    tracker: https://github.com/BIG-MAP/BattINFO/issues
    uri_format: https://w3id.org/emmo/domain/battery#$1
    version.iri: https://w3id.org/battinfo/0.8.0-beta/battinfo
  uri_format: https://w3id.org/emmo/domain/battery#battery_$1
bbkg:
  mappings:
    miriam: bbkg
  miriam:
    deprecated: true
    description: Blue Brain Project's published data as knowledge graphs and Web Studios.
    homepage: https://portal.bluebrain.epfl.ch
    id: 00000903
    name: Blue Brain Project Knowledge Graph
    namespaceEmbeddedInLui: false
    pattern: ^[-\w]+(?:\/[-\w]+)(?:\/\b[0-9a-f]{8}\b-[0-9a-f]{4}-[0-9a-f]{4}-[0-9a-f]{4}-\b[0-9a-f]{12}\b)$
    prefix: bbkg
    sampleId: topological-sampling/studios/f0ba2f3e-aa6f-4264-8d18-8ee65cf6f61a
    uri_format: https://bbp.epfl.ch/nexus/web/studios/public/$1
  prefix: bbkg
bbtp:
  mappings:
    miriam: bbtp
  miriam:
    deprecated: true
    description: Input data and analysis results for the paper "Topology of synaptic
      connectivity constrains neuronal stimulus representation, predicting two complementary
      coding strategies (https://www.biorxiv.org/content/10.1101/2020.11.02.363929v2
      ).
    homepage: https://portal.bluebrain.epfl.ch
    id: 00000889
    name: Blue Brain Project Topological sampling Knowledge Graph
    namespaceEmbeddedInLui: false
    pattern: ^\b[0-9a-f]{8}\b-[0-9a-f]{4}-[0-9a-f]{4}-[0-9a-f]{4}-\b[0-9a-f]{12}\b$
    prefix: bbtp
    sampleId: f0ba2f3e-aa6f-4264-8d18-8ee65cf6f61a
    uri_format: https://bbp.epfl.ch/nexus/web/studios/public/topological-sampling/studios/data:$1
  prefix: bbtp
bcbc:
  description: One of the many goals of the BCBC was to develop and maintain databases
    of useful research resources. A total of 813 different scientific resources were
    generated and submitted by BCBC investigators over the 14 years it existed. Information
    pertaining to 495 selected resources, judged to be the most scientifically-useful,
    has been converted into a static catalog, as shown below. In addition, the metadata
    for these 495 resources have been transferred to dkNET in the form of RDF descriptors,
    and all genomics data have been deposited to either ArrayExpress or GEO. [from
    homepage]
  example: '4623'
  integbio:
    alt_name: Beta Cell Biology Consortium
    description: The Beta Cell Biology Consortium was to advance understanding associated
      with the development and function of the islets of Langerhans through functional
      genomics research data and distribution of resources; however, they have stopped
      operations as of August 1, 2015. The database contains information about antibodies,
      genomics study, mouse ECS lines, and mouse strains as screenshots.
    homepage: http://www.betacell.org/
    information_keywords:
    - Bioresource
    - Method
    maintainer: Beta Cell Biology Consortium
    name: BCBC
    prefix: nbdc00375
    status: Active
    target_keywords:
    - Cell/Organelle
  mappings:
    integbio: nbdc00375
    rrid: BCBC
  pattern: ^\d+$
  prefix: bcbc
  rrid:
    homepage: http://www.betacell.org/
    keywords:
    - adenovirus
    - antibody
    - basic research
    - basic science
    - beta cell
    - cell line
    - cell regeneration
    - cell replacement
    - cell reprogramming
    - data set
    - data sharing
    - embryonic stem cell
    - embryonic stem cell line
    - functional genomics
    - gene
    - gene expression
    - genomics
    - mouse
    - mouse embryonic stem cell line
    - mouse strain
    - pancreas
    - pancreatic development
    - pancreatic islet
    - pancreatic islet development
    - pancreatic islet function
    - protocol
    name: Beta Cell Biology Consortium
    prefix: BCBC
    scr: '005136'
  uri_format: https://scicrunch.org/resolver/RRID:BCBC_$1
bcgo:
  aberowl:
    description: An application ontology built for beta cell genomics studies.
    download_owl: http://aber-owl.net/media/ontologies/BCGO/3/bcgo.owl
    homepage: https://github.com/obi-bcgo/bcgo
    name: Beta Cell Genomics Ontology
    prefix: BCGO
  biocontext:
    prefix: BCGO
  bioportal:
    contact:
      email: alex27bulzan@yahoo.com
      name: Alexandra Bulzan
    description: assigns a grade to a tumor starting from the 3 criteria of the NGS
    name: Breast Cancer Grading Ontology
    prefix: BCGO
    version: '1.5'
  cellosaurus:
    category: Anatomy/cell type resources
    homepage: https://github.com/obi-bcgo/bcgo
    name: Beta Cell Genomics Ontology
    prefix: BCGO
  download_owl: https://github.com/obi-bcgo/bcgo/raw/master/ontology/bcgo.owl
  example: '0000015'
  mappings:
    aberowl: BCGO
    biocontext: BCGO
    bioportal: BCGO
    cellosaurus: BCGO
    obofoundry: bcgo
    ols: bcgo
    ontobee: BCGO
  obofoundry:
    contact: jiezheng@pennmedicine.upenn.edu
    contact.github: zhengj2007
    contact.label: Jie Zheng
    contact.orcid: 0000-0002-2999-0103
    deprecated: true
    description: An application ontology built for beta cell genomics studies.
    domain: anatomy and development
    download.owl: http://purl.obolibrary.org/obo/bcgo.owl
    homepage: https://github.com/obi-bcgo/bcgo
    license: CC BY 3.0
    license.url: http://creativecommons.org/licenses/by/3.0/
    name: Beta Cell Genomics Ontology
    prefix: bcgo
    repository: https://github.com/obi-bcgo/bcgo
  ols:
    description: An application ontology built for beta cell genomics studies.
    homepage: https://github.com/obi-bcgo/bcgo
    name: Beta Cell Genomics Ontology
    prefix: bcgo
    tracker: https://github.com/obi-bcgo/bcgo/issues
    version: '2015-07-08'
    version.iri: http://purl.obolibrary.org/obo/bcgo/2015-07-08/bcgo.owl
  ontobee:
    library: Library
    name: Beta Cell Genomics Ontology
    prefix: BCGO
  pattern: ^\d{7}$
  prefix: bcgo
bcio:
  aberowl:
    description: The Human Behaviour Change Project (HBCP) funded by the Wellcome
      Trust, and the Advancing Prevention Research in Cancer through Ontology Tools
      (APRICOT) Project funded by the US National Institutes of Health, are developing
      the Behaviour Change Intervention Ontology and associated tools and resources
      to be used in reporting research; linking datasets and synthesising evidence;
      and AI/machine learning algorithms to predict intervention outcomes in novel
      scenarios. The overall aim of these projects is to automate evidence searching,
      synthesis and interpretation to rapidly address questions from policy-makers,
      practitioners and others to answer ‘What works, compared with what, how well,
      with what exposure, with what behaviours (for how long), for whom, in what settings
      and why?’. To achieve this, ontologies can help structure evidence, i.e., link
      evidence with a shared formal description of classes and relationships capturing
      domain knowledge in order to enable aggregation and semantic querying. We are
      developing and maintaining the Behaviour Change Intervention Ontology (BCIO)
      to do this.
    download_owl: http://aber-owl.net/media/ontologies/BCIO/1/bcio.owl
    homepage: https://www.humanbehaviourchange.org/
    name: Behaviour Change Intervention Ontology
    prefix: BCIO
  bioportal:
    contact:
      email: janna.hastings@uzh.ch
      name: Janna Hastings
    description: The Human Behaviour Change Project (HBCP) funded by the Wellcome
      Trust, and the Advancing Prevention Research in Cancer through Ontology Tools
      (APRICOT) Project funded by the US National Institutes of Health, are developing
      the Behaviour Change Intervention Ontology and associated tools and resources
      to be used in reporting research; linking datasets and synthesising evidence;
      and AI/machine learning algorithms to predict intervention outcomes in novel
      scenarios. The overall aim of these projects is to automate evidence searching,
      synthesis and interpretation to rapidly address questions from policy-makers,
      practitioners and others to answer ‘What works, compared with what, how well,
      with what exposure, with what behaviours (for how long), for whom, in what settings
      and why?’. To achieve this, ontologies can help structure evidence, i.e., link
      evidence with a shared formal description of classes and relationships capturing
      domain knowledge in order to enable aggregation and semantic querying. We are
      developing and maintaining the Behaviour Change Intervention Ontology (BCIO)
      to do this.
    homepage: https://www.humanbehaviourchange.org/
    license: CC-BY-4.0
    name: Behaviour Change Intervention Ontology
    prefix: BCIO
    publications:
    - https://doi.org/10.12688/wellcomeopenres.21252.2
    repository: https://github.com/HumanBehaviourChangeProject/ontologies
  contact:
    email: srodriguez142857@gmail.com
    github: null
    name: Sergio José Rodríguez Méndez
    orcid: 0000-0001-7203-8399
  download_owl: http://humanbehaviourchange.org/ontology/bcio.owl
  example: '040000'
  mappings:
    aberowl: BCIO
    bioportal: BCIO
    ols: bcio
  ols:
    description: The Behaviour Change Intervention Ontology is an ontology for all
      aspects of human behaviour change interventions and their evaluation.
    download_owl: http://humanbehaviourchange.org/ontology/bcio.owl
    homepage: https://www.humanbehaviourchange.org/
    name: The Behaviour Change Intervention Ontology
    prefix: bcio
    uri_format: http://humanbehaviourchange.org/ontology/BCIO_$1
    version: '2025-12-05'
    version.iri: http://humanbehaviourchange.org/ontology/bcio.owl/2025-12-05
  pattern: ^\d{6}$
  prefix: bcio
  providers:
  - code: website
    description: null
    example: null
    first_party: null
    homepage: null
    name: null
    publications: null
    status: null
    uri_format: http://humanbehaviourchange.org/ontology/BCIO_$1
  uri_format: https://w3id.org/BCI-ontology#$1
bco:
  aberowl:
    description: An ontology to support the interoperability of biodiversity data,
      including data on museum collections, environmental/metagenomic samples, and
      ecological surveys.
    download_owl: http://aber-owl.net/media/ontologies/BCO/12/bco.owl
    homepage: https://github.com/tucotuco/bco
    name: Biological Collections Ontology
    prefix: BCO
  agroportal:
    contact:
      email: rwalls2008@gmail.com
      name: Ramona Walls
    description: The goal of the BCO is to support the interoperability of biodiversity
      data, including data on museum collections, environmental/metagenomic samples,
      and ecological surveys. The BCO covers distinctions between individuals, organisms,
      voucher specimens, lots, samples, the relations between these entities, and
      the processes governing the creation and use of "samples". Also within scope
      are properties including collector, location, time, storage environment, containers,
      institution, and collection identifiers., The BCO supports the interoperability
      of biodiversity and biodiversity related data, and ecological surveys. A key
      aspect of the BCO is distinguishing among material samples (i.e. specimens),
      observing processes, and data about either of those entities.
    example_uri: http://purl.obolibrary.org/obo/bco_0000036
    homepage: https://github.com/BiodiversityOntologies
    license: CC0-1.0
    name: Biological Collections Ontology
    prefix: BCO
    repository: https://github.com/BiodiversityOntologies/bco
    version: '2021-11-14'
  biocontext:
    prefix: BCO
  bioportal:
    contact:
      email: bco-discuss@googlegroups.com
      name: bco-discuss list
    description: BCO supports the interoperability of biodiversity data, including
      data on museum collections, environmental/metagenomic samples, and ecological
      surveys. A key feature of BCO is an ontological interpretation of Darwin Core
      terms.
    homepage: https://github.com/BiodiversityOntologies/bcom/p/bco/
    name: Biological Collections Ontology
    prefix: BCO
    version: '2021-11-14'
  ecoportal:
    contact:
      email: rlwalls2008@gmail.com
      name: Ramona Walls
    description: The goal of the BCO is to support the interoperability of biodiversity
      data, including data on museum collections, environmental/metagenomic samples,
      and ecological surveys. The BCO covers distinctions between individuals, organisms,
      voucher specimens, lots, samples, the relations between these entities, and
      the processes governing the creation and use of "samples". Also within scope
      are properties including collector, location, time, storage environment, containers,
      institution, and collection identifiers., The BCO supports the interoperability
      of biodiversity and biodiversity related data, and ecological surveys. A key
      aspect of the BCO is distinguishing among material samples (i.e. specimens),
      observing processes, and data about either of those entities.
    example_uri: http://purl.obolibrary.org/obo/bco_0000036
    homepage: https://github.com/BiodiversityOntologies/bco
    license: CC0-1.0
    name: BioCollections Ontology
    prefix: BCO
    publications:
    - https://doi.org/10.1371/journal.pone.0089606
    repository: https://github.com/BiodiversityOntologies/bco
    version: '2021-11-14'
  example: 0000081
  fairsharing:
    abbreviation: BCO
    description: The Biological Collections Ontology (BCO) supports the interoperability
      of biodiversity data, including data on museum collections, environmental/metagenomic
      samples, and ecological surveys. The BCO covers distinctions between individuals,
      organisms, voucher specimens, lots, samples, the relations between these entities,
      and the processes governing the creation and use of "samples". Also within scope
      are properties including collector, location, time, storage environment, containers,
      institution, and collection identifiers.
    domains:
    - Taxonomic classification
    - Sample annotation
    - environmental material
    - Biospecimen
    homepage: https://github.com/BiodiversityOntologies/bco
    license: CC0-1.0
    name: Biological Collections Ontology
    prefix: FAIRsharing.8ktkqy
    publications:
    - doi: 10.1371/journal.pone.0089606
      pubmed: '24595056'
      title: 'Semantics in support of biodiversity knowledge discovery: an introduction
        to the biological collections ontology and related ontologies'
      year: 2014
    subjects:
    - Taxonomy
    - Biodiversity
    - Metagenomics
    - Ecology
  mappings:
    aberowl: BCO
    agroportal: BCO
    biocontext: BCO
    bioportal: BCO
    ecoportal: BCO
    fairsharing: FAIRsharing.8ktkqy
    obofoundry: bco
    ols: bco
    ontobee: BCO
    tib: bco
    wikidata.entity: Q55118250
  obofoundry:
    appears_in:
    - fovt
    contact: rlwalls2008@gmail.com
    contact.github: ramonawalls
    contact.label: Ramona Walls
    contact.orcid: 0000-0001-8815-0078
    deprecated: false
    description: An ontology to support the interoperability of biodiversity data,
      including data on museum collections, environmental/metagenomic samples, and
      ecological surveys.
    domain: organisms
    download.owl: http://purl.obolibrary.org/obo/bco.owl
    homepage: https://github.com/BiodiversityOntologies/bco
    license: CC0 1.0
    license.url: https://creativecommons.org/publicdomain/zero/1.0/
    name: Biological Collections Ontology
    preferredPrefix: BCO
    prefix: bco
    publications:
    - id: https://doi.org/10.1371/journal.pone.0089606
      title: 'Semantics in Support of Biodiversity Knowledge Discovery: An Introduction
        to the Biological Collections Ontology and Related Ontologies'
    repository: https://github.com/BiodiversityOntologies/bco
  ols:
    description: An ontology to support the interoperability of biodiversity data,
      including data on museum collections, environmental/metagenomic samples, and
      ecological surveys.
    download_owl: http://purl.obolibrary.org/obo/bco.owl
    homepage: https://github.com/BiodiversityOntologies/bco
    name: Biological Collections Ontology
    prefix: bco
    tracker: https://github.com/BiodiversityOntologies/bco/issues
    version: '2021-11-14'
    version.iri: http://purl.obolibrary.org/obo/bco/releases/2021-11-14/bco.owl
  ontobee:
    library: Library
    name: Biological Collections Ontology
    prefix: BCO
  pattern: ^\d{7}$
  prefix: bco
  publications:
  - doi: 10.1371/journal.pone.0089606
    pmc: PMC3940615
    pubmed: '24595056'
    title: 'Semantics in support of biodiversity knowledge discovery: an introduction
      to the biological collections ontology and related ontologies'
    year: 2014
  - doi: 10.1371/journal.pone.0089606
    pmc: null
    pubmed: null
    title: 'Semantics in Support of Biodiversity Knowledge Discovery: An Introduction
      to the Biological Collections Ontology and Related Ontologies'
    year: null
  - doi: 10.1371/journal.pone.0089606
    pmc: null
    pubmed: '24595056'
    title: 'Semantics in support of biodiversity knowledge discovery: an introduction
      to the biological collections ontology and related ontologies'
    year: 2014
  tib:
    description: 'The BCO supports the interoperability of biodiversity and biodiversity
      related data, including data on museum collections, environmental/metagenomic
      samples, and ecological surveys. A key aspect of the BCO is distinguishing among
      material samples (i.e. specimens), observing processes, and data about either
      of those entities. See also: Walls RL, Deck J, Guralnick R, Baskauf S, Beaman
      R, et al. (2014) Semantics in Support of Biodiversity Knowledge Discovery: An
      Introduction to the Biological Collections Ontology and Related Ontologies.
      PLOS ONE 9(3): e89606. https://doi.org/10.1371/journal.pone.0089606'
    download_owl: https://purl.obolibrary.org/obo/bco.owl
    keywords:
    - ESS
    - DataPLANT
    - earth sciences
    name: The Biological Collections Ontology
    prefix: bco
    tracker: https://github.com/BiodiversityOntologies/bco/issues
    version.iri: http://purl.obolibrary.org/obo/bco/releases/2021-11-14/bco.owl
  uri_format: http://purl.obolibrary.org/obo/BCO_$1
bcrc:
  cellosaurus:
    category: Cell line collections (Providers)
    homepage: https://catalog.bcrc.firdi.org.tw/
    name: Taiwan Bioresource Collection and Research Center
    prefix: BCRC
    uri_format: https://catalog.bcrc.firdi.org.tw/BcrcContent?bid=$1
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  example: '60316'
  homepage: https://catalog.bcrc.firdi.org.tw
  keywords:
  - cell lines
  mappings:
    cellosaurus: BCRC
  name: BCRC Strain Collection Catalog
  pattern: ^\d+$
  prefix: bcrc
  uri_format: https://catalog.bcrc.firdi.org.tw/BcrcContent?bid=$1
bcrj:
  cellosaurus:
    category: Cell line collections (Providers)
    homepage: https://bcrj.org.br/pesquisa/
    name: Banco de Celulas do Rio de Janeiro
    prefix: BCRJ
    uri_format: https://bcrj.org.br/pesquisa/?search=$1
  example: 0278
  mappings:
    cellosaurus: BCRJ
  pattern: ^\d{4}$
  prefix: bcrj
bdgp.est:
  biocontext:
    prefix: BDGP.EST
  has_canonical: dbest
  mappings:
    biocontext: BDGP.EST
    miriam: bdgp.est
    n2t: bdgp.est
    ncbi: BDGP_EST
    prefixcommons: flybase.est
  miriam:
    deprecated: false
    description: The BDGP EST database collects the expressed sequence tags (ESTs)
      derived from a variety of tissues and developmental stages for Drosophila melanogaster.
      All BDGP ESTs are available at dbEST (NCBI).
    homepage: https://www.ncbi.nlm.nih.gov/dbEST/index.html
    id: 00000285
    name: BDGP EST
    namespaceEmbeddedInLui: false
    pattern: ^\w+(\.)?(\d+)?$
    prefix: bdgp.est
    sampleId: EY223054.1
    uri_format: https://www.ncbi.nlm.nih.gov/nucest/$1
  n2t:
    description: The BDGP EST database collects the expressed sequence tags (ESTs)
      derived from a variety of tissues and developmental stages for Drosophila melanogaster.
      All BDGP ESTs are available at dbEST (NCBI).
    example: EY223054.1
    homepage: https://www.ncbi.nlm.nih.gov/dbEST/index.html
    name: BDGP EST at NCBI
    namespaceEmbeddedInLui: false
    pattern: ^\w+(\.)?(\d+)?$
    prefix: bdgp.est
    uri_format: https://www.ncbi.nlm.nih.gov/nucest/$1
  ncbi:
    example: '123456'
    homepage: http://www.fruitfly.org/EST/index.shtml
    name: Berkeley Drosophila Genome Project EST database
    prefix: BDGP_EST
  prefix: bdgp.est
  prefixcommons:
    description: The goals of the Drosophila Genome Center are to finish the sequence
      of the euchromatic genome of Drosophila melanogaster to high quality and to
      generate and maintain biological annotations of this sequence.
    example: '123456'
    homepage: http://www.fruitfly.org/EST/index.shtml
    keywords:
    - genome
    name: Berkeley Drosophila Genome Project EST database
    pattern: ^\d+$
    prefix: flybase.est
    synonyms:
    - bdgp_est
bdgp.insertion:
  biocontext:
    prefix: BDGP.INSERTION
  contact:
    email: spradling@ciwemb.edu
    github: null
    name: Allan Spradling
    orcid: 0000-0002-5251-1801
  mappings:
    biocontext: BDGP.INSERTION
    miriam: bdgp.insertion
    n2t: bdgp.insertion
    prefixcommons: bdgp
  miriam:
    deprecated: false
    description: BDGP gene disruption collection provides a public resource of gene
      disruptions of Drosophila genes using a single transposable element.
    homepage: http://flypush.imgen.bcm.tmc.edu/pscreen/
    id: '00000156'
    name: BDGP insertion DB
    namespaceEmbeddedInLui: false
    pattern: ^\w+$
    prefix: bdgp.insertion
    sampleId: KG09531
    uri_format: http://flypush.imgen.bcm.tmc.edu/pscreen/details.php?line=$1
  n2t:
    description: BDGP gene disruption collection provides a public resource of gene
      disruptions of Drosophila genes using a single transposable element.
    example: KG09531
    homepage: http://flypush.imgen.bcm.tmc.edu/pscreen/
    name: BDGP Gene Disruption Project
    namespaceEmbeddedInLui: false
    pattern: ^\w+$
    prefix: bdgp.insertion
    uri_format: http://flypush.imgen.bcm.tmc.edu/pscreen/details.php?line=$1
  prefix: bdgp.insertion
  prefixcommons:
    description: BDGP gene disruption collection provides a public resource of gene
      disruptions of Drosophila genes using a single transposable element.
    example: KG09531
    keywords:
    - gene
    - sequence
    name: Drosphila Gene Disruption Database
    pattern: ^\w+$
    prefix: bdgp
    pubmed_ids:
    - '15238527'
    synonyms:
    - BDGP.insertion
    uri_format: http://flypush.imgen.bcm.tmc.edu/pscreen/details.php?line=$1
  publications:
  - doi: 10.1534/genetics.104.026427
    pmc: PMC1470905
    pubmed: '15238527'
    title: 'The BDGP gene disruption project: single transposon insertions associated
      with 40% of Drosophila genes'
    year: 2004
  - doi: null
    pmc: null
    pubmed: '15238527'
    title: null
    year: null
bdsc:
  mappings:
    miriam: bdsc
    n2t: bdsc
    rrid: BDSC
  miriam:
    deprecated: false
    description: The Bloomington Drosophila Stock Center collects, maintains and distributes
      Drosophila melanogaster strains for research.
    homepage: https://bdsc.indiana.edu/about/mission.html
    id: '00000332'
    name: Bloomington Drosophila Stock Center
    namespaceEmbeddedInLui: false
    pattern: ^\d+$
    prefix: bdsc
    sampleId: '33607'
    uri_format: https://bdsc.indiana.edu/stocks/$1
  n2t:
    description: The Bloomington Drosophila Stock Center collects, maintains and distributes
      Drosophila melanogaster strains for research.
    example: '33607'
    homepage: https://bdsc.indiana.edu/about/mission.html
    name: BDSC at Indiana University
    namespaceEmbeddedInLui: false
    pattern: ^\d+$
    prefix: bdsc
    uri_format: https://bdsc.indiana.edu/stocks/$1
  prefix: bdsc
  rrid:
    homepage: https://bdsc.indiana.edu/
    keywords:
    - FASEB list
    - database
    - deficiency
    - deletion
    - disease model
    - duplication
    - fly
    - gene
    - genetic
    - genetic analysis
    - genetic construct
    - germline
    - human disease model
    - insertion
    - invertebrate
    - mutation
    - protein trap
    - scientist
    - sequenced strain
    - somatic
    - stock
    - transposon
    - transposon insertion
    name: Bloomington Drosophila Stock Center
    prefix: BDSC
    scr: '006457'
beetlebase:
  biocontext:
    prefix: BEETLEBASE
  contact:
    email: sjbrown@ksu.edu
    github: null
    name: Susan J. Brown
    orcid: 0000-0002-7984-0445
  fairsharing:
    abbreviation: BeetleBase
    description: BeetleBase is a community resource for Tribolium genetics, genomics
      and developmental biology. The database is built on the Chado generic data model,
      and is able to store various types of data, ranging from genome sequences to
      mutant phenotypes.
    homepage: http://www.beetlebase.org/
    name: BeetleBase
    prefix: FAIRsharing.h5f091
    publications:
    - doi: 10.1093/nar/gkp807
      pubmed_id: 19820115
      title: 'BeetleBase in 2010: revisions to provide comprehensive genomic information
        for Tribolium castaneum.'
    subjects:
    - Computational Biology
    - Life Science
  integbio:
    description: BeetleBase is a community resource for Tribolium genetics, genomics
      and developmental biology. The database is built on the Chado generic data model,
      and is able to store various types of data, ranging from genome sequences to
      mutant phenotypes.
    fairsharing: FAIRsharing.h5f091
    homepage: http://www.beetlebase.org/
    information_keywords:
    - Sequence
    - Interaction/Pathway
    maintainer: Kansas State University
    name: BeetleBase
    prefix: nbdc01820
    pubmeds:
    - '19820115'
    status: Inactive
    target_keywords:
    - Genome/Gene
    - cDNA/EST
    - Protein
  mappings:
    biocontext: BEETLEBASE
    fairsharing: FAIRsharing.h5f091
    integbio: nbdc01820
    miriam: beetlebase
    n2t: beetlebase
    ncbi: BEETLEBASE
    prefixcommons: beetlebase
    re3data: r3d100010921
  miriam:
    deprecated: true
    description: BeetleBase is a comprehensive sequence database and community resource
      for Tribolium genetics, genomics and developmental biology. It incorporates
      information about genes, mutants, genetic markers, expressed sequence tags and
      publications.
    homepage: http://beetlebase.org/
    id: '00000157'
    name: BeetleBase
    namespaceEmbeddedInLui: false
    pattern: ^TC\d+$
    prefix: beetlebase
    sampleId: TC010103
    uri_format: http://beetlebase.org/cgi-bin/gbrowse/BeetleBase3.gff3/?name=$1
  n2t:
    description: BeetleBase is a comprehensive sequence database and community resource
      for Tribolium genetics, genomics and developmental biology. It incorporates
      information about genes, mutants, genetic markers, expressed sequence tags and
      publications.
    example: TC010103
    homepage: http://beetlebase.org/
    name: BeetleBase at Kansas State University
    namespaceEmbeddedInLui: false
    pattern: ^TC\d+$
    prefix: beetlebase
    uri_format: http://beetlebase.org/cgi-bin/gbrowse/BeetleBase3.gff3/?name=$1
  ncbi:
    example: TC030551
    homepage: http://www.beetlebase.org/
    name: Tribolium Genome Database -- Insertion
    prefix: BEETLEBASE
  prefix: beetlebase
  prefixcommons:
    description: BeetleBase is being developed as an important community resource
      for Tribolium genetics, genomics and developmental biology.The database is built
      on the Chado generic data model, and is able to store various types of data,
      ranging from genome sequences to mutant phenotypes.
    example: TC010103
    homepage: http://www.beetlebase.org/
    keywords:
    - genome
    name: BeetleBase
    pattern: ^TC\d+$
    prefix: beetlebase
    pubmed_ids:
    - '19820115'
    uri_format: http://www.beetlebase.org/cgi-bin/gbrowse/BeetleBase3.gff3/?name=$1
  publications:
  - doi: 10.1093/nar/gkp807
    pmc: PMC2808946
    pubmed: '19820115'
    title: 'BeetleBase in 2010: revisions to provide comprehensive genomic information
      for Tribolium castaneum'
    year: 2009
  re3data:
    description: <<<!!!<<< This database doesn't exist anymore.  2017-09-05  >>>!!!>>>
    doi: 10.17616/R3G61K
    homepage: http://beetlebase.org/
    name: BeetleBase
    prefix: r3d100010921
    xrefs:
      nif: 0000-02599
      omics: 03118
begdb:
  biocontext:
    prefix: BEGDB
  contact:
    email: pavel.hobza@uochb.cas.cz
    github: null
    name: Pavel Hobza
    orcid: 0000-0001-5292-6719
  fairsharing:
    abbreviation: BEGDB
    description: The Benchmark Energy & Geometry Database (BEGDB) collects results
      of highly accurate QM calculations of molecular structures, energies and properties.
      These data can serve as benchmarks for testing and parameterization of other
      computational methods.
    homepage: http://www.begdb.org/
    name: The Benchmark Energy & Geometry Database
    prefix: FAIRsharing.nbe4fq
    publications:
    - doi: 10.1135/cccc20081261
      pubmed_id: null
      title: 'Quantum Chemical Benchmark Energy and Geometry Database for Molecular
        Clusters and Complex Molecular Systems (www.begdb.com): A Users Manual and
        Examples'
    subjects:
    - Life Science
  mappings:
    biocontext: BEGDB
    fairsharing: FAIRsharing.nbe4fq
    miriam: begdb
    n2t: begdb
    re3data: r3d100011166
  miriam:
    deprecated: false
    description: The Benchmark Energy & Geometry Database (BEGDB) collects results
      of highly accurate quantum mechanics (QM) calculations of molecular structures,
      energies and properties. These data can serve as benchmarks for testing and
      parameterization of other computational methods.
    homepage: http://www.begdb.com
    id: '00000622'
    name: Benchmark Energy & Geometry Database
    namespaceEmbeddedInLui: false
    pattern: ^[0-9]+$
    prefix: begdb
    sampleId: '4214'
    uri_format: http://www.begdb.com/index.php?action=oneMolecule&state=show&id=$1
  n2t:
    description: The Benchmark Energy & Geometry Database (BEGDB) collects results
      of highly accurate quantum mechanics (QM) calculations of molecular structures,
      energies and properties. These data can serve as benchmarks for testing and
      parameterization of other computational methods.
    example: '4214'
    homepage: http://www.begdb.com
    name: Benchmark Energy & Geometry Database
    namespaceEmbeddedInLui: false
    pattern: ^[0-9]+$
    prefix: begdb
    uri_format: http://www.begdb.com/index.php?action=oneMolecule&state=show&id=$1
  prefix: begdb
  publications:
  - doi: 10.1135/cccc20081261
    pmc: null
    pubmed: null
    title: 'Quantum Chemical Benchmark Energy and Geometry Database for Molecular
      Clusters and Complex Molecular Systems (www.begdb.com): A Users Manual and Examples'
    year: 2008
  - doi: 10.1135/cccc20081261
    pmc: null
    pubmed: null
    title: 'Quantum Chemical Benchmark Energy and Geometry Database for Molecular
      Clusters and Complex Molecular Systems (www.begdb.com): A Users Manual and Examples'
    year: null
  - doi: 10.1135/cccc20081261
    pmc: null
    pubmed: null
    title: 'Quantum Chemical Benchmark Energy and Geometry Database for Molecular
      Clusters and Complex Molecular Systems (www.begdb.com): A Users Manual and Examples'
    year: null
  re3data:
    description: The Benchmark Energy & Geometry Database (BEGDB) collects results
      of highly accurate QM calculations of molecular structures, energies and properties.
      These data can serve as benchmarks for testing and parameterization of other
      computational methods.
    doi: 10.17616/R3Z90K
    homepage: http://www.begdb.org/
    name: Benchmark Energy & Geometry Database
    prefix: r3d100011166
    synonyms:
    - BEGDB
beiresources:
  cellosaurus:
    category: Cell line collections (Providers)
    homepage: https://www.beiresources.org/Home.aspx
    name: BEI Resources cell line products
    prefix: BEI_Resources
    uri_format: https://www.beiresources.org/Catalog/cellBanks/$1.aspx
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  example: MRA-253
  homepage: https://www.beiresources.org
  keywords:
  - cell lines
  mappings:
    cellosaurus: BEI_Resources
  name: BEI Resources
  prefix: beiresources
  synonyms:
  - BEI_Resources
  uri_format: https://www.beiresources.org/Catalog/cellBanks/$1.aspx
bel:
  comment: INDRA uses bel as a catch-all for scomp/sfam
  contact:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: The Biological Expression Language is a domain-specific language for
    describing causal, correlative, and associative relationships between a variety
    of biological agents.
  example: 9-1-1 Complex
  fairsharing:
    abbreviation: BEL
    contact:
      email: support@bel.bio
      name: William Hayes
      orcid: 0000-0003-0728-781X
    description: BEL is a language for representing scientific findings in the life
      sciences in a reusable, shareable, and computable form. BEL is designed to represent
      scientific findings by capturing causal and correlative relationships in context,
      where context can include information about the biological and experimental
      system in which the relationships were observed, the supporting publications
      cited and the process of curation. BEL is intended as a knowledge capture and
      interchange medium, supporting the operation of systems that integrate knowledge
      derived from independent efforts. The language is designed to be use-neutral,
      facilitating the storage and use of structured knowledge for inference by applications
      through a knowledge assembly process that can create computable biological networks.
      While BEL does not prescribe any particular assembly process or any particular
      knowledge format for the output of an assembly process, a suite of software
      components called the BEL Framework provides everything necessary to create,
      compile, assemble, and deliver computable knowledge models to BEL-aware applications.
      The current version of BEL provides the means to describe biological interactions
      qualitatively but not to quantify the magnitude or rate of these interactions.
      This limitation is by design because this quantitative information has significant
      variability and is not consistently reported in the literature. It is our hope
      that future versions of BEL can accommodate these additional data.
    homepage: https://bel.bio
    license: CC-BY-4.0
    name: Biological Expression Language
    prefix: FAIRsharing.dp0jvd
    publications: []
    subjects:
    - Biology
  homepage: https://biological-expression-language.github.io
  logo: https://biological-expression-language.github.io/img/bel300.png
  mappings:
    fairsharing: FAIRsharing.dp0jvd
  name: Biological Expression Language
  prefix: bel
bervo:
  aberowl:
    description: The Biological and Environmental Research Variable Ontology (BERVO)
      is a model of the experimental variables, conditions, and concepts used in the
      study of environmental research, including studies in earth science, plant science,
      and geochemistry. , None
    download_owl: http://aber-owl.net/media/ontologies/BERVO/4/bervo.owl
    name: The Biological and Environmental Research Variable Ontology
    prefix: BERVO
    version: '2025-11-07'
  bioportal:
    contact:
      email: jhc@lbl.gov
      name: Harry Caufield
    description: The Biological and Environmental Research Variable Ontology (BERVO)
      is a model of the experimental variables, conditions, and concepts used in the
      study of environmental research, including studies in earth science, plant science,
      and geochemistry. , None
    name: The Biological and Environmental Research Variable Ontology
    prefix: BERVO
    version: '2025-11-07'
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: A representation of variables appearing in models in the environmental
    research space.
  download_json: https://github.com/bioepic-data/bervo/raw/refs/heads/main/bervo.json
  download_obo: https://github.com/bioepic-data/bervo/raw/refs/heads/main/bervo.obo
  download_owl: https://github.com/bioepic-data/bervo/raw/refs/heads/main/bervo.owl
  example: '0000001'
  homepage: https://github.com/bioepic-data/bervo
  mappings:
    aberowl: BERVO
    bioportal: BERVO
  name: Biological and Environmental Research Variable Ontology
  pattern: ^\d{7}$
  preferred_prefix: BERVO
  prefix: bervo
  repository: https://github.com/bioepic-data/bervo
  uri_format: https://w3id.org/bervo/BERVO_$1
bfo:
  aberowl:
    description: The upper level ontology upon which OBO Foundry ontologies are built.
    download_owl: http://aber-owl.net/media/ontologies/BFO/5/bfo.owl
    homepage: http://ifomis.org/bfo/
    name: Basic Formal Ontology
    prefix: BFO
  agroportal:
    contact:
      email: phismith@buffalo.edu
      name: Barry Smith
    description: BFO grows out of a philosophical orientation which overlaps with
      that of DOLCE and SUMO. Unlike these, however, it is narrowly focused on the
      task of providing a genuine upper ontology which can be used in support of domain
      ontologies developed for scientific research, as for example in biomedicine
      within the framework of the OBO Foundry. Thus BFO does not contain physical,
      chemical, biological or other terms which would properly fall within the special
      sciences domains. BFO is the upper level ontology upon which OBO Foundry ontologies
      are built.
    example_uri: http://purl.obolibrary.org/obo/BFO_0000140
    homepage: http://ifomis.org/bfo
    license: CC-BY-4.0
    name: Basic Formal Ontology
    prefix: BFO
    publications:
    - http://ifomis.uni-saarland.de/bfo/publications
    repository: https://github.com/BFO-ontology/BFO
    version: '1.1'
  biocontext:
    prefix: BFO
  bioportal:
    contact:
      email: phismith@buffalo.edu
      name: Barry Smith
    description: BFO grows out of a philosophical orientation which overlaps with
      that of DOLCE and SUMO. Unlike these, however, it is narrowly focused on the
      task of providing a genuine upper ontology which can be used in support of domain
      ontologies developed for scientific research, as for example in biomedicine
      within the framework of the OBO Foundry. Thus BFO does not contain physical,
      chemical, biological or other terms which would properly fall within the special
      sciences domains.
    homepage: http://www.ifomis.org/bfo
    name: Basic Formal Ontology
    prefix: BFO
    version: '2.0'
  domain: classification
  example: '0000001'
  fairsharing:
    abbreviation: BFO
    description: 'The Basic Formal Ontology (BFO, also known via its ISO label as
      ''ISO/IEC 21838-2:2021 Information technology — Top-level ontologies (TLO) —
      Part 2: Basic Formal Ontology (BFO)'') is an ontology that is conformant to
      the requirements specified for top-level ontologies in ISO/IEC 21838‑1. BFO
      is a small, upper level ontology that is designed for use in supporting information
      retrieval, analysis and integration in scientific and other domains. BFO is
      a genuine upper ontology. Thus it does not contain physical, chemical, biological
      or other terms which would properly fall within the coverage domains of the
      special sciences. BFO is used by more than 250 ontology-driven endeavors throughout
      the world. '
    domains:
    - Data retrieval
    - Data identity and mapping
    homepage: https://www.iso.org/standard/74572.html
    license: CC-BY-4.0
    name: Basic Formal Ontology
    prefix: FAIRsharing.wcpd6f
    repository: https://github.com/bfo-ontology/BFO
    subjects:
    - Subject Agnostic
  go:
    description: An upper ontology used by Open Bio Ontologies (OBO) Foundry. BFO
      contains upper-level classes as well as core relations such as part_of (BFO_0000050)
    name: Basic Formal Ontology
    prefix: BFO
  mappings:
    aberowl: BFO
    agroportal: BFO
    biocontext: BFO
    bioportal: BFO
    fairsharing: FAIRsharing.wcpd6f
    go: BFO
    obofoundry: bfo
    ols: bfo
    ontobee: BFO
    tib: bfo
    wikidata.entity: Q4866972
  obofoundry:
    appears_in:
    - ado
    - agro
    - aism
    - cdno
    - colao
    - duo
    - ecocore
    - epio
    - foodon
    - fovt
    - hso
    - lepao
    - mco
    - ons
    - pcl
    - pco
    - psdo
    - rbo
    - uberon
    - xpo
    - zp
    contact: phismith@buffalo.edu
    contact.github: phismith
    contact.label: Barry Smith
    contact.orcid: 0000-0003-1384-116X
    deprecated: false
    description: The upper level ontology upon which OBO Foundry ontologies are built.
    domain: upper
    download.obo: http://purl.obolibrary.org/obo/bfo.obo
    download.owl: http://purl.obolibrary.org/obo/bfo.owl
    homepage: http://ifomis.org/bfo/
    license: CC BY 4.0
    license.url: http://creativecommons.org/licenses/by/4.0/
    logo: https://avatars2.githubusercontent.com/u/12972134?v=3&s=200
    name: Basic Formal Ontology
    preferredPrefix: BFO
    prefix: bfo
    repository: https://github.com/BFO-ontology/BFO
  ols:
    description: The upper level ontology upon which OBO Foundry ontologies are built.
    download_owl: http://purl.obolibrary.org/obo/bfo.owl
    homepage: http://ifomis.org/bfo/
    name: Basic Formal Ontology
    prefix: bfo
    tracker: https://github.com/BFO-ontology/BFO/issues
    version: '2019-08-26'
    version.iri: http://purl.obolibrary.org/obo/bfo/2019-08-26/bfo.owl
  ontobee:
    library: Foundry
    name: Basic Formal Ontology
    prefix: BFO
  pattern: ^\d{7}$
  prefix: bfo
  tib:
    description: The upper level ontology upon which OBO Foundry ontologies are built.
    download_owl: http://purl.obolibrary.org/obo/bfo.owl
    homepage: http://ifomis.org/bfo/
    keywords:
    - NFDI4CHEM
    - NFDI4ING
    - NFDI4CAT
    - Foundational Ontologies
    - DataPLANT
    - FAIRmat
    name: Basic Formal Ontology
    prefix: bfo
    tracker: https://github.com/BFO-ontology/BFO/issues
    version.iri: http://purl.obolibrary.org/obo/bfo/2019-08-26/bfo.owl
  uri_format: http://purl.obolibrary.org/obo/BFO_$1
bgee.family:
  biocontext:
    prefix: BGEE.FAMILY
  contributor_extras:
  - email: sebastien.moretti@sib.swiss
    github: smoretti
    name: Sébastien Moretti
    orcid: 0000-0003-3947-488X
  deprecated: true
  mappings:
    biocontext: BGEE.FAMILY
    miriam: bgee.family
    n2t: bgee.family
  miriam:
    deprecated: true
    description: Bgee is a database of gene expression patterns within particular
      anatomical structures within a species, and between different animal species.
      This collection refers to expression across species.
    homepage: http://bgee.unil.ch/bgee/bgee
    id: '00000417'
    name: Bgee family
    namespaceEmbeddedInLui: false
    pattern: ^(ENSFM|ENSGTV:)\d+$
    prefix: bgee.family
    sampleId: ENSFM00500000270089
    uri_format: http://bgee.unil.ch/bgee/bgee?page=gene_family&action=family_details&gene_family_id=$1
  n2t:
    description: Bgee is a database of gene expression patterns within particular
      anatomical structures within a species, and between different animal species.
      This collection refers to expression across species.
    example: ENSFM00500000270089
    homepage: http://bgee.unil.ch/bgee/bgee
    name: Bgee at Lausanne
    namespaceEmbeddedInLui: false
    pattern: ^(ENSFM|ENSGTV:)\d+$
    prefix: bgee.family
    uri_format: http://bgee.unil.ch/bgee/bgee?page=gene_family&action=family_details&gene_family_id=$1
  prefix: bgee.family
  references:
  - https://github.com/biopragmatics/bioregistry/issues/889
bgee.gene:
  biocontext:
    prefix: BGEE.GENE
  contact:
    email: sebastien.moretti@sib.swiss
    github: smoretti
    name: Sébastien Moretti
    orcid: 0000-0003-3947-488X
  contributor_extras:
  - email: sebastien.moretti@sib.swiss
    github: smoretti
    name: Sébastien Moretti
    orcid: 0000-0003-3947-488X
  description: Bgee is a database to retrieve and compare gene expression patterns
    in multiple species, produced from multiple data types (bulk RNA-Seq, scRNA-Seq,
    Affymetrix, in situ hybridization, and EST data). This collection references genes
    in Bgee.
  homepage: https://www.bgee.org
  mappings:
    biocontext: BGEE.GENE
    miriam: bgee.gene
    n2t: bgee.gene
    prefixcommons: bgee
  miriam:
    deprecated: false
    description: Bgee is a database to retrieve and compare gene expression patterns
      in multiple species, produced from multiple data types (bulk RNA-Seq, scRNA-Seq,
      Affymetrix, in situ hybridization, and EST data). This collection references
      genes in Bgee.
    homepage: https://www.bgee.org/
    id: 00000418
    name: Bgee gene
    namespaceEmbeddedInLui: false
    pattern: ^[A-Za-z0-9]+$
    prefix: bgee.gene
    sampleId: FBgn0000015
    uri_format: https://www.bgee.org/gene/$1
  n2t:
    description: Bgee is a database to retrieve and compare gene expression patterns
      in multiple species, produced from multiple data types (RNA-Seq, Affymetrix,
      in situ hybridization, and EST data). This collection references genes in Bgee.
    example: FBgn0000015
    homepage: https://bgee.org/
    name: Bgee gene
    namespaceEmbeddedInLui: false
    pattern: ^[A-Za-z]+\d+$
    prefix: bgee.gene
    uri_format: https://bgee.org/?page=gene&gene_id=$1
  pattern: ^[A-Za-z0-9]+$
  prefix: bgee.gene
  prefixcommons:
    description: Bgee is a database to retrieve and compare gene expression patterns
      between animal species. Bgee first maps heterogeneous expression data (currently
      EST, Affymetrix, and in situ hybridization data) on anatomical and developmental
      ontologies. Then, in order to perform automated cross species comparisons, homology
      relationships across anatomical ontologies, and comparison criteria between
      developmental ontologies, are designed.
    example: FBgn0041195
    homepage: http://bgee.unil.ch
    keywords:
    - gene expression
    name: Bgee DataBase for Gene Expression Evolution
    pattern: ^[A-Z]+\d+$
    prefix: bgee
    uri_format: http://bgee.unil.ch/bgee/bgee?page=gene&action=expression&gene_id=$1
  references:
  - https://github.com/biopragmatics/bioregistry/issues/890
  uri_format: https://www.bgee.org/gene/$1
bgee.organ:
  biocontext:
    prefix: BGEE.ORGAN
  contributor_extras:
  - email: sebastien.moretti@sib.swiss
    github: smoretti
    name: Sébastien Moretti
    orcid: 0000-0003-3947-488X
  deprecated: true
  mappings:
    biocontext: BGEE.ORGAN
    miriam: bgee.organ
    n2t: bgee.organ
  miriam:
    deprecated: true
    description: Bgee is a database of gene expression patterns within particular
      anatomical structures within a species, and between different animal species.
      This collection refers to anatomical structures.
    homepage: http://bgee.unil.ch/bgee/bgee
    id: '00000420'
    name: Bgee organ
    namespaceEmbeddedInLui: false
    pattern: ^(XAO|ZFA|EHDAA|EMAPA|EV|MA)\:\d+$
    prefix: bgee.organ
    sampleId: EHDAA:2185
    uri_format: http://bgee.unil.ch/bgee/bgee?page=anatomy&action=organ_details&organ_id=$1&organ_children=on
  n2t:
    description: Bgee is a database of gene expression patterns within particular
      anatomical structures within a species, and between different animal species.
      This collection refers to anatomical structures.
    example: EHDAA:2185
    homepage: http://bgee.unil.ch/bgee/bgee
    name: Bgee at Lausanne
    namespaceEmbeddedInLui: false
    pattern: ^(XAO|ZFA|EHDAA|EMAPA|EV|MA)\:\d+$
    prefix: bgee.organ
    uri_format: http://bgee.unil.ch/bgee/bgee?page=anatomy&action=organ_details&organ_id=$1&organ_children=on
  prefix: bgee.organ
  references:
  - https://github.com/biopragmatics/bioregistry/issues/889
  uri_format: http://bgee.unil.ch/bgee/bgee?page=anatomy&action=organ_details&organ_children=on&organ_id=$1
bgee.stage:
  biocontext:
    prefix: BGEE.STAGE
  contributor_extras:
  - email: sebastien.moretti@sib.swiss
    github: smoretti
    name: Sébastien Moretti
    orcid: 0000-0003-3947-488X
  deprecated: true
  mappings:
    biocontext: BGEE.STAGE
    miriam: bgee.stage
    n2t: bgee.stage
  miriam:
    deprecated: true
    description: Bgee is a database of gene expression patterns within particular
      anatomical structures within a species, and between different animal species.
      This collection refers to developmental stages.
    homepage: http://bgee.unil.ch/bgee/bgee
    id: 00000419
    name: Bgee stage
    namespaceEmbeddedInLui: false
    pattern: ^(FBvd|XtroDO|HsapDO|MmusDO)\:\d+$
    prefix: bgee.stage
    sampleId: HsapDO:0000004
    uri_format: http://bgee.unil.ch/bgee/bgee?page=anatomy&action=organs&stage_id=$1&stage_children=on
  n2t:
    description: Bgee is a database of gene expression patterns within particular
      anatomical structures within a species, and between different animal species.
      This collection refers to developmental stages.
    example: HsapDO:0000004
    homepage: http://bgee.unil.ch/bgee/bgee
    name: Bgee at Lausanne
    namespaceEmbeddedInLui: false
    pattern: ^(FBvd|XtroDO|HsapDO|MmusDO)\:\d+$
    prefix: bgee.stage
    uri_format: http://bgee.unil.ch/bgee/bgee?page=anatomy&action=organs&stage_id=$1&stage_children=on
  prefix: bgee.stage
  references:
  - https://github.com/biopragmatics/bioregistry/issues/889
  uri_format: http://bgee.unil.ch/bgee/bgee?page=anatomy&action=organs&stage_children=on&stage_id=$1
bibframe:
  aberowl:
    description: Initiated by the Library of Congress, BIBFRAME provides a foundation
      for the future of bibliographic description, both on the web, and in the broader
      networked world. In addition to being a replacement for MARC, BIBFRAME serves
      as a general model for expressing and connecting bibliographic data. A major
      focus of the initiative will be to determine a transition path for the MARC
      21 formats while preserving a robust data exchange that has supported resource
      sharing and cataloging cost savings in recent decades.
    download_owl: http://aber-owl.net/media/ontologies/BIBFRAME/3/bibframe.owl
    homepage: https://www.loc.gov/bibframe/
    name: BIBFRAME 2.0
    prefix: BIBFRAME
    version: '2017-05-04T14:49:12.796-04:00'
  bioportal:
    contact:
      email: khes@loc.gov
      name: Kirk Hess
    description: Initiated by the Library of Congress, BIBFRAME provides a foundation
      for the future of bibliographic description, both on the web, and in the broader
      networked world. In addition to being a replacement for MARC, BIBFRAME serves
      as a general model for expressing and connecting bibliographic data. A major
      focus of the initiative will be to determine a transition path for the MARC
      21 formats while preserving a robust data exchange that has supported resource
      sharing and cataloging cost savings in recent decades.
    name: BIBFRAME 2.0
    prefix: BIBFRAME
    version: 2.2.0
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: 'The Bibframe vocabulary consists of RDF classes and properties used
    for the description of items cataloged principally by libraries, but may also
    be used to describe items cataloged by museums and archives. Classes include the
    three core classes - Work, Instance, and Item - in addition to many more classes
    to support description. Properties describe characteristics of the resource being
    described as well as relationships among resources. For example: one Work might
    be a "translation of" another Work; an Instance may be an "instance of" a particular
    Bibframe Work. Other properties describe attributes of Works and Instances. For
    example: the Bibframe property "subject" expresses an important attribute of a
    Work (what the Work is about), and the property "extent" (e.g. number of pages)
    expresses an attribute of an Instance.'
  download_owl: https://id.loc.gov/ontologies/bibframe.rdf
  example: DescriptionLevel
  fairsharing:
    abbreviation: BIBFRAME
    description: Initiated by the Library of Congress, BIBFRAME provides a foundation
      for the future of bibliographic description, both on the web, and in the broader
      networked world. This site presents general information about the project, including
      presentations, FAQs, and links to working documents. In addition to being a
      replacement for MARC, BIBFRAME serves as a general model for expressing and
      connecting bibliographic data. A major focus of the initiative will be to determine
      a transition path for the MARC 21 formats while preserving a robust data exchange
      that has supported resource sharing and cataloging cost savings in recent decades.
    homepage: https://www.loc.gov/bibframe/
    name: BIBFRAME 2.0
    prefix: FAIRsharing.xj5egt
    subjects:
    - Subject Agnostic
  homepage: https://id.loc.gov/ontologies/bibframe.html
  license: CC0-1.0
  mappings:
    aberowl: BIBFRAME
    bioportal: BIBFRAME
    fairsharing: FAIRsharing.xj5egt
    tib: bf
  name: Bibliographic Framework Initiative Vocabulary
  prefix: bibframe
  rdf_uri_format: http://id.loc.gov/ontologies/bibframe/$1
  references:
  - https://www.loc.gov/bibframe/
  repository: https://github.com/lcnetdev/bibframe-ontology
  synonyms:
  - bf
  tib:
    description: 'The Bibframe vocabulary consists of RDF classes and properties used
      for the description of items cataloged principally by libraries, but may also
      be used to describe items cataloged by museums and archives. Classes include
      the three core classes - Work, Instance, and Item - in addition to many more
      classes to support description. Properties describe characteristics of the resource
      being described as well as relationships among resources. For example: one Work
      might be a "translation of" another Work; an Instance may be an "instance of"
      a particular Bibframe Work. Other properties describe attributes of Works and
      Instances. For example: the Bibframe property "subject" expresses an important
      attribute of a Work (what the Work is about), and the property "extent" (e.g.
      number of pages) expresses an attribute of an Instance.'
    homepage: https://www.loc.gov/bibframe/
    keywords:
    - TIB
    - computer science
    name: BIBFRAME vocabulary
    prefix: bf
    tracker: https://github.com/lcnetdev/bibframe-ontology/issues
    uri_format: http://id.loc.gov/ontologies/bibframe/$1
    version.iri: http://id.loc.gov/ontologies/bibframe-2-6-0/
  uri_format: http://id.loc.gov/ontologies/bibframe/$1
bibo:
  bartoc:
    abbreviation: bibo
    description: The Bibliographic Ontology describes bibliographic things on the
      semantic Web in RDF. This ontology can be used as a citation ontology, as a
      document classification ontology, or simply as a way to describe any kind of
      document in RDF. It has been inspired by many existing document description
      metadata formats, and can be used as a common ground for converting other bibliographic
      data sources.
    homepage: https://www.dublincore.org/specifications/bibo/bibo/
    name: The Bibliographic Ontology
    prefix: '17844'
  contact:
    email: fred@fgiasson.com
    github: fgiasson
    name: Frédérick Giasson
    orcid: null
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: The Bibliographic Ontology Specification provides main concepts and
    properties for describing citations and bibliographic references (i.e. quotes,
    books, articles, etc) on the Semantic Web.
  download_owl: https://www.dublincore.org/specifications/bibo/bibo/bibo.rdf.xml
  example: authorList
  homepage: http://purl.org/ontology/bibo/
  keywords:
  - bibliometrics
  lov:
    description: The Bibliographic Ontology Specification provides main concepts and
      properties for describing citations and bibliographic references (i.e. quotes,
      books, articles, etc) on the Semantic Web.
    homepage: http://purl.org/ontology/bibo/
    keywords:
    - Catalogs
    modified: '2009-11-04'
    name: The Bibliographic Ontology
    prefix: bibo
    uri_prefix: http://purl.org/ontology/bibo/$1
  mappings:
    bartoc: '17844'
    lov: bibo
    zazuko: bibo
  name: The Bibliographic Ontology
  preferred_prefix: bibo
  prefix: bibo
  repository: https://github.com/dcmi/bibo
  uri_format: http://purl.org/ontology/bibo/$1
  zazuko:
    prefix: bibo
    uri_format: http://purl.org/ontology/bibo/$1
bido:
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: An ontology that allows the description of numerical and categorical
    bibliometric data (e.g., journal impact factor, author h-index, categories describing
    research careers) in RDF.
  example: CategorialBibliometricData
  fairsharing:
    abbreviation: BiDO
    contact:
      email: silvio.peroni@unibo.it
      name: Silvio Peroni
      orcid: 0000-0003-0530-4305
    description: The Bibliometric Data Ontology (BiDO) is a modular ontology that
      allows the description of numerical and categorical bibliometric data (e.g.,
      journal impact factor, author h-index, categories describing research careers)
      in RDF.
    homepage: http://www.sparontologies.net/ontologies/bido
    license: CC-BY-4.0
    name: 'Bibliometric Data Ontology '
    prefix: FAIRsharing.d7f0a9
    repository: https://github.com/sparontologies/bido
    subjects:
    - Subject Agnostic
    twitter: sparontologies
  homepage: http://www.sparontologies.net/ontologies/bido
  mappings:
    fairsharing: FAIRsharing.d7f0a9
    ontobee: BIDO
  name: Bibliometric Data Ontology
  ontobee:
    library: Not Specified/No
    name: Bacteria Infectious Disease Ontology
    prefix: BIDO
  preferred_prefix: BiDO
  prefix: bido
  repository: https://github.com/sparontologies/bido
  uri_format: http://purl.org/spar/bido/$1
bigg.compartment:
  biocontext:
    prefix: BIGG.COMPARTMENT
  contact:
    email: zaking@ucsd.edu
    github: zakandrewking
    name: Zachary King
    orcid: 0000-0003-1238-1499
  domain: cellular component
  keywords:
  - cellular component
  - compartment
  - subcellular compartment
  license: http://bigg.ucsd.edu/license#license
  logo: https://lh3.googleusercontent.com/proxy/vQjhtm8lVovH27pBaBSbAx_50uQbOvjubQM4s-R3-6JLiEzlozInmDfqGpp7OwbbkwxbTwfqie4g1GSGOG-vryt20uzT
  mappings:
    biocontext: BIGG.COMPARTMENT
    miriam: bigg.compartment
    n2t: bigg.compartment
  miriam:
    deprecated: false
    description: BiGG is a knowledgebase of Biochemically, Genetically and Genomically
      structured genome-scale metabolic network reconstructions. It more published
      genome-scale metabolic networks into a single database with a set of stardized
      identifiers called BiGG IDs. Genes in the BiGG models are mapped to NCBI genome
      annotations, and metabolites are linked to many external databases (KEGG, PubChem,
      and many more). This collection references model compartments.
    homepage: http://bigg.ucsd.edu/compartments/
    id: '00000555'
    name: BiGG Compartment
    namespaceEmbeddedInLui: false
    pattern: ^[a-z_A-Z]+$
    prefix: bigg.compartment
    sampleId: c
    uri_format: http://bigg.ucsd.edu/compartments/$1
  n2t:
    description: BiGG is a knowledgebase of Biochemically, Genetically and Genomically
      structured genome-scale metabolic network reconstructions. It more published
      genome-scale metabolic networks into a single database with a set of stardized
      identifiers called BiGG IDs. Genes in the BiGG models are mapped to NCBI genome
      annotations, and metabolites are linked to many external databases (KEGG, PubChem,
      and many more). This collection references model compartments.
    example: c
    homepage: http://bigg.ucsd.edu/compartments/
    name: BiGG Compartment at University of California
    namespaceEmbeddedInLui: false
    pattern: ^[a-z_A-Z]+$
    prefix: bigg.compartment
    uri_format: http://bigg.ucsd.edu/compartments/$1
  part_of_database: bigg
  pattern: ^c|cm|cx|e|f|g|h|i|im|l|m|mm|n|p|r|s|u|um|v|w|x|y$
  prefix: bigg.compartment
bigg.metabolite:
  biocontext:
    prefix: BIGG.METABOLITE
  contact:
    email: zaking@ucsd.edu
    github: zakandrewking
    name: Zachary King
    orcid: 0000-0003-1238-1499
  domain: chemical
  example_extras:
  - 12dgr161[c]
  keywords:
  - chemical
  - compound
  - metabolite
  - small molecule
  license: http://bigg.ucsd.edu/license#license
  logo: https://lh3.googleusercontent.com/proxy/vQjhtm8lVovH27pBaBSbAx_50uQbOvjubQM4s-R3-6JLiEzlozInmDfqGpp7OwbbkwxbTwfqie4g1GSGOG-vryt20uzT
  mappings:
    biocontext: BIGG.METABOLITE
    miriam: bigg.metabolite
    n2t: bigg.metabolite
  miriam:
    deprecated: false
    description: BiGG is a knowledgebase of Biochemically, Genetically and Genomically
      structured genome-scale metabolic network reconstructions. It published genome-scale
      metabolic networks into a single database with a set of standardized identifiers
      called BiGG IDs. Genes in the BiGG models are mapped to NCBI genome annotations,
      and metabolites are linked to many external databases (KEGG, PubChem, and many
      more). This collection references individual metabolites.
    homepage: http://bigg.ucsd.edu/universal/metabolites
    id: '00000556'
    name: BiGG Metabolite
    namespaceEmbeddedInLui: false
    pattern: ^[a-z_A-Z0-9]+$
    prefix: bigg.metabolite
    sampleId: 12dgr161
    uri_format: http://bigg.ucsd.edu/models/universal/metabolites/$1
  n2t:
    description: BiGG is a knowledgebase of Biochemically, Genetically and Genomically
      structured genome-scale metabolic network reconstructions. It more published
      genome-scale metabolic networks into a single database with a set of stardized
      identifiers called BiGG IDs. Genes in the BiGG models are mapped to NCBI genome
      annotations, and metabolites are linked to many external databases (KEGG, PubChem,
      and many more). This collection references individual metabolotes.
    example: 12dgr161
    homepage: http://bigg.ucsd.edu/universal/metabolites
    name: BiGG Metabolite at University of Cakifornia
    namespaceEmbeddedInLui: false
    pattern: ^[a-z_A-Z0-9]+$
    prefix: bigg.metabolite
    uri_format: http://bigg.ucsd.edu/models/universal/metabolites/$1
  pattern: ^[a-z_A-Z0-9]+(\[[c|cm|cx|e|f|g|h|i|im|l|m|mm|n|p|r|s|u|um|v|w|x|y]\])?$
  prefix: bigg.metabolite
bigg.model:
  biocontext:
    prefix: BIGG.MODEL
  contact:
    email: zaking@ucsd.edu
    github: zakandrewking
    name: Zachary King
    orcid: 0000-0003-1238-1499
  domain: model
  keywords:
  - metabolic model
  - pathway
  license: http://bigg.ucsd.edu/license#license
  logo: https://lh3.googleusercontent.com/proxy/vQjhtm8lVovH27pBaBSbAx_50uQbOvjubQM4s-R3-6JLiEzlozInmDfqGpp7OwbbkwxbTwfqie4g1GSGOG-vryt20uzT
  mappings:
    biocontext: BIGG.MODEL
    miriam: bigg.model
    n2t: bigg.model
  miriam:
    deprecated: false
    description: BiGG is a knowledgebase of Biochemically, Genetically and Genomically
      structured genome-scale metabolic network reconstructions. It more published
      genome-scale metabolic networks into a single database with a set of stardized
      identifiers called BiGG IDs. Genes in the BiGG models are mapped to NCBI genome
      annotations, and metabolites are linked to many external databases (KEGG, PubChem,
      and many more). This collection references individual models.
    homepage: http://bigg.ucsd.edu/models
    id: '00000554'
    name: BiGG Model
    namespaceEmbeddedInLui: false
    pattern: ^[a-z_A-Z0-9]+$
    prefix: bigg.model
    sampleId: iECABU_c1320
    uri_format: http://bigg.ucsd.edu/models/$1
  n2t:
    description: BiGG is a knowledgebase of Biochemically, Genetically and Genomically
      structured genome-scale metabolic network reconstructions. It more published
      genome-scale metabolic networks into a single database with a set of stardized
      identifiers called BiGG IDs. Genes in the BiGG models are mapped to NCBI genome
      annotations, and metabolites are linked to many external databases (KEGG, PubChem,
      and many more). This collection references individual models.
    example: iECABU_c1320
    homepage: http://bigg.ucsd.edu/models
    name: BiGG Model at University of California
    namespaceEmbeddedInLui: false
    pattern: ^[a-z_A-Z0-9]+$
    prefix: bigg.model
    uri_format: http://bigg.ucsd.edu/models/$1
  prefix: bigg.model
bigg.reaction:
  biocontext:
    prefix: BIGG.REACTION
  contact:
    email: zaking@ucsd.edu
    github: zakandrewking
    name: Zachary King
    orcid: 0000-0003-1238-1499
  domain: reaction
  keywords:
  - reaction
  license: http://bigg.ucsd.edu/license#license
  logo: https://lh3.googleusercontent.com/proxy/vQjhtm8lVovH27pBaBSbAx_50uQbOvjubQM4s-R3-6JLiEzlozInmDfqGpp7OwbbkwxbTwfqie4g1GSGOG-vryt20uzT
  mappings:
    biocontext: BIGG.REACTION
    miriam: bigg.reaction
    n2t: bigg.reaction
  miriam:
    deprecated: false
    description: BiGG is a knowledgebase of Biochemically, Genetically and Genomically
      structured genome-scale metabolic network reconstructions. It more published
      genome-scale metabolic networks into a single database with a set of stardized
      identifiers called BiGG IDs. Genes in the BiGG models are mapped to NCBI genome
      annotations, and metabolites are linked to many external databases (KEGG, PubChem,
      and many more). This collection references reactions.
    homepage: http://bigg.ucsd.edu/universal/reactions
    id: '00000557'
    name: BiGG Reaction
    namespaceEmbeddedInLui: false
    pattern: ^[a-z_A-Z0-9]+$
    prefix: bigg.reaction
    sampleId: 13GS
    uri_format: http://bigg.ucsd.edu/models/universal/reactions/$1
  n2t:
    description: BiGG is a knowledgebase of Biochemically, Genetically and Genomically
      structured genome-scale metabolic network reconstructions. It more published
      genome-scale metabolic networks into a single database with a set of stardized
      identifiers called BiGG IDs. Genes in the BiGG models are mapped to NCBI genome
      annotations, and metabolites are linked to many external databases (KEGG, PubChem,
      and many more). This collection references reactions.
    example: 13GS
    homepage: http://bigg.ucsd.edu/universal/reactions
    name: BiGG Reaction at University of California
    namespaceEmbeddedInLui: false
    pattern: ^[a-z_A-Z0-9]+$
    prefix: bigg.reaction
    uri_format: http://bigg.ucsd.edu/models/universal/reactions/$1
  prefix: bigg.reaction
bila:
  biocontext:
    prefix: BILA
  deprecated: true
  example: '0000000'
  fairsharing:
    abbreviation: BILA
    description: This is a record of the Bilateria anatomy terminology and ontology.
      We have been unable to find any further information about this resource.
    homepage: http://purl.bioontology.org/ontology/BILA
    name: Bilateria anatomy
    prefix: FAIRsharing.eqgjeq
    subjects:
    - Anatomy
  mappings:
    biocontext: BILA
    fairsharing: FAIRsharing.eqgjeq
    obofoundry: bila
    ols: bila
    prefixcommons: 4dxpress
    wikidata.entity: Q114677880
  obofoundry:
    contact: henrich@embl.de
    contact.github: ThorstenHen
    contact.label: Thorsten Henrich
    contact.orcid: 0000-0002-1548-3290
    deprecated: true
    domain: anatomy and development
    download.owl: http://purl.obolibrary.org/obo/bila.owl
    homepage: http://4dx.embl.de/4DXpress
    name: Bilateria anatomy
    prefix: bila
  ols:
    homepage: http://4dx.embl.de/4DXpress
    name: Bilateria anatomy
    prefix: bila
    version: '2019-06-12'
    version.iri: http://purl.obolibrary.org/obo/bila/releases/2019-06-12/bila.owl
  pattern: ^\d{7}$
  prefix: bila
  prefixcommons:
    description: This database provides a platform to query and compare gene expression
      data during the development of the major model animals (zebrafish, drosophila,
      medaka, mouse). The high resolution expression data was acquired through whole
      mount in situ hybridsation-, antibody- or transgenic experiments.
    example: '98967'
    homepage: http://4dx.embl.de/4DXpress
    keywords:
    - gene expression
    name: 4DXpress gene expression in major animals
    pattern: ^\d+$
    prefix: 4dxpress
    pubmed_ids:
    - '17916571'
    uri_format: http://4dx.embl.de/4DXpress/reg/all/cview/gene.do?geneID=$1
  publications:
  - doi: 10.1093/nar/gkm797
    pmc: PMC2238840
    pubmed: '17916571'
    title: '4DXpress: a database for cross-species expression pattern comparisons'
    year: 2007
  - doi: null
    pmc: null
    pubmed: '17916571'
    title: null
    year: null
bind:
  biocontext:
    prefix: BIND
  deprecated: true
  edam:
    description: Accession number of an entry from the BIND database.
    name: BIND accession number
    obsolete: false
    prefix: '1129'
  homepage: http://bind.ca
  mappings:
    biocontext: BIND
    edam: '1129'
    pathguide: '1'
    prefixcommons: bind
  pathguide:
    abbreviation: BIND
    homepage: http://bond.unleashedinformatics.com/
    keywords:
    - PSI-MI
    name: Biomolecular Interaction Network Database
    prefix: '1'
  prefix: bind
  prefixcommons:
    description: BIND is a database designed to store full descriptions of interactions,
      molecular complexes and pathways.
    example: '98346'
    homepage: http://bond.unleashedinformatics.com/
    keywords:
    - interaction
    - small molecule
    - pathway
    name: Biomolecular Interaction Network Databank
    pattern: ^\d+$
    prefix: bind
    uri_format: http://www.bind.ca/Action?identifier=bindid&idsearch=$1
  publications:
  - doi: 10.1093/nar/gkg056
    pmc: PMC165503
    pubmed: '12519993'
    title: 'BIND: the Biomolecular Interaction Network Database'
    year: 2003
  - doi: 10.1093/bioinformatics/16.5.465
    pmc: null
    pubmed: '10871269'
    title: BIND--a data specification for storing and describing biomolecular interactions,
      molecular complexes and pathways
    year: 2000
  uri_format: http://www.bind.ca/Action?identifier=bindid&idsearch=$1
bindingdb:
  biocontext:
    prefix: BINDINGDB
  fairsharing:
    abbreviation: BindingDB
    contact:
      email: mgilson@health.ucsd.edu
      name: Michael K. Gilson
      orcid: 0000-0002-3375-1738
    description: BindingDB enables research by making a growing collection of high-quality,
      quantitative, protein-ligand binding data findable and usable. Funded by NIGMS/NIH.
    homepage: http://www.bindingdb.org
    license: https://creativecommons.org/licenses/by-nc-nd/2.5
    name: BindingDB database of measured binding affinities
    prefix: FAIRsharing.3b36hk
    publications:
    - doi: 10.1093/nar/gkl999
      pubmed_id: 17145705
      title: 'BindingDB: a web-accessible database of experimentally determined protein-ligand
        binding affinities.'
    subjects:
    - Drug Discovery
    - Chemistry
    - Life Science
    - Computational Chemistry
    - Medicinal Chemistry
  mappings:
    biocontext: BINDINGDB
    fairsharing: FAIRsharing.3b36hk
    miriam: bindingdb
    n2t: bindingdb
    pathguide: '50'
    prefixcommons: bindingdb
    re3data: r3d100012074
    uniprot: DB-0127
  miriam:
    deprecated: false
    description: BindingDB is the first public database of protein-small molecule
      affinity data.
    homepage: https://www.bindingdb.org
    id: '00000264'
    name: BindingDB
    namespaceEmbeddedInLui: false
    pattern: ^\d+$
    prefix: bindingdb
    sampleId: '999'
    uri_format: http://www.bindingdb.org/rwd/entry/$1
  n2t:
    description: BindingDB is the first public database of protein-small molecule
      affinity data.
    example: e999
    homepage: https://www.bindingdb.org
    name: BindingDB
    namespaceEmbeddedInLui: false
    pattern: ^\w\d+$
    prefix: bindingdb
    uri_format: http://www.bindingdb.org/compact/$1
  pathguide:
    abbreviation: BindingDB
    homepage: https://www.bindingdb.org/bind/index.jsp
    name: The Binding Database
    prefix: '50'
  prefix: bindingdb
  prefixcommons:
    description: BindingDB is a public, web-accessible database of measured binding
      affinities, focusing chiefly on the interactions of protein considered to be
      drug-targets with small, drug-like molecules.
    example: '22360'
    homepage: http://www.bindingdb.org
    keywords:
    - protein
    - interaction
    name: BindingDB database of measured binding affinities
    pattern: ^\d+$
    prefix: bindingdb
    pubmed_ids:
    - '17145705'
    uri_format: http://www.bindingdb.org/bind/chemsearch/marvin/MolStructure.jsp?monomerid=$1
  publications:
  - doi: 10.1093/nar/gkae1075
    pmc: null
    pubmed: '39574417'
    title: 'BindingDB in 2024: a FAIR knowledgebase of protein-small molecule binding
      data'
    year: 2024
  - doi: 10.1093/nar/gkv1072
    pmc: PMC4702793
    pubmed: '26481362'
    title: 'BindingDB in 2015: A public database for medicinal chemistry, computational
      chemistry and systems pharmacology'
    year: 2015
  - doi: 10.1093/nar/gkl999
    pmc: PMC1751547
    pubmed: '17145705'
    title: 'BindingDB: a web-accessible database of experimentally determined protein-ligand
      binding affinities'
    year: 2006
  re3data:
    description: 'BindingDB is a public, web-accessible knowledgebase of measured
      binding affinities, focusing chiefly on the interactions of proteins considered
      to be candidate drug-targets with ligands that are small, drug-like molecules.
      BindingDB supports medicinal chemistry and drug discovery via literature awareness
      and development of structure-activity relations (SAR and QSAR); validation of
      computational chemistry and molecular modeling approaches such as docking, scoring
      and free energy methods; chemical biology and chemical genomics; and basic studies
      of the physical chemistry of molecular recognition. BindingDB also includes
      a small collection of host-guest binding data of interest to chemists studying
      supramolecular systems.

      The data collection derives from a variety of measurement techniques, including
      enzyme inhibition and kinetics, isothermal titration calorimetry, NMR, and radioligand
      and competition assays. BindingDB includes data extracted from the literature
      and from US Patents by the BindingDB project, selected PubChem confirmatory
      BioAssays, and ChEMBL entries for which a well defined protein target ("TARGET_TYPE=''PROTEIN''")
      is provided.'
    doi: 10.17616/R3ZS9T
    homepage: https://www.bindingdb.org/rwd/bind/index.jsp
    name: BindingDB
    prefix: r3d100012074
    synonyms:
    - BDB
    - The Binding Database
    xrefs:
      nif: 0000-02603
  uniprot:
    abbreviation: BindingDB
    category: Chemistry databases
    homepage: https://www.bindingdb.org/
    name: BindingDB database of measured binding affinities
    prefix: DB-0127
    publications:
    - doi: 10.1093/nar/gkae1075
      pubmed: '39574417'
    uri_format: https://www.bindingdb.org/rwd/uniprot/$1
biocarta.pathway:
  biocontext:
    prefix: BIOCARTA.PATHWAY
  mappings:
    biocontext: BIOCARTA.PATHWAY
    miriam: biocarta.pathway
    n2t: biocarta.pathway
  miriam:
    deprecated: false
    description: BioCarta is a supplier and distributor of characterized reagents
      and assays for biopharmaceutical and academic research. It catalogs community
      produced online maps depicting molecular relationships from areas of active
      research, generating classical pathways as well as suggestions for new pathways.
      This collections references pathway maps.
    homepage: https://www.biocarta.com/
    id: '00000421'
    name: BioCarta Pathway
    namespaceEmbeddedInLui: false
    pattern: ^([hm]\_)?\w+Pathway$
    prefix: biocarta.pathway
    sampleId: h_aktPathway
    uri_format: https://cgap.nci.nih.gov/Pathways/BioCarta/$1
  n2t:
    description: BioCarta is a supplier and distributor of characterized reagents
      and assays for biopharmaceutical and academic research. It catalogs community
      produced online maps depicting molecular relationships from areas of active
      research, generating classical pathways as well as suggestions for new pathways.
      This collections references pathway maps.
    example: h_aktPathway
    homepage: https://www.biocarta.com/
    name: BioCarta Pathway at NCI
    namespaceEmbeddedInLui: false
    pattern: ^([hm]\_)?\w+Pathway$
    prefix: biocarta.pathway
    uri_format: https://cgap.nci.nih.gov/Pathways/BioCarta/$1
  prefix: biocarta.pathway
biocatalogue.service:
  biocontext:
    prefix: BIOCATALOGUE.SERVICE
  contact:
    email: carole.goble@manchester.ac.uk
    github: CaroleGoble
    name: Carole Goble
    orcid: 0000-0003-1219-2137
  mappings:
    biocontext: BIOCATALOGUE.SERVICE
    miriam: biocatalogue.service
    n2t: biocatalogue.service
    prefixcommons: biocatalogue
  miriam:
    deprecated: false
    description: The BioCatalogue provides a common interface for registering, browsing
      and annotating Web Services to the Life Science community. Registered services
      are monitored, allowing the identification of service problems and changes and
      the filtering-out of unavailable or unreliable resources. BioCatalogue is free
      to use, for all.
    homepage: https://www.biocatalogue.org/
    id: '00000140'
    name: BioCatalogue
    namespaceEmbeddedInLui: false
    pattern: ^\d+$
    prefix: biocatalogue.service
    sampleId: '614'
    uri_format: https://www.biocatalogue.org/services/$1
  n2t:
    description: The BioCatalogue provides a common interface for registering, browsing
      and annotating Web Services to the Life Science community. Registered services
      are monitored, allowing the identification of service problems and changes and
      the filtering-out of unavailable or unreliable resources. BioCatalogue is free
      to use, for all.
    example: '614'
    homepage: https://www.biocatalogue.org/
    name: BioCatalogue at EMBL-EBI
    namespaceEmbeddedInLui: false
    pattern: ^\d+$
    prefix: biocatalogue.service
    uri_format: https://www.biocatalogue.org/services/$1
  name: BioCatalogue Service
  prefix: biocatalogue.service
  prefixcommons:
    description: The BioCatalogue provides a common interface for registering, browsing
      and annotating Web Services to the Life Science community. Registered services
      are monitored, allowing the identification of service problems and changes and
      the filtering-out of unavailable or unreliable resources. BioCatalogue is free
      to use, for all.
    example: '614'
    homepage: http://www.biocatalogue.org/
    keywords:
    - registry
    name: Curated catalogue of Life Science Web Services
    pattern: ^\d+$
    prefix: biocatalogue
    pubmed_ids:
    - '20484378'
    uri_format: http://www.biocatalogue.org/services/$1
  publications:
  - doi: 10.1093/nar/gkq394
    pmc: PMC2896129
    pubmed: '20484378'
    title: 'BioCatalogue: a universal catalogue of web services for the life sciences'
    year: 2010
  - doi: null
    pmc: null
    pubmed: '20484378'
    title: null
    year: null
biocompute:
  contact:
    email: mazumder@gwu.edu
    github: null
    name: Raja Mazumder
    orcid: 0000-0001-8823-9945
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: BioCompute is shorthand for the IEEE 2791-2020 standard for Bioinformatics
    Analyses Generated by High-Throughput Sequencing (HTS) to facilitate communication.
    This pipeline documentation approach has been adopted by a few FDA centers. The
    goal is to ease the communication burdens between research centers, organizations,
    and industries. This web portal allows users to build a BioCompute Objects through
    the interface in a human and machine readable format.
  example: '000001'
  homepage: https://biocomputeobject.org
  name: Biocompute Object
  pattern: ^\d+$
  prefix: biocompute
  publications:
  - doi: null
    pmc: null
    pubmed: '27974626'
    title: BioCompute objects - a step towards evaluation and validation of bio-medical
      scientific computations
    year: 2017
  repository: https://github.com/biocompute-objects/BCO_Specification
  uri_format: https://biocomputeobject.org/BCO_$1
biocyc:
  biocontext:
    prefix: BIOCYC
  contact:
    email: pkarp@ai.sri.com
    github: pkarp111
    name: Peter D. Karp
    orcid: 0000-0002-5876-6418
  edam:
    description: Identifier of an object from one of the BioCyc databases.
    name: BioCyc
    obsolete: false
    prefix: '2104'
  go:
    homepage: http://biocyc.org/
    name: BioCyc collection of metabolic pathway databases
    prefix: BioCyc
    uri_format: http://biocyc.org/META/NEW-IMAGE?type=PATHWAY&object=$1
  integbio:
    description: This is a collection of metabolic pathways and their genomes for
      each species. It contains predictions of metabolic pathways, genome regions
      of unidentified enzymes, and operons for species, about organisms which sequence
      analysis is completed. Furthermore, the site has the information on metabolic
      pathway collected from journal articles, a genome browser, visualization tools,
      and a search tool.
    homepage: http://biocyc.org/
    information_keywords:
    - Sequence
    - Interaction/Pathway
    - Bibliography/Documents
    maintainer: SRI International
    name: BioCyc
    prefix: nbdc00252
    pubmeds:
    - '22102576'
    - '16246909'
    status: Active
    target_keywords:
    - Genome/Gene
    - DNA
    - RNA
    - Protein
  logo: https://biocyc.org/graphics2021/BioCyc-logo-color-genome.svg
  mappings:
    biocontext: BIOCYC
    edam: '2104'
    go: BioCyc
    integbio: nbdc00252
    miriam: biocyc
    n2t: biocyc
    pathguide: '8'
    prefixcommons: biocyc
    uniprot: DB-0005
  miriam:
    deprecated: false
    description: BioCyc is a collection of Pathway/Genome Databases (PGDBs) which
      provides an electronic reference source on the genomes and metabolic pathways
      of sequenced organisms.
    homepage: http://biocyc.org
    id: 00000194
    name: BioCyc
    namespaceEmbeddedInLui: false
    pattern: ^[A-Z-0-9]+(\:)?[A-Za-z0-9+_.%-:]+$
    prefix: biocyc
    sampleId: ECOLI:CYT-D-UBIOX-CPLX
    uri_format: http://biocyc.org/getid?id=$1
  n2t:
    description: BioCyc is a collection of Pathway/Genome Databases (PGDBs) which
      provides an electronic reference source on the genomes and metabolic pathways
      of sequenced organisms.
    example: ECOLI:CYT-D-UBIOX-CPLX
    homepage: http://biocyc.org
    name: BioCyc at SRI International
    namespaceEmbeddedInLui: false
    pattern: ^[A-Z-0-9]+(\:)?[A-Za-z0-9+_.%-:]+$
    prefix: biocyc
    uri_format: http://biocyc.org/getid?id=$1
  pathguide:
    abbreviation: BioCyc
    homepage: http://biocyc.org/
    keywords:
    - BioPAX
    - SBML
    name: BioCyc Knowledge Library
    prefix: '8'
  prefix: biocyc
  prefixcommons:
    description: The BioCyc collection of Pathway/Genome Databases (PGDBs) provides
      electronic reference sources on the pathways and genomes of different organisms.
    example: ECOLI:CYT-D-UBIOX-CPLX
    homepage: http://www.biocyc.org/
    keywords:
    - genome
    - pathway
    - sequence
    name: BioCyc Database Collection
    pattern: ^\w+\:[A-Za-z0-9-]+$
    prefix: biocyc
    pubmed_ids:
    - '16246909'
    uri_format: http://biocyc.org/ECOLI/NEW-IMAGE?object=$1
  publications:
  - doi: 10.1093/bib/bbx085
    pmc: PMC6781571
    pubmed: '29447345'
    title: The BioCyc collection of microbial genomes and metabolic pathways
    year: 2019
  - doi: 10.1093/nar/gkv1164
    pmc: PMC4702838
    pubmed: '26527732'
    title: The MetaCyc database of metabolic pathways and enzymes and the BioCyc collection
      of pathway/genome databases
    year: 2015
  - doi: 10.1093/nar/gki892
    pmc: PMC1266070
    pubmed: '16246909'
    title: Expansion of the BioCyc collection of pathway/genome databases to 160 genomes
    year: 2005
  uniprot:
    abbreviation: BioCyc
    category: Enzyme and pathway databases
    homepage: https://www.biocyc.org/
    name: BioCyc Collection of Pathway/Genome Databases
    prefix: DB-0005
    publications:
    - doi: 10.1093/bib/bbx085
      pubmed: '29447345'
    uri_format: https://biocyc.org/getid?id=$1
biodeep:
  banana: BioDeep
  banana_peel: _
  example: '00000000001'
  mappings:
    miriam: biodeep
  miriam:
    deprecated: false
    description: 'The BioDeep database is a comprehensive database of metabolite information
      in living organisms: by aggregating metabolite information from multiple public
      databases and large-scale natural language text mining work, we have built a
      large scale knowledge network for biological knowledge interpretation. By using
      the BioDeep database, it is possible to query such large scale metabolic knowledge
      network.'
    homepage: https://en.panomix.com/
    id: 00001080
    name: BioDeep Database
    namespaceEmbeddedInLui: false
    pattern: ^BioDeep_\d{11}$
    prefix: biodeep
    sampleId: BioDeep_00000000001
    uri_format: https://query.biodeep.cn/metabolite/$1
  pattern: ^\d{11}$
  prefix: biodeep
biodolphin:
  contact:
    email: andrew.mcshan@chemistry.gatech.edu
    github: null
    name: Andrew C. McShan
    orcid: 0000-0002-3212-9867
  contributor:
    email: m.naguthana@hotmail.com
    github: nagutm
    name: Mufaddal Naguthanawala
    orcid: 0009-0009-5240-7463
  description: Identifiers for lipid-protein interactions, including details about
    protein functions, protein families, lipid classifications, lipid-protein binding
    affinities, membrane association type, and atomic structures.
  example: BD1a05-A-A-IPM1
  github_request_issue: 1327
  homepage: https://biodolphin.chemistry.gatech.edu
  name: BioDolphin
  pattern: ^BD\d[a-zA-Z0-9]+-[A-Za-z]-[A-Za-z]-[A-Za-z0-9]+$
  prefix: biodolphin
  publications:
  - doi: 10.1038/s42004-024-01384-z
    pmc: PMC11618342
    pubmed: '39633021'
    title: BioDolphin as a comprehensive database of lipid-protein binding interactions
    year: 2024
  reviewer:
    email: b.gyori@northeastern.edu
    github: bgyori
    name: Benjamin M. Gyori
    orcid: 0000-0001-9439-5346
  uri_format: https://biodolphin.chemistry.gatech.edu/detail/$1
biofactoid:
  contact:
    email: jeffvin.wong@utoronto.ca
    github: jvwong
    name: Jeffrey Wong
    orcid: 0000-0002-8912-5699
  contributor:
    email: benjamin_gyori@hms.harvard.edu
    github: bgyori
    name: Benjamin M. Gyori
    orcid: 0000-0001-9439-5346
  description: Biofactoid is a web-based system that empowers authors to capture and
    share machine-readable summaries of molecular-level interactions described in
    their publications.
  example: fdb8a927-45c3-48b7-9743-cbb5e16837fa
  github_request_issue: 700
  homepage: https://biofactoid.org/
  keywords:
  - biocuration
  - database
  - relationships
  license: CC0-1.0
  mappings:
    miriam: biofactoid
  miriam:
    deprecated: false
    description: 'Biofactoid is a resource of biological pathways, assembled from
      author-curated results in papers.

      '
    homepage: https://thedonnellycentre.utoronto.ca/
    id: '00001074'
    name: Biofactoid
    namespaceEmbeddedInLui: false
    pattern: ^[0-9a-f]{8}-[0-9a-f]{4}-[1-5][0-9a-f]{3}-[89ab][0-9a-f]{3}-[0-9a-f]{12}$
    prefix: biofactoid
    sampleId: 5df17c41-acb7-4c42-a37b-fe323688bc64
    uri_format: https://biofactoid.org/document/$1
  name: Biofactoid
  pattern: ^[0-9a-fA-F]{8}\-[0-9a-fA-F]{4}\-[0-9a-fA-F]{4}\-[0-9a-fA-F]{4}\-[0-9a-fA-F]{12}$
  prefix: biofactoid
  publications:
  - doi: 10.7554/elife.68292
    pmc: PMC8683078
    pubmed: '34860157'
    title: Author-sourced capture of pathway knowledge in computable form using Biofactoid
    year: 2021
  repository: https://github.com/PathwayCommons/factoid
  reviewer:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  uri_format: https://biofactoid.org/document/$1
biogrid:
  biocontext:
    prefix: BIOGRID
    uri_format: http://thebiogrid.org/$1
  contact:
    email: md.tyers@umontreal.ca
    github: null
    name: Mike Tyers
    orcid: 0000-0002-9713-9994
  fairsharing:
    abbreviation: BioGRID
    description: The Biological General Repository for Interaction Datasets (BioGRID)
      is a public database that archives and disseminates genetic and protein interaction
      data from model organisms and humans. BioGRID currently holds over 1,740,000
      interactions curated from both high-throughput datasets and individual focused
      studies, as derived from over 70,000+ publications in the primary literature.
      Complete coverage of the entire literature is maintained for budding yeast (S.
      cerevisiae), fission yeast (S. pombe) and thale cress (A. thaliana), and efforts
      to expand curation across multiple metazoan species are underway. All data are
      freely provided via our search index and available for download in many standardized
      formats.
    homepage: http://www.thebiogrid.org
    name: Biological General Repository for Interaction Datasets
    prefix: FAIRsharing.9d5f5r
    publications:
    - doi: 10.1093/nar/gkj109
      pubmed_id: 16381927
      title: 'BioGRID: a general repository for interaction datasets.'
    - doi: 10.1186/gb-2003-4-3-r23
      pubmed_id: 12620108
      title: 'The GRID: the General Repository for Interaction Datasets.'
    - doi: 10.1002/pro.3978
      pubmed_id: 33070389
      title: 'The BioGRID database: A comprehensive biomedical resource of curated
        protein, genetic, and chemical interactions.'
    - doi: 10.1093/nar/gky1079
      pubmed_id: 30476227
      title: 'The BioGRID interaction database: 2019 update'
    repository: https://github.com/BioGRID
    subjects:
    - Cheminformatics
    - Biochemistry
    - Bioinformatics
    - Chemical Biology
    - Proteomics
    - Life Science
    - Systems Biology
    twitter: biogrid
  mappings:
    biocontext: BIOGRID
    fairsharing: FAIRsharing.9d5f5r
    miriam: biogrid
    n2t: biogrid
    pathguide: '7'
    prefixcommons: biogrid
    re3data: r3d100010350
    uniprot: DB-0184
  miriam:
    deprecated: false
    description: BioGRID is a database of physical and genetic interactions in Saccharomyces
      cerevisiae, Caenorhabditis elegans, Drosophila melanogaster, Homo sapiens, and
      Schizosaccharomyces pombe.
    homepage: http://thebiogrid.org/
    id: 00000058
    name: BioGRID
    namespaceEmbeddedInLui: false
    pattern: ^\d+$
    prefix: biogrid
    sampleId: '31623'
    uri_format: http://thebiogrid.org/$1
  n2t:
    description: BioGRID is a database of physical and genetic interactions in Saccharomyces
      cerevisiae, Caenorhabditis elegans, Drosophila melanogaster, Homo sapiens, and
      Schizosaccharomyces pombe.
    example: '31623'
    homepage: http://thebiogrid.org/
    name: BioGRID database of physical and genetic interactions
    namespaceEmbeddedInLui: false
    pattern: ^\d+$
    prefix: biogrid
    uri_format: http://thebiogrid.org/$1
  part_of_database: biogrid
  pathguide:
    abbreviation: BioGRID
    homepage: http://www.thebiogrid.org/
    keywords:
    - PSI-MI
    name: Biological General Repository for Interaction Datasets
    prefix: '7'
  prefix: biogrid
  prefixcommons:
    description: BioGRID is a database of physical and genetic interactions in Saccharomyces
      cerevisiae, Caenorhabditis elegans, Drosophila melanogaster, Homo sapiens, and
      Schizosaccharomyces pombe.
    example: '31623'
    homepage: http://www.thebiogrid.org
    keywords:
    - protein
    - gene
    - interaction
    name: Biological General Repository for Interaction Datasets
    pattern: ^\d+$
    prefix: biogrid
    pubmed_ids:
    - '16381927'
    uri_format: http://thebiogrid.org/$1
  publications:
  - doi: 10.1002/pro.3978
    pmc: PMC7737760
    pubmed: '33070389'
    title: 'The BioGRID database: A comprehensive biomedical resource of curated protein,
      genetic, and chemical interactions'
    year: 2020
  - doi: 10.1093/nar/gky1079
    pmc: PMC6324058
    pubmed: '30476227'
    title: 'The BioGRID interaction database: 2019 update'
    year: 2019
  - doi: 10.1093/nar/gkq1116
    pmc: PMC3013707
    pubmed: '21071413'
    title: 'The BioGRID Interaction Database: 2011 update'
    year: 2010
  - doi: 10.1093/nar/gkj109
    pmc: PMC1347471
    pubmed: '16381927'
    title: 'BioGRID: a general repository for interaction datasets'
    year: 2006
  - doi: 10.1186/gb-2003-4-3-r23
    pmc: PMC153463
    pubmed: '12620108'
    title: 'The GRID: the General Repository for Interaction Datasets'
    year: 2003
  re3data:
    description: The Biological General Repository for Interaction Datasets (BioGRID)
      is a public database that archives and disseminates genetic and protein interaction
      data from model organisms and humans. BioGRID is an online interaction repository
      with data compiled through comprehensive curation efforts. All interaction data
      are freely provided through our search index and available via download in a
      wide variety of standardized formats.
    doi: 10.17616/R34C7G
    homepage: https://thebiogrid.org/
    name: BioGRID
    prefix: r3d100010350
    synonyms:
    - Biological General Repository for Interaction Datasets
    xrefs:
      nif: 0000-00432
      omics: 01901
  twitter: biogrid
  uniprot:
    abbreviation: BioGRID
    category: Protein-protein interaction databases
    homepage: https://thebiogrid.org/
    name: The Biological General Repository for Interaction Datasets (BioGRID)
    prefix: DB-0184
    publications:
    - doi: 10.1002/pro.3978
      pubmed: '33070389'
    uri_format: https://thebiogrid.org/$1
biogrid.interaction:
  contact:
    email: md.tyers@umontreal.ca
    github: null
    name: Mike Tyers
    orcid: 0000-0002-9713-9994
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: BioGRID is a database of physical and genetic interactions in Saccharomyces
    cerevisiae, Caenorhabditis elegans, Drosophila melanogaster, Homo sapiens, and
    Schizosaccharomyces pombe.
  edam:
    description: A unique identifier of an interaction from the BioGRID database.
    name: BioGRID interaction
    obsolete: false
    prefix: '2628'
  example: '2649230'
  homepage: https://thebiogrid.org/
  mappings:
    edam: '2628'
  name: BioGRID Interactions
  part_of_database: biogrid
  pattern: ^\d+$
  prefix: biogrid.interaction
  twitter: biogrid
  uri_format: https://thebiogrid.org/interaction/$1
biokc:
  mappings:
    miriam: biokc
  miriam:
    deprecated: false
    description: BioKC (Biological Knowledge Curation), is a web-based collaborative
      platform for the curation and annotation of biomedical knowledge following the
      standard data model from Systems Biology Markup Language (SBML).
    homepage: https://wwwen.uni.lu/lcsb
    id: 00000995
    name: BioKC
    namespaceEmbeddedInLui: false
    pattern: ^bkc[0-9]*$
    prefix: biokc
    sampleId: bkc640
    uri_format: https://biokb.lcsb.uni.lu/fact/$1
  prefix: biokc
biolegend:
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: BioLegend is a life sciences supply vendor.
  example: '3403'
  homepage: https://www.biolegend.com
  keywords:
  - antibodies
  - assays
  - life sciences
  - reagents
  - vendor
  name: BioLegend
  pattern: ^\d+$
  prefix: biolegend
  uri_format: https://www.biolegend.com/Default.aspx?ID=6664&productid=$1
biolink:
  aberowl:
    description: A high level datamodel of biological entities (genes, diseases, phenotypes,
      pathways, individuals, substances, etc) and their associations
    download_owl: http://aber-owl.net/media/ontologies/BIOLINK/75/biolink.owl
    homepage: https://biolink.github.io/biolink-model/
    name: Biolink Model
    prefix: BIOLINK
    version: 4.3.6
  biolink:
    is_identifiers: false
    is_obo: false
    prefix: biolink
    uri_format: https://w3id.org/biolink/vocab/$1
  bioportal:
    contact:
      email: cjmungall@lbl.gov
      name: Chris Mungall
    description: A high level datamodel of biological entities (genes, diseases, phenotypes,
      pathways, individuals, substances, etc) and their associations
    homepage: https://biolink.github.io/biolink-model/
    license: CC0-1.0
    name: Biolink Model
    prefix: BIOLINK
    version: 4.3.4
  contact:
    email: cjmungall@lbl.gov
    github: cmungall
    name: Chris Mungall
    orcid: 0000-0002-6601-2165
  fairsharing:
    abbreviation: biolink
    contact:
      email: smoxon@lbl.gov
      name: Sierra Moxon
      orcid: 0000-0002-8719-7760
    description: 'A high level datamodel of biological entities (genes, diseases,
      phenotypes, pathways, individuals, substances, etc) and their associations.

      Biolink Model is designed as a way of standardizing types and relational structures
      in knowledge graphs (KGs), where the KG may be either a property graph or RDF
      triple store.


      The schema is expressed as a YAML, which may be translated into a number of
      different representations including OWL, Python dataclasses, GraphQL and more.
      The schema assumes a property graph, where nodes represent individual entities,
      and edges represent relationship between entities. Biolink Model provides a
      schema for representing both nodes and edges. The model itself can be divided
      into a few parts: Entities (subjects and objects), Predicates (relationships
      between core concepts), Associations (statements including evidence and provenance),
      Entity Slots (node properties), and Edge Slots (edge properties).'
    homepage: https://biolink.github.io/biolink-model/
    license: Apache 2.0 License
    name: Biolink Model
    prefix: FAIRsharing.ad9d85
    publications: []
    repository: https://github.com/biolink/biolink-model
    subjects:
    - Functional Genomics
    - Medical Biotechnology
    - Biomedical Science
    - Translational Medicine
    - Medical Informatics
  homepage: https://biolink.github.io/biolink-model/
  mappings:
    aberowl: BIOLINK
    biolink: biolink
    bioportal: BIOLINK
    fairsharing: FAIRsharing.ad9d85
    miriam: biolink
    ols: biolink
  miriam:
    deprecated: false
    description: A high level datamodel of biological entities (genes, diseases, phenotypes,
      pathways, individuals, substances, etc) and their associations.
    homepage: https://biolink.github.io/biolink-model
    id: 00000782
    name: BioLink Model
    namespaceEmbeddedInLui: false
    pattern: ^\S+$
    prefix: biolink
    sampleId: Gene
    uri_format: https://w3id.org/biolink/vocab/$1
  ols:
    download_rdf: https://w3id.org/biolink/biolink-model.owl.ttl
    homepage: https://biolink.github.io/biolink-model/
    prefix: biolink
  preferred_prefix: biolink
  prefix: biolink
biomagresbank:
  mappings:
    prefixcommons: biomagresbank
  prefix: biomagresbank
  prefixcommons:
    description: A repository for Data from NMR Spectroscopy on Proteins, Peptides,
      and Nucleic Acids.
    example: '10046'
    homepage: http://www.bmrb.wisc.edu/
    keywords:
    - protein
    name: BioMagResBank
    pattern: ^\d+$
    prefix: biomagresbank
    uri_format: http://www.bmrb.wisc.edu/data_library/generate_summary.php?bmrbId=$1
  reviewer:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
biomarkerkb.biomarker:
  contact:
    email: mazumder@gwu.edu
    github: null
    name: Raja Mazumder
    orcid: 0000-0001-8823-9945
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  contributor_extras:
  - email: jeetvora@email.gwu.edu
    github: jeet-vora
    name: Jeet Kiran Vora
    orcid: 0000-0002-5317-1458
  description: A disease/condition-specific instantiation of a canonical biomarker
  example: AN6278-5
  example_extras:
  - AO2172-10
  github_request_issue: 1526
  homepage: https://biomarkerkb.org
  keywords:
  - biomarker
  name: Biomarker Knowledgebase - Biomarker
  part_of_database: biomarkerkb
  pattern: ^A(N|O)\d+-\d+$
  prefix: biomarkerkb.biomarker
  uri_format: https://biomarkerkb.org/biomarker/$1
biomarkerkb.canonical:
  contact:
    email: mazumder@gwu.edu
    github: null
    name: Raja Mazumder
    orcid: 0000-0001-8823-9945
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  contributor_extras:
  - email: jeetvora@email.gwu.edu
    github: jeet-vora
    name: Jeet Kiran Vora
    orcid: 0000-0002-5317-1458
  description: A canonical biomarker, which describes the composition of a measurement
    on a change to an entity. For example, the increase in IL6 level
  example: AN6278
  example_extras:
  - AO1391
  github_request_issue: 1526
  homepage: https://biomarkerkb.org
  keywords:
  - biomarker
  name: Biomarker Knowledgebase - Canonical Biomarker
  part_of_database: biomarkerkb
  pattern: ^A(N|O)\d+$
  prefix: biomarkerkb.canonical
  uri_format: https://biomarkerkb.org/canonical/$1
biominder:
  biocontext:
    prefix: BIOMINDER
  mappings:
    biocontext: BIOMINDER
    miriam: biominder
    n2t: biominder
  miriam:
    deprecated: false
    description: Database of the dielectric properties of biological tissues.
    homepage: https://datalab.rwth-aachen.de/MINDER
    id: '00000634'
    name: Bio-MINDER Tissue Database
    namespaceEmbeddedInLui: false
    pattern: ^[a-z0-9\-]+$
    prefix: biominder
    sampleId: aef4c195-9cf9-46db-a12a-7cfd1ff3eec3
    uri_format: https://datalab.rwth-aachen.de/MINDER/resource/$1
  n2t:
    description: Database of the dielectric properties of biological tissues.
    example: aef4c195-9cf9-46db-a12a-7cfd1ff3eec3
    homepage: https://datalab.rwth-aachen.de/MINDER
    name: Bio-MINDER Tissue Database
    namespaceEmbeddedInLui: false
    pattern: ^[a-z0-9\-]+$
    prefix: biominder
    uri_format: https://datalab.rwth-aachen.de/MINDER/resource/$1
  prefix: biominder
biomodels.db:
  biocontext:
    prefix: BIOMODELS.DB
  contact:
    email: mhucka@caltech.edu
    github: mhucka
    name: Michael Hucka
    orcid: 0000-0001-9105-5960
  go:
    homepage: https://www.ebi.ac.uk/biomodels/
    name: BioModels Database
    prefix: BIOMD
    synonyms:
    - BIOMDID
    uri_format: https://www.ebi.ac.uk/biomodels/$1
  mappings:
    biocontext: BIOMODELS.DB
    go: BIOMD
    miriam: biomodels.db
    n2t: biomodels.db
    prefixcommons: biomodels
  miriam:
    deprecated: false
    description: BioModels Database is a data resource that allows biologists to store,
      search and retrieve published mathematical models of biological interests.
    homepage: https://www.ebi.ac.uk/biomodels/
    id: '00000007'
    name: BioModels Database
    namespaceEmbeddedInLui: false
    pattern: ^((BIOMD|MODEL)\d{10})|(BMID\d{12})$
    prefix: biomodels.db
    providers:
    - code: omicsdi
      description: BioModels through OmicsDI
      homepage: https://www.omicsdi.org/
      name: BioModels through OmicsDI
      uri_format: https://www.omicsdi.org/dataset/biomodels/$1
    sampleId: BIOMD0000000048
    uri_format: https://www.ebi.ac.uk/biomodels/$1
  n2t:
    description: BioModels Database is a data resource that allows biologists to store,
      search and retrieve published mathematical models of biological interests.
    example: BIOMD0000000048
    homepage: https://www.ebi.ac.uk/biomodels/
    name: BioModels Database
    namespaceEmbeddedInLui: false
    pattern: ^((BIOMD|MODEL)\d{10})|(BMID\d{12})$
    prefix: biomodels.db
    uri_format: https://www.ebi.ac.uk/biomodels/$1
  prefix: biomodels.db
  prefixcommons:
    alt_uri_formats:
    - http://biomodels.caltech.edu/$1
    bioportal: '3022'
    description: BioModels Database is a data resource that allows biologists to store,
      search and retrieve published mathematical models of biological interests.
    example: BIOMD0000000048
    homepage: http://www.ebi.ac.uk/biomodels/
    keywords:
    - model
    license: http://www.ebi.ac.uk/Information/termsofuse.html
    name: A Database of Annotated Published Models
    pattern: ^((BIOMD|MODEL)\d{10})|(BMID\d{12})$
    prefix: biomodels
    pubmed_ids:
    - '16381960'
    synonyms:
    - biomodelsdatabase
    - biomodels.db
    uri_format: http://www.ebi.ac.uk/biomodels-main/$1
  publications:
  - doi: 10.1093/nar/gkj092
    pmc: PMC1347454
    pubmed: '16381960'
    title: 'BioModels Database: a free, centralized database of curated, published,
      quantitative kinetic models of biochemical and cellular systems'
    year: 2006
  - doi: null
    pmc: null
    pubmed: '16381960'
    title: null
    year: null
  synonyms:
  - BIOMD
biomodels.kisao:
  aberowl:
    description: A classification of algorithms for simulating biology, their parameters,
      and their outputs
    download_owl: http://aber-owl.net/media/ontologies/KISAO/37/kisao.owl
    homepage: https://github.com/SED-ML/KiSAO
    name: Kinetic Simulation Algorithm Ontology
    prefix: KISAO
  banana: KISAO
  banana_peel: _
  biocontext:
    prefix: KISAO
  bioportal:
    contact:
      email: sed-ml-editors@googlegroups.com
      name: SED-ML Editors
    description: The Kinetic Simulation Algorithm Ontology (KiSAO) is an ontology
      of algorithms for simulating and analyzing biological models, as well as the
      characteristics of these algorithms, their input parameters, and their outputs.
      In addition, KiSAO captures relationships among algorithms, their parameters,
      and their outputs.
    homepage: http://biomodels.net/kisao/
    name: Kinetic Simulation Algorithm Ontology
    prefix: KISAO
    publications:
    - https://doi.org/10.1038/msb.2011.77
    version: '2.34'
  example: '0000057'
  fairsharing:
    abbreviation: KiSAO
    contact:
      email: lenov@ebi.ac.uk
      name: Nicolas Le Novère
      orcid: 0000-0002-6309-7327
    description: The Kinetic Simulation Algorithm Ontology aims at providing support
      in unambiguously referring to simulation algorithms when describing a simulation
      experiment. It describes and classifies existing algorithms and their inter-relationships
      through the algorithm characteristics and parameters.
    domains:
    - algorithm
    homepage: https://github.com/SED-ML/KiSAO
    name: Kinetic Simulation Algorithm Ontology
    prefix: FAIRsharing.jcg19w
    publications:
    - doi: 10.1038/msb.2011.77
      pubmed: '22027554'
      title: Controlled vocabularies and semantics in systems biology
      year: 2011
    repository: https://github.com/SED-ML/KiSAO
    subjects:
    - Computer Science
    - Bioinformatics
  logo: https://upload.wikimedia.org/wikipedia/commons/6/63/KiSAO_logo.svg
  mappings:
    aberowl: KISAO
    biocontext: KISAO
    bioportal: KISAO
    fairsharing: FAIRsharing.jcg19w
    miriam: biomodels.kisao
    n2t: biomodels.kisao
    obofoundry: kisao
    ols: kisao
    ontobee: KISAO
    prefixcommons: kisao
  miriam:
    deprecated: false
    description: The Kinetic Simulation Algorithm Ontology (KiSAO) is an ontology
      that describes simulation algorithms and methods used for biological kinetic
      models, and the relationships between them. This provides a means to unambiguously
      refer to simulation algorithms when describing a simulation experiment.
    homepage: http://bioportal.bioontology.org/ontologies/KISAO
    id: 00000108
    name: KiSAO
    namespaceEmbeddedInLui: false
    pattern: ^KISAO_\d+$
    prefix: biomodels.kisao
    sampleId: KISAO_0000057
    uri_format: http://purl.bioontology.org/ontology/KISAO/kisao:$1
  n2t:
    description: The Kinetic Simulation Algorithm Ontology (KiSAO) is an ontology
      that describes simulation algorithms and methods used for biological kinetic
      models, and the relationships between them. This provides a means to unambiguously
      refer to simulation algorithms when describing a simulation experiment.
    example: KISAO_0000057
    homepage: http://bioportal.bioontology.org/ontologies/KISAO
    name: KiSAO via NCBO's Bioportal
    namespaceEmbeddedInLui: false
    pattern: ^KISAO_\d+$
    prefix: biomodels.kisao
    uri_format: http://purl.bioontology.org/ontology/KISAO/kisao:$1
  namespace_in_lui: true
  obofoundry:
    contact: jonrkarr@gmail.com
    contact.github: jonrkarr
    contact.label: Jonathan Karr
    contact.orcid: 0000-0002-2605-5080
    deprecated: false
    description: A classification of algorithms for simulating biology, their parameters,
      and their outputs
    domain: simulation
    download.owl: http://purl.obolibrary.org/obo/kisao.owl
    homepage: https://github.com/SED-ML/KiSAO
    license: Artistic License 2.0
    license.url: http://opensource.org/licenses/Artistic-2.0
    name: Kinetic Simulation Algorithm Ontology
    preferredPrefix: KISAO
    prefix: kisao
    publications:
    - id: https://www.ncbi.nlm.nih.gov/pubmed/22027554
      title: Controlled vocabularies and semantics in systems biology
    repository: https://github.com/SED-ML/KiSAO
  ols:
    description: A classification of algorithms for simulating biology, their parameters,
      and their outputs
    download_owl: http://purl.obolibrary.org/obo/kisao.owl
    homepage: https://github.com/SED-ML/KiSAO
    name: Kinetic Simulation Algorithm Ontology
    prefix: kisao
    tracker: https://github.com/SED-ML/KiSAO/issues
    version: '2.34'
  ontobee:
    library: Library
    name: Kinetic Simulation Algorithm Ontology
    prefix: KISAO
  pattern: ^\d+$
  preferred_prefix: biomodels.kisao
  prefix: biomodels.kisao
  prefixcommons:
    bioportal: '1410'
    description: The Kinetic Simulation Algorithm Ontology (KiSAO) is an ontology
      that describes simulation algorithms and methods used for biological kinetic
      models, and the relationships between them. This provides a means to unambiguously
      refer to simulation algorithms when describing a simulation experiment.
    example: KISAO_0000057
    homepage: http://biomodels.net/kisao/
    keywords:
    - ontology
    name: Kinetic Simulation Algorithm Ontology
    pattern: ^KISAO_\d+$
    prefix: kisao
    rdf_uri_format: http://www.biomodels.net/kisao/KISAO#$1
    synonyms:
    - biomodels.kisao
  providers:
  - code: legacy
    description: This is the URI scheme used in the ontology but it does not resolve.
    example: null
    first_party: null
    homepage: https://www.biomodels.net
    name: Legacy Biomodels URL
    publications: null
    status: null
    uri_format: https://www.biomodels.net/kisao/KISAO#KISAO_$1
  publications:
  - doi: 10.1038/msb.2011.77
    pmc: PMC3261705
    pubmed: '22027554'
    title: Controlled vocabularies and semantics in systems biology
    year: 2011
  synonyms:
  - biomodels.kisao
  - kisao
  uri_format: http://purl.obolibrary.org/obo/KISAO_$1
biomodels.teddy:
  aberowl:
    description: The TErminology for the Description of DYnamics (TEDDY) project aims
      to provide an ontology for dynamical behaviours, observable dynamical phenomena,
      and control elements of bio-models and biological systems in Systems Biology
      and Synthetic Biology.
    download_owl: http://aber-owl.net/media/ontologies/TEDDY/11/teddy.owl
    homepage: http://teddyontology.sourceforge.net/
    name: Terminology for the Description of Dynamics
    prefix: TEDDY
    version: rel-2014-04-24 (inferred)
  banana: TEDDY
  banana_peel: _
  biocontext:
    prefix: BIOMODELS.TEDDY
  bioportal:
    contact:
      email: biomodels-net-support@lists.sf.net
      name: BioModels.net team
    description: The TErminology for the Description of DYnamics (TEDDY) project aims
      to provide an ontology for dynamical behaviours, observable dynamical phenomena,
      and control elements of bio-models and biological systems in Systems Biology
      and Synthetic Biology.
    homepage: http://teddyontology.sourceforge.net/
    name: Terminology for the Description of Dynamics
    prefix: TEDDY
    publications:
    - http://www.nature.com/msb/journal/v7/n1/full/msb201177.html
    version: rel-2014-04-24 (inferred)
  contact:
    email: mhucka@caltech.edu
    github: mhucka
    name: Michael Hucka
    orcid: 0000-0001-9105-5960
  download_owl: http://svn.code.sf.net/p/teddyontology/code/teddy/tags/current/teddy-inferred.owl
  example: '0000066'
  fairsharing:
    abbreviation: TEDDY
    description: The TErminology for the Description of DYnamics (TEDDY) project aims
      to provide an ontology for dynamical behaviours, observable dynamical phenomena,
      and control elements of bio-models and biological systems in Systems Biology
      and Synthetic Biology.
    homepage: https://sourceforge.net/projects/teddyontology/
    name: TErminology for the Description of DYnamics
    prefix: FAIRsharing.w9jvbt
    publications:
    - doi: 10.1038/msb.2011.77
      pubmed: '22027554'
      title: Controlled vocabularies and semantics in systems biology
      year: 2011
    repository: https://github.com/combine-org/combine-specifications/blob/main/specifications/teddy.md
    subjects:
    - Systems Biology
    - Neurophysiology
    - Synthetic Biology
  mappings:
    aberowl: TEDDY
    biocontext: BIOMODELS.TEDDY
    bioportal: TEDDY
    fairsharing: FAIRsharing.w9jvbt
    miriam: biomodels.teddy
    n2t: biomodels.teddy
    ols: teddy
    prefixcommons: teddy
  miriam:
    deprecated: false
    description: The Terminology for Description of Dynamics (TEDDY) is an ontology
      for dynamical behaviours, observable dynamical phenomena, and control elements
      of bio-models and biological systems in Systems Biology and Synthetic Biology.
    homepage: http://teddyontology.sourceforge.net/
    id: '00000107'
    name: TEDDY
    namespaceEmbeddedInLui: false
    pattern: ^TEDDY_\d{7}$
    prefix: biomodels.teddy
    sampleId: TEDDY_0000066
    uri_format: http://purl.bioontology.org/ontology/TEDDY/$1
  n2t:
    description: The Terminology for Description of Dynamics (TEDDY) is an ontology
      for dynamical behaviours, observable dynamical phenomena, and control elements
      of bio-models and biological systems in Systems Biology and Synthetic Biology.
    example: TEDDY_0000066
    homepage: http://teddyontology.sourceforge.net/
    name: TEDDY through BioPortal
    namespaceEmbeddedInLui: false
    pattern: ^TEDDY_\d{7}$
    prefix: biomodels.teddy
    uri_format: http://purl.bioontology.org/ontology/TEDDY/$1
  ols:
    description: TEDDY is an ontology for dynamical behaviours, observable dynamical
      phenomena, and control elements of bio-models and biological systems in Systems
      and Synthetic Biology.
    name: Terminology for Description of Dynamics
    prefix: teddy
    uri_format: http://identifiers.org/teddy/TEDDY_$1
    version: '2014-04-24'
    version.iri: http://identifiers.org/combine.specifications/teddy.rel-2014-04-24
  pattern: ^\d+$
  prefix: biomodels.teddy
  prefixcommons:
    alt_uri_formats:
    - http://purl.org/obo/owl/TEDDY#$1
    - http://biomodels.net/teddy/TEDDY#$1
    bioportal: '1407'
    description: The Terminology for Description of Dynamics (TEDDY) is an ontology
      for dynamical behaviours, observable dynamical phenomena, and control elements
      of bio-models and biological systems in Systems Biology and Synthetic Biology.
    example: TEDDY_0000066
    homepage: http://teddyontology.sourceforge.net/
    keywords:
    - ontology
    license: http://www.ebi.ac.uk/Information/termsofuse.html
    name: Terminology for the Description of Dynamics
    pattern: ^TEDDY_\d{7}$
    prefix: teddy
    synonyms:
    - biomodels.teddy
  providers:
  - code: legacy
    description: null
    example: null
    first_party: null
    homepage: null
    name: null
    publications: null
    status: null
    uri_format: http://identifiers.org/teddy/TEDDY_$1
  publications:
  - doi: 10.1038/msb.2011.77
    pmc: PMC3261705
    pubmed: '22027554'
    title: Controlled vocabularies and semantics in systems biology
    year: 2011
  synonyms:
  - teddy
  uri_format: https://www.ebi.ac.uk/ols/ontologies/teddy/terms?iri=http://identifiers.org/teddy/TEDDY_$1
biomodels.vocabulary:
  biocontext:
    prefix: BIOMODELS.VOCABULARY
  mappings:
    biocontext: BIOMODELS.VOCABULARY
    miriam: biomodels.vocabulary
    n2t: biomodels.vocabulary
  miriam:
    deprecated: false
    description: Vocabulary used in the RDF representation of SBML models.
    homepage: http://biomodels.net/rdf/vocabulary.rdf
    id: '00000514'
    name: SBML RDF Vocabulary
    namespaceEmbeddedInLui: false
    pattern: ^[A-Za-z]+$
    prefix: biomodels.vocabulary
    sampleId: rateRule
    uri_format: http://biomodels.net/rdf/vocabulary.rdf#$1
  n2t:
    description: Vocabulary used in the RDF representation of SBML models.
    example: rateRule
    homepage: http://biomodels.net/rdf/vocabulary.rdf
    name: Vocabulary via BioModels.net
    namespaceEmbeddedInLui: false
    pattern: ^[A-Za-z]+$
    prefix: biomodels.vocabulary
    uri_format: http://biomodels.net/rdf/vocabulary.rdf#$1
  prefix: biomodels.vocabulary
bionumbers:
  biocontext:
    prefix: BIONUMBERS
  edam:
    description: Identifier of an entry from the BioNumbers database of key numbers
      and associated data in molecular biology.
    name: BioNumbers
    obsolete: false
    prefix: '2660'
  mappings:
    biocontext: BIONUMBERS
    edam: '2660'
    miriam: bionumbers
    n2t: bionumbers
    prefixcommons: bionumbers
  miriam:
    deprecated: false
    description: BioNumbers is a database of key numberical information that may be
      used in molecular biology. Along with the numbers, it contains references to
      the original literature, useful comments, and related numeric data.
    homepage: https://bionumbers.hms.harvard.edu
    id: '00000101'
    name: BioNumbers
    namespaceEmbeddedInLui: false
    pattern: ^\d+$
    prefix: bionumbers
    sampleId: '104674'
    uri_format: https://bionumbers.hms.harvard.edu/bionumber.aspx?id=$1
  n2t:
    description: BioNumbers is a database of key numberical information that may be
      used in molecular biology. Along with the numbers, it contains references to
      the original literature, useful comments, and related numeric data.
    example: '104674'
    homepage: https://bionumbers.hms.harvard.edu
    name: BioNumbers database
    namespaceEmbeddedInLui: false
    pattern: ^\d+$
    prefix: bionumbers
    uri_format: https://bionumbers.hms.harvard.edu/bionumber.aspx?id=$1
  prefix: bionumbers
  prefixcommons:
    description: BioNumbers is a database of key numberical information that may be
      used in molecular biology. Along with the numbers, it contains references to
      the original literature, useful comments, and related numeric data.
    example: '104674'
    homepage: http://www.bionumbers.hms.harvard.edu/search.aspx
    name: The Database of Useful Biological Numbers
    pattern: ^\d+$
    prefix: bionumbers
    uri_format: http://www.bionumbers.hms.harvard.edu/bionumber.aspx?s=y&id=$1&ver=1
biopixie:
  comment: This resource doesn't exist on the web anymore
  deprecated: true
  mappings:
    prefixcommons: biopixie
  prefix: biopixie
  prefixcommons:
    description: bioPIXIE is a novel system for biological data integration and visualization.
      It allows you to discover interaction networks and pathways in which your gene(s)
      (e.g. BNI1, YFL039C) of interest participate.
    example: '12'
    homepage: http://pixie.princeton.edu/pixie/
    keywords:
    - gene
    - interaction
    name: biological Process Inference from eXperimental Interaction Evidence/Microarray
      Experiment Functional Integration Technology
    pattern: ^\d+$
    prefix: biopixie
    synonyms:
    - biopixie_mefit
    uri_format: http://avis.princeton.edu/pixie/viewgraph.php?graphID=$1
  reviewer:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
bioportal:
  biocontext:
    prefix: BIOPORTAL
  contact:
    email: jgraybeal@stanford.edu
    github: null
    name: John Graybeal
    orcid: 0000-0001-6875-5360
  contact_group_email: support@bioontology.org
  example_extras:
  - SEPIO
  - pseudo
  - FBBi
  fairsharing:
    abbreviation: BioPortal
    contact:
      email: support@bioontology.org
      name: John Graybeal
      orcid: 0000-0001-6875-5360
    description: BioPortal is a library of biomedical ontologies and terminologies
      developed in Web Ontology Language (OWL), Resource Description Framework (RDF)(S),
      Open Biological and Biomedical Ontologies (OBO) format, and Protégé frames and
      Rich Release Format. BioPortal groups ontologies by domain to aid discoverability
      and allows users to browse, search and visualize the content of ontologies.
      BioPortal also provides ontology recommendation, text annotation, ontology mapping,
      and a reference index to resources like PubMed.
    homepage: http://bioportal.bioontology.org/
    name: BioPortal
    prefix: FAIRsharing.4m97ah
    publications:
    - doi: 10.1093/nar/gkr469
      pubmed_id: 21672956
      title: 'BioPortal: enhanced functionality via new Web services from the National
        Center for Biomedical Ontology to access and use ontologies in software applications.'
    repository: http://github.com/ncbo
    subjects:
    - Life Science
    - Ontology and Terminology
    twitter: bioontology
  integbio:
    description: BioPortal is a library of biomedical ontologies and terminologies
      developed in Web Ontology Language (OWL), Resource Description Framework (RDF)(S),
      Open Biological and Biomedical Ontologies (OBO) format, and Protégé frames and
      Rich Release Format. BioPortal groups ontologies by domain to aid discoverability
      and allows users to browse, search and visualize the content of ontologies.
      BioPortal also provides ontology recommendation, text annotation, ontology mapping,
      and a reference index to resources like PubMed.
    fairsharing: FAIRsharing.4m97ah
    homepage: http://bioportal.bioontology.org/
    information_keywords:
    - Ontology/Terminology/Nomenclature
    - Bibliography/Documents
    - Portal
    maintainer: Stanford Center for Biomedical Informatics Research
    name: BioPortal
    prefix: nbdc02144
    pubmeds:
    - '21672956'
    status: Active
    target_keywords:
    - Health/Disease
  mappings:
    biocontext: BIOPORTAL
    fairsharing: FAIRsharing.4m97ah
    integbio: nbdc02144
    miriam: bioportal
    n2t: bioportal
    prefixcommons: bioportal
    re3data: r3d100012344
  miriam:
    deprecated: true
    description: BioPortal is an open repository of biomedical ontologies that provides
      access via Web services and Web browsers to ontologies developed in OWL, RDF,
      OBO format and Protégé frames. BioPortal functionality includes the ability
      to browse, search and visualize ontologies.
    homepage: http://bioportal.bioontology.org/
    id: 00000187
    name: BioPortal
    namespaceEmbeddedInLui: false
    pattern: ^\d+$
    prefix: bioportal
    sampleId: '1046'
    uri_format: http://bioportal.bioontology.org/ontologies/$1
  n2t:
    description: BioPortal is an open repository of biomedical ontologies that provides
      access via Web services and Web browsers to ontologies developed in OWL, RDF,
      OBO format and Prot&#xE9;g&#xE9; frames. BioPortal functionality includes the
      ability to browse, search and visualize ontologies.
    example: '1046'
    homepage: http://bioportal.bioontology.org/
    name: BioPortal at National Center for Biomedical Ontology
    namespaceEmbeddedInLui: false
    pattern: ^\d+$
    prefix: bioportal
    uri_format: http://bioportal.bioontology.org/ontologies/$1
  pattern: ^(\d+)|(\w+)$
  prefix: bioportal
  prefixcommons:
    description: BioPortal is an open repository of biomedical ontologies that provides
      access via Web services and Web browsers to ontologies developed in OWL, RDF,
      OBO format and Protege frames. BioPortal functionality includes the ability
      to browse, search and visualize ontologies.
    example: '1046'
    homepage: http://bioportal.bioontology.org/
    keywords:
    - ontology
    name: BioPortal
    pattern: ^\d+$
    prefix: bioportal
    pubmed_ids:
    - '19483092'
    uri_format: http://bioportal.bioontology.org/ontologies/$1
  publications:
  - doi: 10.1093/nar/gkr469
    pmc: PMC3125807
    pubmed: '21672956'
    title: 'BioPortal: enhanced functionality via new Web services from the National
      Center for Biomedical Ontology to access and use ontologies in software applications'
    year: 2011
  - doi: 10.1093/nar/gkp440
    pmc: PMC2703982
    pubmed: '19483092'
    title: 'BioPortal: ontologies and integrated data resources at the click of a
      mouse'
    year: 2009
  re3data:
    description: 'BioPortal is an open repository of biomedical ontologies, a service
      that provides access to those ontologies, and a set of tools for working with
      them. BioPortal provides a wide range of such tools, either directly via the
      BioPortal web site, or using the BioPortal web service REST API. BioPortal also
      includes community features for adding notes, reviews, and even mappings to
      specific ontologies.

      BioPortal has four major product components: the web application; the API services;
      widgets, or applets, that can be installed on your own site; and a Virtual Appliance
      version that is available for download or through Amazon Web Services machine
      instance (AMI). There is also a beta release SPARQL endpoint.'
    doi: 10.17616/R3J362
    homepage: https://bioportal.bioontology.org/
    name: BioPortal
    prefix: r3d100012344
    xrefs:
      nif: 0000-23346
bioproject:
  biocontext:
    prefix: BIOPROJECT
  contact:
    email: mizrachi@ncbi.nlm.nih.gov
    github: null
    name: Ilene Karsch-Mizrachi
    orcid: 0000-0002-0289-7101
  fairsharing:
    abbreviation: BioProject
    description: A BioProject is a collection of biological data related to a single
      initiative, originating from a single organization or from a consortium. A BioProject
      record provides users a single place to find links to the diverse data types
      generated for that project. The BioProject database is a searchable collection
      of complete and incomplete (in-progress) large-scale sequencing, assembly, annotation,
      and mapping projects for cellular organisms.
    homepage: https://www.ncbi.nlm.nih.gov/bioproject/
    name: NCBI BioProject
    prefix: FAIRsharing.aqhv1y
    publications:
    - doi: 10.1093/nar/gkr1163
      pubmed_id: 22139929
      title: 'BioProject and BioSample databases at NCBI: facilitating capture and
        organization of metadata.'
    subjects:
    - Life Science
  mappings:
    biocontext: BIOPROJECT
    fairsharing: FAIRsharing.aqhv1y
    miriam: bioproject
    n2t: bioproject
    re3data: r3d100013330
    togoid: Bioproject
  miriam:
    deprecated: false
    description: BioProject provides an organizational framework to access metadata
      about research projects and the data from the projects that are deposited into
      different databases. It provides information about a project’s scope, material,
      objectives, funding source and general relevance categories.
    homepage: https://www.ncbi.nlm.nih.gov/bioproject
    id: 00000349
    name: BioProject
    namespaceEmbeddedInLui: false
    pattern: ^PRJ[DEN][A-Z]\d+$
    prefix: bioproject
    sampleId: PRJDB3
    uri_format: https://www.ncbi.nlm.nih.gov/bioproject?term=$1
  n2t:
    description: BioProject provides an organizational framework to access metadata
      about research projects and the data from the projects that are deposited into
      different databases. It provides information about a project&#x2019;s scope,
      material, objectives, funding source and general relevance categories.
    example: PRJDB3
    homepage: https://www.ncbi.nlm.nih.gov/bioproject
    name: BioProject at NCBI
    namespaceEmbeddedInLui: false
    pattern: ^PRJ[DEN][A-Z]\d+$
    prefix: bioproject
    uri_format: https://www.ncbi.nlm.nih.gov/bioproject?term=$1
  prefix: bioproject
  publications:
  - doi: 10.1093/nar/gkr1163
    pmc: PMC3245069
    pubmed: '22139929'
    title: 'BioProject and BioSample databases at NCBI: facilitating capture and organization
      of metadata'
    year: 2011
  re3data:
    description: The BioProject database is a searcheable collection of complete and
      incomplete (in-progress) large-scale molecular projects including genome sequencing
      and assembly, transcriptome, metagenomic, annotation, expression and mapping
      projects. BioProject provides a central point to link to all data associated
      with a project in the NCBI molecular and literature databases.
    doi: 10.17616/R31NJMS2
    homepage: https://www.ncbi.nlm.nih.gov/bioproject/
    name: BioProject
    prefix: r3d100013330
  togoid:
    catalog: nbdc00476
    description: BioProject is a database which collects the results of research projects
      under the umbrella of the project or initiative. The database consists of tables
      of projects, which users can search or browse to find all data outputs related
      to that project. Users can submit projects or download data via FTP.
    examples:
    - PRJDB575
    - PRJDB1880
    - PRJDB478
    - PRJDA45949
    - PRJEB6285
    - PRJEA28961
    - PRJEB2222
    - PRJNA30641
    - PRJNA68235
    - PRJNA42549
    keywords:
    - Project
    name: BioProject
    pattern: ^(?PRJ[DEN][A-Z]\d+)$
    prefix: Bioproject
    uri_format: http://identifiers.org/bioproject/$1
  uri_format: https://www.ncbi.nlm.nih.gov/bioproject/?term=$1
bioregistry:
  contact:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: The Bioregistry is integrative meta-registry of biological databases,
    ontologies, and nomenclatures that is backed by an open database.
  example: bioregistry
  fairsharing:
    abbreviation: bioregistry
    contact:
      email: cthoyt@gmail.com
      name: Charles Tapley Hoyt
      orcid: 0000-0003-4423-4370
    description: The Bioregistry is an open source, community curated registry, meta-registry,
      and compact identifier resolver.
    homepage: https://bioregistry.io
    license: CC0-1.0
    name: Bioregistry
    prefix: FAIRsharing.250a8c
    publications:
    - doi: 10.1101/2022.07.08.499378
      pubmed_id: null
      title: Unifying the Identification of Biomedical Entities with the Bioregistry
    repository: https://github.com/biopragmatics/bioregistry
    subjects:
    - Cheminformatics
    - Bioinformatics
    - Computational Biology
    - Life Science
    - Ontology and Terminology
    - Computational Chemistry
    twitter: bioregistry
  homepage: https://bioregistry.io
  mappings:
    bartoc: '18951'
    fairsharing: FAIRsharing.250a8c
    wikidata.entity: Q109302681
  mastodon: bioregistry@fosstodon.org
  name: Bioregistry
  part_of_database: bioregistry
  pattern: ^[A-Za-z_][A-Za-z0-9\.\-_]*$
  prefix: bioregistry
  publications:
  - doi: 10.1101/2022.07.08.499378
    pmc: null
    pubmed: null
    title: Unifying the Identification of Biomedical Entities with the Bioregistry
    year: 2022
  - doi: 10.1101/2022.07.08.499378
    pmc: null
    pubmed: null
    title: Unifying the Identification of Biomedical Entities with the Bioregistry
    year: null
  repository: https://github.com/biopragmatics/bioregistry
  uri_format: https://bioregistry.io/registry/$1
bioregistry.collection:
  contact:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: Manually curated collections of resources stored in the bioregistry
  example: '0000001'
  homepage: https://bioregistry.io/collection
  keywords:
  - registry
  name: Bioregistry Collections
  part_of_database: bioregistry
  pattern: ^\d{7}$
  prefix: bioregistry.collection
  uri_format: https://bioregistry.io/collection/$1
bioregistry.registry:
  contact:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: The Bioregistry's meta-registry
  example: miriam
  homepage: https://bioregistry.io/metaregistry/
  keywords:
  - data integration
  - data science
  - metaregistry
  - registry
  name: Bioregistry Metaregistry
  part_of_database: bioregistry
  prefix: bioregistry.registry
  uri_format: https://bioregistry.io/metaregistry/$1
bioregistry.schema:
  contact:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: Schema for the export of the Bioregistry as RDF
  example: '0000001'
  homepage: https://bioregistry.io/schema
  keywords:
  - registry
  name: Bioregistry Schema
  part_of_database: bioregistry
  pattern: ^\d{7}$
  prefix: bioregistry.schema
  uri_format: https://bioregistry.io/schema/#$1
biorxiv:
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: The bioRxiv is a preprint server for biology
  example: 2022.07.08.499378
  example_extras:
  - 000091
  - 000091v1
  - 2022.07.08.499378v2
  go:
    homepage: https://www.biorxiv.org/
    name: bioRxiv
    prefix: bioRxiv
    synonyms:
    - BIORXIV
    uri_format: https://www.biorxiv.org/content/$1
  homepage: https://biorxiv.org
  keywords:
  - preprints
  - publishing
  mappings:
    go: bioRxiv
    wikidata: P3951
  name: bioRxiv
  pattern: ^(\d{4}\.\d{2}\.\d{2}\.)?\d{6,8}(v\d{1,3})?$
  prefix: biorxiv
  providers:
  - code: scholia
    description: Scholia is a service that creates visual scholarly profiles for topic,
      people, organizations, species, chemicals, etc using bibliographic and other
      information in Wikidata.
    example: null
    first_party: null
    homepage: https://scholia.toolforge.org/
    name: Scholia
    publications: null
    status: null
    uri_format: https://scholia.toolforge.org/biorxiv/$1
  uri_format: https://www.biorxiv.org/content/10.1101/$1
  wikidata:
    description: identifier of a document in BioRxiv, a preprint repository for the
      biological sciences launched in November 2013
    example:
    - 028522
    - 2021.09.10.459803
    homepage: http://biorxiv.org/search/limit_from:2010-01-01%20limit_to:2017-02-16%20numresults:10%20sort:relevance-rank%20format_result:standard
    name: BioRxiv ID
    pattern: ^(\d{4}\.\d{2}\.\d{2}\.)?\d{6}$
    prefix: P3951
    uri_format: https://doi.org/10.1101/$1
    uri_format_rdf: http://dx.doi.org/10.1101/$1
biosample:
  biocontext:
    prefix: BIOSAMPLE
  cellosaurus:
    category: Biological sample resources
    homepage: https://www.ebi.ac.uk/biosamples/
    name: BioSamples database
    prefix: BioSamples
    uri_format: https://www.ebi.ac.uk/biosamples/samples/$1
  contact:
    email: mizrachi@ncbi.nlm.nih.gov
    github: null
    name: Ilene Karsch-Mizrachi
    orcid: 0000-0002-0289-7101
  fairsharing:
    abbreviation: BioSample
    description: The NCBI BioSample database stores submitter-supplied descriptive
      information, or metadata, about the biological materials from which data stored
      in NCBI’s primary data archives are derived. NCBI’s archives host data from
      diverse types of samples from any species, so the BioSample database is similarly
      diverse; typical examples of a BioSample include a cell line, a primary tissue
      biopsy, an individual organism or an environmental isolate. The BioSample database
      promotes the use of structured and consistent attribute names and values that
      describe what the samples are as well as information about their provenance,
      where appropriate.
    homepage: https://www.ncbi.nlm.nih.gov/biosample
    name: NCBI BioSample
    prefix: FAIRsharing.qr6pqk
    publications:
    - doi: 10.1093/nar/gkr1163
      pubmed_id: 22139929
      title: 'BioProject and BioSample databases at NCBI: facilitating capture and
        organization of metadata.'
    subjects:
    - Biology
  mappings:
    biocontext: BIOSAMPLE
    cellosaurus: BioSamples
    fairsharing: FAIRsharing.qr6pqk
    miriam: biosample
    n2t: biosample
    re3data: r3d100012828
    rrid: SAMN
    togoid: Biosample
  miriam:
    deprecated: false
    description: The BioSample Database stores information about biological samples
      used in molecular experiments, such as sequencing, gene expression or proteomics.
      It includes reference samples, such as cell lines, which are repeatedly used
      in experiments. Accession numbers for the reference samples will be exchanged
      with a similar database at NCBI, and DDBJ (Japan). Record access may be affected
      due to different release cycles and inter-institutional synchronisation.
    homepage: https://www.ebi.ac.uk/biosamples/
    id: '00000350'
    name: BioSample
    namespaceEmbeddedInLui: false
    pattern: ^SAM[NED](\w)?\d+$
    prefix: biosample
    providers:
    - code: ncbi
      description: BioSample at NCBI
      homepage: http://www.ncbi.nlm.nih.gov/biosample
      name: BioSample at NCBI
      uri_format: http://www.ncbi.nlm.nih.gov/biosample?term=$1
    - code: ddbj
      description: BioSample at DNA Data Bank of Japan
      homepage: https://www.ddbj.nig.ac.jp/biosample
      name: BioSample at DNA Data Bank of Japan
      uri_format: https://ddbj.nig.ac.jp/search/entry/biosample/$1
    sampleId: SAMEA2397676
    uri_format: https://www.ebi.ac.uk/biosamples/sample/$1
  n2t:
    description: The BioSample Database stores information about biological samples
      used in molecular experiments, such as sequencing, gene expression or proteomics.
      It includes reference samples, such as cell lines, which are repeatedly used
      in experiments. Accession numbers for the reference samples will be exchanged
      with a similar database at NCBI, and DDBJ (Japan). Record access may be affected
      due to different release cycles and inter-institutional synchronisation.
    example: SAMEA2397676
    homepage: https://www.ebi.ac.uk/biosamples/
    name: BioSamples Database at EBI
    namespaceEmbeddedInLui: false
    pattern: ^SAM[NED](\w)?\d+$
    prefix: biosample
    uri_format: https://www.ebi.ac.uk/biosamples/sample/$1
  prefix: biosample
  publications:
  - doi: 10.1093/nar/gkr1163
    pmc: PMC3245069
    pubmed: '22139929'
    title: 'BioProject and BioSample databases at NCBI: facilitating capture and organization
      of metadata'
    year: 2011
  re3data:
    description: The BioSample database contains descriptions of biological source
      materials used in experimental assays.
    doi: 10.17616/R31NJME4
    homepage: https://www.ncbi.nlm.nih.gov/biosample/
    name: BioSample
    prefix: r3d100012828
    synonyms:
    - BioSample at the NCBI
  rrid:
    abbreviation: BioSample
    homepage: http://www.ncbi.nlm.nih.gov/biosample
    keywords:
    - biomaterial
    - cell
    - cell line
    - dna
    - gold standard
    - rna
    - stem cell
    name: NCBI BioSample
    prefix: SAMN
    pubmeds:
    - '22139929'
    scr: 004854
  synonyms:
  - biosamples
  togoid:
    catalog: nbdc01983
    examples:
    - SAMD00003683
    - SAMD00006315
    - SAMD00003741
    - SAMD00011226
    - SAMN13091859
    - SAMN05877962
    - SAMN05877838
    - SAMEA104232303
    - SAMEA4760552
    - SAMEA1572228
    keywords:
    - Sample
    name: BioSample
    pattern: ^(?SAM[NED]\w?\d+)$
    prefix: Biosample
    uri_format: http://identifiers.org/biosample/$1
bioschemas:
  biolink:
    is_identifiers: false
    is_obo: false
    prefix: bioschemas
    uri_format: https://bioschemas.org/$1
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: Bioschemas aims to improve the Findability on the Web of life sciences
    resources such as datasets, software, and training materials. It does this by
    encouraging people in the life sciences to use Schema.org markup in their websites
    so that they are indexable by search engines and other services. Bioschemas encourages
    the consistent use of markup to ease the consumption of the contained markup across
    many sites. This structured information then makes it easier to discover, collate,
    and analyse distributed resources. [from BioSchemas.org]
  download_rdf: https://bioschemas.org/types/bioschemas_types.ttl
  example: Dataset
  homepage: https://bioschemas.org
  mappings:
    biolink: bioschemas
  name: BioSchemas
  prefix: bioschemas
  providers:
  - code: draft
    description: BioSchemas makes a difference between its draft and released terms
      by putting them in different namespaces. This causes problems when consuming
      it, so this URI format maps them all into a unified semantic space
    example: null
    first_party: null
    homepage: https://bioschemas.org
    name: BioSchemas Draft
    publications: null
    status: null
    uri_format: https://bioschemas.org/draft_terms/$1
  - code: w3id
    description: null
    example: null
    first_party: null
    homepage: null
    name: null
    publications: null
    status: null
    uri_format: https://w3id.org/bioschemas/terms/$1
  - code: term
    description: null
    example: null
    first_party: null
    homepage: null
    name: null
    publications: null
    status: null
    uri_format: https://bioschemas.org/terms/$1
  - code: biothings
    description: null
    example: null
    first_party: null
    homepage: null
    name: null
    publications: null
    status: null
    uri_format: https://discovery.biothings.io/view/bioschemastypes/$1
  repository: https://github.com/BioSchemas/specifications
  synonyms:
  - bioschema
  - bioschemas_draft
  twitter: bioschemas
  uri_format: https://bioschemas.org/profiles/$1
biosimulations:
  mappings:
    miriam: biosimulations
    re3data: r3d100013361
  miriam:
    deprecated: false
    description: BioSimulations is an open repository of simulation projects, including
      simulation experiments, their results, and data visualizations of their results.
      BioSimulations supports a broad range of model languages, modeling frameworks,
      simulation algorithms, and simulation software tools.
    homepage: https://icahn.mssm.edu/
    id: 00000880
    name: biosimulations
    namespaceEmbeddedInLui: false
    pattern: ^[a-zA-Z0-9_-]{3,}$
    prefix: biosimulations
    sampleId: Yeast-cell-cycle-Irons-J-Theor-Biol-2009
    uri_format: https://biosimulations.org/projects/$1
  prefix: biosimulations
  re3data:
    description: BioSimulations is a web application for sharing and re-using biomodels,
      simulations, and visualizations of simulations results. BioSimulations supports
      a wide range of modeling frameworks (e.g., kinetic, constraint-based, and logical
      modeling), model formats (e.g., BNGL, CellML, SBML), and simulation tools (e.g.,
      COPASI, libRoadRunner/tellurium, NFSim, VCell). BioSimulations aims to help
      researchers discover published models that might be useful for their research
      and quickly try them via a simple web-based interface.
    doi: 10.17616/R31NJMSX
    homepage: https://biosimulations.org/
    name: BioSimulations
    prefix: r3d100013361
    xrefs:
      fairsharing.legacy: '3208'
biosimulators:
  fairsharing:
    abbreviation: BioSimulators
    contact:
      email: karr@mssm.edu
      name: Jonathan Karr
      orcid: 0000-0002-2605-5080
    description: BioSimulators is a registry of containerized biosimulation tools
      that provide consistent command-line interfaces. The BioSimulations web application
      helps investigators browse this registry to find simulation tools that have
      the capabilities (supported modeling frameworks, simulation algorithms, and
      modeling formats) needed for specific modeling projects.
    homepage: https://biosimulators.org
    name: BioSimulators
    prefix: FAIRsharing.pwEima
    publications: []
    repository: https://github.com/biosimulators/Biosimulators/issues/new/choose
    subjects:
    - Computational Biology
    - Systems Biology
  mappings:
    fairsharing: FAIRsharing.pwEima
    miriam: biosimulators
    re3data: r3d100013432
  miriam:
    deprecated: false
    description: BioSimulators is a registry of containerized simulation tools that
      support a common interface. The containers in BioSimulators support a range
      of modeling frameworks (e.g., logical, constraint-based, continuous kinetic,
      discrete kinetic), simulation algorithms (e.g., CVODE, FBA, SSA), and modeling
      formats (e.g., BGNL, SBML, SED-ML).
    homepage: https://biosimulators.org/
    id: '00000767'
    name: BioSimulators
    namespaceEmbeddedInLui: false
    pattern: ^[a-zA-Z0-9-_]+$
    prefix: biosimulators
    sampleId: vcell
    uri_format: https://biosimulators.org/simulators/$1
  prefix: biosimulators
  re3data:
    description: BioSimulators is a registry of containerized biosimulation tools
      that provide consistent command-line interfaces. The BioSimulations web application
      helps investigators browse this registry to find simulation tools that have
      the capabilities (supported modeling frameworks, simulation algorithms, and
      modeling formats) needed for specific modeling projects.
    doi: 10.17616/R31NJMUW
    homepage: https://biosimulators.org
    name: BioSimulators
    prefix: r3d100013432
biostudies:
  contact:
    email: ugis@ebi.ac.uk
    github: null
    name: Ugis Sarkans
    orcid: 0000-0001-9227-8488
  fairsharing:
    abbreviation: BioStudies
    description: The BioStudies database holds descriptions of biological studies,
      links to data from these studies in other databases at EMBL-EBI or outside,
      as well as data that do not fit in the structured archives at EMBL-EBI. The
      database can accept a wide range of types of studies described via a simple
      format. It also enables manuscript authors to submit supplementary information
      and link to it from the publication.
    homepage: https://www.ebi.ac.uk/biostudies/
    name: BioStudies
    prefix: FAIRsharing.mtjvme
    publications:
    - doi: 10.1093/nar/gkx965
      pubmed_id: 29069414
      title: The BioStudies database-one stop shop for all data supporting a life
        sciences study.
    - doi: 10.15252/msb.20156658
      pubmed_id: 26700850
      title: The BioStudies database.
    subjects:
    - Life Science
    - Biomedical Science
  integbio:
    description: The BioStudies database holds descriptions of biological studies,
      links to data from these studies in other databases at EMBL-EBI or outside,
      as well as data that do not fit in the structured archives at EMBL-EBI. The
      database can accept a wide range of types of studies described via a simple
      format. It also enables manuscript authors to submit supplementary information
      and link to it from the publication.
    fairsharing: FAIRsharing.mtjvme
    homepage: https://www.ebi.ac.uk/biostudies/
    information_keywords:
    - Portal
    maintainer: European Commission FP7||EMBL (European Molecular Biology Laboratory)
    name: BioStudies
    prefix: nbdc02279
    pubmeds:
    - '26700850'
    - '29069414'
    status: Active
  mappings:
    fairsharing: FAIRsharing.mtjvme
    integbio: nbdc02279
    miriam: biostudies
    n2t: biostudies
    re3data: r3d100012627
  miriam:
    deprecated: false
    description: The BioStudies database holds descriptions of biological studies,
      links to data from these studies in other databases at EMBL-EBI or outside,
      as well as data that do not fit in the structured archives at EMBL-EBI. The
      database can accept a wide range of types of studies described via a simple
      format. It also enables manuscript authors to submit supplementary information
      and link to it from the publication.
    homepage: https://www.ebi.ac.uk/biostudies/
    id: 00000694
    name: BioStudies database
    namespaceEmbeddedInLui: false
    pattern: ^S-[A-Z]{4}[\-\_A-Z\d]+$
    prefix: biostudies
    sampleId: S-EPMC6266652
    uri_format: https://www.ebi.ac.uk/biostudies/studies/$1
  n2t:
    description: The BioStudies database holds descriptions of biological studies,
      links to data from these studies in other databases at EMBL-EBI or outside,
      as well as data that do not fit in the structured archives at EMBL-EBI. The
      database can accept a wide range of types of studies described via a simple
      format. It also enables manuscript authors to submit supplementary information
      and link to it from the publication.
    example: S-EPMC6266652
    homepage: https://www.ebi.ac.uk/biostudies/
    name: BioStudies database
    namespaceEmbeddedInLui: false
    pattern: ^S-[A-Z]{4}[A-Z\d\-]+$
    prefix: biostudies
    uri_format: https://www.ebi.ac.uk/biostudies/studies/$1
  prefix: biostudies
  publications:
  - doi: 10.1093/nar/gkx965
    pmc: PMC5753238
    pubmed: '29069414'
    title: The BioStudies database-one stop shop for all data supporting a life sciences
      study
    year: 2018
  - doi: 10.15252/msb.20156658
    pmc: PMC4704487
    pubmed: '26700850'
    title: The BioStudies database
    year: 2015
  - doi: 10.1093/nar/gkx965
    pmc: null
    pubmed: null
    title: The BioStudies database-one stop shop for all data supporting a life sciences
      study.
    year: null
  - doi: 10.15252/msb.20156658
    pmc: null
    pubmed: null
    title: The BioStudies database.
    year: null
  - doi: 10.1093/nar/gkx965
    pmc: null
    pubmed: null
    title: The BioStudies database-one stop shop for all data supporting a life sciences
      study.
    year: null
  - doi: 10.15252/msb.20156658
    pmc: null
    pubmed: null
    title: The BioStudies database.
    year: null
  - doi: 10.1093/nar/gkx965
    pmc: null
    pubmed: null
    title: The BioStudies database-one stop shop for all data supporting a life sciences
      study.
    year: null
  - doi: 10.15252/msb.20156658
    pmc: null
    pubmed: null
    title: The BioStudies database.
    year: null
  re3data:
    description: The BioStudies database holds descriptions of biological studies,
      links to data from these studies in other databases at EMBL-EBI or outside,
      as well as data that do not fit in the structured archives at EMBL-EBI. The
      database accepts submissions via an online tool, or in a simple tab-delimited
      format. It also enables authors to submit supplementary information and link
      to it from the publication.
    doi: 10.17616/R3CF7B
    homepage: https://www.ebi.ac.uk/biostudies/
    name: BioStudies
    prefix: r3d100012627
biosystems:
  biocontext:
    prefix: BIOSYSTEMS
  contact:
    email: lewis.geer@nih.gov
    github: null
    name: Aron Marchler-Bauer
    orcid: 0000-0003-1516-0712
  contributor_extras:
  - email: egon.willighagen@gmail.com
    github: egonw
    name: Egon Willighagen
    orcid: 0000-0001-7542-0286
  fairsharing:
    abbreviation: BioSystems
    description: The NCBI BioSystems database centralizes and cross-links existing
      biological systems databases, increasing their utility and target audience by
      integrating their pathways and systems into NCBI resources. The resource provides
      categorical information on genes, proteins and small molecules of biosystems.
    homepage: https://www.ncbi.nlm.nih.gov/biosystems/
    license: http://opendatacommons.org/licenses/pddl/1.0
    name: NCBI BioSystems Database
    prefix: FAIRsharing.w2eeqr
    publications:
    - doi: 10.1093/nar/gkp858
      pubmed_id: 19854944
      title: The NCBI BioSystems database.
    subjects:
    - Biology
    - Systems Biology
  homepage: https://www.ncbi.nlm.nih.gov/Structure/biosystems/docs/biosystems_about.html
  integbio:
    description: This database is a collection of metabolic and signaling pathways
      in organisms, as well as interaction sets between biological molecules associated
      with disease and other biological processes. Each entry contains information
      including pathway maps, relevant citations, genes, proteins sequences, and data
      on compounds.
    fairsharing: biodbcore-000430
    homepage: http://www.ncbi.nlm.nih.gov/biosystems/
    information_keywords:
    - Interaction/Pathway
    - Image/Movie
    - Bibliography/Documents
    maintainer: NCBI (National Center for Biotechnology Information)
    name: BioSystems
    prefix: nbdc00379
    pubmeds:
    - '19854944'
    target_keywords:
    - Protein
    - Health/Disease
    - Metabolite
    - Cell/Organelle
  mappings:
    biocontext: BIOSYSTEMS
    fairsharing: FAIRsharing.w2eeqr
    integbio: nbdc00379
    miriam: biosystems
    n2t: biosystems
    prefixcommons: biosystems
    re3data: r3d100011033
  miriam:
    deprecated: true
    description: The NCBI BioSystems database centralizes and cross-links existing
      biological systems databases, increasing their utility and target audience by
      integrating their pathways and systems into NCBI resources.
    homepage: https://www.ncbi.nlm.nih.gov/biosystems/
    id: 00000097
    name: BioSystems
    namespaceEmbeddedInLui: false
    pattern: ^\d+$
    prefix: biosystems
    sampleId: '001'
    uri_format: https://www.ncbi.nlm.nih.gov/biosystems/$1
  n2t:
    description: The NCBI BioSystems database centralizes and cross-links existing
      biological systems databases, increasing their utility and target audience by
      integrating their pathways and systems into NCBI resources.
    example: '001'
    homepage: https://www.ncbi.nlm.nih.gov/biosystems/
    name: BioSystems database at NCBI
    namespaceEmbeddedInLui: false
    pattern: ^\d+$
    prefix: biosystems
    uri_format: https://www.ncbi.nlm.nih.gov/biosystems/$1
  prefix: biosystems
  prefixcommons:
    description: The NCBI BioSystems database centralizes and cross-links existing
      biological systems databases, increasing their utility and target audience by
      integrating their pathways and systems into NCBI resources.
    example: '1'
    homepage: http://www.ncbi.nlm.nih.gov/biosystems/
    keywords:
    - molecules
    - pathways
    license: http://www.nlm.nih.gov/copyright.html
    name: BioSystems
    pattern: ^\d+$
    prefix: biosystems
    pubmed_ids:
    - '19854944'
    synonyms:
    - bsid
    uri_format: http://www.ncbi.nlm.nih.gov/biosystems/$1
  publications:
  - doi: 10.1093/nar/gkp858
    pmc: PMC2808896
    pubmed: '19854944'
    title: The NCBI BioSystems database
    year: 2009
  re3data:
    description: "<<<!!!<<<  The NCBI BioSystems Database will be retired in March\
      \ 2022. >>>!!!>>>\nThis retirement includes the representation of BioSystems\
      \ records in the NCBI Entrez system and viewers of BioSystems content. \nNCBI\
      \ now provides metabolic pathway and other biosystems data through the regularly\
      \ updated PubChem Pathways resource (https://pubchemdocs.ncbi.nlm.nih.gov/pathways)\
      \ that offers a fresh, extended, and more modern interface."
    doi: 10.17616/R31K80
    homepage: https://www.ncbi.nlm.nih.gov/biosystems/
    name: NCBI BioSystems Database
    prefix: r3d100011033
    synonyms:
    - NCBI BioSystems
biotools:
  biocontext:
    prefix: BIOTOOLS
  contact:
    email: haiiu@dtu.dk
    github: hansioan
    name: Hans Ienasescu
    orcid: 0000-0001-9727-2544
  description: BioTools is a registry of databases and software with tools, services,
    and workflows for biological and biomedical research.
  example: bioregistry
  fairsharing:
    abbreviation: bio.tools
    description: bio.tools is a registry of information about bioinformatics software
      and data services. It was created to help researchers in biological and biomedical
      science to find and use such resources.
    homepage: https://bio.tools/
    license: CC-BY-4.0
    name: bio.tools
    prefix: FAIRsharing.63520c
    publications:
    - doi: 10.1093/nar/gkv1116
      pubmed_id: 26538599
      title: 'Tools and data services registry: a community effort to document bioinformatics
        resources.'
    repository: http://github.com/bio-tools/biotoolsregistry/
    subjects:
    - Bioinformatics
    - Biomedical Science
    - Biology
  mappings:
    biocontext: BIOTOOLS
    fairsharing: FAIRsharing.63520c
    miriam: biotools
    n2t: biotools
    re3data: r3d100013668
  miriam:
    deprecated: false
    description: Tool and data services registry.
    homepage: https://bio.tools/
    id: '00000616'
    name: BioTools
    namespaceEmbeddedInLui: false
    pattern: ^[-A-Za-z0-9\_]*$
    prefix: biotools
    sampleId: uniprotkb
    uri_format: https://bio.tools/$1
  n2t:
    description: Tool and data services registry.
    example: uniprotkb
    homepage: https://bio.tools/
    name: BioTools
    namespaceEmbeddedInLui: false
    pattern: ^[A-Za-z0-9\_]*$
    prefix: biotools
    uri_format: https://bio.tools/$1
  pattern: ^[-A-Za-z0-9\_]*$
  prefix: biotools
  publications:
  - doi: 10.1093/nar/gkv1116
    pmc: PMC4702812
    pubmed: '26538599'
    title: 'Tools and data services registry: a community effort to document bioinformatics
      resources'
    year: 2015
  - doi: 10.1093/nar/gkv1116
    pmc: null
    pubmed: null
    title: 'Tools and data services registry: a community effort to document bioinformatics
      resources.'
    year: null
  re3data:
    description: bio.tools is a software registry for bioinformatics and the life
      sciences.
    doi: 10.17616/R31NJN1G
    homepage: https://bio.tools
    license: CC
    name: bio.tools
    prefix: r3d100013668
biotop:
  contact:
    email: stefan.schulz@medunigraz.at
    github: steschu63
    name: Stefan Schulz
    orcid: 0000-0001-7222-3287
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: Upper-Level ontology for Biology and Medicine. Compatible with BFO,
    DOLCE, and the UMLS Semantic Network
  download_owl: https://raw.githubusercontent.com/BioTopOntology/biotop/master/biotop.owl
  example: attachedTo
  github_request_issue: 1312
  homepage: http://purl.org/biotop
  license: CC-BY-3.0
  lov:
    description: Upper-Level ontology for Biology and Medicine. Compatible with BFO,
      DOLCE, and the UMLS Semantic Network
    homepage: http://purl.org/biotop
    keywords:
    - Biology
    modified: '2012-04-24'
    name: BioTop
    prefix: biotop
    uri_prefix: http://purl.org/biotop/biotop.owl#$1
  mappings:
    lov: biotop
  name: BioTop
  prefix: biotop
  publications:
  - doi: 10.1093/bioinformatics/btp194
    pmc: PMC2687948
    pubmed: '19478019'
    title: 'Alignment of the UMLS semantic network with BioTop: methodology and assessment'
    year: 2009
  - doi: 10.1093/bioinformatics/btn158
    pmc: PMC2718636
    pubmed: '18586729'
    title: The ontology of biological taxa
    year: 2008
  repository: https://github.com/BioTopOntology/biotop
  uri_format: http://purl.org/biotop/biotop.owl#$1
biozil:
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: Redistributor of bilogics and biomedical supplies
  example: ls-c35719-120
  homepage: https://www.biozol.de/en
  keywords:
  - biologics
  - life sciences
  - vendor
  name: BIOZIL
  prefix: biozil
  uri_format: https://www.biozol.de/en/product/$1
birnlex:
  aberowl:
    description: The BIRN Project lexicon will provide entities for data and database
      annotation for the BIRN project, covering anatomy, disease, data collection,
      project management and experimental design.
    download_owl: http://aber-owl.net/media/ontologies/BIRNLEX/1/birnlex.owl
    homepage: http://xwiki.nbirn.net:8080/xwiki/bin/view/%20BIRN-OTF-Public/Home
    name: Biomedical Informatics Research Network Project Lexicon
    prefix: BIRNLEX
    version: 1.3.1
  bioportal:
    contact:
      email: wbug@ncmir.ucsd.edu
      name: William Bug
    description: The BIRN Project lexicon will provide entities for data and database
      annotation for the BIRN project, covering anatomy, disease, data collection,
      project management and experimental design.
    homepage: http://xwiki.nbirn.net:8080/xwiki/bin/view/%20BIRN-OTF-Public/Home
    name: Biomedical Informatics Research Network Project Lexicon
    prefix: BIRNLEX
    version: 1.3.1
  comment: Part of the NeuroLex namespace now
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: The BIRN Project lexicon will provide entities for data and database
    annotation for the BIRN project, covering anatomy, disease, data collection, project
    management and experimental design.
  example: '2023'
  fairsharing:
    abbreviation: BIRNLEX
    description: 'This resource is no longer available because its underlying source
      material is not in scope for FAIRsharing.Records previously linked: [1032, 333]. '
    domains:
    - study design
    - disease
    homepage: http://xwiki.nbirn.net:8080/xwiki/bin/view/%20BIRN-OTF-Public/Home
    name: Biomedical Informatics Research Network Project Lexicon
    prefix: FAIRsharing.jedbbt
    subjects:
    - Anatomy
    - Biomedical Science
  homepage: https://bioportal.bioontology.org/ontologies/BIRNLEX
  mappings:
    aberowl: BIRNLEX
    bioportal: BIRNLEX
    fairsharing: FAIRsharing.jedbbt
  name: Biomedical Informatics Research Network Lexicon
  pattern: ^\d+$
  prefix: birnlex
  providers:
  - code: bioportal.purl
    description: Pseudo-BioPortal PURL assigned to BirnLex
    example: null
    first_party: null
    homepage: http://bioontology.org/projects/ontologies/birnlex
    name: BioPortal
    publications: null
    status: null
    uri_format: http://bioontology.org/projects/ontologies/birnlex#$1
  uri_format: http://uri.neuinfo.org/nif/nifstd/birnlex_$1
biro:
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: An ontology meant to define bibliographic records, bibliographic references,
    and their compilation into bibliographic collections and bibliographic lists,
    respectively.
  example: BibliographicRecord
  fairsharing:
    abbreviation: BiRO
    contact:
      email: silvio.peroni@unibo.it
      name: Silvio Peroni
      orcid: 0000-0003-0530-4305
    description: 'the Bibliographic Reference Ontology (BiRO) is an ontology meant
      to define bibliographic records, bibliographic references, and their compilation
      into bibliographic collections and bibliographic lists, respectively.


      '
    homepage: http://www.sparontologies.net/ontologies/biro
    license: CC-BY-4.0
    name: 'Bibliographic Reference Ontology '
    prefix: FAIRsharing.99da5f
    repository: https://github.com/sparontologies/biro
    subjects:
    - Subject Agnostic
    twitter: sparontologies
  homepage: http://www.sparontologies.net/ontologies/biro
  lov:
    description: BiRO, the Bibliographic Reference Ontology, is an ontology structured
      according to the FRBR model to define bibliographic records (as subclasses of
      frbr:Work) and bibliographic references (as subclasses of frbr:Expression),
      and their compilations into bibliographic collections such as library catalogues,
      and into bibliographic lists such as reference lists in journal articles, respectively.
    homepage: http://purl.org/spar/biro
    keywords:
    - SPAR
    modified: '2013-05-11'
    name: The Bibliographic Reference Ontology
    prefix: biro
    uri_prefix: http://purl.org/spar/biro/$1
  mappings:
    fairsharing: FAIRsharing.99da5f
    lov: biro
  name: Bibliographic Reference Ontology
  preferred_prefix: BiRO
  prefix: biro
  repository: https://github.com/sparontologies/biro
  uri_format: http://purl.org/spar/biro/$1
bitbucket:
  fairsharing:
    abbreviation: Bitbucket
    description: Bitbucket is a Git-based source code repository hosting service owned
      by Atlassian. It provides a number of different access levels, from free through
      to premium paid services. Users can create public or private repositories, the
      latter of which is restricted to 5 users under the free plan.
    homepage: https://bitbucket.org/
    name: Bitbucket
    prefix: FAIRsharing.fc3431
    publications: []
    subjects:
    - Knowledge and Information Systems
    - Subject Agnostic
    - Software Engineering
  mappings:
    fairsharing: FAIRsharing.fc3431
    miriam: bitbucket
    re3data: r3d100013478
  miriam:
    deprecated: false
    description: Bitbucket is a Git-based source code repository hosting service owned
      by Atlassian.
    homepage: https://www.atlassian.com/
    id: 00000899
    name: Bitbucket
    namespaceEmbeddedInLui: false
    pattern: ^[0-9A-Za-z-_\.]+/[0-9A-Za-z-_\.]+$
    prefix: bitbucket
    sampleId: andreadega/systems-biology-compiler
    uri_format: https://bitbucket.org/$1
  prefix: bitbucket
  re3data:
    description: Bitbucket is a web-based version control repository hosting service
      owned by Atlassian, for source code and development projects that use either
      Mercurial or Git revision control systems.
    doi: 10.17616/R31NJMW6
    homepage: https://bitbucket.org/
    name: Bitbucket
    prefix: r3d100013478
    synonyms:
    - Atlassian Bitbucket
bitterdb.cpd:
  biocontext:
    prefix: BITTERDB.CPD
  mappings:
    biocontext: BITTERDB.CPD
    miriam: bitterdb.cpd
    n2t: bitterdb.cpd
  miriam:
    deprecated: false
    description: BitterDB is a database of compounds reported to taste bitter to humans.
      The compounds can be searched by name, chemical structure, similarity to other
      bitter compounds, association with a particular human bitter taste receptor,
      and so on. The database also contains information on mutations in bitter taste
      receptors that were shown to influence receptor activation by bitter compounds.
      The aim of BitterDB is to facilitate studying the chemical features associated
      with bitterness. This collection references compounds.
    homepage: http://bitterdb.agri.huji.ac.il/dbbitter.php
    id: 00000348
    name: BitterDB Compound
    namespaceEmbeddedInLui: false
    pattern: ^\d+$
    prefix: bitterdb.cpd
    sampleId: '46'
    uri_format: http://bitterdb.agri.huji.ac.il/bitterdb/compound.php?id=$1
  n2t:
    description: BitterDB is a database of compounds reported to taste bitter to humans.
      The compounds can be searched by name, chemical structure, similarity to other
      bitter compounds, association with a particular human bitter taste receptor,
      and so on. The database also contains information on mutations in bitter taste
      receptors that were shown to influence receptor activation by bitter compounds.
      The aim of BitterDB is to facilitate studying the chemical features associated
      with bitterness. This collection references compounds.
    example: '46'
    homepage: http://bitterdb.agri.huji.ac.il/dbbitter.php
    name: BitterDB Compound at The Hebrew University of Jerusalem
    namespaceEmbeddedInLui: false
    pattern: ^\d+$
    prefix: bitterdb.cpd
    uri_format: http://bitterdb.agri.huji.ac.il/bitterdb/compound.php?id=$1
  prefix: bitterdb.cpd
bitterdb.rec:
  biocontext:
    prefix: BITTERDB.REC
  mappings:
    biocontext: BITTERDB.REC
    miriam: bitterdb.rec
    n2t: bitterdb.rec
  miriam:
    deprecated: false
    description: BitterDB is a database of compounds reported to taste bitter to humans.
      The compounds can be searched by name, chemical structure, similarity to other
      bitter compounds, association with a particular human bitter taste receptor,
      and so on. The database also contains information on mutations in bitter taste
      receptors that were shown to influence receptor activation by bitter compounds.
      The aim of BitterDB is to facilitate studying the chemical features associated
      with bitterness. This collection references receptors.
    homepage: http://bitterdb.agri.huji.ac.il/dbbitter.php
    id: '00000347'
    name: BitterDB Receptor
    namespaceEmbeddedInLui: false
    pattern: ^\d+$
    prefix: bitterdb.rec
    sampleId: '1'
    uri_format: http://bitterdb.agri.huji.ac.il/Receptor.php?id=$1
  n2t:
    description: BitterDB is a database of compounds reported to taste bitter to humans.
      The compounds can be searched by name, chemical structure, similarity to other
      bitter compounds, association with a particular human bitter taste receptor,
      and so on. The database also contains information on mutations in bitter taste
      receptors that were shown to influence receptor activation by bitter compounds.
      The aim of BitterDB is to facilitate studying the chemical features associated
      with bitterness. This collection references receptors.
    example: '1'
    homepage: http://bitterdb.agri.huji.ac.il/dbbitter.php
    name: BitterDB Receptor at The Hebrew University of Jerusalem
    namespaceEmbeddedInLui: false
    pattern: ^\d+$
    prefix: bitterdb.rec
    uri_format: http://bitterdb.agri.huji.ac.il/Receptor.php?id=$1
  prefix: bitterdb.rec
bko:
  aberowl:
    description: The BricKs Ontology (BKO) provides Systems Biology Graphical Notation
      representations of recurring concepts in molecular networks. These representations,
      called bricks, are associated in the ontology with terms describing the concepts.
      Part of these terms are borrowed from the Gene Ontology and the Systems Biology
      Ontology. The bricks can be used for both the template-based construction of
      molecular networks maps as well as for their annotation.
    download_owl: http://aber-owl.net/media/ontologies/BKO/1/bko.owl
    homepage: http://sbgnbricks.org
    name: Bricks ontology
    prefix: BKO
    version: 13:07:2018 10:45
  bioportal:
    contact:
      email: adrienrougny@gmail.com
      name: Adrien Rougny
    description: The BricKs Ontology (BKO) provides Systems Biology Graphical Notation
      representations of recurring concepts in molecular networks. These representations,
      called bricks, are associated in the ontology with terms describing the concepts.
      Part of these terms are borrowed from the Gene Ontology and the Systems Biology
      Ontology. The bricks can be used for both the template-based construction of
      molecular networks maps as well as for their annotation.
    homepage: http://sbgnbricks.org
    name: Bricks ontology
    prefix: BKO
    version: 13:07:2018 10:45
  comment: This resource also uses SBO terms and resolves them, e.g., http://www.sbgnbricks.org/BKO/full/entry/all/SBO:0000177/.
  contact:
    email: adrienrougny@gmail.com
    github: adrienrougny
    name: Adrien Rougny
    orcid: 0000-0002-2118-035X
  contributor:
    email: benjamin_gyori@hms.harvard.edu
    github: bgyori
    name: Benjamin M. Gyori
    orcid: 0000-0001-9439-5346
  description: SBGN bricks represent biomolecular or biological concepts. BKO formally
    associates bricks with the concepts they represent. BKO includes terms that describe
    concepts, the template bricks representing these concepts, and categories that
    gather bricks in a broader way.
  example: '0000204'
  github_request_issue: 283
  homepage: http://www.sbgnbricks.org/
  mappings:
    aberowl: BKO
    bioportal: BKO
  name: SBGN Bricks data and ontology
  pattern: ^\d+$
  prefix: bko
  reviewer:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  uri_format: http://www.sbgnbricks.org/BKO/full/entry/all/BKO:$1
blastrule:
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: BlastRules (identifiers starting with the “NBR” prefix) are a type
    of evidence for functional classification of proteins based on BLAST (Basic Local
    Alignment Search Tool). A BlastRule consists of one or more 'model' proteins with
    known biological function, and BLAST identity and coverage cutoffs. Any protein
    aligning to a model protein above the cutoffs is considered a BlastRule hit. [from
    homepage]
  example: NBR016799
  github_request_issue: 1522
  homepage: https://www.ncbi.nlm.nih.gov/genome/annotation_prok/evidence/
  name: BlastRule
  pattern: ^NBR\d+$
  prefix: blastrule
  references:
  - https://ftp.ncbi.nlm.nih.gov/pub/blastrules/
  uri_format: https://www.ncbi.nlm.nih.gov/genome/annotation_prok/evidence/$1
bmbf.glossary:
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: A german-language glossary provides you with definitions of the terms
    used in the portal in the fields of education, science, research and innovation
    and is updated regularly.
  example: G1
  homepage: https://www.datenportal.bmbf.de/portal/de/glossary.html
  name: German Federal Ministry of Education and Research Glossary
  prefix: bmbf.glossary
  uri_format: https://www.datenportal.bmbf.de/portal/de/$1.html
bmont:
  aberowl:
    description: An application ontology that represents comprehensive knowledge involving
      a variety of fields of medical and biological aspects.
    download_owl: http://aber-owl.net/media/ontologies/BMONT/3/bmont.owl
    homepage: https://github.com/SCAI-BIO/BiomarkerOntology
    name: Biomarker Ontology
    prefix: BMONT
  bioportal:
    contact:
      email: alpha.tom.kodamullil@scai.fraunhofer.de
      name: Alpha Tom Kodamullil
    description: The Biomarker Ontology (BMONT) is a comprehensive knowledge representation
      involving a variety of fields of medical and biological aspects. BMONT is built
      in line with Basic Formal Ontology (BFO) and Open Biological and Biomedical
      Ontology (OBO) principles. Entities and definitions are added by reviewing the
      biomarker ontology (created by Fraunhofer SCAI 10 years ago and used for the
      validation of the companion biomarker for a anticancer drug), as well as collected
      from scientific publications and books from different fields capturing various
      diseases.
    name: The Biomarker Ontology
    prefix: BMONT
    version: 'Version Release: 0.5.8'
  example: '0000006'
  mappings:
    aberowl: BMONT
    bioportal: BMONT
    obofoundry: bmont
    ols: bmont
    ontobee: BMONT
  obofoundry:
    contact: alpha.tom.kodamullil@scai.fraunhofer.de
    contact.github: akodamullil
    contact.label: Alpha Tom Kodamullil
    contact.orcid: 0000-0001-9896-3531
    deprecated: false
    description: An application ontology that represents comprehensive knowledge involving
      a variety of fields of medical and biological aspects.
    domain: health
    homepage: https://github.com/SCAI-BIO/BiomarkerOntology
    license: CC BY 4.0
    license.url: http://creativecommons.org/licenses/by/4.0/
    name: Biomarker Ontology
    preferredPrefix: BMONT
    prefix: bmont
    repository: https://github.com/SCAI-BIO/BiomarkerOntology
  ols:
    description: An application ontology that represents comprehensive knowledge involving
      a variety of fields of medical and biological aspects.
    download_owl: http://purl.obolibrary.org/obo/bmont.owl
    homepage: https://github.com/SCAI-BIO/BiomarkerOntology
    name: Biomarker Ontology (BMONT)
    prefix: bmont
    tracker: https://github.com/SCAI-BIO/BiomarkerOntology/issues
    version.iri: http://purl.obolibrary.org/obo/bmont/releases/2025-06-20/bmont.owl
  ontobee:
    library: Library
    name: Biomarker Ontology
    prefix: BMONT
  prefix: bmont
bmrb.entry:
  contact:
    email: markley@nmrfam.wisc.edu
    github: null
    name: John L. Markley
    orcid: 0000-0003-1799-6134
  fairsharing:
    abbreviation: BMRB
    description: BMRB collects, annotates, archives, and disseminates (worldwide in
      the public domain) the important spectral and quantitative data derived from
      NMR spectroscopic investigations of biological macromolecules and metabolites.
      Its goal is to empower scientists in their analysis of the structure, dynamics,
      and chemistry of biological systems and to support further development of the
      field of biomolecular NMR spectroscopy.
    homepage: https://bmrb.io/
    license: CC0-1.0
    name: Biological Magnetic Resonance Data Bank
    prefix: FAIRsharing.p06nme
    publications:
    - doi: 10.1007/s10858-008-9221-y
      pubmed_id: 18288446
      title: 'BioMagResBank (BMRB) as a partner in the Worldwide Protein Data Bank
        (wwPDB): new policies affecting biomolecular NMR depositions.'
    - doi: 10.1093/nar/gkm957
      pubmed_id: 17984079
      title: BioMagResBank.
    subjects:
    - Structural Biology
  integbio:
    alt_name: Biological Magnetic Resonance Data Bank
    description: BMRB is a database of biomolecular magnetic resonance data. Proteins,
      peptides, and nucleic acids, and other molecules are represented in NMR and
      PDB data form. Several search functions are supported and users can upload or
      download data.
    fairsharing: biodbcore-000584
    homepage: http://www.bmrb.wisc.edu/
    information_keywords:
    - 3D structure
    - Repository
    maintainer: University of Wisconsin System Board of Regents
    name: BMRB
    prefix: nbdc00380
    pubmeds:
    - '17984079'
    status: Inactive
    target_keywords:
    - DNA
    - RNA
    - Protein
  mappings:
    fairsharing: FAIRsharing.p06nme
    integbio: nbdc00380
    miriam: bmrb
    re3data: r3d100010191
    uniprot: DB-0256
  miriam:
    deprecated: false
    description: BMRB collects, annotates, archives, and disseminates (worldwide in
      the public domain) the important spectral and quantitative data derived from
      NMR spectroscopic investigations of biological macromolecules and metabolites.
      The goal is to empower scientists in their analysis of the structure, dynamics,
      and chemistry of biological systems and to support further development of the
      field of biomolecular NMR spectroscopy.
    homepage: https://bmrb.io/
    id: '00000716'
    name: Biological Magnetic Resonance Data Bank
    namespaceEmbeddedInLui: false
    pattern: ^(bmr|bmse|bmst)?[0-9]{1,6}$
    prefix: bmrb
    sampleId: '15000'
    uri_format: https://bmrb.io/data_library/summary/index.php?bmrbId=$1
  part_of_database: bmrb
  prefix: bmrb.entry
  publications:
  - doi: 10.1007/s10858-008-9221-y
    pmc: PMC2268728
    pubmed: '18288446'
    title: 'BioMagResBank (BMRB) as a partner in the Worldwide Protein Data Bank (wwPDB):
      new policies affecting biomolecular NMR depositions'
    year: 2008
  - doi: 10.1093/nar/gkm957
    pmc: PMC2238925
    pubmed: '17984079'
    title: BioMagResBank
    year: 2007
  - doi: 10.1007/s10858-008-9221-y
    pmc: null
    pubmed: null
    title: 'BioMagResBank (BMRB) as a partner in the Worldwide Protein Data Bank (wwPDB):
      new policies affecting biomolecular NMR depositions.'
    year: null
  - doi: 10.1093/nar/gkm957
    pmc: null
    pubmed: null
    title: BioMagResBank.
    year: null
  - doi: 10.1093/nar/gkm957
    pmc: null
    pubmed: '17984079'
    title: null
    year: null
  re3data:
    description: BioMagResBank (BMRB) is the publicly-accessible depository for NMR
      results from peptides, proteins, and nucleic acids recognized by the International
      Society of Magnetic Resonance and by the IUPAC-IUBMB-IUPAB Inter-Union Task
      Group on the Standardization of Data Bases of Protein and Nucleic Acid Structures
      Determined by NMR Spectroscopy. In addition, BMRB provides reference information
      and maintains a collection of NMR pulse sequences and computer software for
      biomolecular NMR
    doi: 10.17616/R3ZC7X
    homepage: https://bmrb.io/
    name: Biological Magnetic Resonance Data Bank
    prefix: r3d100010191
    synonyms:
    - BMRB
    - BioMagResBank
    - Biological Magnetic Resonance Databank
    xrefs:
      nif: 0000-21058
      omics: 02858
  synonyms:
  - bmrb
  uniprot:
    abbreviation: BMRB
    category: 3D structure databases
    homepage: https://bmrb.io/
    name: Biological Magnetic Resonance Data Bank
    prefix: DB-0256
    publications:
    - doi: 10.1093/nar/gkm957
      pubmed: '17984079'
    uri_format: https://bmrb.io/data_library/summary/protein.php?uniprot=$1
bmrb.restraint:
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: The NMR Restraints Grid contains the original NMR data as collected
    for over 2500 protein and nucleic acid structures with corresponding PDB entries.
    In addition to the original restraints, most of the distance, dihedral angle and
    RDC restraint data (>85%) were parsed, and those in over 500 entries were converted
    and filtered. The converted and filtered data sets constitute the DOCR and FRED
    databases respectively.
  example: '28789'
  homepage: https://restraintsgrid.bmrb.io/NRG/MRGridServlet
  keywords:
  - chemistry
  - nmr
  - spectrometry
  name: NMR Restraints Grid
  part_of_database: bmrb
  pattern: ^\d+$
  prefix: bmrb.restraint
  uri_format: https://restraintsgrid.bmrb.io/NRG/MRGridServlet?block_text_type=2-parsed&db_username=wattos1&file_detail=2-parsed&format=n%2Fa&program=STAR&request_type=block&subtype=full&type=entry&mrblock_id=$1
bodc.cf:
  example: MIKUZ25U
  mappings:
    tib: cf
  prefix: bodc.cf
  tib:
    description: Ontology representation of the Climate and Forecast (CF) standard
      names parameter vocabulary, which is intended for use with climate and forecast
      data in the atmosphere, surface and ocean domains. Every CF parameter is captured
      as a SKOS concept.This vocabulary is a simplified version of the CF vocabulary
      P07 from the NERC Vocabulary Server (NVS), National Oceanography Centre - British
      Oceanographic Data Centre (BODC), https://vocab.nerc.ac.uk.
    homepage: http://vocab.nerc.ac.uk/collection/P07/current
    keywords:
    - ESS
    - earth sciences
    name: Climate and Forecast Standard Names
    prefix: cf
    uri_format: http://vocab.nerc.ac.uk/collection/P07/current/$1
bodc.sdn:
  example: '101'
  homepage: http://vocab.nerc.ac.uk/collection/L05
  mappings:
    tib: sdn
  prefix: bodc.sdn
  tib:
    description: Terms used to classify groups of sensors, instruments, sources of
      algorithmically computed data (numerical models) or samplers (collectors of
      water, SPM, sediment, rock, air or biota samples).
    keywords:
    - ESS
    - earth sciences
    name: SeaDataNet device categories
    prefix: sdn
    uri_format: http://vocab.nerc.ac.uk/collection/L05/current/$1
bodc.unit:
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: terms approved for use by BODC to describe the measurement units for
    data held in its repositories.
  example: UMKS
  github_request_issue: 1643
  homepage: https://vocab.nerc.ac.uk/collection/P06/current/
  keywords:
  - unit
  - units
  license: CC-BY-4.0
  name: British Oceanographic Data Centre data storage units
  prefix: bodc.unit
  synonyms:
  - nvs.P06
  uri_format: http://vocab.nerc.ac.uk/collection/P06/current/$1
bold.taxonomy:
  biocontext:
    prefix: BOLD.TAXONOMY
  contact:
    email: phebert@uoguelph.ca
    github: null
    name: Paul David Neil Hebert
    orcid: 0000-0002-3081-6700
  mappings:
    biocontext: BOLD.TAXONOMY
    miriam: bold.taxonomy
    n2t: bold.taxonomy
    ncbi: BOLD
    prefixcommons: bold
    wikidata: P3606
  miriam:
    deprecated: false
    description: The Barcode of Life Data System (BOLD) is an informatics workbench
      aiding the acquisition, storage, analysis and publication of DNA barcode records.
      The associated taxonomy browser shows the progress of DNA barcoding and provides
      sample collection site distribution, and taxon occurence information.
    homepage: http://www.boldsystems.org/
    id: 00000158
    name: BOLD Taxonomy
    namespaceEmbeddedInLui: false
    pattern: ^\d+$
    prefix: bold.taxonomy
    sampleId: '27267'
    uri_format: http://www.boldsystems.org/index.php/Taxbrowser_Taxonpage?taxid=$1
  n2t:
    description: The Barcode of Life Data System (BOLD) is an informatics workbench
      aiding the acquisition, storage, analysis and publication of DNA barcode records.
      The associated taxonomy browser shows the progress of DNA barcoding and provides
      sample collection site distribution, and taxon occurence information.
    example: '27267'
    homepage: http://www.boldsystems.org/
    name: BOLD taxonomy browser
    namespaceEmbeddedInLui: false
    pattern: ^\d+$
    prefix: bold.taxonomy
    uri_format: http://www.boldsystems.org/index.php/Taxbrowser_Taxonpage?taxid=$1
  name: BOLD Systems taxon
  ncbi:
    example: EPAF263
    homepage: http://www.barcodinglife.com
    name: Barcode of Life database
    prefix: BOLD
  prefix: bold.taxonomy
  prefixcommons:
    description: The Barcode of Life Data Systems (BOLD) is an online workbench that
      aids collection, management, analysis, and use of DNA barcodes. It consists
      of 3 components (MAS, IDS, and ECS) that each address the needs of various groups
      in the barcoding community.
    example: '27267'
    homepage: http://www.barcodinglife.com
    keywords:
    - DNA
    name: The Barcode of Life Data Systems
    pattern: ^\d+$
    prefix: bold
    pubmed_ids:
    - '18784790'
    synonyms:
    - bold.taxonomy
    uri_format: http://www.barcodinglife.com/views/taxbrowser.php?taxid=$1
  publications:
  - doi: 10.1111/j.1471-8286.2007.01678.x
    pmc: PMC1890991
    pubmed: '18784790'
    title: 'bold: The Barcode of Life Data System (http://www.barcodinglife.org)'
    year: 2007
  - doi: null
    pmc: null
    pubmed: '18784790'
    title: null
    year: null
  wikidata:
    description: identifier for a taxon in boldsystems.org
    example:
    - '286001'
    - '38074'
    name: BOLD Systems taxon ID
    prefix: P3606
    uri_format: https://bench.boldsystems.org/index.php/TaxBrowser_TaxonPage?taxid=$1
bonsai:
  example: Activity
  mappings:
    tib: bont
  name: Big Open Network of Sustainability Assessment Information Ontology
  prefix: bonsai
  repository: https://github.com/BONSAMURAIS/ontology
  tib:
    description: The BONSAI ontologies provides elements of description for product
      footprint concepts defined in the bonsai.uno data base
    download_rdf: https://raw.githubusercontent.com/BONSAMURAIS/ontology/master/core/ontology_v0.2.ttl
    homepage: https://github.com/BONSAMURAIS/BONSAI-ontology-RDF-framework
    keywords:
    - NFDI4ING
    - NFDI4Energy
    - engineering
    name: The BONSAI ontology
    prefix: bont
    tracker: https://github.com/BONSAMURAIS/ontology/issues
    uri_format: http://ontology.bonsai.uno/core#$1
bot:
  example: Building
  mappings:
    tib: bot
  prefix: bot
  repository: https://github.com/w3c-lbd-cg/bot
  tib:
    description: The Building Topology Ontology (BOT) is a minimal ontology for describing
      the core topological concepts of a building.
    download_rdf: https://w3c-lbd-cg.github.io/bot/bot.ttl
    homepage: https://w3c-lbd-cg.github.io/bot/
    keywords:
    - NFDI4ING
    - NFDI4CULTURE
    - Digital Planning and Construction
    - FID BAUdigital
    - civil engineering
    - architecture
    name: Building Topology Ontology
    prefix: bot
    uri_format: https://w3id.org/bot#$1
    version.iri: https://w3id.org/bot-0.3.2
bpdb:
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: Database of biopesticides maintained by the University of Hertfordshire
  example: '2404'
  homepage: https://sitem.herts.ac.uk/aeru/bpdb/index.htm
  keywords:
  - biology
  - biopesticides
  - pesticides
  name: Bio-Pesticides DataBase
  pattern: ^\d+$
  prefix: bpdb
  uri_format: https://sitem.herts.ac.uk/aeru/bpdb/Reports/$1.htm
brenda:
  biocontext:
    prefix: BRENDA
  contact:
    email: D.Schomburg@tu-braunschweig.de
    github: null
    name: Dietmar Schomburg
    orcid: 0000-0002-3354-822X
  fairsharing:
    abbreviation: BRENDA
    description: BRENDA is the main collection of enzyme functional data available
      to the scientific community.
    homepage: https://www.brenda-enzymes.org/
    license: CC-BY-4.0
    name: BRENDA Enzyme Database
    prefix: FAIRsharing.etp533
    publications:
    - doi: 10.1016/S0968-0004(01)02027-8
      pubmed_id: 11796225
      title: 'BRENDA: a resource for enzyme data and metabolic information.'
    - doi: 10.1093/nar/30.1.47
      pubmed_id: 11752250
      title: BRENDA, enzyme data and metabolic information.
    - doi: 10.1093/nar/gkh081
      pubmed_id: 14681450
      title: 'BRENDA, the enzyme database: updates and major new developments.'
    - doi: 10.1016/S1096-7176(03)00008-9
      pubmed_id: 12850129
      title: Review of the BRENDA Database.
    - doi: 10.1093/nar/gku1068
      pubmed_id: 25378310
      title: 'BRENDA in 2015: exciting developments in its 25th year of existence.'
    - doi: 10.1093/nar/gkl972
      pubmed_id: 17202167
      title: 'BRENDA, AMENDA and FRENDA: the enzyme information system in 2007.'
    - doi: 10.1093/nar/gkn820
      pubmed_id: 18984617
      title: 'BRENDA, AMENDA and FRENDA the enzyme information system: new content
        and tools in 2009.'
    - doi: 10.1093/nar/gks1049
      pubmed_id: 23203881
      title: 'BRENDA in 2013: integrated reactions, kinetic data, enzyme function
        data, improved disease classification: new options and contents in BRENDA.'
    - doi: 10.1093/nar/gkq1089
      pubmed_id: 21062828
      title: BRENDA, the enzyme information system in 2011.
    - doi: S0168-1656(17)30183-9
      pubmed_id: 28438579
      title: The BRENDA enzyme information system-From a database to an expert system.
    subjects:
    - Life Science
  go:
    homepage: http://www.brenda-enzymes.info
    name: BRENDA, The Comprehensive Enzyme Information System
    prefix: BRENDA
    uri_format: https://www.brenda-enzymes.info/enzyme.php?ecno=$1
  mappings:
    biocontext: BRENDA
    fairsharing: FAIRsharing.etp533
    go: BRENDA
    miriam: brenda
    n2t: brenda
    pathguide: '51'
    prefixcommons: brenda
    re3data: r3d100010616
  miriam:
    deprecated: false
    description: BRENDA is a collection of enzyme functional data available to the
      scientific community. Data on enzyme function are extracted directly from the
      primary literature The database covers information on classification and nomenclature,
      reaction and specificity, functional parameters, occurrence, enzyme structure
      and stability, mutants and enzyme engineering, preparation and isolation, the
      application of enzymes, and ligand-related data.
    homepage: https://www.brenda-enzymes.org/
    id: '00000071'
    name: BRENDA
    namespaceEmbeddedInLui: false
    pattern: ^((\d+\.-\.-\.-)|(\d+\.\d+\.-\.-)|(\d+\.\d+\.\d+\.-)|(\d+\.\d+\.\d+\.\d+))$
    prefix: brenda
    sampleId: 1.1.1.1
    uri_format: https://www.brenda-enzymes.org/php/result_flat.php4?ecno=$1
  n2t:
    description: BRENDA is a collection of enzyme functional data available to the
      scientific community. Data on enzyme function are extracted directly from the
      primary literature The database covers information on classification and nomenclature,
      reaction and specificity, functional parameters, occurrence, enzyme structure
      and stability, mutants and enzyme engineering, preparation and isolation, the
      application of enzymes, and ligand-related data.
    example: 1.1.1.1
    homepage: https://www.brenda-enzymes.org/
    name: Brenda enzyme database
    namespaceEmbeddedInLui: false
    pattern: ^((\d+\.-\.-\.-)|(\d+\.\d+\.-\.-)|(\d+\.\d+\.\d+\.-)|(\d+\.\d+\.\d+\.\d+))$
    prefix: brenda
    uri_format: https://www.brenda-enzymes.org/php/result_flat.php4?ecno=$1
  name: BRENDA Enzyme
  pathguide:
    abbreviation: BRENDA
    homepage: http://www.brenda-enzymes.info/
    keywords:
    - SBML
    name: BRaunschweig ENzyme DAtabase
    prefix: '51'
  prefix: brenda
  prefixcommons:
    description: BRENDA is the main collection of enzyme functional data available
      to the scientific community.
    example: 1.1.1.1
    homepage: http://www.brenda-enzymes.org
    keywords:
    - enzyme
    license: http://www.brenda-enzymes.org
    name: The Comprehensive Enzyme Information System
    pattern: ^((\d+\.-\.-\.-)|(\d+\.\d+\.-\.-)|(\d+\.\d+\.\d+\.-)|(\d+\.\d+\.\d+\.\d+))$
    prefix: brenda
    pubmed_ids:
    - '18984617'
    uri_format: http://www.brenda-enzymes.org/php/result_flat.php4?ecno=$1
  provides: ec
  publications:
  - doi: 10.1016/j.jbiotec.2017.04.020
    pmc: null
    pubmed: '28438579'
    title: The BRENDA enzyme information system-From a database to an expert system
    year: 2017
  - doi: 10.1093/nar/gku1068
    pmc: PMC4383907
    pubmed: '25378310'
    title: 'BRENDA in 2015: exciting developments in its 25th year of existence'
    year: 2014
  - doi: 10.1093/nar/gks1049
    pmc: PMC3531171
    pubmed: '23203881'
    title: 'BRENDA in 2013: integrated reactions, kinetic data, enzyme function data,
      improved disease classification: new options and contents in BRENDA'
    year: 2012
  - doi: 10.1093/nar/gkq1089
    pmc: PMC3013686
    pubmed: '21062828'
    title: BRENDA, the enzyme information system in 2011
    year: 2010
  - doi: 10.1093/nar/gkn820
    pmc: PMC2686525
    pubmed: '18984617'
    title: 'BRENDA, AMENDA and FRENDA the enzyme information system: new content and
      tools in 2009'
    year: 2008
  - doi: 10.1093/nar/gkl972
    pmc: PMC1899097
    pubmed: '17202167'
    title: 'BRENDA, AMENDA and FRENDA: the enzyme information system in 2007'
    year: 2007
  - doi: 10.1093/nar/gkh081
    pmc: PMC308815
    pubmed: '14681450'
    title: 'BRENDA, the enzyme database: updates and major new developments'
    year: 2004
  - doi: 10.1016/s1096-7176(03)00008-9
    pmc: null
    pubmed: '12850129'
    title: Review of the BRENDA Database
    year: 2003
  - doi: 10.1093/nar/30.1.47
    pmc: PMC99121
    pubmed: '11752250'
    title: BRENDA, enzyme data and metabolic information
    year: 2002
  - doi: 10.1016/s0968-0004(01)02027-8
    pmc: null
    pubmed: '11796225'
    title: 'BRENDA: a resource for enzyme data and metabolic information'
    year: 2002
  - doi: 10.1016/S0968-0004(01)02027-8
    pmc: null
    pubmed: null
    title: 'BRENDA: a resource for enzyme data and metabolic information.'
    year: null
  - doi: 10.1093/nar/30.1.47
    pmc: null
    pubmed: null
    title: BRENDA, enzyme data and metabolic information.
    year: null
  - doi: 10.1093/nar/gkh081
    pmc: null
    pubmed: null
    title: 'BRENDA, the enzyme database: updates and major new developments.'
    year: null
  - doi: 10.1016/S1096-7176(03)00008-9
    pmc: null
    pubmed: null
    title: Review of the BRENDA Database.
    year: null
  - doi: 10.1093/nar/gku1068
    pmc: null
    pubmed: null
    title: 'BRENDA in 2015: exciting developments in its 25th year of existence.'
    year: null
  - doi: 10.1093/nar/gkl972
    pmc: null
    pubmed: null
    title: 'BRENDA, AMENDA and FRENDA: the enzyme information system in 2007.'
    year: null
  - doi: 10.1093/nar/gkn820
    pmc: null
    pubmed: null
    title: 'BRENDA, AMENDA and FRENDA the enzyme information system: new content and
      tools in 2009.'
    year: null
  - doi: 10.1093/nar/gks1049
    pmc: null
    pubmed: null
    title: 'BRENDA in 2013: integrated reactions, kinetic data, enzyme function data,
      improved disease classification: new options and contents in BRENDA.'
    year: null
  - doi: 10.1093/nar/gkq1089
    pmc: null
    pubmed: null
    title: BRENDA, the enzyme information system in 2011.
    year: null
  - doi: S0168-1656(17)30183-9
    pmc: null
    pubmed: null
    title: The BRENDA enzyme information system-From a database to an expert system.
    year: null
  - doi: null
    pmc: null
    pubmed: '18984617'
    title: null
    year: null
  - doi: 10.1016/S0968-0004(01)02027-8
    pmc: null
    pubmed: null
    title: 'BRENDA: a resource for enzyme data and metabolic information.'
    year: null
  - doi: 10.1093/nar/30.1.47
    pmc: null
    pubmed: null
    title: BRENDA, enzyme data and metabolic information.
    year: null
  - doi: 10.1093/nar/gkh081
    pmc: null
    pubmed: null
    title: 'BRENDA, the enzyme database: updates and major new developments.'
    year: null
  - doi: 10.1016/S1096-7176(03)00008-9
    pmc: null
    pubmed: null
    title: Review of the BRENDA Database.
    year: null
  - doi: 10.1093/nar/gku1068
    pmc: null
    pubmed: null
    title: 'BRENDA in 2015: exciting developments in its 25th year of existence.'
    year: null
  - doi: 10.1093/nar/gkl972
    pmc: null
    pubmed: null
    title: 'BRENDA, AMENDA and FRENDA: the enzyme information system in 2007.'
    year: null
  - doi: 10.1093/nar/gkn820
    pmc: null
    pubmed: null
    title: 'BRENDA, AMENDA and FRENDA the enzyme information system: new content and
      tools in 2009.'
    year: null
  - doi: 10.1093/nar/gks1049
    pmc: null
    pubmed: null
    title: 'BRENDA in 2013: integrated reactions, kinetic data, enzyme function data,
      improved disease classification: new options and contents in BRENDA.'
    year: null
  - doi: 10.1093/nar/gkq1089
    pmc: null
    pubmed: null
    title: BRENDA, the enzyme information system in 2011.
    year: null
  - doi: S0168-1656(17)30183-9
    pmc: null
    pubmed: null
    title: The BRENDA enzyme information system-From a database to an expert system.
    year: null
  - doi: null
    pmc: null
    pubmed: '18984617'
    title: null
    year: null
  - doi: 10.1016/S0968-0004(01)02027-8
    pmc: null
    pubmed: null
    title: 'BRENDA: a resource for enzyme data and metabolic information.'
    year: null
  - doi: 10.1093/nar/30.1.47
    pmc: null
    pubmed: null
    title: BRENDA, enzyme data and metabolic information.
    year: null
  - doi: 10.1093/nar/gkh081
    pmc: null
    pubmed: null
    title: 'BRENDA, the enzyme database: updates and major new developments.'
    year: null
  - doi: 10.1016/S1096-7176(03)00008-9
    pmc: null
    pubmed: null
    title: Review of the BRENDA Database.
    year: null
  - doi: 10.1093/nar/gku1068
    pmc: null
    pubmed: null
    title: 'BRENDA in 2015: exciting developments in its 25th year of existence.'
    year: null
  - doi: 10.1093/nar/gkl972
    pmc: null
    pubmed: null
    title: 'BRENDA, AMENDA and FRENDA: the enzyme information system in 2007.'
    year: null
  - doi: 10.1093/nar/gkn820
    pmc: null
    pubmed: null
    title: 'BRENDA, AMENDA and FRENDA the enzyme information system: new content and
      tools in 2009.'
    year: null
  - doi: 10.1093/nar/gks1049
    pmc: null
    pubmed: null
    title: 'BRENDA in 2013: integrated reactions, kinetic data, enzyme function data,
      improved disease classification: new options and contents in BRENDA.'
    year: null
  - doi: 10.1093/nar/gkq1089
    pmc: null
    pubmed: null
    title: BRENDA, the enzyme information system in 2011.
    year: null
  - doi: S0168-1656(17)30183-9
    pmc: null
    pubmed: null
    title: The BRENDA enzyme information system-From a database to an expert system.
    year: null
  - doi: null
    pmc: null
    pubmed: '18984617'
    title: null
    year: null
  - doi: 10.1016/S0968-0004(01)02027-8
    pmc: null
    pubmed: null
    title: 'BRENDA: a resource for enzyme data and metabolic information.'
    year: null
  - doi: 10.1093/nar/30.1.47
    pmc: null
    pubmed: null
    title: BRENDA, enzyme data and metabolic information.
    year: null
  - doi: 10.1093/nar/gkh081
    pmc: null
    pubmed: null
    title: 'BRENDA, the enzyme database: updates and major new developments.'
    year: null
  - doi: 10.1016/S1096-7176(03)00008-9
    pmc: null
    pubmed: null
    title: Review of the BRENDA Database.
    year: null
  - doi: 10.1093/nar/gku1068
    pmc: null
    pubmed: null
    title: 'BRENDA in 2015: exciting developments in its 25th year of existence.'
    year: null
  - doi: 10.1093/nar/gkl972
    pmc: null
    pubmed: null
    title: 'BRENDA, AMENDA and FRENDA: the enzyme information system in 2007.'
    year: null
  - doi: 10.1093/nar/gkn820
    pmc: null
    pubmed: null
    title: 'BRENDA, AMENDA and FRENDA the enzyme information system: new content and
      tools in 2009.'
    year: null
  - doi: 10.1093/nar/gks1049
    pmc: null
    pubmed: null
    title: 'BRENDA in 2013: integrated reactions, kinetic data, enzyme function data,
      improved disease classification: new options and contents in BRENDA.'
    year: null
  - doi: 10.1093/nar/gkq1089
    pmc: null
    pubmed: null
    title: BRENDA, the enzyme information system in 2011.
    year: null
  - doi: S0168-1656(17)30183-9
    pmc: null
    pubmed: null
    title: The BRENDA enzyme information system-From a database to an expert system.
    year: null
  - doi: null
    pmc: null
    pubmed: '18984617'
    title: null
    year: null
  re3data:
    description: BRENDA is the main collection of enzyme functional data available
      to the scientific community worldwide.  The enzymes are classified according
      to the Enzyme Commission list of enzymes. It is available free of charge for
      via the internet (http://www.brenda-enzymes.org/) and as an in-house database
      for commercial users (requests to our distributor Biobase). The enzymes are
      classified according to the Enzyme Commission list of enzymes. Some 5000 "different"
      enzymes are covered. Frequently enzymes with very different properties are included
      under the same EC number. BRENDA includes biochemical and molecular information
      on classification, nomenclature, reaction, specificity, functional parameters,
      occurrence, enzyme structure, application, engineering, stability, disease,
      isolation, and preparation. The database also provides additional information
      on ligands, which function as natural or in vitro substrates/products, inhibitors,
      activating compounds, cofactors, bound metals, and other attributes.
    doi: 10.17616/R39W42
    homepage: https://www.brenda-enzymes.org
    name: BRENDA
    prefix: r3d100010616
    synonyms:
    - BRENDA Enzyme Database
    - BRaunschweig ENzyme DAtabase
    xrefs:
      nif: 0000-30222
      omics: 02681
brenda.ligand:
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: Information for ligands in the BRENDA database.
  example: '278'
  homepage: https://www.brenda-enzymes.de/ligand.php
  keywords:
  - chemistry
  - structrual bioinformatics
  name: BRENDA Ligand
  part_of_database: brenda
  pattern: ^\d+$
  prefix: brenda.ligand
  uri_format: https://www.brenda-enzymes.de/ligand.php?brenda_ligand_id=$1
brenda.ligandgroup:
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: Information for ligand groups (chemical classes).
  example: '18030'
  homepage: https://www.brenda-enzymes.de/ligand.php
  keywords:
  - chemistry
  - grouping
  - structrual bioinformatics
  name: BRENDA Ligand Group
  part_of_database: brenda
  pattern: ^\d+$
  prefix: brenda.ligandgroup
  uri_format: https://www.brenda-enzymes.de/ligand.php?brenda_group_id=$1
brick:
  example: Ablutions_Room
  fairsharing:
    abbreviation: Brick
    description: 'Brick is an open-source effort to standardize semantic descriptions
      of the physical, logical and virtual assets in buildings and the relationships
      between them. Brick consists of an extensible dictionary of terms and concepts
      in and around buildings, a set of relationships for linking and composing concepts
      together, and a flexible data model permitting seamless integration of Brick
      with existing tools and databases. Through the use of powerful Semantic Web
      technology, Brick can describe the broad set of idiosyncratic and custom features,
      assets and subsystems found across the building stock in a consistent matter.
      Adopting Brick as the canonical description of a building enables the following:
      1) Brick lowers the cost of deploying analytics, energy efficiency measures
      and intelligent controls across buildings, 2) Brick presents an integrated,
      cross-vendor representation of the multitude of subsystems in modern buildings:
      HVAC, lighting, fire, security and so on, 3) Brick simplifies the development
      of smart analytics and control applications, and 4) Brick reduces the reliance
      upon the non-standard, unstructured labels endemic to building management systems.

      '
    homepage: https://brickschema.org/
    logo: https://api.fairsharing.org/rails/active_storage/blobs/redirect/eyJfcmFpbHMiOnsibWVzc2FnZSI6IkJBaHBBYXc9IiwiZXhwIjpudWxsLCJwdXIiOiJibG9iX2lkIn19--5c7080d13b18a371dfa46816c406e7c896c6f921/Brick.png?disposition=inline
    name: Brick - A Uniform Metadata Schema For Buildings
    prefix: FAIRsharing.e1c595
    publications:
    - doi: 10.1145/2993422.2993577
      title: Brick
      year: 2016
    - doi: 10.1016/j.apenergy.2018.02.091
      title: 'Brick : Metadata schema for portable smart building applications'
      year: 2018
    - doi: 10.1145/3408308.3427627
      title: Shepherding Metadata Through the Building Lifecycle
      year: 2020
    - doi: 10.1145/3137133.3141449
      title: HodDB
      year: 2018
    - doi: 10.1145/3276774.3276794
      title: Plaster
      year: 2018
    - doi: 10.1145/3276774.3276795
      title: Scrabble
      year: 2018
    - doi: 10.1145/3276774.3276796
      title: Mortar
      year: 2018
    - doi: 10.1145/3199666
      title: Design and Analysis of a Query Processor for Brick
      year: 2018
    - doi: 10.1016/j.aei.2018.04.010
      title: A large-scale evaluation of automated metadata inference approaches on
        sensors from air handling units
      year: 2018
    - doi: 10.1145/3360322.3360862
      title: Beyond a House of Sticks
      year: 2019
    - doi: 10.1145/3408308.3431125
      title: Interactive Metadata Integration with Brick
      year: 2020
    repository: https://github.com/BrickSchema/brick
    subjects:
    - Industrial Engineering
    - Energy Engineering
    - Systems Engineering
    - Power Engineering
    - Building Informatics
    - Building Design
    user_defined_tags:
    - building information modeling
  mappings:
    fairsharing: FAIRsharing.e1c595
    tib: brick
  prefix: brick
  repository: https://github.com/BrickSchema/Brick
  tib:
    description: Brick is an open-source, BSD-licensed development effort to create
      a uniform schema for representing metadata in buildings.
    download_rdf: https://brickschema.org/schema/1.3.0/Brick.ttl
    homepage: https://brickschema.org/ontology/
    keywords:
    - NFDI4ING
    - Digital Planning and Construction
    - FID BAUdigital
    - NFDI4Energy
    - engineering
    - civil engineering
    - architecture
    name: Brick Ontology
    prefix: brick
    tracker: https://github.com/BrickSchema/Brick/issues
    uri_format: https://brickschema.org/schema/Brick#$1
bridgedb:
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: A vocabulary about resources, similar to bioregistry.schema, venn,
    idot, etc.
  example: hasPrimaryUriPattern
  homepage: https://bridgedb.org
  name: BridgeDb Vocabulary
  prefix: bridgedb
  references:
  - https://github.com/bridgedb/BridgeDb/blob/master/org.bridgedb.rdf/resources/IdentifiersOrgDataSource.ttl
  uri_format: http://vocabularies.bridgedb.org/ops#$1
broad:
  biocontext:
    prefix: BROAD
  mappings:
    biocontext: BROAD
    miriam: broad
    n2t: broad
  miriam:
    deprecated: false
    description: Magnaporthe grisea, the causal agent of rice blast disease, is one
      of the most devasting threats to food security worldwide and is a model organism
      for studying fungal phytopathogenicity and host-parasite interactions. The Magnaporthe
      comparative genomics database provides accesses to multiple fungal genomes from
      the Magnaporthaceae family to facilitate the comparative analysis. As part of
      the Broad Fungal Genome Initiative, the Magnaporthe comparative project includes
      the finished M. oryzae (formerly M. grisea) genome, as well as the draft assemblies
      of Gaeumannomyces graminis var. tritici and M. poae.
    homepage: https://www.broadinstitute.org/annotation/genome/magnaporthe_grisea/
    id: 00000438
    name: Broad Fungal Genome Initiative
    namespaceEmbeddedInLui: false
    pattern: ^S\d+$
    prefix: broad
    sampleId: S7000002168151102
    uri_format: https://www.broadinstitute.org/annotation/genome/magnaporthe_grisea/GeneDetails.html?sp=$1
  n2t:
    description: Magnaporthe grisea, the causal agent of rice blast disease, is one
      of the most devasting threats to food security worldwide and is a model organism
      for studying fungal phytopathogenicity and host-parasite interactions. The Magnaporthe
      comparative genomics database provides accesses to multiple fungal genomes from
      the Magnaporthaceae family to facilitate the comparative analysis. As part of
      the Broad Fungal Genome Initiative, the Magnaporthe comparative project includes
      the finished M. oryzae (formerly M. grisea) genome, as well as the draft assemblies
      of Gaeumannomyces graminis var. tritici and M. poae.
    example: S7000002168151102
    homepage: https://www.broadinstitute.org/annotation/genome/magnaporthe_grisea/
    name: Broad Fungal Genome Initiative at Broad Institute
    namespaceEmbeddedInLui: false
    pattern: ^S\d+$
    prefix: broad
    uri_format: https://www.broadinstitute.org/annotation/genome/magnaporthe_grisea/GeneDetails.html?sp=$1
  prefix: broad
bs:
  comment: An alernative vocabulary that has been aligned and integrated in Sequence
    Ontology (SO).
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: SO is a collaborative ontology project for the definition of sequence
    features used in biological sequence annotation. It is part of the Open Biomedical
    Ontologies library.
  download_obo: https://raw.githubusercontent.com/The-Sequence-Ontology/SO-Ontologies/master/Ontology_Files/subsets/biosapiens.obo
  example: '00042'
  homepage: https://github.com/The-Sequence-Ontology/SO-Ontologies
  name: Biosapiens Protein Feature Ontology
  pattern: ^\d+$
  prefix: bs
  repository: https://github.com/The-Sequence-Ontology/SO-Ontologies
  uri_format: https://biopragmatics.github.io/providers/bs/$1
bspo:
  aberowl:
    description: An ontology for representing spatial concepts, anatomical axes, gradients,
      regions, planes, sides, and surfaces
    download_owl: http://aber-owl.net/media/ontologies/BSPO/31/bspo.owl
    homepage: https://github.com/obophenotype/biological-spatial-ontology
    name: Biological Spatial Ontology
    prefix: BSPO
  biocontext:
    prefix: BSPO
  bioportal:
    contact:
      email: cjmungall@lbl.gov
      name: Chris Mungall
    description: An ontology for respresenting spatial concepts, anatomical axes,
      gradients, regions, planes, sides, and surfaces. These concepts can be used
      at multiple biological scales and in a diversity of taxa, including plants,
      animals and fungi. The BSPO is used to provide a source of anatomical location
      descriptors for logically defining anatomical entity classes in anatomy ontologies.
    homepage: https://github.com/obophenotype/biological-spatial-ontology
    name: Spatial Ontology
    prefix: BSPO
    version: '2023-05-27'
  download_json: http://purl.obolibrary.org/obo/bspo.json
  download_obo: https://raw.githubusercontent.com/obophenotype/biological-spatial-ontology/master/bspo.obo
  example: 0000029
  fairsharing:
    abbreviation: BSPO
    contact:
      email: cjmungall@lbl.gov
      name: Chris Mungall
      orcid: 0000-0002-6601-2165
    description: The Biological SPatial Ontology (BSPO) ontology is representative
      of spatial concepts, anatomical axes, gradients, regions, planes, sides and
      surfaces. These concepts can be used at multiple biological scales and in a
      diversity of taxa, including plants, animals and fungi. The BSPO is used to
      provide a source of anatomical location descriptors for logically defining anatomical
      entity classes in anatomy ontologies.
    domains:
    - functional domain
    - phenotype
    homepage: https://github.com/obophenotype/biological-spatial-ontology
    license: CC-BY-3.0
    name: Biological SPatial Ontology
    prefix: FAIRsharing.newa3z
    publications:
    - doi: 10.1186/2041-1480-5-34
      pubmed: '25140222'
      title: 'Nose to tail, roots to shoots: spatial descriptors for phenotypic diversity
        in the Biological Spatial Ontology'
      year: 2014
    repository: https://github.com/obophenotype/biological-spatial-ontology/issues
    subjects:
    - Life Science
    - Systems Biology
    - Anatomy
    - Phenomics
    - Physiology
  mappings:
    aberowl: BSPO
    biocontext: BSPO
    bioportal: BSPO
    fairsharing: FAIRsharing.newa3z
    obofoundry: bspo
    ols: bspo
    ontobee: BSPO
    wikidata.entity: Q81661546
  obofoundry:
    appears_in:
    - aism
    - colao
    - fovt
    - lepao
    - uberon
    - zp
    contact: cjmungall@lbl.gov
    contact.github: cmungall
    contact.label: Chris Mungall
    contact.orcid: 0000-0002-6601-2165
    deprecated: false
    description: An ontology for representing spatial concepts, anatomical axes, gradients,
      regions, planes, sides, and surfaces
    domain: anatomy and development
    download.obo: http://purl.obolibrary.org/obo/bspo.obo
    download.owl: http://purl.obolibrary.org/obo/bspo.owl
    homepage: https://github.com/obophenotype/biological-spatial-ontology
    license: CC BY 3.0
    license.url: http://creativecommons.org/licenses/by/3.0/
    name: Biological Spatial Ontology
    preferredPrefix: BSPO
    prefix: bspo
    publications:
    - id: https://www.ncbi.nlm.nih.gov/pubmed/25140222
      title: 'Nose to tail, roots to shoots: spatial descriptors for phenotypic diversity
        in the Biological Spatial Ontology.'
    repository: https://github.com/obophenotype/biological-spatial-ontology
  ols:
    description: An ontology for respresenting spatial concepts, anatomical axes,
      gradients, regions, planes, sides and surfaces. These concepts can be used at
      multiple biological scales and in a diversity of taxa, including plants, animals
      and fungi. The BSPO is used to provide a source of anatomical location descriptors
      for logically defining anatomical entity classes in anatomy ontologies.
    download_owl: http://purl.obolibrary.org/obo/bspo.owl
    homepage: https://github.com/obophenotype/biological-spatial-ontology
    name: Biological Spatial Ontology
    prefix: bspo
    tracker: https://github.com/obophenotype/biological-spatial-ontology/issues
    version: '2023-05-27'
    version.iri: http://purl.obolibrary.org/obo/bspo/releases/2023-05-27/bspo.owl
  ontobee:
    library: Library
    name: Biological Spatial Ontology
    prefix: BSPO
  pattern: ^\d{7}$
  prefix: bspo
  publications:
  - doi: 10.1186/2041-1480-5-34
    pmc: PMC4137724
    pubmed: '25140222'
    title: 'Nose to tail, roots to shoots: spatial descriptors for phenotypic diversity
      in the Biological Spatial Ontology'
    year: 2014
  - doi: null
    pmc: null
    pubmed: '25140222'
    title: 'Nose to tail, roots to shoots: spatial descriptors for phenotypic diversity
      in the Biological Spatial Ontology'
    year: null
  - doi: 10.1186/2041-1480-5-34
    pmc: null
    pubmed: '25140222'
    title: 'Nose to tail, roots to shoots: spatial descriptors for phenotypic diversity
      in the Biological Spatial Ontology'
    year: 2014
  uri_format: http://purl.obolibrary.org/obo/BSPO_$1
bto:
  aberowl:
    description: A structured controlled vocabulary for the source of an enzyme comprising
      tissues, cell lines, cell types and cell cultures.
    download_owl: http://aber-owl.net/media/ontologies/BTO/39/bto.owl
    homepage: http://www.brenda-enzymes.org
    name: BRENDA tissue / enzyme source
    prefix: BTO
  biocontext:
    prefix: BTO
  bioportal:
    contact:
      email: antje.jaede@online.de
      name: BrendaTissue Administrators
    description: A structured controlled vocabulary for the source of an enzyme. It
      comprises terms for tissues, cell lines, cell types and cell cultures from uni-
      and multicellular organisms.
    homepage: http://www.brenda-enzymes.info
    name: BRENDA Tissue and Enzyme Source Ontology
    prefix: BTO
    version: releases/2021-10-26
  cellosaurus:
    category: Anatomy/cell type resources
    homepage: https://bioportal.bioontology.org/ontologies/BTO
    name: BRENDA Tissue Ontology
    prefix: BTO
  example: 0000590
  fairsharing:
    abbreviation: BTO
    contact:
      email: c.dudek@tu-braunschweig.de
      name: Christian-Alexander Dudek
      orcid: 0000-0001-9117-7909
    description: A structured controlled vocabulary for the source of an enzyme. It
      comprises terms for tissues, cell lines, cell types and cell cultures from uni-
      and multicellular organisms.
    domains:
    - Experimental measurement
    - Sample annotation
    - cell
    - enzyme
    - organ
    - tissue
    homepage: https://www.brenda-enzymes.org
    license: CC-BY-4.0
    name: The BRENDA Tissue Ontology
    prefix: FAIRsharing.1414v8
    publications:
    - doi: 10.1093/nar/gkq968
      pubmed: '21030441'
      title: 'The BRENDA Tissue Ontology (BTO): the first all-integrating ontology
        of all organisms for enzyme sources'
      year: 2010
    - doi: 10.1093/nar/gky1048
      pubmed: '30395242'
      title: 'BRENDA in 2019: a European ELIXIR core data resource'
      year: 2018
    - doi: 10.1093/nar/gkh081
      pubmed: '14681450'
      title: 'BRENDA, the enzyme database: updates and major new developments'
      year: 2003
    - doi: 10.1093/nar/gku1068
      pubmed: '25378310'
      title: 'BRENDA in 2015: exciting developments in its 25th year of existence'
      year: 2014
    - doi: 10.1093/nar/gks1049
      pubmed: '23203881'
      title: 'BRENDA in 2013: integrated reactions, kinetic data, enzyme function
        data, improved disease classification: new options and contents in BRENDA'
      year: 2012
    - doi: 10.1093/nar/gkaa1025
      title: 'BRENDA, the ELIXIR core data resource in 2021: new developments and
        updates'
      year: 2021
    repository: https://github.com/BRENDA-Enzymes/BTO
    subjects:
    - Life Science
    - Anatomy
    - Omics
    - Cell Biology
    - Enzymology
    - Proteomics
    - Genomics
  go:
    description: A structured controlled vocabulary for the source of an enzyme comprising
      tissues, cell lines, cell types and cell cultures.
    name: BRENDA tissue / enzyme ontology
    prefix: BTO
  logo: https://www.brenda-enzymes.org/images/brenda_logo.svg
  mappings:
    aberowl: BTO
    biocontext: BTO
    bioportal: BTO
    cellosaurus: BTO
    fairsharing: FAIRsharing.1414v8
    go: BTO
    miriam: bto
    n2t: bto
    obofoundry: bto
    ols: bto
    ontobee: BTO
    prefixcommons: bto
    tib: bto
    wikidata: P5501
    wikidata.entity: Q4836352
  miriam:
    deprecated: false
    description: The Brenda tissue ontology is a structured controlled vocabulary
      eastablished to identify the source of an enzyme cited in the Brenda enzyme
      database. It comprises terms of tissues, cell lines, cell types and cell cultures
      from uni- and multicellular organisms.
    homepage: http://bioportal.bioontology.org/ontologies/BTO
    id: '00000111'
    name: Brenda Tissue Ontology
    namespaceEmbeddedInLui: true
    pattern: ^BTO:\d{7}$
    prefix: bto
    sampleId: '0000146'
    uri_format: http://purl.bioontology.org/ontology/BTO/BTO:$1
  n2t:
    description: The Brenda tissue ontology is a structured controlled vocabulary
      eastablished to identify the source of an enzyme cited in the Brenda enzyme
      database. It comprises terms of tissues, cell lines, cell types and cell cultures
      from uni- and multicellular organisms.
    example: '0000146'
    homepage: http://bioportal.bioontology.org/ontologies/BTO
    name: Brenda Tissue Ontology through BioPortal
    namespaceEmbeddedInLui: true
    pattern: ^BTO:\d{7}$
    prefix: bto
    uri_format: http://purl.bioontology.org/ontology/BTO/BTO:$1
  name: BRENDA Tissue Ontology
  obofoundry:
    contact: c.dudek@tu-braunschweig.de
    contact.github: chdudek
    contact.label: Christian-Alexander Dudek
    contact.orcid: 0000-0001-9117-7909
    deprecated: false
    description: A structured controlled vocabulary for the source of an enzyme comprising
      tissues, cell lines, cell types and cell cultures.
    domain: anatomy and development
    download.json: http://purl.obolibrary.org/obo/bto.json
    download.obo: http://purl.obolibrary.org/obo/bto.obo
    download.owl: http://purl.obolibrary.org/obo/bto.owl
    homepage: http://www.brenda-enzymes.org
    license: CC BY 4.0
    license.url: https://creativecommons.org/licenses/by/4.0/
    name: BRENDA tissue / enzyme source
    preferredPrefix: BTO
    prefix: bto
    publications:
    - id: https://www.ncbi.nlm.nih.gov/pubmed/21030441
      title: 'The BRENDA Tissue Ontology (BTO): the first all-integrating ontology
        of all organisms for enzyme sources'
    repository: https://github.com/BRENDA-Enzymes/BTO
  ols:
    description: A structured controlled vocabulary for the source of an enzyme comprising
      tissues, cell lines, cell types and cell cultures.
    download_owl: http://purl.obolibrary.org/obo/bto.owl
    homepage: http://www.brenda-enzymes.org
    name: The BRENDA Tissue Ontology (BTO)
    prefix: bto
    tracker: https://github.com/BRENDA-Enzymes/BTO/issues
    version: '2021-10-26'
    version.iri: http://purl.obolibrary.org/obo/bto/releases/2021-10-26/bto.owl
  ontobee:
    library: Library
    name: BRENDA tissue / enzyme source
    prefix: BTO
  pattern: ^\d{7}$
  prefix: bto
  prefixcommons:
    alt_uri_formats:
    - http://purl.org/obo/owl/BTO#$1
    bioportal: '1005'
    description: The Brenda tissue ontology is a structured controlled vocabulary
      established to identify the source of an enzyme cited in the Brenda enzyme database.
      It comprises terms of tissues, cell lines, cell types and cell cultures from
      uni- and multicellular organisms.
    example: BTO:0000146
    homepage: http://www.brenda-enzymes.info
    keywords:
    - obo
    - tissue
    name: BRENDA Tissue Ontology
    pattern: ^BTO:\d{7}$
    prefix: bto
    synonyms:
    - brendatissueontology
    - obo.bto
  providers:
  - code: miriam_obo_legacy
    description: An old URI style for MIRIAM
    example: null
    first_party: null
    homepage: https://identifiers.org/
    name: MIRIAM OBO Legacy
    publications: null
    status: null
    uri_format: http://identifiers.org/obo.bto/BTO:$1
  publications:
  - doi: 10.1093/nar/gky1048
    pmc: PMC6323942
    pubmed: '30395242'
    title: 'BRENDA in 2019: a European ELIXIR core data resource'
    year: 2019
  - doi: 10.1093/nar/gku1068
    pmc: PMC4383907
    pubmed: '25378310'
    title: 'BRENDA in 2015: exciting developments in its 25th year of existence'
    year: 2014
  - doi: 10.1093/nar/gks1049
    pmc: PMC3531171
    pubmed: '23203881'
    title: 'BRENDA in 2013: integrated reactions, kinetic data, enzyme function data,
      improved disease classification: new options and contents in BRENDA'
    year: 2012
  - doi: 10.1093/nar/gkq968
    pmc: PMC3013802
    pubmed: '21030441'
    title: 'The BRENDA Tissue Ontology (BTO): the first all-integrating ontology of
      all organisms for enzyme sources'
    year: 2010
  - doi: 10.1093/nar/gkh081
    pmc: PMC308815
    pubmed: '14681450'
    title: 'BRENDA, the enzyme database: updates and major new developments'
    year: 2004
  - doi: null
    pmc: null
    pubmed: '21030441'
    title: 'The BRENDA Tissue Ontology (BTO): the first all-integrating ontology of
      all organisms for enzyme sources'
    year: null
  - doi: 10.1093/nar/gkq968
    pmc: null
    pubmed: '21030441'
    title: 'The BRENDA Tissue Ontology (BTO): the first all-integrating ontology of
      all organisms for enzyme sources'
    year: 2010
  - doi: 10.1093/nar/gky1048
    pmc: null
    pubmed: '30395242'
    title: 'BRENDA in 2019: a European ELIXIR core data resource'
    year: 2018
  - doi: 10.1093/nar/gkh081
    pmc: null
    pubmed: '14681450'
    title: 'BRENDA, the enzyme database: updates and major new developments'
    year: 2003
  - doi: 10.1093/nar/gku1068
    pmc: null
    pubmed: '25378310'
    title: 'BRENDA in 2015: exciting developments in its 25th year of existence'
    year: 2014
  - doi: 10.1093/nar/gks1049
    pmc: null
    pubmed: '23203881'
    title: 'BRENDA in 2013: integrated reactions, kinetic data, enzyme function data,
      improved disease classification: new options and contents in BRENDA'
    year: 2012
  - doi: 10.1093/nar/gkaa1025
    pmc: null
    pubmed: null
    title: 'BRENDA, the ELIXIR core data resource in 2021: new developments and updates'
    year: 2021
  - doi: null
    pmc: null
    pubmed: '21030441'
    title: 'The BRENDA Tissue Ontology (BTO): the first all-integrating ontology of
      all organisms for enzyme sources'
    year: null
  - doi: 10.1093/nar/gkq968
    pmc: null
    pubmed: '21030441'
    title: 'The BRENDA Tissue Ontology (BTO): the first all-integrating ontology of
      all organisms for enzyme sources'
    year: 2010
  - doi: 10.1093/nar/gky1048
    pmc: null
    pubmed: '30395242'
    title: 'BRENDA in 2019: a European ELIXIR core data resource'
    year: 2018
  - doi: 10.1093/nar/gkh081
    pmc: null
    pubmed: '14681450'
    title: 'BRENDA, the enzyme database: updates and major new developments'
    year: 2003
  - doi: 10.1093/nar/gku1068
    pmc: null
    pubmed: '25378310'
    title: 'BRENDA in 2015: exciting developments in its 25th year of existence'
    year: 2014
  - doi: 10.1093/nar/gks1049
    pmc: null
    pubmed: '23203881'
    title: 'BRENDA in 2013: integrated reactions, kinetic data, enzyme function data,
      improved disease classification: new options and contents in BRENDA'
    year: 2012
  - doi: 10.1093/nar/gkaa1025
    pmc: null
    pubmed: null
    title: 'BRENDA, the ELIXIR core data resource in 2021: new developments and updates'
    year: 2021
  - doi: null
    pmc: null
    pubmed: '21030441'
    title: 'The BRENDA Tissue Ontology (BTO): the first all-integrating ontology of
      all organisms for enzyme sources'
    year: null
  - doi: 10.1093/nar/gkq968
    pmc: null
    pubmed: '21030441'
    title: 'The BRENDA Tissue Ontology (BTO): the first all-integrating ontology of
      all organisms for enzyme sources'
    year: 2010
  - doi: 10.1093/nar/gky1048
    pmc: null
    pubmed: '30395242'
    title: 'BRENDA in 2019: a European ELIXIR core data resource'
    year: 2018
  - doi: 10.1093/nar/gkh081
    pmc: null
    pubmed: '14681450'
    title: 'BRENDA, the enzyme database: updates and major new developments'
    year: 2003
  - doi: 10.1093/nar/gku1068
    pmc: null
    pubmed: '25378310'
    title: 'BRENDA in 2015: exciting developments in its 25th year of existence'
    year: 2014
  - doi: 10.1093/nar/gks1049
    pmc: null
    pubmed: '23203881'
    title: 'BRENDA in 2013: integrated reactions, kinetic data, enzyme function data,
      improved disease classification: new options and contents in BRENDA'
    year: 2012
  - doi: 10.1093/nar/gkaa1025
    pmc: null
    pubmed: null
    title: 'BRENDA, the ELIXIR core data resource in 2021: new developments and updates'
    year: 2021
  synonyms:
  - BTO
  tib:
    description: A structured controlled vocabulary for the source of an enzyme comprising
      tissues, cell lines, cell types and cell cultures.
    download_owl: http://purl.obolibrary.org/obo/bto.owl
    homepage: http://www.brenda-enzymes.org
    keywords:
    - NFDI4CHEM
    - DataPLANT
    - life sciences, biology
    - medicine
    name: The BRENDA Tissue Ontology (BTO)
    prefix: bto
    tracker: https://github.com/BRENDA-Enzymes/BTO/issues
    version.iri: http://purl.obolibrary.org/obo/bto/releases/2021-10-26/bto.owl
  uri_format: http://purl.obolibrary.org/obo/BTO_$1
  wikidata:
    database: Q4836352
    description: identifier in the Brenda Tissue Ontology
    example:
    - BTO:0000562
    - BTO:0001172
    homepage: https://www.brenda-enzymes.org/ontology.php?ontology_id=3
    name: Brenda Tissue Ontology ID
    pattern: ^BTO:\d+$
    prefix: P5501
    uri_format: https://www.brenda-enzymes.org/ontology.php?ontology_id=3&id_go=$1
bugbase.expt:
  biocontext:
    prefix: BUGBASE.EXPT
  mappings:
    biocontext: BUGBASE.EXPT
    miriam: bugbase.expt
    n2t: bugbase.expt
  miriam:
    deprecated: true
    description: BugBase is a MIAME-compliant microbial gene expression and comparative
      genomic database. It stores experimental annotation and multiple raw and analysed
      data formats, as well as protocols for bacterial microarray designs. This collection
      references microarray experiments.
    homepage: http://bugs.sgul.ac.uk/E-BUGS
    id: '00000404'
    name: BugBase Expt
    namespaceEmbeddedInLui: false
    pattern: ^\d+$
    prefix: bugbase.expt
    sampleId: '288'
    uri_format: http://bugs.sgul.ac.uk/bugsbase/tabs/experiment.php?expt_id=$1&action=view
  n2t:
    description: BugBase is a MIAME-compliant microbial gene expression and comparative
      genomic database. It stores experimental annotation and multiple raw and analysed
      data formats, as well as protocols for bacterial microarray designs. This collection
      references microarray experiments.
    example: '288'
    homepage: http://bugs.sgul.ac.uk/E-BUGS
    name: BugBase Expt at University of London
    namespaceEmbeddedInLui: false
    pattern: ^\d+$
    prefix: bugbase.expt
    uri_format: http://bugs.sgul.ac.uk/bugsbase/tabs/experiment.php?expt_id=$1&action=view
  prefix: bugbase.expt
  uri_format: http://bugs.sgul.ac.uk/bugsbase/tabs/experiment.php?action=view&expt_id=$1
bugbase.protocol:
  biocontext:
    prefix: BUGBASE.PROTOCOL
  mappings:
    biocontext: BUGBASE.PROTOCOL
    miriam: bugbase.protocol
    n2t: bugbase.protocol
  miriam:
    deprecated: true
    description: BugBase is a MIAME-compliant microbial gene expression and comparative
      genomic database. It stores experimental annotation and multiple raw and analysed
      data formats, as well as protocols for bacterial microarray designs. This collection
      references design protocols.
    homepage: http://bugs.sgul.ac.uk/E-BUGS
    id: '00000403'
    name: BugBase Protocol
    namespaceEmbeddedInLui: false
    pattern: ^\d+$
    prefix: bugbase.protocol
    sampleId: '67'
    uri_format: http://bugs.sgul.ac.uk/bugsbase/tabs/protocol.php?protocol_id=$1&amp;action=view
  n2t:
    description: BugBase is a MIAME-compliant microbial gene expression and comparative
      genomic database. It stores experimental annotation and multiple raw and analysed
      data formats, as well as protocols for bacterial microarray designs. This collection
      references design protocols.
    example: '67'
    homepage: http://bugs.sgul.ac.uk/E-BUGS
    name: BugBase Protocol at University of London
    namespaceEmbeddedInLui: false
    pattern: ^\d+$
    prefix: bugbase.protocol
    uri_format: http://bugs.sgul.ac.uk/bugsbase/tabs/protocol.php?protocol_id=$1&amp;action=view
  prefix: bugbase.protocol
  uri_format: http://bugs.sgul.ac.uk/bugsbase/tabs/protocol.php?action=view&protocol_id=$1
building:
  aberowl:
    download_owl: http://aber-owl.net/media/ontologies/building/1/building.owl
    name: Building and Sub Elements
    prefix: building
    version: '1.0'
  example: AirConditioningUnit
  mappings:
    aberowl: building
    tib: building
  prefix: building
  tib:
    description: The Building ontology has been developed to perform as the core module
      of the BIMERR Ontology Network, containing information related to building topology,
      and components. The model is constructed as an extention of the BOT ontology
      that provides the vocabulary to describe the topology of a building as well
      as the relationships between their main components such as zones, spaces, and
      building elements. The taxonomy of building components is based on the proposed
      by the IFC 4.1 standard.
    homepage: https://bimerr.iot.linkeddata.es/def/building/
    keywords:
    - NFDI4ING
    - Digital Planning and Construction
    - FID BAUdigital
    - civil engineering
    - architecture
    name: Building Ontology
    prefix: building
    uri_format: http://bimerr.iot.linkeddata.es/def/building#$1
bykdb:
  biocontext:
    prefix: BYKDB
  contact:
    email: cozzone@ibcp.fr
    github: null
    name: Alain J. Cozzone
    orcid: null
  fairsharing:
    abbreviation: BYKdb
    description: The Bacterial protein tYrosine Kinase database (BYKdb) contains computer-annotated
      BY-kinase sequences. The database web interface allows static and dynamic queries
      and provides integrated analysis tools including sequence annotation.
    homepage: http://bykdb.ibcp.fr
    name: Bacterial protein tYrosine Kinase database
    prefix: FAIRsharing.jr30xc
    publications:
    - doi: 10.1016/s0378-1119(97)00554-4
      pubmed_id: 9434192
      title: Characterization of a bacterial gene encoding an autophosphorylating
        protein tyrosine kinase.
    - doi: 10.1093/bioinformatics/btn462
      pubmed_id: 18772155
      title: Identification of the idiosyncratic bacterial protein tyrosine kinase
        (BY-kinase) family signature.
    - doi: 10.1007/s00726-009-0237-8
      pubmed_id: 19189200
      title: 'Tyrosine-kinases in bacteria: from a matter of controversy to the status
        of key regulatory enzymes.'
    - doi: 10.1093/nar/gkr915
      pubmed_id: 22080550
      title: 'BYKdb: the Bacterial protein tYrosine Kinase database.'
    subjects:
    - Life Science
  mappings:
    biocontext: BYKDB
    fairsharing: FAIRsharing.jr30xc
    miriam: bykdb
    n2t: bykdb
    prefixcommons: bykdb
  miriam:
    deprecated: false
    description: The bacterial tyrosine kinase database (BYKdb) that collects sequences
      of putative and authentic bacterial tyrosine kinases,  providing structural
      and functional information.
    homepage: https://bykdb.lyon.inserm.fr/BYKdb/BYKdbIndex
    id: '00000253'
    name: BYKdb
    namespaceEmbeddedInLui: false
    pattern: ^[A-Z0-9]+$
    prefix: bykdb
    sampleId: A0A009HB13
    uri_format: https://bykdb.lyon.inserm.fr/data/html/annotated/$1.html
  n2t:
    description: The bacterial tyrosine kinase database (BYKdb) that collects sequences
      of putative and authentic bacterial tyrosine kinases,  providing structural
      and functional information.
    example: A0A009E7X8
    homepage: https://bykdb.ibcp.fr/BYKdb/
    name: BYKdb at CNRS
    namespaceEmbeddedInLui: false
    pattern: ^[A-Z0-9]+$
    prefix: bykdb
    uri_format: https://bykdb.ibcp.fr/data/html/annotated/$1.html
  name: Bacterial Tyrosine Kinase Database
  prefix: bykdb
  prefixcommons:
    description: The bacterial tyrosine kinase database (BYKdb) that collects sequences
      of putative and authentic bacterial tyrosine kinases,  providing structural
      and functional information.
    example: A0AYT5
    homepage: http://bykdb.ibcp.fr/BYKdb/
    keywords:
    - domain
    - microbial
    - sequence
    name: Bacterial Tyrosine Kinase Database
    pattern: ^\w+$
    prefix: bykdb
    pubmed_ids:
    - '22080550'
    uri_format: http://bykdb.ibcp.fr/data/html/$1.html
  provides: uniprot
  publications:
  - doi: 10.1093/nar/gkr915
    pmc: PMC3245071
    pubmed: '22080550'
    title: 'BYKdb: the Bacterial protein tYrosine Kinase database'
    year: 2011
  - doi: 10.1007/s00726-009-0237-8
    pmc: null
    pubmed: '19189200'
    title: 'Tyrosine-kinases in bacteria: from a matter of controversy to the status
      of key regulatory enzymes'
    year: 2009
  - doi: 10.1093/bioinformatics/btn462
    pmc: null
    pubmed: '18772155'
    title: Identification of the idiosyncratic bacterial protein tyrosine kinase (BY-kinase)
      family signature
    year: 2008
  - doi: 10.1016/s0378-1119(97)00554-4
    pmc: null
    pubmed: '9434192'
    title: Characterization of a bacterial gene encoding an autophosphorylating protein
      tyrosine kinase
    year: 1997
  - doi: 10.1016/s0378-1119(97)00554-4
    pmc: null
    pubmed: null
    title: Characterization of a bacterial gene encoding an autophosphorylating protein
      tyrosine kinase.
    year: null
  - doi: 10.1093/bioinformatics/btn462
    pmc: null
    pubmed: null
    title: Identification of the idiosyncratic bacterial protein tyrosine kinase (BY-kinase)
      family signature.
    year: null
  - doi: 10.1007/s00726-009-0237-8
    pmc: null
    pubmed: null
    title: 'Tyrosine-kinases in bacteria: from a matter of controversy to the status
      of key regulatory enzymes.'
    year: null
  - doi: 10.1093/nar/gkr915
    pmc: null
    pubmed: null
    title: 'BYKdb: the Bacterial protein tYrosine Kinase database.'
    year: null
  - doi: null
    pmc: null
    pubmed: '22080550'
    title: null
    year: null
  - doi: 10.1016/s0378-1119(97)00554-4
    pmc: null
    pubmed: null
    title: Characterization of a bacterial gene encoding an autophosphorylating protein
      tyrosine kinase.
    year: null
  - doi: 10.1093/bioinformatics/btn462
    pmc: null
    pubmed: null
    title: Identification of the idiosyncratic bacterial protein tyrosine kinase (BY-kinase)
      family signature.
    year: null
  - doi: 10.1007/s00726-009-0237-8
    pmc: null
    pubmed: null
    title: 'Tyrosine-kinases in bacteria: from a matter of controversy to the status
      of key regulatory enzymes.'
    year: null
  - doi: 10.1093/nar/gkr915
    pmc: null
    pubmed: null
    title: 'BYKdb: the Bacterial protein tYrosine Kinase database.'
    year: null
  - doi: null
    pmc: null
    pubmed: '22080550'
    title: null
    year: null
c4o:
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: An ontology that permits the number of in-text citations of a cited
    source to be recorded, together with their textual citation contexts, along with
    the number of citations a cited entity has received globally on a particular date.
  example: InTextReferencePointer
  fairsharing:
    abbreviation: C4O
    contact:
      email: silvio.peroni@unibo.it
      name: Silvio Peroni
      orcid: 0000-0003-0530-4305
    description: The Citation Counting and Context Characterisation Ontology (C4O)
      is an ontology that permits the number of in-text citations of a cited source
      to be recorded, together with their textual citation contexts, along with the
      number of citations a cited entity has received globally on a particular date;
    homepage: http://www.sparontologies.net/ontologies/c4o
    license: CC-BY-4.0
    name: 'Citation Counting and Context Characterization Ontology '
    prefix: FAIRsharing.beb855
    repository: https://github.com/sparontologies/c4o
    subjects:
    - Subject Agnostic
    twitter: sparontologies
  homepage: http://www.sparontologies.net/ontologies/c4o
  lov:
    description: C4O allows the characterization of bibliographic citations in terms
      of their number and their context.
    homepage: http://purl.org/spar/c4o
    keywords:
    - SPAR
    modified: '2013-05-11'
    name: C4O, the Citation Counting and Context Characterization Ontology
    prefix: c4o
    uri_prefix: http://purl.org/spar/c4o/$1
  mappings:
    fairsharing: FAIRsharing.beb855
    lov: c4o
  name: Citation Counting and Context Characterisation Ontology
  preferred_prefix: C4O
  prefix: c4o
  repository: https://github.com/sparontologies/c4o
  uri_format: http://purl.org/spar/c4o/$1
cabi:
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: Research and learning in agriculture, the environment and the applied
    life sciences
  example: '20000614040'
  github_request_issue: 1313
  homepage: https://www.cabidigitallibrary.org
  name: CABI Digital Library
  pattern: ^\d+$
  prefix: cabi
  uri_format: https://www.cabi.org/cabebooks/ebook/$1
cabri:
  biocontext:
    prefix: CABRI
  edam:
    description: A unique identifier of an item from the CABRI database.
    name: CABRI
    obsolete: false
    prefix: '2380'
  fairsharing:
    abbreviation: CABRI
    contact:
      email: paolo.romano@hsanmartino.it
      name: Paolo Romano
      orcid: 0000-0003-4694-3883
    description: CABRI provides an integrated resource including catalogues of strains
      of different organism types, genetic materials and other biologicals resources
      of European culture collections so that the user world-wide can access these
      relevant data during one searching session through a common entry point and
      get in touch with collections for ordering products to be delivered to their
      place of work.
    homepage: http://www.cabri.org
    name: Common Access to Biological Resources and Information
    prefix: FAIRsharing.qx2rvz
    publications:
    - doi: 10.1002/cfg.376
      pubmed_id: 18629057
      title: Interoperability of CABRI Services and Biochemical Pathways Databases.
    - doi: null
      pubmed_id: 16231959
      title: The role of informatics in the coordinated management of biological resources
        collections.
    subjects:
    - Molecular biology
    - Medical Microbiology
    - Applied Microbiology
    - Virology
    - Molecular Microbiology
    - Microbiology
  mappings:
    biocontext: CABRI
    edam: '2380'
    fairsharing: FAIRsharing.qx2rvz
    miriam: cabri
    n2t: cabri
    ncbi: CABRI
  miriam:
    deprecated: false
    description: CABRI (Common Access to Biotechnological Resources and Information)
      is an online service where users can search a number of European Biological
      Resource Centre catalogues. It lists the availability of a particular organism
      or genetic resource and defines the set of technical specifications and procedures
      which should be used to handle it.
    homepage: http://www.cabri.org/
    id: '00000261'
    name: CABRI
    namespaceEmbeddedInLui: false
    pattern: ^([A-Za-z]+)?(\_)?([A-Za-z-]+)\:([A-Za-z0-9 ]+)$
    prefix: cabri
    providers:
    - code: ''
      description: CABRI Cell Lines catalogue in Brussels (SRS)
      homepage: http://www.be.cabri.org/
      name: CABRI Cell Lines catalogue in Brussels (SRS)
      uri_format: http://www.be.cabri.org/CABRI/srs-bin/wgetz?-e+-page+EntryPage+[$1]
    sampleId: dsmz_mutz-id:ACC 291
    uri_format: http://www.cabri.org/CABRI/srs-bin/wgetz?-e+-page+EntryPage+[$1]
  n2t:
    description: CABRI (Common Access to Biotechnological Resources and Information)
      is an online service where users can search a number of European Biological
      Resource Centre catalogues. It lists the availability of a particular organism
      or genetic resource and defines the set of technical specifications and procedures
      which should be used to handle it.
    example: dsmz_mutz-id:ACC 291
    homepage: http://www.cabri.org/
    name: CABRI Cell Lines catalogue in Genova (SRS)
    namespaceEmbeddedInLui: false
    pattern: ^([A-Za-z]+)?(\_)?([A-Za-z-]+)\:([A-Za-z0-9 ]+)$
    prefix: cabri
    uri_format: http://www.cabri.org/CABRI/srs-bin/wgetz?-e+-page+EntryPage+[$1]
  ncbi:
    example: ACC 424
    name: Common Access to Biological Resources and Information Project
    prefix: CABRI
  prefix: cabri
  publications:
  - doi: 10.2165/00822942-200594030-00002
    pmc: null
    pubmed: '16231959'
    title: The role of informatics in the coordinated management of biological resources
      collections
    year: 2005
  - doi: 10.1002/cfg.376
    pmc: PMC2447341
    pubmed: '18629057'
    title: Interoperability of CABRI Services and Biochemical Pathways Databases
    year: 2004
cadsr:
  mappings:
    miriam: cadsr
    n2t: cadsr
  miriam:
    deprecated: false
    description: The US National Cancer Institute (NCI) maintains and administers
      data elements, forms, models, and components of these items in a metadata registry
      referred to as the Cancer Data Standards Registry and Repository, or caDSR.
    homepage: https://wiki.nci.nih.gov/display/caDSR/caDSR+Wiki
    id: 00000695
    name: Cancer Data Standards Registry and Repository
    namespaceEmbeddedInLui: false
    pattern: ^[0-9]*$
    prefix: cadsr
    sampleId: '3771992'
    uri_format: https://cadsrapi.nci.nih.gov/cadsrapi4/GetXML?query=DataElement[@publicId=$1]
  n2t:
    description: The US National Cancer Institute (NCI) maintains and administers
      data elements, forms, models, and components of these items in a metadata registry
      referred to as the Cancer Data Standards Registry and Repository, or caDSR.
    example: '3771992'
    homepage: https://wiki.nci.nih.gov/display/caDSR/caDSR+Wiki
    name: Cancer Data Standards Registry and Repository
    namespaceEmbeddedInLui: false
    pattern: ^[0-9]*$
    prefix: cadsr
    uri_format: https://cadsrapi.nci.nih.gov/cadsrapi4/GetXML?query=DataElement[@publicId=$1]
  prefix: cadsr
caloha:
  contact:
    email: Paula.Duek@sib.swiss
    github: paulacalipho
    name: Paula Duek Roggli
    orcid: 0000-0002-0819-0473
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: This is a code repository for the SIB - Swiss Institute of Bioinformatics
    CALIPHO group neXtProt project, which is a comprehensive human-centric discovery
    platform, that offers a integration of and navigation through protein-related
    data. CALIPHO is an interdisciplinary team which aims to use a variety of methodologies
    to help uncover the function of uncharacterized human proteins.
  download_obo: https://raw.githubusercontent.com/calipho-sib/controlled-vocabulary/master/caloha.obo
  example: TS-0001
  homepage: https://github.com/calipho-sib/controlled-vocabulary
  keywords:
  - anatomy
  - human
  - physiology
  license: CC-BY-4.0
  name: CALIPHO Group Ontology of Human Anatomy
  pattern: ^TS-\d+$
  prefix: caloha
  providers:
  - code: biopragmatics
    description: A static site generated from the CALOHA OBO flat file
    example: null
    first_party: null
    homepage: https://biopragmatics.github.io/providers
    name: Biopragmatics Browser
    publications: null
    status: null
    uri_format: https://biopragmatics.github.io/providers/caloha/$1
  references:
  - https://twitter.com/neXtProt_news/status/1350105997633867781
  - https://github.com/biopragmatics/bioregistry/issues/721
  repository: https://github.com/calipho-sib/controlled-vocabulary
  twitter: neXtProt_news
  uri_format: https://www.nextprot.org/term/$1
cameo:
  biocontext:
    prefix: CAMEO
  fairsharing:
    abbreviation: CAMEO
    contact:
      email: torsten.schwede@unibas.ch
      name: Torsten Schwede
      orcid: 0000-0003-2715-335X
    description: Continuous automated benchmarking of computational protein structure
      prediction methods (and model quality estimation techniques). CAMEO assessment
      is based on blind predictions for weekly pre-released targets from PDB. Benchmarking
      results are made available as reference data for methods development.
    homepage: http://cameo3d.org/
    license: http://cameo3d.org/cameong_terms
    name: Continuously Automated Model Evaluation
    prefix: FAIRsharing.dq34p2
    publications:
    - doi: 10.1093/database/bat031
      pubmed_id: 23624946
      title: The Protein Model Portal--a comprehensive resource for protein structure
        and model information.
    subjects:
    - Life Science
  mappings:
    biocontext: CAMEO
    fairsharing: FAIRsharing.dq34p2
    miriam: cameo
    n2t: cameo
  miriam:
    deprecated: false
    description: The goal of the CAMEO (Continuous Automated Model EvaluatiOn) community
      project is to continuously evaluate the accuracy and reliability of protein
      structure prediction servers, offering scores on  tertiary and quaternary structure
      prediction, model quality estimation, accessible surface area prediction, ligand
      binding site residue prediction and contact prediction services in a fully automated
      manner. These predictions are regularly compared against reference structures
      from PDB.
    homepage: https://cameo3d.org
    id: '00000623'
    name: CAMEO
    namespaceEmbeddedInLui: false
    pattern: ^[0-9\-_]+$
    prefix: cameo
    sampleId: 2019-08-03_00000089_1
    uri_format: https://www.cameo3d.org/sp/targets/target/$1
  n2t:
    description: The goal of the CAMEO (Continuous Automated Model EvaluatiOn) community
      project is to continuously evaluate the accuracy and reliability of protein
      structure prediction servers, offering scores on  tertiary and quaternary structure
      prediction, model quality estimation, accessible surface area prediction, ligand
      binding site residue prediction and contact prediction services in a fully automated
      manner. These predictions are regularly compared against reference structures
      from PDB.
    example: 2018-03-24_00000030_1
    homepage: https://cameo3d.org
    name: CAMEO
    namespaceEmbeddedInLui: false
    pattern: ^[0-9\-_]+$
    prefix: cameo
    uri_format: https://www.cameo3d.org/sp/targets/target/$1
  name: Continuous Automated Model Evaluation
  prefix: cameo
  publications:
  - doi: 10.1093/database/bat031
    pmc: PMC3889916
    pubmed: '23624946'
    title: The Protein Model Portal--a comprehensive resource for protein structure
      and model information
    year: 2013
  - doi: 10.1093/database/bat031
    pmc: null
    pubmed: null
    title: The Protein Model Portal--a comprehensive resource for protein structure
      and model information.
    year: null
cao:
  aberowl:
    description: CAO ontology is designed for supporting the COG enrichment study
      by using Fisher's exact test
    download_owl: http://aber-owl.net/media/ontologies/CAO/3/cao.owl
    homepage: http://cao.sourceforge.net/
    name: Clusters of Orthologous Groups (COG) Analysis Ontology
    prefix: CAO
    version: '1.4'
  bartoc:
    abbreviation: CAO
    description: The Chemical Analysis Ontology (CAO) is organized using the BFO framework
      with entries primarily under concepts (not complete by any means), material
      entities, information content entities (data items), roles, and processes. Currently,
      the ontology is more of a vocabulary in that development of predicates (ontology
      properties) that relate subjects to objects has not been a focal point.
    homepage: https://champ.stuchalk.domains.unf.edu/cao
    license: CC-BY-3.0
    name: Chemical Analysis Ontology
    prefix: '20701'
  bioportal:
    contact:
      email: linikujp@gmail.com
      name: Asiyah Yu Lin
    description: CAO ontology is designed for supporting the COG enrichment study
      by using Fisher's exact test
    homepage: http://cao.sourceforge.net/
    name: Clusters of Orthologous Groups (COG) Analysis Ontology
    prefix: CAO
    publications:
    - http://www.hegroup.org/docs/OntoCOG_ICBO-2011_Proceeding.pdf
    version: '1.4'
  contact:
    email: williams.antony@epa.gov
    github: null
    name: Antony Williams
    orcid: 0000-0002-2668-4821
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: 'An ontology developed as part of the Chemical Analysis Metadata Project
    (ChAMP) as a resource to semantically annotate standards developed using the ChAMP
    platform. (source: CAO ontology)'
  example: '000064'
  fairsharing:
    abbreviation: CAO
    description: CAO ontology is designed for supporting the COG enrichment study
      by using Fisher's exact test. It is used for the ontology based application
      for statistical analysis on COG db.
    domains:
    - Annotation
    - protein
    - transcript
    - gene
    - polypeptide region
    - orthologous
    homepage: http://sourceforge.net/projects/cao/
    name: Clusters of Orthologous Groups (COG) Analysis Ontology
    prefix: FAIRsharing.wp0134
    publications:
    - doi: 10.1126/science.278.5338.631
      pubmed: '9381173'
      title: A genomic perspective on protein families
      year: 1997
    subjects:
    - Life Science
    - Phylogenetics
    - Genetics
  homepage: https://champ.stuchalk.domains.unf.edu
  keywords:
  - characterisation data heat
  - transport and kinetic data
  license: CC-BY-3.0
  mappings:
    aberowl: CAO
    bartoc: '20701'
    bioportal: CAO
    fairsharing: FAIRsharing.wp0134
    ols: cao
    tib: cao
  name: Chemical Analysis Ontology
  ols:
    contact: schalk@unf.edu
    description: The Chemical Analysis Ontology (CAO) is an ontology developed as
      part of the Chemical Analaysis Metadata Project (ChAMP) as a resource to semantically
      annotate standards developed using the ChAMP platform.  For more information
      go to http://champ-project.org.
    download_owl: https://champ.stuchalk.domains.unf.edu/images/ontology/cao.owl
    homepage: https://champ.stuchalk.domains.unf.edu/cao
    name: Chemical Analysis Metadata Platform (ChAMP) Ontology version 0.2
    prefix: cao
    uri_format: http://champ-project.org/images/ontology/cao.owl#CAO_$1
    version: '0.2'
  pattern: ^\d+$
  prefix: cao
  repository: https://github.com/stuchalk/chemical-analysis-ontology
  tib:
    description: The Chemical Analysis Ontology (CAO) is an ontology developed as
      part of the Chemical Analaysis Metadata Project (ChAMP) as a resource to semantically
      annotate standards developed using the ChAMP platform.  For more information
      go to http://champ-project.org.
    download_owl: https://champ.stuchalk.domains.unf.edu/images/ontology/cao.owl
    keywords:
    - NFDI4CAT
    - chemistry
    license: http://creativecommons.org/licenses/by/3.0/
    name: Chemical Analysis Metadata Platform (ChAMP) Ontology version 0.2
    prefix: cao
    uri_format: http://champ-project.org/images/ontology/cao.owl#CAO_$1
  uri_format: http://champ-project.org/images/ontology/cao.owl#CAO_$1
caps:
  biocontext:
    prefix: CAPS
  mappings:
    biocontext: CAPS
    miriam: caps
    n2t: caps
  miriam:
    deprecated: false
    description: CAPS-DB is a structural classification of helix-cappings or caps
      compiled from protein structures. The regions of the polypeptide chain immediately
      preceding or following an alpha-helix are known as Nt- and Ct cappings, respectively.
      Caps extracted from protein structures have been structurally classified based
      on geometry and conformation and organized in a tree-like hierarchical classification
      where the different levels correspond to different properties of the caps.
    homepage: http://www.bioinsilico.org/cgi-bin/CAPSDB/staticHTML/home
    id: 00000396
    name: CAPS-DB
    namespaceEmbeddedInLui: false
    pattern: ^\d+$
    prefix: caps
    sampleId: '434'
    uri_format: http://www.bioinsilico.org/cgi-bin/CAPSDB/getCAPScluster?nidcl=$1
  n2t:
    description: CAPS-DB is a structural classification of helix-cappings or caps
      compiled from protein structures. The regions of the polypeptide chain immediately
      preceding or following an alpha-helix are known as Nt- and Ct cappings, respectively.
      Caps extracted from protein structures have been structurally classified based
      on geometry and conformation and organized in a tree-like hierarchical classification
      where the different levels correspond to different properties of the caps.
    example: '434'
    homepage: http://www.bioinsilico.org/cgi-bin/CAPSDB/staticHTML/home
    name: CAPS-DB at Leeds Institute of Molecular Medicine
    namespaceEmbeddedInLui: false
    pattern: ^\d+$
    prefix: caps
    uri_format: http://www.bioinsilico.org/cgi-bin/CAPSDB/getCAPScluster?nidcl=$1
  prefix: caps
carnegie.stage:
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: One of the 23 stages of embryo development
  example: '20'
  github_request_issue: 1325
  homepage: https://embryology.med.unsw.edu.au/embryology/index.php/Carnegie_Stages
  name: Carnegie Stage
  pattern: ^\d+$
  prefix: carnegie.stage
  uri_format: https://embryology.med.unsw.edu.au/embryology/index.php/Carnegie_Stages#Stage_$1
caro:
  aberowl:
    description: An upper level ontology to facilitate interoperability between existing
      anatomy ontologies for different species
    download_owl: http://aber-owl.net/media/ontologies/CARO/17/caro.owl
    homepage: https://github.com/obophenotype/caro/
    name: Common Anatomy Reference Ontology
    prefix: CARO
  biocontext:
    prefix: CARO
  bioportal:
    contact:
      email: haendel@ohsu.edu
      name: Melissa Haendel
    description: 'The Common Anatomy Reference Ontology (CARO) is being developed
      to facilitate interoperability between existing anatomy ontologies for different
      species, and will provide a template for building new anatomy ontologies. CARO
      will be described in Anatomy Ontologies for Bioinformatics: Principles and Practice
      Albert Burger, Duncan Davidson and Richard Baldock (Editors)'
    homepage: https://github.com/obophenotype/caro/
    name: Common Anatomy Reference Ontology
    prefix: CARO
    version: '2023-03-15'
  download_json: http://purl.obolibrary.org/obo/caro.json
  download_obo: http://purl.obolibrary.org/obo/caro.obo
  example: '0000000'
  fairsharing:
    abbreviation: CARO
    contact:
      email: haendel@ohsu.edu
      name: Melissa Haendel
      orcid: 0000-0001-9114-8737
    description: The Common Anatomy Reference Ontology (CARO) is being developed to
      facilitate interoperability between existing anatomy ontologies for different
      species, and will provide a template for building new anatomy ontologies.
    domains:
    - Annotation
    homepage: http://bioportal.bioontology.org/ontologies/CARO?p=summary
    name: Common Anatomy Reference Ontology
    prefix: FAIRsharing.3kcgmr
    publications:
    - doi: 10.1007/978-1-84628-885-2_16
      title: CARO – The Common Anatomy Reference Ontology
      year: 2008
    subjects:
    - Life Science
    - Anatomy
  go:
    description: An upper ontology for anatomy used by OBO Foundry ontologies. Used
      to facilitate interoperability between existing anatomy ontologies for different
      species
    name: Common Anatomy Reference Ontology
    prefix: CARO
  mappings:
    aberowl: CARO
    biocontext: CARO
    bioportal: CARO
    fairsharing: FAIRsharing.3kcgmr
    go: CARO
    obofoundry: caro
    ols: caro
    ontobee: CARO
    wikidata.entity: Q55118319
  obofoundry:
    appears_in:
    - aism
    - colao
    - gallont
    - lepao
    - pco
    - ehdaa2
    contact: haendel@ohsu.edu
    contact.github: mellybelly
    contact.label: Melissa Haendel
    contact.orcid: 0000-0001-9114-8737
    deprecated: true
    description: An upper level ontology to facilitate interoperability between existing
      anatomy ontologies for different species
    domain: anatomy and development
    download.owl: http://purl.obolibrary.org/obo/caro.owl
    homepage: https://github.com/obophenotype/caro/
    license: CC BY 4.0
    license.url: https://creativecommons.org/licenses/by/4.0/
    name: Common Anatomy Reference Ontology
    preferredPrefix: CARO
    prefix: caro
    repository: https://github.com/obophenotype/caro
  ols:
    description: The Common Anatomy Reference Ontology (CARO) is being developed to
      facilitate interoperability between existing anatomy ontologies for different
      species, and will provide a template for building new anatomy ontologies.
    homepage: https://github.com/obophenotype/caro/
    name: Common Anatomy Reference Ontology
    prefix: caro
    tracker: https://github.com/obophenotype/caro/issues
    version: '2023-03-15'
    version.iri: http://purl.obolibrary.org/obo/caro/releases/2023-03-15/caro.owl
  ontobee:
    library: Library
    name: Common Anatomy Reference Ontology
    prefix: CARO
  pattern: ^\d{7}$
  prefix: caro
  providers:
  - code: obo.1
    description: This incorrect encoding was found inside IDO-COVID-19
    example: null
    first_party: null
    homepage: http://purl.obolibrary.org
    name: Nonstandard OBO PURL
    publications: null
    status: null
    uri_format: http://purl.obolibrary.org/obo/ido.owl/CARO_$1
  publications:
  - doi: 10.1007/978-1-84628-885-2_16
    pmc: null
    pubmed: null
    title: CARO – The Common Anatomy Reference Ontology
    year: 2008
  - doi: 10.1007/978-1-84628-885-2_16
    pmc: null
    pubmed: null
    title: CARO – The Common Anatomy Reference Ontology
    year: 2008
  uri_format: http://purl.obolibrary.org/obo/CARO_$1
cas:
  biocontext:
    prefix: CAS
  cheminf:
    description: Identifier used by the Chemical Abstracts Service database.
    name: CAS registry number
    obsolete: false
    prefix: '000446'
  contact:
    email: ajacobs@cas.org
    github: null
    name: Andrea Jacobs
    orcid: 0000-0001-9316-9400
  edam:
    description: CAS registry number of a chemical compound; a unique numerical identifier
      of chemicals in the scientific literature, as assigned by the Chemical Abstracts
      Service.
    name: CAS number
    obsolete: false
    prefix: '1002'
  fairsharing:
    abbreviation: CAS RN
    description: Identifier used by the Chemical Abstracts Service Registry. A CAS
      Registry Number is a numeric identifier that can contain up to 10 digits, divided
      by hyphens into three parts. The right-most digit is a check digit used to verify
      the validity and uniqueness of the entire number.
    domains:
    - chemical entity
    homepage: https://www.cas.org/cas-data/cas-registry
    name: CAS Registry Number
    prefix: FAIRsharing.r7Kwy7
    publications:
    - doi: 10.1021/acs.jcim.2c00268
      title: 'CAS Common Chemistry in 2021: Expanding Access to Trusted Chemical Information
        for the Scientific Community'
      year: 2022
    subjects:
    - Physical Chemistry
  go:
    description: CAS REGISTRY is the most authoritative collection of disclosed chemical
      substance information, containing more than 54 million organic and inorganic
      substances and 62 million sequences. CAS REGISTRY covers substances identified
      from the scientific literature from 1957 to the present, with additional substances
      going back to the early 1900s.
    homepage: http://www.cas.org/expertise/cascontent/registry/index.html
    name: CAS Chemical Registry
    prefix: CAS
  hl7:
    description: Chemical abstract codes
    name: CAS
    preferred_prefix: CAS
    prefix: 2.16.840.1.113883.6.61
    status: Pending
  logo: https://upload.wikimedia.org/wikipedia/en/2/2a/Chemical_Abstracts_Service_logo.svg
  mappings:
    biocontext: CAS
    cheminf: '000446'
    edam: '1002'
    fairsharing: FAIRsharing.r7Kwy7
    go: CAS
    hl7: 2.16.840.1.113883.6.61
    miriam: cas
    n2t: cas
    prefixcommons: cas
    wikidata: P231
  miriam:
    deprecated: false
    description: CAS (Chemical Abstracts Service) is a division of the American Chemical
      Society and is the producer of comprehensive databases of chemical information.
    homepage: https://commonchemistry.cas.org/
    id: '00000237'
    name: CAS
    namespaceEmbeddedInLui: false
    pattern: ^\d{1,7}\-\d{2}\-\d$
    prefix: cas
    providers:
    - code: scholia
      description: Scholia is a service that creates visual scholarly profiles for
        topic, people, organizations, species, chemicals, etc using bibliographic
        and other information in Wikidata.
      homepage: https://scholia.toolforge.org/
      name: Scholia
      uri_format: https://scholia.toolforge.org/cas/$1
    sampleId: 50-00-0
    uri_format: https://commonchemistry.cas.org/detail?cas_rn=$1
  n2t:
    description: CAS (Chemical Abstracts Service) is a division of the American Chemical
      Society and is the producer of comprehensive databases of chemical information.
    example: 50-00-0
    homepage: http://commonchemistry.org
    name: CAS through Common Chemistry
    namespaceEmbeddedInLui: false
    pattern: ^\d{1,7}\-\d{2}\-\d$
    prefix: cas
    uri_format: http://commonchemistry.org/ChemicalDetail.aspx?ref=$1
  prefix: cas
  prefixcommons:
    description: CAS (Chemical Abstracts Service) is a division of the American Chemical
      Society and is the producer of comprehensive databases of chemical information.
    example: 50-00-0
    homepage: http://www.cas.org/
    keywords:
    - chemical
    - structure
    name: 'CAS: A Divison of the American Chemical Society'
    pattern: ^\d{1,7}\-\d{2}\-\d$
    prefix: cas
    synonyms:
    - chemicalabstractscas
    uri_format: http://commonchemistry.org/ChemicalDetail.aspx?ref=$1
  providers:
  - code: hoelzel
    description: Vendor page
    example: null
    first_party: null
    homepage: https://www.hoelzel-biotech.com
    name: Hölzel Diagnostika
    publications: null
    status: null
    uri_format: https://www.hoelzel-biotech.com/de/casinfo/cas/index/number/$1
  publications:
  - doi: 10.1021/acs.jcim.2c00268
    pmc: PMC9199008
    pubmed: '35559614'
    title: 'CAS Common Chemistry in 2021: Expanding Access to Trusted Chemical Information
      for the Scientific Community'
    year: 2022
  - doi: 10.1021/acs.jcim.2c00268
    pmc: null
    pubmed: null
    title: 'CAS Common Chemistry in 2021: Expanding Access to Trusted Chemical Information
      for the Scientific Community'
    year: 2022
  - doi: 10.1021/acs.jcim.2c00268
    pmc: null
    pubmed: null
    title: 'CAS Common Chemistry in 2021: Expanding Access to Trusted Chemical Information
      for the Scientific Community'
    year: 2022
  - doi: 10.1021/acs.jcim.2c00268
    pmc: null
    pubmed: null
    title: 'CAS Common Chemistry in 2021: Expanding Access to Trusted Chemical Information
      for the Scientific Community'
    year: 2022
  synonyms:
  - CASID
  - CAS_RN
  - SECONDARY_CAS_RN
  - cas_id
  uri_format: https://commonchemistry.cas.org/detail?cas_rn=$1
  wikidata:
    description: identifier for a chemical substance or compound per Chemical Abstract
      Service's Registry database
    example:
    - 1474034-05-3
    - 15307-86-5
    homepage: https://scifinder.cas.org
    name: CAS Registry Number
    pattern: ^[1-9]\d{1,6}-\d{2}-\d$
    prefix: P231
    uri_format: https://commonchemistry.cas.org/detail?cas_rn=$1
casspc:
  comment: Jim Balhoff said that Catalog of Fishes does not publish their data in
    a machine readable format, but a long time ago they sent a CSV dump to help in
    the development of TTO and VTO. These ontologies are effectively retired and CASSPC
    terms are only also used in Phenoscape. Note that the github request issue is
    not correct, since this was made on a commit (but, fishbase is related).
  contributor:
    email: benjamin_gyori@hms.harvard.edu
    github: bgyori
    name: Benjamin M. Gyori
    orcid: 0000-0001-9439-5346
  contributor_extras:
  - email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  deprecated: true
  example: '5359'
  github_request_issue: 149
  go:
    homepage: https://researcharchive.calacademy.org/research/ichthyology/catalog/fishcatmain.asp
    name: Catalog of Fishes species database
    prefix: CASSPC
    synonyms:
    - CAS_SPC
    uri_format: https://researcharchive.calacademy.org/research/ichthyology/catalog/fishcatget.asp?spid=$1
  homepage: https://researcharchive.calacademy.org/research/ichthyology/catalog/fishcatmain.asp
  mappings:
    go: CASSPC
  name: Eschmeyer's Catalog of Fishes
  pattern: ^\d+$
  prefix: casspc
  reviewer:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  synonyms:
  - CASGEN
cath:
  biocontext:
    prefix: CATH
  contact:
    email: c.orengo@ucl.ac.uk
    github: null
    name: Christine Orengo
    orcid: 0000-0002-7141-8936
  edam:
    description: Identifier of a protein domain (or other node) from the CATH database.
    name: CATH
    obsolete: false
    prefix: '2700'
  fairsharing:
    abbreviation: CATH
    description: The CATH database is a free, publicly available online resource that
      provides information on the evolutionary relationships of protein domains. It
      provides a hierarchical domain classification of protein structures in the Protein
      Data Bank. Protein structures are classified using a combination of automated
      and manual procedures. There are four major levels in this hierarchy; Class
      (secondary structure classification, e.g. mostly alpha), Architecture (classification
      based on overall shape), Topology (fold family) and Homologous superfamily (protein
      domains which are thought to share a common ancestor).
    homepage: http://www.cathdb.info/
    name: CATH
    prefix: FAIRsharing.xgcyyn
    publications:
    - doi: 10.1093/nar/gkw1098
      pubmed_id: 27899584
      title: 'CATH: an expanded resource to predict protein function through structure
        and sequence.'
    - doi: 10.1016/s0969-2126(97)00260-8
      pubmed_id: 9309224
      title: CATH--a hierarchic classification of protein domain structures.
    - doi: 10.1016/j.biochi.2015.08.004
      pubmed_id: 26253692
      title: The history of the CATH structural classification of protein domains.
    - doi: 10.1093/bioinformatics/btw473
      pubmed_id: 27477482
      title: 'Functional classification of CATH superfamilies: a domain-based approach
        for protein function annotation.'
    - doi: 10.1093/nar/gkx1069
      pubmed_id: 29112716
      title: 'Gene3D: Extensive prediction of globular domains in proteins.'
    - doi: 10.1093/nar/gky1097
      pubmed_id: 30398663
      title: 'CATH: expanding the horizons of structure-based functional annotations
        for genome sequences.'
    - doi: 10.1093/nar/gkaa1079
      pubmed_id: 33237325
      title: 'CATH: increased structural coverage of functional space.'
    - doi: 10.1093/nar/gku947
      pubmed_id: 25348408
      title: 'CATH: comprehensive structural and functional annotations for genome
        sequences.'
    - doi: null
      pubmed_id: 11788987
      title: 'The CATH protein family database: a resource for structural and functional
        annotation of genomes.'
    subjects:
    - Evolutionary Biology
    - Biology
    twitter: CATHDatabase
  integbio:
    description: The CATH database is a free, publicly available online resource that
      provides information on the evolutionary relationships of protein domains. It
      provides a hierarchical domain classification of protein structures in the Protein
      Data Bank. Protein structures are classified using a combination of automated
      and manual procedures. There are four major levels in this hierarchy; Class
      (secondary structure classification, e.g. mostly alpha), Architecture (classification
      based on overall shape), Topology (fold family) and Homologous superfamily (protein
      domains which are thought to share a common ancestor).
    fairsharing: FAIRsharing.xgcyyn
    homepage: http://www.cathdb.info/
    information_keywords:
    - Sequence
    - 3D structure
    - Classification
    maintainer: University College London
    name: CATH
    prefix: nbdc01888
    pubmeds:
    - '9309224'
    - '27477482'
    - '26253692'
    - '25348408'
    - '11788987'
    - '27899584'
    - '29112716'
    status: Active
    target_keywords:
    - Protein
  mappings:
    biocontext: CATH
    edam: '2700'
    fairsharing: FAIRsharing.xgcyyn
    integbio: nbdc01888
    miriam: cath
    n2t: cath
    prefixcommons: cath
    re3data: r3d100012629
  miriam:
    deprecated: false
    description: CATH is a classification of protein structural domains. We group
      protein domains into superfamilies when there is sufficient evidence they have
      diverged from a common ancestor. CATH can be used to predict structural and
      functional information directly from protein sequence.
    homepage: http://www.cathdb.info
    id: '00000612'
    name: CATH Protein Structural Domain Superfamily
    namespaceEmbeddedInLui: false
    pattern: ^[1-6]\.[0-9]+\.[0-9]+\.[0-9]+$
    prefix: cath
    sampleId: 1.10.8.10
    uri_format: http://www.cathdb.info/cathnode/$1
  n2t:
    description: CATH is a classification of protein structural domains. We group
      protein domains into superfamilies when there is sufficient evidence they have
      diverged from a common ancestor. CATH can be used to predict structural and
      functional information directly from protein sequence.
    example: 1.10.8.10
    homepage: http://www.cathdb.info
    name: CATH Node through UCL
    namespaceEmbeddedInLui: false
    pattern: ^[1-4]\.[0-9]+\.[0-9]+\.[0-9]+$
    prefix: cath
    uri_format: http://www.cathdb.info/cathnode/$1
  prefix: cath
  prefixcommons:
    description: The CATH database is a hierarchical domain classification of protein
      structures in the Protein Data Bank. Protein structures are classified using
      a combination of automated and manual procedures. There are four major levels
      in this hierarchy; Class (secondary structure classification, e.g. mostly alpha),
      Architecture (classification based on overall shape), Topology (fold family)
      and  Homologous superfamily (protein domains which are thought to share a common
      ancestor). This collection is concerned with superfamily classification.
    example: '3.15'
    homepage: http://www.cathdb.info/
    keywords:
    - classification
    - protein
    - structure
    name: CATH Protein Structure Classification
    pattern: ^\d+(\.\d+(\.\d+(\.\d+)?)?)?$
    prefix: cath
    pubmed_ids:
    - '9309224'
    uri_format: http://www.cathdb.info/cathnode/$1
  publications:
  - doi: 10.1093/nar/gkae1087
    pmc: null
    pubmed: '39565206'
    title: 'CATH v4.4: major expansion of CATH by experimental and predicted structural
      data'
    year: 2024
  - doi: 10.1093/nar/gkaa1079
    pmc: PMC7778904
    pubmed: '33237325'
    title: 'CATH: increased structural coverage of functional space'
    year: 2021
  - doi: 10.1093/nar/gky1097
    pmc: PMC6323983
    pubmed: '30398663'
    title: 'CATH: expanding the horizons of structure-based functional annotations
      for genome sequences'
    year: 2019
  - doi: 10.1093/nar/gkx1069
    pmc: PMC5753370
    pubmed: '29112716'
    title: 'Gene3D: Extensive prediction of globular domains in proteins'
    year: 2018
  - doi: 10.1093/nar/gkw1098
    pmc: PMC5210570
    pubmed: '27899584'
    title: 'CATH: an expanded resource to predict protein function through structure
      and sequence'
    year: 2016
  - doi: 10.1093/bioinformatics/btw473
    pmc: PMC5018379
    pubmed: '27477482'
    title: 'Functional classification of CATH superfamilies: a domain-based approach
      for protein function annotation'
    year: 2016
  - doi: 10.1016/j.biochi.2015.08.004
    pmc: PMC4678953
    pubmed: '26253692'
    title: The history of the CATH structural classification of protein domains
    year: 2015
  - doi: 10.1093/nar/gku947
    pmc: PMC4384018
    pubmed: '25348408'
    title: 'CATH: comprehensive structural and functional annotations for genome sequences'
    year: 2014
  - doi: null
    pmc: null
    pubmed: '11788987'
    title: 'The CATH protein family database: a resource for structural and functional
      annotation of genomes'
    year: 2002
  - doi: 10.1016/s0969-2126(97)00260-8
    pmc: null
    pubmed: '9309224'
    title: CATH--a hierarchic classification of protein domain structures
    year: 1997
  - doi: 10.1093/nar/gkw1098
    pmc: null
    pubmed: null
    title: 'CATH: an expanded resource to predict protein function through structure
      and sequence.'
    year: null
  - doi: 10.1016/s0969-2126(97)00260-8
    pmc: null
    pubmed: null
    title: CATH--a hierarchic classification of protein domain structures.
    year: null
  - doi: 10.1016/j.biochi.2015.08.004
    pmc: null
    pubmed: null
    title: The history of the CATH structural classification of protein domains.
    year: null
  - doi: 10.1093/bioinformatics/btw473
    pmc: null
    pubmed: null
    title: 'Functional classification of CATH superfamilies: a domain-based approach
      for protein function annotation.'
    year: null
  - doi: 10.1093/nar/gkx1069
    pmc: null
    pubmed: null
    title: 'Gene3D: Extensive prediction of globular domains in proteins.'
    year: null
  - doi: 10.1093/nar/gky1097
    pmc: null
    pubmed: null
    title: 'CATH: expanding the horizons of structure-based functional annotations
      for genome sequences.'
    year: null
  - doi: 10.1093/nar/gkaa1079
    pmc: null
    pubmed: null
    title: 'CATH: increased structural coverage of functional space.'
    year: null
  - doi: 10.1093/nar/gku947
    pmc: null
    pubmed: null
    title: 'CATH: comprehensive structural and functional annotations for genome sequences.'
    year: null
  - doi: null
    pmc: null
    pubmed: '9309224'
    title: null
    year: null
  re3data:
    description: The CATH database is a hierarchical domain classification of protein
      structures in the Protein Data Bank. Protein structures are classified using
      a combination of automated and manual procedures.  There are four major levels
      in the CATH hierarchy; Class, Architecture, Topology and Homologous superfamily.
    doi: 10.17616/R32Z1F
    homepage: https://www.cathdb.info/
    name: CATH
    prefix: r3d100012629
    synonyms:
    - CATH-Gene3D
    - Class  Architecture Topology  Homologous superfamily
    xrefs:
      nif: 0000-02640
cath.domain:
  biocontext:
    prefix: CATH.DOMAIN
  edam:
    description: Identifier of a protein domain from CATH.
    name: CATH domain
    obsolete: false
    prefix: '1040'
  mappings:
    biocontext: CATH.DOMAIN
    edam: '1040'
    miriam: cath.domain
    n2t: cath.domain
  miriam:
    deprecated: false
    description: The CATH database is a hierarchical domain classification of protein
      structures in the Protein Data Bank. Protein structures are classified using
      a combination of automated and manual procedures. There are four major levels
      in this hierarchy; Class (secondary structure classification, e.g. mostly alpha),
      Architecture (classification based on overall shape), Topology (fold family)
      and Homologous superfamily (protein domains which are thought to share a common
      ancestor). This colelction is concerned with CATH domains.
    homepage: http://www.cathdb.info/
    id: '00000210'
    name: CATH domain
    namespaceEmbeddedInLui: false
    pattern: ^\w+$
    prefix: cath.domain
    sampleId: 1cukA01
    uri_format: http://www.cathdb.info/domain/$1
  n2t:
    description: The CATH database is a hierarchical domain classification of protein
      structures in the Protein Data Bank. Protein structures are classified using
      a combination of automated and manual procedures. There are four major levels
      in this hierarchy; Class (secondary structure classification, e.g. mostly alpha),
      Architecture (classification based on overall shape), Topology (fold family)
      and Homologous superfamily (protein domains which are thought to share a common
      ancestor). This colelction is concerned with CATH domains.
    example: 1cukA01
    homepage: http://www.cathdb.info/
    name: CATH domain at UCL
    namespaceEmbeddedInLui: false
    pattern: ^\w+$
    prefix: cath.domain
    uri_format: http://www.cathdb.info/domain/$1
  part_of_database: cath
  prefix: cath.domain
cath.superfamily:
  biocontext:
    prefix: CATH.SUPERFAMILY
  mappings:
    biocontext: CATH.SUPERFAMILY
    miriam: cath.superfamily
    n2t: cath.superfamily
  miriam:
    deprecated: false
    description: The CATH database is a hierarchical domain classification of protein
      structures in the Protein Data Bank. Protein structures are classified using
      a combination of automated and manual procedures. There are four major levels
      in this hierarchy; Class (secondary structure classification, e.g. mostly alpha),
      Architecture (classification based on overall shape), Topology (fold family)
      and  Homologous superfamily (protein domains which are thought to share a common
      ancestor). This colelction is concerned with superfamily classification.
    homepage: http://www.cathdb.info/
    id: 00000209
    name: CATH superfamily
    namespaceEmbeddedInLui: false
    pattern: ^\d+(\.\d+(\.\d+(\.\d+)?)?)?$
    prefix: cath.superfamily
    sampleId: 1.10.10.200
    uri_format: http://www.cathdb.info/cathnode/$1
  n2t:
    description: The CATH database is a hierarchical domain classification of protein
      structures in the Protein Data Bank. Protein structures are classified using
      a combination of automated and manual procedures. There are four major levels
      in this hierarchy; Class (secondary structure classification, e.g. mostly alpha),
      Architecture (classification based on overall shape), Topology (fold family)
      and  Homologous superfamily (protein domains which are thought to share a common
      ancestor). This colelction is concerned with superfamily classification.
    example: 1.10.10.200
    homepage: http://www.cathdb.info/
    name: CATH superfamily at UCL
    namespaceEmbeddedInLui: false
    pattern: ^\d+(\.\d+(\.\d+(\.\d+)?)?)?$
    prefix: cath.superfamily
    uri_format: http://www.cathdb.info/cathnode/$1
  part_of: cath
  part_of_database: cath
  prefix: cath.superfamily
cattleqtldb:
  biocontext:
    prefix: CATTLEQTLDB
  mappings:
    biocontext: CATTLEQTLDB
    miriam: cattleqtldb
    n2t: cattleqtldb
    prefixcommons: cattleqtldb
  miriam:
    deprecated: false
    description: The Animal Quantitative Trait Loci (QTL) database (Animal QTLdb)
      is designed to house publicly all available QTL and single-nucleotide polymorphism/gene
      association data on livestock animal species. This collection references cattle
      QTLs.
    homepage: https://www.animalgenome.org/QTLdb
    id: '00000504'
    name: Animal Genome Cattle QTL
    namespaceEmbeddedInLui: false
    pattern: ^\d+$
    prefix: cattleqtldb
    sampleId: '4685'
    uri_format: https://www.animalgenome.org/QTLdb/q?id=QTL_ID:$1
  n2t:
    description: The Animal Quantitative Trait Loci (QTL) database (Animal QTLdb)
      is designed to house publicly all available QTL and single-nucleotide polymorphism/gene
      association data on livestock animal species. This collection references cattle
      QTLs.
    example: '4685'
    homepage: http://www.animalgenome.org/cgi-bin/QTLdb/BT/index
    name: Animal QTL Cattle at Iowa State University
    namespaceEmbeddedInLui: false
    pattern: ^\d+$
    prefix: cattleqtldb
    uri_format: http://www.animalgenome.org/cgi-bin/QTLdb/BT/qdetails?QTL_ID=$1
  part_of: qtldb
  prefix: cattleqtldb
  prefixcommons:
    description: This Cattle Quantitative Trait Locus (QTL) database (Cattle QTLdb)
      has gathered all cattle QTL data published during the past 10+ years. The database
      and its peripheral tools make it possible to compare, confirm and locate on
      cattle chromosomes the most feasible location for genes responsible for quantitative
      trait important to cattle production.
    example: '66'
    homepage: http://www.animalgenome.org/cgi-bin/QTLdb/BT/index
    keywords:
    - DNA
    - genome
    name: Cattle Quantitative Trait Locus database
    pattern: ^\d+$
    prefix: cattleqtldb
    uri_format: http://www.animalgenome.org/cgi-bin/QTLdb/BT/qdetails?QTL_ID=$1
cazy:
  biocontext:
    prefix: CAZY
  contact:
    email: nicolas.terrapon@univ-amu.fr
    github: gandarath
    name: Nicolas Terrapon
    orcid: 0000-0002-3693-6017
  fairsharing:
    abbreviation: CAZy
    description: The CAZy database describes the families of structurally-related
      catalytic and carbohydrate-binding modules (or functional domains) of enzymes
      that degrade, modify, or create glycosidic bonds.
    homepage: http://www.cazy.org/
    name: The Carbohydrate-Active enZYmes Database
    prefix: FAIRsharing.ntyq70
    publications:
    - doi: 10.1093/nar/gkn663
      pubmed_id: 18838391
      title: 'The Carbohydrate-Active EnZymes database (CAZy): an expert resource
        for Glycogenomics.'
    - doi: 10.1093/nar/gkt1178
      pubmed_id: 24270786
      title: The carbohydrate-active enzymes database (CAZy) in 2013.
    subjects:
    - Life Science
    - Glycomics
  go:
    description: The CAZy database describes the families of structurally-related
      catalytic and carbohydrate-binding modules (or functional domains) of enzymes
      that degrade, modify, or create glycosidic bonds.
    homepage: http://www.cazy.org/
    name: Carbohydrate Active EnZYmes
    prefix: CAZY
    uri_format: http://www.cazy.org/$1.html
  mappings:
    biocontext: CAZY
    fairsharing: FAIRsharing.ntyq70
    go: CAZY
    miriam: cazy
    n2t: cazy
    prefixcommons: cazy
    re3data: r3d100012321
    uniprot: DB-0136
  miriam:
    deprecated: false
    description: The Carbohydrate-Active Enzyme (CAZy) database is a resource specialized
      in enzymes that build and breakdown complex carbohydrates and glycoconjugates.
      These enzymes are classified into families based on structural features.
    homepage: http://www.cazy.org/
    id: 00000195
    name: CAZy
    namespaceEmbeddedInLui: false
    pattern: ^(GT|GH|PL|CE|CBM)\d+(\_\d+)?$
    prefix: cazy
    sampleId: GT10
    uri_format: http://www.cazy.org/$1.html
  n2t:
    description: The Carbohydrate-Active Enzyme (CAZy) database is a resource specialized
      in enzymes that build and breakdown complex carbohydrates and glycoconjugates.
      These enzymes are classified into families based on structural features.
    example: GT10
    homepage: http://www.cazy.org/
    name: CAZy at CNRS
    namespaceEmbeddedInLui: false
    pattern: ^(GT|GH|PL|CE|CBM)\d+(\_\d+)?$
    prefix: cazy
    uri_format: http://www.cazy.org/$1.html
  prefix: cazy
  prefixcommons:
    description: The CAZy database describes the families of structurally-related
      catalytic and carbohydrate-binding modules (or functional domains) of enzymes
      that degrade, modify, or create glycosidic bonds.
    example: GT10
    homepage: http://www.cazy.org/
    keywords:
    - classification
    - polysaccharide
    name: The Carbohydrate-Active enZYmes Database
    pattern: ^GT\d+$
    prefix: cazy
    pubmed_ids:
    - '18838391'
    uri_format: http://www.cazy.org/$1.html
  publications:
  - doi: 10.1093/nar/gkt1178
    pmc: PMC3965031
    pubmed: '24270786'
    title: The carbohydrate-active enzymes database (CAZy) in 2013
    year: 2013
  - doi: 10.1093/nar/gkn663
    pmc: PMC2686590
    pubmed: '18838391'
    title: 'The Carbohydrate-Active EnZymes database (CAZy): an expert resource for
      Glycogenomics'
    year: 2008
  - doi: 10.1093/nar/gkn663
    pmc: null
    pubmed: null
    title: 'The Carbohydrate-Active EnZymes database (CAZy): an expert resource for
      Glycogenomics.'
    year: null
  - doi: 10.1093/nar/gkt1178
    pmc: null
    pubmed: null
    title: The carbohydrate-active enzymes database (CAZy) in 2013.
    year: null
  - doi: null
    pmc: null
    pubmed: '18838391'
    title: null
    year: null
  - doi: 10.1093/nar/gkab1045
    pmc: null
    pubmed: '34850161'
    title: null
    year: null
  re3data:
    description: CAZy is a specialist database dedicated to the display and analysis
      of genomic, structural and biochemical information on Carbohydrate-Active Enzymes
      (CAZymes).  CAZy data are accessible either by browsing sequence-based families
      or by browsing the content of genomes in carbohydrate-active enzymes. New genomes
      are added regularly shortly after they appear in the daily releases of GenBank.
      New families are created based on published evidence for the activity of at
      least one member of the family and all families are regularly updated, both
      in content and in description.
    doi: 10.17616/R38W88
    homepage: http://www.cazy.org/
    name: Carbohydrate-Active enZYmes Database
    prefix: r3d100012321
    synonyms:
    - CAZy
    xrefs:
      nif: 0000-02642
      omics: '01677'
  uniprot:
    abbreviation: CAZy
    category: Protein family/group databases
    homepage: https://www.cazy.org/
    name: Carbohydrate-Active enZymes
    prefix: DB-0136
    publications:
    - doi: 10.1093/nar/gkab1045
      pubmed: '34850161'
    uri_format: https://www.cazy.org/$1.html
cba:
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: 'CBA: http://www.cba.ac.cn/ and the Shanghai Institutes for Biological
    Sciences (SIBS at http://www.sibs.ac.cn/) provide EBI with citation data not available
    in MEDLINE.'
  example: '375364'
  homepage: http://www.cba.ac.cn
  keywords:
  - bibliography
  name: Chinese Biological Abstracts
  pattern: ^\d+$
  prefix: cba
  uri_format: https://europepmc.org/article/CBA/$1
cbioportal:
  contact:
    email: gaoj@mskcc.org
    github: jjgao
    name: Jianjiong Gao
    orcid: 0000-0002-5739-1781
  fairsharing:
    abbreviation: cBioPortal
    description: The cBioPortal for Cancer Genomics provides visualization, analysis
      and download of large-scale cancer genomics data sets.
    homepage: http://www.cbioportal.org
    name: cBioPortal for Cancer Genomics
    prefix: FAIRsharing.6L6MjA
    publications:
    - doi: 10.1126/scisignal.2004088
      pubmed_id: 23550210
      title: Integrative analysis of complex cancer genomics and clinical profiles
        using the cBioPortal.
    - doi: 10.1158/2159-8290.CD-12-0095
      pubmed_id: 22588877
      title: 'The cBio cancer genomics portal: an open platform for exploring multidimensional
        cancer genomics data.'
    repository: https://github.com/cBioPortal/cbioportal
    subjects:
    - Genomics
    - Proteomics
    - Biomedical Science
    - Preclinical Studies
    twitter: cbioportal
  mappings:
    fairsharing: FAIRsharing.6L6MjA
    miriam: cbioportal
    n2t: cbioportal
  miriam:
    deprecated: false
    description: The cBioPortal for Cancer Genomics provides visualization, analysis
      and download of large-scale cancer genomics data sets.
    homepage: http://www.cbioportal.org
    id: 00000679
    name: The cBioPortal for Cancer Genomics
    namespaceEmbeddedInLui: false
    pattern: ^[a-z0-9\_]+$
    prefix: cbioportal
    sampleId: laml_tcga_pub
    uri_format: http://www.cbioportal.org/study?id=$1#summary
  n2t:
    description: The cBioPortal for Cancer Genomics provides visualization, analysis
      and download of large-scale cancer genomics data sets.
    example: laml_tcga_pub
    homepage: http://www.cbioportal.org
    name: The cBioPortal for Cancer Genomics
    namespaceEmbeddedInLui: false
    pattern: ^[a-z0-9\_]+$
    prefix: cbioportal
    uri_format: http://www.cbioportal.org/study?id=$1#summary
  prefix: cbioportal
  publications:
  - doi: 10.1126/scisignal.2004088
    pmc: PMC4160307
    pubmed: '23550210'
    title: Integrative analysis of complex cancer genomics and clinical profiles using
      the cBioPortal
    year: 2013
  - doi: 10.1158/2159-8290.cd-12-0095
    pmc: PMC3956037
    pubmed: '22588877'
    title: 'The cBio cancer genomics portal: an open platform for exploring multidimensional
      cancer genomics data'
    year: 2012
  - doi: 10.1126/scisignal.2004088
    pmc: null
    pubmed: null
    title: Integrative analysis of complex cancer genomics and clinical profiles using
      the cBioPortal.
    year: null
  - doi: 10.1158/2159-8290.CD-12-0095
    pmc: null
    pubmed: null
    title: 'The cBio cancer genomics portal: an open platform for exploring multidimensional
      cancer genomics data.'
    year: null
  uri_format: https://www.cbioportal.org/study/summary?id=$1
cc:
  aberowl:
    description: Client category
    name: CC
    prefix: CC
    version: '1'
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: The Creative Commons Rights Expression Language (ccREL) lets you describe
    copyright licenses in RDF. For more information on describing licenses in RDF
    and attaching those descriptions to digital works, see [ccREL](https://wiki.creativecommons.org/CC_REL)
    in the [Creative Commons wiki](https://wiki.creativecommons.org/).
  download_rdf: https://creativecommons.org/schema.rdf
  example: Work
  homepage: https://creativecommons.org/ns
  license: CC0-1.0
  lov:
    description: The Creative Commons Rights Expression Language (CC REL) lets you
      describe copyright licenses in RDF
    homepage: http://creativecommons.org/ns
    keywords:
    - Metadata
    modified: '2008-03-03'
    name: Creative Commons Rights Expression Language
    prefix: cc
    uri_prefix: http://creativecommons.org/ns#$1
  mappings:
    aberowl: CC
    lov: cc
    tib: ccrel
    zazuko: cc
  name: Creative Commons Rights Expression Language
  pattern: ^\w+$
  prefix: cc
  synonyms:
  - ccrel
  tib:
    description: The Creative Commons Rights Expression Language (CC REL) lets you
      describe copyright licenses in RDF. For more information on describing licenses
      in RDF and attaching those descriptions to digital works, see CC REL (https://wiki.creativecommons.org/CC_REL)
      in the Creative Commons wiki (https://wiki.creativecommons.org/).
    homepage: https://creativecommons.org/ns
    keywords:
    - NFDI4ING
    - law
    name: Describing Copyright in RDF - Creative Commons Rights Expression Language
    prefix: ccrel
    uri_format: http://creativecommons.org/ns#$1
  twitter: cc_opensource
  uri_format: https://creativecommons.org/ns#$1
  zazuko:
    prefix: cc
    uri_format: http://creativecommons.org/ns#$1
cc.legacy:
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  deprecated: true
  description: A precursor that was later replaced with the Creative Commons Rights
    Expression Language (ccREL)
  download_rdf: https://web.resource.org/cc/schema.rdf
  example: License
  github_request_issue: 1639
  homepage: https://web.resource.org/cc/
  keywords:
  - license
  - schema
  name: Creative Commons Schema
  prefix: cc.legacy
  uri_format: http://web.resource.org/cc/$1
ccdc:
  mappings:
    miriam: ccdc
  miriam:
    deprecated: false
    description: The Cambridge Crystallographic Data Centre (CCDC) develops and maintains
      the Cambridge Stuctural Database, the world's most comprehensive archive of
      small-molecule crystal structure data. A CCDC Number is a unique identifier
      assigned to a dataset deposited with the CCDC.
    homepage: https://www.ccdc.cam.ac.uk/
    id: 00000818
    name: CCDC Number
    namespaceEmbeddedInLui: false
    pattern: ^\d{6,7}$
    prefix: ccdc
    sampleId: '1829126'
    uri_format: https://www.ccdc.cam.ac.uk/services/structures?pid=ccdc:$1&sid=IDORG
  prefix: ccdc
ccds:
  biocontext:
    prefix: CCDS
    uri_format: http://www.ncbi.nlm.nih.gov/CCDS/CcdsBrowse.cgi?REQUEST=CCDS&DATA=$1
  contact:
    email: murphyte@ncbi.nlm.nih.gov
    github: murphyte
    name: Terence D. Murphy
    orcid: 0000-0001-9311-9745
  example: CCDS12976
  example_extras:
  - CCDS12976.1
  fairsharing:
    abbreviation: CCDS
    description: The Consensus CDS (CCDS) project is a collaborative effort to identify
      a core set of human and mouse protein coding regions that are consistently annotated
      and of high quality. The long term goal is to support convergence towards a
      standard set of gene annotations.
    homepage: http://www.ncbi.nlm.nih.gov/CCDS/
    license: http://opendatacommons.org/licenses/pddl/1.0
    name: The Consensus CDS
    prefix: FAIRsharing.46s4nt
    publications:
    - doi: 10.1101/gr.080531.108
      pubmed_id: 19498102
      title: 'The consensus coding sequence (CCDS) project: Identifying a common protein-coding
        gene set for the human and mouse genomes.'
    subjects:
    - Life Science
  integbio:
    alt_name: Consensus CDS
    description: This database seeks to identify a core set of human and mouse protein
      coding regions of high quality that are consistently annotated.
    fairsharing: biodbcore-000432
    homepage: http://www.ncbi.nlm.nih.gov/projects/CCDS/CcdsBrowse.cgi
    information_keywords:
    - Sequence
    maintainer: NCBI (National Center for Biotechnology Information)
    name: CCDS
    prefix: nbdc00023
    pubmeds:
    - '19498102'
    status: Active
    target_keywords:
    - Genome/Gene
    - Protein
  mappings:
    biocontext: CCDS
    fairsharing: FAIRsharing.46s4nt
    integbio: nbdc00023
    miriam: ccds
    n2t: ccds
    prefixcommons: ccds
    togoid: Ccds
    uniprot: DB-0187
  miriam:
    deprecated: false
    description: The Consensus CDS (CCDS) project is a collaborative effort to identify
      a core set of human and mouse protein coding regions that are consistently annotated
      and of high quality. The CCDS set is calculated following coordinated whole
      genome annotation updates carried out by the NCBI, WTSI, and Ensembl. The long
      term goal is to support convergence towards a standard set of gene annotations.
    homepage: http://www.ncbi.nlm.nih.gov/CCDS/
    id: '00000375'
    name: Consensus CDS
    namespaceEmbeddedInLui: false
    pattern: ^CCDS\d+\.\d+$
    prefix: ccds
    sampleId: CCDS13573.1
    uri_format: http://www.ncbi.nlm.nih.gov/CCDS/CcdsBrowse.cgi?REQUEST=CCDS&DATA=$1
  n2t:
    description: The Consensus CDS (CCDS) project is a collaborative effort to identify
      a core set of human and mouse protein coding regions that are consistently annotated
      and of high quality. The CCDS set is calculated following coordinated whole
      genome annotation updates carried out by the NCBI, WTSI, and Ensembl. The long
      term goal is to support convergence towards a standard set of gene annotations.
    example: CCDS13573.1
    homepage: http://www.ncbi.nlm.nih.gov/CCDS/
    name: Consensus CDS at NCBI
    namespaceEmbeddedInLui: false
    pattern: ^CCDS\d+\.\d+$
    prefix: ccds
    uri_format: http://www.ncbi.nlm.nih.gov/CCDS/CcdsBrowse.cgi?REQUEST=CCDS&DATA=$1
  pattern: ^CCDS\d+(\.\d+)?$
  prefix: ccds
  prefixcommons:
    description: The Consensus CDS (CCDS) project is a collaborative effort to identify
      a core set of human and mouse protein coding regions that are consistently annotated
      and of high quality. The long term goal is to support convergence towards a
      standard set of gene annotations.
    example: '4824'
    homepage: http://www.ncbi.nlm.nih.gov/CCDS/
    keywords:
    - protein
    - gene
    name: The Consensus CDS
    pattern: ^\d+$
    prefix: ccds
    pubmed_ids:
    - '19498102'
    uri_format: http://www.ncbi.nlm.nih.gov/projects/CCDS/CcdsBrowse.cgi?REQUEST=CCDS&DATA=$1
  publications:
  - doi: 10.1101/gr.080531.108
    pmc: PMC2704439
    pubmed: '19498102'
    title: 'The consensus coding sequence (CCDS) project: Identifying a common protein-coding
      gene set for the human and mouse genomes'
    year: 2009
  togoid:
    catalog: nbdc00023
    description: This database seeks to identify a core set of human and mouse protein
      coding regions of high quality that are consistently annotated.
    examples:
    - CCDS1471
    - CCDS10913
    - CCDS14790
    - CCDS35175
    - CCDS2395
    - CCDS58412
    - CCDS55555
    - CCDS34401
    - CCDS41889
    - CCDS9052
    keywords:
    - Gene
    name: Consensus CDS
    pattern: ^(?CCDS\d+)(?:\.\d+)?$
    prefix: Ccds
    uri_format: http://identifiers.org/ccds/$1
  uniprot:
    abbreviation: CCDS
    category: Sequence databases
    homepage: https://www.ncbi.nlm.nih.gov/projects/CCDS/CcdsBrowse.cgi
    name: The Consensus CDS (CCDS) project
    prefix: DB-0187
    publications:
    - doi: 10.1093/nar/gkx1031
      pubmed: '29126148'
    uri_format: https://www.ncbi.nlm.nih.gov/CCDS/CcdsBrowse.cgi?REQUEST=CCDS&GO=MainBrowse&DATA=$1
ccf:
  aberowl:
    description: The Common Coordinate Framework (CCF) Ontology is an application
      ontology built to support the development of the Human Reference Atlas (HRA).
      It unifies vocabulary for HRA construction and usage—making it possible to ingest
      external data sources; supporting uniform tissue sample registration that includes
      the spatial positioning and semantic annotations within 3D reference organs;
      and supporting user-formulated cross-domain queries over tissue donor properties,
      anatomical structures, cell types, biomarkers, and 3D space. The CCF Ontology
      consists of three major ontologies. The Biological Structure Ontology records
      anatomical structures, cell types, and biomarkers (ASCT+B) and the relationships
      between them. The ASCT+B tables are authored by human experts using templated
      Google Sheets. The biomarkers, cell types, and anatomical structures are mapped
      to existing ontologies (Uberon/FMA, CL, HGNC) whenever possible. All relationships
      between anatomical structures and from cell types to anatomical structures are
      valid Uberon and CL relationships. The Spatial Ontology defines the shape, size,
      location, and rotation of experimental tissue and data major anatomical structures
      in the 3D Reference Object Library. The Specimen Ontology captures the sex,
      age, and other information on donors that provided tissue data used in the construction
      of the HRA.
    download_owl: http://aber-owl.net/media/ontologies/CCF/16/ccf.owl
    homepage: https://lod.humanatlas.io/vocab/ccf/latest
    name: Human Reference Atlas Common Coordinate Framework Ontology
    prefix: CCF
    version: 3.0.0
  bioportal:
    contact:
      email: anitac@ebi.ac.uk
      name: Anita R. Caron
    description: The Common Coordinate Framework (CCF) Ontology is an application
      ontology built to support the development of the Human Reference Atlas (HRA).
      It unifies vocabulary for HRA construction and usage—making it possible to ingest
      external data sources; supporting uniform tissue sample registration that includes
      the spatial positioning and semantic annotations within 3D reference organs;
      and supporting user-formulated cross-domain queries over tissue donor properties,
      anatomical structures, cell types, biomarkers, and 3D space. The CCF Ontology
      consists of three major ontologies. The Biological Structure Ontology records
      anatomical structures, cell types, and biomarkers (ASCT+B) and the relationships
      between them. The ASCT+B tables are authored by human experts using templated
      Google Sheets. The biomarkers, cell types, and anatomical structures are mapped
      to existing ontologies (Uberon/FMA, CL, HGNC) whenever possible. All relationships
      between anatomical structures and from cell types to anatomical structures are
      valid Uberon and CL relationships. The Spatial Ontology defines the shape, size,
      location, and rotation of experimental tissue and data major anatomical structures
      in the 3D Reference Object Library. The Specimen Ontology captures the sex,
      age, and other information on donors that provided tissue data used in the construction
      of the HRA.
    homepage: https://purl.humanatlas.io/vocab/ccf
    name: Human Reference Atlas Common Coordinate Framework Ontology
    prefix: CCF
    publications:
    - https://humanatlas.io/ccf-ontology
    version: 3.0.0
  contact:
    email: katy@indiana.edu
    github: katyb
    name: Katy Börner
    orcid: 0000-0002-3321-6137
  contributor:
    email: benjamin_gyori@hms.harvard.edu
    github: bgyori
    name: Benjamin M. Gyori
    orcid: 0000-0001-9439-5346
  example: extraction_set
  github_request_issue: 879
  homepage: https://bioportal.bioontology.org/ontologies/CCF
  license: CC-BY-4.0
  mappings:
    aberowl: CCF
    bioportal: CCF
    ols: ccf
    re3data: r3d100012657
  name: Human Reference Atlas Common Coordinate Framework Ontology
  ols:
    contact: infoccf@iu.edu
    description: The Common Coordinate Framework (CCF) Ontology is an application
      ontology built to support the development of the Human Reference Atlas (HRA).  It
      unifies vocabulary for HRA construction and usage—making it possible to ingest
      external data sources; supporting uniform tissue sample registration that includes
      the spatial positioning and semantic annotations within 3D reference organs;
      and supporting user-formulated cross-domain queries over tissue donor properties,
      anatomical structures, cell types, biomarkers, and 3D space. The CCF Ontology
      consists of three major ontologies. The Biological Structure Ontology records
      anatomical structures, cell types, and biomarkers (ASCT+B) and the relationships
      between them.  The ASCT+B tables are authored by human experts using templated
      Google Sheets. The biomarkers, cell types, and anatomical structures are mapped
      to existing ontologies (Uberon/FMA, CL, HGNC) whenever possible.  All relationships
      between anatomical structures and from cell types to anatomical structures are
      valid Uberon and CL relationships. The Spatial Ontology defines the shape, size,
      location, and rotation of experimental tissue and data major anatomical structures
      in the 3D Reference Object Library. The Specimen Ontology captures the sex,
      age, and other information on donors that provided tissue data used in the construction
      of the HRA.
    homepage: https://humanatlas.io/ccf-ontology
    name: Human Reference Atlas Common Coordinate Framework Ontology
    prefix: ccf
    uri_format: https://purl.org/ccf/$1
  pattern: ^\S+$
  prefix: ccf
  rdf_uri_format: http://purl.org/ccf/$1
  re3data:
    description: The Connectome Coordination Facility (CCF) houses and distributes
      public research data for a series of studies that focus on the connections within
      the human brain. These are known as Human Connectome Projects. he Connectome
      Coordination Facility (CCF) was chartered to help coordinate myriad research
      projects, harmonize their data, and facilitate the dissemination of results.
    doi: 10.17616/R31NJM9D
    homepage: https://nda.nih.gov/ccf
    name: CCF
    prefix: r3d100012657
    synonyms:
    - Connectome Coordination Facility
  repository: https://github.com/hubmapconsortium/ccf-ontology
  reviewer:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  uri_format: https://bioportal.bioontology.org/ontologies/CCF/?p=classes&conceptid=http%3A%2F%2Fpurl.org%2Fccf%2F$1
ccle:
  cellosaurus:
    category: Cell line databases/resources
    homepage: https://portals.broadinstitute.org/ccle
    name: Cancer Cell Line Encyclopedia
    prefix: CCLE
    uri_format: https://portals.broadinstitute.org/ccle/page?cell_line=$1
  contact:
    email: wsellers@broadinstitute.org
    github: null
    name: William R. Sellers
    orcid: 0000-0002-3539-9803
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: Datasets around different cancer cell lines generated by the Broad
    Institute and Novartis
  domain: cell and cell line
  example: BT20_BREAST
  homepage: https://www.cbioportal.org/study/summary?id=ccle_broad_2019
  keywords:
  - cancer cell line
  - cell
  - cell line
  license: ODbL-1.0
  logo: https://sites.broadinstitute.org/files/files/ccle/files/cclelogo_200h_4.jpg
  mappings:
    cellosaurus: CCLE
  name: Cancer Cell Line Encyclopedia Cells
  prefix: ccle
  publications:
  - doi: 10.1016/j.cell.2019.12.023
    pmc: PMC7339254
    pubmed: '31978347'
    title: Quantitative Proteomics of the Cancer Cell Line Encyclopedia
    year: 2020
  - doi: 10.1038/s41586-019-1186-3
    pmc: PMC6697103
    pubmed: '31068700'
    title: Next-generation characterization of the Cancer Cell Line Encyclopedia
    year: 2019
  synonyms:
  - ccle.cell
  uri_format: https://www.cbioportal.org/patient?studyId=ccle_broad_2019&caseId=$1
cco:
  aberowl:
    description: An application ontology integrating knowledge about the eukaryotic
      cell cycle.
    download_owl: http://aber-owl.net/media/ontologies/CCO/9/cco.owl
    homepage: http://www.semantic-systems-biology.org/apo/
    name: Cell Cycle Ontology
    prefix: CCO
    version: '2015'
  banana: CCO
  bartoc:
    abbreviation: CCO
    description: A manual to help you describe, document, and catalog cultural artifacts
      (like art and architecture) and visual media that represent them.
    homepage: https://www.vraweb.org/cco
    license: CC BY-NC-SA 3.0
    name: Cataloging Cultural Objects
    prefix: '20461'
  biocontext:
    prefix: CCO
  bioportal:
    contact:
      email: mironov@bio.ntnu.no
      name: Vladimir Mironov
    description: An application ontology integrating knowledge about the eukaryotic
      cell cycle.
    homepage: http://www.semantic-systems-biology.org/cco/
    name: Cell Cycle Ontology
    prefix: CCO
    publications:
    - http://genomebiology.com/2009/10/5/R58
    version: '2.10'
  contact:
    email: kuiper@bio.ntnu.no
    github: makuintnu
    name: Martin Kuiper
    orcid: 0000-0002-1171-9876
  download_obo: https://www.bio.ntnu.no/ontology/CCO/cco.obo
  download_owl: https://www.bio.ntnu.no/ontology/CCO/cco.owl
  fairsharing:
    abbreviation: CCO
    contact:
      email: kuiper@bio.ntnu.no
      name: Martin Kuiper
      orcid: 0000-0002-1171-9876
    description: CCO contains genes, proteins, interactions (comprising genes or proteins
      that participate in them), processes from the cell cycle subtree of GO, molecular
      functions (GO), taxa, and ontological constructs (like an upper level ontology
      and relationships) to stick everything together.
    domains:
    - cell
    - molecular_function
    - cell cycle
    homepage: https://www.biogateway.eu/tools/#CCO
    name: Cell Cycle Ontology
    prefix: FAIRsharing.xhwrnr
    publications:
    - doi: 10.1186/gb-2009-10-5-r58
      pubmed: '19480664'
      title: 'The Cell Cycle Ontology: an application ontology for the representation
        and integrated analysis of the cell cycle process'
      year: 2009
    subjects:
    - Life Science
    - Functional Genomics
    - Proteomics
    - Genomics
  mappings:
    aberowl: CCO
    bartoc: '20461'
    biocontext: CCO
    bioportal: CCO
    fairsharing: FAIRsharing.xhwrnr
    miriam: cco
    n2t: cco
    ols: cco
    prefixcommons: cco
  miriam:
    deprecated: false
    description: The Cell Cycle Ontology is an application ontology that captures
      and integrates detailed knowledge on the cell cycle process.
    homepage: https://www.ebi.ac.uk/ontology-lookup/browse.do?ontName=CCO
    id: '00000234'
    name: Cell Cycle Ontology
    namespaceEmbeddedInLui: true
    pattern: ^CCO:\w+$
    prefix: cco
    sampleId: '0000003'
    uri_format: https://www.ebi.ac.uk/ols4/ontologies/cco/terms?obo_id=CCO:$1
  n2t:
    description: The Cell Cycle Ontology is an application ontology that captures
      and integrates detailed knowledge on the cell cycle process.
    example: '0000003'
    homepage: https://www.ebi.ac.uk/ontology-lookup/browse.do?ontName=CCO
    name: Cell Cycle Ontology through OLS
    namespaceEmbeddedInLui: true
    pattern: ^CCO\:\w+$
    prefix: cco
    uri_format: https://www.ebi.ac.uk/ols/ontologies/cco/terms?obo_id=CCO:$1
  ols:
    contact: vladimir.n.mironov@gmail.com
    description: The Cell Cycle Ontology extends existing ontologies for cell cycle
      knowledge building a resource that integrates and manages knowledge about the
      cell cycle components and regulatory aspects.
    download_owl: http://www.bio.ntnu.no/ontology/CCO/cco.owl
    homepage: http://www.semantic-systems-biology.org/apo
    name: Cell Cycle Ontology
    prefix: cco
    uri_format: http://purl.obolibrary.org/obo/CCO_$1
  pattern: ^\w+$
  prefix: cco
  prefixcommons:
    alt_uri_formats:
    - http://purl.org/obo/owl/CCO#$1
    bioportal: '1507'
    description: An application ontology integrating knowledge about the eukaryotic
      cell cycle.
    example: CCO:P0000023
    homepage: http://www.semantic-systems-biology.org/cco/
    keywords:
    - obo
    - cell cycle
    name: Cell Cycle Ontology
    pattern: ^CCO\:\w+$
    prefix: cco
    pubmed_ids:
    - '19480664'
  publications:
  - doi: 10.1186/gb-2009-10-5-r58
    pmc: PMC2718524
    pubmed: '19480664'
    title: 'The Cell Cycle Ontology: an application ontology for the representation
      and integrated analysis of the cell cycle process'
    year: 2009
  - doi: 10.1186/gb-2009-10-5-r58
    pmc: null
    pubmed: '19480664'
    title: 'The Cell Cycle Ontology: an application ontology for the representation
      and integrated analysis of the cell cycle process'
    year: 2009
  - doi: null
    pmc: null
    pubmed: '19480664'
    title: null
    year: null
ccrid:
  cellosaurus:
    category: Cell line databases/resources
    homepage: http://cellresource.cn/
    name: Chinese Cell Resource Information Database
    prefix: CCRID
    uri_format: http://www.cellresource.cn/cellsearch.aspx?sc=1&where=$1
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  example: 4201PAT-CCTCC00348
  homepage: http://www.cellresource.cn
  mappings:
    cellosaurus: CCRID
  name: National Experimental Cell Resource Sharing Platform
  prefix: ccrid
  uri_format: http://www.cellresource.cn/cellsearch.aspx?sc=1&where=$1
ccso:
  contact:
    email: merocknyxta@gmail.com
    github: vkreations
    name: Evangelos Katis
    orcid: null
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: CCSO is an educational ontology acting as a data model for concepts
    and entities within an academic setting, enabling also the annotation of potentially
    available resources. The ontology aims to conceptualize educational entities within
    Curriculum and Syllabus with appropriate coverage and quality, in order to support
    rich services on top for improving curriculum management and automatically enabling
    syllabus semantic processes. (from homepage)
  download_owl: https://vkreations.github.io/CCSO/CCSO_071owl.owl
  example: AcademicStaff
  homepage: https://vkreations.github.io/CCSO/
  keywords:
  - curricula
  - curriculum
  - education
  - oer
  - oers
  - open educational resources
  license: GPL-3.0
  name: Curriculum Course Syllabus Ontology
  prefix: ccso
  rdf_uri_format: https://w3id.org/ccso/ccso#$1
  repository: https://github.com/Vkreations/CCSO
  uri_format: https://w3id.org/ccso/ccso#$1
cdao:
  aberowl:
    description: a formalization of concepts and relations relevant to evolutionary
      comparative analysis
    download_owl: http://aber-owl.net/media/ontologies/CDAO/11/cdao.owl
    homepage: https://github.com/evoinfo/cdao
    name: Comparative Data Analysis Ontology
    prefix: CDAO
  agroportal:
    contact:
      email: balhoff@nescent.org
      name: Jim Balhoff
    description: The Comparative Data Analysis Ontology (CDAO) provides a framework
      for understanding data in the context of evolutionary-comparative analysis.
      This comparative approach is used commonly in bioinformatics and other areas
      of biology to draw inferences from a comparison of differently evolved versions
      of something, such as differently evolved versions of a protein. In this kind
      of analysis, the things-to-be-compared typically are classes called 'OTUs' (Operational
      Taxonomic Units). The OTUs can represent biological species, but also may be
      drawn from higher or lower in a biological hierarchy, anywhere from molecules
      to communities. The features to be compared among OTUs are rendered in an entity-attribute-value
      model sometimes referred to as the 'character-state data model'. For a given
      character, such as 'beak length', each OTU has a state, such as 'short' or 'long'.
      The differences between states are understood to emerge by a historical process
      of evolutionary transitions in state, represented by a model (or rules) of transitions
      along with a phylogenetic tree. CDAO provides the framework for representing
      OTUs, trees, transformations, and characters. The representation of characters
      and transformations may depend on imported ontologies for a specific type of
      character.
    example_uri: http://purl.obolibrary.org/obo/CDAO_0000098
    homepage: http://www.evolutionaryontology.org/
    license: CC0-1.0
    name: Comparative Data Analysis Ontology
    prefix: CDAO
    publications:
    - http://www.evolutionaryontology.org
    repository: https://sourceforge.net/projects/cdao/
    version: '2013-02-01'
  biocontext:
    prefix: CDAO
  bioportal:
    contact:
      email: balhoff@renci.org
      name: Jim Balhoff
    description: A formalization of concepts and relations relevant to evolutionary
      comparative analysis, such as phylogenetic trees, OTUs (operational taxonomic
      units) and compared characters (including molecular characters as well as other
      types). CDAO is being developed by scientists in biology, evolution, and computer
      science.
    homepage: https://github.com/evoinfo/cdao
    name: Comparative Data Analysis Ontology
    prefix: CDAO
    version: $Revision$
  example: '0000072'
  fairsharing:
    abbreviation: CDAO
    contact:
      email: balhoff@gmail.com
      name: Jim Balhoff
      orcid: 0000-0002-8688-6599
    description: Comparative Data Analysis Ontology (CDAO) is a formalization of concepts
      and relations relevant to evolutionary comparative analysis, such as phylogenetic
      trees, OTUs (operational taxonomic units) and compared characters (including
      molecular characters as well as other types).
    domains:
    - Evolution
    homepage: https://github.com/evoinfo/cdao
    license: CC0-1.0
    name: Comparative Data Analysis Ontology
    prefix: FAIRsharing.kay31r
    publications:
    - doi: 10.4137/ebo.s2320
      pubmed: '19812726'
      title: Initial implementation of a comparative data analysis ontology
      year: 2009
    repository: https://github.com/evoinfo/cdao/issues
    subjects:
    - Life Science
    - Taxonomy
    - Molecular biology
    - Phylogenetics
    - Evolutionary Biology
    - Biomedical Science
    - Bioinformatics
  mappings:
    aberowl: CDAO
    agroportal: CDAO
    biocontext: CDAO
    bioportal: CDAO
    fairsharing: FAIRsharing.kay31r
    obofoundry: cdao
    ols: cdao
    ontobee: CDAO
    wikidata.entity: Q55118328
  obofoundry:
    contact: balhoff@renci.org
    contact.github: balhoff
    contact.label: Jim Balhoff
    contact.orcid: 0000-0002-8688-6599
    deprecated: false
    description: a formalization of concepts and relations relevant to evolutionary
      comparative analysis
    domain: organisms
    download.owl: http://purl.obolibrary.org/obo/cdao.owl
    homepage: https://github.com/evoinfo/cdao
    license: CC0 1.0
    license.url: https://creativecommons.org/publicdomain/zero/1.0/
    name: Comparative Data Analysis Ontology
    preferredPrefix: CDAO
    prefix: cdao
    publications:
    - id: https://doi.org/10.4137/EBO.S2320
      title: Initial Implementation of a Comparative Data Analysis Ontology
    repository: https://github.com/evoinfo/cdao
  ols:
    description: a formalization of concepts and relations relevant to evolutionary
      comparative analysis
    download_owl: http://purl.obolibrary.org/obo/cdao.owl
    homepage: https://github.com/evoinfo/cdao
    name: Comparative Data Analysis Ontology
    prefix: cdao
    tracker: https://github.com/evoinfo/cdao/issues
    version: '2024-01-25'
    version.iri: http://purl.obolibrary.org/obo/cdao/2024-01-25/cdao.owl
  ontobee:
    library: Library
    name: Comparative Data Analysis Ontology
    prefix: CDAO
  pattern: ^\d{7}$
  prefix: cdao
  publications:
  - doi: 10.4137/ebo.s2320
    pmc: PMC2747124
    pubmed: '19812726'
    title: Initial implementation of a comparative data analysis ontology
    year: 2009
  uri_format: http://purl.obolibrary.org/obo/CDAO_$1
cdd:
  biocontext:
    prefix: CDD
  edam:
    description: Identifier of a conserved domain from the Conserved Domain Database.
    name: CDD
    obsolete: false
    prefix: '2666'
  fairsharing:
    abbreviation: CDD
    description: The Canadian Disaster Database (CDD) contains detailed disaster information
      on more than 1000 natural, technological and conflict events (excluding war)
      that have happened since 1900 at home or abroad and that have directly affected
      Canadians. The database describes where and when a disaster occurred, the number
      of injuries, evacuations, and fatalities, as well as a rough estimate of the
      costs. As much as possible, the CDD contains primary data that is valid, current
      and supported by reliable and traceable sources, including federal institutions,
      provincial/territorial governments, non-governmental organizations and media
      sources. Data is updated and reviewed on a semi-annual basis.
    homepage: https://www.publicsafety.gc.ca/cnt/rsrcs/cndn-dsstr-dtbs/index-en.aspx
    name: Canadian Disaster Database
    prefix: FAIRsharing.ea287c
    publications: []
    subjects:
    - Geology
    - Earth Science
  go:
    homepage: https://www.ncbi.nlm.nih.gov/cdd
    name: Conserved Domain Database at NCBI
    prefix: CDD
    uri_format: http://www.ncbi.nlm.nih.gov/Structure/cdd/cddsrv.cgi?uid=$1
  integbio:
    alt_name: Conserved Domain Database
    description: This is a collection of muliple sequence alignment models for ancient
      domains and full-length proteins, for the purpose of giving annotations for
      proteins. This database includes domain information curated by NCBI as well
      as those imported from the external sources; Pfam, SMART, COG, PRK, and TIGRFAM.
    homepage: http://www.ncbi.nlm.nih.gov/cdd
    information_keywords:
    - Sequence
    - Image/Movie
    - Classification
    maintainer: NCBI (National Center for Biotechnology Information)
    name: CDD
    prefix: nbdc00401
    pubmeds:
    - '18984618'
    - '17135202'
    - '15215404'
    - '12368255'
    status: Active
    target_keywords:
    - Protein
  mappings:
    biocontext: CDD
    edam: '2666'
    fairsharing: FAIRsharing.ea287c
    go: CDD
    integbio: nbdc00401
    miriam: cdd
    n2t: cdd
    ncbi: CDD
    prefixcommons: cdd
    re3data: r3d100012041
    uniprot: DB-0214
  miriam:
    deprecated: false
    description: The Conserved Domain Database (CDD) is a collection of multiple sequence
      alignments and derived database search models, which represent protein domains
      conserved in molecular evolution.
    homepage: https://www.ncbi.nlm.nih.gov/sites/entrez?db=cdd
    id: 00000119
    name: Conserved Domain Database
    namespaceEmbeddedInLui: false
    pattern: ^(cd)?\d{5}$
    prefix: cdd
    sampleId: cd00400
    uri_format: https://www.ncbi.nlm.nih.gov/Structure/cdd/cddsrv.cgi?uid=$1
  n2t:
    description: The Conserved Domain Database (CDD) is a collection of multiple sequence
      alignments and derived database search models, which represent protein domains
      conserved in molecular evolution.
    example: cd00400
    homepage: https://www.ncbi.nlm.nih.gov/sites/entrez?db=cdd
    name: Conserved Domain Database at NCBI
    namespaceEmbeddedInLui: false
    pattern: ^(cd)?\d{5}$
    prefix: cdd
    uri_format: https://www.ncbi.nlm.nih.gov/Structure/cdd/cddsrv.cgi?uid=$1
  ncbi:
    example: 02194
    homepage: https://www.ncbi.nlm.nih.gov/Structure/cdd/cdd.shtml
    name: Conserved Domain Database
    prefix: CDD
  prefix: cdd
  prefixcommons:
    description: The Conserved Domain Database (CDD) brings together several collections
      of multiple sequence alignments representing conserved domains, including NCBI-curated
      domains, which use 3D-structure information to explicitly to define domain boundaries
      and provide insights into sequence/structure/function relationships, as well
      as domain models imported from a number of external source databases (Pfam,
      SMART, COG, PRK, TIGRFAM).
    example: cd00400
    homepage: http://www.ncbi.nlm.nih.gov/Structure/cdd/cdd.shtml
    keywords:
    - protein
    - structure
    license: http://www.nlm.nih.gov/copyright.html
    name: Conserved Domain Database
    pattern: ^cd\d{5}$
    prefix: cdd
    pubmed_ids:
    - '18984618'
    uri_format: http://www.ncbi.nlm.nih.gov/Structure/cdd/cddsrv.cgi?uid=$1
  publications:
  - doi: 10.1093/nar/gku1221
    pmc: PMC4383992
    pubmed: '25414356'
    title: 'CDD: NCBI''s conserved domain database'
    year: 2014
  - doi: 10.1093/nar/gkn845
    pmc: PMC2686570
    pubmed: '18984618'
    title: 'CDD: specific functional annotation with the Conserved Domain Database'
    year: 2008
  re3data:
    description: 'The Canadian Disaster Database (CDD) contains detailed disaster
      information on more than 1000 natural, technological and conflict events (excluding
      war) that have happened since 1900 at home or abroad and that have directly
      affected Canadians.

      Message since 2022-01: The Canadian Disaster Database geospatial view is temporarily
      out of service. We apologize for the inconvenience. The standard view of the
      database is still available.'
    doi: 10.17616/R3S65W
    homepage: https://www.publicsafety.gc.ca/cnt/rsrcs/cndn-dsstr-dtbs/index-en.aspx
    name: Canadian Disaster Database
    prefix: r3d100012041
    synonyms:
    - BDC
    - Base de données canadienne sur les catastrophes
    - CDD
  uniprot:
    abbreviation: CDD
    category: Family and domain databases
    homepage: https://www.ncbi.nlm.nih.gov/cdd
    name: Conserved Domains Database
    prefix: DB-0214
    publications:
    - doi: 10.1093/nar/gkac1096
      pubmed: '36477806'
    uri_format: https://www.ncbi.nlm.nih.gov/Structure/cdd/cddsrv.cgi?uid=$1
cdno:
  aberowl:
    description: CDNO provides structured terminologies to describe nutritional attributes
      of material entities that contribute to human diet.
    download_owl: http://aber-owl.net/media/ontologies/CDNO/19/cdno.owl
    homepage: https://cdno.info/
    name: Compositional Dietary Nutrition Ontology
    prefix: CDNO
  agroportal:
    contact:
      email: landreshdz@gmail.com
      name: Liliana Andrés‐Hernández
    description: The CDNO provides structured terminologies to describe nutritional
      attributes of material entities that contribute to human diet. These terms are
      intended primarily to be associated with datasets that quantify concentration
      of chemical nutritional components derived from samples taken from any stage
      in the production of food raw materials (including from crops, livestock, fisheries)
      and through processing and supply chains. Additional knowledge associated with
      these dietary sources may be represented by terms that describe functional,
      physical and other attributes. Whilst recognising that dietary nutrients within
      food substrates may be present as complex and dynamic physical and chemical
      structures or mixtures, CDNO focuses on components typically quantified in an
      analytical chemistry laboratory. The primary CDNO class ‘dietary nutritional
      component’ contains hierarchical sets of terms organised to reflect commonly
      used classifications of chemical food composition. This class does not represent
      an exhaustive classification of chemical components, but focuses on structuring
      terms according to widely accepted categories. This class is independent of,
      but may be used in conjunction with, classes that describe ‘analytical methods’
      for quantification, ‘physical properties’ or ‘dietary function’. Quantification
      data may be used and reported in research literature, to inform food composition
      tables and labelling, or for supply chain quality assurance and control. More
      specifically, terms within the ‘nutritional component concentration’ class may
      be used to represent quantification of components described in the ‘dietary
      nutritional component’ class. Concentration data are intended to be described
      in conjunction with post-composed metadata concepts, such as represented by
      the Food Ontology (FoodOn) ‘Food product by organism’, which derives from some
      food or anatomical entity and a NCBI organismal classification ontology (NCBITaxon)
      entity. The common vocabulary and relationships defined within CDNO should facilitate
      description, communication and exchange of material entity-derived nutritional
      composition datasets typically generated by analytical laboratories. The organisation
      of the vocabulary is structured to reflect common categories variously used
      by those involved in crop, livestock or other organismal production, associated
      R&D and breeding, as well as the food processing and supply sector, and nutritionists,
      inlcuding compilers and users of food composition databases. The CDNO therefore
      supports characterisation of genetic diversity and management of biodiversity
      collections, as well as sharing of knowledge relating to dietary composition
      between a wider set of researchers, breeders, farmers, processors and other
      stakeholders. Further development of the functional class should also assist
      in understanding how interactions between organismal genetic and environmental
      variation contribute to human diet and health in the farm to fork continuum.,
      None
    example_uri: http://purl.obolibrary.org/obo/CDNO_0200815
    homepage: https://cdno.info/
    license: CC-BY-3.0
    name: Compositional Dietary Nutrition Ontology
    prefix: CDNO
    repository: https://github.com/Southern-Cross-Plant-Science/cdno
  bioportal:
    contact:
      email: l.andres.hernandez.18@student.scu.edu.au
      name: Liliana Andres Hernandez
    description: CDNO provides structured terminologies to describe nutritional attributes
      of material entities that contribute to human diet.
    homepage: https://github.com/Southern-Cross-Plant-Science/cdno
    name: Compositional Dietary Nutrition Ontology
    prefix: CDNO
  example: '0000013'
  mappings:
    aberowl: CDNO
    agroportal: CDNO
    bioportal: CDNO
    obofoundry: cdno
    ols: cdno
    ontobee: CDNO
    wikidata.entity: Q111272479
  obofoundry:
    contact: landreshdz@gmail.com
    contact.github: LilyAndres
    contact.label: Liliana Andres Hernandez
    contact.orcid: 0000-0002-7696-731X
    depends_on:
    - bfo
    - chebi
    - envo
    - pato
    - ro
    deprecated: false
    description: CDNO provides structured terminologies to describe nutritional attributes
      of material entities that contribute to human diet.
    domain: diet, metabolomics, and nutrition
    download.obo: http://purl.obolibrary.org/obo/cdno.obo
    download.owl: http://purl.obolibrary.org/obo/cdno.owl
    homepage: https://cdno.info/
    license: CC BY 3.0
    license.url: https://creativecommons.org/licenses/by/3.0/
    name: Compositional Dietary Nutrition Ontology
    preferredPrefix: CDNO
    prefix: cdno
    publications:
    - id: https://doi.org/10.3389/fnut.2022.928837
      title: Establishing a Common Nutritional Vocabulary - From Food Production to
        Diet
    repository: https://github.com/CompositionalDietaryNutritionOntology/cdno
  ols:
    description: The CDNO provides structured terminologies to describe nutritional
      attributes of material entities that contribute to human diet. These terms are
      intended primarily to be associated with datasets that quantify concentration
      of chemical nutritional components derived from samples taken from any stage
      in the production of food raw materials (including from crops, livestock, fisheries)
      and through processing and supply chains. Additional knowledge associated with
      these dietary sources may be represented by terms that describe functional,
      physical and other attributes. Whilst recognising that dietary nutrients within
      food substrates may be present as complex and dynamic physical and chemical
      structures or mixtures, CDNO focuses on components typically quantified in an
      analytical chemistry laboratory. The primary CDNO class ‘dietary nutritional
      component’ contains hierarchical sets of terms organised to reflect commonly
      used classifications of chemical food composition. This class does not represent
      an exhaustive classification of chemical components, but focuses on structuring
      terms according to widely accepted categories. This class is independent of,
      but may be used in conjunction with, classes that describe ‘analytical methods’
      for quantification, ‘physical properties’ or ‘dietary function’. Quantification
      data may be used and reported in research literature, to inform food composition
      tables and labelling, or for supply chain quality assurance and control. More
      specifically, terms within the ‘nutritional component concentration’ class may
      be used to represent quantification of components described in the ‘dietary
      nutritional component’ class. Concentration data are intended to be described
      in conjunction with post-composed metadata concepts, such as represented by
      the Food Ontology (FoodOn) ‘Food product by organism’, which derives from some
      food or anatomical entity and a NCBI organismal classification ontology (NCBITaxon)
      entity. The common vocabulary and relationships defined within CDNO should facilitate
      description, communication and exchange of material entity-derived nutritional
      composition datasets typically generated by analytical laboratories. The organisation
      of the vocabulary is structured to reflect common categories variously used
      by those involved in crop, livestock or other organismal production, associated
      R&D and breeding, as well as the food processing and supply sector, and nutritionists,
      inlcuding compilers and users of food composition databases. The CDNO therefore
      supports characterisation of genetic diversity and management of biodiversity
      collections, as well as sharing of knowledge relating to dietary composition
      between a wider set of researchers, breeders, farmers, processors and other
      stakeholders. Further development of the functional class should also assist
      in understanding how interactions between organismal genetic and environmental
      variation contribute to human diet and health in the farm to fork continuum.
    download_owl: http://purl.obolibrary.org/obo/cdno.owl
    homepage: https://cdno.info/
    name: Compositional Dietary Nutrition Ontology
    prefix: cdno
    tracker: https://github.com/CompositionalDietaryNutritionOntology/cdno/issues
    version: '2025-06-09'
    version.iri: http://purl.obolibrary.org/obo/cdno/releases/2025-06-09/cdno.owl
  ontobee:
    library: Library
    name: Compositional Dietary Nutrition Ontology
    prefix: CDNO
  pattern: ^\d{7}$
  prefix: cdno
  publications:
  - doi: 10.1002/csc2.20092
    pmc: null
    pubmed: null
    title: Knowledge representation and data sharing to unlock crop variation for
      nutritional food security
    year: 2020
  - doi: 10.3389/fnut.2022.928837
    pmc: null
    pubmed: null
    title: Establishing a Common Nutritional Vocabulary - From Food Production to
      Diet
    year: null
  uri_format: http://purl.obolibrary.org/obo/CDNO_$1
cdpd:
  biocontext:
    prefix: CDPD
  mappings:
    biocontext: CDPD
    miriam: cdpd
    n2t: cdpd
  miriam:
    deprecated: false
    description: The Canadian Drug Product Database (DPD) contains product specific
      information on drugs approved for use in Canada, and includes human pharmaceutical
      and biological drugs, veterinary drugs and disinfectant products. This information
      includes 'brand name', 'route of administration' and a Canadian 'Drug Identification
      Number' (DIN).
    homepage: https://www.canada.ca/en/health-canada/services/drugs-health-products/drug-products/drug-product-database.html
    id: '00000272'
    name: Canadian Drug Product Database
    namespaceEmbeddedInLui: false
    pattern: ^\d+$
    prefix: cdpd
    sampleId: '63250'
    uri_format: https://health-products.canada.ca/dpd-bdpp/info?lang=eng&code=$1
  n2t:
    description: The Canadian Drug Product Database (DPD) contains product specific
      information on drugs approved for use in Canada, and includes human pharmaceutical
      and biological drugs, veterinary drugs and disinfectant products. This information
      includes 'brand name', 'route of administration' and a Canadian 'Drug Identification
      Number' (DIN).
    example: '63250'
    homepage: http://webprod3.hc-sc.gc.ca/dpd-bdpp/index-eng.jsp
    name: Canadian Drug Identification Number at Health Canada
    namespaceEmbeddedInLui: false
    pattern: ^\d+$
    prefix: cdpd
    uri_format: http://webprod3.hc-sc.gc.ca/dpd-bdpp/info.do?lang=eng&code=$1
  prefix: cdpd
cdt:
  appears_in:
  - ohd
  bartoc:
    abbreviation: CDT
    description: The Code on Dental Procedures and Nomenclature is used to provide
      for the efficient processing of dental claims, and to populate an Electronic
      Health Record.
    homepage: http://www.ada.org/en/publications/cdt
    license: http://rightsstatements.org/vocab/InC/1.0
    name: Code on Dental Procedures and Nomenclature
    prefix: '20299'
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: 'The Code on Dental Procedures and Nomenclature (the CDT Code) assures
    consistency in documenting dental treatment.


    Note that CDT codes should look like D2150 but for some reason the ontology conversion
    that is reused across OBO rewrites them as CPT_000 + the four numbers without
    the leading D.'
  download_owl: https://raw.githubusercontent.com/oral-health-and-disease-ontologies/ohd-ontology/f19378ff192b6f9ea16133e85671e8359fc371cd/src/ontology/archive/CDTCodes%20as%20Classes_pruned.owl
  example: '1000001'
  hl7:
    description: Version of Current Dental Terminology (CDT) version 4, included in
      the Healthcare Common Procedure Coding System (HCPCS).Request rejected.  This
      is a duplicate of OID 2.16.840.1.113883.6.13
    name: Current Dental Terminology
    preferred_prefix: CDT
    prefix: 2.16.840.1.113883.6.116
    status: Rejected
  homepage: https://www.ada.org/publications/CDT
  mappings:
    bartoc: '20299'
    hl7: 2.16.840.1.113883.6.116
  name: Current Dental Terminology
  pattern: ^\d{7}$
  prefix: cdt
ceds.element:
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: The Common Entity Data Standards (CEDS) Domain Entity Schema (DES)
    provides a hierarchy of domains, entities, categories, and elements. It is intended
    for use primarily by people as an index to search, map, and organize elements
    in a logical way. [from homepage]
  example: '000254'
  homepage: https://ceds.ed.gov/domainEntitySchema.aspx
  name: Common Entity Data Standards - Domain Entity Schema
  pattern: ^\d+$
  prefix: ceds.element
  uri_format: https://ceds.ed.gov/element/$1
ceds.learning_resource_type:
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: A vocabulary for learning resource types
  example: AlternateAssessment
  homepage: https://ceds.ed.gov/element/000928
  keywords:
  - educational resources
  - learning materials
  - open educational resources
  name: CEDS Learning Resource Type
  prefix: ceds.learning_resource_type
  uri_format: https://ceds.ed.gov/element/000928#$1
cell_biolabs:
  cellosaurus:
    category: Cell line collections (Providers)
    homepage: https://www.cellbiolabs.com
    name: Cell Biolabs cell line products
    prefix: Cell_Biolabs
    uri_format: https://www.cellbiolabs.com/search?keywords=$1
  example: AKR-270
  mappings:
    cellosaurus: Cell_Biolabs
  prefix: cell_biolabs
cell_model_passport:
  cellosaurus:
    category: Cell line databases/resources
    homepage: https://cellmodelpassports.sanger.ac.uk/
    name: Sanger Cell Model Passports
    prefix: Cell_Model_Passport
    uri_format: https://cellmodelpassports.sanger.ac.uk/passports/$1
  example: SIDM01262
  mappings:
    cellosaurus: Cell_Model_Passport
  prefix: cell_model_passport
cellbank.australia:
  cellosaurus:
    category: Cell line collections (Providers)
    homepage: https://www.cellbankaustralia.com/cellbank-australia-exclusive-lines/
    name: CellBank Australia
    prefix: CBA
    uri_format: https://www.cellbankaustralia.com/$1
  description: CellBank Australia collects novel cell lines, developed by Australian
    researchers, submits these cell lines to rigorous testing to confirm their integrity,
    and then distributes the cell lines to researchers throughout the world.
  example: ab-1-ha
  mappings:
    cellosaurus: CBA
  prefix: cellbank.australia
  uri_format: https://www.cellbankaustralia.com/$1.html
cellimage:
  biocontext:
    prefix: CELLIMAGE
  contact:
    email: dorloff@ncmir.ucsd.edu
    github: null
    name: David N. Orloff
    orcid: 0000-0001-7594-0820
  fairsharing:
    abbreviation: null
    description: This library is a public and easily accessible resource database
      of images, videos, and animations of cells, capturing a wide diversity of organisms,
      cell types, and cellular processes. The purpose of this database is to advance
      research on cellular activity, with the ultimate goal of improving human health.
      It is a repository for images, movies, and animations of cells from a variety
      of organisms that demonstrate cellular architecture and functions. This comprehensive
      library is designed as a public resource first and foremost for research, and
      secondarily as a tool for education. The long-term goal is the construction
      of a library of images that will serve as primary data for research.
    homepage: http://www.cellimagelibrary.org
    name: Cell Image Library
    prefix: FAIRsharing.8t18te
    publications:
    - doi: 10.1093/nar/gks1257
      pubmed_id: 23203874
      title: 'The cell: an image library-CCDB: a curated repository of microscopy
        data.'
    subjects:
    - Life Science
    - Cell Biology
    twitter: CellImageLibrar
  mappings:
    biocontext: CELLIMAGE
    fairsharing: FAIRsharing.8t18te
    miriam: cellimage
    n2t: cellimage
    prefixcommons: cellimage
    re3data: r3d100000023
  miriam:
    deprecated: false
    description: 'The Cell: An Image Library™ is a freely accessible, public repository
      of reviewed and annotated images, videos, and animations of cells from a variety
      of organisms, showcasing cell architecture, intracellular functionalities, and
      both normal and abnormal processes.'
    homepage: http://cellimagelibrary.org/
    id: '00000257'
    name: Cell Image Library
    namespaceEmbeddedInLui: false
    pattern: ^\d+$
    prefix: cellimage
    sampleId: '24801'
    uri_format: http://cellimagelibrary.org/images/$1
  n2t:
    description: 'The Cell: An Image Library&#x2122; is a freely accessible, public
      repository of reviewed and annotated images, videos, and animations of cells
      from a variety of organisms, showcasing cell architecture, intracellular functionalities,
      and both normal and abnormal processes.'
    example: '24801'
    homepage: http://cellimagelibrary.org/
    name: Cell Image Library at American Society for Cell Biology
    namespaceEmbeddedInLui: false
    pattern: ^\d+$
    prefix: cellimage
    uri_format: http://cellimagelibrary.org/images/$1
  prefix: cellimage
  prefixcommons:
    description: 'The Cell: An Image Library™ is a freely accessible, public repository
      of reviewed and annotated images, videos, and animations of cells from a variety
      of organisms, showcasing cell architecture, intracellular functionalities, and
      both normal and abnormal processes.'
    example: '24801'
    keywords:
    - image
    name: 'The Cell: An Image Library'
    pattern: ^\d+$
    prefix: cellimage
    uri_format: http://cellimagelibrary.org/images/$1
  publications:
  - doi: 10.1093/nar/gks1257
    pmc: PMC3531121
    pubmed: '23203874'
    title: 'The cell: an image library-CCDB: a curated repository of microscopy data'
    year: 2012
  - doi: 10.1093/nar/gks1257
    pmc: null
    pubmed: null
    title: 'The cell: an image library-CCDB: a curated repository of microscopy data.'
    year: null
  re3data:
    description: This library is a public and easily accessible resource database
      of images, videos, and animations of cells, capturing a wide diversity of organisms,
      cell types, and cellular processes. The Cell Image Library has been merged with
      "Cell Centered Database" in 2017. The purpose of the database is to advance
      research on cellular activity, with the ultimate goal of improving human health.
    doi: 10.17616/R3Z59M
    homepage: http://www.cellimagelibrary.org/home
    name: Cell Image Library
    prefix: r3d100000023
    synonyms:
    - CIL
    - The Cell
    xrefs:
      nif: 0000-37639
cellopub:
  cellosaurus:
    category: Reference resources
    homepage: https://www.cellosaurus.org/
    name: Cellosaurus Publication
    prefix: CelloPub
    uri_format: https://www.cellosaurus.org/cellopub/$1
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: Cellosaurus identifeirs for publications, like Pubmed
  example: CLPUB00496
  homepage: https://web.expasy.org/cellosaurus/
  mappings:
    cellosaurus: CelloPub
  name: Cellosaurus Publication
  pattern: ^CLPUB\d+$
  prefix: cellopub
  uri_format: https://web.expasy.org/cellosaurus/cellopub/$1
cellosaurus:
  banana: CVCL
  banana_peel: _
  biocontext:
    prefix: CELLOSAURUS
  cellosaurus:
    category: Cell line databases/resources
    homepage: https://www.cellosaurus.org/
    name: Cellosaurus - a knowledge resource on cell lines
    prefix: Cellosaurus
    uri_format: https://www.cellosaurus.org/$1
  contact:
    email: Amos.Bairoch@sib.swiss
    github: AmosBairoch
    name: Amos Bairoch
    orcid: 0000-0003-2826-6444
  download_obo: https://ftp.expasy.org/databases/cellosaurus/cellosaurus.obo
  example: '0440'
  fairsharing:
    abbreviation: Cellosaurus
    contact:
      email: Amos.Bairoch@sib.swiss
      name: Amos Bairoch
      orcid: 0000-0003-2826-6444
    description: 'The Cellosaurus is a knowledge resource on cell lines. It attempts
      to describe all cell lines used in biomedical research. Its scope includes:
      Immortalized cell lines; naturally immortal cell lines (example: stem cell lines);
      finite life cell lines when those are distributed and used widely; vertebrate
      cell line with an emphasis on human, mouse and rat cell lines; and invertebrate
      (insects and ticks) cell lines. Its scope does not include primary cell lines
      (with the exception of the finite life cell lines described above) and plant
      cell lines.'
    homepage: https://www.cellosaurus.org
    license: CC-BY-4.0
    name: Cellosaurus
    prefix: FAIRsharing.hkk309
    publications:
    - doi: 10.1002/ijc.32639
      pubmed_id: 31444973
      title: 'CLASTR: The Cellosaurus STR similarity search tool - A precious help
        for cell line authentication.'
    - doi: 10.7171/jbt.18-2902-002
      pubmed_id: 29805321
      title: The Cellosaurus, a Cell-Line Knowledge Resource.
    subjects:
    - Life Science
  homepage: https://cellosaurus.org
  integbio:
    description: 'The Cellosaurus is a knowledge resource on cell lines. It attempts
      to describe all cell lines used in biomedical research. Its scope includes:
      Immortalized cell lines; naturally immortal cell lines (example: stem cell lines);
      finite life cell lines when those are distributed and used widely; vertebrate
      cell line with an emphasis on human, mouse and rat cell lines; and invertebrate
      (insects and ticks) cell lines. Its scope does not include primary cell lines
      (with the exception of the finite life cell lines described above) and plant
      cell lines.'
    fairsharing: FAIRsharing.hkk309
    homepage: https://www.cellosaurus.org
    information_keywords:
    - Bioresource
    maintainer: CALIPHO (Computer and Laboratory Investigation of Proteins of Human
      Origin Group, Swiss Institute of Bioinformatics)
    name: Cellosaurus
    prefix: nbdc02180
    status: Active
    target_keywords:
    - Cell/Organelle
    - Organism
  license: CC-BY-4.0
  logo: https://www.cellosaurus.org/images/cellosaurus/cellosaurus.png
  mappings:
    biocontext: CELLOSAURUS
    cellosaurus: Cellosaurus
    fairsharing: FAIRsharing.hkk309
    integbio: nbdc02180
    miriam: cellosaurus
    n2t: cellosaurus
    re3data: r3d100013293
    rrid: CVCL
    togoid: Cellosaurus
    wikidata: P3289
    wikidata.entity: Q21014462
  mastodon: cellosaurus@fediscience.org
  miriam:
    deprecated: false
    description: 'The Cellosaurus is a knowledge resource on cell lines. It attempts
      to describe all cell lines used in biomedical research. Its scope includes:
      Immortalized cell lines; naturally immortal cell lines (example: stem cell lines);
      finite life cell lines when those are distributed and used widely; vertebrate
      cell line with an emphasis on human, mouse and rat cell lines; and invertebrate
      (insects and ticks) cell lines. Its scope does not include primary cell lines
      (with the exception of the finite life cell lines described above) and plant
      cell lines.'
    homepage: https://www.cellosaurus.org/
    id: 00000598
    name: Cellosaurus
    namespaceEmbeddedInLui: false
    pattern: ^CVCL_[A-Z0-9]{4}(\.txt)?$
    prefix: cellosaurus
    sampleId: CVCL_0030
    uri_format: https://www.cellosaurus.org/$1
  n2t:
    description: 'The Cellosaurus is a knowledge resource on cell lines. It attempts
      to describe all cell lines used in biomedical research. Its scope includes:
      Immortalized cell lines; naturally immortal cell lines (example: stem cell lines);
      finite life cell lines when those are distributed and used widely; vertebrate
      cell line with an emphasis on human, mouse and rat cell lines; and invertebrate
      (insects and ticks) cell lines. Its scope does not include primary cell lines
      (with the exception of the finite life cell lines described above) and plant
      cell lines.'
    example: CVCL_0030
    homepage: https://web.expasy.org/cellosaurus/
    name: Cellosaurus through SIB
    namespaceEmbeddedInLui: false
    pattern: CVCL_[A-Z0-9]{4}
    prefix: cellosaurus
    uri_format: https://web.expasy.org/cellosaurus/$1
  name: Cellosaurus
  pattern: ^[A-Z0-9]{4}$
  prefix: cellosaurus
  providers:
  - code: legacy
    description: The legacy URI for the Cellosaurus website, updated on August 30,
      2022 [ref](https://twitter.com/Cellosaurus/status/1564658792691810305).
    example: null
    first_party: null
    homepage: https://web.expasy.org/cellosaurus
    name: Legacy Endpoint
    publications: null
    status: null
    uri_format: https://web.expasy.org/cellosaurus/CVCL_$1
  - code: obo.incorrect
    description: OBO PURL generated by incorrectly configured OBO file - this is not
      registered in OBO Foundry.
    example: null
    first_party: null
    homepage: http://purl.obolibrary.org
    name: OBO (Incorrect)
    publications: null
    status: null
    uri_format: http://purl.obolibrary.org/obo/Cellosaurus#CVCL_$1
  - code: nextprot
    description: The neXtProt endpoint for exploring Cellosaurus
    example: null
    first_party: null
    homepage: https://www.nextprot.org/
    name: neXtProt Cellosaurus Browser
    publications: null
    status: null
    uri_format: https://www.nextprot.org/term/CVCL_$1
  - code: obo
    description: Incorrectly encoded OBO PURL - do not use!
    example: null
    first_party: null
    homepage: http://purl.obolibrary.org
    name: OBO PURL
    publications: null
    status: null
    uri_format: http://purl.obolibrary.org/obo/Cellosaurus#CVCL_$1
  publications:
  - doi: 10.1002/ijc.32639
    pmc: null
    pubmed: '31444973'
    title: 'CLASTR: The Cellosaurus STR similarity search tool - A precious help for
      cell line authentication'
    year: 2019
  - doi: 10.7171/jbt.18-2902-002
    pmc: PMC5945021
    pubmed: '29805321'
    title: The Cellosaurus, a Cell-Line Knowledge Resource
    year: 2018
  - doi: 10.1002/ijc.32639
    pmc: null
    pubmed: null
    title: 'CLASTR: The Cellosaurus STR similarity search tool - A precious help for
      cell line authentication.'
    year: null
  - doi: 10.7171/jbt.18-2902-002
    pmc: null
    pubmed: null
    title: The Cellosaurus, a Cell-Line Knowledge Resource.
    year: null
  - doi: null
    pmc: null
    pubmed: '29805321'
    title: null
    year: null
  - doi: 10.1002/ijc.32639
    pmc: null
    pubmed: null
    title: 'CLASTR: The Cellosaurus STR similarity search tool - A precious help for
      cell line authentication.'
    year: null
  - doi: 10.7171/jbt.18-2902-002
    pmc: null
    pubmed: null
    title: The Cellosaurus, a Cell-Line Knowledge Resource.
    year: null
  - doi: null
    pmc: null
    pubmed: '29805321'
    title: null
    year: null
  re3data:
    description: 'The Cellosaurus is a knowledge resource on cell lines. It attempts
      to describe all cell lines used in biomedical research. Its scope includes:
      Immortalized cell lines, Naturally immortal cell lines (example: stem cell lines),
      Finite life cell lines when those are distributed and used widely, Vertebrate
      cell line with an emphasis on human, mouse and rat cell lines, Invertebrate
      (insects and ticks) cell lines. Its scope does not include: Primary cell lines
      (with the exception of the finite life cell lines described above), Plant cell
      lines.  Cellosaurus was initiated to be used as a cell line controlled vocabulary
      in the context of the neXtProt knowledgebase, but it quickly become apparent
      that there was a need for a cell line knowledge resource that would serve the
      needs of individual researchers, cell line distributors and bioinformatic resources.
      This leads to an increase of the scope and depth of the content of the Cellosaurus.
      The Cellosaurus is a participant of the Resource Identification Initiative and
      contributes actively to the work of the International Cell Line Authentication
      Committee (ICLAC). It is a Global Core Biodata Resource, an ELIXIR Core Data
      Resource and an IRDiRC Recognized Resource.'
    doi: 10.17616/R31NJMR1
    homepage: https://www.cellosaurus.org/
    name: Cellosaurus
    prefix: r3d100013293
    synonyms:
    - Cellosaurus - a knowledge resource on cell lines
  repository: https://github.com/calipho-sib/cellosaurus
  rrid:
    homepage: https://web.expasy.org/cellosaurus/
    keywords:
    - cell lines
    - controlled vocabularies
    - ontologies
    - thesaurus
    name: Cellosaurus
    prefix: CVCL
    pubmeds:
    - '29805321'
    scr: 013869
    twitter: Cellosaurus
  synonyms:
  - CVCL
  togoid:
    catalog: nbdc02180
    examples:
    - CVCL:7T24
    - CVCL:SE45
    - CVCL:XG73
    - CVCL:B6HT
    - CVCL:WM34
    - CVCL:7891
    - CVCL:FV52
    - CVCL:0367
    - CVCL:9Z18
    - CVCL:CG19
    keywords:
    - CellLine
    name: Cellosaurus
    pattern: ^CVCL[:_](?[A-Z0-9]{4})$
    prefix: Cellosaurus
    uri_format: http://www.cellosaurus.org/CVCL_$1
  twitter: cellosaurus
  uri_format: https://www.cellosaurus.org/CVCL_$1
  wikidata:
    database: Q21014462
    description: Cellosaurus cell line identifier
    example:
    - CVCL_0030
    - CVCL_0440
    name: Cellosaurus ID
    pattern: ^CVCL_[A-Z\d][A-Z\d][A-Z\d][A-Z\d]$
    prefix: P3289
    uri_format: https://www.cellosaurus.org/$1
cellosaurus.resource:
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: The set of prefixes used in the Cellosaurus resource
  example: 4DN
  homepage: https://web.expasy.org/cellosaurus/
  keywords:
  - cell lines
  - cells
  - registry
  name: Cellosaurus Registry
  part_of_database: cellosaurus
  prefix: cellosaurus.resource
  uri_format: https://bioregistry.io/metaregistry/cellosaurus/$1
cellrepo:
  mappings:
    miriam: cellrepo
  miriam:
    deprecated: false
    description: The Cell Version Control Repository is the single worldwide version
      control repository for engineered and natural cell lines
    homepage: https://www.cellrepo.com/
    id: 00000829
    name: Cell Version Control Repository
    namespaceEmbeddedInLui: false
    pattern: ^[0-9]+$
    prefix: cellrepo
    sampleId: '82'
    uri_format: https://www.cellrepo.com/repositories/$1
  prefix: cellrepo
cellxgene.collection:
  contact:
    email: acarr@chanzuckerberg.com
    github: ambrosejcarr
    name: Ambrose Carr
    orcid: 0000-0002-8457-2836
  contributor:
    email: robert.j.allaway@gmail.com
    github: allaway
    name: Robert Allaway
    orcid: 0000-0003-3573-3565
  description: 'Assigns identifiers to collections of datasets indexed by CELLxGENE.


    CELLxGENE is an interactive data visualization and exploration tool developed
    by the Chan Zuckerberg Initiative that enables researchers to analyze and share
    single-cell genomics datasets. It provides a user-friendly interface for biologists
    and computational scientists to interrogate gene expression patterns across different
    cell types.'
  example: 436154da-bcf1-4130-9c8b-120ff9a888f2
  github_request_issue: 1541
  homepage: https://cellxgene.cziscience.com/collections
  license: CC-BY-4.0
  name: Chan Zuckerberg CELLxGENE Collection
  part_of_database: cellxgene
  pattern: ^[0-9a-f]{8}-[0-9a-f]{4}-[0-9a-f]{4}-[0-9a-f]{4}-[0-9a-f]{12}$
  prefix: cellxgene.collection
  publications:
  - doi: 10.1093/nar/gkae1142
    pmc: PMC11701654
    pubmed: '39607691'
    title: 'CZ CELLxGENE Discover: a single-cell data platform for scalable exploration,
      analysis and modeling of aggregated data'
    year: 2024
  reviewer:
    email: b.gyori@northeastern.edu
    github: bgyori
    name: Benjamin M. Gyori
    orcid: 0000-0001-9439-5346
  reviewer_extras:
  - email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  uri_format: https://cellxgene.cziscience.com/collections/$1
cellxgene.dataset:
  contact:
    email: acarr@chanzuckerberg.com
    github: ambrosejcarr
    name: Ambrose Carr
    orcid: 0000-0002-8457-2836
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: Assigns identifiers to datasets indexed by CELLxGENE, such those resulting
    from scRNA-seq experiments
  example: f72958f5-7f42-4ebb-98da-445b0c6de516
  github_request_issue: 1541
  homepage: https://cellxgene.cziscience.com
  name: Chan Zuckerberg CELLxGENE Dataset
  part_of_database: cellxgene
  prefix: cellxgene.dataset
  publications:
  - doi: 10.1093/nar/gkae1142
    pmc: PMC11701654
    pubmed: '39607691'
    title: 'CZ CELLxGENE Discover: a single-cell data platform for scalable exploration,
      analysis and modeling of aggregated data'
    year: 2024
  uri_format: https://cellxgene.cziscience.com/e/$1
cemo:
  contact:
    email: n.queralt_rosinach@lumc.nl
    github: NuriaQueralt
    name: Núria Queralt Rosinach
    orcid: 0000-0003-0169-8159
  contributor:
    email: benjamin_gyori@hms.harvard.edu
    github: bgyori
    name: Benjamin M. Gyori
    orcid: 0000-0001-9439-5346
  description: The covid-19 epidemiology and monitoring ontology (cemo) provides a
    common ontological model to make epidemiological quantitative data for monitoring
    the covid-19 outbreak machine-readable and interoperable to facilitate its exchange,
    integration and analysis, to eventually support evidence-based rapid response.
  download_json: https://raw.githubusercontent.com/cthoyt/covid19-epidemiology-ontology/add-artifacts/owl/cemo.json
  download_owl: https://raw.githubusercontent.com/NuriaQueralt/covid19-epidemiology-ontology/main/owl/cemo.owl
  example: secondary_attack_rate
  github_request_issue: 593
  homepage: https://github.com/NuriaQueralt/covid19-epidemiology-ontology
  license: CC0-1.0
  name: The COVID-19 epidemiology and monitoring ontology
  pattern: ^[0-9a-z_-]+$
  prefix: cemo
  providers:
  - code: obo
    description: This represents misconfigured base IRIs, even though this ontology
      isn't an OBO Foundry ontology
    example: null
    first_party: null
    homepage: http://purl.obolibrary.org/obo/
    name: Legacy OBO PURL
    publications: null
    status: null
    uri_format: http://purl.obolibrary.org/obo/cemo.owl#$1
  repository: https://github.com/NuriaQueralt/covid19-epidemiology-ontology
  reviewer:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  uri_format: https://biopragmatics.github.io/providers/cemo/$1
ceph:
  aberowl:
    description: An anatomical and developmental ontology for cephalopods
    download_owl: http://aber-owl.net/media/ontologies/CEPH/2/ceph.owl
    homepage: https://github.com/obophenotype/cephalopod-ontology
    name: Cephalopod Ontology
    prefix: CEPH
  biocontext:
    prefix: CEPH
  bioportal:
    contact:
      email: cjmungall@lbl.gov
      name: Chris Mungall
    description: An anatomical and developmental ontology for cephalopods
    homepage: https://github.com/obophenotype/cephalopod-ontology
    name: Cephalopod Ontology
    prefix: CEPH
  download_obo: https://raw.githubusercontent.com/obophenotype/cephalopod-ontology/master/ceph.obo
  example: 0000109
  fairsharing:
    abbreviation: CEPH
    description: An anatomical and developmental ontology for cephalopods
    domains:
    - life cycle
    homepage: https://github.com/obophenotype/cephalopod-ontology
    name: Cephalopod Ontology
    prefix: FAIRsharing.p58bm4
    subjects:
    - Fisheries Science
    - Anatomy
    - Zoology
  mappings:
    aberowl: CEPH
    biocontext: CEPH
    bioportal: CEPH
    fairsharing: FAIRsharing.p58bm4
    obofoundry: ceph
    ols: ceph
    ontobee: CEPH
    wikidata.entity: Q104030182
  obofoundry:
    contact: cjmungall@lbl.gov
    contact.github: cmungall
    contact.label: Chris Mungall
    contact.orcid: 0000-0002-6601-2165
    deprecated: true
    description: An anatomical and developmental ontology for cephalopods
    domain: anatomy and development
    download.obo: http://purl.obolibrary.org/obo/ceph.obo
    download.owl: http://purl.obolibrary.org/obo/ceph.owl
    homepage: https://github.com/obophenotype/cephalopod-ontology
    license: CC BY 3.0
    license.url: http://creativecommons.org/licenses/by/3.0/
    name: Cephalopod Ontology
    prefix: ceph
    repository: https://github.com/obophenotype/cephalopod-ontology
  ols:
    description: An anatomical and developmental ontology for cephalopods
    download_owl: http://purl.obolibrary.org/obo/ceph.owl
    homepage: https://github.com/obophenotype/cephalopod-ontology
    name: Cephalopod Ontology
    prefix: ceph
    tracker: https://github.com/obophenotype/cephalopod-ontology/issues
    version: '2016-01-12'
    version.iri: http://purl.obolibrary.org/obo/ceph/releases/2016-01-12/ceph.owl
  ontobee:
    library: Library
    name: Cephalopod Ontology
    prefix: CEPH
  pattern: ^\d{7}$
  prefix: ceph
cert:
  example: Certificate
  lov:
    description: Ontology for Certificates and crypto stuff.
    homepage: http://www.w3.org/ns/auth/cert#
    keywords:
    - Quality
    modified: '2008-11-13'
    name: The Cert Ontology
    prefix: cert
    uri_prefix: http://www.w3.org/ns/auth/cert#$1
  mappings:
    lov: cert
    zazuko: cert
  prefix: cert
  zazuko:
    prefix: cert
    uri_format: http://www.w3.org/ns/auth/cert#$1
cessda:
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: A vocabulary service for the social sciences, covering the Data Documentation
    Initiative (DDI) is an international standard for describing data produced by
    surveys and other observational methods in the social, behavioural, economic,
    and health sciences.
  example: TopicClassification
  homepage: https://vocabularies.cessda.eu
  keywords:
  - registry
  name: Consortium of European Social Science Data Archives Vocabulary
  prefix: cessda
  uri_format: https://vocabularies.cessda.eu/vocabulary/$1
cessda.cdcpublishernames:
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: Names of organisations providing metadata for CESSDA Data Catalogue.
  example: AUSSDA
  homepage: https://vocabularies.cessda.eu/vocabulary/CdcPublisherNames
  license: CC-BY-4.0
  name: CDC Publisher Names
  owners:
  - name: Consortium of European Social Science Data Archives
    partnered: false
    ror: 02wg9xc72
    wikidata: null
  part_of_database: cessda
  prefix: cessda.cdcpublishernames
  uri_format: https://vocabularies.cessda.eu/vocabulary/CdcPublisherNames?lang=en#code_$1
  version: 6.0.0
cessda.cessdadatacataloguecollections:
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: This vocabulary holds the definitions and descriptions of the collections
    included in the CESSDA Data Catalogue.
  example: BY-COVID
  homepage: https://vocabularies.cessda.eu/vocabulary/CESSDADataCatalogueCollections
  license: CC-BY-4.0
  name: CESSDA Data Catalogue Collections
  owners:
  - name: Consortium of European Social Science Data Archives
    partnered: false
    ror: 02wg9xc72
    wikidata: null
  part_of_database: cessda
  prefix: cessda.cessdadatacataloguecollections
  uri_format: https://vocabularies.cessda.eu/vocabulary/CESSDADataCatalogueCollections?lang=en#code_$1
  version: 1.0.0
cessda.cessdapersistentidentifiertypes:
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: Lists the types of persistent identifiers that CESSDA accepts as study
    level PIDs in its data catalogue.
  example: ARK
  homepage: https://vocabularies.cessda.eu/vocabulary/CessdaPersistentIdentifierTypes
  license: CC-BY-4.0
  name: CESSDA Persistent Identifier Types
  owners:
  - name: Consortium of European Social Science Data Archives
    partnered: false
    ror: 02wg9xc72
    wikidata: null
  part_of_database: cessda
  prefix: cessda.cessdapersistentidentifiertypes
  uri_format: https://vocabularies.cessda.eu/vocabulary/CessdaPersistentIdentifierTypes?lang=en#code_$1
  version: 1.0.0
cessda.countrynamesandcodes:
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: ISO 3166-1 alpha-2 country codes and names.
  example: AF
  homepage: https://vocabularies.cessda.eu/vocabulary/CountryNamesAndCodes
  license: CC-BY-4.0
  name: Country Names and Codes
  owners:
  - name: Consortium of European Social Science Data Archives
    partnered: false
    ror: 02wg9xc72
    wikidata: null
  part_of_database: cessda
  prefix: cessda.countrynamesandcodes
  uri_format: https://vocabularies.cessda.eu/vocabulary/CountryNamesAndCodes?lang=en#code_$1
  version: 1.1.0
cessda.topicclassification:
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: A typology of main themes or subjects of data.
  example: Demography
  homepage: https://vocabularies.cessda.eu/vocabulary/TopicClassification
  license: CC-BY-4.0
  name: CESSDA Topic Classification
  owners:
  - name: Consortium of European Social Science Data Archives
    partnered: false
    ror: 02wg9xc72
    wikidata: null
  part_of_database: cessda
  prefix: cessda.topicclassification
  uri_format: https://vocabularies.cessda.eu/vocabulary/TopicClassification?lang=en#code_$1
  version: 4.2.3
cgd:
  biocontext:
    prefix: CGD
  contact:
    email: gsherloc@stanford.edu
    github: null
    name: Gavin Sherlock
    orcid: 0000-0002-1692-4983
  fairsharing:
    abbreviation: CGD
    description: The Candida Genome Database (CGD) provides access to genomic sequence
      data and manually curated functional information about genes and proteins of
      the human pathogen Candida albicans. It collects gene names and aliases, and
      assigns gene ontology terms to describe the molecular function, biological process,
      and subcellular localization of gene products.
    homepage: http://www.candidagenome.org/
    name: Candida Genome Database
    prefix: FAIRsharing.j7j53
    publications:
    - doi: 10.1093/nar/gki003
      pubmed_id: 15608216
      title: The Candida Genome Database (CGD), a community resource for Candida albicans
        gene and protein information.
    - doi: 10.1093/nar/gkr945
      pubmed_id: 22064862
      title: 'The Candida genome database incorporates multiple Candida species: multispecies
        search and analysis tools with curated gene and protein information for Candida
        albicans and Candida glabrata.'
    subjects:
    - Life Science
  go:
    homepage: http://www.candidagenome.org/
    name: Candida Genome Database
    prefix: CGD
    synonyms:
    - CGDID
    uri_format: http://www.candidagenome.org/cgi-bin/locus.pl?dbid=$1
  integbio:
    alt_name: Candida Genome Database
    description: This database is a genome database for Candida. It contains manually
      curated annotations on genes and proteins, as well as genomic sequences of the
      human pathogen Candida. Users can view the information of four strains of Candida,
      including C. albicans, C. dubliniensis, C. glabrata, and C. parapsilosis, which
      are metabolic pathways, experimental data, and full text of publications as
      well as genomic information.
    fairsharing: biodbcore-000276
    homepage: http://www.candidagenome.org
    information_keywords:
    - Sequence
    - Interaction/Pathway
    - Bibliography/Documents
    - Repository
    maintainer: Stanford University
    name: CGD
    prefix: nbdc00391
    pubmeds:
    - '19808938'
    - '19577928'
    - '19465905'
    - '17090582'
    - '16879419'
    - '15608216'
    - '22064862'
    status: Active
    target_keywords:
    - Genome/Gene
    - DNA
    - Protein
    - Health/Disease
  mappings:
    biocontext: CGD
    fairsharing: FAIRsharing.j7j53
    go: CGD
    integbio: nbdc00391
    miriam: cgd
    n2t: cgd
    ncbi: CGD
    prefixcommons: cgd
    re3data: r3d100010617
    uniprot: DB-0126
  miriam:
    deprecated: false
    description: The Candida Genome Database (CGD) provides access to genomic sequence
      data and manually curated functional information about genes and proteins of
      the human pathogen Candida albicans. It collects gene names and aliases, and
      assigns gene ontology terms to describe the molecular function, biological process,
      and subcellular localization of gene products.
    homepage: http://www.candidagenome.org/
    id: '00000145'
    name: Candida Genome Database
    namespaceEmbeddedInLui: false
    pattern: ^CAL\d{7}$
    prefix: cgd
    sampleId: CAL0003079
    uri_format: http://www.candidagenome.org/cgi-bin/locus.pl?dbid=$1
  n2t:
    description: The Candida Genome Database (CGD) provides access to genomic sequence
      data and manually curated functional information about genes and proteins of
      the human pathogen Candida albicans. It collects gene names and aliases, and
      assigns gene ontology terms to describe the molecular function, biological process,
      and subcellular localization of gene products.
    example: CAL0003079
    homepage: http://www.candidagenome.org/
    name: Candida Genome Database at Stanford University
    namespaceEmbeddedInLui: false
    pattern: ^CAL\d{7}$
    prefix: cgd
    uri_format: http://www.candidagenome.org/cgi-bin/locus.pl?dbid=$1
  ncbi:
    example: CAL0005934
    homepage: http://www.candidagenome.org/
    name: Candida Genome Database
    prefix: CGD
  prefix: cgd
  prefixcommons:
    description: The Candida Genome Database (CGD) provides access to genomic sequence
      data and manually curated functional information about genes and proteins of
      the human pathogen Candida albicans. It collects gene names and aliases, and
      assigns gene ontology terms to describe the molecular function, biological process,
      and subcellular localization of gene products.
    example: CAL0003079
    homepage: http://www.candidagenome.org/
    keywords:
    - eukaryotic
    - genome
    - nucleotide
    name: Candida Genome Database
    pattern: ^CAL\d{7}$
    prefix: cgd
    pubmed_ids:
    - '15608216'
    uri_format: http://www.candidagenome.org/cgi-bin/locus.pl?dbid=$1
  publications:
  - doi: 10.1093/nar/gkw924
    pmc: PMC5210628
    pubmed: '27738138'
    title: 'The Candida Genome Database (CGD): incorporation of Assembly 22, systematic
      identifiers and visualization of high throughput sequencing data'
    year: 2016
  - doi: 10.1093/nar/gkr945
    pmc: PMC3245171
    pubmed: '22064862'
    title: 'The Candida genome database incorporates multiple Candida species: multispecies
      search and analysis tools with curated gene and protein information for Candida
      albicans and Candida glabrata'
    year: 2011
  - doi: 10.1093/nar/gki003
    pmc: PMC539957
    pubmed: '15608216'
    title: The Candida Genome Database (CGD), a community resource for Candida albicans
      gene and protein information
    year: 2005
  re3data:
    description: Candida Genome Database, a resource for genomic sequence data and
      gene and protein information for Candida albicans and related species. CGD is
      based on the Saccharomyces Genome Database. The Candida Genome Database (CGD)
      provides online access to genomic sequence data and manually curated functional
      information about genes and proteins of the human pathogen Candida albicans
      and related species. C. albicans is the best studied of the human fungal pathogens.
      It is a common commensal organism of healthy individuals, but can cause debilitating
      mucosal infections and life-threatening systemic infections, especially in immunocompromised
      patients. C. albicans also serves as a model organism for the study of other
      fungal pathogens.
    doi: 10.17616/R36312
    homepage: http://www.candidagenome.org/
    name: Candida Genome Database
    prefix: r3d100010617
    synonyms:
    - CGD
    xrefs:
      nif: 0000-02634
      omics: 03098
  uniprot:
    abbreviation: CGD
    category: Organism-specific databases
    homepage: http://www.candidagenome.org/
    name: Candida Genome Database
    prefix: DB-0126
    publications:
    - doi: 10.1093/nar/gkw924
      pubmed: '27738138'
    uri_format: http://www.candidagenome.org/cgi-bin/locus.pl?dbid=$1
cghdb:
  cellosaurus:
    category: Cell line databases/resources
    homepage: https://web.archive.org/web/20190222051223/http://www.cghtmd.jp/CGHDatabase/index_e.jsp
    name: CGH Data Base
    prefix: CGH-DB
  example: 300165/p13898_2106T
  mappings:
    cellosaurus: CGH-DB
  prefix: cghdb
cgnc:
  cellosaurus:
    category: Organism-specific databases
    homepage: http://birdgenenames.org/cgnc/
    name: Chicken Gene Nomenclature Consortium Database
    prefix: CGNC
    uri_format: http://birdgenenames.org/cgnc/GeneReport?id=$1
  contact:
    email: fionamcc@arizona.edu
    github: null
    name: Fiona M McCarthy
    orcid: 0000-0003-2175-5464
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: Nomenclature Consortium around Chicken genes (analogous to the HGNC
    for humans)
  domain: gene
  example: '10087'
  homepage: http://birdgenenames.org
  license: CC-BY-4.0
  logo: https://birdgenenames.org/img/CGNC.png
  mappings:
    cellosaurus: CGNC
    prefixcommons: cgnc
    re3data: r3d100012429
  name: Chicken Gene Nomenclature Consortium
  pattern: ^\d+$
  prefix: cgnc
  prefixcommons:
    description: The Chicken Gene Nomenclature Consortium (CGNC) provides standardized
      gene nomenclature for chicken genes.
    example: '2218'
    homepage: http://www.agnc.msstate.edu/
    keywords:
    - gene
    license: http://www.agnc.msstate.edu/About.htm
    name: Chicken Gene Nomenclature Consortium
    pattern: ^\d+$
    prefix: cgnc
    pubmed_ids:
    - '19607656'
    uri_format: http://www.agnc.msstate.edu/GeneReport.aspx?a=$1
  publications:
  - doi: 10.1186/1471-2164-10-s2-s5
    pmc: PMC2966335
    pubmed: '19607656'
    title: The Chicken Gene Nomenclature Committee report
    year: 2009
  re3data:
    description: '<<<!!!<<< This repository is no longer available. >>>!!!>>>

      The sequencing of several bird genomes and the anticipated sequencing of many
      more provided the impetus to develop a model organism database devoted to the
      taxonomic class: Aves. Birds provide model organisms important to the study
      of neurobiology, immunology, genetics, development, oncology, virology, cardiovascular
      biology, evolution and a variety of other life sciences. Many bird species are
      also important to agriculture, providing an enormous worldwide food source worldwide.
      Genomic approaches are proving invaluable to studying traits that affect meat
      yield, disease resistance, behavior, and bone development along with many other
      factors affecting productivity. In this context, BirdBase will serve both biomedical
      and agricultural researchers.'
    doi: 10.17616/R3HN34
    homepage: http://birdbase.arizona.edu/birdbase/
    name: Birdbase
    prefix: r3d100012429
    synonyms:
    - A database of avian genes & genomes
  synonyms:
  - BirdBase
  - CGNC
  uri_format: http://birdgenenames.org/cgnc/GeneReport?id=$1
cgsc:
  biocontext:
    prefix: CGSC
  contact:
    email: kelly.hughes@utah.edu
    github: null
    name: Kelly T. Hughes
    orcid: 0000-0003-1546-6746
  fairsharing:
    abbreviation: CGSC
    description: The CGSC Database of E. coli genetic information includes genotypes
      and reference information for the strains in the CGSC collection, the names,
      synonyms, properties, and map position for genes, gene product information,
      and information on specific mutations and references to primary literature.
    homepage: https://cgsc.biology.yale.edu/
    name: Coli Genetic Stock Center
    prefix: FAIRsharing.1tbrdz
    publications:
    - doi: 10.1016/S0076-6879(06)21001-2
      pubmed_id: 17352909
      title: Strain collections and genetic nomenclature.
    subjects:
    - Life Science
  go:
    homepage: http://cgsc.biology.yale.edu/
    name: CGSC
    prefix: CGSC
  mappings:
    biocontext: CGSC
    fairsharing: FAIRsharing.1tbrdz
    go: CGSC
    miriam: cgsc
    n2t: cgsc
    prefixcommons: cgsc
    re3data: r3d100010585
  miriam:
    deprecated: true
    description: The CGSC Database of E. coli genetic information includes genotypes
      and reference information for the strains in the CGSC collection, the names,
      synonyms, properties, and map position for genes, gene product information,
      and information on specific mutations and references to primary literature.
    homepage: http://cgsc.biology.yale.edu/index.php
    id: 00000295
    name: CGSC Strain
    namespaceEmbeddedInLui: false
    pattern: ^\d+$
    prefix: cgsc
    sampleId: '74'
    uri_format: http://cgsc.biology.yale.edu/Site.php?ID=$1
  n2t:
    description: The CGSC Database of E. coli genetic information includes genotypes
      and reference information for the strains in the CGSC collection, the names,
      synonyms, properties, and map position for genes, gene product information,
      and information on specific mutations and references to primary literature.
    example: '74'
    homepage: http://cgsc.biology.yale.edu/index.php
    name: CGSC at Yale university
    namespaceEmbeddedInLui: false
    pattern: ^\d+$
    prefix: cgsc
    uri_format: http://cgsc.biology.yale.edu/Site.php?ID=$1
  name: Coli Genetic Stock Center
  prefix: cgsc
  prefixcommons:
    description: The CGSC Database of E. coli genetic information includes genotypes
      and reference information for the strains in the CGSC collection, the names,
      synonyms, properties, and map position for genes, gene product information,
      and information on specific mutations and references to primary literature.
    example: '96846'
    homepage: http://cgsc.biology.yale.edu/
    keywords:
    - gene
    name: The Coli Genetic Stock Center
    pattern: ^\d+$
    prefix: cgsc
    uri_format: http://cgsc.biology.yale.edu/Site.php?ID=$1
  publications:
  - doi: 10.1016/s0076-6879(06)21001-2
    pmc: null
    pubmed: '17352909'
    title: Strain collections and genetic nomenclature
    year: 2007
  - doi: 10.1016/S0076-6879(06)21001-2
    pmc: null
    pubmed: null
    title: Strain collections and genetic nomenclature.
    year: null
  re3data:
    description: The CGSC Database of E. coli genetic information includes genotypes
      and reference information for the strains in the CGSC collection, the names,
      synonyms, properties, and map position for genes, gene product information,
      and information on specific mutations and references to primary literature.
      The public version of the database includes this information and can be queried
      directly via this CGSC DB WebServer
    doi: 10.17616/R32G7W
    homepage: https://cgsc2.biology.yale.edu/
    name: E. coli Genetic Resources at Yale
    prefix: r3d100010585
    synonyms:
    - CGSC
    - The Coli Genetic Stock Center
    xrefs:
      nif: 0000-21083
charprot:
  biocontext:
    prefix: CHARPROT
  mappings:
    biocontext: CHARPROT
    miriam: charprot
    n2t: charprot
  miriam:
    deprecated: true
    description: CharProt is a database of biochemically characterized proteins designed
      to support automated annotation pipelines. Entries are annotated with gene name,
      symbol and various controlled vocabulary terms, including Gene Ontology terms,
      Enzyme Commission number and TransportDB accession.
    homepage: http://www.jcvi.org/charprotdb
    id: '00000341'
    name: CharProt
    namespaceEmbeddedInLui: false
    pattern: ^CH_\d+$
    prefix: charprot
    sampleId: CH_001923
    uri_format: http://www.jcvi.org/charprotdb/index.cgi/view/$1
  n2t:
    description: CharProt is a database of biochemically characterized proteins designed
      to support automated annotation pipelines. Entries are annotated with gene name,
      symbol and various controlled vocabulary terms, including Gene Ontology terms,
      Enzyme Commission number and TransportDB accession.
    example: CH_001923
    homepage: http://www.jcvi.org/charprotdb
    name: CharProt at JCVI
    namespaceEmbeddedInLui: false
    pattern: ^CH_\d+$
    prefix: charprot
    uri_format: http://www.jcvi.org/charprotdb/index.cgi/view/$1
  prefix: charprot
chebi:
  aberowl:
    description: A structured classification of molecular entities of biological interest
      focusing on 'small' chemical compounds.
    download_owl: http://aber-owl.net/media/ontologies/CHEBI/209/chebi.owl
    homepage: http://www.ebi.ac.uk/chebi
    name: Chemical Entities of Biological Interest
    prefix: CHEBI
  bartoc:
    abbreviation: ChEBI
    description: Chemical Entities of Biological Interest (ChEBI) is a freely available
      dictionary of molecular entities focused on ‘small’ chemical compounds. The
      term ‘molecular entity’ refers to any constitutionally or isotopically distinct
      atom, molecule, ion, ion pair, radical, radical ion, complex, conformer, etc.,
      identifiable as a separately distinguishable entity. The molecular entities
      in question are either products of nature or synthetic products used to intervene
      in the processes of living organisms. ChEBI incorporates an ontological classification,
      whereby the relationships between molecular entities or classes of entities
      and their parents and/or children are specified.
    homepage: http://www.ebi.ac.uk/chebi/
    name: Chemical Entities of Biological Interest
    prefix: '558'
    wikidata_database: Q902623
  biocontext:
    prefix: CHEBI
  bioportal:
    contact:
      email: amalik@ebi.ac.uk
      name: Adnan Malik
    description: A structured classification of chemical compounds of biological relevance.
    homepage: http://www.ebi.ac.uk/chebi
    name: Chemical Entities of Biological Interest Ontology
    prefix: CHEBI
    repository: https://github.com/ebi-chebi/ChEBI
    version: '246.0'
  cellosaurus:
    category: Chemistry resources
    homepage: https://www.ebi.ac.uk/chebi/
    name: Chemical Entities of Biological Interest
    prefix: ChEBI
    uri_format: https://www.ebi.ac.uk/chebi/search?query=$1
  cheminf:
    description: Database identifier used by ChEBI.
    name: ChEBI
    obsolete: false
    prefix: '000407'
  contributor_extras:
  - email: muhammad@ebi.ac.uk
    github: theArsalanM
    name: Muhammad Arsalan
    orcid: 0009-0005-4625-8212
  edam:
    description: Identifier of an entry from the ChEBI database.
    name: ChEBI
    obsolete: false
    prefix: '1174'
  example: '138488'
  fairsharing:
    abbreviation: ChEBI
    contact:
      email: venkat@ebi.ac.uk
      name: Venkat
      orcid: 0000-0002-6850-9888
    description: Chemical Entities of Biological Interest (ChEBI) is a free dictionary
      that describes 'small’ chemical compounds. These compound includes distinct
      synthetic or natural atoms, molecules, ions, ion pair, radicals, radical ions,
      complexes, conformers, etc.. These molecular entities can interact with or affect
      the processes of living organisms.
    domains:
    - Structure
    - Taxonomic classification
    - molecular entity
    - small molecule
    - Natural Product
    homepage: http://www.ebi.ac.uk/chebi/
    license: CC-BY-4.0
    name: Chemical Entities of Biological Interest
    prefix: FAIRsharing.62qk8w
    publications:
    - doi: 10.1002/0471250953.bi1409s26
      pubmed: '19496059'
      title: 'ChEBI: an open bioinformatics and cheminformatics resource'
      year: 2009
    - doi: 10.1093/nar/gkm791
      pubmed: '17932057'
      title: 'ChEBI: a database and ontology for chemical entities of biological interest'
      year: 2007
    - doi: 10.1093/nar/gkv1031
      pubmed: '26467479'
      title: 'ChEBI in 2016: Improved services and an expanding collection of metabolites'
      year: 2015
    - doi: 10.1093/nar/gkp886
      pubmed: '19854951'
      title: 'Chemical Entities of Biological Interest: an update'
      year: 2009
    - doi: 10.1093/nar/gks1146
      pubmed: '23180789'
      title: 'The ChEBI reference database and ontology for biologically relevant
        chemistry: enhancements for 2013'
      year: 2012
    repository: https://github.com/ebi-chebi/ChEBI
    subjects:
    - Lipidomics
    - Metabolomics
    - Biochemistry
    - Chemistry
    - Proteomics
    twitter: chebit
  go:
    homepage: http://www.ebi.ac.uk/chebi/
    name: Chemical Entities of Biological Interest
    prefix: CHEBI
    synonyms:
    - ChEBI
    uri_format: http://www.ebi.ac.uk/chebi/searchId.do?chebiId=CHEBI:$1
  integbio:
    alt_name: Chemical Entities of Biological Interest
    description: 'ChEBI is a collection of data on entities of biological interest.

      This database concentrates on assembling data on smaller chemical compounds,
      such as atoms, molecules, ions, radicals etc. These should be produced in nature
      or be synthetic molecules affecting biological processes in living organisms.

      ChEBI does not generally include molecules directly encoded by the genome.

      The database contains 31,651 entries with annotations.

      A keyword search option is available.

      In addition to this an advanced search option, which includes a structure drawing
      tool, is provided.

      The ChEBI database can be searched individually or in combination with other
      databases.'
    homepage: http://www.ebi.ac.uk/chebi/
    information_keywords:
    - Ontology/Terminology/Nomenclature
    maintainer: EMBL-EBI (European Bioinformatics Institute)
    name: ChEBI
    prefix: nbdc00027
    pubmeds:
    - '17932057'
    - '19496059'
    - '19854951'
    status: Active
    target_keywords:
    - Carbohydrate
    - Lipid
    - Metabolite
    - Chemical compound
  mappings:
    aberowl: CHEBI
    bartoc: '558'
    biocontext: CHEBI
    bioportal: CHEBI
    cellosaurus: ChEBI
    cheminf: '000407'
    edam: '1174'
    fairsharing: FAIRsharing.62qk8w
    go: CHEBI
    integbio: nbdc00027
    miriam: chebi
    n2t: chebi
    obofoundry: chebi
    ols: chebi
    ontobee: CHEBI
    prefixcommons: chebi
    re3data: r3d100012626
    tib: chebi
    togoid: Chebi
    wikidata: P683
    wikidata.entity: Q902623
  miriam:
    deprecated: false
    description: Chemical Entities of Biological Interest (ChEBI) is a freely available
      dictionary of molecular entities focused on 'small' chemical compounds.
    homepage: https://www.ebi.ac.uk/chebi/
    id: '00000002'
    name: ChEBI
    namespaceEmbeddedInLui: true
    pattern: ^CHEBI:\d+$
    prefix: chebi
    sampleId: '36927'
    uri_format: https://www.ebi.ac.uk/chebi/searchId.do?chebiId=CHEBI:$1
  n2t:
    description: Chemical Entities of Biological Interest (ChEBI) is a freely available
      dictionary of molecular entities focused on 'small' chemical compounds.
    example: '36927'
    homepage: https://www.ebi.ac.uk/chebi/
    name: ChEBI (Chemical Entities of Biological Interest)
    namespaceEmbeddedInLui: true
    pattern: ^CHEBI:\d+$
    prefix: chebi
    uri_format: https://www.ebi.ac.uk/chebi/searchId.do?chebiId=CHEBI:$1
  name: Chemical Entities of Biological Interest
  obofoundry:
    appears_in:
    - cdno
    - chiro
    - ecocore
    - ecto
    - envo
    - fobi
    - foodon
    - genepio
    - maxo
    - mco
    - ons
    - pcl
    - proco
    - uberon
    - xpo
    - scdo
    contact: amalik@ebi.ac.uk
    contact.github: amalik01
    contact.label: Adnan Malik
    contact.orcid: 0000-0001-8123-5351
    deprecated: false
    description: A structured classification of molecular entities of biological interest
      focusing on 'small' chemical compounds.
    domain: chemistry and biochemistry
    download.obo: http://purl.obolibrary.org/obo/chebi.obo
    download.owl: http://purl.obolibrary.org/obo/chebi.owl
    homepage: http://www.ebi.ac.uk/chebi
    license: CC BY 4.0
    license.url: https://creativecommons.org/licenses/by/4.0/
    logo: https://www.ebi.ac.uk/chebi/chebi_logo.svg
    name: Chemical Entities of Biological Interest
    preferredPrefix: CHEBI
    prefix: chebi
    publications:
    - id: https://doi.org/10.1093/nar/gkaf1271
      title: 'ChEBI: re-engineered for a sustainable future'
    - id: https://www.ncbi.nlm.nih.gov/pubmed/26467479
      title: 'ChEBI in 2016: Improved services and an expanding collection of metabolites.'
    repository: https://github.com/ebi-chebi/ChEBI
    twitter: chebit
  ols:
    description: A structured classification of molecular entities of biological interest
      focusing on 'small' chemical compounds.
    download_owl: http://purl.obolibrary.org/obo/chebi.owl
    homepage: http://www.ebi.ac.uk/chebi
    name: Chemical Entities of Biological Interest
    prefix: chebi
    tracker: https://github.com/ebi-chebi/ChEBI/issues
    version: '247'
  ontobee:
    library: Foundry
    name: Chemical Entities of Biological Interest
    prefix: CHEBI
  pattern: ^\d+$
  prefix: chebi
  prefixcommons:
    alt_uri_formats:
    - http://www.ebi.ac.uk/chebi/searchId.do;?chebiId=$1
    - http://www.loria.fr/~coulet/ontology/sopharm$1
    - http://www.ebi.ac.uk/ontology-lookup//version2.1/chebi.owl#$1
    - http://purl.org/obo/owl/CHEBI#$1
    - http://www.ebi.ac.uk/ontology-lookup/?termId=CHEBI:#$1
    bioportal: '1007'
    description: A structured classification of chemical compounds of biological relevance.
    example: '17234'
    homepage: http://www.ebi.ac.uk/chebi/
    keywords:
    - obo
    - chemical
    license: http://www.ebi.ac.uk/Information/termsofuse.html
    name: Chemical Entities of Biological Interest
    pattern: ^\d+$
    prefix: chebi
    pubmed_ids:
    - '23180789'
    synonyms:
    - atp_chebi
    uri_format: http://www.ebi.ac.uk/chebi/searchId.do?chebiId=$1
  providers:
  - code: iedb.antigen
    description: A comprehensive collection of data on immune epitopes, covering experimental
      data and resources, including antigens
    example: '60327'
    first_party: null
    homepage: https://www.iedb.org
    name: Immune Epitope Database
    publications: null
    status: null
    uri_format: https://www.iedb.org/antigen/ChEBI:$1
  - code: chebi-img
    description: Image server from chebi
    example: null
    first_party: true
    homepage: https://www.ebi.ac.uk/chebi/
    name: ChEBI
    publications: null
    status: null
    uri_format: https://www.ebi.ac.uk/chebi/backend/api/public/compound/$1/structure/?width=300&height=300
  publications:
  - doi: 10.1093/nar/gkv1031
    pmc: PMC4702775
    pubmed: '26467479'
    title: 'ChEBI in 2016: Improved services and an expanding collection of metabolites'
    year: 2015
  - doi: 10.1093/nar/gks1146
    pmc: PMC3531142
    pubmed: '23180789'
    title: 'The ChEBI reference database and ontology for biologically relevant chemistry:
      enhancements for 2013'
    year: 2012
  - doi: 10.1002/0471250953.bi1409s26
    pmc: null
    pubmed: '19496059'
    title: 'ChEBI: an open bioinformatics and cheminformatics resource'
    year: 2009
  - doi: 10.1093/nar/gkp886
    pmc: PMC2808869
    pubmed: '19854951'
    title: 'Chemical Entities of Biological Interest: an update'
    year: 2009
  - doi: 10.1093/nar/gkm791
    pmc: PMC2238832
    pubmed: '17932057'
    title: 'ChEBI: a database and ontology for chemical entities of biological interest'
    year: 2007
  - doi: 10.1093/nar/gkaf1271
    pmc: null
    pubmed: null
    title: 'ChEBI: re-engineered for a sustainable future'
    year: null
  - doi: null
    pmc: null
    pubmed: '26467479'
    title: 'ChEBI in 2016: Improved services and an expanding collection of metabolites'
    year: null
  - doi: 10.1002/0471250953.bi1409s26
    pmc: null
    pubmed: '19496059'
    title: 'ChEBI: an open bioinformatics and cheminformatics resource'
    year: 2009
  - doi: 10.1093/nar/gkm791
    pmc: null
    pubmed: '17932057'
    title: 'ChEBI: a database and ontology for chemical entities of biological interest'
    year: 2007
  - doi: 10.1093/nar/gkv1031
    pmc: null
    pubmed: '26467479'
    title: 'ChEBI in 2016: Improved services and an expanding collection of metabolites'
    year: 2015
  - doi: 10.1093/nar/gkp886
    pmc: null
    pubmed: '19854951'
    title: 'Chemical Entities of Biological Interest: an update'
    year: 2009
  - doi: 10.1093/nar/gks1146
    pmc: null
    pubmed: '23180789'
    title: 'The ChEBI reference database and ontology for biologically relevant chemistry:
      enhancements for 2013'
    year: 2012
  - doi: null
    pmc: null
    pubmed: '23180789'
    title: null
    year: null
  - doi: 10.1093/nar/gkaf1271
    pmc: null
    pubmed: null
    title: 'ChEBI: re-engineered for a sustainable future'
    year: null
  - doi: null
    pmc: null
    pubmed: '26467479'
    title: 'ChEBI in 2016: Improved services and an expanding collection of metabolites'
    year: null
  - doi: 10.1002/0471250953.bi1409s26
    pmc: null
    pubmed: '19496059'
    title: 'ChEBI: an open bioinformatics and cheminformatics resource'
    year: 2009
  - doi: 10.1093/nar/gkm791
    pmc: null
    pubmed: '17932057'
    title: 'ChEBI: a database and ontology for chemical entities of biological interest'
    year: 2007
  - doi: 10.1093/nar/gkv1031
    pmc: null
    pubmed: '26467479'
    title: 'ChEBI in 2016: Improved services and an expanding collection of metabolites'
    year: 2015
  - doi: 10.1093/nar/gkp886
    pmc: null
    pubmed: '19854951'
    title: 'Chemical Entities of Biological Interest: an update'
    year: 2009
  - doi: 10.1093/nar/gks1146
    pmc: null
    pubmed: '23180789'
    title: 'The ChEBI reference database and ontology for biologically relevant chemistry:
      enhancements for 2013'
    year: 2012
  - doi: null
    pmc: null
    pubmed: '23180789'
    title: null
    year: null
  re3data:
    description: Chemical Entities of Biological Interest (ChEBI) is a freely available
      dictionary of 'small molecular entities'. The term 'molecular entity' encompasses
      any constitutionally or isotopically distinct atom, molecule, ion, ion pair,
      radical, radical ion, complex, conformer, etc., identifiable as a separately
      distinguishable entity. The molecular entities in question are either products
      of nature or synthetic products used to intervene in the processes of living
      organisms (either deliberately, as for drugs, or unintentionally', as for chemicals
      in the environment). The qualifier 'small' implies the exclusion of entities
      directly encoded by the genome, and thus as a rule nucleic acids, proteins and
      peptides derived from proteins by cleavage are not included.
    doi: 10.17616/R3H78W
    homepage: https://www.ebi.ac.uk/chebi/
    license: CC
    name: ChEBI
    prefix: r3d100012626
    synonyms:
    - Chemical Entities of Biological Interest
    xrefs:
      nif: 0000-02655
      omics: '02752'
  references:
  - https://github.com/biopragmatics/bioregistry/issues/1760
  synonyms:
  - CHEBI
  - CHEBIID
  - ChEBI
  tib:
    description: ChEBI (Chemical Entities of Biological Interest) is a free dictionary
      of small molecular entities, including distinct atoms, molecules, ions, radicals,
      and complexes. These entities can be natural or synthetic, used in or affecting
      biological processes. The term "small" excludes genome-encoded entities like
      nucleic acids and proteins. ChEBI also includes classes of molecular entities
      and their parts, such as substituent groups or atoms.
    download_owl: http://purl.obolibrary.org/obo/chebi.owl
    homepage: http://www.ebi.ac.uk/chebi
    keywords:
    - NFDI4CHEM
    - ESS
    - DataPLANT
    - NFDI4CAT
    - chemistry
    - earth sciences
    name: Chemical Entities of Biological Interest
    prefix: chebi
    tracker: https://github.com/ebi-chebi/ChEBI/issues
  togoid:
    catalog: nbdc00027
    description: ChEBI is a collection of data on entities of biological interest.
      This database concentrates on assembling data on smaller chemical compounds,
      such as atoms, molecules, ions, radicals etc. These should be produced in nature
      or be synthetic molecules affecting biological processes in living organisms.
      ChEBI does not generally include molecules directly encoded by the genome. The
      database contains 31,651 entries with annotations. A keyword search option is
      available. In addition to this an advanced search option, which includes a structure
      drawing tool, is provided. The ChEBI database can be searched individually or
      in combination with other databases.
    examples:
    - '84824'
    - '40167'
    - '32807'
    - '87666'
    - '57524'
    - '64860'
    - '94440'
    - '18005'
    - '4806'
    - '50158'
    keywords:
    - Compound
    name: ChEBI compound
    pattern: ^(?:CHEBI[:_])?(?\d+)$
    prefix: Chebi
    uri_format: http://purl.obolibrary.org/obo/CHEBI_$1
  uri_format: http://purl.obolibrary.org/obo/CHEBI_$1
  wikidata:
    description: identifier from database and ontology of molecular entities focused
      on 'small' chemical compounds
    example:
    - '18153'
    - '27518'
    - '28969'
    homepage: https://www.ebi.ac.uk/chebi
    miriam: chebi
    name: ChEBI ID
    pattern: ^\d+$
    prefix: P683
    uri_format: https://www.ebi.ac.uk/chebi/searchId.do?chebiId=CHEBI:$1
    uri_format_rdf: http://purl.obolibrary.org/obo/CHEBI_$1
chembank:
  biocontext:
    prefix: CHEMBANK
  biolink:
    is_identifiers: false
    is_obo: false
    prefix: ChemBank
    uri_format: http://chembank.broadinstitute.org/chemistry/viewMolecule.htm?cbid=$1
  comment: This resource doesn't exist on the web anymore
  deprecated: true
  mappings:
    biocontext: CHEMBANK
    biolink: ChemBank
    prefixcommons: chembank
  prefix: chembank
  prefixcommons:
    description: ChemBank is a public, web-based informatics environment created by
      the Broad Institute's Chemical Biology Program and funded in large part by the
      National Cancer Institute's Initiative for Chemical Genetics (ICG).
    example: '1000000'
    homepage: http://chembank.broad.harvard.edu
    keywords:
    - chemical
    - metabolite
    name: ChemBank
    pattern: ^\d+$
    prefix: chembank
    pubmed_ids:
    - '17947324'
    uri_format: http://chembank.broadinstitute.org/chemistry/viewMolecule.htm?cbid=$1
  publications:
  - doi: 10.1093/nar/gkm843
    pmc: PMC2238881
    pubmed: '17947324'
    title: 'ChemBank: a small-molecule screening and cheminformatics resource database'
    year: 2007
  - doi: null
    pmc: null
    pubmed: '17947324'
    title: null
    year: null
  reviewer:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
chembiosys.assay:
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: A assay in the ChemBioSys data platform
  example: '31'
  homepage: https://data.chembiosys.de/assays
  name: ChemBioSys Assay
  part_of_database: chembiosys
  pattern: ^\d+$
  prefix: chembiosys.assay
  uri_format: https://data.chembiosys.de/assays/$1
chembiosys.data:
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: A dataset in the ChemBioSys data platform
  example: '103'
  homepage: https://data.chembiosys.de/data_files
  name: ChemBioSys Dataset
  part_of_database: chembiosys
  pattern: ^\d+$
  prefix: chembiosys.data
  uri_format: https://data.chembiosys.de/data_files/$1
chembiosys.institution:
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: An institution in the ChemBioSys data platform
  example: '13'
  homepage: https://data.chembiosys.de/institutions
  name: ChemBioSys Institution
  part_of_database: chembiosys
  pattern: ^\d+$
  prefix: chembiosys.institution
  uri_format: https://data.chembiosys.de/institutions/$1
chembiosys.investigation:
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: An investigation in the ChemBioSys data platform
  example: '27'
  homepage: https://data.chembiosys.de/investigations
  name: ChemBioSys Investigation
  part_of_database: chembiosys
  pattern: ^\d+$
  prefix: chembiosys.investigation
  uri_format: https://data.chembiosys.de/investigations/$1
chembiosys.model:
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: A model in the ChemBioSys data platform
  example: '11'
  homepage: https://data.chembiosys.de/models
  name: ChemBioSys Model
  part_of_database: chembiosys
  pattern: ^\d+$
  prefix: chembiosys.model
  uri_format: https://data.chembiosys.de/models/$1
chembiosys.organism:
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: An organism in the ChemBioSys data platform
  example: '604090889'
  homepage: https://data.chembiosys.de/
  name: ChemBioSys Organism
  part_of_database: chembiosys
  pattern: ^\d+$
  prefix: chembiosys.organism
  uri_format: https://data.chembiosys.de/organisms/$1
chembiosys.project:
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: A project in the ChemBioSys data platform
  example: '15'
  homepage: https://data.chembiosys.de/projects
  name: ChemBioSys Project
  part_of_database: chembiosys
  pattern: ^\d+$
  prefix: chembiosys.project
  uri_format: https://data.chembiosys.de/projects/$1
chembiosys.publication:
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: A publication in the ChemBioSys data platform
  example: '157'
  homepage: https://data.chembiosys.de/publications
  name: ChemBioSys Publication
  part_of_database: chembiosys
  pattern: ^\d+$
  prefix: chembiosys.publication
  uri_format: https://data.chembiosys.de/publications/$1
chembiosys.strain:
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: A strain in the ChemBioSys data platform
  example: '33'
  homepage: https://data.chembiosys.de/strains
  name: ChemBioSys Strain
  part_of_database: chembiosys
  pattern: ^\d+$
  prefix: chembiosys.strain
  uri_format: https://data.chembiosys.de/strains/$1
chembiosys.study:
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: A study in the ChemBioSys data platform
  example: '20'
  homepage: https://data.chembiosys.de/studies
  name: ChemBioSys Study
  part_of_database: chembiosys
  pattern: ^\d+$
  prefix: chembiosys.study
  uri_format: https://data.chembiosys.de/studies/$1
chembiosys.tag:
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: A tag in the ChemBioSys data platform
  example: '59'
  homepage: https://data.chembiosys.de/tags
  name: ChemBioSys Tag
  part_of_database: chembiosys
  pattern: ^\d+$
  prefix: chembiosys.tag
  uri_format: https://data.chembiosys.de/tags/$1
chembl:
  cheminf:
    description: Identifier used by the ChEMBL database for compounds, assays, target,
      etc.
    name: ChEMBL
    obsolete: false
    prefix: '000412'
  contact:
    email: dmendez@ebi.ac.uk
    github: nclopezo
    name: David Mendez Lopez
    orcid: 0000-0002-0294-5484
  contact_group_email: chembl-help@ebi.ac.uk
  fairsharing:
    abbreviation: ChEMBL
    description: ChEMBL is an open, manually-curated, large-scale bioactivity database
      integrating data records extracted from medicinal chemistry literature, from
      deposited data sets, as well as other public data sources. It brings together
      chemical, bioactivity and genomic data to aid the translation of genomic information
      into effective new drugs. Information regarding the compounds tested (including
      their chemical structures), the biological or physicochemical assays performed
      on these and the targets of these assays are recorded in a structured form,
      standardized, and annotated with controlled vocabularies to allow users to address
      a broad range of drug discovery questions.
    homepage: https://www.ebi.ac.uk/chembl
    license: CC BY-SA 3.0
    name: ChEMBL
    prefix: FAIRsharing.m3jtpg
    publications:
    - doi: 10.1093/nar/gkr777
      pubmed_id: 21948594
      title: 'ChEMBL: a large-scale bioactivity database for drug discovery.'
    - doi: 10.1093/nar/gky1075
      pubmed_id: 30398643
      title: 'ChEMBL: towards direct deposition of bioassay data.'
    - doi: 10.1093/nar/gkt1031
      pubmed_id: 24214965
      title: 'The ChEMBL bioactivity database: an update'
    - doi: 10.1093/nar/gkw1074
      pubmed_id: 27899562
      title: The ChEMBL database in 2017.
    repository: https://github.com/chembl/GLaDOS
    subjects:
    - Drug Discovery
    - Biochemistry
    - Genomics
    - Medicinal Chemistry
    twitter: chembl
  homepage: https://www.ebi.ac.uk/chembl
  integbio:
    description: ChEMBL is a database for bioactive molecules. It collects information
      of small molecules, such as calculated properties (e.g. logP, Molecular Weight,
      Lipinski Parameters, etc.) and abstracted bioactivities (e.g. binding constants,
      pharmacology and ADMET data), and the target information. Metadata of assays
      for small molecule activities or assays for binding activities between small
      molecules and its targets are also provided.
    fairsharing: FAIRsharing.m3jtpg
    homepage: https://www.ebi.ac.uk/chembl/
    information_keywords:
    - Chemical structure
    - Interaction/Pathway
    - Repository
    maintainer: EMBL-EBI (European Bioinformatics Institute)
    name: ChEMBL
    prefix: nbdc02555
    pubmeds:
    - '33507738'
    - '30398643'
    - '25883136'
    status: Active
    target_keywords:
    - Chemical compound
    - Drug
    - Protein
  license: CC-BY-SA-3.0
  mappings:
    cheminf: '000412'
    fairsharing: FAIRsharing.m3jtpg
    integbio: nbdc02555
    miriam: chembl
    prefixcommons: chembl
    re3data: r3d100010539
    uniprot: DB-0174
  miriam:
    deprecated: false
    description: ChEMBL is a database of bioactive compounds, their quantitative properties
      and bioactivities (binding constants, pharmacology and ADMET, etc). The data
      is abstracted and curated from the primary scientific literature.
    homepage: https://www.ebi.ac.uk/chembl
    id: 00000799
    name: ChEMBL
    namespaceEmbeddedInLui: false
    pattern: ^CHEMBL\d+$
    prefix: chembl
    sampleId: CHEMBL4303805
    uri_format: https://www.ebi.ac.uk/chembl/id_lookup/$1
  prefix: chembl
  prefixcommons:
    description: ChEMBL is a database of bioactive compounds, their quantitative properties
      and bioactivities (binding constants, pharmacology and ADMET, etc). The data
      is abstracted and curated from the primary scientific literature.
    example: '210313'
    homepage: https://www.ebi.ac.uk/chembldb/
    keywords:
    - molecules
    license: http://www.ebi.ac.uk/Information/termsofuse.html
    name: chEMBL
    pattern: ^\d+$
    prefix: chembl
    synonyms:
    - chembldb
    uri_format: https://www.ebi.ac.uk/chembldb/index.php/compound/inspect/$1
  publications:
  - doi: 10.1093/nar/gky1075
    pmc: PMC6323927
    pubmed: '30398643'
    title: 'ChEMBL: towards direct deposition of bioassay data'
    year: 2019
  - doi: 10.1093/nar/gkw1074
    pmc: PMC5210557
    pubmed: '27899562'
    title: The ChEMBL database in 2017
    year: 2016
  - doi: 10.1093/nar/gkt1031
    pmc: PMC3965067
    pubmed: '24214965'
    title: 'The ChEMBL bioactivity database: an update'
    year: 2013
  - doi: 10.1093/nar/gkr777
    pmc: PMC3245175
    pubmed: '21948594'
    title: 'ChEMBL: a large-scale bioactivity database for drug discovery'
    year: 2011
  - doi: 10.1093/nar/gkr777
    pmc: null
    pubmed: null
    title: 'ChEMBL: a large-scale bioactivity database for drug discovery.'
    year: null
  - doi: 10.1093/nar/gky1075
    pmc: null
    pubmed: null
    title: 'ChEMBL: towards direct deposition of bioassay data.'
    year: null
  - doi: 10.1093/nar/gkt1031
    pmc: null
    pubmed: null
    title: 'The ChEMBL bioactivity database: an update'
    year: null
  - doi: 10.1093/nar/gkw1074
    pmc: null
    pubmed: null
    title: The ChEMBL database in 2017.
    year: null
  - doi: 10.1093/nar/gkad1004
    pmc: null
    pubmed: '37933841'
    title: null
    year: null
  re3data:
    description: 'ChEMBL is a database of bioactive drug-like small molecules, it
      contains 2-D structures, calculated properties (e.g. logP, Molecular Weight,
      Lipinski Parameters, etc.) and abstracted bioactivities (e.g. binding constants,
      pharmacology and ADMET data).

      The data is abstracted and curated from the primary scientific literature, and
      cover a significant fraction of the SAR and discovery of modern drugs

      We attempt to normalise the bioactivities into a uniform set of end-points and
      units where possible, and also to tag the links between a molecular target and
      a published assay with a set of varying confidence levels. Additional data on
      clinical progress of compounds is being integrated into ChEMBL at the current
      time.'
    doi: 10.17616/R3C320
    homepage: https://www.ebi.ac.uk/chembl/
    license: CC
    name: ChEMBL
    prefix: r3d100010539
    xrefs:
      omics: '02731'
  synonyms:
  - ChEMBL
  - ChEMBL_ID
  - chembl
  uniprot:
    abbreviation: ChEMBL
    category: Chemistry databases
    homepage: https://www.ebi.ac.uk/chembl
    name: ChEMBL database of bioactive drug-like small molecules
    prefix: DB-0174
    publications:
    - doi: 10.1093/nar/gkad1004
      pubmed: '37933841'
    uri_format: https://www.ebi.ac.uk/chembl/target_report_card/$1
chembl.cell:
  cellosaurus:
    category: Chemistry resources
    homepage: https://www.ebi.ac.uk/chembldb
    name: ChEMBL database of bioactive drug-like small molecules - Cell lines section
    prefix: ChEMBL-Cells
    uri_format: https://www.ebi.ac.uk/chembldb/cell/inspect/$1
  contact:
    email: dmendez@ebi.ac.uk
    github: nclopezo
    name: David Mendez Lopez
    orcid: 0000-0002-0294-5484
  contact_group_email: chembl-help@ebi.ac.uk
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  domain: cell and cell line
  example: CHEMBL3307800
  keywords:
  - bioactivities
  - cell lines
  license: CC-BY-SA-3.0
  logo: https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEg5LCdi4mEW56jpmM0YDjEwLtGUUy2F9I7m02I9hygI0OPugnZKlTrAgfBtug5yJS5RbpCXifID0pzA5Wxdc6un1UjCCtOJcvlkeoAFgzQspvplZcstYNwx8lBtvlYY8WJ-kLj-I891VIAO/s1600/Screenshot+2018-12-20+at+10.30.09.png
  mappings:
    cellosaurus: ChEMBL-Cells
  pattern: ^CHEMBL\d+$
  prefix: chembl.cell
  synonyms:
  - ChEMBL-Cells
  uri_format: https://www.ebi.ac.uk/chembl/cell_line_report_card/$1
chembl.compound:
  biocontext:
    prefix: CHEMBL.COMPOUND
  contact:
    email: dmendez@ebi.ac.uk
    github: nclopezo
    name: David Mendez Lopez
    orcid: 0000-0002-0294-5484
  contact_group_email: chembl-help@ebi.ac.uk
  domain: chemical
  edam:
    description: Identifier of a small molecular from the ChEMBL database.
    name: Compound ID (ChEMBL)
    obsolete: false
    prefix: '2646'
  example: CHEMBL465070
  keywords:
  - chemical
  - compound
  - small molecule
  license: CC-BY-SA-3.0
  logo: https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEg5LCdi4mEW56jpmM0YDjEwLtGUUy2F9I7m02I9hygI0OPugnZKlTrAgfBtug5yJS5RbpCXifID0pzA5Wxdc6un1UjCCtOJcvlkeoAFgzQspvplZcstYNwx8lBtvlYY8WJ-kLj-I891VIAO/s1600/Screenshot+2018-12-20+at+10.30.09.png
  mappings:
    biocontext: CHEMBL.COMPOUND
    edam: '2646'
    miriam: chembl.compound
    n2t: chembl.compound
    togoid: ChemblCompound
    wikidata: P592
  miriam:
    deprecated: false
    description: ChEMBL is a database of bioactive compounds, their quantitative properties
      and bioactivities (binding constants, pharmacology and ADMET, etc). The data
      is abstracted and curated from the primary scientific literature.
    homepage: https://www.ebi.ac.uk/chembldb/
    id: 00000084
    name: ChEMBL compound
    namespaceEmbeddedInLui: false
    pattern: ^CHEMBL\d+$
    prefix: chembl.compound
    sampleId: CHEMBL308052
    uri_format: https://www.ebi.ac.uk/chembl/compound/inspect/$1
  n2t:
    description: ChEMBL is a database of bioactive compounds, their quantitative properties
      and bioactivities (binding constants, pharmacology and ADMET, etc). The data
      is abstracted and curated from the primary scientific literature.
    example: CHEMBL308052
    homepage: https://www.ebi.ac.uk/chembldb/
    name: ChEMBL compound database at EBI
    namespaceEmbeddedInLui: false
    pattern: ^CHEMBL\d+$
    prefix: chembl.compound
    uri_format: https://www.ebi.ac.uk/chembl/compound/inspect/$1
  name: ChEMBL Compound
  pattern: ^CHEMBL\d+$
  prefix: chembl.compound
  togoid:
    catalog: nbdc02555
    description: ChEMBL is a database for bioactive molecules. It collects information
      of small molecules, such as calculated properties (e.g. logP, Molecular Weight,
      Lipinski Parameters, etc.) and abstracted bioactivities (e.g. binding constants,
      pharmacology and ADMET data), and the target information. Metadata of assays
      for small molecule activities or assays for binding activities between small
      molecules and its targets are also provided.
    examples:
    - CHEMBL121649
    - CHEMBL190334
    - CHEMBL3103282
    - CHEMBL69329
    - CHEMBL2105131
    - CHEMBL2177390
    - CHEMBL3091820
    - CHEMBL1200335
    - CHEMBL3094412
    - CHEMBL67367
    keywords:
    - Compound
    name: ChEMBL compound
    pattern: ^(?CHEMBL\d+)$
    prefix: ChemblCompound
    uri_format: http://identifiers.org/chembl.compound/$1
  wikidata:
    description: identifier from a chemical database of bioactive molecules with drug-like
      properties
    example:
    - CHEMBL113
    - CHEMBL1200604
    - CHEMBL417016
    homepage: https://www.ebi.ac.uk/chembl
    miriam: chembl
    name: ChEMBL ID
    pattern: ^CHEMBL\d+$
    prefix: P592
    uri_format: https://www.ebi.ac.uk/chembl/compound_report_card/$1/
    uri_format_rdf: http://rdf.ebi.ac.uk/resource/chembl/molecule/$1
chembl.mechanism:
  contact:
    email: dmendez@ebi.ac.uk
    github: nclopezo
    name: David Mendez Lopez
    orcid: 0000-0002-0294-5484
  contact_group_email: chembl-help@ebi.ac.uk
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: This controlled vocabulary contains terms to describe the mechanism
    of action for a chemical-target interaction. The terms can be retrieved from ACTION_TYPE
    table in ChEMBL's SQL dump and are used to annotate the DRUG_MECHANISM table.
    Because these aren't really identifiers, they are transformed by lowercasing and
    replacing spaces with dashes to form 'identifiers'. The pattern in the Bioregistry
    record contains an enumeration of the 33 allowed values as of ChEMBL v35.
  domain: relationship type
  example: activator
  example_extras:
  - cross-linking-agent
  - negative-allosteric-modulator
  homepage: https://www.ebi.ac.uk/chembl
  license: CC-BY-SA-3.0
  logo: https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEg5LCdi4mEW56jpmM0YDjEwLtGUUy2F9I7m02I9hygI0OPugnZKlTrAgfBtug5yJS5RbpCXifID0pzA5Wxdc6un1UjCCtOJcvlkeoAFgzQspvplZcstYNwx8lBtvlYY8WJ-kLj-I891VIAO/s1600/Screenshot+2018-12-20+at+10.30.09.png
  name: ChEMBL mechanism
  part_of: chembl
  pattern: ^activator|agonist|allosteric-antagonist|antagonist|antisense-inhibitor|binding-agent|blocker|chelating-agent|cross-linking-agent|degrader|disrupting-agent|exogenous-gene|exogenous-protein|hydrolytic-enzyme|inhibitor|inverse-agonist|methylating-agent|modulator|negative-allosteric-modulator|negative-modulator|opener|other|oxidative-enzyme|partial-agonist|positive-allosteric-modulator|positive-modulator|proteolytic-enzyme|reducing-agent|releasing-agent|rnai-inhibitor|sequestering-agent|stabiliser|substrate|vaccine-antigen$
  prefix: chembl.mechanism
chembl.target:
  biocontext:
    prefix: CHEMBL.TARGET
  cellosaurus:
    category: Chemistry resources
    homepage: https://www.ebi.ac.uk/chembldb
    name: ChEMBL database of bioactive drug-like small molecules - Targets section
    prefix: ChEMBL-Targets
    uri_format: https://www.ebi.ac.uk/chembldb/target/inspect/$1
  contact:
    email: dmendez@ebi.ac.uk
    github: nclopezo
    name: David Mendez Lopez
    orcid: 0000-0002-0294-5484
  contact_group_email: chembl-help@ebi.ac.uk
  domain: protein
  keywords:
  - cell
  - cell line
  - protein
  - protein complex
  license: CC-BY-SA-3.0
  logo: https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEg5LCdi4mEW56jpmM0YDjEwLtGUUy2F9I7m02I9hygI0OPugnZKlTrAgfBtug5yJS5RbpCXifID0pzA5Wxdc6un1UjCCtOJcvlkeoAFgzQspvplZcstYNwx8lBtvlYY8WJ-kLj-I891VIAO/s1600/Screenshot+2018-12-20+at+10.30.09.png
  mappings:
    biocontext: CHEMBL.TARGET
    cellosaurus: ChEMBL-Targets
    miriam: chembl.target
    n2t: chembl.target
    togoid: ChemblTarget
  miriam:
    deprecated: false
    description: ChEMBL is a database of bioactive compounds, their quantitative properties
      and bioactivities (binding constants, pharmacology and ADMET, etc). The data
      is abstracted and curated from the primary scientific literature.
    homepage: https://www.ebi.ac.uk/chembldb/
    id: 00000085
    name: ChEMBL target
    namespaceEmbeddedInLui: false
    pattern: ^CHEMBL\d+$
    prefix: chembl.target
    sampleId: CHEMBL3467
    uri_format: https://www.ebi.ac.uk/chembl/target/inspect/$1
  n2t:
    description: ChEMBL is a database of bioactive compounds, their quantitative properties
      and bioactivities (binding constants, pharmacology and ADMET, etc). The data
      is abstracted and curated from the primary scientific literature.
    example: CHEMBL3467
    homepage: https://www.ebi.ac.uk/chembldb/
    name: ChEMBL targets database at EBI
    namespaceEmbeddedInLui: false
    pattern: ^CHEMBL\d+$
    prefix: chembl.target
    uri_format: https://www.ebi.ac.uk/chembl/target/inspect/$1
  prefix: chembl.target
  synonyms:
  - ChEMBL-Targets
  togoid:
    catalog: nbdc02555
    description: ChEMBL is a database for bioactive molecules. It collects information
      of small molecules, such as calculated properties (e.g. logP, Molecular Weight,
      Lipinski Parameters, etc.) and abstracted bioactivities (e.g. binding constants,
      pharmacology and ADMET data), and the target information. Metadata of assays
      for small molecule activities or assays for binding activities between small
      molecules and its targets are also provided.
    examples:
    - CHEMBL2788
    - CHEMBL3091264
    - CHEMBL3831324
    - CHEMBL5524
    - CHEMBL5597
    - CHEMBL3983
    - CHEMBL4187
    - CHEMBL3391681
    - CHEMBL5135
    - CHEMBL1255130
    keywords:
    - Protein
    name: ChEMBL target
    pattern: ^(?CHEMBL\d+)$
    prefix: ChemblTarget
    uri_format: http://identifiers.org/chembl.target/$1
chembl.tissue:
  contact:
    email: dmendez@ebi.ac.uk
    github: nclopezo
    name: David Mendez Lopez
    orcid: 0000-0002-0294-5484
  contact_group_email: chembl-help@ebi.ac.uk
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: Tissues used to annotate cells and cell lines, cross-referenced to
    EFO, BTO, UBERON, and CALOHA
  domain: tissue
  example: CHEMBL3559721
  homepage: https://www.ebi.ac.uk/chembl
  logo: https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEg5LCdi4mEW56jpmM0YDjEwLtGUUy2F9I7m02I9hygI0OPugnZKlTrAgfBtug5yJS5RbpCXifID0pzA5Wxdc6un1UjCCtOJcvlkeoAFgzQspvplZcstYNwx8lBtvlYY8WJ-kLj-I891VIAO/s1600/Screenshot+2018-12-20+at+10.30.09.png
  name: ChEMBL tissue
  part_of: chembl
  pattern: ^CHEMBL\d+$
  prefix: chembl.tissue
  references:
  - https://chembl.blogspot.com/2018/03/chembl-tissues-increasing-depth-breadth.html
chemdb:
  biocontext:
    prefix: CHEMDB
  contact:
    email: pfbaldi@uci.edu
    github: null
    name: Pierre Baldi
    orcid: 0000-0001-8752-4664
  fairsharing:
    abbreviation: ChemDB
    description: ChemDB is a chemical database containing nearly 5M commercially available
      small molecules, important for use as synthetic building blocks, probes in systems
      biology and as leads for the discovery of drugs and other useful compounds.
    homepage: http://cdb.ics.uci.edu
    license: http://opendatacommons.org/licenses/pddl/1.0
    name: The UC Irvine ChemDB
    prefix: FAIRsharing.dstf7h
    publications:
    - doi: 10.1093/bioinformatics/bti683
      pubmed_id: 16174682
      title: 'ChemDB: a public database of small molecules and related chemoinformatics
        resources.'
    - doi: 10.1093/bioinformatics/btm341
      pubmed_id: 17599932
      title: ChemDB update--full-text search and virtual chemical space.
    subjects:
    - Biochemistry
    - Life Science
    - Biomedical Science
    - Systems Biology
    - Preclinical Studies
  mappings:
    biocontext: CHEMDB
    fairsharing: FAIRsharing.dstf7h
    miriam: chemdb
    n2t: chemdb
    prefixcommons: chemdb
  miriam:
    deprecated: false
    description: ChemDB is a chemical database containing commercially available small
      molecules, important for use as synthetic building blocks, probes in systems
      biology and as leads for the discovery of drugs and other useful compounds.
    homepage: http://cdb.ics.uci.edu/
    id: 00000279
    name: ChemDB
    namespaceEmbeddedInLui: false
    pattern: ^\d+$
    prefix: chemdb
    sampleId: '3966782'
    uri_format: http://cdb.ics.uci.edu/cgibin/ChemicalDetailWeb.py?chemical_id=$1
  n2t:
    description: ChemDB is a chemical database containing commercially available small
      molecules, important for use as synthetic building blocks, probes in systems
      biology and as leads for the discovery of drugs and other useful compounds.
    example: '3966782'
    homepage: http://cdb.ics.uci.edu/
    name: ChemDB at UC Irvine
    namespaceEmbeddedInLui: false
    pattern: ^\d+$
    prefix: chemdb
    uri_format: http://cdb.ics.uci.edu/cgibin/ChemicalDetailWeb.py?chemical_id=$1
  prefix: chemdb
  prefixcommons:
    description: ChemDB is a chemical database containing nearly 5M commercially available
      small molecules, important for use as synthetic building blocks, probes in systems
      biology and as leads for the discovery of drugs and other useful compounds.
    example: '3965223'
    homepage: http://cdb.ics.uci.edu
    keywords:
    - small molecule
    name: The UC Irvine ChemDB
    pattern: ^\d+$
    prefix: chemdb
    pubmed_ids:
    - '17599932'
    uri_format: http://cdb.ics.uci.edu/cgibin/ChemicalDetailWeb.py?chemical_id=$1
  publications:
  - doi: 10.1093/bioinformatics/btm341
    pmc: null
    pubmed: '17599932'
    title: ChemDB update--full-text search and virtual chemical space
    year: 2007
  - doi: 10.1093/bioinformatics/bti683
    pmc: null
    pubmed: '16174682'
    title: 'ChemDB: a public database of small molecules and related chemoinformatics
      resources'
    year: 2005
  - doi: 10.1093/bioinformatics/bti683
    pmc: null
    pubmed: null
    title: 'ChemDB: a public database of small molecules and related chemoinformatics
      resources.'
    year: null
  - doi: 10.1093/bioinformatics/btm341
    pmc: null
    pubmed: null
    title: ChemDB update--full-text search and virtual chemical space.
    year: null
  - doi: null
    pmc: null
    pubmed: '17599932'
    title: null
    year: null
chemfont.chemical:
  contact:
    email: david.wishart@ualberta.ca
    github: DavidWishartLab
    name: David S. Wishart
    orcid: 0000-0002-3207-2434
  contributor:
    email: b.gyori@northeastern.edu
    github: bgyori
    name: Benjamin M. Gyori
    orcid: 0000-0001-9439-5346
  description: The Chemical Functional Ontology (ChemFOnt) is a hierarchical, OWL-compatible
    ontology describing the functions and actions of biologically important chemicals
    including primary metabolites, secondary metabolites, natural products, food chemicals,
    synthetic food additives, drugs, herbicides, pesticides and environmental chemicals.
    The identifiers in this semantic space correspond to individual chemicals.
  example: CFc000239295
  github_request_issue: 1617
  homepage: https://www.chemfont.ca/chemicals
  keywords:
  - chemical
  - ontology
  name: ChemFOnt Chemical
  part_of_database: chemfont
  pattern: ^CFc\d{9}$
  prefix: chemfont.chemical
  publications:
  - doi: 10.1093/nar/gkac919
    pmc: PMC9825615
    pubmed: '36305829'
    title: 'ChemFOnt: the chemical functional ontology resource'
    year: 2023
  reviewer:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  uri_format: https://www.chemfont.ca/chemicals/$1
chemfont.ontology:
  contact:
    email: david.wishart@ualberta.ca
    github: DavidWishartLab
    name: David S. Wishart
    orcid: 0000-0002-3207-2434
  contributor:
    email: b.gyori@northeastern.edu
    github: bgyori
    name: Benjamin M. Gyori
    orcid: 0000-0001-9439-5346
  description: The Chemical Functional Ontology (ChemFOnt) is a hierarchical, OWL-compatible
    ontology describing the functions and actions of biologically important chemicals
    including primary metabolites, secondary metabolites, natural products, food chemicals,
    synthetic food additives, drugs, herbicides, pesticides and environmental chemicals.
    The identifiers in this semantic space correspond to entries in the ChemFOnt ontology
    that are used to organize individual chemicals. Terms can be looked up using the
    following URL (https://www.chemfont.ca/ontology_browse/term_info/18), but not
    directly by ID
  download_owl: https://www.chemfont.ca/system/downloads/1.0/chemfont.owl.zip
  example: CFo000000197
  github_request_issue: 1617
  homepage: https://www.chemfont.ca/ontology_browse
  keywords:
  - chemical
  - ontology
  name: ChemFOnt Ontology
  part_of_database: chemfont
  pattern: ^CFo\d{9}$
  prefix: chemfont.ontology
  publications:
  - doi: 10.1093/nar/gkac919
    pmc: PMC9825615
    pubmed: '36305829'
    title: 'ChemFOnt: the chemical functional ontology resource'
    year: 2023
  reviewer:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
chemicalbook:
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: A hybrid chemical enyclopedia and supplier advertizing system for chemicals.
  example: CB82546919
  github_request_issue: 1311
  homepage: https://www.chemicalbook.com
  name: Chemical Book
  prefix: chemicalbook
  synonyms:
  - ChemicalBookNo
  uri_format: https://www.chemicalbook.com/ChemicalProductProperty_IN_$1.htm
chemidplus:
  biocontext:
    prefix: CHEMIDPLUS
  edam:
    description: Identifier of a chemical from the ChemIDplus database.
    name: Compound ID (ChemIDplus)
    obsolete: false
    prefix: '2658'
  fairsharing:
    abbreviation: ChemIDplus
    description: ChemIDplus is a web-based search system that provides access to structure
      and nomenclature authority files used for the identification of chemical substances
      cited in National Library of Medicine (NLM) databases. It also provides structure
      searching and direct links to many biomedical resources at NLM and on the Internet
      for chemicals of interest.
    homepage: https://chem.nlm.nih.gov/chemidplus/
    name: ChemIDplus
    prefix: FAIRsharing.5949vn
    publications:
    - doi: 10.1300/J115v21n01_04
      pubmed_id: 11989279
      title: ChemIDplus-super source for chemical and drug information.
    subjects:
    - Chemistry
    - Biomedical Science
  integbio:
    description: ChemIDplus is a web-based search system that provides access to structure
      and nomenclature authority files used for the identification of chemical substances
      cited in National Library of Medicine (NLM) databases. It also provides structure
      searching and direct links to many biomedical resources at NLM and on the Internet
      for chemicals of interest.
    fairsharing: FAIRsharing.5949vn
    homepage: https://www.nlm.nih.gov/pubs/techbull/ja22/ja22_pubchem.html#note
    information_keywords:
    - 3D structure
    - Image/Movie
    - Chemical structure
    maintainer: NLM (National Library of Medicine)
    name: ChemIDplus
    prefix: nbdc01837
    pubmeds:
    - '11989279'
    status: Active
    target_keywords:
    - Chemical compound
  mappings:
    biocontext: CHEMIDPLUS
    edam: '2658'
    fairsharing: FAIRsharing.5949vn
    integbio: nbdc01837
    miriam: chemidplus
    n2t: chemidplus
    prefixcommons: chemidplus
  miriam:
    deprecated: false
    description: ChemIDplus is a web-based search system that provides access to structure
      and nomenclature authority files used for the identification of chemical substances
      cited in National Library of Medicine (NLM) databases. It also provides structure
      searching and direct links to many biomedical resources at NLM and on the Internet
      for chemicals of interest.
    homepage: https://chem.nlm.nih.gov/chemidplus/chemidheavy.jsp
    id: 00000096
    name: ChemIDplus
    namespaceEmbeddedInLui: false
    pattern: ^\d+\-\d+\-\d+$
    prefix: chemidplus
    sampleId: 57-27-2
    uri_format: https://chem.nlm.nih.gov/chemidplus/rn/$1
  n2t:
    description: ChemIDplus is a web-based search system that provides access to structure
      and nomenclature authority files used for the identification of chemical substances
      cited in National Library of Medicine (NLM) databases. It also provides structure
      searching and direct links to many biomedical resources at NLM and on the Internet
      for chemicals of interest.
    example: 57-27-2
    homepage: https://chem.nlm.nih.gov/chemidplus/chemidheavy.jsp
    name: ChemIDplus at National Library of Medicine
    namespaceEmbeddedInLui: false
    pattern: ^\d+\-\d+\-\d+$
    prefix: chemidplus
    uri_format: https://chem.nlm.nih.gov/chemidplus/rn/$1
  prefix: chemidplus
  prefixcommons:
    description: ChemIDplus is a web-based search system that provides access to structure
      and nomenclature authority files used for the identification of chemical substances
      cited in National Library of Medicine (NLM) databases. It also provides structure
      searching and direct links to many biomedical resources at NLM and on the Internet
      for chemicals of interest.
    example: '000057272'
    homepage: http://chem.sis.nlm.nih.gov/chemidplus/chemidheavy.jsp
    keywords:
    - structure
    - molecules
    license: http://www.nlm.nih.gov/copyright.html
    name: ChemIDplus
    pattern: ^\d+$
    prefix: chemidplus
    uri_format: http://chem.sis.nlm.nih.gov/chemidplus/direct.jsp?regno=$1
  publications:
  - doi: 10.1300/j115v21n01_04
    pmc: null
    pubmed: '11989279'
    title: ChemIDplus-super source for chemical and drug information
    year: 2002
  synonyms:
  - ChemIDplus
cheminf:
  aberowl:
    description: Includes terms for the descriptors commonly used in cheminformatics
      software applications and the algorithms which generate them.
    download_owl: http://aber-owl.net/media/ontologies/CHEMINF/50/cheminf.owl
    homepage: https://github.com/semanticchemistry/semanticchemistry
    name: Chemical Information Ontology
    prefix: CHEMINF
  bartoc:
    abbreviation: CHEMINF
    description: The Chemical Information Ontology (CHEMINF) aims to establish a standard
      in representing chemical information. In particular, it aims to produce an ontology
      to represent chemical structure and to richly describe chemical properties,
      whether intrinsic or computed.
    homepage: https://github.com/egonw/semanticchemistry
    license: CC_MARK
    prefix: '20702'
  biocontext:
    prefix: CHEMINF
  bioportal:
    contact:
      email: egon.willighagen@maastrichtuniversity.nl
      name: Egon Willighagen
    description: Includes terms for the descriptors commonly used in cheminformatics
      software applications and the algorithms which generate them.
    homepage: https://github.com/semanticchemistry/semanticchemistry
    name: Chemical Information Ontology
    prefix: CHEMINF
    publications:
    - https://github.com/semanticchemistry/semanticchemistry
    version: 2.1.0
  download_owl: https://github.com/semanticchemistry/semanticchemistry/raw/master/ontology/cheminf.owl
  example: '000410'
  fairsharing:
    abbreviation: CHEMINF
    contact:
      email: egon.willighagen@gmail.com
      name: Egon Willighagen
      orcid: 0000-0001-7542-0286
    description: The Chemical Information Ontology (CHEMINF) aims to establish a standard
      in representing chemical information. In particular, it aims to produce an ontology
      to represent chemical structure and to richly describe chemical properties,
      whether intrinsic or computed.
    domains:
    - Structure
    - molecular entity
    homepage: https://github.com/semanticchemistry/semanticchemistry
    license: CC0-1.0
    name: CHEMical INFormation Ontology
    prefix: FAIRsharing.sjhvyy
    publications:
    - doi: 10.1371/journal.pone.0025513
      pubmed: '21991315'
      title: 'The chemical information ontology: provenance and disambiguation for
        chemical data on the biological semantic web'
      year: 2011
    subjects:
    - Life Science
    - Biochemistry
    - Chemistry
  mappings:
    aberowl: CHEMINF
    bartoc: '20702'
    biocontext: CHEMINF
    bioportal: CHEMINF
    fairsharing: FAIRsharing.sjhvyy
    miriam: cheminf
    obofoundry: cheminf
    ols: cheminf
    ontobee: CHEMINF
    tib: cheminf
    wikidata.entity: Q55118298
  miriam:
    deprecated: false
    description: The chemical information ontology (cheminf) describes information
      entities about chemical entities. It provides qualitative and quantitative attributes
      to richly describe chemicals.
    homepage: https://www.ebi.ac.uk/ols4/ontologies/cheminf
    id: '00001045'
    name: Chemical Information Ontology
    namespaceEmbeddedInLui: true
    pattern: ^CHEMINF:\d+$
    prefix: cheminf
    sampleId: '000306'
    uri_format: https://www.ebi.ac.uk/ols4/ontologies/cheminf/classes?obo_id=CHEMINF:$1
  name: Chemical Information Ontology
  obofoundry:
    appears_in:
    - proco
    contact: egon.willighagen@gmail.com
    contact.github: egonw
    contact.label: Egon Willighagen
    contact.orcid: 0000-0001-7542-0286
    deprecated: false
    description: Includes terms for the descriptors commonly used in cheminformatics
      software applications and the algorithms which generate them.
    domain: chemistry and biochemistry
    download.owl: http://purl.obolibrary.org/obo/cheminf.owl
    homepage: https://github.com/semanticchemistry/semanticchemistry
    license: CC0 1.0
    license.url: http://creativecommons.org/publicdomain/zero/1.0/
    name: Chemical Information Ontology
    preferredPrefix: CHEMINF
    prefix: cheminf
    publications:
    - id: https://www.ncbi.nlm.nih.gov/pubmed/21991315
      title: 'The chemical information ontology: provenance and disambiguation for
        chemical data on the biological semantic web'
    repository: https://github.com/semanticchemistry/semanticchemistry
  ols:
    description: Includes terms for the descriptors commonly used in cheminformatics
      software applications and the algorithms which generate them.
    download_owl: http://purl.obolibrary.org/obo/cheminf.owl
    homepage: https://github.com/semanticchemistry/semanticchemistry
    name: chemical information ontology (cheminf) - information entities about chemical
      entities
    prefix: cheminf
    tracker: https://github.com/semanticchemistry/semanticchemistry/issues
    version: 2.1.0
  ontobee:
    library: Library
    name: Chemical Information Ontology
    prefix: CHEMINF
  pattern: ^\d{6}$
  prefix: cheminf
  providers:
  - code: semanticscience
    description: Legacy URLs before conversion of CHEMINF to OBO PURLs
    example: null
    first_party: null
    homepage: http://semanticscience.org
    name: Semantic Science
    publications: null
    status: null
    uri_format: http://semanticscience.org/resource/CHEMINF_$1
  publications:
  - doi: 10.1371/journal.pone.0025513
    pmc: PMC3184996
    pubmed: '21991315'
    title: 'The chemical information ontology: provenance and disambiguation for chemical
      data on the biological semantic web'
    year: 2011
  tib:
    description: The chemical information ontology (cheminf) describes information
      entities about chemical entities. It provides qualitative and quantitative attributes
      to richly describe chemicals. Includes terms for the descriptors commonly used
      in cheminformatics software applications and the algorithms which generate them.
    download_owl: http://purl.obolibrary.org/obo/cheminf.owl
    homepage: https://github.com/semanticchemistry/semanticchemistry
    keywords:
    - NFDI4CHEM
    - NFDI4CAT
    - chemistry
    name: chemical information ontology (cheminf) - information entities about chemical
      entities
    prefix: cheminf
    tracker: https://github.com/semanticchemistry/semanticchemistry/issues
  uri_format: http://purl.obolibrary.org/obo/CHEMINF_$1
chempro.competitor:
  contact:
    email: zhufeng@zju.edu.cn
    github: null
    name: Feng Zhu
    orcid: 0000-0001-8069-0053
  contributor:
    email: m.naguthana@hotmail.com
    github: nagutm
    name: Mufaddal Naguthanawala
    orcid: 0009-0009-5240-7463
  description: ChemPro is a database of chemoproteomic probes. This prefix provides
    identifiers for compounds that compete with probes for binding to target proteins.
  example: LDCM0160
  github_request_issue: 1424
  homepage: https://chemprosquare.idrblab.net
  name: ChemPro Competitor
  pattern: ^LDCM\d+$
  prefix: chempro.competitor
  publications:
  - doi: 10.1093/nar/gkae943
    pmc: PMC11701659
    pubmed: '39436046'
    title: 'Chem(Pro)2: the atlas of chemoproteomic probes labelling human proteins'
    year: 2024
  reviewer:
    email: b.gyori@northeastern.edu
    github: bgyori
    name: Benjamin M. Gyori
    orcid: 0000-0001-9439-5346
  uri_format: https://chemprosquare.idrblab.net/data/competitor/details/$1
chempro.probe:
  contact:
    email: zhufeng@zju.edu.cn
    github: null
    name: Feng Zhu
    orcid: 0000-0001-8069-0053
  contributor:
    email: m.naguthana@hotmail.com
    github: nagutm
    name: Mufaddal Naguthanawala
    orcid: 0009-0009-5240-7463
  description: ChemPro is a database of chemoproteomic probes. This prefix provides
    identifiers for chemoproteomic probes used to label human proteins in living cells.
  example: LDPC0032
  github_request_issue: 1424
  homepage: https://chemprosquare.idrblab.net
  name: ChemPro Probe
  pattern: ^LDPC\d+$
  prefix: chempro.probe
  publications:
  - doi: 10.1093/nar/gkae943
    pmc: PMC11701659
    pubmed: '39436046'
    title: 'Chem(Pro)2: the atlas of chemoproteomic probes labelling human proteins'
    year: 2024
  reviewer:
    email: b.gyori@northeastern.edu
    github: bgyori
    name: Benjamin M. Gyori
    orcid: 0000-0001-9439-5346
  uri_format: https://chemprosquare.idrblab.net/data/probe/details/$1
chempro.target:
  contact:
    email: zhufeng@zju.edu.cn
    github: null
    name: Feng Zhu
    orcid: 0000-0001-8069-0053
  contributor:
    email: m.naguthana@hotmail.com
    github: nagutm
    name: Mufaddal Naguthanawala
    orcid: 0009-0009-5240-7463
  description: ChemPro is a database of chemoproteomic probes. This prefix provides
    identifiers for human proteins that interact with chemoproteomic probes.
  example: LDTP03903
  github_request_issue: 1424
  homepage: https://chemprosquare.idrblab.net
  name: ChemPro Target
  pattern: ^LDTP\d+$
  prefix: chempro.target
  publications:
  - doi: 10.1093/nar/gkae943
    pmc: PMC11701659
    pubmed: '39436046'
    title: 'Chem(Pro)2: the atlas of chemoproteomic probes labelling human proteins'
    year: 2024
  reviewer:
    email: b.gyori@northeastern.edu
    github: bgyori
    name: Benjamin M. Gyori
    orcid: 0000-0001-9439-5346
  uri_format: https://chemprosquare.idrblab.net/data/target/details/$1
chemrof:
  aberowl:
    description: CHEMROF is an ontological framework for Chemical Entities Mixtures
      Reactions Ontological Framework. This OWL ontology is an automated Translation
      of the source LinkML schema, https://w3id.org/chemrof
    download_owl: http://aber-owl.net/media/ontologies/CHEMROF/4/chemrof.owl
    homepage: https://w3id.org/chemrof
    name: CHEMROF
    prefix: CHEMROF
  bioportal:
    contact:
      email: cjmungall@lbl.gov
      name: Chris Mungall
    description: CHEMROF is an ontological framework for Chemical Entities Mixtures
      Reactions Ontological Framework. This OWL ontology is an automated Translation
      of the source LinkML schema, https://w3id.org/chemrof
    homepage: https://w3id.org/chemrof
    license: CC0-1.0
    name: CHEMROF
    prefix: CHEMROF
    version: 0.0.1
  contact:
    email: cjmungall@lbl.gov
    github: cmungall
    name: Chris Mungall
    orcid: 0000-0002-6601-2165
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: A data model for managing information about chemical entities, ranging
    from atoms through molecules to complex mixtures.
  download_owl: https://raw.githubusercontent.com/chemkg/chemrof/main/schema/owl/chemrof.owl.ttl
  example: FullySpecifiedAtom
  homepage: https://chemkg.github.io/chemrof/
  mappings:
    aberowl: CHEMROF
    bioportal: CHEMROF
    tib: chemrof
  name: Chemical Entity Materials and Reactions Ontological Framework
  preferred_prefix: ChEMROF
  prefix: chemrof
  rdf_uri_format: https://w3id.org/chemrof/$1
  repository: https://github.com/chemkg/chemrof
  tib:
    description: "A data model for managing information about chemical entities, ranging\
      \ from atoms through molecules to complex mixtures. \nAspects of this have been\
      \ cribbed from various sources including CHEBI, SIO, \nWikipedia/Wikidata, the\
      \ NCATS Translator Chemical Working Group, but all mistakes, \nare my own. \n\
      For full context/motivation see the [GitHub repo](https://github.com/chemkg/chemrof)."
    download_rdf: https://w3id.org/chemrof/chemrof.owl.ttl
    homepage: https://chemkg.github.io/chemrof/
    keywords:
    - NFDI4CHEM
    - chemistry
    name: Chemical Entities Mixtures and Reactions Ontological Framework
    prefix: chemrof
    tracker: https://github.com/chemkg/chemrof/issues
    uri_format: https://w3id.org/chemrof/$1
  uri_format: https://chemkg.github.io/chemrof/$1
chemspider:
  biocontext:
    prefix: CHEMSPIDER
  cheminf:
    description: Database identifier used by ChemSpider.
    name: ChemSpider
    obsolete: false
    prefix: '000405'
  contact:
    email: pencehe@oneonta.edu
    github: null
    name: Harry E. Pence
    orcid: 0000-0002-0412-9018
  edam:
    description: Identifier of an entry from the ChemSpider database.
    name: ChemSpider
    obsolete: false
    prefix: '1173'
  fairsharing:
    abbreviation: ChemSpider
    description: ChemSpider is a freely available collection of compound data from
      across the web, which aggregates chemical structures and their associated information
      into a single searchable repository entry. These entries are supplemented with
      additional properties, related information and links back to original data sources.
    homepage: http://www.chemspider.com/
    name: ChemSpider
    prefix: FAIRsharing.96f3gm
    publications:
    - doi: 10.1021/ed100697w
      pubmed_id: null
      title: 'ChemSpider: An Online Chemical Information Resource'
    subjects:
    - Chemistry
    - Life Science
    twitter: ChemSpider
  integbio:
    description: ChemSpider is a freely available collection of compound data from
      across the web, which aggregates chemical structures and their associated information
      into a single searchable repository entry. These entries are supplemented with
      additional properties, related information and links back to original data sources.
    fairsharing: FAIRsharing.96f3gm
    homepage: http://www.chemspider.com/
    information_keywords:
    - 3D structure
    - Image/Movie
    maintainer: Royal Society of Chemistry
    name: ChemSpider
    prefix: nbdc01863
    status: Active
    target_keywords:
    - Chemical compound
  mappings:
    biocontext: CHEMSPIDER
    cheminf: '000405'
    edam: '1173'
    fairsharing: FAIRsharing.96f3gm
    integbio: nbdc01863
    miriam: chemspider
    n2t: chemspider
    prefixcommons: chemspider
    re3data: r3d100010205
    wikidata: P661
  miriam:
    deprecated: false
    description: ChemSpider is a collection of compound data from across the web,
      which aggregates chemical structures and their associated information into a
      single searchable repository entry. These entries are supplemented with additional
      properties, related information and links back to original data sources.
    homepage: http://www.chemspider.com/
    id: 00000138
    name: ChemSpider
    namespaceEmbeddedInLui: false
    pattern: ^\d+$
    prefix: chemspider
    sampleId: '56586'
    uri_format: http://www.chemspider.com/Chemical-Structure.$1.html
  n2t:
    description: ChemSpider is a collection of compound data from across the web,
      which aggregates chemical structures and their associated information into a
      single searchable repository entry. These entries are supplemented with additional
      properties, related information and links back to original data sources.
    example: '56586'
    homepage: http://www.chemspider.com/
    name: ChemSpider at RSC
    namespaceEmbeddedInLui: false
    pattern: ^\d+$
    prefix: chemspider
    uri_format: http://www.chemspider.com/Chemical-Structure.$1.html
  name: ChemSpider
  prefix: chemspider
  prefixcommons:
    description: ChemSpider is a collection of compound data from across the web,
      which aggregates chemical structures and their associated information into a
      single searchable repository entry. These entries are supplemented with additional
      properties, related information and links back to original data sources.
    example: '56586'
    homepage: http://www.chemspider.com/
    keywords:
    - structure
    - molecules
    license: http://www.rsc.org/Help/termsconditions.asp
    name: ChemSpider - Database of Chemical Structures and Property Predictions
    pattern: ^\d+$
    prefix: chemspider
    uri_format: http://www.chemspider.com/Chemical-Structure.$1.html
  publications:
  - doi: 10.1021/ed100697w
    pmc: null
    pubmed: null
    title: 'ChemSpider: An Online Chemical Information Resource'
    year: 2010
  - doi: 10.1021/ed100697w
    pmc: null
    pubmed: null
    title: 'ChemSpider: An Online Chemical Information Resource'
    year: null
  - doi: 10.1021/ed100697w
    pmc: null
    pubmed: null
    title: 'ChemSpider: An Online Chemical Information Resource'
    year: null
  - doi: 10.1021/ed100697w
    pmc: null
    pubmed: null
    title: 'ChemSpider: An Online Chemical Information Resource'
    year: null
  - doi: 10.1021/ed100697w
    pmc: null
    pubmed: null
    title: 'ChemSpider: An Online Chemical Information Resource'
    year: null
  re3data:
    description: 'ChemSpider is a free chemical structure database providing fast
      access to over 130 million structures, properties and associated information.
      By integrating and linking compounds from more than 270 data sources, ChemSpider
      enables researchers to discover the most comprehensive view of freely available
      chemical data from a single online search. It is owned by the Royal Society
      of Chemistry.

      ChemSpider builds on the collected sources by adding additional properties,
      related information and links back to original data sources. ChemSpider offers
      text and structure searching to find compounds of interest and provides unique
      services to improve this data by curation and annotation and to integrate it
      with users’ applications.'
    doi: 10.17616/R38P4P
    homepage: https://www.chemspider.com/
    license: Copyrights
    name: ChemSpider
    prefix: r3d100010205
    synonyms:
    - Search and share chemistry
  synonyms:
  - ChemSpiderID
  - Chemspider
  wikidata:
    description: identifier in a free chemical database, owned by the Royal Society
      of Chemistry
    example:
    - '10189562'
    - '1086'
    - '3953'
    homepage: https://www.chemspider.com/
    name: ChemSpider ID
    pattern: ^[1-9]\d*$
    prefix: P661
    uri_format: https://www.chemspider.com/Chemical-Structure.$1.html
    uri_format_rdf: http://rdf.chemspider.com/$1
chickenqtldb:
  biocontext:
    prefix: CHICKENQTLDB
  mappings:
    biocontext: CHICKENQTLDB
    miriam: chickenqtldb
    n2t: chickenqtldb
    prefixcommons: chickenqtldb
  miriam:
    deprecated: false
    description: The Animal Quantitative Trait Loci (QTL) database (Animal QTLdb)
      is designed to house publicly all available QTL and single-nucleotide polymorphism/gene
      association data on livestock animal species. This collection references chicken
      QTLs.
    homepage: https://www.animalgenome.org/QTLdb
    id: '00000505'
    name: Animal Genome Chicken QTL
    namespaceEmbeddedInLui: false
    pattern: ^\d+$
    prefix: chickenqtldb
    sampleId: '14362'
    uri_format: https://www.animalgenome.org/QTLdb/q?id=QTL_ID:$1
  n2t:
    description: The Animal Quantitative Trait Loci (QTL) database (Animal QTLdb)
      is designed to house publicly all available QTL and single-nucleotide polymorphism/gene
      association data on livestock animal species. This collection references chicken
      QTLs.
    example: '14362'
    homepage: http://www.animalgenome.org/cgi-bin/QTLdb/GG/index
    name: Animal QTL Chicken at Iowa State University
    namespaceEmbeddedInLui: false
    pattern: ^\d+$
    prefix: chickenqtldb
    uri_format: http://www.animalgenome.org/cgi-bin/QTLdb/GG/qdetails?QTL_ID=$1
  part_of: qtldb
  prefix: chickenqtldb
  prefixcommons:
    description: This Chicken Quantitative Trait Locus (QTL) database (Chicken QTLdb)
      has gathered all chicken QTL data published during the past 10+ years. The database
      and its peripheral tools make it possible to compare, confirm and locate on
      chicken chromosomes the most feasible location for genes responsible for quantitative
      trait important to chicken production.
    example: '66'
    homepage: http://www.animalgenome.org/cgi-bin/QTLdb/GG/index
    keywords:
    - DNA
    - genome
    name: Chicken Quantitative Trait Locus database
    pattern: ^\d+$
    prefix: chickenqtldb
    uri_format: http://www.animalgenome.org/cgi-bin/QTLdb/GG/qdetails?QTL_ID=$1
chictr:
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: Established in 2005 by professor Wu Taixiang and Li Youping team, West
    China Hospital, Sichuan University, and the Ministry of Health of China assigned
    it to be the representative of China to join WHO ICTRP in 2007. The Chinese Clinical
    Trial Registry provides the services include register for trials, consultation
    for trial design, central randomization for an allocation sequence, peer review
    for draft articles and training for peer reviewers. (from website)
  domain: clinical trial
  example: ChiCTR2300070727
  homepage: https://www.chictr.org.cn
  logo: https://www.chictr.org.cn/images/top.jpg
  name: Chinese Clinical Trial Registry
  pattern: ^ChiCTR(-[A-Z]+-)?\d+$
  prefix: chictr
  references:
  - https://www.chictr.org.cn/showproj.html?proj=187605
chiro:
  aberowl:
    description: CHEBI provides a distinct role hierarchy. Chemicals in the structural
      hierarchy are connected via a 'has role' relation. CHIRO provides links from
      these roles to useful other classes in other ontologies. This will allow direct
      connection between chemical structures (small molecules, drugs) and what they
      do. This could be formalized using 'capable of', in the same way Uberon and
      the Cell Ontology link structures to processes.
    download_owl: http://aber-owl.net/media/ontologies/CHIRO/1/chiro.owl
    homepage: https://github.com/obophenotype/chiro
    name: CHEBI Integrated Role Ontology
    prefix: CHIRO
  bioportal:
    contact:
      email: vasilevs@ohsu.edu
      name: Nicole Vasilevsky
    description: CHEBI provides a distinct role hierarchy. Chemicals in the structural
      hierarchy are connected via a 'has role' relation. CHIRO provides links from
      these roles to useful other classes in other ontologies. This will allow direct
      connection between chemical structures (small molecules, drugs) and what they
      do. This could be formalized using 'capable of', in the same way Uberon and
      the Cell Ontology link structures to processes.
    homepage: https://github.com/obophenotype/chiro
    name: CHEBI Integrated Role Ontology
    prefix: CHIRO
  mappings:
    aberowl: CHIRO
    bioportal: CHIRO
    obofoundry: chiro
    ols: chiro
    ontobee: CHIRO
    tib: chiro
    wikidata.entity: Q113006226
  name: ChEBI Integrated Role Ontology
  no_own_terms: true
  obofoundry:
    contact: vasilevs@ohsu.edu
    contact.github: nicolevasilevsky
    contact.label: Nicole Vasilevsky
    contact.orcid: 0000-0001-5208-3432
    depends_on:
    - chebi
    - go
    - hp
    - mp
    - ncbitaxon
    - pr
    - uberon
    deprecated: false
    description: CHEBI provides a distinct role hierarchy. Chemicals in the structural
      hierarchy are connected via a 'has role' relation. CHIRO provides links from
      these roles to useful other classes in other ontologies. This will allow direct
      connection between chemical structures (small molecules, drugs) and what they
      do. This could be formalized using 'capable of', in the same way Uberon and
      the Cell Ontology link structures to processes.
    domain: chemistry and biochemistry
    download.obo: http://purl.obolibrary.org/obo/chiro.obo
    download.owl: http://purl.obolibrary.org/obo/chiro.owl
    homepage: https://github.com/obophenotype/chiro
    license: CC0 1.0
    license.url: http://creativecommons.org/publicdomain/zero/1.0/
    name: CHEBI Integrated Role Ontology
    preferredPrefix: CHIRO
    prefix: chiro
    publications:
    - id: https://doi.org/10.26434/chemrxiv.12591221
      title: Extension of Roles in the ChEBI Ontology
    repository: https://github.com/obophenotype/chiro
  ols:
    description: CHEBI provides a distinct role hierarchy. Chemicals in the structural
      hierarchy are connected via a 'has role' relation. CHIRO provides links from
      these roles to useful other classes in other ontologies. This will allow direct
      connection between chemical structures (small molecules, drugs) and what they
      do. This could be formalized using 'capable of', in the same way Uberon and
      the Cell Ontology link structures to processes.
    download_owl: http://purl.obolibrary.org/obo/chiro.owl
    homepage: https://github.com/obophenotype/chiro
    name: CHEBI Integrated Role Ontology
    prefix: chiro
    tracker: https://github.com/obophenotype/chiro/issues
    version: '2015-11-23'
    version.iri: http://purl.obolibrary.org/obo/chiro/releases/2015-11-23/chiro.owl
  ontobee:
    library: Library
    name: CHEBI Integrated Role Ontology
    prefix: CHIRO
  prefix: chiro
  publications:
  - doi: 10.26434/chemrxiv.12591221
    pmc: null
    pubmed: null
    title: Extension of Roles in the ChEBI Ontology
    year: 2020
  tib:
    description: CHEBI provides a distinct role hierarchy. Chemicals in the structural
      hierarchy are connected via a 'has role' relation. CHIRO provides links from
      these roles to useful other classes in other ontologies. This will allow direct
      connection between chemical structures (small molecules, drugs) and what they
      do. This could be formalized using 'capable of', in the same way Uberon and
      the Cell Ontology link structures to processes.
    download_owl: http://purl.obolibrary.org/obo/chiro.owl
    homepage: https://github.com/obophenotype/chiro
    keywords:
    - NFDI4CHEM
    - chemistry
    name: CHEBI Integrated Role Ontology
    prefix: chiro
    tracker: https://github.com/obophenotype/chiro/issues
    uri_format: http://purl.obolibrary.org/obo/chiro#$1
    version.iri: http://purl.obolibrary.org/obo/chiro/releases/2015-11-23/chiro.owl
chmo:
  aberowl:
    description: CHMO, the chemical methods ontology, describes methods used to
    download_owl: http://aber-owl.net/media/ontologies/CHMO/34/chmo.owl
    homepage: https://github.com/rsc-ontologies/rsc-cmo
    name: Chemical Methods Ontology
    prefix: CHMO
  bartoc:
    abbreviation: CHMO
    description: CHMO, the chemical methods ontology, describes methods used to collect
      data in chemical experiments, such as mass spectrometry and electron microscopy
      prepare and separate material for further analysis, such as sample ionisation,
      chromatography, and electrophoresis synthesise materials, such as epitaxy and
      continuous vapour deposition It also describes the instruments used in these
      experiments, such as mass spectrometers and chromatography columns. It is intended
      to be complementary to the Ontology for Biomedical Investigations (OBI).
    homepage: https://obofoundry.org/ontology/chmo
    license: CC-BY-4.0
    prefix: '20703'
  biocontext:
    prefix: CHMO
  bioportal:
    contact:
      email: batchelorc@rsc.org
      name: Colin Batchelor
    description: CMO, the chemical methods ontology, describes methods used to collect
      data in chemical experiments, such as mass spectrometry and electron microscopy
      prepare and separate material for further analysis, such as sample ionisation,
      chromatography, and electrophoresis synthesise materials, such as epitaxy and
      continuous vapour deposition It also describes the instruments used in these
      experiments, such as mass spectrometers and chromatography columns. It is intended
      to be complementary to the Ontology for Biomedical Investigations (OBI)., CHMO,
      describes methods used to collect data in chemical experiments, such as mass
      spectrometry and electron microscopy prepare and separate material for further
      analysis, and electrophoresis synthesise materials, such as epitaxy and continuous
      vapour deposition It also describes the instruments used in these experiments
    homepage: https://code.google.com/p/rsc-cmo/
    license: CC-BY-4.0
    name: Chemical Methods Ontology
    prefix: CHMO
    version: '2025-10-21'
  download_obo: http://purl.obolibrary.org/obo/chmo.obo
  example: 0002902
  fairsharing:
    abbreviation: CHMO
    description: CHMO, the chemical methods ontology, describes methods used to collect
      data in chemical experiments, such as mass spectrometry and electron microscopy;
      prepare and separate material for further analysis, such as sample ionisation,
      chromatography, and electrophoresis; and synthesise materials such as epitaxy
      and continuous vapour deposition. It also describes the instruments used in
      these experiments, such as mass spectrometers and chromatography columns. It
      is intended to be complementary to the Ontology for Biomedical Investigations
      (OBI).
    domains:
    - electron microscopy
    - chromatography
    - assay
    - mass spectrometry assay
    homepage: https://github.com/rsc-ontologies/rsc-cmo
    license: CC-BY-4.0
    name: Chemical Methods Ontology
    prefix: FAIRsharing.9j4wh2
    repository: https://github.com/rsc-ontologies/rsc-cmo/issues
    subjects:
    - Chemistry
  mappings:
    aberowl: CHMO
    bartoc: '20703'
    biocontext: CHMO
    bioportal: CHMO
    fairsharing: FAIRsharing.9j4wh2
    obofoundry: chmo
    ols: chmo
    ontobee: CHMO
    tib: chmo
    wikidata.entity: Q55118301
  obofoundry:
    appears_in:
    - rbo
    - scdo
    contact: batchelorc@rsc.org
    contact.github: batchelorc
    contact.label: Colin Batchelor
    contact.orcid: 0000-0001-5985-7429
    deprecated: false
    description: CHMO, the chemical methods ontology, describes methods used to
    domain: health
    download.owl: http://purl.obolibrary.org/obo/chmo.owl
    homepage: https://github.com/rsc-ontologies/rsc-cmo
    license: CC BY 4.0
    license.url: http://creativecommons.org/licenses/by/4.0/
    name: Chemical Methods Ontology
    preferredPrefix: CHMO
    prefix: chmo
    repository: https://github.com/rsc-ontologies/rsc-cmo
  ols:
    contact: chemistry-ontologies@googlegroups.com
    description: CHMO, the chemical methods ontology, describes methods used to
    download_owl: http://purl.obolibrary.org/obo/chmo.owl
    homepage: https://github.com/rsc-ontologies/rsc-cmo
    name: Chemical Methods Ontology
    prefix: chmo
    tracker: https://github.com/rsc-ontologies/rsc-cmo/issues
    version: '2025-10-21'
    version.iri: http://purl.obolibrary.org/obo/chmo/releases/2025-10-21/chmo.owl
  ontobee:
    library: Library
    name: Chemical Methods Ontology
    prefix: CHMO
  pattern: ^\d{7}$
  prefix: chmo
  tib:
    contact: chemistry-ontologies@googlegroups.com
    description: CHMO, the chemical methods ontology, describes methods used to collect
      data in chemical experiments, such as mass spectrometry and electron microscopy
      prepare and separate material for further analysis, such as sample ionisation,
      chromatography, and electrophoresis synthesise materials, such as epitaxy and
      continuous vapour deposition It also describes the instruments used in these
      experiments, such as mass spectrometers and chromatography columns. It is intended
      to be complementary to the Ontology for Biomedical Investigations (OBI).
    download_owl: http://purl.obolibrary.org/obo/chmo.owl
    homepage: https://github.com/rsc-ontology/rsc-cmo
    keywords:
    - NFDI4CHEM
    - NFDI4CAT
    - DataPLANT
    - chemistry
    name: Chemical Methods Ontology
    prefix: chmo
    tracker: https://github.com/rsc-ontology/rsc-cmo/issues
    version.iri: http://purl.obolibrary.org/obo/chmo/releases/2025-10-21/chmo.owl
  uri_format: http://purl.obolibrary.org/obo/CHMO_$1
chr:
  aberowl:
    description: Ontological representation of chromosomes in major species, Automatic
      translation of UCSC chromosome bands to OWL classes
    download_owl: http://aber-owl.net/media/ontologies/CHR/4/chr.owl
    homepage: https://github.com/monarch-initiative/monochrom/
    name: Monochrom
    prefix: CHR
    version: '2025-10-15'
  biocontext:
    prefix: CHR
  bioportal:
    contact:
      email: cjmungall@lbl.gov
      name: Chris Mungall
    description: Ontological representation of chromosomes in major species, Automatic
      translation of UCSC chromosome bands to OWL classes
    homepage: https://github.com/monarch-initiative/monochrom/
    license: CC0-1.0
    name: Monochrom
    prefix: CHR
    version: '2025-10-15'
  contact:
    email: cjmungall@lbl.gov
    github: cmungall
    name: Chris Mungall
    orcid: 0000-0002-6601-2165
  contributor:
    email: jhc@lbl.gov
    github: caufieldjh
    name: Harry Caufield
    orcid: 0000-0001-5705-7831
  description: The Chromosome Ontology is an automatically derived ontology of chromosomes
    and chromosome parts.
  download_json: https://raw.githubusercontent.com/monarch-initiative/monochrom/refs/heads/master/chr.json
  download_obo: https://raw.githubusercontent.com/monarch-initiative/monochrom/refs/heads/master/chr.obo
  download_owl: https://raw.githubusercontent.com/monarch-initiative/monochrom/refs/heads/master/chr.owl
  example: 10090-chr10qC
  github_request_issue: 1265
  homepage: https://github.com/monarch-initiative/monochrom
  license: BSD-3
  mappings:
    aberowl: CHR
    biocontext: CHR
    bioportal: CHR
  name: Chromosome Ontology
  preferred_prefix: CHR
  prefix: chr
  repository: https://github.com/monarch-initiative/monochrom
  reviewer:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
cido:
  aberowl:
    description: The Coronavirus Infectious Disease Ontology (CIDO) aims to ontologically
      represent and standardize various aspects of coronavirus infectious diseases,
      including their etiology, transmission, epidemiology, pathogenesis, diagnosis,
      prevention, and treatment.
    download_owl: http://aber-owl.net/media/ontologies/CIDO/35/cido.owl
    homepage: https://github.com/cido-ontology/cido
    name: Coronavirus Infectious Disease Ontology
    prefix: CIDO
  bioportal:
    contact:
      email: yongqunh@med.umich.edu
      name: Yongqun Oliver He
    description: The Ontology of Coronavirus Infectious Disease (CIDO) is a community-driven
      open-source biomedical ontology in the area of coronavirus infectious disease.
      The CIDO is developed to provide standardized human- and computer-interpretable
      annotation and representation of various coronavirus infectious diseases, including
      their etiology, transmission, pathogenesis, diagnosis, prevention, and treatment.
    homepage: https://github.com/CIDO-ontology/cido
    name: Coronavirus Infectious Disease Ontology
    prefix: CIDO
    publications:
    - http://www.example.com
    version: '2024-02-16'
  download_owl: https://github.com/CIDO-ontology/cido/raw/master/cido.owl
  example: '0000005'
  fairsharing:
    abbreviation: CIDO
    description: The Ontology of Coronavirus Infectious Disease (CIDO) is a community-driven
      open-source biomedical ontology in the area of coronavirus infectious disease.
      The CIDO is developed to provide standardized human- and computer-interpretable
      annotation and representation of various coronavirus infectious diseases, including
      their etiology, transmission, epidemiology, pathogenesis, diagnosis, prevention,
      and treatment. Its development follows the OBO Foundry Principles.
    domains:
    - drug
    - infection process
    - disease
    - drug interaction
    homepage: https://github.com/cido-ontology/cido
    license: CC-BY-4.0
    name: Coronavirus Infectious Disease Ontology
    prefix: FAIRsharing.aVmpKl
    publications:
    - doi: 10.1038/s41597-020-0523-6
      pubmed: '32533075'
      title: CIDO, a community-based ontology for coronavirus disease knowledge and
        data integration, sharing, and analysis
      year: 2020
    repository: https://github.com/CIDO-ontology/cido/issues
    subjects:
    - Virology
    - Drug Discovery
    - Epidemiology
    - Bioinformatics
    - Drug Repositioning
    user_defined_tags:
    - COVID-19
  mappings:
    aberowl: CIDO
    bioportal: CIDO
    fairsharing: FAIRsharing.aVmpKl
    obofoundry: cido
    ols: cido
    ontobee: CIDO
    wikidata.entity: Q110998476
  obofoundry:
    contact: yongqunh@med.umich.edu
    contact.github: yongqunh
    contact.label: Yongqun Oliver He
    contact.orcid: 0000-0001-9189-9661
    deprecated: false
    description: The Coronavirus Infectious Disease Ontology (CIDO) aims to ontologically
      represent and standardize various aspects of coronavirus infectious diseases,
      including their etiology, transmission, epidemiology, pathogenesis, diagnosis,
      prevention, and treatment.
    domain: health
    download.owl: http://purl.obolibrary.org/obo/cido.owl
    homepage: https://github.com/cido-ontology/cido
    license: CC BY 4.0
    license.url: http://creativecommons.org/licenses/by/4.0/
    name: Coronavirus Infectious Disease Ontology
    preferredPrefix: CIDO
    prefix: cido
    publications:
    - id: https://www.ncbi.nlm.nih.gov/pubmed/36271389
      title: 'A comprehensive update on CIDO: the community-based coronavirus infectious
        disease ontology'
    repository: https://github.com/cido-ontology/cido
  ols:
    contact: cido-discuss@googlegroups.com
    description: The Ontology of Coronavirus Infectious Disease (CIDO) is a community-driven
      open-source biomedical ontology in the area of coronavirus infectious disease.
      The CIDO is developed to provide standardized human- and computer-interpretable
      annotation and representation of various coronavirus infectious diseases, including
      their etiology, transmission, pathogenesis, diagnosis, prevention, and treatment.
    download_owl: http://purl.obolibrary.org/obo/cido.owl
    homepage: https://github.com/cido-ontology/cido
    name: 'CIDO: Ontology of Coronavirus Infectious Disease'
    prefix: cido
    tracker: https://github.com/cido-ontology/cido/issues
    version: '2024-02-16'
    version.iri: http://purl.obolibrary.org/obo/cido/releases/2024-02-16/cido.owl
  ontobee:
    library: Library
    name: Coronavirus Infectious Disease Ontology
    prefix: CIDO
  pattern: ^\d{7}$
  prefix: cido
  publications:
  - doi: 10.1186/s13326-022-00279-z
    pmc: PMC9585694
    pubmed: '36271389'
    title: 'A comprehensive update on CIDO: the community-based coronavirus infectious
      disease ontology'
    year: 2022
  - doi: 10.1038/s41597-020-0523-6
    pmc: PMC7293349
    pubmed: '32533075'
    title: CIDO, a community-based ontology for coronavirus disease knowledge and
      data integration, sharing, and analysis
    year: 2020
  uri_format: http://purl.obolibrary.org/obo/CIDO_$1
cidoc.crm:
  aberowl:
    description: The CIDOC Conceptual Reference Model (CRM) provides definitions and
      a formal structure for describing the implicit and explicit concepts and relationships
      used in cultural heritage documentation. The CIDOC CRM is intended to promote
      a shared understanding of cultural heritage information by providing a common
      and extensible semantic framework that any cultural heritage information can
      be mapped to. It is intended to be a common language for domain experts and
      implementers to formulate requirements for information systems and to serve
      as a guide for good practice of conceptual modelling. In this way, it can provide
      the "semantic glue" needed to mediate between different sources of cultural
      heritage information, such as that published by museums, libraries and archives.
    download_owl: http://aber-owl.net/media/ontologies/CIDOC-CRM/2/cidoc-crm.owl
    homepage: http://www.cidoc-crm.org/
    name: CIDOC Conceptual Reference Model
    prefix: CIDOC-CRM
    version: v6.2
  bioportal:
    contact:
      email: patrick.le-boeuf@bnf.fr
      name: Patrick Le Bœuf
    description: The CIDOC Conceptual Reference Model (CRM) provides definitions and
      a formal structure for describing the implicit and explicit concepts and relationships
      used in cultural heritage documentation. The CIDOC CRM is intended to promote
      a shared understanding of cultural heritage information by providing a common
      and extensible semantic framework that any cultural heritage information can
      be mapped to. It is intended to be a common language for domain experts and
      implementers to formulate requirements for information systems and to serve
      as a guide for good practice of conceptual modelling. In this way, it can provide
      the "semantic glue" needed to mediate between different sources of cultural
      heritage information, such as that published by museums, libraries and archives.
    homepage: http://www.cidoc-crm.org/
    name: CIDOC Conceptual Reference Model
    prefix: CIDOC-CRM
    version: v6.2
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: The CIDOC Conceptual Reference Model (CRM) is a theoretical and practical
    tool for information integration in the field of cultural heritage. It can help
    researchers, administrators and the public explore complex questions with regards
    to our past across diverse and dispersed datasets. The CIDOC CRM achieves this
    by providing definitions and a formal structure for describing the implicit and
    explicit concepts and relationships used in cultural heritage documentation and
    of general interest for the querying and exploration of such data. Such models
    are also known as formal ontologies. These formal descriptions allow the integration
    of data from multiple sources in a software and schema agnostic fashion. [from
    homepage]
  example: E1
  fairsharing:
    abbreviation: CIDOC-CRM
    description: 'The CIDOC Conceptual Reference Model (CRM) provides definitions
      and a formal structure for describing the implicit and explicit concepts and
      relationships used in cultural heritage documentation. The overall scope of
      the CIDOC CRM can be summarised in simple terms as the curated, factual knowledge

      about the past at a human scale. The CIDOC CRM is intended to promote a shared
      understanding of cultural heritage information by providing a common and extensible
      semantic framework that any cultural heritage information can be mapped to.
      It is intended to be a common language for domain experts and implementers to
      formulate requirements for information systems and to serve as a guide for good
      practice of conceptual modelling. In this way, it can provide the "semantic
      glue" needed to mediate between different sources of cultural heritage information,
      such as that published by museums, libraries and archives. The ISO 21127:2014
      specification (Information and documentation — A reference ontology for the
      interchange of cultural heritage information) was created from the CIDOC CRM,
      although the CIDOC CRM Special Interest Group continues to maintain this original
      document as well.'
    homepage: https://www.cidoc-crm.org/
    logo: https://api.fairsharing.org/rails/active_storage/blobs/redirect/eyJfcmFpbHMiOnsibWVzc2FnZSI6IkJBaHBBZUk9IiwiZXhwIjpudWxsLCJwdXIiOiJibG9iX2lkIn19--057a21005e538cb21742ec8a475bf44a6228c707/cidoc.png?disposition=inline
    name: CIDOC Conceptual Reference Model
    prefix: FAIRsharing.9xcr4z
    subjects:
    - Anthropology
    - Culture
    - Humanities and Social Science
    - Cultural Studies
  homepage: https://cidoc-crm.org
  logo: https://cidoc-crm.org/sites/default/files/logo3.png
  mappings:
    aberowl: CIDOC-CRM
    bioportal: CIDOC-CRM
    fairsharing: FAIRsharing.9xcr4z
    tib: cidoc
    zazuko: crm
  name: CIDOC Conceptual Reference Model
  prefix: cidoc.crm
  tib:
    description: The CIDOC Conceptual Reference Model (CRM) is a theoretical and practical
      tool for information integration in the field of cultural heritage
    download_rdf: https://gitlab.isl.ics.forth.gr/cidoc-crm/cidoc_crm_rdf/-/raw/master/7.1.1/CIDOC_CRM_v7.1.1.rdf
    homepage: https://gitlab.isl.ics.forth.gr/cidoc-crm/cidoc_crm_rdf/
    keywords:
    - NFDI4CULTURE
    - CoyPu
    - Digital Planning and Construction
    - FID BAUdigital
    - history
    name: The CIDOC Conceptual Reference Model (CRM)
    prefix: cidoc
    tracker: https://gitlab.isl.ics.forth.gr/cidoc-crm/cidoc_crm_rdf/issues
    uri_format: http://www.cidoc-crm.org/cidoc-crm/$1
    version.iri: http://www.cidoc-crm.org/cidoc-crm/7.1.1/
  uri_format: http://www.cidoc-crm.org/cidoc-crm/$1
  zazuko:
    prefix: crm
    uri_format: http://www.cidoc-crm.org/cidoc-crm/$1
cienciavitae:
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  keywords:
  - person
  - researcher
  mappings:
    wikidata: P7893
  prefix: cienciavitae
  references:
  - https://github.com/biopragmatics/bioregistry/pull/1171
  wikidata:
    description: identifier of scientific author in www.cienciavitae.pt
    example:
    - 0C1F-DA6C-4B02
    - 7510-6641-5A42
    - A11B-38F7-A1B1
    homepage: https://www.ciencia-id.pt
    name: CIÊNCIAVITAE ID
    pattern: ^([0-9A-F]{4}-){2}[0-9A-F]{4}$
    prefix: P7893
    uri_format: https://www.cienciavitae.pt/$1
cio:
  aberowl:
    description: An ontology to capture confidence information about annotations.
    download_owl: http://aber-owl.net/media/ontologies/CIO/2/cio.owl
    homepage: https://github.com/BgeeDB/confidence-information-ontology
    name: Confidence Information Ontology
    prefix: CIO
  biocontext:
    prefix: CIO
  bioportal:
    contact:
      email: frederic.bastian@unil.ch
      name: Frederic Bastian
    description: An ontology to capture confidence information about annotations
    homepage: https://github.com/BgeeDB/confidence-information-ontology
    name: Confidence Information Ontology
    prefix: CIO
  example: '0000040'
  fairsharing:
    abbreviation: CIO
    description: The Confidence Information Ontology (CIO) is an ontology to capture
      confidence information about annotations. Please note that the last update to
      the ontology files were in 2015.
    domains:
    - Annotation
    homepage: https://github.com/BgeeDB/confidence-information-ontology
    license: CC0-1.0
    name: Confidence Information Ontology
    prefix: FAIRsharing.e3t0yw
    publications:
    - doi: 10.1093/database/bav043
      title: 'The Confidence Information Ontology: a step towards a standard for asserting
        confidence in annotations'
      year: 2015
    subjects:
    - Biology
  mappings:
    aberowl: CIO
    biocontext: CIO
    bioportal: CIO
    fairsharing: FAIRsharing.e3t0yw
    obofoundry: cio
    ols: cio
    ontobee: CIO
    wikidata.entity: Q81661853
  obofoundry:
    contact: frederic.bastian@unil.ch
    contact.github: fbastian
    contact.label: Frédéric Bastian
    contact.orcid: 0000-0002-9415-5104
    deprecated: false
    description: An ontology to capture confidence information about annotations.
    domain: information
    download.obo: http://purl.obolibrary.org/obo/cio.obo
    download.owl: http://purl.obolibrary.org/obo/cio.owl
    homepage: https://github.com/BgeeDB/confidence-information-ontology
    license: CC0 1.0
    license.url: https://creativecommons.org/publicdomain/zero/1.0/
    name: Confidence Information Ontology
    preferredPrefix: CIO
    prefix: cio
    publications:
    - id: https://www.ncbi.nlm.nih.gov/pubmed/25957950
      title: 'The Confidence Information Ontology: a step towards a standard for asserting
        confidence in annotations'
    repository: https://github.com/BgeeDB/confidence-information-ontology
  ols:
    description: An ontology to capture confidence information about annotations.
    download_owl: http://purl.obolibrary.org/obo/cio.owl
    homepage: https://github.com/BgeeDB/confidence-information-ontology
    name: Confidence Information Ontology
    prefix: cio
    tracker: https://github.com/BgeeDB/confidence-information-ontology
    version: '2015-03-10'
    version.iri: http://purl.obolibrary.org/obo/cio/releases/2015-03-10/cio.owl
  ontobee:
    library: Library
    name: Confidence Information Ontology
    prefix: CIO
  pattern: ^\d{7}$
  prefix: cio
  publications:
  - doi: 10.1093/database/bav043
    pmc: PMC4425939
    pubmed: '25957950'
    title: 'The Confidence Information Ontology: a step towards a standard for asserting
      confidence in annotations'
    year: 2015
  - doi: null
    pmc: null
    pubmed: '25957950'
    title: 'The Confidence Information Ontology: a step towards a standard for asserting
      confidence in annotations'
    year: null
  - doi: 10.1093/database/bav043
    pmc: null
    pubmed: null
    title: 'The Confidence Information Ontology: a step towards a standard for asserting
      confidence in annotations'
    year: 2015
  - doi: null
    pmc: null
    pubmed: '25957950'
    title: 'The Confidence Information Ontology: a step towards a standard for asserting
      confidence in annotations'
    year: null
  - doi: 10.1093/database/bav043
    pmc: null
    pubmed: null
    title: 'The Confidence Information Ontology: a step towards a standard for asserting
      confidence in annotations'
    year: 2015
  uri_format: http://purl.obolibrary.org/obo/CIO_$1
citedcat:
  contact:
    email: andrea.perego@jrc.ec.europa.eu
    github: andrea-perego
    name: Andrea Perego
    orcid: 0000-0001-9300-2694
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: A vocabuarly for describing the background and methodology for the
    design of the DataCite profile of DCAT-AP (CiteDCAT-AP), as well as the defined
    mappings.
  download_rdf: https://ec-jrc.github.io/datacite-to-dcat-ap/citedcat-ap.ttl
  example: isSupplementedBy
  homepage: https://ec-jrc.github.io/datacite-to-dcat-ap/
  lov:
    description: CiteDCAT-AP is an extension of the DCAT application profile for data
      portals in Europe (DCAT-AP) for describing resources documented by using the
      DataCite metadata schema - the de facto standard for data citation, and used
      across scientific disciplines. Its basic use case is to make research data searchable
      on general data portals, thereby bridging the gap between scientific and public
      sector information. For this purpose, CiteDCAT-AP provides an RDF vocabulary
      and the corresponding RDF syntax binding for the metadata elements defined in
      DataCite.
    homepage: https://ec-jrc.github.io/datacite-to-dcat-ap/
    keywords:
    - Catalogs
    - Methods
    modified: '2021-03-28'
    name: CiteDCAT-AP Vocabulary
    prefix: citedcat
    uri_prefix: https://w3id.org/citedcat-ap/$1
  mappings:
    lov: citedcat
  name: DataCite to DCAT-AP Mapping
  prefix: citedcat
  rdf_uri_format: https://w3id.org/citedcat-ap/$1
  uri_format: https://w3id.org/citedcat-ap/$1
citexplore:
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: One of the precursors to the EuropePMC project. Now EuropePMC is able
    to resolve CiteXplore codes.
  example: C6155
  fairsharing:
    abbreviation: CTX
    contact:
      email: maria.taboada@usc.es
      name: Maria Taboada
      orcid: 0000-0002-2353-596X
    description: The ontology represents CTX phenotypes, genetic variants, and bidirectional
      relationships between them though a patient model. The CTX ontology was build
      reusing the Human Phenotype Ontology (HPO) and the Snomed ct ontologies. A set
      of temporal clinical manifestations are semantically annotated with a domain
      phenotype ontology and registered with a time-stamped value.
    domains:
    - lipid
    - phenotype
    - disease
    - brain
    homepage: http://bioportal.bioontology.org/ontologies/CTX
    name: Cerebrotendinous Xanthomatosis Ontology
    prefix: FAIRsharing.619eqr
    publications:
    - doi: 10.1097/mol.0b013e328362df13
      pubmed: '23759795'
      title: Cerebrotendinous xanthomatosis
      year: 2013
    subjects:
    - Preclinical Studies
    - Biomedical Science
    - Genetics
  homepage: https://www.ebi.ac.uk/citexplore/
  mappings:
    fairsharing: FAIRsharing.619eqr
    prefixcommons: citexplore
  name: CiteXplore
  prefix: citexplore
  prefixcommons:
    description: PubMed is a service of the U.S. National Library of Medicine that
      includes citations from MEDLINE and other life science journals for biomedical
      articles back to the 1950s.
    example: '16333295'
    homepage: http://www.ebi.ac.uk/citexplore/
    license: http://www.ebi.ac.uk/Information/termsofuse.html
    name: CiteXplore
    pattern: ^\d+$
    prefix: citexplore
    uri_format: http://www.ebi.ac.uk/citexplore/citationDetails.do?dataSource=MED&externalId=$1
  publications:
  - doi: 10.1097/mol.0b013e328362df13
    pmc: null
    pubmed: '23759795'
    title: Cerebrotendinous xanthomatosis
    year: 2013
  references:
  - https://www.embl.de/aboutus/communication_outreach/media_relations/2006/061127_hinxton/
  synonyms:
  - CTX
  uri_format: https://europepmc.org/article/CTX/$1
cito:
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: An ontology that enables characterization of the nature or type of
    citations, both factually and rhetorically.
  download_owl: https://github.com/SPAROntologies/cito/raw/refs/heads/master/docs/current/cito.owl
  example: sharesAuthorInstitutionWith
  fairsharing:
    abbreviation: CiTO
    contact:
      email: silvio.peroni@unibo.it
      name: Silvio Peroni
      orcid: 0000-0003-0530-4305
    description: 'The Citation Typing Ontology (CiTO) is an ontology that enables
      the characterization of the nature or type of citations, both factually and
      rhetorically. It is intended to allow authors (or others) to mark citation links
      and to capture citation intent when someone cites a particular publication.
      In particular, CiTO allows the creation of metadata describing citations that
      are distinct from metadata describing the cited works themselves, and permits
      the motives of an author when referring to another document to be captured.

      '
    homepage: http://www.sparontologies.net/ontologies/cito
    license: CC-BY-4.0
    name: 'Citation Typing Ontology '
    prefix: FAIRsharing.b220d4
    publications:
    - doi: 10.1016/j.websem.2012.08.001
      title: 'FaBiO and CiTO: Ontologies for describing bibliographic resources and
        citations'
      year: 2012
    repository: https://github.com/sparontologies/cito
    subjects:
    - Knowledge and Information Systems
    twitter: sparontologies
  homepage: http://www.sparontologies.net/ontologies/cito
  lov:
    description: The Citation Typing Ontology enables characterization of the nature
      or type of citations
    homepage: http://www.sparontologies.net/ontologies/cito
    keywords:
    - SPAR
    modified: '2018-02-16'
    name: CiTO, the Citation Typing Ontology
    prefix: cito
    uri_prefix: http://purl.org/spar/cito/$1
  mappings:
    fairsharing: FAIRsharing.b220d4
    lov: cito
    tib: cito
  name: Citation Typing Ontology
  preferred_prefix: CiTO
  prefix: cito
  publications:
  - doi: 10.1016/j.websem.2012.08.001
    pmc: null
    pubmed: null
    title: 'FaBiO and CiTO: Ontologies for describing bibliographic resources and
      citations'
    year: 2012
  - doi: 10.1016/j.websem.2012.08.001
    pmc: null
    pubmed: null
    title: 'FaBiO and CiTO: Ontologies for describing bibliographic resources and
      citations'
    year: 2012
  - doi: 10.1016/j.websem.2012.08.001
    pmc: null
    pubmed: null
    title: 'FaBiO and CiTO: Ontologies for describing bibliographic resources and
      citations'
    year: 2012
  repository: https://github.com/sparontologies/cito
  tib:
    description: "CiTO, the Citation Typing Ontology, is an ontology written in OWL\
      \ 2 DL to enable characterization of the nature or type of citations, both factually\
      \ and rhetorically, and to permit these descriptions to be published on the\
      \ Web.  \n\nThe citations characterized may be either direct and explicit (as\
      \ in the reference list of a journal article), indirect (e.g. a citation to\
      \ a more recent paper by the same research group on the same topic), or implicit\
      \ (e.g. as in artistic quotations or parodies, or in cases of plagiarism).\n\
      \nCiTO contains the object property cito:cites and its sub-properties, and its\
      \ inverse property cito:isCitedBy, from the original Citation Typing Ontology,\
      \ CiTO v1.6.  Upon the creation of version 2.0 of CiTO, a number of new sub-properties\
      \ of cito:cites were added, and the inverse properties of all the sub-properties\
      \ of cito:cites were created, all of which are sub-properties of cito:isCitedBy.\
      \  The ontology has also been integrated with the SWAN Discourse Relationships\
      \ Ontology by making cito:cites a sub-property of http://purl.org/swan/2.0/discourse-relationships/refersTo.\n\
      \nRestrictions of domain and range present in the previous version of CiTO were\
      \ removed from the object properties when creating CiTO v 2.0, permitting its\
      \ independent use in other contexts, in addition to conventional bibliographic\
      \ citations.  \n\nSo that they can be used independently, other entities that\
      \ were previously included in CiTO v1.6 have now been made components of other\
      \ SPAR ontologies: FaBiO, the FRBR-aligned Bibliographic Ontology; C4O, the\
      \ Citation Counting and Context Characterization Ontology; and PSO, the Publication\
      \ Status Ontology. \n\nThe addition of two new properties:cito:usesConclusionsFrom\
      \ and its inverse cito:providesConclusionsFor on 09Dec2011 led to a version\
      \ number increment from v2.0 to v2.1.\n\nThe addition of two additional properties,\
      \ cito:compiles and cito:isCompiledBy, previously in the deprecated CiTO4Data\
      \ ontology, on 03 July 2012 led to a version increment from v2.1 to v2.2.\n\n\
      Subsequent expansions include:\n\nin versions 2.3 and 2.4 the addition of the\
      \ object properties cito:citesAsPotentialSolution, cito:citesAsRecommendedReading,\
      \ cito:repliesTo, cito:retracts, cito:speculates on, and their inverse properties;\n\
      \nin v2.5 the addition of cito:CitationAct, cito:hasCitationEvent, cito:hasCitedEntity\
      \ and cito:hasCitingEntity;\n\nin v 2.6: \nrenaming cito:hasCitationEvent to\
      \ become cito:hasCitationCharacterization;\nimproving definitions of cito:CitationAct,\
      \ cito:hasCitationCharacterization, cito:hasCitedEntity and cito:hasCitingEntity;\n\
      revising the definition of cito:isCompiledBy to correct it and bring it into\
      \ line with the DataCite Metadata Kernel v2.2 definition;\nchanging the definition\
      \ of cito:sharesAuthorsWith from 'An object property indicating that the citing\
      \ entity has at least one author in common with the cited entity.' to 'An object\
      \ property between two entities indicating that they have at least one author\
      \ in common.' so that it can be used when one entity does not actually cite\
      \ the other;\nadding the object properties cito:hasRelatedEntity, cito:sharesFundingAgencyWith\
      \ and cito:sharesAuthorInstitutionWith;\nand adding the text 'An object property\
      \ indicating that . . .' at the beginning of the textual definition (rdfs:comment)\
      \ for each CiTO object property.\n\nin v 2.6.1:\nRemoved text 'An object property\
      \ indicating that . . .' added in v 2.6 at the beginning of the textual definition\
      \ (rdfs:comment) for each CiTO object property, so that each definition is just\
      \ a direct statement of the relationship.  \nRemoved the property cito:hasRelatedEntity\
      \ (in favour of using dcterms:relation).\nRenamed cito:hasReply to become cito:hasReplyFrom.\n\
      Improved the textual definitions of cito:derides and its inverse property.\n\
      \nin v 2.6.2:\nImproved definitions of of cito:CitationAct, cito:hasCitationCharacterization,\
      \ cito:hasCitedEntity and cito:hasCitingEntity.\n\nin v 2.6.3:\nAdded examples\
      \ for each citation type (i.e., all the subproperties of cito:cites).\n\nin\
      \ v 2.6.4:\nAdded alignment with schema:citation.\n\nin v 2.7.0:\nAdded new\
      \ property cito:linksTo, and corrected some property URL.\n\nin v 2.7.1\nCorrected\
      \ some typos in property comments.\n\nin v 2.7.2\nThe name of the class cito:CitationAct\
      \ has been changed to cito:Citation, and its definition has been modified. The\
      \ property cito:hasCitationTimeSpan has been added.\n\nin v 2.7.3\nAdded the\
      \ class cito:SelfCitation, i.e. citation in which the citing and the cited entities\
      \ have at least one author in common.\n\nin v 2.8\nRenamed the class cito:SelfCitation\
      \ in cito:AuthorSelfCitation. Created a new class cito:SelfCitation with a more\
      \ general definition (citation in which the citing and the cited entities have\
      \ something significant in common with one another), which now includes five\
      \ subclasses: cito:AuthorSelfCitation, cito:JournalSelfCitation, cito:FunderSelfCitation,\
      \ cito:AffiliationSelfCitation, cito:AuthorNetworkSelfCitation. The latter class\
      \ is also accompanied by the new data property cito:hasCoAuthorCitationLevel,\
      \ which specifies the minimal distance that one of the authors of a citing entity\
      \ has with regards to one of the authors of a cited entity according to their\
      \ co-author network. Added the object properties cito:sharesPublicationVenueWith\
      \ and its subproperty cito:sharesJournalWith. Added the data property cito:hasCitationCreationDate,\
      \ and changed the domain of cito:hasCitationTimeSpan with xsd:duration.\n\n\
      in v 2.8.1\nRenamed the property cito:hasCoAuthorCitationLevel in cito:hasCoAuthorshipCitationLevel."
    homepage: http://www.sparontologies.net/ontologies/cito
    keywords:
    - TIB
    name: CiTO, the Citation Typing Ontology
    prefix: cito
    tracker: https://github.com/SPAROntologies/cito/issues
    uri_format: http://purl.org/spar/cito/$1
    version.iri: http://purl.org/spar/cito/2018-02-16
  uri_format: http://purl.org/spar/cito/$1
civic.aid:
  contact:
    email: mgriffit@wustl.edu
    github: malachig
    name: Malachi Griffith
    orcid: 0000-0002-6388-446X
  license: CC0-1.0
  logo: https://civic.readthedocs.io/en/latest/_images/CIViC_logo_for-light-bg_LG_v5a1.png
  mappings:
    miriam: civic.aid
  miriam:
    deprecated: false
    description: 'A CIViC assertion classifies the clinical significance of a variant-disease
      relationship under recognized guidelines. The CIViC Assertion (AID) summarizes
      a collection of Evidence Items (EIDs) that covers predictive/therapeutic, diagnostic,
      prognostic or predisposing clinical information for a variant in a specific
      cancer context. CIViC currently has two main types of Assertions: those based
      on variants of primarily somatic origin (predictive/therapeutic, prognostic,
      and diagnostic) and those based on variants of primarily germline origin (predisposing).
      When the number and quality of Predictive, Prognostic, Diagnostic or Predisposing
      Evidence Items (EIDs) in CIViC sufficiently cover what is known for a particular
      variant and cancer type, then a corresponding assertion be created in CIViC.'
    homepage: https://civicdb.org/
    id: 00000835
    name: CIViC Assertion
    namespaceEmbeddedInLui: false
    pattern: ^[0-9]+$
    prefix: civic.aid
    sampleId: '3'
    uri_format: https://civicdb.org/links/assertions/$1
  part_of_database: civic
  prefix: civic.aid
  synonyms:
  - civic.assertion
civic.did:
  contact:
    email: mgriffit@wustl.edu
    github: malachig
    name: Malachi Griffith
    orcid: 0000-0002-6388-446X
  license: CC0-1.0
  logo: https://civic.readthedocs.io/en/latest/_images/CIViC_logo_for-light-bg_LG_v5a1.png
  mappings:
    miriam: civic.did
  miriam:
    deprecated: false
    description: Within the CIViC database, the disease should be the cancer or cancer
      subtype that is a result of the described variant. The disease selected should
      be as specific as possible should reflect the disease type used in the source
      that supports the evidence statement.
    homepage: https://civicdb.org/
    id: 00000957
    name: CIViC Disease
    namespaceEmbeddedInLui: false
    pattern: ^[0-9]+$
    prefix: civic.did
    sampleId: '46'
    uri_format: https://civicdb.org/links/diseases/$1
  part_of_database: civic
  prefix: civic.did
  synonyms:
  - civic.disease
civic.eid:
  contact:
    email: mgriffit@wustl.edu
    github: malachig
    name: Malachi Griffith
    orcid: 0000-0002-6388-446X
  license: CC0-1.0
  logo: https://civic.readthedocs.io/en/latest/_images/CIViC_logo_for-light-bg_LG_v5a1.png
  mappings:
    miriam: civic.eid
  miriam:
    deprecated: false
    description: Evidence Items are the central building block of the Clinical Interpretation
      of Variants in Cancer (CIViC) knowledgebase. The clinical Evidence Item is a
      piece of information that has been manually curated from trustable medical literature
      about a Variant or genomic ‘event’ that has implications in cancer Predisposition,
      Diagnosis (aka molecular classification), Prognosis, Predictive response to
      therapy, Oncogenicity or protein Function. For example, an Evidence Item might
      describe a line of evidence supporting the notion that tumors with a somatic
      BRAF V600 mutation generally respond well to the drug dabrafenib. A Variant
      may be a single nucleotide substitution, a small insertion or deletion, an RNA
      gene fusion, a chromosomal rearrangement, an RNA expression pattern (e.g. over-expression),
      etc. Each clinical Evidence statement corresponds to a single citable Source
      (a publication or conference abstract).
    homepage: https://civicdb.org/
    id: 00000839
    name: CIViC Evidence
    namespaceEmbeddedInLui: false
    pattern: ^[0-9]+$
    prefix: civic.eid
    sampleId: '1199'
    uri_format: https://civicdb.org/links/evidence/$1
  part_of_database: civic
  prefix: civic.eid
  synonyms:
  - civic.evidence
civic.gid:
  contact:
    email: mgriffit@wustl.edu
    github: malachig
    name: Malachi Griffith
    orcid: 0000-0002-6388-446X
  contact_group_email: help@civicdb.org
  domain: gene
  keywords:
  - gene
  license: CC0-1.0
  logo: https://civic.readthedocs.io/en/latest/_images/CIViC_logo_for-light-bg_LG_v5a1.png
  mappings:
    miriam: civic.gid
    wikidata: P11277
  miriam:
    deprecated: false
    description: A CIViC Gene Summary is created to provide a high-level overview
      of clinical relevance of cancer variants for the gene. Gene Summaries in CIViC
      focus on emphasizing the clinical relevance from a molecular perspective rather
      than describing the biological function of the gene unless necessary to contextualize
      its clinical relevance in cancer. Gene Summaries include relevant cancer subtypes,
      specific treatments for the gene’s associated variants, pathway interactions,
      functional alterations caused by the variants in the gene, and normal/abnormal
      functions of the gene with associated roles in oncogenesis
    homepage: https://civicdb.org/
    id: 00000907
    name: CIViC Gene
    namespaceEmbeddedInLui: false
    pattern: ^[0-9]+$
    prefix: civic.gid
    sampleId: '272'
    uri_format: https://civicdb.org/links/gene/$1
  name: CIViC gene
  part_of_database: civic
  prefix: civic.gid
  synonyms:
  - civic.gene
  wikidata:
    description: identifier for a human gene in the CIViC database
    example:
    - '1134'
    - '14221'
    - '2'
    - '3'
    - '4'
    homepage: https://civic.genome.wustl.edu/#/home
    name: CIViC gene ID
    pattern: ^[1-9]\d*$
    prefix: P11277
    uri_format: https://civicdb.org/genes/$1/summary
civic.mpid:
  contact:
    email: mgriffit@wustl.edu
    github: malachig
    name: Malachi Griffith
    orcid: 0000-0002-6388-446X
  contact_group_email: help@civicdb.org
  license: CC0-1.0
  logo: https://civic.readthedocs.io/en/latest/_images/CIViC_logo_for-light-bg_LG_v5a1.png
  mappings:
    miriam: civic.mpid
  miriam:
    deprecated: false
    description: CIViC Molecular Profiles are combinations of one or more CIViC variants.
      Most Molecular Profiles are “Simple” Molecular Profiles comprised of a single
      variant. In most cases, these can be considered equivalent to the CIViC concept
      of a Variant. However, increasingly clinical significance must be considered
      in the context of multiple variants simultaneously. Complex Molecular Profiles
      in CIViC allow for curation of such variant combinations. Regardless of the
      nature of the Molecular Profile (Simple or Complex), it must have a Predictive,
      Prognostic, Predisposing, Diagnostic, Oncogenic, or Functional clinical relevance
      to be entered in CIViC.
    homepage: https://civicdb.org/
    id: 00000981
    name: CIViC Molecular Profile
    namespaceEmbeddedInLui: false
    pattern: ^[0-9]+$
    prefix: civic.mpid
    sampleId: '559'
    uri_format: https://civicdb.org/links/molecular_profile/$1
  prefix: civic.mpid
  synonyms:
  - civic.molecularprofile
civic.sid:
  contact:
    email: mgriffit@wustl.edu
    github: malachig
    name: Malachi Griffith
    orcid: 0000-0002-6388-446X
  license: CC0-1.0
  logo: https://civic.readthedocs.io/en/latest/_images/CIViC_logo_for-light-bg_LG_v5a1.png
  mappings:
    miriam: civic.sid
  miriam:
    deprecated: false
    description: In CIViC, each Evidence Item must be associated with a Source Type
      and Source ID, which link the Evidence Item to the original source of information
      supporting clinical claims. Currently, CIViC accepts publications indexed on
      PubMed OR abstracts published through the American Society of Clinical Oncology
      (ASCO). Each such source entered into CIViC is assigned a unique identifier
      and expert curators can curate guidance that assists future curators in the
      interpretation of information from this source.
    homepage: https://civicdb.org/
    id: 00000953
    name: CIViC Source
    namespaceEmbeddedInLui: false
    pattern: ^[0-9]+$
    prefix: civic.sid
    sampleId: '62'
    uri_format: https://civicdb.org/links/sources/$1
  part_of_database: civic
  prefix: civic.sid
  synonyms:
  - civic.source
civic.tid:
  contact:
    email: mgriffit@wustl.edu
    github: malachig
    name: Malachi Griffith
    orcid: 0000-0002-6388-446X
  contact_group_email: help@civicdb.org
  license: CC0-1.0
  logo: https://civic.readthedocs.io/en/latest/_images/CIViC_logo_for-light-bg_LG_v5a1.png
  mappings:
    miriam: civic.tid
  miriam:
    deprecated: false
    description: Therapies (often drugs) in CIViC are associated with Predictive Evidence
      Types, which describe sensitivity, resistance or adverse response to therapies
      when a given variant is present. The Therapy field may also be used to describe
      more general treatment types and regimes, such as FOLFOX or Radiation, as long
      as the literature derived Evidence Item makes a scientific association between
      the Therapy (treatment type) and the presence of the variant.
    homepage: https://civicdb.org/
    id: 00000955
    name: CIViC Therapy
    namespaceEmbeddedInLui: false
    pattern: ^[0-9]+$
    prefix: civic.tid
    sampleId: '14'
    uri_format: https://civicdb.org/links/drugs/$1
  part_of_database: civic
  prefix: civic.tid
  synonyms:
  - civic.therapy
civic.vgid:
  contact:
    email: mgriffit@wustl.edu
    github: malachig
    name: Malachi Griffith
    orcid: 0000-0002-6388-446X
  contact_group_email: help@civicdb.org
  license: CC0-1.0
  logo: https://civic.readthedocs.io/en/latest/_images/CIViC_logo_for-light-bg_LG_v5a1.png
  mappings:
    miriam: civic.vgid
  miriam:
    deprecated: false
    description: Variant Groups in CIViC provide user-defined grouping of Variants
      within and between genes based on unifying characteristics. CIViC curators are
      required to define a cohesive rationale for grouping these variants together,
      summarize their relevance to cancer diagnosis, prognosis or treatment and highlight
      any treatments or cancers of particular relevance
    homepage: https://civicdb.org/
    id: 00000979
    name: CIViC Variant Group
    namespaceEmbeddedInLui: false
    pattern: ^[0-9]+$
    prefix: civic.vgid
    sampleId: '16'
    uri_format: https://civicdb.org/links/variant_group/$1
  prefix: civic.vgid
  synonyms:
  - civic.variantgroup
civic.vid:
  contact:
    email: mgriffit@wustl.edu
    github: malachig
    name: Malachi Griffith
    orcid: 0000-0002-6388-446X
  contact_group_email: help@civicdb.org
  license: CC0-1.0
  logo: https://civic.readthedocs.io/en/latest/_images/CIViC_logo_for-light-bg_LG_v5a1.png
  mappings:
    miriam: civic.vid
    wikidata: P3329
  miriam:
    deprecated: false
    description: CIViC variants are usually genomic alterations, including single
      nucleotide variants (SNVs), insertion/deletion events (indels), copy number
      alterations (CNV’s such as amplification or deletion), structural variants (SVs
      such as translocations and inversions), and other events that differ from the
      “normal” genome. In some cases a CIViC variant may represent events of the transcriptome
      or proteome. For example, ‘expression’ or ‘over-expression’ is a valid variant.
      Regardless of the variant, it must have a Predictive, Prognostic, Predisposing,
      Diagnostic, Oncogenic, or Functional relevance that is clinical in nature to
      be entered in CIViC. i.e. There must be some rationale for why curation of this
      variant could ultimately aid clinical decision making.
    homepage: https://civicdb.org/
    id: 00000909
    name: CIViC Variant
    namespaceEmbeddedInLui: false
    pattern: ^[0-9]+$
    prefix: civic.vid
    sampleId: '12'
    uri_format: https://civicdb.org/links/variant/$1
  name: CIViC variant
  part_of_database: civic
  prefix: civic.vid
  synonyms:
  - civic.variant
  wikidata:
    description: identifier used in the CIViC database to identify specific variant
    example:
    - '12'
    - '2416'
    - '2979'
    homepage: https://civic.genome.wustl.edu/#/home
    name: CIViC variant ID
    pattern: ^[1-9]\d*$
    prefix: P3329
    uri_format: https://civicdb.org/molecular-profiles/$1
cl:
  aberowl:
    description: The Cell Ontology is a structured controlled vocabulary for cell
      types in animals.
    download_owl: http://aber-owl.net/media/ontologies/CL/117/cl.owl
    homepage: https://obophenotype.github.io/cell-ontology/
    name: Cell Ontology
    prefix: CL
  agroportal:
    contact:
      email: addiehl@buffalo.edu
      name: Alex Diehl
    description: An ontology of cell types.
    example_uri: http://purl.obolibrary.org/obo/CL_0000000
    homepage: https://cell-ontology.github.io/
    license: CC-BY-4.0
    name: Cell Ontology
    prefix: CL
    repository: https://github.com/obophenotype/cell-ontology
    version: '2025-12-17'
  biocontext:
    prefix: CL
  bioportal:
    contact:
      email: addiehl@buffalo.edu
      name: Alexander Diehl
    description: The Cell Ontology is a structured controlled vocabulary for cell
      types in animals. The Cell Ontology is designed as a structured controlled vocabulary
      for cell types. This ontology was constructed for use by the model organism
      and other bioinformatics databases, where there is a need for a controlled vocabulary
      of cell types. This ontology is not organism specific. It covers cell types
      from prokaryotes to mammals. However, it excludes plant cell types, which are
      covered by PO. , An ontology of cell types.
    homepage: https://obophenotype.github.io/cell-ontology/
    license: CC-BY-4.0
    name: Cell Ontology
    prefix: CL
    publications:
    - https://www.ncbi.nlm.nih.gov/pubmed/27377652
    version: '2025-11-25'
  cellosaurus:
    category: Anatomy/cell type resources
    homepage: https://obophenotype.github.io/cell-ontology/
    name: Cell Ontology
    prefix: CL
  contributor_extras:
  - email: null
    github: anitacaron
    name: Anita Caron
    orcid: 0000-0002-6523-4866
  download_obo: https://github.com/obophenotype/cell-ontology/raw/master/cl.obo
  example: '0000062'
  fairsharing:
    abbreviation: CL
    contact:
      email: addiehl@buffalo.edu
      name: Alexander Diehl
      orcid: 0000-0001-9990-8331
    description: The Cell Ontology (CL) is a candidate OBO Foundry ontology for the
      representation of cell types. First described in 2005, the CL integrates cell
      types from the prokaryotic, fungal, and eukaryotic organisms. As a core component
      of the OBO Foundry, the CL merges information contained in species-specific
      anatomical ontologies as well as referencing other OBO Foundry ontologies such
      as the Protein Ontology (PR) for uniquely expressed biomarkers and the Gene
      Ontology (GO) for the biological processes a cell type participates in. The
      CL is under continuous revision to expand representation of cell types and to
      better integrate with other biomedical ontologies.
    domains:
    - Annotation
    - cell
    - morphology
    homepage: https://github.com/obophenotype/cell-ontology
    license: CC-BY-3.0
    name: Cell Ontology
    prefix: FAIRsharing.j9y503
    publications:
    - doi: 10.1186/1471-2105-12-6
      pubmed: '21208450'
      title: Logical development of the cell ontology
      year: 2011
    - doi: 10.1186/s13326-016-0088-7
      pubmed: '27377652'
      title: 'The Cell Ontology 2016: enhanced content, modularization, and ontology
        interoperability'
      year: 2016
    repository: https://github.com/obophenotype/cell-ontology/issues
    subjects:
    - Life Science
    - Anatomy
    - Omics
    - Immunogenetics
    - Cell Biology
    - Immunology
  go:
    homepage: http://cellontology.org
    name: Cell Type Ontology
    prefix: CL
  mappings:
    aberowl: CL
    agroportal: CL
    biocontext: CL
    bioportal: CL
    cellosaurus: CL
    fairsharing: FAIRsharing.j9y503
    go: CL
    miriam: cl
    n2t: cl
    obofoundry: cl
    ols: cl
    ontobee: CL
    prefixcommons: cl
    wikidata: P7963
    wikidata.entity: Q55118285
  miriam:
    deprecated: false
    description: The Cell Ontology is designed as a structured controlled vocabulary
      for cell types. The ontology was constructed for use by the model organism and
      other bioinformatics databases, incorporating cell types from prokaryotes to
      mammals, and includes plants and fungi.
    homepage: http://bioportal.bioontology.org/ontologies/CL
    id: '00000110'
    name: Cell Type Ontology
    namespaceEmbeddedInLui: true
    pattern: ^CL:\d{7}$
    prefix: cl
    sampleId: '0000232'
    uri_format: http://purl.bioontology.org/ontology/CL/CL:$1
  n2t:
    description: The Cell Ontology is designed as a structured controlled vocabulary
      for cell types. The ontology was constructed for use by the model organism and
      other bioinformatics databases, incorporating cell types from prokaryotes to
      mammals, and includes plants and fungi.
    example: '0000232'
    homepage: http://bioportal.bioontology.org/ontologies/CL
    name: Cell Type Ontology through BioPortal
    namespaceEmbeddedInLui: true
    pattern: ^CL:\d{7}$
    prefix: cl
    uri_format: http://purl.bioontology.org/ontology/CL/CL:$1
  obofoundry:
    appears_in:
    - clo
    - ecao
    - go
    - mco
    - pcl
    - uberon
    - xpo
    - ehdaa2
    contact: do12@sanger.ac.uk
    contact.github: dosumis
    contact.label: David Osumi-Sutherland
    contact.orcid: 0000-0002-7073-9172
    depends_on:
    - go
    - ncbitaxon
    - omo
    - pato
    - pr
    - ro
    - uberon
    deprecated: false
    description: The Cell Ontology is a structured controlled vocabulary for cell
      types in animals.
    domain: anatomy and development
    download.json: http://purl.obolibrary.org/obo/cl.json
    download.obo: http://purl.obolibrary.org/obo/cl.obo
    download.owl: http://purl.obolibrary.org/obo/cl.owl
    homepage: https://obophenotype.github.io/cell-ontology/
    license: CC BY 4.0
    license.url: http://creativecommons.org/licenses/by/4.0/
    logo: https://obofoundry.org/images/CL-logo.jpg
    name: Cell Ontology
    preferredPrefix: CL
    prefix: cl
    publications:
    - id: https://www.ncbi.nlm.nih.gov/pubmed/27377652
      title: 'The Cell Ontology 2016: enhanced content, modularization, and ontology
        interoperability.'
    repository: https://github.com/obophenotype/cell-ontology
    twitter: CellOntology
  ols:
    description: An ontology of cell types.
    download_owl: http://purl.obolibrary.org/obo/cl.owl
    homepage: https://obophenotype.github.io/cell-ontology/
    name: Cell Ontology
    prefix: cl
    tracker: https://github.com/obophenotype/cell-ontology/issues
    version: '2025-12-17'
    version.iri: http://purl.obolibrary.org/obo/cl/releases/2025-12-17/cl.owl
  ontobee:
    library: Library
    name: Cell Ontology
    prefix: CL
  pattern: ^\d{7}$
  prefix: cl
  prefixcommons:
    bioportal: '1006'
    description: The Cell Ontology is designed as a structured controlled vocabulary
      for cell types. The ontology was constructed for use by the model organism and
      other bioinformatics databases, incorporating cell types from prokaryotes to
      mammals, and includes plants and fungi.
    example: CL:0000232
    homepage: http://lists.sourceforge.net/lists/listinfo/obo-cell-type
    keywords:
    - obo
    - cell
    name: Cell Ontology
    pattern: ^CL:\d+$
    prefix: cl
  providers:
  - code: cellguide
    description: CellGuide is a comprehensive resource for knowledge about cell types.
    example: null
    first_party: null
    homepage: https://cellxgene.cziscience.com/cellguide
    name: Cell Guide
    publications: null
    status: null
    uri_format: https://cellxgene.cziscience.com/cellguide/CL_$1
  publications:
  - doi: 10.1186/s13326-016-0088-7
    pmc: PMC4932724
    pubmed: '27377652'
    title: 'The Cell Ontology 2016: enhanced content, modularization, and ontology
      interoperability'
    year: 2016
  - doi: 10.1186/1471-2105-12-6
    pmc: PMC3024222
    pubmed: '21208450'
    title: Logical development of the cell ontology
    year: 2011
  - doi: null
    pmc: null
    pubmed: '27377652'
    title: 'The Cell Ontology 2016: enhanced content, modularization, and ontology
      interoperability'
    year: null
  - doi: 10.1186/1471-2105-12-6
    pmc: null
    pubmed: '21208450'
    title: Logical development of the cell ontology
    year: 2011
  - doi: 10.1186/s13326-016-0088-7
    pmc: null
    pubmed: '27377652'
    title: 'The Cell Ontology 2016: enhanced content, modularization, and ontology
      interoperability'
    year: 2016
  uri_format: http://purl.obolibrary.org/obo/CL_$1
  wikidata:
    description: ID in the Cell Ontology
    example:
    - CL_0000148
    - CL_0000232
    - CL_0000235
    - CL_0000540
    - CL_0002328
    homepage: https://github.com/obophenotype/cell-ontology
    miriam: cl
    name: Cell Ontology ID
    pattern: ^CL_[0-9]{7}$
    prefix: P7963
clao:
  aberowl:
    description: 'CLAO is an ontology of anatomical terms employed in morphological
      descriptions for the Class Collembola (Arthropoda: Hexapoda).'
    download_owl: http://aber-owl.net/media/ontologies/CLAO/2/clao.owl
    homepage: https://github.com/luis-gonzalez-m/Collembola
    name: Collembola Anatomy Ontology
    prefix: CLAO
  bioportal:
    contact:
      email: lagonzalezmo@unal.edu.co
      name: Luis A. González-Montaña
    description: Collembola Anatomy Ontology (CLAO) includes anatomical terms to refer
      to sclerites, anatomical systems, cell components, and chaetotaxy. CLAO is directed
      towards building semantic annotations or the production of morphological data
      employing a standardized language. CLAO is intended as a complementary tool
      to morhological descriptions during taxonomic work, before obtaining phylogenetic
      characters.
    homepage: http://github/luis-gonzalez-m
    name: Collembola Anatomy Ontology
    prefix: CLAO
    version: '2021-09-27'
  example: 0000088
  mappings:
    aberowl: CLAO
    bioportal: CLAO
    obofoundry: clao
    ols: clao
    ontobee: CLAO
    wikidata.entity: Q111274067
  obofoundry:
    contact: lagonzalezmo@unal.edu.co
    contact.github: luis-gonzalez-m
    contact.label: Luis González-Montaña
    contact.orcid: 0000-0002-9136-9932
    depends_on:
    - ro
    deprecated: false
    description: 'CLAO is an ontology of anatomical terms employed in morphological
      descriptions for the Class Collembola (Arthropoda: Hexapoda).'
    domain: anatomy and development
    download.obo: http://purl.obolibrary.org/obo/clao.obo
    download.owl: http://purl.obolibrary.org/obo/clao.owl
    homepage: https://github.com/luis-gonzalez-m/Collembola
    license: CC0 1.0
    license.url: http://creativecommons.org/publicdomain/zero/1.0/
    name: Collembola Anatomy Ontology
    preferredPrefix: CLAO
    prefix: clao
    repository: https://github.com/luis-gonzalez-m/Collembola
  ols:
    description: 'CLAO is an ontology of anatomical terms employed in morphological
      descriptions for the Class Collembola (Arthropoda: Hexapoda).'
    download_owl: http://purl.obolibrary.org/obo/clao.owl
    homepage: https://github.com/luis-gonzalez-m/Collembola
    name: Collembola Anatomy Ontology
    prefix: clao
    tracker: https://github.com/luis-gonzalez-m/Collembola/issues
    version: '2021-09-27'
    version.iri: http://purl.obolibrary.org/obo/clao/releases/2021-09-27/clao.owl
  ontobee:
    library: Library
    name: Collembola Anatomy Ontology
    prefix: CLAO
  pattern: ^\d{7}$
  prefix: clao
  uri_format: http://purl.obolibrary.org/obo/CLAO_$1
clarin.clavas:
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: Representation of languages
  example: CDB-00133756-001
  homepage: https://vocabularies.clarin.eu/clavas/ISO639-3/en/
  keywords:
  - language
  name: 'CLAVAS: ISO 639-3 Language Codes'
  prefix: clarin.clavas
  uri_format: http://cdb.iso.org/lg/$1
clarin.concept:
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: Concepts for encoding bibliometric information
  example: CCR_C-3784_55fa12c9-35ad-7b55-b7a5-f9926c801952
  homepage: https://vocabularies.clarin.eu/clavas/ccr/en/
  name: CLARIN Concept Registry
  prefix: clarin.concept
  uri_format: http://hdl.handle.net/11459/$1
classyfire:
  banana: C
  comment: There's a mismatch between the MIRIAM URI format string, which has a C
    prefix in front of class identifiers and the ontology which does not use them.
  download_obo: http://classyfire.wishartlab.com/system/downloads/1_0/chemont/ChemOnt_2_1.obo.zip
  example: 0004828
  mappings:
    miriam: classyfire
  miriam:
    deprecated: false
    description: ClassyFire is a web-based application for automated structural classification
      of chemical entities. This application uses a rule-based approach that relies
      on a comprehensible, comprehensive, and computable chemical taxonomy. ClassyFire
      provides a hierarchical chemical classification of chemical entities (mostly
      small molecules and short peptide sequences), as well as a structure-based textual
      description, based on a chemical taxonomy named ChemOnt, which covers 4825 chemical
      classes of organic and inorganic compounds. Moreover, ClassyFire allows for
      text-based search via its web interface. It can be accessed via the web interface
      or via the ClassyFire API.
    homepage: http://classyfire.wishartlab.com/
    id: '00000770'
    name: ClassyFire
    namespaceEmbeddedInLui: false
    pattern: ^C[0-9]{7}$
    prefix: classyfire
    sampleId: C0004828
    uri_format: http://classyfire.wishartlab.com/tax_nodes/$1
  pattern: ^\d{7}$
  prefix: classyfire
  synonyms:
  - CHEMONTID
  - chemont
  uri_format: http://classyfire.wishartlab.com/tax_nodes/C$1
clb:
  mappings:
    miriam: clb
  miriam:
    deprecated: false
    description: ChecklistBank is an index and repository for taxonomic and nomenclatural
      datasets
    homepage: https://www.checklistbank.org
    id: 00000964
    name: ChecklistBank
    namespaceEmbeddedInLui: false
    pattern: ^[0-9]+(LR)?$
    prefix: clb
    sampleId: '1010'
    uri_format: https://www.checklistbank.org/dataset/$1
  prefix: clb
cldb:
  biocontext:
    prefix: CLDB
  cellosaurus:
    category: Cell line databases/resources
    homepage: https://bioinformatics.hsanmartino.it/hypercldb/
    name: Cell Line Data Base
    prefix: CLDB
    uri_format: https://bioinformatics.hsanmartino.it/hypercldb/$1.html
  mappings:
    biocontext: CLDB
    cellosaurus: CLDB
    miriam: cldb
    n2t: cldb
  miriam:
    deprecated: false
    description: The Cell Line Data Base (CLDB) is a reference information source
      for human and animal cell lines. It provides the characteristics of the cell
      lines and their availability through  distributors, allowing cell line requests
      to be made from collections and laboratories.
    homepage: http://bioinformatics.hsanmartino.it/hypercldb/indexes.html
    id: 00000390
    name: CLDB
    namespaceEmbeddedInLui: false
    pattern: ^(cl|tum)\d+$
    prefix: cldb
    sampleId: cl3603
    uri_format: http://bioinformatics.hsanmartino.it/hypercldb/$1.html
  n2t:
    description: The Cell Line Data Base (CLDB) is a reference information source
      for human and animal cell lines. It provides the characteristics of the cell
      lines and their availability through  distributors, allowing cell line requests
      to be made from collections and laboratories.
    example: cl3603
    homepage: http://bioinformatics.hsanmartino.it/hypercldb/indexes.html
    name: CLDB at Genova
    namespaceEmbeddedInLui: false
    pattern: ^(cl|tum)\d+$
    prefix: cldb
    uri_format: http://bioinformatics.hsanmartino.it/hypercldb/$1.html
  name: Cell Line Database
  prefix: cldb
  synonyms:
  - hypercldb
clingen.affiliation:
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: ClinGen is a National Institutes of Health (NIH)-funded resource that
    defines the clinical relevance of genes and variants for use in precision medicine
    and research. This prefix provides identifiers for a panel of experts performing
    variant pathogenecity evaluation.
  example: '40135'
  github_request_issue: 1314
  homepage: https://clinicalgenome.org/affiliation
  name: ClinGen Clinical Genome Expert Panel
  prefix: clingen.affiliation
  uri_format: https://clinicalgenome.org/affiliation/$1/
clingen.allele:
  biolink:
    is_identifiers: false
    is_obo: false
    prefix: CAID
    uri_format: http://reg.clinicalgenome.org/redmine/projects/registry/genboree_registry/by_caid?caid=$1
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  contributor_extras:
  - email: smoxon@lbl.gov
    github: sierra-moxon
    name: Sierra Moxon
    orcid: 0000-0002-8719-7760
  description: ClinGen is a National Institutes of Health (NIH)-funded resource that
    defines the clinical relevance of genes and variants for use in precision medicine
    and research. This prefix provides and maintains identifiers for alleles.
  example: CA981206459
  homepage: https://reg.clinicalgenome.org
  keywords:
  - alleles
  - genetics
  - mutations
  mappings:
    biolink: CAID
  name: ClinGen Allele Registry
  pattern: ^CA\d+$
  prefix: clingen.allele
  references:
  - https://github.com/biopragmatics/bioregistry/issues/647
  synonyms:
  - CAID
  - clingene
  uri_format: https://reg.clinicalgenome.org/redmine/projects/registry/genboree_registry/by_caid?caid=$1
clingen.curation:
  banana: CCID
  banana_peel: ':'
  contributor:
    email: m.naguthana@hotmail.com
    github: nagutm
    name: Mufaddal Naguthanawala
    orcid: 0009-0009-5240-7463
  description: ClinGen is a National Institutes of Health (NIH)-funded resource that
    defines the clinical relevance of genes and variants for use in precision medicine
    and research. This prefix provides identifiers for curations representing evidence
    aggregation and expert panel assertions based on standardized evaluation procedures
  example: '004126'
  github_request_issue: 1414
  homepage: https://search.clinicalgenome.org/kb/gene-validity
  name: ClinGen Curation
  pattern: ^\d{6}$
  prefix: clingen.curation
  reviewer:
    email: b.gyori@northeastern.edu
    github: bgyori
    name: Benjamin M. Gyori
    orcid: 0000-0001-9439-5346
  uri_format: https://search.clinicalgenome.org/CCID:$1
clinicaltrials:
  biocontext:
    prefix: CLINICALTRIALS
  contact:
    email: register@clinicaltrials.gov
    github: null
    name: ClinicalTrials.gov Helpdesk
    orcid: null
  domain: clinical trial
  license: https://clinicaltrials.gov/about-site/terms-conditions#availability
  logo: https://clinicaltrials.gov/assets/images/ctg-header-logo.svg
  mappings:
    biocontext: CLINICALTRIALS
    miriam: clinicaltrials
    n2t: clinicaltrials
    prefixcommons: clinicaltrials
    wikidata: P3098
  miriam:
    deprecated: false
    description: ClinicalTrials.gov provides free access to information on clinical
      studies for a wide range of diseases and conditions. Studies listed in the database
      are conducted in 175 countries
    homepage: https://clinicaltrials.gov/
    id: '00000137'
    name: ClinicalTrials.gov
    namespaceEmbeddedInLui: false
    pattern: ^NCT\d{8}$
    prefix: clinicaltrials
    sampleId: NCT00222573
    uri_format: https://clinicaltrials.gov/ct2/show/$1
  n2t:
    description: ClinicalTrials.gov provides free access to information on clinical
      studies for a wide range of diseases and conditions. Studies listed in the database
      are conducted in 175 countries
    example: NCT00222573
    homepage: https://clinicaltrials.gov/
    name: ClinicalTrials.gov at NIH
    namespaceEmbeddedInLui: false
    pattern: ^NCT\d{8}$
    prefix: clinicaltrials
    uri_format: https://clinicaltrials.gov/ct2/show/$1
  name: ClinicalTrials.gov
  prefix: clinicaltrials
  prefixcommons:
    description: ClinicalTrials.gov is a registry and results database of publicly
      and privately supported clinical studies of human participants conducted around
      the world.
    example: NCT00050895
    homepage: http://clinicaltrials.gov/
    keywords:
    - disease
    - drug
    - human
    license: http://www.nlm.nih.gov/copyright.html
    name: ClinicalTrials.gov
    pattern: ^NCT\d{8}$
    prefix: clinicaltrials
    uri_format: http://clinicaltrials.gov/ct2/show/$1
  providers:
  - code: smartpatients
    description: Smart Patients is an online community for patients and their families.
      Join us to talk with other patients about the latest research for your condition.
    example: null
    first_party: null
    homepage: https://www.smartpatients.com
    name: Smart Patients
    publications: null
    status: null
    uri_format: https://www.smartpatients.com/trials/$1
  synonyms:
  - NCT
  - clinicaltrial
  - ctgov
  uri_format: https://www.clinicaltrials.gov/study/$1
  wikidata:
    description: identifier in the ClinicalTrials.gov database
    example:
    - NCT00243178
    - NCT04315948
    name: ClinicalTrials.gov ID
    pattern: ^NCT(\d{8})$
    prefix: P3098
    uri_format: https://clinicaltrials.gov/show/$1
clinvar.record:
  biocontext:
    prefix: CLINVAR.RECORD
  mappings:
    biocontext: CLINVAR.RECORD
    miriam: clinvar.record
    n2t: clinvar.record
  miriam:
    deprecated: false
    description: ClinVar archives reports of relationships among medically important
      variants and phenotypes. It records human variation, interpretations of the
      relationship specific variations to human health, and supporting evidence for
      each interpretation. Each ClinVar record (RCV identifier) represents an aggregated
      view of interpretations of  the same variation and condition from one or more
      submitters. Submissions for individual variation/phenotype combinations (SCV
      identifier) are also collected and made available separately. This collection
      references the Record Report, based on RCV accession.
    homepage: http://www.ncbi.nlm.nih.gov/clinvar/
    id: '00000534'
    name: ClinVar Record
    namespaceEmbeddedInLui: false
    pattern: ^RCV\d+(\.\d+)?$
    prefix: clinvar.record
    sampleId: RCV000033555.3
    uri_format: http://www.ncbi.nlm.nih.gov/clinvar/$1/
  n2t:
    description: ClinVar archives reports of relationships among medically important
      variants and phenotypes. It records human variation, interpretations of the
      relationship specific variations to human health, and supporting evidence for
      each interpretation. Each ClinVar record (RCV identifier) represents an aggregated
      view of interpretations of  the same variation and condition from one or more
      submitters. Submissions for individual variation/phenotype combinations (SCV
      identifier) are also collected and made available separately. This collection
      references the Record Report, based on RCV accession.
    example: RCV000033555.3
    homepage: http://www.ncbi.nlm.nih.gov/clinvar/
    name: ClinVar Record at NCBI
    namespaceEmbeddedInLui: false
    pattern: ^RCV\d+(\.\d+)?$
    prefix: clinvar.record
    uri_format: http://www.ncbi.nlm.nih.gov/clinvar/$1/
  part_of_database: clinvar
  prefix: clinvar.record
  uri_format: http://www.ncbi.nlm.nih.gov/clinvar/$1
clinvar.submission:
  biocontext:
    prefix: CLINVAR.SUBMISSION
  mappings:
    biocontext: CLINVAR.SUBMISSION
    miriam: clinvar.submission
    n2t: clinvar.submission
  miriam:
    deprecated: false
    description: ClinVar archives reports of relationships among medically important
      variants and phenotypes. It records human variation, interpretations of the
      relationship specific variations to human health, and supporting evidence for
      each interpretation. Each ClinVar record (RCV identifier) represents an aggregated
      view of interpretations of the same variation and condition from one or more
      submitters. Submissions for individual variation/phenotype combinations (SCV
      identifier) are also collected and made available separately. This collection
      references submissions, and is based on SCV accession.
    homepage: http://www.ncbi.nlm.nih.gov/clinvar/
    id: 00000595
    name: ClinVar Submission
    namespaceEmbeddedInLui: false
    pattern: ^SCV\d+(\.\d+)?$
    prefix: clinvar.submission
    sampleId: SCV000151292
    uri_format: http://www.ncbi.nlm.nih.gov/clinvar?term=$1
  n2t:
    description: ClinVar archives reports of relationships among medically important
      variants and phenotypes. It records human variation, interpretations of the
      relationship specific variations to human health, and supporting evidence for
      each interpretation. Each ClinVar record (RCV identifier) represents an aggregated
      view of interpretations of the same variation and condition from one or more
      submitters. Submissions for individual variation/phenotype combinations (SCV
      identifier) are also collected and made available separately. This collection
      references submissions, and is based on SCV accession.
    example: SCV000151292
    homepage: http://www.ncbi.nlm.nih.gov/clinvar/
    name: ClinVar Submission at NCBI
    namespaceEmbeddedInLui: false
    pattern: ^SCV\d+(\.\d+)?$
    prefix: clinvar.submission
    uri_format: http://www.ncbi.nlm.nih.gov/clinvar?term=$1
  part_of_database: clinvar
  prefix: clinvar.submission
clinvar.submitter:
  mappings:
    miriam: clinvar.submitter
  miriam:
    deprecated: false
    description: ClinVar archives reports of relationships among medically important
      variants and phenotypes. It records human variation, interpretations of the
      relationship specific variations to human health, and supporting evidence for
      each interpretation. Each ClinVar record (RCV identifier) represents an aggregated
      view of interpretations of the same variation and condition from one or more
      submitters (Submitter IDs). Submissions for individual variation/phenotype combinations
      (SCV identifier) are also collected and made available separately. This collection
      references submitters (submitter ids) that submit the submissions (SCVs).
    homepage: https://www.ncbi.nlm.nih.gov/clinvar/
    id: 00000769
    name: ClinVar Submitter
    namespaceEmbeddedInLui: false
    pattern: ^\d+$
    prefix: clinvar.submitter
    sampleId: '26957'
    uri_format: https://www.ncbi.nlm.nih.gov/clinvar/submitters/$1
  part_of_database: clinvar
  prefix: clinvar.submitter
clinvar.variation:
  biocontext:
    prefix: ClinVarVariant
    uri_format: http://www.ncbi.nlm.nih.gov/clinvar/variation/$1
  biolink:
    is_identifiers: true
    is_obo: false
    prefix: CLINVAR
    uri_format: http://identifiers.org/clinvar$1
  cellosaurus:
    category: Polymorphism and mutation databases
    homepage: https://www.ncbi.nlm.nih.gov/clinvar/
    name: ClinVar
    prefix: ClinVar
    uri_format: https://www.ncbi.nlm.nih.gov/clinvar/variation/$1
  contact:
    email: maglott@ncbi.nlm.nih.gov
    github: null
    name: Donna R. Maglott
    orcid: 0000-0001-7451-4467
  fairsharing:
    abbreviation: ClinVar
    description: ClinVar is a freely accessible, public archive of reports of the
      relationships among human variations and phenotypes, with supporting evidence.
      ClinVar thus facilitates access to and communication about the relationships
      asserted between human variation and observed health status, and the history
      of that interpretation. ClinVar processes submissions reporting variants found
      in patient samples, assertions made regarding their clinical significance, information
      about the submitter, and other supporting data. The alleles described in submissions
      are mapped to reference sequences, and reported according to the HGVS standard.
      ClinVar then presents the data for interactive users as well as those wishing
      to use ClinVar in daily workflows and other local applications. ClinVar works
      in collaboration with interested organizations to meet the needs of the medical
      genetics community as efficiently and effectively as possible.
    homepage: http://www.ncbi.nlm.nih.gov/clinvar/
    license: https://www.ncbi.nlm.nih.gov/home/about/policies
    name: ClinVar
    prefix: FAIRsharing.wx5r6f
    publications:
    - doi: 10.1093/nar/gkt1113
      pubmed_id: 24234437
      title: 'ClinVar: public archive of relationships among sequence variation and
        human phenotype.'
    subjects:
    - Genomics
    - Clinical Studies
    - Biomedical Science
    - Preclinical Studies
  hl7:
    description: 'ClinVar processes submissions reporting variants found in patient
      samples, assertions made regarding their clinical significance, information
      about the submitter, and other supporting data. The alleles described in submissions
      are mapped to reference sequences, and reported according to the HGVS standard.
      The ClinVar records have a field for Allele ID and for Variant ID. All simple
      variants have an Allele ID. At present, all complex  and most simple variants
      also have a Variant ID, and by the end of 2016, all variants will have a variant
      ID. This coding system uses the variant ID as the code and the variant name
      ( field TBD) from the "variant_summary" file as the code print string. The "variant_summary"
      file caries more than 20 fields , including the seperate components of the variant
      nane, the cytogenomic locatiaon, the genomic reference etc. Many of these attributes
      have been indexed to assist users and applications that need to find the  ID
      for a particular variant. '
    homepage: https://lhncbc.nlm.nih.gov/
    name: ClinVar Variant ID
    organization: National Lister Hill Center of Biomedical Communications, National
      Library of Medicine
    preferred_prefix: clinVar-V
    prefix: 2.16.840.1.113883.6.319
    status: Complete
  integbio:
    description: ClinVar is a freely available archive describing relationships between
      medically important variants and phenotypes. Submissions report human variation,
      interpretations of the relationship of that variation to human health, and the
      evidence supporting each interpretation. ClinVar is tightly coupled with dbSNP
      and dbVar, which maintain information about locations of variations on human
      assemblies, and also based on the phenotypic descriptions maintained in MedGen
      (http://www.ncbi.nlm.nih.gov/medgen). Each record contains the submitter, the
      variation and the phenotype. Furthermore, to facilitate evaluation of the medical
      importance of each variant, ClinVar aggregates submissions with the same variation/phenotype
      combination, adds value from other NCBI databases, and reports if there are
      conflicting clinical interpretations. Data in ClinVar are available in multiple
      formats, including html, download as XML, VCF or tab-delimited subsets.
    fairsharing: biodbcore-000739
    homepage: http://www.ncbi.nlm.nih.gov/clinvar/
    information_keywords:
    - Phenotype
    - Bibliography/Documents
    - Repository
    maintainer: NCBI (National Center for Biotechnology Information)
    name: ClinVar
    prefix: nbdc01514
    pubmeds:
    - '24234437'
    status: Active
    target_keywords:
    - Genome/Gene
    - Genetic variation
    - Health/Disease
  mappings:
    biocontext: ClinVarVariant
    biolink: CLINVAR
    cellosaurus: ClinVar
    fairsharing: FAIRsharing.wx5r6f
    hl7: 2.16.840.1.113883.6.319
    integbio: nbdc01514
    miriam: clinvar
    n2t: clinvar
    re3data: r3d100013331
    togoid: Clinvar
    wikidata: P1929
  miriam:
    deprecated: false
    description: ClinVar archives reports of relationships among medically important
      variants and phenotypes. It records human variation, interpretations of the
      relationship specific variations to human health, and supporting evidence for
      each interpretation. Each ClinVar record (RCV identifier) represents an aggregated
      view of interpretations of the same variation and condition from one or more
      submitters. Submissions for individual variation/phenotype combinations (SCV
      identifier) are also collected and made available separately. This collection
      references the Variant identifier.
    homepage: http://www.ncbi.nlm.nih.gov/clinvar/
    id: 00000596
    name: ClinVar Variant
    namespaceEmbeddedInLui: false
    pattern: ^\d+$
    prefix: clinvar
    sampleId: '12345'
    uri_format: https://www.ncbi.nlm.nih.gov/clinvar/variation/$1
  n2t:
    description: ClinVar archives reports of relationships among medically important
      variants and phenotypes. It records human variation, interpretations of the
      relationship specific variations to human health, and supporting evidence for
      each interpretation. Each ClinVar record (RCV identifier) represents an aggregated
      view of interpretations of the same variation and condition from one or more
      submitters. Submissions for individual variation/phenotype combinations (SCV
      identifier) are also collected and made available separately. This collection
      references the Variant identifier.
    example: '12345'
    homepage: http://www.ncbi.nlm.nih.gov/clinvar/
    name: ClinVar Variant at NCBI
    namespaceEmbeddedInLui: false
    pattern: ^\d+$
    prefix: clinvar
    uri_format: https://www.ncbi.nlm.nih.gov/clinvar/variation/$1
  name: ClinVar Variation
  prefix: clinvar.variation
  publications:
  - doi: 10.1093/nar/gkt1113
    pmc: PMC3965032
    pubmed: '24234437'
    title: 'ClinVar: public archive of relationships among sequence variation and
      human phenotype'
    year: 2013
  - doi: 10.1093/nar/gkt1113
    pmc: null
    pubmed: null
    title: 'ClinVar: public archive of relationships among sequence variation and
      human phenotype.'
    year: null
  - doi: 10.1093/nar/gkt1113
    pmc: null
    pubmed: null
    title: 'ClinVar: public archive of relationships among sequence variation and
      human phenotype.'
    year: null
  - doi: 10.1093/nar/gkt1113
    pmc: null
    pubmed: null
    title: 'ClinVar: public archive of relationships among sequence variation and
      human phenotype.'
    year: null
  re3data:
    description: ClinVar is a freely accessible, public archive of reports of the
      relationships among human variations and phenotypes, with supporting evidence.
      ClinVar thus facilitates access to and communication about the relationships
      asserted between human variation and observed health status, and the history
      of that interpretation. ClinVar processes submissions reporting variants found
      in patient samples, assertions made regarding their clinical significance, information
      about the submitter, and other supporting data. The alleles described in submissions
      are mapped to reference sequences, and reported according to the HGVS standard.
      ClinVar then presents the data for interactive users as well as those wishing
      to use ClinVar in daily workflows and other local applications. ClinVar works
      in collaboration with interested organizations to meet the needs of the medical
      genetics community as efficiently and effectively as possible
    doi: 10.17616/R31NJMS3
    homepage: https://www.ncbi.nlm.nih.gov/clinvar/
    name: ClinVar
    prefix: r3d100013331
  synonyms:
  - clinvar
  - clinvar.variant
  togoid:
    catalog: nbdc01514
    description: ClinVar is a freely available archive describing relationships between
      medically important variants and phenotypes. Submissions report human variation,
      interpretations of the relationship of that variation to human health, and the
      evidence supporting each interpretation. ClinVar is tightly coupled with dbSNP
      and dbVar, which maintain information about locations of variations on human
      assemblies, and also based on the phenotypic descriptions maintained in MedGen
      (http://www.ncbi.nlm.nih.gov/medgen). Each record contains the submitter, the
      variation and the phenotype. Furthermore, to facilitate evaluation of the medical
      importance of each variant, ClinVar aggregates submissions with the same variation/phenotype
      combination, adds value from other NCBI databases, and reports if there are
      conflicting clinical interpretations. Data in ClinVar are available in multiple
      formats, including html, download as XML, VCF or tab-delimited subsets.
    examples:
    - '658761'
    - '619209'
    - '745342'
    - '11955'
    - '731668'
    - '724289'
    - '725734'
    - '743127'
    - '789913'
    - '5302'
    keywords:
    - Variant
    name: ClinVar variant
    pattern: ^(VCV0*)?(?(\d{1,9}))$
    prefix: Clinvar
    uri_format: http://identifiers.org/clinvar/$1
  wikidata:
    description: identifier in the ClinVar database for human genomic variation
    example:
    - '13961'
    - '586'
    - '7105'
    homepage: https://www.ncbi.nlm.nih.gov/clinvar/
    name: ClinVar Variation ID
    prefix: P1929
    uri_format: https://www.ncbi.nlm.nih.gov/clinvar/variation/$1/
clm:
  contact:
    email: davidos@ebi.ac.uk
    github: dosumis
    name: David Osumi-Sutherland
    orcid: 0000-0002-7073-9172
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: This ontology integrates cell type markers for cells in the Cell Ontology
    from various sources along with details of marker context (anatomical context,
    assay), confidence (where available) and provenance. [from repository]
  download_json: https://github.com/Cellular-Semantics/CellMark/raw/refs/heads/main/clm.json
  download_obo: https://github.com/Cellular-Semantics/CellMark/raw/refs/heads/main/clm.obo
  download_owl: https://github.com/Cellular-Semantics/CellMark/raw/refs/heads/main/clm.owl
  example: '1000003'
  github_request_issue: 1551
  homepage: https://github.com/Cellular-Semantics/CellMark
  name: Cell Markers Ontology
  pattern: ^\d{7}$
  preferred_prefix: CLM
  prefix: clm
  repository: https://github.com/Cellular-Semantics/CellMark
  uri_format: http://purl.obolibrary.org/obo/CLM_$1
clo:
  aberowl:
    description: An ontology to standardize and integrate cell line information and
      to support computer-assisted reasoning.
    download_owl: http://aber-owl.net/media/ontologies/CLO/7/clo.owl
    homepage: https://github.com/CLO-Ontology/CLO
    name: Cell Line Ontology
    prefix: CLO
  biocontext:
    prefix: CLO
  bioportal:
    contact:
      email: yongqunh@med.umich.edu
      name: Oliver He
    description: The Cell Line Ontology (CLO) is a community-based ontology in domain
      of biological cell lines with a focus on permanent cell lines from culture collections.
      Upper ontology structures that frame the skeleton of CLO include Basic Formal
      Ontology and Relation Ontology. Cell lines contained in CLO are associated with
      terms from other ontologies such as Cell Type Ontology, NCBI Taxonomy, and Ontology
      for Biomedical Investigation. A common design pattern for the cell line is used
      to model cell lines and their attributes, the Jurkat cell line provides ane
      xample. Currently CLO contains over 36,000 cell line entries obtained from ATCC,
      HyperCLDB, Coriell, and bymanual curation. The cell lines are derived from 194
      cell types, 656 anatomical entries, and 217 organisms. The OWL-based CLO is
      machine-readable and can be used in various applications.
    homepage: http://www.clo-ontology.org/
    name: Cell Line Ontology
    prefix: CLO
    publications:
    - http://www.jbiomedsem.com/content/5/1/37
    version: 2.1.188
  cellosaurus:
    category: Cell line databases/resources
    homepage: https://bioportal.bioontology.org/ontologies/CLO
    name: Cell Line Ontology
    prefix: CLO
  domain: cell and cell line
  example: 0000091
  fairsharing:
    abbreviation: CLO
    contact:
      email: Sirarat.Sarntivijai@fda.hhs.gov
      name: Sirarat Sarntivijai
      orcid: 0000-0002-2548-641X
    description: The Cell Line Ontology (CLO) is a community-driven ontology that
      is developed to standardize and integrate cell line information and support
      computer-assisted reasoning. Thousands of cell lines have been artificially
      developed and used for different applications. Integration of data from multiple
      sources is a challenge, confounded by lack of consistent naming conventions,
      contamination of cell lines, and provision of the same cell lines by multiple
      commercial sources but with different biological attributes. CLO is a community-based
      effort to represent all cell lines in a standard ontology approach.
    domains:
    - cell line
    - cell
    - morphology
    homepage: https://github.com/CLO-ontology/CLO
    license: CC-BY-3.0
    name: Cell Line Ontology
    prefix: FAIRsharing.4dvtcz
    publications:
    - doi: 10.1186/2041-1480-5-37
      pubmed: '25852852'
      title: 'CLO: The cell line ontology'
      year: 2014
    repository: https://github.com/CLO-ontology/CLO/issues
    subjects:
    - Life Science
    - Cell Biology
  logo: https://avatars.githubusercontent.com/u/12410534
  mappings:
    aberowl: CLO
    biocontext: CLO
    bioportal: CLO
    cellosaurus: CLO
    fairsharing: FAIRsharing.4dvtcz
    miriam: clo
    obofoundry: clo
    ols: clo
    ontobee: CLO
    prefixcommons: clo
    wikidata: P2158
    wikidata.entity: Q21039006
  miriam:
    deprecated: false
    description: The Cell Line Ontology is a community-based ontology of cell lines.
      The CLO is developed to unify publicly available cell line entry data from multiple
      sources to a standardized logically defined format based on consensus design
      patterns.
    homepage: https://www.ebi.ac.uk/ols4/ontologies/clo
    id: 00000983
    name: Cell Line Ontology
    namespaceEmbeddedInLui: false
    pattern: ^\d{7}$
    prefix: clo
    providers:
    - code: bioportal
      description: Our vision is that all biomedical knowledge and data are disseminated
        on the Internet using principled ontologies in such a way that the knowledge
        and data are semantically interoperable and useful for furthering biomedical
        science and clinical care. Our mission is to create software and support services
        for the application of principled ontologies in biomedical science and clinical
        care, ranging from tools for application developers to software for end-users.
      homepage: https://bioportal.bioontology.org
      name: Center for Biomedical Informatics Research, Stanford
      uri_format: https://bioportal.bioontology.org/ontologies/CLO/?p=classes&conceptid=http://purl.obolibrary.org/obo/CLO_$1
    sampleId: 0000091
    uri_format: https://www.ebi.ac.uk/ols4/ontologies/clo/terms?short_form=CLO_$1
  obofoundry:
    appears_in:
    - mco
    contact: zhengj2007@gmail.com
    contact.github: zhengj2007
    contact.label: Jie Zheng
    contact.orcid: 0000-0002-2999-0103
    depends_on:
    - cl
    - doid
    - ncbitaxon
    - uberon
    deprecated: false
    description: An ontology to standardize and integrate cell line information and
      to support computer-assisted reasoning.
    domain: anatomy and development
    download.owl: http://purl.obolibrary.org/obo/clo.owl
    homepage: https://github.com/CLO-Ontology/CLO
    license: CC BY 3.0
    license.url: http://creativecommons.org/licenses/by/3.0/
    name: Cell Line Ontology
    preferredPrefix: CLO
    prefix: clo
    publications:
    - id: https://www.ncbi.nlm.nih.gov/pubmed/25852852
      title: 'CLO: The Cell Line Ontology'
    repository: https://github.com/CLO-Ontology/CLO
  ols:
    description: The Cell Line Ontology (CLO) is a community-based ontology of cell
      lines. The CLO is developed to unify publicly available cell line entry data
      from multiple sources to a standardized logically defined format based on consensus
      design patterns.
    download_owl: http://purl.obolibrary.org/obo/clo.owl
    homepage: https://github.com/CLO-Ontology/CLO
    name: 'CLO: Cell Line Ontology'
    prefix: clo
    tracker: https://github.com/CLO-Ontology/CLO/issues
    version: 2.1.188
  ontobee:
    library: Library
    name: Cell Line Ontology
    prefix: CLO
  pattern: ^\d{7}$
  prefix: clo
  prefixcommons:
    alt_uri_formats:
    - http://purl.org/obo/owl/CL#$1
    - http://purl.org/obo/owl/CLO#$1
    bioportal: '1314'
    description: The Cell Line Ontology (CLO) is a community-based ontology in domain
      of biological cell lines with a focus on permanent cell lines from culture collections.
      Upper ontology structures that frame the skeleton of CLO include Basic Formal
      Ontology and Relation Ontology. Cell lines contained in CLO are associated with
      terms from other ontologies such as Cell Type Ontology, NCBI Taxonomy, and Ontology
      for Biomedical Investigation. A common design pattern for the cell line is used
      to model cell lines and their attributes, the Jurkat cell line provides ane
      xample.  Currently CLO contains over 36,000 cell line entries obtained from
      ATCC, HyperCLDB, Coriell, and bymanual curation. The cell lines are derived
      from 194 cell types, 656 anatomical entries, and 217 organisms. The OWL-based
      CLO is machine-readable and can be used in various applications.
    example: CL:0000232
    homepage: http://sourceforge.net/projects/clo-ontology/
    keywords:
    - ontology
    name: Cell Line Ontology
    pattern: ^CL:\d{7}$
    prefix: clo
    pubmed_ids:
    - '15693950'
    synonyms:
    - obo.clo
  publications:
  - doi: 10.1186/2041-1480-5-37
    pmc: PMC4387853
    pubmed: '25852852'
    title: 'CLO: The cell line ontology'
    year: 2014
  - doi: 10.1186/gb-2005-6-2-r21
    pmc: PMC551541
    pubmed: '15693950'
    title: An ontology for cell types
    year: 2005
  - doi: null
    pmc: null
    pubmed: '25852852'
    title: 'CLO: The Cell Line Ontology'
    year: null
  - doi: 10.1186/2041-1480-5-37
    pmc: null
    pubmed: '25852852'
    title: 'CLO: The cell line ontology'
    year: 2014
  - doi: null
    pmc: null
    pubmed: '15693950'
    title: null
    year: null
  - doi: null
    pmc: null
    pubmed: '25852852'
    title: 'CLO: The Cell Line Ontology'
    year: null
  - doi: 10.1186/2041-1480-5-37
    pmc: null
    pubmed: '25852852'
    title: 'CLO: The cell line ontology'
    year: 2014
  - doi: null
    pmc: null
    pubmed: '15693950'
    title: null
    year: null
  - doi: null
    pmc: null
    pubmed: '25852852'
    title: 'CLO: The Cell Line Ontology'
    year: null
  - doi: 10.1186/2041-1480-5-37
    pmc: null
    pubmed: '25852852'
    title: 'CLO: The cell line ontology'
    year: 2014
  - doi: null
    pmc: null
    pubmed: '15693950'
    title: null
    year: null
  synonyms:
  - CLO
  uri_format: http://purl.obolibrary.org/obo/CLO_$1
  wikidata:
    description: identifier for the Cell Line Ontology which describes anatomic origin
      and nature of eukaryotic cell lines
    example:
    - CLO_0004283
    - CLO_0007043
    - CLO_0008177
    homepage: http://www.clo-ontology.org/
    name: Cell Line Ontology ID
    pattern: ^CLO_\d{7}$
    prefix: P2158
cls:
  cellosaurus:
    category: Cell line collections (Providers)
    homepage: https://www.cytion.com/
    name: Cell Lines Service
    prefix: CLS
    uri_format: https://www.cytion.com/$1
  example: 300108/p3934_A-172
  mappings:
    cellosaurus: CLS
  prefix: cls
clyh:
  aberowl:
    description: The Clytia hemisphaerica Development and Anatomy Ontology (CLYH)
      describes the anatomical and developmental features of the Clytia hemisphaerica
      life cycle.
    download_owl: http://aber-owl.net/media/ontologies/CLYH/3/clyh.owl
    homepage: https://github.com/EBISPOT/clyh_ontology
    name: Clytia hemisphaerica Development and Anatomy Ontology
    prefix: CLYH
  bioportal:
    contact:
      email: lucas.leclere@obs-vlfr.fr
      name: Lucas Leclere
    description: The Clytia hemisphaerica Development and Anatomy Ontology (CLYH)
      describes the anatomical and developmental features of the Clytia hemisphaerica
      life cycle.
    homepage: https://github.com/EBISPOT/clyh_ontology
    name: Clytia hemisphaerica Development and Anatomy Ontology
    prefix: CLYH
  example: '1000100'
  mappings:
    aberowl: CLYH
    bioportal: CLYH
    obofoundry: clyh
    ols: clyh
    ontobee: CLYH
    wikidata.entity: Q111274068
  obofoundry:
    contact: lucas.leclere@obs-banyuls.fr
    contact.github: Leclere-L
    contact.label: Lucas Leclere
    contact.orcid: 0000-0002-7440-0467
    depends_on:
    - iao
    - ro
    - uberon
    deprecated: false
    description: The Clytia hemisphaerica Development and Anatomy Ontology (CLYH)
      describes the anatomical and developmental features of the Clytia hemisphaerica
      life cycle.
    domain: anatomy and development
    download.obo: http://purl.obolibrary.org/obo/clyh.obo
    download.owl: http://purl.obolibrary.org/obo/clyh.owl
    homepage: https://github.com/EBISPOT/clyh_ontology
    license: CC BY 3.0
    license.url: http://creativecommons.org/licenses/by/3.0/
    name: Clytia hemisphaerica Development and Anatomy Ontology
    preferredPrefix: CLYH
    prefix: clyh
    repository: https://github.com/EBISPOT/clyh_ontology
  ols:
    description: Anatomy, development and life cycle stages - planula, polyp, medusa/jellyfish
      - of the cnidarian hydrozoan species, Clytia hemiphaerica.
    download_owl: http://purl.obolibrary.org/obo/clyh.owl
    homepage: https://github.com/EBISPOT/clyh_ontology
    name: Clytia hemisphaerica Development and Anatomy Ontology (CLYH)
    prefix: clyh
    tracker: https://github.com/EBISPOT/clyh_ontology/issues
    uri_format: http://purl.obolibrary.org/obo/CLYH_$1
    version: '2020-05-29'
    version.iri: http://purl.obolibrary.org/obo/clyh/releases/2020-05-29/clyh.owl
  ontobee:
    library: Library
    name: Clytia hemisphaerica Development and Anatomy Ontology
    prefix: CLYH
  pattern: ^\d+$
  prefix: clyh
  uri_format: http://purl.obolibrary.org/obo/CLYH_$1
cmecs:
  aberowl:
    description: The Coastal and Marine Ecological Classification Standard (CMECS,
      FGDC-STD-018-2012) is collection of defined terms ("units") used to describe
      and classify marine ecological data. It is a national scheme for classifying
      and integrating observational data collected in coastal, marine, and lacustrine
      environments in U.S. waters. CMECS was published by the U.S. Federal Geographic
      Data Committee (FGDC) in 2012.
    download_owl: http://aber-owl.net/media/ontologies/CMECS/2/cmecs.owl
    homepage: https://github.com/NCEI-NOAAGov/cmecs
    name: Coastal and Marine Ecological Classification Standard Catalog
    prefix: CMECS
    version: 1.1.0
  bioportal:
    contact:
      email: kate.rose@noaa.gov
      name: Kate Rose
    description: The Coastal and Marine Ecological Classification Standard (CMECS,
      FGDC-STD-018-2012) is collection of defined terms ("units") used to describe
      and classify marine ecological data. It is a national scheme for classifying
      and integrating observational data collected in coastal, marine, and lacustrine
      environments in U.S. waters. CMECS was published by the U.S. Federal Geographic
      Data Committee (FGDC) in 2012.
    homepage: https://github.com/NOAA-OCM/cmecs
    name: Coastal and Marine Ecological Classification Standard Catalog
    prefix: CMECS
    version: 1.1.0
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: Use this database to browse the CMECS classification and to get definitions
    for individual CMECS Units. This database contains the units that were published
    in the Coastal and Marine Ecological Classification Standard.
  ecoportal:
    contact:
      email: kater@ngi.msstate.edu
      name: Kate Rose
    description: The Coastal and Marine Ecological Classification Standard (CMECS,
      FGDC-STD-018-2012) ) is a collection of terms and and definitions (units) for
      classifying and describing aquatic environments. Units are organized in a framework
      of thematic, interrelated, semi-hierarchical components and settings designed
      for analyzing and mapping observational data within geographic information systems
      (GIS). CMECS is a U.S. National Ecological Classification Standard published
      by the US Federal Geographic Data Committee (FGDC). , The Coastal and Marine
      Ecological Classification Standard (CMECS) is a collection of terms and and
      definitions for classifying and describing aquatic environments. The vocabulary
      is organized in a framework of thematic, semi-hierarchical Components and Settings
      categories., The Coastal and Marine Ecological Classifcation Standard (CMECS)
      is a collection of terms and and defintions for classifying and describing aquatic
      environments. The vocabulary is organized in a framework of thematic, semi-heirarchical
      components and settings.
    example_uri: http://purl.obolibrary.org/obo/*Chaetomorpha*Communities
    homepage: https://iocm.noaa.gov/standards/cmecs-home.html
    license: CC0-1.0
    name: Coastal and Marine Ecological Classification Standard Catalog
    prefix: CMECS
    publications:
    - https://repository.library.noaa.gov/view/noaa/27552
    repository: https://github.com/NOAA-OCM/cmecs
    version: 1.1.0
  example: '595'
  homepage: https://cmecscatalog.org/cmecs
  keywords:
  - ecology
  - marine ecology
  mappings:
    aberowl: CMECS
    bioportal: CMECS
    ecoportal: CMECS
  name: Costal and Marine Ecological Classification Standard
  pattern: ^\d+$
  prefix: cmecs
  rdf_uri_format: https://w3id.org/CMECS/CMECS_$1
  references:
  - http://www.natureserve.org/sites/default/files/publications/files/cmecs_version_06-2012_final.pdf
  repository: https://github.com/NOAA-OCM/cmecs
  uri_format: https://cmecscatalog.org/cmecs/classification/unit/$1.html
cmf:
  aberowl:
    name: CranioMaxilloFacial ontology
    prefix: CMF
  biocontext:
    prefix: CMF
  deprecated: true
  description: This ontology represents the clinical findings and procedures used
    in the oral and maxillo-facial surgical domain
  mappings:
    aberowl: CMF
    biocontext: CMF
    obofoundry: cmf
    ontobee: CMF
    wikidata.entity: Q114677881
  obofoundry:
    contact: engelsta@ohsu.edu
    contact.label: Mark Engelstad
    contact.orcid: 0000-0001-5889-4463
    deprecated: true
    domain: health
    homepage: https://code.google.com/p/craniomaxillofacial-ontology/
    name: CranioMaxilloFacial ontology
    prefix: cmf
  ontobee:
    library: Library
    name: CranioMaxilloFacial ontology
    prefix: CMF
  prefix: cmf
cmo:
  aberowl:
    description: Morphological and physiological measurement records generated from
      clinical and model organism research and health programs.
    download_owl: http://aber-owl.net/media/ontologies/CMO/167/cmo.owl
    homepage: http://rgd.mcw.edu/rgdweb/ontology/search.html
    name: Clinical measurement ontology
    prefix: CMO
  biocontext:
    prefix: CMO
  bioportal:
    contact:
      email: akwitek@mcw.edu
      name: Anne Kwitek
    description: The Clinical Measurement Ontology is designed to be used to standardize
      morphological and physiological measurement records generated from clinical
      and model organism research and health programs.
    homepage: https://rgd.mcw.edu/rgdweb/ontology/search.html
    name: Clinical Measurement Ontology
    prefix: CMO
    publications:
    - http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3361058/
    version: '2.247'
  example: '0001350'
  fairsharing:
    abbreviation: CMO
    contact:
      email: shimoyama@mcw.edu
      name: Mary Shimoyama
      orcid: 0000-0003-1176-0796
    description: The Clinical Measurement Ontology is designed to be used to standardize
      morphological and physiological measurement records generated from clinical
      and model organism research and health programs.
    domains:
    - Model organisms
    - Electronic Health Record
    - phenotype
    - disease
    homepage: http://rgd.mcw.edu/rgdweb/ontology/view.html?acc_id=CMO:0000000
    license: CC0-1.0
    name: Clinical Measurement Ontology
    prefix: FAIRsharing.dq78pn
    publications:
    - doi: 10.3389/fgene.2012.00087
      pubmed: '22654893'
      title: Three ontologies to define phenotype measurement data
      year: 2012
    - doi: 10.1186/2041-1480-4-26
      pubmed: '24103152'
      title: 'The clinical measurement, measurement method and experimental condition
        ontologies: expansion, improvements and new applications'
      year: 2013
    subjects:
    - Life Science
    - Preclinical Studies
    - Biomedical Science
  mappings:
    aberowl: CMO
    biocontext: CMO
    bioportal: CMO
    fairsharing: FAIRsharing.dq78pn
    obofoundry: cmo
    ols: cmo
    ontobee: CMO
    wikidata.entity: Q81661570
  obofoundry:
    appears_in:
    - scdo
    contact: jrsmith@mcw.edu
    contact.github: jrsjrs
    contact.label: Jennifer Smith
    contact.orcid: 0000-0002-6443-9376
    deprecated: false
    description: Morphological and physiological measurement records generated from
      clinical and model organism research and health programs.
    domain: health
    download.obo: http://purl.obolibrary.org/obo/cmo.obo
    download.owl: http://purl.obolibrary.org/obo/cmo.owl
    homepage: http://rgd.mcw.edu/rgdweb/ontology/search.html
    license: CC0 1.0
    license.url: http://creativecommons.org/publicdomain/zero/1.0/
    logo: http://rgd.mcw.edu/common/images/rgd_LOGO_blue_rgd.gif
    name: Clinical measurement ontology
    preferredPrefix: CMO
    prefix: cmo
    publications:
    - id: https://www.ncbi.nlm.nih.gov/pubmed/22654893
      title: Three ontologies to define phenotype measurement data.
    - id: https://www.ncbi.nlm.nih.gov/pubmed/24103152
      title: 'The clinical measurement, measurement method and experimental condition
        ontologies: expansion, improvements and new applications.'
    repository: https://github.com/rat-genome-database/CMO-Clinical-Measurement-Ontology
  ols:
    description: Morphological and physiological measurement records generated from
      clinical and model organism research and health programs.
    download_owl: http://purl.obolibrary.org/obo/cmo.owl
    homepage: http://rgd.mcw.edu/rgdweb/ontology/search.html
    name: Clinical measurement ontology
    prefix: cmo
    tracker: https://github.com/rat-genome-database/CMO-Clinical-Measurement-Ontology/issues
    version: '2.260'
    version.iri: http://purl.obolibrary.org/obo/cmo/2.260/cmo.owl
  ontobee:
    library: Library
    name: Clinical measurement ontology
    prefix: CMO
  pattern: ^\d{7}$
  prefix: cmo
  publications:
  - doi: 10.1186/2041-1480-4-26
    pmc: PMC3882879
    pubmed: '24103152'
    title: 'The clinical measurement, measurement method and experimental condition
      ontologies: expansion, improvements and new applications'
    year: 2013
  - doi: 10.3389/fgene.2012.00087
    pmc: PMC3361058
    pubmed: '22654893'
    title: Three ontologies to define phenotype measurement data
    year: 2012
  twitter: ratgenome
  uri_format: http://purl.obolibrary.org/obo/CMO_$1
cmpo:
  aberowl:
    description: The Cellular Microscopy Phenotype Ontology (CMPO) is a species neutral
      ontology for describing general phenotypic observations relating to the whole
      cell, cellular components, cellular processes and cell populations. CMPO is
      an application ontology developed in OWL that contains precomposed phenotypes
      descriptions that are defined using the Gene Ontology (GO) and the Phenotype
      Trait Ontology (PATO).
    download_owl: http://aber-owl.net/media/ontologies/CMPO/14/cmpo.owl
    homepage: https://github.com/EBISPOT/CMPO
    name: Cellular microscopy phenotype ontology
    prefix: CMPO
    version: '1.3'
  bioportal:
    contact:
      email: jupp@ebi.ac.uk
      name: Simon Jupp
    description: The Cellular Microscopy Phenotype Ontology (CMPO) is a species neutral
      ontology for describing general phenotypic observations relating to the whole
      cell, cellular components, cellular processes and cell populations. CMPO is
      an application ontology developed in OWL that contains precomposed phenotypes
      descriptions that are defined using the Gene Ontology (GO) and the Phenotype
      Trait Ontology (PATO).
    homepage: https://github.com/EBISPOT/CMPO
    name: Cellular microscopy phenotype ontology
    prefix: CMPO
    version: '1.3'
  contact:
    email: jupp@ebi.ac.uk
    github: null
    name: Simon Jupp
    orcid: 0000-0002-0643-3144
  example: '0000435'
  fairsharing:
    abbreviation: CMPO
    contact:
      email: jupp@abi.ac.uk
      name: Simon Jupp
      orcid: 0000-0002-0643-3144
    description: The Cellular Microscopy Phenotype Ontology (CMPO) provides a species-neutral
      controlled vocabulary for describing phenotypic qualities relating to the whole
      cell, cellular components, cellular processes and cell populations. Terms from
      CMPO are being used to annotate phenotype descriptions from high-content screening
      databases and cellular image repositories.
    domains:
    - Imaging
    - Bioimaging
    - microscopy
    - cell
    - cellular_component
    - phenotype
    homepage: http://www.ebi.ac.uk/cmpo/
    license: Apache 2.0 License
    name: The Cellular Microscopy Phenotype Ontology
    prefix: FAIRsharing.knp11s
    publications:
    - doi: 10.1186/s13326-016-0074-0
      pubmed: '27195102'
      title: The cellular microscopy phenotype ontology
      year: 2016
    repository: https://github.com/EBISPOT/CMPO
    subjects:
    - Phenomics
    - Cell Biology
  mappings:
    aberowl: CMPO
    bioportal: CMPO
    fairsharing: FAIRsharing.knp11s
    ols: cmpo
  ols:
    contact: jupp@ebi.ac.uk
    description: CMPO is a species neutral ontology for describing general phenotypic
      observations relating to the whole cell, cellular components, cellular processes
      and cell populations.
    download_owl: http://www.ebi.ac.uk/cmpo/cmpo.owl
    homepage: http://www.ebi.ac.uk/cmpo
    name: Cellular Microscopy Phenotype Ontology
    prefix: cmpo
    uri_format: http://www.ebi.ac.uk/cmpo/CMPO_$1
    version: '2017-12-19'
    version.iri: http://www.ebi.ac.uk/cmpo/releases/2017-12-19/cmpo.owl
  pattern: ^\d{7}$
  prefix: cmpo
  publications:
  - doi: 10.1186/s13326-016-0074-0
    pmc: PMC4870745
    pubmed: '27195102'
    title: The cellular microscopy phenotype ontology
    year: 2016
  repository: https://github.com/EBISPOT/CMPO
  twitter: EBIOLS
  uri_format: http://www.ebi.ac.uk/cmpo/CMPO_$1
cncb.gwh:
  contact:
    email: baoym@big.ac.cn
    github: null
    name: Yiming Bao
    orcid: 0000-0002-9922-9723
  contributor:
    email: palayoor.n@northeastern.edu
    github: nalikapalayoor
    name: Nalika Palayoor
    orcid: 0009-0008-8406-631X
  description: The China National Center for Bioinformation's (CNCB) Genome Warehouse
    (GWH) is a public repository holding genetic information for a wide range of species
    including humans, plants, animals, and microorganisms. Identifiers in this resource
    correspond to genomes of various species. The goal of the resource is to make
    genomic data accessible to researchers in areas like precision medicine and biotechnology.
  example: '167047'
  github_request_issue: 1452
  homepage: https://ngdc.cncb.ac.cn/gwh/browse/genome
  name: CNCB Genome Warehouse
  pattern: ^\d{6}$
  prefix: cncb.gwh
  publications:
  - doi: 10.1093/gpbjnl/qzaf010
    pmc: null
    pubmed: '39977364'
    title: 'The Updated Genome Warehouse: Enhancing Data Value, Security, and Usability
      to Address Data Expansion'
    year: 2025
  reviewer:
    email: b.gyori@northeastern.edu
    github: bgyori
    name: Benjamin M. Gyori
    orcid: 0000-0001-9439-5346
  uri_format: https://ngdc.cncb.ac.cn/gwh/Genome/$1/show
cnrs:
  comment: Motivated to add because of appearance in ROR
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: identifier for an academic research group issued by the CNRS
  example: UMR7315
  example_extras:
  - UPS76
  homepage: https://annuaire.cnrs.fr
  mappings:
    wikidata: P4550
  name: French National Center for Scientific Research - Research Group Identifier
  pattern: ^(UMR|UMS|UMI|UPR|URA|USR|GDR|EA|FR|SNC|ERL|FRC|FRE|IFR|MOY|UPS)\d+$
  prefix: cnrs
  uri_format: https://web-ast.dsi.cnrs.fr/l3c/owa/structure.infos_admin?&p_lab=$1&p_origine_appel=u
  wikidata:
    description: identifier for an academic research group issued by the CNRS
    example:
    - UMR7315
    - UMR7318
    - UMR8627
    name: CNRS research group ID
    pattern: ^(UAR|UMR|UMS|UMI|UPR|URA|USR|GDR|EA|FR|SNC|ERL|FRC|FRE|IFR|MOY)\d+$
    prefix: P4550
    uri_format: https://annuaire.cnrs.fr/NavigationServlet?pageName=resultatMain&type=UNITE&codeUniteStr=$1
cnt:
  bartoc:
    abbreviation: cnt
    description: A vocabulary to represent Content in the Resource Description Framework
      (RDF). There is a wide variety of scenarios where a representation of any type
      of content, either on the Web or in any local storage media, is necessary. The
      vocabulary is built in a flexible manner, thus there are no limitations known
      at the time of writing this specification. It also provides opportunities for
      extensions to match particular needs of its users.
    homepage: https://www.w3.org/TR/Content-in-RDF10/
    name: Representing Content in RDF
    prefix: '17875'
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: This vocabulary is intended to provide a flexible framework within
    different usage scenarios to semantically represent any type of content, be it
    on the Web or in local storage media. For example, it can be used by web quality
    assurance tools such as web accessibility evaluation tools to record a representation
    of the assessed web content, including text, images, or other types of formats.
    In many cases, it can be used together with HTTP Vocabulary in RDF 1.0, which
    allows quality assurance tools to record the HTTP headers that have been exchanged
    between a client and a server. This is particularly useful for quality assurance
    testing, conformance claims, and reporting languages like the W3C Evaluation And
    Report Language (EARL). [from homepage]
  example: Content
  homepage: https://www.w3.org/TR/Pointers-in-RDF/#ref-content
  lov:
    description: Representing Content in RDF as defined by http://www.w3.org/TR/Content-in-RDF/
    homepage: http://www.w3.org/TR/Content-in-RDF10/
    keywords:
    - RDF
    modified: '2011-05-10'
    name: Representing Content in RDF
    prefix: cnt
    uri_prefix: http://www.w3.org/2011/content#$1
  mappings:
    bartoc: '17875'
    lov: cnt
    zazuko: cnt
  name: Representing Content in RDF
  prefix: cnt
  rdf_uri_format: http://www.w3.org/2011/content#$1
  uri_format: http://www.w3.org/2011/content#$1
  version: '2011'
  zazuko:
    prefix: cnt
    uri_format: http://www.w3.org/2011/content#$1
co_320:
  agroportal:
    contact:
      email: j.detras@cgiar.org
      name: Jeffrey A. Detras
    description: Rice Trait Dictionary in template v 5.0 - IRRI - March 2016 - Based
      on SES, RD, UPOV variables and on variables used by CIAT, FLAR and the GRISP
      Phenotyping Network variables
    example_uri: http://www.cropontology.org/rdf/CO_320:0000600/5
    homepage: http://www.cropontology.org/
    license: CC-BY-4.0
    name: Rice Ontology
    prefix: CO_320
    repository: https://github.com/Planteome/CO_320-rice-traits
    version: March 2016
  contact:
    email: j.detras@cgiar.org
    github: null
    name: Jeffrey A. Detras
    orcid: 0000-0002-6680-578X
  cropoct:
    description: Rice Trait Dictionary in template v 5.0 - IRRI - March 2016 - Based
      on SES, RD, UPOV variables and on variables used by CIAT, FLAR and the GRISP
      Phenotyping Network variables
    download_owl: http://cropontology.org/rdf/CO_320.owl
    homepage: http://cropontology.org/term/CO_320:ROOT
    name: Rice ontology
    prefix: CO_320
  example: 0000618
  fairsharing:
    abbreviation: CO_320
    description: Reference Plant Ontologies are being developed in the context of
      the Planteome project and are being integrated with the Crop Ontology, which
      provides harmonized breeders’ trait names, measurement methods, scales and standard
      variables for many crops. The IBP Rice Trait Ontology is one of these reference
      plant ontologies integrated within the Crop Ontology. Based on SES, Rice Descriptor
      and IRIS DB.
    domains:
    - food
    - phenotype
    homepage: https://cropontology.org/term/CO_320:ROOT
    license: CC-BY-4.0
    name: Rice Ontology
    prefix: FAIRsharing.2jkxp5
    subjects:
    - Agriculture
    - Life Science
    - Botany
    user_defined_tags:
    - Plant Phenotypes and Traits
  license: CC-BY-4.0
  mappings:
    agroportal: CO_320
    cropoct: CO_320
    fairsharing: FAIRsharing.2jkxp5
    ols: co_320
  ols:
    contact: helpdesk@cropontology-curationtool.org
    description: Rice Trait Dictionary in template v 5.0 - IRRI - March 2016 - Based
      on SES, RD, UPOV variables and on variables used by CIAT, FLAR and the GRISP
      Phenotyping Network variables
    download: https://cropontology.org/ontology/CO_320/Rice/owl
    homepage: https://cropontology.org/ontology/CO_320/Rice
    name: Rice ontology
    prefix: co_320
    version: '2019-10-09'
  pattern: ^\d{7}$
  preferred_prefix: CO_320
  prefix: co_320
  repository: https://github.com/bioversity/Crop-Ontology
  uri_format: https://cropontology.org/rdf/CO_320:$1
co_321:
  agroportal:
    contact:
      email: helpdesk@cropontology-curationtool.org
      name: Crop Ontology Helpdesk
    description: Wheat Trait Dictionary in template v5.
    example_uri: http://www.cropontology.org/rdf/CO_321:0000238
    homepage: http://www.cropontology.org/
    license: CC-BY-4.0
    name: Wheat Ontology
    prefix: CO_321
    repository: https://github.com/Planteome/CO_321-wheat-traits
    version: Feb 2016
  contact:
    email: r.shrestha2@cgiar.org
    github: null
    name: Rosemary Shrestha
    orcid: 0000-0002-9399-8003
  contact_group_email: helpdesk@cropontology-curationtool.org
  cropoct:
    description: July 2018
    download_owl: http://cropontology.org/rdf/CO_321.owl
    homepage: http://cropontology.org/term/CO_321:ROOT
    name: Wheat ontology
    prefix: CO_321
  example: 0000449
  fairsharing:
    abbreviation: CO_321
    contact:
      email: R.Shrestha2@cgiar.org
      name: Rosemary Shrestha
      orcid: 0000-0002-9399-8003
    description: This ontology defines traits of the International Wheat Information
      System (IWIS) database and wheat descriptor. The Wheat Ontology is part of the
      Crop Ontology (CO) project. The Crop Ontology has been created to compile validated
      concepts along with their inter-relationships on anatomy, structure and phenotype
      of Crops, on trait measurement and methods as well as on Germplasm with the
      multi-crop passport terms. The concepts of the CO are being used to curate agronomic
      databases and describe the data. The use of ontology terms to describe agronomic
      phenotypes and the accurate mapping of these descriptions into databases is
      important in comparative phenotypic and genotypic studies across species and
      gene-discovery experiments as it provides harmonized description of the data
      and therefore facilitates the retrieval of information.
    domains:
    - food
    - phenotype
    homepage: https://cropontology.org/term/CO_321:ROOT
    license: CC-BY-4.0
    name: Wheat Ontology
    prefix: FAIRsharing.czzmpg
    publications:
    - doi: 10.1093/aobpla/plq008
      pubmed: '22476066'
      title: 'Multifunctional crop trait ontology for breeders'' data: field book,
        annotation, data discovery and semantic enrichment of the literature'
      year: 2010
    subjects:
    - Agriculture
    - Life Science
  license: CC-BY-4.0
  mappings:
    agroportal: CO_321
    cropoct: CO_321
    fairsharing: FAIRsharing.czzmpg
    ols: co_321
  ols:
    contact: helpdesk@cropontology-curationtool.org
    description: July 2018
    download: https://cropontology.org/ontology/CO_321/Wheat/owl
    homepage: https://cropontology.org/ontology/CO_321/Wheat
    name: Wheat ontology
    prefix: co_321
    version: '2019-10-09'
  pattern: ^\d{7}$
  preferred_prefix: CO_321
  prefix: co_321
  publications:
  - doi: 10.1093/aobpla/plq008
    pmc: PMC3000699
    pubmed: '22476066'
    title: 'Multifunctional crop trait ontology for breeders'' data: field book, annotation,
      data discovery and semantic enrichment of the literature'
    year: 2010
  repository: https://github.com/bioversity/Crop-Ontology
  uri_format: https://cropontology.org/rdf/CO_321:$1
co_322:
  agroportal:
    contact:
      email: helpdesk@cropontology-curationtool.org
      name: Crop Ontology Helpdesk
    description: This ontology is a part of the the Crop Ontology project (http://www.cropontology.org),as
      an essential source of traits and variables to support the standardization of
      the breeding databases.
    example_uri: http://www.cropontology.org/rdf/CO_322:0000850
    homepage: http://www.cropontology.org/
    license: CC-BY-4.0
    name: Maize Ontology
    prefix: CO_322
    repository: https://github.com/Planteome/CO_322-maize-traits
    version: September 2016
  contact:
    email: e.arnaud@cgiar.org
    github: null
    name: Elizabeth Arnaud
    orcid: 0000-0002-6020-5919
  contact_group_email: helpdesk@cropontology-curationtool.org
  cropoct:
    description: Maize Trait Dictionary in template 5 - CIMMYT- September 2016- Updated
      nov 2023 Updated Nov 2023 with the traits and variables for on farm comparative
      ranking of varieties
    download_owl: http://cropontology.org/rdf/CO_322.owl
    homepage: http://cropontology.org/term/CO_322:ROOT
    name: Maize ontology
    prefix: CO_322
  example: '0000773'
  fairsharing:
    abbreviation: CO_322
    description: The Maize Ontology is part of the Crop Ontology (CO) project. The
      Crop Ontology has been created to compile validated concepts along with their
      inter-relationships on anatomy, structure and phenotype of Crops, on trait measurement
      and methods as well as on Germplasm with the multi-crop passport terms. The
      concepts of the CO are being used to curate agronomic databases and describe
      the data. The use of ontology terms to describe agronomic phenotypes and the
      accurate mapping of these descriptions into databases is important in comparative
      phenotypic and genotypic studies across species and gene-discovery experiments
      as it provides harmonized description of the data and therefore facilitates
      the retrieval of information.
    domains:
    - food
    - phenotype
    homepage: https://cropontology.org/term/CO_322:ROOT
    license: CC-BY-4.0
    name: Maize Ontology
    prefix: FAIRsharing.eeyne8
    subjects:
    - Agriculture
    - Life Science
    - Botany
    user_defined_tags:
    - Plant Phenotypes and Traits
  license: CC-BY-4.0
  mappings:
    agroportal: CO_322
    cropoct: CO_322
    fairsharing: FAIRsharing.eeyne8
    ols: co_322
  ols:
    contact: helpdesk@cropontology-curationtool.org
    description: Maize Trait Dictionary in template 5 - CIMMYT- September 2016
    download: https://cropontology.org/ontology/CO_322/Maize/owl
    homepage: https://cropontology.org/ontology/CO_322/Maize
    name: Maize ontology
    prefix: co_322
    version: '2019-10-09'
  pattern: ^\d{7}$
  preferred_prefix: CO_322
  prefix: co_322
  repository: https://github.com/bioversity/Crop-Ontology
  uri_format: https://cropontology.org/rdf/CO_322:$1
co_323:
  agroportal:
    contact:
      email: f.nawar@cgiar.org
      name: Fawzy Nawar
    description: Reference Plant Ontologies are being developed in the context of
      the Plantome project and are being integrated with the Crop Ontology, which
      provides harmonized breeder's trait names, measurement methods, scales, and
      standard variables for many crops. The barley Ontology is one of these reference
      plant ontologies integrated within the Crop Ontology.
    example_uri: http://www.cropontology.org/rdf/CO_323:0000005/4
    homepage: http://www.cropontology.org/
    license: CC-BY-4.0
    name: Barley Ontology
    prefix: CO_323
    repository: https://github.com/Planteome/CO_323-barley-traits
    version: '1.2'
  cropoct:
    description: ICARDA - TDv5 - Sept 2018
    download_owl: http://cropontology.org/rdf/CO_323.owl
    homepage: http://cropontology.org/term/CO_323:ROOT
    name: Barley ontology
    prefix: CO_323
  example: '0000252'
  fairsharing:
    abbreviation: CO_323
    description: Reference Plant Ontologies are being developed in the context of
      the Planteome project and are being integrated with the Crop Ontology, which
      provides harmonized breeders’ trait names, measurement methods, scales and standard
      variables for many crops. The Barley Ontology is one of these reference plant
      ontologies integrated within the Crop Ontology. Its focus is on traits and variable
      used in field trials for breeding.
    domains:
    - phenotype
    homepage: https://cropontology.org/term/CO_323:ROOT
    license: CC-BY-4.0
    name: Barley Ontology
    prefix: FAIRsharing.f69084
    subjects:
    - Agriculture
    - Botany
    user_defined_tags:
    - Plant Phenotypes and Traits
  license: CC-BY-4.0
  mappings:
    agroportal: CO_323
    cropoct: CO_323
    fairsharing: FAIRsharing.f69084
    ols: co_323
  ols:
    contact: helpdesk@cropontology-curationtool.org
    description: ICARDA - TDv5 - Sept 2018
    download: https://cropontology.org/ontology/CO_323/Barley/owl
    homepage: https://cropontology.org/ontology/CO_323/Barley
    name: Barley ontology
    prefix: co_323
    version: '2019-11-20'
  pattern: ^\d{7}$
  preferred_prefix: CO_323
  prefix: co_323
  repository: https://github.com/bioversity/Crop-Ontology
  uri_format: https://cropontology.org/rdf/CO_323:$1
co_324:
  agroportal:
    contact:
      email: helpdesk@cropontology-curationtool.org
      name: Crop Ontology Helpdesk
    description: Sorghum TDv5 Ontology
    example_uri: http://www.cropontology.org/rdf/CO_324:0000660
    homepage: http://www.cropontology.org/
    license: CC-BY-4.0
    name: Sorghum Ontology
    prefix: CO_324
    repository: https://github.com/Planteome/CO_324-sorghum-traits
    version: '1.0'
  contact:
    email: e.arnaud@cgiar.org
    github: null
    name: Elizabeth Arnaud
    orcid: 0000-0002-6020-5919
  contact_group_email: helpdesk@cropontology-curationtool.org
  cropoct:
    description: Sorghum TDv5 - Oct 2019- Updated January 2024 with the Traits of
      1000Farms project trials using comparative ranking by farmers method
    download_owl: http://cropontology.org/rdf/CO_324.owl
    homepage: http://cropontology.org/term/CO_324:ROOT
    name: Sorghum ontology
    prefix: CO_324
  example: '0000111'
  fairsharing:
    abbreviation: CO_324
    description: The Sorghum Ontology is part of the Crop Ontology (CO) project. The
      Crop Ontology has been created to compile validated concepts along with their
      inter-relationships on anatomy, structure and phenotype of Crops, on trait measurement
      and methods as well as on Germplasm with the multi-crop passport terms. The
      concepts of the CO are being used to curate agronomic databases and describe
      the data. The use of ontology terms to describe agronomic phenotypes and the
      accurate mapping of these descriptions into databases is important in comparative
      phenotypic and genotypic studies across species and gene-discovery experiments
      as it provides harmonized description of the data and therefore facilitates
      the retrieval of information.
    domains:
    - food
    - phenotype
    homepage: https://cropontology.org/term/CO_324:ROOT
    license: CC-BY-4.0
    name: Sorghum Ontology
    prefix: FAIRsharing.dxx0c
    repository: https://github.com/Planteome/CO_324-sorghum-traits
    subjects:
    - Agriculture
    - Botany
  license: CC-BY-4.0
  mappings:
    agroportal: CO_324
    cropoct: CO_324
    fairsharing: FAIRsharing.dxx0c
    ols: co_324
  ols:
    contact: helpdesk@cropontology-curationtool.org
    description: Sorghum TDv5 - Oct 2019
    download: https://cropontology.org/ontology/CO_324/Sorghum/owl
    homepage: https://cropontology.org/ontology/CO_324/Sorghum
    name: Sorghum ontology
    prefix: co_324
    version: '2019-10-09'
  pattern: ^\d{7}$
  preferred_prefix: CO_324
  prefix: co_324
  repository: https://github.com/bioversity/Crop-Ontology
  uri_format: https://cropontology.org/rdf/CO_324:$1
co_325:
  agroportal:
    contact:
      email: helpdesk@cropontology-curationtool.org
      name: Crop Ontology Helpdesk
    description: Banana Trait Dictionary in template 5 - characterization and breeding
      variables, drought experiment variables.
    example_uri: http://www.cropontology.org/rdf/CO_325:0000267
    homepage: http://www.cropontology.org/
    license: CC-BY-4.0
    name: Banana Ontology
    prefix: CO_325
    repository: https://github.com/Planteome/CO_325-banana-traits
    version: April 2019
  contact:
    email: e.arnaud@cgiar.org
    github: null
    name: Elizabeth Arnaud
    orcid: 0000-0002-6020-5919
  contact_group_email: helpdesk@cropontology-curationtool.org
  cropoct:
    description: Banana Trait Dictionary in template 5 - Bioversity & IITA - April
      2019
    download_owl: http://cropontology.org/rdf/CO_325.owl
    homepage: http://cropontology.org/term/CO_325:ROOT
    name: Banana ontology
    prefix: CO_325
  example: 0000519
  fairsharing:
    abbreviation: CO_325
    contact:
      email: e.arnaud@cgiar.org
      name: Elizabeth Arnaud
      orcid: 0000-0002-6020-5919
    description: The Banana Ontology is part of the Crop Ontology (CO) project. The
      Crop Ontology has been created to compile validated concepts along with their
      inter-relationships on anatomy, structure and phenotype of Crops, on trait measurement
      and methods as well as on Germplasm with the multi-crop passport terms. The
      concepts of the CO are being used to curate agronomic databases and describe
      the data. The use of ontology terms to describe agronomic phenotypes and the
      accurate mapping of these descriptions into databases is important in comparative
      phenotypic and genotypic studies across species and gene-discovery experiments
      as it provides harmonized description of the data and therefore facilitates
      the retrieval of information.
    domains:
    - food
    - phenotype
    homepage: https://cropontology.org/term/CO_325:ROOT
    license: CC-BY-4.0
    name: Banana Ontology
    prefix: FAIRsharing.gdszhh
    subjects:
    - Agriculture
    - Life Science
    user_defined_tags:
    - Plant Phenotypes and Traits
  license: CC-BY-4.0
  mappings:
    agroportal: CO_325
    cropoct: CO_325
    fairsharing: FAIRsharing.gdszhh
    ols: co_325
  ols:
    contact: helpdesk@cropontology-curationtool.org
    description: Banana Trait Dictionary in template 5 - Bioversity & IITA - April
      2019
    download: https://cropontology.org/ontology/CO_325/Banana/owl
    homepage: https://cropontology.org/ontology/CO_325/Banana
    name: Banana ontology
    prefix: co_325
    version: '2019-10-09'
  pattern: ^\d{7}$
  preferred_prefix: CO_325
  prefix: co_325
  repository: https://github.com/bioversity/Crop-Ontology
  uri_format: https://cropontology.org/rdf/CO_325:$1
co_326:
  agroportal:
    contact:
      email: helpdesk@cropontology-curationtool.org
      name: Crop Ontology Helpdesk
    description: Coconut Ontology v1.0 - Coconut trait dictionary started by CIRAD,
      based on the "Guidelines for collecting coconut germplasm characterisation data
      during prospecting missions", COGENT (to be published); the "Descriptors for
      Coconut, (Cocos nucifera L.)", IPGRI (1995); and the "Manual on standardized
      research techniques in coconut breeding", IPGRI (1996).
    homepage: https://cropontology.org/term/CO_326:ROOT
    license: CC-BY-4.0
    name: Coconut Ontology
    prefix: CO_326
    version: '1.0'
  contact:
    email: e.arnaud@cgiar.org
    github: null
    name: Elizabeth Arnaud
    orcid: 0000-0002-6020-5919
  contact_group_email: helpdesk@cropontology-curationtool.org
  cropoct:
    download_owl: http://cropontology.org/rdf/CO_326.owl
    homepage: http://cropontology.org/term/CO_326:ROOT
    name: Coconut ontology
    prefix: CO_326
  example: '0000254'
  license: CC-BY-4.0
  mappings:
    agroportal: CO_326
    cropoct: CO_326
    ols: co_326
  ols:
    contact: helpdesk@cropontology-curationtool.org
    description: Draft version
    download: https://cropontology.org/ontology/CO_326/Coconut/owl
    homepage: https://cropontology.org/ontology/CO_326/Coconut
    name: Coconut ontology
    prefix: co_326
  pattern: ^\d{7}$
  preferred_prefix: CO_326
  prefix: co_326
  repository: https://github.com/bioversity/Crop-Ontology
  uri_format: https://cropontology.org/rdf/CO_326:$1
co_327:
  agroportal:
    contact:
      email: helpdesk@cropontology-curationtool.org
      name: Crop Ontology Helpdesk
    description: Pearl millet Trait Dictionary in template 5.
    example_uri: http://www.cropontology.org/rdf/CO_327:0000185
    homepage: http://www.cropontology.org/
    license: CC-BY-4.0
    name: Pearl Millet Ontology
    prefix: CO_327
    repository: https://github.com/Planteome/CO_327-pearl-millet-traits
    version: April 2016
  contact:
    email: e.arnaud@cgiar.org
    github: null
    name: Elizabeth Arnaud
    orcid: 0000-0002-6020-5919
  contact_group_email: helpdesk@cropontology-curationtool.org
  cropoct:
    description: Pearl millet Trait Dictionary in template 5 - ICRISAT/INERA - April
      2016 - Updated with onfarm trial traits from 1000Farms project, 2024
    download_owl: http://cropontology.org/rdf/CO_327.owl
    homepage: http://cropontology.org/term/CO_327:ROOT
    name: Pearl millet ontology
    prefix: CO_327
  example: 0000095
  fairsharing:
    abbreviation: CO_327
    description: The goal of the CGIAR Pearl Millet Ontology is to help improve food
      security for subsistence smallholder farmers in East and West Africa with productive
      and nutritious pearl millet food and fodder production technologies.
    domains:
    - phenotype
    homepage: https://cropontology.org/term/CO_327:ROOT
    license: CC-BY-4.0
    name: Pearl Millet Ontology
    prefix: FAIRsharing.4e3qh9
    subjects:
    - Agriculture
    - Botany
    user_defined_tags:
    - Plant Phenotypes and Traits
  license: CC-BY-4.0
  mappings:
    agroportal: CO_327
    cropoct: CO_327
    fairsharing: FAIRsharing.4e3qh9
    ols: co_327
  ols:
    contact: helpdesk@cropontology-curationtool.org
    description: Pearl millet Trait Dictionary in template 5 - ICRISAT/INERA - April
      2016
    download: http://www.cropontology.org/ontology/CO_327/Pearl%20millet/owl
    homepage: http://www.cropontology.org/ontology/CO_327/Pearl%20millet
    name: Pearl millet ontology
    prefix: co_327
  pattern: ^\d{7}$
  preferred_prefix: CO_327
  prefix: co_327
  repository: https://github.com/bioversity/Crop-Ontology
  uri_format: https://cropontology.org/rdf/CO_327:$1
co_330:
  agroportal:
    contact:
      email: helpdesk@cropontology-curationtool.org
      name: Crop Ontology Helpdesk
    description: (to come)
    example_uri: http://www.cropontology.org/rdf/CO_330:0000056/2
    homepage: http://www.cropontology.org/
    license: CC-BY-4.0
    name: Potato Ontology
    prefix: CO_330
    repository: https://github.com/Planteome/CO_330-potato-traits
    version: december 2017
  contact:
    email: e.arnaud@cgiar.org
    github: null
    name: Elizabeth Arnaud
    orcid: 0000-0002-6020-5919
  contact_group_email: helpdesk@cropontology-curationtool.org
  cropoct:
    description: CIP - potato ontology - december 2018
    download_owl: http://cropontology.org/rdf/CO_330.owl
    homepage: http://cropontology.org/term/CO_330:ROOT
    name: Potato ontology
    prefix: CO_330
  example: '0000106'
  fairsharing:
    abbreviation: CO_330
    description: Reference Plant Ontologies are being developed in the context of
      the Planteome project and are being integrated with the Crop Ontology, which
      provides harmonized breeders’ trait names, measurement methods, scales and standard
      variables for many crops. The Potato Ontology is one of these reference plant
      ontologies integrated within the Crop Ontology.
    domains:
    - phenotype
    homepage: https://cropontology.org/term/CO_330:ROOT
    license: CC-BY-4.0
    name: Potato Ontology
    prefix: FAIRsharing.4fa657
    subjects:
    - Agriculture
    - Life Science
    - Botany
    user_defined_tags:
    - Plant Phenotypes and Traits
  license: CC-BY-4.0
  mappings:
    agroportal: CO_330
    cropoct: CO_330
    fairsharing: FAIRsharing.4fa657
    ols: co_330
  ols:
    contact: helpdesk@cropontology-curationtool.org
    description: CIP - potato ontology - december 2018
    download: https://cropontology.org/ontology/CO_330/Potato/owl
    homepage: https://cropontology.org/ontology/CO_330/Potato
    name: Potato ontology
    prefix: co_330
    version: '2019-10-09'
  pattern: ^\d{7}$
  preferred_prefix: CO_330
  prefix: co_330
  repository: https://github.com/bioversity/Crop-Ontology
  uri_format: https://cropontology.org/rdf/CO_330:$1
co_331:
  agroportal:
    contact:
      email: helpdesk@cropontology-curationtool.org
      name: Crop Ontology Helpdesk
    description: Sweet Potato Trait Dictionary in template v5
    example_uri: http://www.cropontology.org/rdf/CO_331:0000601/1
    homepage: http://www.cropontology.org/
    license: CC-BY-4.0
    name: Sweet Potato Ontology
    prefix: CO_331
    repository: https://github.com/Planteome/CO_331-sweetpotato-traits
    version: June 2016
  cropoct:
    description: Sweetpotato Trait Dictionary in template v5 - CIP - November 2019
    download_owl: http://cropontology.org/rdf/CO_331.owl
    homepage: http://cropontology.org/term/CO_331:ROOT
    name: Sweet Potato ontology
    prefix: CO_331
  example: 0000088
  fairsharing:
    abbreviation: CO_331
    contact:
      email: V.Hualla@cgiar.org
      name: Vilma Hualla Mamani
      orcid: 0000-0003-0595-5271
    description: Reference Plant Ontologies are being developed in the context of
      the Planteome project and are being integrated with the Crop Ontology, which
      provides harmonized breeders’ trait names, measurement methods, scales and standard
      variables for many crops. The Sweet Potato Ontology is one of these reference
      plant ontologies integrated within the Crop Ontology.
    domains:
    - food
    homepage: https://cropontology.org/term/CO_331:ROOT
    license: CC-BY-4.0
    name: Sweet Potato Ontology
    prefix: FAIRsharing.4g5qcw
    subjects:
    - Agriculture
    - Life Science
    - Botany
  license: CC-BY-4.0
  mappings:
    agroportal: CO_331
    cropoct: CO_331
    fairsharing: FAIRsharing.4g5qcw
    ols: co_331
  ols:
    contact: helpdesk@cropontology-curationtool.org
    description: Sweet Potato Trait Dictionary in template v5 - CIP - November 2019
    download: http://www.cropontology.org/ontology/CO_331/Sweet%20Potato/owl
    homepage: http://www.cropontology.org/ontology/CO_331/Sweet%20Potato
    name: Sweet Potato ontology
    prefix: co_331
  pattern: ^\d{7}$
  preferred_prefix: CO_331
  prefix: co_331
  repository: https://github.com/bioversity/Crop-Ontology
  uri_format: https://cropontology.org/rdf/CO_331:$1
co_333:
  agroportal:
    contact:
      email: helpdesk@cropontology-curationtool.org
      name: Crop Ontology Helpdesk
    description: This ontology was built as part of the AKER project. It describes
      variables used in beet phenotyping (experimental properties and measurement
      scale) for each institution (INRA, Geves, ITB, Unversité d'Angers) and breeding
      companies (Florimond Desprez).
    example_uri: http://www.cropontology.org/rdf/CO_333:0001137
    homepage: http://www.cropontology.org/
    license: CC-BY-4.0
    name: Beet Ontology
    prefix: CO_333
    repository: https://forgemia.inra.fr/urgi-is/ontologies/-/tree/develop/Beet
    version: November 2017
  contact:
    email: e.arnaud@cgiar.org
    github: null
    name: Elizabeth Arnaud
    orcid: 0000-0002-6020-5919
  contact_group_email: helpdesk@cropontology-curationtool.org
  cropoct:
    description: 'This ontology was built as part of the AKER project. It describes
      variables used in beet phenotyping (experimental properties and measurement
      scale) for each institution (INRAE, Geves, ITB) and breeding companies (Florimond
      Desprez). Curator: Dorothee Charruaud (ADRINORD - URGI) Daphne Verdelet (Florimond
      Desprez) - First submission in November 2017.'
    download_owl: http://cropontology.org/rdf/CO_333.owl
    homepage: http://cropontology.org/term/CO_333:ROOT
    name: Beet Ontology ontology
    prefix: CO_333
  example: '3000045'
  fairsharing:
    abbreviation: CO_333
    description: This ontology was built as part of the AKER project. It describes
      variables used in beet phenotyping (experimental properties and measurement
      scale) for each institution and breeding company within the project. Reference
      Plant Ontologies are being developed in the context of the Planteome project
      and are being integrated with the Crop Ontology, which provides harmonized breeders’
      trait names, measurement methods, scales and standard variables for many crops.
      The Beet Ontology is one of these reference plant ontologies integrated within
      the Crop Ontology.
    domains:
    - food
    - phenotype
    homepage: https://cropontology.org/term/CO_333:ROOT
    license: CC-BY-4.0
    name: Beet Ontology
    prefix: FAIRsharing.af5655
    subjects:
    - Agriculture
    - Life Science
    - Plant Breeding
    - Botany
    user_defined_tags:
    - Plant Phenotypes and Traits
  license: CC-BY-4.0
  mappings:
    agroportal: CO_333
    cropoct: CO_333
    fairsharing: FAIRsharing.af5655
    ols: co_333
  ols:
    contact: helpdesk@cropontology-curationtool.org
    description: 'This ontology was built as part of the AKER project. It describes
      variables used in beet phenotyping (experimental properties and measurement
      scale) for each institution (INRAE, Geves, ITB) and breeding companies (Florimond
      Desprez). Curator: Dorothee Charruaud (ADRINORD - URGI) Daphne Verdelet (Florimond
      Desprez) - First submission in November 2017.'
    download: http://www.cropontology.org/ontology/CO_333/Beet%20Ontology/owl
    homepage: http://www.cropontology.org/ontology/CO_333/Beet%20Ontology
    name: Beet Ontology ontology
    prefix: co_333
  pattern: ^\d+$
  preferred_prefix: CO_333
  prefix: co_333
  repository: https://github.com/bioversity/Crop-Ontology
  uri_format: https://cropontology.org/rdf/CO_333:$1
co_334:
  agroportal:
    contact:
      email: helpdesk@cropontology-curationtool.org
      name: Crop Ontology Helpdesk
    description: This ontology is a part of the the Crop Ontology project, as an essential
      source of traits and variables to support the standardization of the breeding
      databases.
    example_uri: http://www.cropontology.org/rdf/CO_334:0100676
    homepage: http://www.cropontology.org/
    license: CC-BY-4.0
    name: Cassava Ontology
    prefix: CO_334
    publications:
    - http://www.cropontology.org/
    repository: https://github.com/Planteome/CO_334-cassava-traits
    version: February 2016
  contact:
    email: e.arnaud@cgiar.org
    github: null
    name: Elizabeth Arnaud
    orcid: 0000-0002-6020-5919
  contact_group_email: helpdesk@cropontology-curationtool.org
  cropoct:
    description: Cassava Trait Dictionary in template 5 - IITA - July 2015, updated
      in February 2016,   and in 2023 for the traits from on farm trials
    download_owl: http://cropontology.org/rdf/CO_334.owl
    homepage: http://cropontology.org/term/CO_334:ROOT
    name: Cassava ontology
    prefix: CO_334
  example: '0000070'
  fairsharing:
    abbreviation: CO_334
    description: Crop-specific trait ontologies enhance the interoperability and effectiveness
      of data exchange between the data sources which adopt it, by providing standard
      concepts that are use to describe phenotypes stored in those sources. As one
      of them, the Cassava Ontology is actively used and shared in different databases
      such as the BMS (Breeding Management system) of the IBP or the CassavaBase.
      Cassava, a major staple crop, is the main source of calories for 500 million
      people across the globe. A perennial woody shrub native to Latin America, cassava
      is primarily grown as an annual crop in the humid tropics. A cash crop as well
      as a subsistence crop, cassava's large edible starchy roots are a source of
      low-cost carbohydrates for millions. Cassava end products range from fresh roots
      cooked, boiled, baked or fried at the household level, to highly processed starch
      as a food additive.
    domains:
    - food
    - phenotype
    homepage: https://cropontology.org/term/CO_334:ROOT
    license: CC-BY-4.0
    name: IBP Cassava Trait Ontology
    prefix: FAIRsharing.v06c4q
    repository: https://github.com/Planteome/ibp-cassava-traits
    subjects:
    - Agriculture
    - Botany
    - Nutritional Science
    user_defined_tags:
    - Plant Phenotypes and Traits
  license: CC-BY-4.0
  mappings:
    agroportal: CO_334
    cropoct: CO_334
    fairsharing: FAIRsharing.v06c4q
    ols: co_334
  ols:
    contact: helpdesk@cropontology-curationtool.org
    description: Cassava Trait Dictionary in template 5 - IITA - July 2015, updated
      in February 2016
    download: https://cropontology.org/ontology/CO_334/Cassava/owl
    homepage: https://cropontology.org/ontology/CO_334/Cassava
    name: Cassava ontology
    prefix: co_334
    version: '2019-10-09'
  pattern: ^\d{7}$
  preferred_prefix: CO_334
  prefix: co_334
  repository: https://github.com/bioversity/Crop-Ontology
  uri_format: https://cropontology.org/rdf/CO_334:$1
co_335:
  agroportal:
    contact:
      email: helpdesk@cropontology-curationtool.org
      name: Crop Ontology Helpdesk
    description: This ontology is a part of the the Crop Ontology project, as an essential
      source of traits and variables to support the standardization of the breeding
      databases.
    example_uri: http://www.cropontology.org/rdf/CO_335:0000475/4
    homepage: http://www.cropontology.org/
    license: CC-BY-4.0
    name: Common Bean Ontology
    prefix: CO_335
    repository: https://github.com/Planteome/CO_335-common-bean-traits
    version: August 2014
  contact:
    email: e.arnaud@cgiar.org
    github: null
    name: Elizabeth Arnaud
    orcid: 0000-0002-6020-5919
  contact_group_email: helpdesk@cropontology-curationtool.org
  cropoct:
    description: CIAT Common bean trait dictionary - Updated  version Nov. 2023,  with
      the traits and variables for on farm comparative ranking of varieties
    download_owl: http://cropontology.org/rdf/CO_335.owl
    homepage: http://cropontology.org/term/CO_335:ROOT
    name: Common bean ontology
    prefix: CO_335
  example: 0000189
  fairsharing:
    abbreviation: CO_335
    description: Reference Plant Ontologies are being developed in the context of
      the Planteome project and are being integrated with the Crop Ontology, which
      provides harmonized breeders’ trait names, measurement methods, scales and standard
      variables for many crops. The Common Bean Ontology is one of these reference
      plant ontologies integrated within the Crop Ontology.
    domains:
    - food
    homepage: https://cropontology.org/term/CO_335:ROOT
    license: CC-BY-4.0
    name: Common Bean Ontology
    prefix: FAIRsharing.a14123
    subjects:
    - Agriculture
    - Botany
  license: CC-BY-4.0
  mappings:
    agroportal: CO_335
    cropoct: CO_335
    fairsharing: FAIRsharing.a14123
    ols: co_335
  ols:
    contact: helpdesk@cropontology-curationtool.org
    description: CIAT Common bean trait dictionary - version August 2014
    download: http://www.cropontology.org/ontology/CO_335/Common%20Bean/owl
    homepage: http://www.cropontology.org/ontology/CO_335/Common%20Bean
    name: Common Bean ontology
    prefix: co_335
  pattern: ^\d{7}$
  preferred_prefix: CO_335
  prefix: co_335
  repository: https://github.com/bioversity/Crop-Ontology
  uri_format: https://cropontology.org/rdf/CO_335:$1
co_336:
  agroportal:
    contact:
      email: helpdesk@cropontology-curationtool.org
      name: Crop Ontology Helpdesk
    description: Soybean Trait Dictionary in template v5
    example_uri: http://www.cropontology.org/rdf/CO_336:0000230/2
    homepage: http://www.cropontology.org/
    license: CC-BY-4.0
    name: Soybean Ontology
    prefix: CO_336
    repository: https://github.com/Planteome/CO_336-soybean-traits
    version: July 2015
  contact:
    email: e.arnaud@cgiar.org
    github: null
    name: Elizabeth Arnaud
    orcid: 0000-0002-6020-5919
  contact_group_email: helpdesk@cropontology-curationtool.org
  cropoct:
    description: Soybean Trait Dictionary in template v5 - IITA - July 2015
    download_owl: http://cropontology.org/rdf/CO_336.owl
    homepage: http://cropontology.org/term/CO_336:ROOT
    name: Soybean ontology
    prefix: CO_336
  example: 0000339
  fairsharing:
    abbreviation: CO_336
    contact:
      email: e.arnaud@cgiar.org
      name: Elizabeth Arnaud
      orcid: 0000-0002-6020-5919
    description: The Soybean Ontology is part of the Crop Ontology (CO) project. The
      Crop Ontology has been created to compile validated concepts along with their
      inter-relationships on anatomy, structure and phenotype of Crops, on trait measurement
      and methods as well as on Germplasm with the multi-crop passport terms. The
      concepts of the CO are being used to curate agronomic databases and describe
      the data. The use of ontology terms to describe agronomic phenotypes and the
      accurate mapping of these descriptions into databases is important in comparative
      phenotypic and genotypic studies across species and gene-discovery experiments
      as it provides harmonized description of the data and therefore facilitates
      the retrieval of information.
    domains:
    - food
    - phenotype
    homepage: https://cropontology.org/term/CO_336:ROOT
    license: CC-BY-4.0
    name: Soybean Ontology
    prefix: FAIRsharing.j75srj
    subjects:
    - Agriculture
    - Life Science
    user_defined_tags:
    - Plant Phenotypes and Traits
  license: CC-BY-4.0
  mappings:
    agroportal: CO_336
    cropoct: CO_336
    fairsharing: FAIRsharing.j75srj
    ols: co_336
  ols:
    contact: helpdesk@cropontology-curationtool.org
    description: Soybean Trait Dictionary in template v5 - IITA - July 2015
    download: https://cropontology.org/ontology/CO_336/Soybean/owl
    homepage: https://cropontology.org/ontology/CO_336/Soybean
    name: Soybean ontology
    prefix: co_336
  pattern: ^\d{7}$
  preferred_prefix: CO_336
  prefix: co_336
  repository: https://github.com/bioversity/Crop-Ontology
  uri_format: https://cropontology.org/rdf/CO_336:$1
co_337:
  agroportal:
    contact:
      email: tm.shah@cgiar.org
      name: Trushar Shah
    description: This ontology is a part of the the Crop Ontology project , as an
      essential source of traits and variables to support the standardization of the
      breeding databases.
    example_uri: http://www.cropontology.org/rdf/CO_337:0000006
    homepage: http://www.cropontology.org/
    license: CC-BY-4.0
    name: Groundnut Ontology
    prefix: CO_337
    repository: https://github.com/Planteome/CO_337-groundnut-traits
    version: Sept 2015
  contact:
    email: tm.shah@cgiar.org
    github: null
    name: Trushar Shah
    orcid: 0000-0002-0091-7981
  cropoct:
    description: Groundnut Trait Dictionary in template v5 - ICRISAT/ISRA/DARS - Sept
      2015 -Updated Nov 2023 with traits from the on farm trials for the comparative
      ranking of varieties
    download_owl: http://cropontology.org/rdf/CO_337.owl
    homepage: http://cropontology.org/term/CO_337:ROOT
    name: Groundnut ontology
    prefix: CO_337
  example: '0000054'
  fairsharing:
    abbreviation: CO_337
    description: The Groundnut Ontology is part of the Crop Ontology (CO) project.
      The Crop Ontology has been created to compile validated concepts along with
      their inter-relationships on anatomy, structure and phenotype of Crops, on trait
      measurement and methods as well as on Germplasm with the multi-crop passport
      terms. The concepts of the CO are being used to curate agronomic databases and
      describe the data. The use of ontology terms to describe agronomic phenotypes
      and the accurate mapping of these descriptions into databases is important in
      comparative phenotypic and genotypic studies across species and gene-discovery
      experiments as it provides harmonized description of the data and therefore
      facilitates the retrieval of information.
    domains:
    - food
    - phenotype
    homepage: https://cropontology.org/term/CO_337:ROOT
    license: CC-BY-4.0
    name: Groundnut Ontology
    prefix: FAIRsharing.ge8y23
    subjects:
    - Agriculture
    - Life Science
    - Botany
    user_defined_tags:
    - Plant Phenotypes and Traits
  license: CC-BY-4.0
  mappings:
    agroportal: CO_337
    cropoct: CO_337
    fairsharing: FAIRsharing.ge8y23
    ols: co_337
  ols:
    contact: helpdesk@cropontology-curationtool.org
    description: Groundnut Trait Dictionary in template v5 - ICRISAT/ISRA/DARS - Sept
      2015
    download: https://cropontology.org/ontology/CO_337/Groundnut/owl
    homepage: https://cropontology.org/ontology/CO_337/Groundnut
    name: Groundnut ontology
    prefix: co_337
    version: '2019-10-09'
  pattern: ^\d{7}$
  preferred_prefix: CO_337
  prefix: co_337
  repository: https://github.com/bioversity/Crop-Ontology
  uri_format: https://cropontology.org/rdf/CO_337:$1
co_338:
  agroportal:
    contact:
      email: tm.shah@cgiar.org
      name: Trushar Shah
    description: This ontology is a part of the the Crop Ontology project, as an essential
      source of traits and variables to support the standardization of the breeding
      databases.
    example_uri: http://www.cropontology.org/rdf/CO_338:0000344
    homepage: http://www.cropontology.org/
    license: CC-BY-4.0
    name: Chickpea Ontology
    prefix: CO_338
    repository: https://github.com/Planteome/CO_338-chickpea-traits
    version: July 2015
  contact:
    email: tm.shah@cgiar.org
    github: null
    name: Trushar Shah
    orcid: 0000-0002-0091-7981
  cropoct:
    description: Chickpea Trait Dictionary in template v5 - ICRISAT - July 2015
    download_owl: http://cropontology.org/rdf/CO_338.owl
    homepage: http://cropontology.org/term/CO_338:ROOT
    name: Chickpea ontology
    prefix: CO_338
  example: 0000138
  fairsharing:
    abbreviation: CO_338
    description: Development of crop-specific trait ontologies including the Chickpea
      Ontology began in 2008 as part of the Crop Ontology (CO) project. The Crop Ontology
      has been created to compile validated concepts along with their inter-relationships
      on anatomy, structure and phenotype of Crops, on trait measurement and methods
      as well as on Germplasm with the multi-crop passport terms. The concepts of
      the CO are being used to curate agronomic databases and describe the data. The
      use of ontology terms to describe agronomic phenotypes and the accurate mapping
      of these descriptions into databases is important in comparative phenotypic
      and genotypic studies across species and gene-discovery experiments as it provides
      harmonized description of the data and therefore facilitates the retrieval of
      information.
    domains:
    - food
    - phenotype
    homepage: https://cropontology.org/term/CO_338:ROOT
    license: CC-BY-4.0
    name: Chickpea Ontology
    prefix: FAIRsharing.js20q3
    subjects:
    - Agriculture
    - Botany
    user_defined_tags:
    - Plant Phenotypes and Traits
  license: CC-BY-4.0
  mappings:
    agroportal: CO_338
    cropoct: CO_338
    fairsharing: FAIRsharing.js20q3
    ols: co_338
  ols:
    contact: helpdesk@cropontology-curationtool.org
    description: Chickpea Trait Dictionary in template v5 - ICRISAT - July 2015
    download: https://cropontology.org/ontology/CO_338/Chickpea/owl
    homepage: https://cropontology.org/ontology/CO_338/Chickpea
    name: Chickpea ontology
    prefix: co_338
    version: '2019-10-09'
  pattern: ^\d{7}$
  preferred_prefix: CO_338
  prefix: co_338
  repository: https://github.com/bioversity/Crop-Ontology
  uri_format: https://cropontology.org/rdf/CO_338:$1
co_339:
  agroportal:
    contact:
      email: helpdesk@cropontology-curationtool.org
      name: Crop Ontology Helpdesk
    description: This ontology is a part of the the Crop Ontology project, as an essential
      source of traits and variables to support the standardization of the breeding
      databases.
    example_uri: http://www.cropontology.org/rdf/CO_339:0000117
    homepage: http://www.cropontology.org/
    license: CC-BY-4.0
    name: Lentil Ontology
    prefix: CO_339
    repository: https://github.com/Planteome/CO_339-lentil-traits
    version: July 2015
  contact:
    email: e.arnaud@cgiar.org
    github: null
    name: Elizabeth Arnaud
    orcid: 0000-0002-6020-5919
  contact_group_email: helpdesk@cropontology-curationtool.org
  cropoct:
    description: Lentil Trait Dictionary in template v5 - ICARDA - July 2015
    download_owl: http://cropontology.org/rdf/CO_339.owl
    homepage: http://cropontology.org/term/CO_339:ROOT
    name: Lentil ontology
    prefix: CO_339
  example: '0000032'
  fairsharing:
    abbreviation: CO_339
    description: The Lentil Ontology is part of the Crop Ontology (CO) project. The
      Crop Ontology has been created to compile validated concepts along with their
      inter-relationships on anatomy, structure and phenotype of Crops, on trait measurement
      and methods as well as on Germplasm with the multi-crop passport terms. The
      concepts of the CO are being used to curate agronomic databases and describe
      the data. The use of ontology terms to describe agronomic phenotypes and the
      accurate mapping of these descriptions into databases is important in comparative
      phenotypic and genotypic studies across species and gene-discovery experiments
      as it provides harmonized description of the data and therefore facilitates
      the retrieval of information.
    domains:
    - food
    - phenotype
    homepage: https://cropontology.org/term/CO_339:ROOT
    license: CC-BY-4.0
    name: Lentil Ontology
    prefix: FAIRsharing.ry1ezg
    subjects:
    - Agriculture
    - Life Science
    - Botany
    user_defined_tags:
    - Plant Phenotypes and Traits
  license: CC-BY-4.0
  mappings:
    agroportal: CO_339
    cropoct: CO_339
    fairsharing: FAIRsharing.ry1ezg
    ols: co_339
  ols:
    contact: helpdesk@cropontology-curationtool.org
    description: Lentil Trait Dictionary in template v5 - ICARDA - July 2015
    download: https://cropontology.org/ontology/CO_339/Lentil/owl
    homepage: https://cropontology.org/ontology/CO_339/Lentil
    name: Lentil ontology
    prefix: co_339
    version: '2019-10-09'
  pattern: ^\d{7}$
  preferred_prefix: CO_339
  prefix: co_339
  repository: https://github.com/bioversity/Crop-Ontology
  uri_format: https://cropontology.org/rdf/CO_339:$1
co_340:
  agroportal:
    contact:
      email: helpdesk@cropontology-curationtool.org
      name: Crop Ontology Helpdesk
    description: This ontology is a part of the the Crop Ontology project (http://www.cropontology.org),
      created in 2008 by the CGIAR, as an essential source of traits and variables
      to support the standardization of the breeding databases.
    example_uri: http://www.cropontology.org/rdf/CO_340:0000388/4
    homepage: http://www.cropontology.org/
    license: CC-BY-4.0
    name: Cowpea Ontology
    prefix: CO_340
    publications:
    - http://www.cropontology.org/
    repository: https://github.com/Planteome/CO_340-cowpea-traits
    version: August 2015
  contact:
    email: e.arnaud@cgiar.org
    github: null
    name: Elizabeth Arnaud
    orcid: 0000-0002-6020-5919
  contact_group_email: helpdesk@cropontology-curationtool.org
  cropoct:
    description: Cowpea Trait Dictionary - IITA - August 2015 - Updated Nov 2023 with
      the traits and variables for on farm comparative ranking of varieties
    download_owl: http://cropontology.org/rdf/CO_340.owl
    homepage: http://cropontology.org/term/CO_340:ROOT
    name: Cowpea ontology
    prefix: CO_340
  example: 0000639
  fairsharing:
    abbreviation: CO_340
    description: The Cowpea Trait Ontology is part of the Crop Ontology (CO) project.
      The Crop Ontology has been created to compile validated concepts along with
      their inter-relationships on anatomy, structure and phenotype of Crops, on trait
      measurement and methods as well as on Germplasm with the multi-crop passport
      terms. The concepts of the CO are being used to curate agronomic databases and
      describe the data. The use of ontology terms to describe agronomic phenotypes
      and the accurate mapping of these descriptions into databases is important in
      comparative phenotypic and genotypic studies across species and gene-discovery
      experiments as it provides harmonized description of the data and therefore
      facilitates the retrieval of information.
    domains:
    - food
    - phenotype
    homepage: https://cropontology.org/term/CO_340:ROOT
    license: CC-BY-4.0
    name: IBP Cowpea Trait Ontology
    prefix: FAIRsharing.31apg2
    publications:
    - doi: 10.3389/fphys.2012.00326
      pubmed: '22934074'
      title: Bridging the phenotypic and genetic data useful for integrated breeding
        through a data annotation using the Crop Ontology developed by the crop communities
        of practice
      year: 2012
    subjects:
    - Agriculture
    - Botany
    user_defined_tags:
    - Plant Phenotypes and Traits
  license: CC-BY-4.0
  mappings:
    agroportal: CO_340
    cropoct: CO_340
    fairsharing: FAIRsharing.31apg2
    ols: co_340
  ols:
    contact: helpdesk@cropontology-curationtool.org
    description: Cowpea Trait Dictionary in template v5 - IITA - August 2015
    download: https://cropontology.org/ontology/CO_340/Cowpea/owl
    homepage: https://cropontology.org/ontology/CO_340/Cowpea
    name: Cowpea ontology
    prefix: co_340
    version: '2019-10-09'
  pattern: ^\d{7}$
  preferred_prefix: CO_340
  prefix: co_340
  publications:
  - doi: 10.3389/fphys.2012.00326
    pmc: PMC3429094
    pubmed: '22934074'
    title: Bridging the phenotypic and genetic data useful for integrated breeding
      through a data annotation using the Crop Ontology developed by the crop communities
      of practice
    year: 2012
  - doi: 10.3389/fphys.2012.00326
    pmc: null
    pubmed: '22934074'
    title: Bridging the phenotypic and genetic data useful for integrated breeding
      through a data annotation using the Crop Ontology developed by the crop communities
      of practice
    year: 2012
  repository: https://github.com/bioversity/Crop-Ontology
  uri_format: https://cropontology.org/rdf/CO_340:$1
co_341:
  agroportal:
    contact:
      email: helpdesk@cropontology-curationtool.org
      name: Crop Ontology Helpdesk
    description: Pigeonpea Trait Dictionary in template v5
    example_uri: http://www.cropontology.org/rdf/CO_341:0000015
    homepage: http://www.cropontology.org/
    license: CC-BY-4.0
    name: Pigeon Pea Ontology
    prefix: CO_341
    repository: https://github.com/Planteome/CO_341-pigeonpea-traits
    version: July 2015
  contact:
    email: e.arnaud@cgiar.org
    github: null
    name: Elizabeth Arnaud
    orcid: 0000-0002-6020-5919
  contact_group_email: helpdesk@cropontology-curationtool.org
  cropoct:
    description: Pigeonpea Trait Dictionary in template v5 - ICRISAT - July 2015
    download_owl: http://cropontology.org/rdf/CO_341.owl
    homepage: http://cropontology.org/term/CO_341:ROOT
    name: Pigeonpea ontology
    prefix: CO_341
  example: '0000140'
  fairsharing:
    abbreviation: CO_341
    contact:
      email: e.arnaud@cgiar.org
      name: Elizabeth Arnaud
      orcid: 0000-0002-6020-5919
    description: Reference Plant Ontologies are being developed in the context of
      the Planteome project and are being integrated with the Crop Ontology, which
      provides harmonized breeders’ trait names, measurement methods, scales and standard
      variables for many crops. The Pigeon Pea Ontology is one of these reference
      plant ontologies integrated within the Crop Ontology.
    domains:
    - food
    - phenotype
    homepage: https://cropontology.org/term/CO_341:ROOT
    license: CC-BY-4.0
    name: Pigeon Pea Ontology
    prefix: FAIRsharing.ehe3yp
    repository: https://github.com/Planteome/CO_341-pigeonpea-traits
    subjects:
    - Agriculture
    - Life Science
    - Botany
    user_defined_tags:
    - Plant Phenotypes and Traits
  license: CC-BY-4.0
  mappings:
    agroportal: CO_341
    cropoct: CO_341
    fairsharing: FAIRsharing.ehe3yp
    ols: co_341
  ols:
    contact: helpdesk@cropontology-curationtool.org
    description: Pigeonpea Trait Dictionary in template v5 - ICRISAT - July 2015
    download: https://cropontology.org/ontology/CO_341/Pigeonpea/owl
    homepage: https://cropontology.org/ontology/CO_341/Pigeonpea
    name: Pigeonpea ontology
    prefix: co_341
    version: '2019-11-18'
  pattern: ^\d{7}$
  preferred_prefix: CO_341
  prefix: co_341
  repository: https://github.com/bioversity/Crop-Ontology
  uri_format: https://cropontology.org/rdf/CO_341:$1
co_343:
  agroportal:
    contact:
      email: helpdesk@cropontology-curationtool.org
      name: Crop Ontology Helpdesk
    description: Yam trait ontology
    example_uri: http://www.cropontology.org/rdf/CO_343:0000357
    homepage: http://www.cropontology.org/
    license: CC-BY-4.0
    name: Yam Ontology
    prefix: CO_343
    repository: https://github.com/Planteome/CO_343-yam-traits
    version: Feb 2017
  contact:
    email: e.arnaud@cgiar.org
    github: null
    name: Elizabeth Arnaud
    orcid: 0000-0002-6020-5919
  contact_group_email: helpdesk@cropontology-curationtool.org
  cropoct:
    description: version 2019 - pvs
    download_owl: http://cropontology.org/rdf/CO_343.owl
    homepage: http://cropontology.org/term/CO_343:ROOT
    name: Yam ontology
    prefix: CO_343
  example: '0100010'
  fairsharing:
    abbreviation: CO_343
    description: Reference Plant Ontologies are being developed in the context of
      the Planteome project and are being integrated with the Crop Ontology, which
      provides harmonized breeders’ trait names, measurement methods, scales and standard
      variables for many crops. The Yam Ontology is one of these reference plant ontologies
      integrated within the Crop Ontology.
    domains:
    - food
    - phenotype
    homepage: https://cropontology.org/term/CO_343:ROOT
    license: CC-BY-4.0
    name: Yam Ontology
    prefix: FAIRsharing.7e9cff
    subjects:
    - Agriculture
    - Life Science
    - Botany
    user_defined_tags:
    - Plant Phenotypes and Traits
  license: CC-BY-4.0
  mappings:
    agroportal: CO_343
    cropoct: CO_343
    fairsharing: FAIRsharing.7e9cff
    ols: co_343
  ols:
    contact: helpdesk@cropontology-curationtool.org
    description: version 2019 - pvs
    download: https://cropontology.org/ontology/CO_343/Yam/owl
    homepage: https://cropontology.org/ontology/CO_343/Yam
    name: Yam ontology
    prefix: co_343
    version: '2019-10-09'
  pattern: ^\d{7}$
  preferred_prefix: CO_343
  prefix: co_343
  repository: https://github.com/bioversity/Crop-Ontology
  uri_format: https://cropontology.org/rdf/CO_343:$1
co_345:
  agroportal:
    contact:
      email: helpdesk@cropontology-curationtool.org
      name: Crop Ontology Helpdesk
    description: This ontology is a part of the the Crop Ontology project (http://www.cropontology.org),
      as an essential source of traits and variables to support the standardization
      of the breeding databases.
    example_uri: http://www.cropontology.org/rdf/CO_345:0000044
    homepage: http://www.cropontology.org/
    license: CC-BY-4.0
    name: Brachiaria Ontology
    prefix: CO_345
    repository: https://github.com/Planteome/CO_345-brachiaria-traits
    version: Oct 2016
  contact:
    email: e.arnaud@cgiar.org
    github: null
    name: Elizabeth Arnaud
    orcid: 0000-0002-6020-5919
  contact_group_email: helpdesk@cropontology-curationtool.org
  cropoct:
    description: Brachiaria (forages) ontology TD v5 - Version Oct 2016
    download_owl: http://cropontology.org/rdf/CO_345.owl
    homepage: http://cropontology.org/term/CO_345:ROOT
    name: Brachiaria ontology
    prefix: CO_345
  example: '0000127'
  fairsharing:
    abbreviation: CO_345
    description: Reference Plant Ontologies are being developed in the context of
      the Planteome project and are being integrated with the Crop Ontology, which
      provides harmonized breeders’ trait names, measurement methods, scales and standard
      variables for many crops. The Brachiaria Ontology is one of these reference
      plant ontologies integrated within the Crop Ontology.
    domains:
    - phenotype
    homepage: https://cropontology.org/term/CO_345:ROOT
    license: CC-BY-4.0
    name: Brachiaria Ontology
    prefix: FAIRsharing.9e9683
    subjects:
    - Agriculture
    - Life Science
    - Botany
    user_defined_tags:
    - Plant Phenotypes and Traits
  license: CC-BY-4.0
  mappings:
    agroportal: CO_345
    cropoct: CO_345
    fairsharing: FAIRsharing.9e9683
    ols: co_345
  ols:
    contact: helpdesk@cropontology-curationtool.org
    description: Brachiaria (forages) ontology TD v5 - Version Oct 2016
    download: https://cropontology.org/ontology/CO_345/Brachiaria/owl
    homepage: https://cropontology.org/ontology/CO_345/Brachiaria
    name: Brachiaria ontology
    prefix: co_345
    version: '2019-10-09'
  pattern: ^\d{7}$
  preferred_prefix: CO_345
  prefix: co_345
  repository: https://github.com/bioversity/Crop-Ontology
  uri_format: https://cropontology.org/rdf/CO_345:$1
co_346:
  agroportal:
    contact:
      email: helpdesk@cropontology-curationtool.org
      name: Crop Ontology Helpdesk
    description: This ontology is a part of the the Crop Ontology project , as an
      essential source of traits and variables to support the standardization of the
      breeding databases.
    example_uri: http://www.cropontology.org/rdf/CO_346:0000095
    homepage: http://www.cropontology.org/
    license: CC-BY-4.0
    name: Mungbean Ontology
    prefix: CO_346
    repository: https://agroportal.lirmm.fr/ontologies/CO_346
    version: Oct 2016
  contact:
    email: e.arnaud@cgiar.org
    github: null
    name: Elizabeth Arnaud
    orcid: 0000-0002-6020-5919
  contact_group_email: helpdesk@cropontology-curationtool.org
  cropoct:
    description: oct 2016
    download_owl: http://cropontology.org/rdf/CO_346.owl
    homepage: http://cropontology.org/term/CO_346:ROOT
    name: Mungbean ontology
    prefix: CO_346
  example: 0000199
  fairsharing:
    abbreviation: CO_346
    description: The Mungbean Ontology is part of the Crop Ontology (CO) project.
      The Crop Ontology has been created to compile validated concepts along with
      their inter-relationships on anatomy, structure and phenotype of Crops, on trait
      measurement and methods as well as on Germplasm with the multi-crop passport
      terms. The concepts of the CO are being used to curate agronomic databases and
      describe data.
    domains:
    - food
    - phenotype
    homepage: https://cropontology.org/term/CO_346:ROOT
    license: CC-BY-4.0
    name: Mungbean Ontology
    prefix: FAIRsharing.fgd5gq
    subjects:
    - Agriculture
    - Life Science
    user_defined_tags:
    - Plant Phenotypes and Traits
  license: CC-BY-4.0
  mappings:
    agroportal: CO_346
    cropoct: CO_346
    fairsharing: FAIRsharing.fgd5gq
    ols: co_346
  ols:
    contact: helpdesk@cropontology-curationtool.org
    description: oct 2016
    download: https://cropontology.org/ontology/CO_346/Mungbean/owl
    homepage: https://cropontology.org/ontology/CO_346/Mungbean
    name: Mungbean ontology
    prefix: co_346
    version: '2019-10-09'
  pattern: ^\d{7}$
  preferred_prefix: CO_346
  prefix: co_346
  repository: https://github.com/bioversity/Crop-Ontology
  uri_format: https://cropontology.org/rdf/CO_346:$1
co_347:
  agroportal:
    contact:
      email: helpdesk@cropontology-curationtool.org
      name: Crop Ontology Helpdesk
    description: This ontology is a part of the the Crop Ontology project, as an essential
      source of traits and variables to support the standardization of the breeding
      databases.
    example_uri: http://www.cropontology.org/rdf/CO_347:0000108
    homepage: http://www.cropontology.org/
    license: CC-BY-4.0
    name: Castor Bean Ontology
    prefix: CO_347
    repository: https://github.com/Planteome/CO_347-castorbean-traits
    version: March 2017
  contact:
    email: e.arnaud@cgiar.org
    github: null
    name: Elizabeth Arnaud
    orcid: 0000-0002-6020-5919
  contact_group_email: helpdesk@cropontology-curationtool.org
  cropoct:
    description: 'March 2017 version '
    download_owl: http://cropontology.org/rdf/CO_347.owl
    homepage: http://cropontology.org/term/CO_347:ROOT
    name: Castor bean ontology
    prefix: CO_347
  example: 0000108
  fairsharing:
    abbreviation: CO_347
    description: The Castor Bean Ontology is part of the Crop Ontology (CO) project.
      The Crop Ontology has been created to compile validated concepts along with
      their inter-relationships on anatomy, structure and phenotype of Crops, on trait
      measurement and methods as well as on Germplasm with the multi-crop passport
      terms. The concepts of the CO are being used to curate agronomic databases and
      describe data.
    domains:
    - food
    - phenotype
    homepage: https://cropontology.org/term/CO_347:ROOT
    license: CC-BY-4.0
    name: Castor Bean Ontology
    prefix: FAIRsharing.qrrvyk
    subjects:
    - Agriculture
    - Life Science
    - Botany
    user_defined_tags:
    - Plant Phenotypes and Traits
  license: CC-BY-4.0
  mappings:
    agroportal: CO_347
    cropoct: CO_347
    fairsharing: FAIRsharing.qrrvyk
    ols: co_347
  ols:
    contact: helpdesk@cropontology-curationtool.org
    description: 'March 2017 version '
    download: http://www.cropontology.org/ontology/CO_347/Castor%20bean/owl
    homepage: http://www.cropontology.org/ontology/CO_347/Castor%20bean
    name: Castor bean ontology
    prefix: co_347
  pattern: ^\d{7}$
  preferred_prefix: CO_347
  prefix: co_347
  repository: https://github.com/bioversity/Crop-Ontology
  uri_format: https://cropontology.org/rdf/CO_347:$1
co_348:
  agroportal:
    contact:
      email: helpdesk@cropontology-curationtool.org
      name: helpdesk cropontology
    description: Brassica Trait Ontology (BRaTO) hosts trait information to describe
      brassica crop data. Terms are collected from various projects including OREGIN,
      RIPR (UK) and Rapsodyn (France). BRATO development is conducted by Earlham Institute
      (UK), Southern Cross University (Australia) and INRA (France).
    example_uri: http://www.cropontology.org/rdf/CO_348:1000012
    homepage: http://www.cropontology.org/
    license: CC-BY-4.0
    name: Brassica Ontology
    prefix: CO_348
    repository: https://github.com/Brassica-Trait-Ontology/brato
    version: November 2017
  contact:
    email: e.arnaud@cgiar.org
    github: null
    name: Elizabeth Arnaud
    orcid: 0000-0002-6020-5919
  contact_group_email: helpdesk@cropontology-curationtool.org
  cropoct:
    description: Brassica Trait Ontology (BRaTO) hosts trait information to describe
      brassica crop data. Terms are collected from various projects including OREGIN,
      RIPR (UK) and Rapsodyn (France). BRATO development is conducted by Earlham Institute
      (UK), Southern Cross University (Australia) and INRA (France).
    download_owl: http://cropontology.org/rdf/CO_348.owl
    homepage: http://cropontology.org/term/CO_348:ROOT
    name: Brassica ontology
    prefix: CO_348
  example: '1100107'
  fairsharing:
    abbreviation: CO_348
    description: Brassica Trait Ontology (BRaTO) hosts trait information to describe
      brassica crop data. Terms are collected from various projects including OREGIN,
      RIPR (UK) and Rapsodyn (France). Reference Plant Ontologies are being developed
      in the context of the Planteome project and are being integrated with the Crop
      Ontology, which provides harmonized breeders’ trait names, measurement methods,
      scales and standard variables for many crops. The Brassica Ontology is one of
      these reference plant ontologies integrated within the Crop Ontology.
    domains:
    - phenotype
    homepage: https://cropontology.org/term/CO_348:ROOT
    license: CC-BY-4.0
    name: Brassica Ontology
    prefix: FAIRsharing.af7a2d
    repository: https://github.com/Brassica-Trait-Ontology/brato
    subjects:
    - Agriculture
    - Life Science
    - Botany
    user_defined_tags:
    - Plant Phenotypes and Traits
  license: CC-BY-4.0
  mappings:
    agroportal: CO_348
    cropoct: CO_348
    fairsharing: FAIRsharing.af7a2d
    ols: co_348
  ols:
    contact: helpdesk@cropontology-curationtool.org
    description: Brassica Trait Ontology (BRaTO) hosts trait information to describe
      brassica crop data. Terms are collected from various projects including OREGIN,
      RIPR (UK) and Rapsodyn (France). BRATO development is conducted by Earlham Institute
      (UK), Southern Cross University (Australia) and INRA (France).
    download: https://cropontology.org/ontology/CO_348/Brassica/owl
    homepage: https://cropontology.org/ontology/CO_348/Brassica
    name: Brassica ontology
    prefix: co_348
    version: '2019-11-29'
  pattern: ^\d+$
  preferred_prefix: CO_348
  prefix: co_348
  repository: https://github.com/bioversity/Crop-Ontology
  uri_format: https://cropontology.org/rdf/CO_348:$1
co_350:
  agroportal:
    contact:
      email: helpdesk@cropontology-curationtool.org
      name: Crop Ontology Helpdesk
    description: Oat trait dictionary commissioned by Oat Global (http://oatglobal.org/)
      to hold the traits used in the T3/Oat database (http://triticeaetoolbox.org/oat/).
    example_uri: http://www.cropontology.org/rdf/CO_350:0000091
    homepage: http://www.cropontology.org/
    license: CC-BY-4.0
    name: Oat Ontology
    prefix: CO_350
    repository: https://github.com/Planteome/CO_350-oat-traits
    version: '1.0'
  cropoct:
    description: Oat trait dictionary started by Oat Global (http://oatglobal.org/)
      and improved by NIAB and PepsiCo
    download_owl: http://cropontology.org/rdf/CO_350.owl
    homepage: http://cropontology.org/term/CO_350:ROOT
    name: Oat ontology
    prefix: CO_350
  example: '0000215'
  fairsharing:
    abbreviation: CO_350
    contact:
      email: jeanluc.work@gmail.com
      name: Jean-Luc Jannink
      orcid: 0000-0003-4849-628X
    description: Reference Plant Ontologies are being developed in the context of
      the Planteome project and are being integrated with the Crop Ontology, which
      provides harmonized breeders’ trait names, measurement methods, scales and standard
      variables for many crops. The Oat Trait Ontology is one of these reference plant
      ontologies integrated within the Crop Ontology. The Oat Trait Dictionary was
      commissioned by Oat Global (http://oatglobal.org/) to hold the traits used in
      the T3/Oat database (http://triticeaetoolbox.org/oat/).
    domains:
    - phenotype
    homepage: https://cropontology.org/term/CO_350:ROOT
    license: CC-BY-4.0
    name: Oat Trait Ontology
    prefix: FAIRsharing.35e1c3
    subjects:
    - Agriculture
    - Life Science
    - Botany
    user_defined_tags:
    - Plant Phenotypes and Traits
  license: CC-BY-4.0
  mappings:
    agroportal: CO_350
    cropoct: CO_350
    fairsharing: FAIRsharing.35e1c3
    ols: co_350
  ols:
    contact: helpdesk@cropontology-curationtool.org
    description: Oat trait dictionary started by Oat Global (http://oatglobal.org/)
      and improved by NIAB and PepsiCo
    download: https://cropontology.org/ontology/CO_350/Oat/owl
    homepage: https://cropontology.org/ontology/CO_350/Oat
    name: Oat ontology
    prefix: co_350
    version: '2019-10-09'
  pattern: ^\d{7}$
  preferred_prefix: CO_350
  prefix: co_350
  repository: https://github.com/bioversity/Crop-Ontology
  uri_format: https://cropontology.org/rdf/CO_350:$1
co_356:
  agroportal:
    contact:
      email: eric.duchene@inrae.fr
      name: Eric Duchêne
    description: Grape Ontology including OIV and bioversity descriptors.
    example_uri: http://www.cropontology.org/rdf/CO_356:1000182
    homepage: http://www.cropontology.org/
    license: CC-BY-4.0
    name: Vitis Ontology
    prefix: CO_356
    repository: https://forgemia.inra.fr/urgi-is/ontologies/-/tree/develop/Vitis
  cropoct:
    description: Grape Ontology including OIV and bioversity descriptors. INRA July
      2017
    download_owl: http://cropontology.org/rdf/CO_356.owl
    homepage: http://cropontology.org/term/CO_356:ROOT
    name: Vitis ontology
    prefix: CO_356
  example: '4000027'
  fairsharing:
    abbreviation: CO_356
    description: Reference Plant Ontologies are being developed in the context of
      the Planteome project and are being integrated with the Crop Ontology, which
      provides harmonized breeders’ trait names, measurement methods, scales and standard
      variables for many crops. The Vitis Ontology is one of these reference plant
      ontologies integrated within the Crop Ontology.
    domains:
    - phenotype
    homepage: https://cropontology.org/term/CO_356:ROOT
    license: CC BY-SA 4.0
    name: Vitis Ontology
    prefix: FAIRsharing.c7f4d7
    subjects:
    - Agriculture
    - Life Science
    - Botany
    user_defined_tags:
    - Plant Phenotypes and Traits
  license: CC-BY-4.0
  mappings:
    agroportal: CO_356
    cropoct: CO_356
    fairsharing: FAIRsharing.c7f4d7
    ols: co_356
  ols:
    contact: helpdesk@cropontology-curationtool.org
    description: Grape Ontology including OIV and bioversity descriptors. INRA July
      2017
    download: https://cropontology.org/ontology/CO_356/Vitis/owl
    homepage: https://cropontology.org/ontology/CO_356/Vitis
    name: Vitis ontology
    prefix: co_356
    version: '2019-11-29'
  pattern: ^\d+$
  preferred_prefix: CO_356
  prefix: co_356
  repository: https://github.com/bioversity/Crop-Ontology
  uri_format: https://cropontology.org/rdf/CO_356:$1
co_357:
  agroportal:
    contact:
      email: celia.michotey@inrae.fr
      name: Célia Michotey
    description: This ontology list all variables used for woody plant observations.
      Terms are collected from various sources (past and ongoing projects at national
      and international levels).
    example_uri: http://www.cropontology.org/rdf/CO_357:0000088
    license: CC-BY-4.0
    name: Woody Plant Ontology
    prefix: CO_357
    repository: https://forgemia.inra.fr/urgi-is/ontologies/-/tree/develop/Tree
    version: August 2017
  contact:
    email: celia.michotey@inrae.fr
    github: null
    name: Célia Michotey
    orcid: 0000-0003-1877-1703
  cropoct:
    description: 'This ontology lists all variables used for woody plant observations.
      Terms are collected from various sources (past and ongoing projects at national
      and international levels). Curators: Celia Michotey (INRAE) & Ines Chaves (ITQB
      NOVA/IBET) - Version 2 submitted on Jun 2020 by INRAE.'
    download_owl: http://cropontology.org/rdf/CO_357.owl
    homepage: http://cropontology.org/term/CO_357:ROOT
    name: Woody Plant Ontology ontology
    prefix: CO_357
  example: '1000290'
  fairsharing:
    abbreviation: CO_357
    description: 'The Woody Plant Ontology lists reference variables used for experimentations
      and observations on woody plants (forest trees and shrubs, and possibly fruit
      trees). It is an international initiative based on various communities (French,
      Portuguese and European). Terms are collected from various sources and organized
      following the Crop Ontology standard which provides harmonized variables composed
      by a triplet: (i) a trait, the studied character, (ii) a method, the measurement
      protocol and (iii) a scale, the unit of measurement or scoring scale. '
    domains:
    - phenotype
    homepage: https://doi.org/10.15454/JB2WCE
    license: CC-BY-4.0
    name: Woody Plant Ontology
    prefix: FAIRsharing.2b04ae
    subjects:
    - Life Science
    - Botany
  license: CC-BY-4.0
  mappings:
    agroportal: CO_357
    cropoct: CO_357
    fairsharing: FAIRsharing.2b04ae
    ols: co_357
  ols:
    contact: helpdesk@cropontology-curationtool.org
    description: 'This ontology lists all variables used for woody plant observations.
      Terms are collected from various sources (past and ongoing projects at national
      and international levels). Curators: Celia Michotey (INRAE) & Ines Chaves (IBET)
      - Version 2 submitted on Jun 2020 by INRAE.'
    download: http://www.cropontology.org/ontology/CO_357/Woody%20Plant%20Ontology/owl
    homepage: http://www.cropontology.org/ontology/CO_357/Woody%20Plant%20Ontology
    name: Woody Plant Ontology ontology
    prefix: co_357
  pattern: ^\d+$
  preferred_prefix: CO_357
  prefix: co_357
  repository: https://github.com/bioversity/Crop-Ontology
  uri_format: https://cropontology.org/rdf/CO_357:$1
co_358:
  agroportal:
    contact:
      email: helpdesk@cropontology-curationtool.org
      name: Crop Ontology Helpdesk
    description: This ontology is a part of the the Crop Ontology project, as an essential
      source of traits and variables to support the standardization of the breeding
      databases.
    example_uri: http://www.cropontology.org/rdf/CO_358:0000215
    homepage: http://www.cropontology.org/
    license: CC-BY-4.0
    name: Cotton Ontology
    prefix: CO_358
    repository: https://github.com/Planteome/CO_358-cotton-traits
    version: '2020-01-03'
  contact:
    email: e.arnaud@cgiar.org
    github: null
    name: Elizabeth Arnaud
    orcid: 0000-0002-6020-5919
  contact_group_email: helpdesk@cropontology-curationtool.org
  cropoct:
    description: Cotton ontology from CottonGen database - June 2019
    download_owl: http://cropontology.org/rdf/CO_358.owl
    homepage: http://cropontology.org/term/CO_358:ROOT
    name: Cotton ontology
    prefix: CO_358
  example: 0000139
  license: CC-BY-4.0
  mappings:
    agroportal: CO_358
    cropoct: CO_358
    ols: co_358
  ols:
    contact: helpdesk@cropontology-curationtool.org
    description: Cotton ontology from CottonGen database - June 2019
    download: https://cropontology.org/ontology/CO_358/Cotton/owl
    homepage: https://cropontology.org/ontology/CO_358/Cotton
    name: Cotton ontology
    prefix: co_358
    version: '2020-01-03'
  pattern: ^\d{7}$
  preferred_prefix: CO_358
  prefix: co_358
  repository: https://github.com/bioversity/Crop-Ontology
  uri_format: https://cropontology.org/rdf/CO_358:$1
co_359:
  agroportal:
    contact:
      email: helpdesk@cropontology-curationtool.org
      name: Crop Ontology Helpdesk
    description: To add
    example_uri: https://cropontology.org/rdf/CO_359:0000568
    homepage: https://www.cropontology.org/
    license: CC-BY-4.0
    name: Sunflower Ontology
    prefix: CO_359
    repository: https://github.com/Planteome/CO_359-sunflower-traits
    version: '2019-12-16'
  contact:
    email: e.arnaud@cgiar.org
    github: null
    name: Elizabeth Arnaud
    orcid: 0000-0002-6020-5919
  contact_group_email: helpdesk@cropontology-curationtool.org
  cropoct:
    description: December 2019
    download_owl: http://cropontology.org/rdf/CO_359.owl
    homepage: http://cropontology.org/term/CO_359:ROOT
    name: Sunflower ontology
    prefix: CO_359
  example: 0000947
  license: CC-BY-4.0
  mappings:
    agroportal: CO_359
    cropoct: CO_359
    ols: co_359
  ols:
    contact: helpdesk@cropontology-curationtool.org
    description: December 2019
    download: https://cropontology.org/ontology/CO_359/Sunflower/owl
    homepage: https://cropontology.org/ontology/CO_359/Sunflower
    name: Sunflower ontology
    prefix: co_359
  pattern: ^\d{7}$
  preferred_prefix: CO_359
  prefix: co_359
  repository: https://github.com/bioversity/Crop-Ontology
  uri_format: https://cropontology.org/rdf/CO_359:$1
co_360:
  agroportal:
    contact:
      email: helpdesk@cropontology-curationtool.org
      name: Crop Ontology Helpdesk
    description: Sugar Kelp trait ontology
    example_uri: http://www.cropontology.org/rdf/CO_360:0000085
    homepage: http://www.cropontology.org/
    license: CC-BY-4.0
    name: Sugar Kelp Ontology
    prefix: CO_360
    repository: https://github.com/Planteome/CO_360-sugar-kelp-traits
    version: June 2019
  contact:
    email: e.arnaud@cgiar.org
    github: null
    name: Elizabeth Arnaud
    orcid: 0000-0002-6020-5919
  contact_group_email: helpdesk@cropontology-curationtool.org
  cropoct:
    description: Sugar Kelp trait ontology
    download_owl: http://cropontology.org/rdf/CO_360.owl
    homepage: http://cropontology.org/term/CO_360:ROOT
    name: Sugar Kelp trait ontology
    prefix: CO_360
  example: '0000071'
  fairsharing:
    abbreviation: CO_360
    description: Reference Plant Ontologies are being developed in the context of
      the Planteome project and are being integrated with the Crop Ontology, which
      provides harmonized breeders’ trait names, measurement methods, scales and standard
      variables for many crops. The Sugar Kelp Trait Ontology is one of these reference
      plant ontologies integrated within the Crop Ontology.
    domains:
    - marine environment
    - phenotype
    homepage: https://cropontology.org/term/CO_360:ROOT
    license: CC-BY-4.0
    name: Sugar Kelp Trait Ontology
    prefix: FAIRsharing.1c1738
    subjects:
    - Life Science
    - Botany
    user_defined_tags:
    - Plant Phenotypes and Traits
  license: CC-BY-4.0
  mappings:
    agroportal: CO_360
    cropoct: CO_360
    fairsharing: FAIRsharing.1c1738
    ols: co_360
  ols:
    contact: helpdesk@cropontology-curationtool.org
    description: Sugar Kelp trait ontology
    download: http://www.cropontology.org/ontology/CO_360/Sugar%20Kelp%20trait/owl
    homepage: http://www.cropontology.org/ontology/CO_360/Sugar%20Kelp%20trait
    name: Sugar Kelp trait ontology
    prefix: co_360
  pattern: ^\d{7}$
  preferred_prefix: CO_360
  prefix: co_360
  repository: https://github.com/bioversity/Crop-Ontology
  uri_format: https://cropontology.org/rdf/CO_360:$1
co_365:
  agroportal:
    contact:
      email: helpdesk@cropontology-curationtool.org
      name: Crop Ontology Helpdesk
    description: to add
    example_uri: http://www.cropontology.org/rdf/CO_365:0000146
    homepage: http://www.cropontology.org
    license: CC-BY-4.0
    name: Fababean Ontology
    prefix: CO_365
    repository: https://github.com/Planteome/CO_365-faba-bean-traits
    version: '2019-10-15'
  contact:
    email: e.arnaud@cgiar.org
    github: null
    name: Elizabeth Arnaud
    orcid: 0000-0002-6020-5919
  contact_group_email: helpdesk@cropontology-curationtool.org
  cropoct:
    description: developed by ICARDA - Dec 2018
    download_owl: http://cropontology.org/rdf/CO_365.owl
    homepage: http://cropontology.org/term/CO_365:ROOT
    name: Fababean ontology
    prefix: CO_365
  example: '0000205'
  license: CC-BY-4.0
  mappings:
    agroportal: CO_365
    cropoct: CO_365
    ols: co_365
  ols:
    contact: helpdesk@cropontology-curationtool.org
    description: developed by ICARDA - Dec 2018
    download: https://cropontology.org/ontology/CO_365/Fababean/owl
    homepage: https://cropontology.org/ontology/CO_365/Fababean
    name: Fababean ontology
    prefix: co_365
    version: '2019-10-15'
  pattern: ^\d{7}$
  preferred_prefix: CO_365
  prefix: co_365
  repository: https://github.com/bioversity/Crop-Ontology
  uri_format: https://cropontology.org/rdf/CO_365:$1
co_366:
  agroportal:
    contact:
      email: helpdesk@cropontology-curationtool.org
      name: Crop Ontology Helpdesk
    description: This ontology is a part of the the Crop Ontology project , as an
      essential source of traits and variables to support the standardization of the
      breeding databases.
    example_uri: http://www.cropontology.org/rdf/CO_366:0000253/9
    homepage: http://www.cropontology.org
    license: CC-BY-4.0
    name: Bambara Groundnut Ontology
    prefix: CO_366
    repository: https://github.com/Planteome/CO_366-bambara-goundnut-traits
    version: '2019-12-23'
  contact:
    email: e.arnaud@cgiar.org
    github: null
    name: Elizabeth Arnaud
    orcid: 0000-0002-6020-5919
  contact_group_email: helpdesk@cropontology-curationtool.org
  cropoct:
    description: version Dec 2019
    download_owl: http://cropontology.org/rdf/CO_366.owl
    homepage: http://cropontology.org/term/CO_366:ROOT
    name: Bambara groundnut ontology
    prefix: CO_366
  example: '0000072'
  license: CC-BY-4.0
  mappings:
    agroportal: CO_366
    cropoct: CO_366
    ols: co_366
  ols:
    contact: helpdesk@cropontology-curationtool.org
    description: version Dec 2019
    download: http://www.cropontology.org/ontology/CO_366/Bambara%20groundnut/owl
    homepage: http://www.cropontology.org/ontology/CO_366/Bambara%20groundnut
    name: Bambara groundnut ontology
    prefix: co_366
  pattern: ^\d{7}$
  preferred_prefix: CO_366
  prefix: co_366
  repository: https://github.com/bioversity/Crop-Ontology
  uri_format: https://cropontology.org/rdf/CO_366:$1
co_367:
  agroportal:
    contact:
      email: helpdesk@cropontology-curationtool.org
      name: Crop Ontology Helpdesk
    description: Quinoa Ontology database of the Crop Ontology (CO_367) of the Generation
      Challenge Program (GCP) describe traits variables of Quinoa Germinate Database
      http://germinate.quinoadb.org. Quinoa Phenotyping Consortium Creation Date 23.05.2021
    homepage: https://cropontology.org/term/CO_367:ROOT
    license: CC-BY-4.0
    name: Quinoa Ontology
    prefix: CO_367
    publications:
    - https://doi.org/10.3390/plants10091759
  contact:
    email: e.arnaud@cgiar.org
    github: null
    name: Elizabeth Arnaud
    orcid: 0000-0002-6020-5919
  contact_group_email: helpdesk@cropontology-curationtool.org
  cropoct:
    description: 'Curator name: Clara S. Stanschewski; Curator Affiliation: King Abdullah
      University of Science and Technology; Contributing Scientists or Crop expert
      group: The Salt Lab and the Quinoa Phenotyping Consortium Creation Date: 23.05.2021'
    download_owl: http://cropontology.org/rdf/CO_367.owl
    homepage: http://cropontology.org/term/CO_367:ROOT
    name: Quinoa Ontology ontology
    prefix: CO_367
  example: '0000004'
  license: CC-BY-4.0
  mappings:
    agroportal: CO_367
    cropoct: CO_367
  pattern: ^\d{7}$
  preferred_prefix: CO_367
  prefix: co_367
  repository: https://github.com/bioversity/Crop-Ontology
  uri_format: https://cropontology.org/rdf/CO_367:$1
co_370:
  agroportal:
    contact:
      email: helpdesk@cropontology-curationtool.org
      name: Crop Ontology Helpdesk
    description: Apple (Malus domestica) defines crop traits and variables to support
      the standardisation of apple breeding databases providing description of agronomic,
      morphological, physiological, quality traits, its methods and scales. This project
      has received funding from the European Union's Horizon 2020 research and innovation
      program under the Marie Skłodowska-Curie grant agreement No 894215.
    example_uri: https://cropontology.org/rdf/CO_370:0001028
    homepage: http://www.cropontology.org/
    license: CC-BY-4.0
    name: Apple Ontology
    prefix: CO_370
    publications:
    - https://doi.org/10.5194/egusphere-egu21-15804
    repository: https://github.com/echuprikova/AppleCropOntology
    version: '1.1'
  contact:
    email: ekaterina.chuprikova@eurac.edu
    github: null
    name: Ekaterina Chuprikova
    orcid: 0000-0002-8981-0442
  cropoct:
    description: Apple (Malus domestica) defines crop traits and variables to support
      the standardisation of apple breeding databases providing description of agronomic,
      morphological, physiological, quality traits, its methods and scales.
    download_owl: http://cropontology.org/rdf/CO_370.owl
    homepage: http://cropontology.org/term/CO_370:ROOT
    name: Apple ontology
    prefix: CO_370
  example: 0000890
  license: CC-BY-4.0
  mappings:
    agroportal: CO_370
    cropoct: CO_370
  pattern: ^\d{7}$
  preferred_prefix: CO_370
  prefix: co_370
  repository: https://github.com/bioversity/Crop-Ontology
  uri_format: https://cropontology.org/rdf/CO_370:$1
cob:
  aberowl:
    description: COB brings together key terms from a wide range of OBO projects to
      improve interoperability.
    download_owl: http://aber-owl.net/media/ontologies/COB/16/cob.owl
    homepage: https://obofoundry.org/COB/
    name: Core Ontology for Biology and Biomedicine
    prefix: COB
  bioportal:
    contact:
      email: bpeters@lji.org
      name: Bjoern Peters
    description: The Core Ontology for Biology and Biomedicine (COB) brings together
      key terms from a wide range of OBO projects into a single, small ontology. The
      goal is to improve interoperabilty and reuse across the OBO community through
      better coordination of key terms., COB brings together key terms from a wide
      range of OBO projects to improve interoperability.
    homepage: https://github.com/OBOFoundry/COB
    license: CC0-1.0
    name: Core Ontology for Biology and Biomedicine
    prefix: COB
    version: '2025-06-30'
  domain: classification
  example: 0000080
  mappings:
    aberowl: COB
    bioportal: COB
    obofoundry: cob
    ols: cob
    ontobee: COB
    tib: cob
    wikidata.entity: Q113006456
  obofoundry:
    contact: bpeters@lji.org
    contact.github: bpeters42
    contact.label: Bjoern Peters
    contact.orcid: 0000-0002-8457-6693
    deprecated: false
    description: COB brings together key terms from a wide range of OBO projects to
      improve interoperability.
    domain: upper
    download.owl: http://purl.obolibrary.org/obo/cob.owl
    homepage: https://obofoundry.org/COB/
    license: CC0 1.0
    license.url: https://creativecommons.org/publicdomain/zero/1.0/
    name: Core Ontology for Biology and Biomedicine
    preferredPrefix: COB
    prefix: cob
    repository: https://github.com/OBOFoundry/COB
  ols:
    description: COB brings together key terms from a wide range of OBO projects to
      improve interoperability.
    download_owl: http://purl.obolibrary.org/obo/cob.owl
    homepage: https://obofoundry.org/COB/
    name: Core Ontology for Biology and Biomedicine
    prefix: cob
    tracker: https://github.com/OBOFoundry/COB/issues
    version: '2025-12-12'
    version.iri: http://purl.obolibrary.org/obo/cob/releases/2025-12-12/cob.owl
  ontobee:
    library: Library
    name: Core Ontology for Biology and Biomedicine
    prefix: COB
  pattern: ^\d{7}$
  prefix: cob
  tib:
    description: COB brings together key terms from a wide range of OBO projects to
      improve interoperability.
    download_owl: http://purl.obolibrary.org/obo/cob.owl
    homepage: https://obofoundry.org/COB/
    keywords:
    - DataPLANT
    - life sciences, biology
    name: Core Ontology for Biology and Biomedicine
    prefix: cob
    tracker: https://github.com/OBOFoundry/COB/issues/
    version.iri: http://purl.obolibrary.org/obo/cob/releases/2025-06-30/cob.owl
  uri_format: http://purl.obolibrary.org/obo/COB_$1
coconut:
  comment: '@mSorok is the dev of the resource, hope I got it right!'
  contributor:
    email: adriano.rutz@ik.me
    github: adafede
    name: Adriano Rutz
    orcid: 0000-0003-0443-9902
  description: COCONUT (COlleCtion of Open Natural ProdUcTs) Online is an open source
    project for Natural Products (NPs) storage, search and analysis. It gathers data
    from over 50 open NP resources and is available free of charge and without any
    restriction. Each entry corresponds to a "flat" NP structure, and is associated,
    when available, to their known stereochemical forms, literature, organisms that
    produce them, natural geographical presence and diverse pre-computed molecular
    properties.
  example: CNP0171505
  example_extras:
  - CNP0018459.2
  github_request_issue: 221
  homepage: https://coconut.naturalproducts.net
  keywords:
  - chemistry
  - natural producs
  - organic chemistry
  mappings:
    re3data: r3d100014517
  name: COlleCtion of Open Natural ProdUcTs
  pattern: ^CNP\d{7}(\.\d+)?$
  prefix: coconut
  publications:
  - doi: 10.1093/nar/gkae1063
    pmc: null
    pubmed: '39588778'
    title: 'COCONUT 2.0: a comprehensive overhaul and curation of the collection of
      open natural products database'
    year: 2024
  - doi: 10.1186/s13321-020-00478-9
    pmc: PMC7798278
    pubmed: '33423696'
    title: 'COCONUT online: Collection of Open Natural Products database'
    year: 2021
  re3data:
    description: A comprehensive platform facilitating natural product research by
      providing data, tools, and services for deposition, curation, and reuse.
    doi: 10.17616/R31NJNP1
    homepage: https://coconut.naturalproducts.net/
    license: CC0
    name: COCONUT
    prefix: r3d100014517
    synonyms:
    - COlleCtion of Open NatUral producTs
  reviewer:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  uri_format: https://coconut.naturalproducts.net/compound/coconut_id/$1
codata.rdmt:
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: "The goal of the CODATA Research Data Management Terminology is to\
    \ gather the key terms needed for a common understanding of the research data\
    \ management domain.  The RDMT was revised by the CODATA RDM Terminology Working\
    \ Group, shared for public review, and then confirmed and finalised in 2023.\n\
    \nThe RDMT grew out of the CASRAI Research Data Management Glossary, which was\
    \ intended as a practical reference for individuals and groups concerned with\
    \ the improvement of research data management (RDM).  In 2020, CASRAI requested\
    \ that CODATA assume responsibility for the curation of this valued resource.\
    \ \n\nTo that end, the RDM Terminology Working Group uses a lightweight and pragmatic\
    \ biennial process to review the resource now restructured as the CODATA RDM Terminology\
    \ and suggest any edits, additions and removals that are required in order to\
    \ develop and improve this important reference resource."
  ecoportal:
    contact:
      email: laura@codata.org
      name: Laura Molloy
    description: The goal of this terminology is to gather the key terms needed for
      a common understanding of the research data management domain. Research data
      management (RDM) refers to the storage, access and preservation of data created
      or collected in the course of research. Research data management practices cover
      the entire lifecycle of the data, from planning the investigation to conducting
      it, and from backing up data as it is created and used to long term preservation
      of data deliverables after the research investigation has concluded.
    homepage: https://codata.org/initiatives/data-science-and-stewardship/rdm-terminology-wg/
    license: CC-BY-4.0
    name: CODATA Research Data Management Terminology
    prefix: CODATA-RDMT
    publications:
    - https://doi.org/10.5281/zenodo.10626170
    version: v002
  example: aggregated-data
  homepage: https://vocabs.ardc.edu.au/viewById/685
  mappings:
    ecoportal: CODATA-RDMT
  name: CODATA Research Data Management Terminology
  prefix: codata.rdmt
  references:
  - https://zenodo.org/records/10626170
  uri_format: https://terms.codata.org/rdmt/$1
codelink:
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: 'GE Healthcare/Amersham Biosciences CodeLink? Human Whole Genome Bioarray
    targets most of the known and predictive genes of the human genome as it is described
    today in the public domain. It is comprised of approximately 55,000 30-mer probes
    designed to conserved exons across the transcripts of targeted genes. These 55,000
    probes represent well annotated, full length, and partial human gene sequences
    from major public databases. GE Healthcare/Amersham Biosciences CodeLink? Human
    Whole Genome Bioarray probe sequences were selected from the NCBI UniGene build
    #165, RefSeq database (January 5, 2004 release) and dbEST database (January 8,
    2004 release).'
  example: GE86325
  homepage: https://www.ebi.ac.uk/arrayexpress/files/A-GEHB-1/A-GEHB-1.adf.txt
  keywords:
  - microarray
  - transcriptomics
  name: GE Healthcare/Amersham Biosciences CodeLink Human Whole Genome Bioarray
  pattern: ^GE\d+$
  prefix: codelink
  references:
  - https://www.ebi.ac.uk/arrayexpress/files/A-GEOD-8060/A-GEOD-8060.adf.txt
  - https://www.ebi.ac.uk/arrayexpress/files/A-GEHB-1/A-GEHB-1.adf.txt
coexistence:
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: 'COEXISTENCE - Thesaurus of intersectionality and decolonial issues:
    black studies, gender, sexuality and feminist studies'
  example: '163'
  github_request_issue: 1310
  homepage: https://mamoura.eci.ufmg.br
  name: COEXISTENCE
  pattern: ^\d+$
  prefix: coexistence
  uri_format: https://mamoura.eci.ufmg.br/tematres/vocab/index.php?tema=$1
cog.category:
  contact:
    email: cogs@ncbi.nlm.nih.gov
    github: null
    name: Michael Y Galperin
    orcid: 0000-0002-2265-5572
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: Higher-level classifications of COG Pathways
  example: K
  homepage: https://www.ncbi.nlm.nih.gov/research/cog/
  keywords:
  - pathways
  name: COG Categories
  part_of_database: cog
  prefix: cog.category
  uri_format: https://www.ncbi.nlm.nih.gov/research/cog/cogcategory/$1
cog.cluster:
  biolink:
    is_identifiers: false
    is_obo: false
    prefix: COG
    uri_format: https://www.ncbi.nlm.nih.gov/research/cog-project/$1
  contact:
    email: cogs@ncbi.nlm.nih.gov
    github: null
    name: Michael Y Galperin
    orcid: 0000-0002-2265-5572
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: 'COGs stands for Clusters of Orthologous Genes. The database was initially
    created in 1997 (Tatusov et al., PMID: 9381173) followed by several updates, most
    recently in 2014 (Galperin et al., PMID: 25428365). The current update includes
    complete genomes of 1,187 bacteria and 122 archaea that map into 1,234 genera.
    The new features include ~250 updated COG annotations with corresponding references
    and PDB links, where available; new COGs for proteins involved in CRISPR-Cas immunity,
    sporulation, and photosynthesis, and the lists of COGs grouped by pathways and
    functional systems.'
  example: COG0001
  fairsharing:
    abbreviation: COG
    contact:
      email: koonin@ncbi.nlm.nih.gov
      name: Eugene V Koonin
      orcid: 0000-0003-3943-8299
    description: Clusters of Orthologous Groups of proteins (COGs) were delineated
      by comparing protein sequences encoded in complete genomes, representing major
      phylogenetic lineages. Each COG consists of individual proteins or groups of
      paralogs from at least 3 lineages and thus corresponds to an ancient conserved
      domain.
    homepage: https://www.ncbi.nlm.nih.gov/research/cog/
    license: http://opendatacommons.org/licenses/pddl/1.0
    name: 'Clusters of Orthologous Groups of Proteins: Phylogenetic classification
      of proteins encoded in complete genomes'
    prefix: FAIRsharing.djsbw2
    publications:
    - doi: 10.1126/science.278.5338.631
      pubmed_id: 9381173
      title: A genomic perspective on protein families.
    - doi: 10.1093/nar/gku1223
      pubmed_id: 25428365
      title: Expanded microbial genome coverage and improved protein family annotation
        in the COG database.
    subjects:
    - Life Science
  go:
    homepage: http://www.ncbi.nlm.nih.gov/COG/
    name: NCBI COG cluster
    prefix: COG_Cluster
    uri_format: https://www.ncbi.nlm.nih.gov/research/cog/cog/$1
  homepage: https://www.ncbi.nlm.nih.gov/research/cog/
  mappings:
    biolink: COG
    fairsharing: FAIRsharing.djsbw2
    go: COG_Cluster
    miriam: cog
    prefixcommons: cog
    togoid: Cog
  miriam:
    deprecated: false
    description: Database of Clusters of Orthologous Genes (COGs). This database defines
      all orthologs of protein sequences coded by known genomes. The species name,
      protein name, and phylogenetic tree of orthologous clusters can be viewed through
      this site. Each cluster is comprised of individual proteins and its paralogs,
      matched to evolutionarily conserved molecular domains.
    homepage: https://www.ncbi.nlm.nih.gov/
    id: 00000930
    name: COG
    namespaceEmbeddedInLui: false
    pattern: ^COG[0-9]+$
    prefix: cog
    sampleId: COG1806
    uri_format: https://www.ncbi.nlm.nih.gov/research/cog/cog/$1/
  name: Cluster of orthologous genes
  part_of_database: cog
  pattern: ^COG\d+$
  prefix: cog.cluster
  prefixcommons:
    description: Clusters of Orthologous Groups of proteins (COGs) were delineated
      by comparing protein sequences encoded in complete genomes, representing major
      phylogenetic lineages. Each COG consists of individual proteins or groups of
      paralogs from at least 3 lineages and thus corresponds to an ancient conserved
      domain.
    example: '145262'
    homepage: http://www.ncbi.nlm.nih.gov/COG
    keywords:
    - protein
    - genome
    name: 'Clusters of Orthologous Groups of Proteins: Phylogenetic classification
      of proteins encoded in complete genomes'
    pattern: ^\d+$
    prefix: cog
    uri_format: http://www.ncbi.nlm.nih.gov/COG/grace/cogenome.cgi?g=$1
  publications:
  - doi: 10.1093/nar/gku1223
    pmc: PMC4383993
    pubmed: '25428365'
    title: Expanded microbial genome coverage and improved protein family annotation
      in the COG database
    year: 2014
  - doi: 10.1126/science.278.5338.631
    pmc: null
    pubmed: '9381173'
    title: A genomic perspective on protein families
    year: 1997
  - doi: 10.1126/science.278.5338.631
    pmc: null
    pubmed: null
    title: A genomic perspective on protein families.
    year: null
  - doi: 10.1093/nar/gku1223
    pmc: null
    pubmed: null
    title: Expanded microbial genome coverage and improved protein family annotation
      in the COG database.
    year: null
  - doi: 10.1126/science.278.5338.631
    pmc: null
    pubmed: null
    title: A genomic perspective on protein families.
    year: null
  - doi: 10.1093/nar/gku1223
    pmc: null
    pubmed: null
    title: Expanded microbial genome coverage and improved protein family annotation
      in the COG database.
    year: null
  synonyms:
  - COG_Cluster
  - cog
  togoid:
    catalog: nbdc00397
    description: This database defines all orthologs of protein sequences coded by
      known genomes. The species name, protein name, and phylogenetic tree of orthologous
      clusters can be viewed through this site. Each cluster is comprised of individual
      proteins and its paralogs, matched to evolutionarily conserved molecular domains.
    examples:
    - COG0130
    - COG0663
    - COG0762
    - COG1186
    - COG1285
    - COG1390
    - COG3079
    - COG3354
    - COG4957
    - COG5379
    keywords:
    - Ortholog
    name: COG
    pattern: ^(?COG\d{4})$
    prefix: Cog
    uri_format: https://www.ncbi.nlm.nih.gov/research/cog/cog/$1
  uri_format: https://www.ncbi.nlm.nih.gov/research/cog/cog/$1
cog.pathway:
  contact:
    email: cogs@ncbi.nlm.nih.gov
    github: null
    name: Michael Y Galperin
    orcid: 0000-0002-2265-5572
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: Database of Clusters of Orthologous Genes grouped by pathways and functional
    systems. It includes the complete genomes of 1,187 bacteria and 122 archaea that
    map into 1,234 genera.
  example: NAD%20biosynthesis
  go:
    homepage: http://www.ncbi.nlm.nih.gov/COG/
    name: NCBI COG pathway
    prefix: COG_Pathway
    uri_format: https://www.ncbi.nlm.nih.gov/research/cog/pathway/$1
  homepage: https://www.ncbi.nlm.nih.gov/research/cog/pathways
  mappings:
    go: COG_Pathway
  name: COG Pathways
  part_of_database: cog
  prefix: cog.pathway
  uri_format: https://www.ncbi.nlm.nih.gov/research/cog/pathway/$1
cohd:
  comment: not really sure where the source is. this also links to a system called
    athena. I was not able to figure out what COHD stands for.
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: MIMIC-III is a dataset comprising health-related data associated with
    over 40,000 patients who stayed in critical care units of the Beth Israel Deaconess
    Medical Center between 2001 and 2012
  homepage: https://github.com/MIT-LCP/mimic-omop
  keywords:
  - clinical data
  - clinical trials
  - health
  - health sciences
  name: MIMIC III Database
  no_own_terms: true
  prefix: cohd
  repository: https://github.com/MIT-LCP/mimic-omop
cohesindb.binding:
  contact:
    email: rnakato@iqb.u-tokyo.ac.jp
    github: null
    name: Ryuichiro Nakato
    orcid: 0000-0003-3019-5817
  contributor:
    email: maaya.m466@gmail.com
    github: maayamanoj466
    name: Maaya Manoj
    orcid: 0009-0000-6974-6386
  description: Contains identifiers of cohesin binding sites in human cells from CohesinDB.
    CohesinDB includes 2043 epigenomics, transcriptomics and 3D genomics datasets
    from 530 studies involving 176 cell types. Each cohesin object is annotated with
    locus, cell type, classification, function, 3D genomics and cis-regulatory information.
  example: CDBP00415501
  github_request_issue: 1646
  homepage: https://cohesindb.iqb.u-tokyo.ac.jp
  keywords:
  - binding site
  - cohesin
  - protein
  name: CohesinDB - cohesin site
  part_of_database: cohesindb
  pattern: ^CDBP00\d{6}$
  prefix: cohesindb.binding
  publications:
  - doi: 10.1093/nar/gkac795
    pmc: PMC9825609
    pubmed: '36162821'
    title: 'CohesinDB: a comprehensive database for decoding cohesin-related epigenomes,
      3D genomes and transcriptomes in human cells'
    year: 2023
  reviewer:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  uri_format: https://cohesindb.iqb.u-tokyo.ac.jp/browsepeak/eachpeak/$1
cohesindb.gene:
  contact:
    email: rnakato@iqb.u-tokyo.ac.jp
    github: null
    name: Ryuichiro Nakato
    orcid: 0000-0003-3019-5817
  contributor:
    email: maaya.m466@gmail.com
    github: maayamanoj466
    name: Maaya Manoj
    orcid: 0009-0000-6974-6386
  description: Contains identifiers for genes that are part of cohesin regulated CRMs
    (cis-regulatory modules) from CohesinDB. CohesinDB includes 2043 epigenomics,
    transcriptomics and 3D genomics datasets from 530 studies involving 176 cell types.
    Each identifier represents a single cohesin-related CRM. Each cohesin object is
    annotated with locus, cell type, classification, function, 3D genomics and cis-regulatory
    information.
  example: CDBG00009781
  github_request_issue: 1646
  homepage: https://cohesindb.iqb.u-tokyo.ac.jp
  keywords:
  - gene
  name: CohesinDB gene
  part_of_database: cohesindb
  pattern: ^CDBG000\d{5}$
  prefix: cohesindb.gene
  publications:
  - doi: 10.1093/nar/gkac795
    pmc: PMC9825609
    pubmed: '36162821'
    title: 'CohesinDB: a comprehensive database for decoding cohesin-related epigenomes,
      3D genomes and transcriptomes in human cells'
    year: 2023
  reviewer:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  uri_format: https://cohesindb.iqb.u-tokyo.ac.jp/browsegene/eachgene/$1
cohesindb.loops:
  contact:
    email: rnakato@iqb.u-tokyo.ac.jp
    github: null
    name: Ryuichiro Nakato
    orcid: 0000-0003-3019-5817
  contributor:
    email: maaya.m466@gmail.com
    github: maayamanoj466
    name: Maaya Manoj
    orcid: 0009-0000-6974-6386
  description: Contains identifiers of cohesin-related chromatin loops from CohesinDB.
    CohesinDB includes 2043 epigenomics, transcriptomics and 3D genomics datasets
    from 530 studies involving 176 cell types. Each identifier represents a single
    cohesin-related chromatin loop. Each cohesin object is annotated with locus, cell
    type, classification, function, 3D genomics and cis-regulatory information.
  example: CDBL00540805
  github_request_issue: 1646
  homepage: https://cohesindb.iqb.u-tokyo.ac.jp
  keywords:
  - chromatin loop
  - cohesin
  - interaction
  - protein
  name: CohesinDB - cohesin-related chromatin loop
  part_of_database: cohesindb
  pattern: ^CDBL00\d{6}$
  prefix: cohesindb.loops
  publications:
  - doi: 10.1093/nar/gkac795
    pmc: PMC9825609
    pubmed: '36162821'
    title: 'CohesinDB: a comprehensive database for decoding cohesin-related epigenomes,
      3D genomes and transcriptomes in human cells'
    year: 2023
  reviewer:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  uri_format: https://cohesindb.iqb.u-tokyo.ac.jp/browseloop/eachloop/$1
coi:
  contact:
    email: coi@bot.uc.pt
    github: null
    name: COI Catalogue
    orcid: null
  contributor:
    email: shah.tanay2@northeastern.edu
    github: tanayshah2
    name: Tanay Shah
    orcid: 0009-0001-1912-5132
  description: COI Catalogue is a herbarium with c. 800.000 specimens, organised in
    separate collections due to the research priorities over the years.
  example: '63812'
  github_request_issue: 1145
  homepage: https://coicatalogue.uc.pt/index.php
  name: COI Catalogue
  prefix: coi
  publications:
  - doi: 10.1038/s41597-024-03520-9
    pmc: PMC11193818
    pubmed: '38909064'
    title: 'O armário: Fruiting phenology data for 4,462 plant taxa in Portugal (1926-2013)'
    year: 2024
  reviewer:
    email: b.gyori@northeastern.edu
    github: bgyori
    name: Benjamin M. Gyori
    orcid: 0000-0001-9439-5346
  uri_format: https://coicatalogue.uc.pt/index.php?t=specimen&COINumber=$1
col:
  bartoc:
    abbreviation: CoL
    description: 'The Catalogue of Life (CoL) is the nearest thing to a comprehensive
      catalogue of all known species of organisms on Earth. Continuous progress is
      made towards completion, and this edition contains 1,639,016 living and 5,763
      extinct species. Please note that this is probably just over three quarters
      of the world''s known species. This means that for many groups it continues
      to be deficient, and users will notice that many species are still missing from
      the Catalogue.


      The present Catalogue is compiled with sectors provided by 157 taxonomic databases
      from around the world. Many of these contain taxonomic data and opinions from
      extensive networks of specialists, so that the complete work contains contributions
      from more than 3,000 specialists from throughout the taxonomic profession. Species
      2000 and ITIS teams peer review databases, select appropriate sectors and integrate
      the sectors into a single coherent catalogue with a single hierarchical classification.'
    homepage: http://www.catalogueoflife.org/col/
    name: Catalogue of Life
    prefix: '1915'
    wikidata_database: Q38840
  mappings:
    bartoc: '1915'
    miriam: col
    wikidata.entity: Q38840
  miriam:
    deprecated: false
    description: Identifier of a taxon or synonym in the Catalogue of Life
    homepage: https://www.checklistbank.org
    id: 00000969
    name: Catalogue of Life
    namespaceEmbeddedInLui: false
    pattern: ^[23456789BCDFGHJKLMNPQRSTVWXYZ]{1,6}$
    prefix: col
    providers:
    - code: col
      description: The Catalogue of Life website providing a view onto the latest
        release of the COL Checklist.
      homepage: https://www.catalogueoflife.org
      name: Catalogue of Life (COL)
      uri_format: https://www.catalogueoflife.org/data/taxon/$1
    sampleId: 4QHKG
    uri_format: https://www.checklistbank.org/dataset/3LR/taxon/$1
  prefix: col
col.taiwan:
  contributor:
    email: meghan.balk@gmail.com
    github: megbalk
    name: Meghan Balk
    orcid: 0000-0003-2699-3066
  description: Identifier (name code) for a taxon in the catalogue of life in taiwan
  example: '431472'
  github_request_issue: 466
  homepage: http://taibnet.sinica.edu.tw/home.php
  mappings:
    wikidata: P3088
  name: Catalogue of Life in Taiwan
  pattern: ^[1-9]\d{5}$
  prefix: col.taiwan
  reviewer:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  uri_format: https://taibnet.sinica.edu.tw/eng/taibnet_species_detail.php?name_code=$1
  wikidata:
    database: Q26218155
    description: identifier (name code) for a taxon in the Catalogue of Life in Taiwan
    example:
    - '421738'
    - '431472'
    homepage: https://taibnet.sinica.edu.tw/home_eng.php
    name: TaiBNET ID
    pattern: ^([1-9]\d{5})$
    prefix: P3088
    uri_format: https://taibnet.sinica.edu.tw/chi/taibnet_species_detail.php?name_code=$1
colao:
  aberowl:
    description: The Coleoptera Anatomy Ontology contains terms used for describing
      the anatomy and phenotype of beetles in biodiversity research. It has been built
      using the Ontology Develoment Kit, with the Ontology for the Anatomy of the
      Insect Skeleto-Muscular system (AISM) as a backbone.
    download_owl: http://aber-owl.net/media/ontologies/COLAO/10/colao.owl
    homepage: https://github.com/insect-morphology/colao
    name: Coleoptera Anatomy Ontology (COLAO)
    prefix: COLAO
  bioportal:
    contact:
      email: entiminae@gmail.com
      name: Jennifer C. Girón
    description: The Coleoptera Anatomy Ontology contains terms used for describing
      the anatomy and phenotype of beetles in biodiversity research. It has been built
      using the Ontology Develoment Kit with the Ontology for the Anatomy of the Insect
      SkeletoMuscular system (AISM) as a backbone. The project is open for collaboration.
    homepage: https://github.com/insect-morphology/colao
    name: Coleoptera Anatomy Ontology
    prefix: COLAO
    version: '2024-06-21'
  example: '0000000'
  mappings:
    aberowl: COLAO
    bioportal: COLAO
    obofoundry: colao
    ols: colao
    ontobee: COLAO
    wikidata.entity: Q113009128
  name: Coleoptera Anatomy Ontology
  obofoundry:
    contact: entiminae@gmail.com
    contact.github: JCGiron
    contact.label: Jennifer C. Giron
    contact.orcid: 0000-0002-0851-6883
    depends_on:
    - aism
    - bfo
    - bspo
    - caro
    - pato
    - ro
    - uberon
    deprecated: false
    description: The Coleoptera Anatomy Ontology contains terms used for describing
      the anatomy and phenotype of beetles in biodiversity research. It has been built
      using the Ontology Develoment Kit, with the Ontology for the Anatomy of the
      Insect Skeleto-Muscular system (AISM) as a backbone.
    domain: anatomy and development
    download.obo: http://purl.obolibrary.org/obo/colao.obo
    download.owl: http://purl.obolibrary.org/obo/colao.owl
    homepage: https://github.com/insect-morphology/colao
    license: CC BY 4.0
    license.url: https://creativecommons.org/licenses/by/4.0/
    name: Coleoptera Anatomy Ontology (COLAO)
    preferredPrefix: COLAO
    prefix: colao
    repository: https://github.com/insect-morphology/colao
  ols:
    description: The Coleoptera Anatomy Ontology contains terms used for describing
      the anatomy and phenotype of beetles in biodiversity research.
    download_owl: http://purl.obolibrary.org/obo/colao.owl
    homepage: https://github.com/insect-morphology/colao
    name: Coleoptera Anatomy Ontology
    prefix: colao
    tracker: https://github.com/insect-morphology/colao/issues
    version: '2024-06-21'
    version.iri: http://purl.obolibrary.org/obo/colao/releases/2024-06-21/colao.owl
  ontobee:
    library: Library
    name: Coleoptera Anatomy Ontology (COLAO)
    prefix: COLAO
  pattern: ^\d{7}$
  prefix: colao
  uri_format: http://purl.obolibrary.org/obo/COLAO_$1
collagenmutdb:
  mappings:
    prefixcommons: cmd
  prefix: collagenmutdb
  prefixcommons:
    description: This database aims to record all published accounts of variants resulting
      in osteogenesis imperfecta. Such variants occur in the COL1A1, COL1A2, CRTAP,
      FKBP10, LEPRE1 and PPIB genes.
    example: COL3A1
    homepage: http://www.le.ac.uk/genetics/collagen/
    keywords:
    - gene
    name: Collagen Mutation Database
    pattern: ^[A-Z,0-9]+$
    prefix: cmd
    uri_format: https://eds.gene.le.ac.uk/home.php?select_db=$1
  provides: hgnc.symbol
  reviewer:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
colonatlas:
  cellosaurus:
    category: Cell line databases/resources
    homepage: http://www.coloncanceratlas.org
    name: Colorectal Cancer Atlas
    prefix: ColonAtlas
    uri_format: http://www.coloncanceratlas.org/search_cell_line?cell_line=$1
  example: ALA
  mappings:
    cellosaurus: ColonAtlas
  prefix: colonatlas
combine.specifications:
  biocontext:
    prefix: COMBINE.SPECIFICATIONS
  mappings:
    biocontext: COMBINE.SPECIFICATIONS
    miriam: combine.specifications
    n2t: combine.specifications
  miriam:
    deprecated: false
    description: The 'COmputational Modeling in BIology' NEtwork (COMBINE) is an initiative
      to coordinate the development of the various community standards and formats
      for computational models, initially in Systems Biology and related fields. This
      collection pertains to specifications of the standard formats developed by the
      Computational Modeling in Biology Network.
    homepage: https://co.mbine.org/standards/
    id: 00000258
    name: COMBINE specifications
    namespaceEmbeddedInLui: false
    pattern: ^\w+(\-|\.|\w)*$
    prefix: combine.specifications
    sampleId: sed-ml.level-1.version-1
    uri_format: https://github.com/combine-org/combine-specifications/blob/main/specifications/$1.md
  n2t:
    description: The 'COmputational Modeling in BIology' NEtwork (COMBINE) is an initiative
      to coordinate the development of the various community standards and formats
      for computational models, initially in Systems Biology and related fields. This
      collection pertains to specifications of the standard formats developed by the
      Computational Modeling in Biology Network.
    example: sbgn.er.level-1.version-1.2
    homepage: https://co.mbine.org/standards/
    name: COMBINE at EBI
    namespaceEmbeddedInLui: false
    pattern: ^\w+(\-|\.|\w)*$
    prefix: combine.specifications
    uri_format: https://co.mbine.org/specifications/$1
  prefix: combine.specifications
come:
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: COMe (Co-Ordination of Metals) at the EBI represents an ontology for
    bioinorganic and other small molecule centres in complex proteins, using a classification
    system based on the concept of a bioinorganic motif.
  example: MOL000160
  homepage: https://www.flymine.org/come
  mappings:
    prefixcommons: come
  name: The Bioinorganic Motif Database
  prefix: come
  prefixcommons:
    description: COMe is an attempt to classify metalloproteins and some other complex
      proteins using the concept of bioinorganic motif.
    example: BIM000347
    homepage: http://www.flymine.org/come/
    keywords:
    - protein
    name: COMe
    pattern: ^BIM\d+$
    prefix: come
    uri_format: http://www.flymine.org/come/entry?gn=$1
  synonyms:
  - COMe
  uri_format: https://www.flymine.org/come/entry?gn=$1
commoncoreontology:
  contact:
    email: mpjensen@buffalo.edu
    github: mark-jensen
    name: Mark Jensen
    orcid: 0000-0001-9228-8838
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: 'The Common Core Ontologies (CCO) comprise twelve ontologies that are
    designed to represent and integrate taxonomies of generic classes and relations
    across all domains of interest.


    CCO is a mid-level extension of Basic Formal Ontology (BFO), an upper-level ontology
    framework widely used to structure and integrate ontologies in the biomedical
    domain (Arp, et al., 2015). BFO aims to represent the most generic categories
    of entity and the most generic types of relations that hold between them, by defining
    a small number of classes and relations. CCO then extends from BFO in the sense
    that every class in CCO is asserted to be a subclass of some class in BFO, and
    that CCO adopts the generic relations defined in BFO (e.g., has_part) (Smith and
    Grenon, 2004). Accordingly, CCO classes and relations are heavily constrained
    by the BFO framework, from which it inherits much of its basic semantic relationships.'
  example: DirectiveInformationContentEntity
  homepage: http://www.ontologyrepository.com
  keywords:
  - ontology
  - upper-level ontology
  license: CC-BY-4.0
  mappings:
    tib: cco
  name: Common Core Ontologies
  prefix: commoncoreontology
  repository: https://github.com/CommonCoreOntology/CommonCoreOntologies
  tib:
    description: An import of all the Common Core mid-level ontologies into a single
      file so that content is easy to view. The All Core Ontology is not an ontology
      in the sense it contains no unique content. As such it should not be added to,
      but can be extended from.
    homepage: https://www.cubrc.org/index.php/data-science-and-information-fusion/ontology
    keywords:
    - NFDI4ING
    - engineering
    name: All Core Ontology
    prefix: cco
    tracker: https://github.com/CommonCoreOntology/CommonCoreOntologies/issues
    uri_format: http://www.ontologyrepository.com/CommonCoreOntologies/$1
    version.iri: http://www.ontologyrepository.com/CommonCoreOntologies/Mid/2024-11-03/AllCoreOntology
  uri_format: http://www.ontologyrepository.com/CommonCoreOntologies/$1
complexportal:
  biocontext:
    prefix: COMPLEXPORTAL
  biolink:
    is_identifiers: false
    is_obo: false
    prefix: ComplexPortal
    uri_format: https://www.ebi.ac.uk/complexportal/complex/$1
  contact:
    email: sbalu@ebi.ac.uk
    github: CP-SB
    name: Sucharitha Balu
    orcid: 0000-0001-7456-0594
  contact_extras:
  - email: jmedina@ebi.ac.uk
    github: jmedinaebi
    name: Juan Jose Medina Reyes
    orcid: 0009-0004-6468-260X
  domain: protein complex
  example: CPX-263
  go:
    homepage: https://www.ebi.ac.uk/complexportal
    name: Complex Portal database of macromolecular complexes
    prefix: ComplexPortal
    uri_format: https://www.ebi.ac.uk/complexportal/complex/$1
  keywords:
  - protein complex
  license: CC0-1.0
  logo: https://www.ebi.ac.uk/complexportal/assets/images/logo.png
  mappings:
    biocontext: COMPLEXPORTAL
    biolink: ComplexPortal
    go: ComplexPortal
    miriam: complexportal
    n2t: complexportal
    re3data: r3d100013295
    uniprot: DB-0228
    wikidata: P7718
  miriam:
    deprecated: false
    description: A database that describes manually curated macromolecular complexes
      and provides links to details about these complexes in other databases.
    homepage: https://www.ebi.ac.uk/complexportal
    id: '00000657'
    name: Complex Portal
    namespaceEmbeddedInLui: false
    pattern: ^CPX-[0-9]+$
    prefix: complexportal
    sampleId: CPX-2158
    uri_format: https://www.ebi.ac.uk/complexportal/complex/$1
  n2t:
    description: A database that describes manually curated macromolecular complexes
      and provides links to details about these complexes in other databases.
    example: CPX-2158
    homepage: https://www.ebi.ac.uk/complexportal
    name: Complex Portal
    namespaceEmbeddedInLui: false
    pattern: ^CPX-[0-9]+$
    prefix: complexportal
    uri_format: https://www.ebi.ac.uk/complexportal/complex/$1
  name: Complex Portal
  prefix: complexportal
  publications:
  - doi: 10.1093/nar/gkae1085
    pmc: PMC11701666
    pubmed: '39558156'
    title: 'Complex portal 2025: predicted human complexes and enhanced visualisation
      tools for the comparison of orthologous and paralogous complexes'
    year: 2025
  - doi: 10.1093/nar/gku975
    pmc: PMC4384031
    pubmed: '25313161'
    title: The complex portal--an encyclopaedia of macromolecular complexes
    year: 2014
  - doi: 10.1093/nar/gky1001
    pmc: null
    pubmed: '30357405'
    title: null
    year: null
  re3data:
    description: The Complex Portal is a manually curated, encyclopaedic resource
      of macromolecular complexes from a number of key model organisms, entered into
      the IntAct molecular interaction database (https://www.ebi.ac.uk/intact/). Data
      includes protein-only complexes as well as protein-small molecule and protein-nucleic
      acid complexes. All complexes are derived from physical molecular interaction
      evidences extracted from the literature and cross-referenced in the entry, or
      by curator inference from information on homologs in closely related species
      or by inference from scientific background. All complexes are tagged with Evidence
      and Conclusion Ontology codes to indicate the type of evidence available for
      each entry.
    doi: 10.17616/R31NJMR3
    homepage: https://www.ebi.ac.uk/complexportal/home
    license: Apache License 2.0
    name: Complex Portal
    prefix: r3d100013295
    synonyms:
    - CP
  synonyms:
  - ComplexPortal
  uniprot:
    abbreviation: ComplexPortal
    category: Protein-protein interaction databases
    homepage: https://www.ebi.ac.uk/complexportal/
    name: ComplexPortal
    prefix: DB-0228
    publications:
    - doi: 10.1093/nar/gky1001
      pubmed: '30357405'
    uri_format: https://www.ebi.ac.uk/complexportal/complex/$1
  wikidata:
    description: accession number of protein complex at the Complex Portal
    example:
    - CPX-2165
    - CPX-577
    - CPX-630
    homepage: https://www.ebi.ac.uk/complexportal/home
    miriam: complexportal
    name: Complex Portal accession ID
    pattern: ^CPX-[0-9]+$
    prefix: P7718
    uri_format: https://www.ebi.ac.uk/complexportal/complex/$1
comptox:
  biocontext:
    prefix: COMPTOX
  mappings:
    biocontext: COMPTOX
    miriam: comptox
    n2t: comptox
    wikidata: P3117
  miriam:
    deprecated: false
    description: The Chemistry Dashboard is a part of a suite of databases and web
      applications developed by the US Environmental Protection Agency's Chemical
      Safety for Sustainability Research Program. These databases and apps support
      EPA's computational toxicology research efforts to develop innovative methods
      to change how chemicals are currently evaluated for potential health risks.
    homepage: https://comptox.epa.gov/dashboard
    id: 00000658
    name: CompTox Chemistry Dashboard
    namespaceEmbeddedInLui: false
    pattern: ^DTXSID\d+$
    prefix: comptox
    sampleId: DTXSID2021028
    uri_format: https://comptox.epa.gov/dashboard/$1
  n2t:
    description: The Chemistry Dashboard is a part of a suite of databases and web
      applications developed by the US Environmental Protection Agency's Chemical
      Safety for Sustainability Research Program. These databases and apps support
      EPA's computational toxicology research efforts to develop innovative methods
      to change how chemicals are currently evaluated for potential health risks.
    example: DTXSID2021028
    homepage: https://comptox.epa.gov/dashboard
    name: CompTox Chemistry Dashboard
    namespaceEmbeddedInLui: false
    pattern: ^DTXSID\d+$
    prefix: comptox
    uri_format: https://comptox.epa.gov/dashboard/$1
  name: DSSTox substance
  prefix: comptox
  wikidata:
    description: DSSTox substance identifier (DTXSID) used in the Environmental Protection
      Agency CompTox Dashboard
    example:
    - DTXSID3039242
    - DTXSID5020108
    - DTXSID6046761
    - DTXSID7020182
    - DTXSID8031865
    - DTXSID9020112
    name: DSSTox substance ID
    pattern: ^DTXSID\d{7,9}$
    prefix: P3117
    uri_format: https://comptox.epa.gov/dashboard/chemical/details/$1
compulyeast:
  biocontext:
    prefix: COMPULYEAST
  fairsharing:
    abbreviation: Compulyeast
    description: Compluyeast-2D-DB is a two-dimensional polyacrylamide gel electrophoresis
      federated database. This collection references a subset of Uniprot, and contains
      general information about the protein record.
    homepage: http://compluyeast2dpage.dacya.ucm.es
    license: http://opendatacommons.org/licenses/pddl/1.0
    name: Compulyeast
    prefix: FAIRsharing.rbjs3e
    publications: []
    subjects: []
  mappings:
    biocontext: COMPULYEAST
    fairsharing: FAIRsharing.rbjs3e
    miriam: compulyeast
    n2t: compulyeast
    prefixcommons: compluyeast2dpage
  miriam:
    deprecated: true
    description: Compluyeast-2D-DB is a two-dimensional polyacrylamide gel electrophoresis
      federated database. This collection references a subset of Uniprot, and contains
      general information about the protein record.
    homepage: http://compluyeast2dpage.dacya.ucm.es/
    id: 00000198
    name: Compulyeast
    namespaceEmbeddedInLui: false
    pattern: ^([A-N,R-Z][0-9][A-Z][A-Z, 0-9][A-Z, 0-9][0-9])|([O,P,Q][0-9][A-Z, 0-9][A-Z,
      0-9][A-Z, 0-9][0-9])$
    prefix: compulyeast
    sampleId: O08709
    uri_format: http://compluyeast2dpage.dacya.ucm.es/cgi-bin/2d/2d.cgi?ac=$1
  n2t:
    description: Compluyeast-2D-DB is a two-dimensional polyacrylamide gel electrophoresis
      federated database. This collection references a subset of Uniprot, and contains
      general information about the protein record.
    example: O08709
    homepage: http://compluyeast2dpage.dacya.ucm.es/
    name: Compluyeast database at Universidad Complutense Madrid
    namespaceEmbeddedInLui: false
    pattern: ^([A-N,R-Z][0-9][A-Z][A-Z, 0-9][A-Z, 0-9][0-9])|([O,P,Q][0-9][A-Z, 0-9][A-Z,
      0-9][A-Z, 0-9][0-9])$
    prefix: compulyeast
    uri_format: http://compluyeast2dpage.dacya.ucm.es/cgi-bin/2d/2d.cgi?ac=$1
  name: Compluyeast-2D-DB
  prefix: compulyeast
  prefixcommons:
    description: Compluyeast-2D-DB is a Two-dimensional polyacrilamide gel electrophoresis
      federated database built with the Make2DDB package and integrated at the WORLD-2DPAGE
      of the ExPASy proteomics web server.
    example: P20029
    homepage: http://compluyeast2dpage.dacya.ucm.es/
    keywords:
    - protein
    name: CompluYeast 2D-PAGE
    pattern: ^P\d+$
    prefix: compluyeast2dpage
    uri_format: http://compluyeast2dpage.dacya.ucm.es/cgi-bin/2d/2d.cgi?ac=$1
  provides: uniprot
condo:
  example: AestheticFunction
  mappings:
    tib: condo
  prefix: condo
  tib:
    description: The COnCEPT upper-level Design Ontology (COnDO).
    download_rdf: https://raw.githubusercontent.com/OntoRep/COnCEPT/master/COnDO.ttl
    homepage: https://github.com/OntoRep/COnCEPT
    keywords:
    - NFDI4ING
    - engineering
    name: The COnCEPT upper-level Design Ontology
    prefix: condo
    uri_format: http://www.w3id.org/Concept/Ontology/COnDO#$1
conference:
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: The conference-ontology is a new self-contained ontology for modelleing
    knowledge about conferences. The conference-ontology adopts best ontology design
    practices (e.g., Ontology Design Patterns, ontology reuse and interlinking) and
    guarantees interoperability with SWC ontology and all other pertinent vocabularies.
    (from homepage)
  download_owl: https://w3id.org/scholarlydata/ontology/conference-ontology.owl
  example: isDocumentRelatedTo
  homepage: http://www.scholarlydata.org/ontology/doc/
  license: CC-BY-3.0
  name: Conference Ontology
  prefix: conference
  uri_format: https://w3id.org/scholarlydata/ontology/conference-ontology.owl#$1
confident.event:
  contact:
    email: philip.stroemert@tib.eu
    github: StroemPhi
    name: Philip Strömert
    orcid: 0000-0002-1595-3213
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: Confident makes descriptive metadata on conferences and other formats
    of scientific events permanently accessible in a high quality through automated
    processes and scientific data curating.
  example: 37af84f2-bfd7-4653-b608-eaff44febba6
  github_request_issue: 519
  homepage: https://www.confident-conference.org/index.php/Category:Event
  keywords:
  - conferences
  - meetings
  - metascience
  name: ConfIDent Event
  pattern: ^[0-9a-f]{8}-[0-9a-f]{4}-[0-9a-f]{4}-[0-9a-f]{4}-[0-9a-f]{12}$
  prefix: confident.event
  uri_format: https://www.confident-conference.org/index.php/Event:$1
confident.series:
  contact:
    email: philip.stroemert@tib.eu
    github: StroemPhi
    name: Philip Strömert
    orcid: 0000-0002-1595-3213
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: Confident makes descriptive metadata on conferences and other formats
    of scientific events permanently accessible in a high quality through automated
    processes and scientific data curating.
  example: AAC
  github_request_issue: 519
  homepage: https://www.confident-conference.org/index.php/Category:Event_Series
  keywords:
  - conferences
  - grouping
  - meetings
  - metascience
  name: ConfIDent Event Series
  prefix: confident.series
  uri_format: https://www.confident-conference.org/index.php/Event_Series:$1
conoserver:
  biocontext:
    prefix: CONOSERVER
  fairsharing:
    abbreviation: ConoServer
    contact:
      email: d.craik@imb.uq.edu.au
      name: David Craik
      orcid: 0000-0003-0007-6796
    description: ConoServer is a database specializing in sequences and structures
      of peptides expressed by marine cone snails. The database gives access to protein
      sequences, nucleic acid sequences and structural information on conopeptides.
      ConoServer's data are first collected from the peer reviewed literature and
      from publicly available databases, including UniProtKB/Swiss-Prot, NCBI nucleotide
      (nt), and the World Wide Protein Data Bank. The data are then curated manually,
      which include the addition of references, the analysis of sequence regions,
      the identification of cysteine frameworks and gene superfamilies, and the identification
      of mature peptides in the precusor sequences.
    homepage: http://www.conoserver.org
    license: http://www.conoserver.org
    name: ConoServer
    prefix: FAIRsharing.y00hz4
    publications:
    - doi: 10.1016/j.toxicon.2010.03.002
      pubmed_id: 20211197
      title: 'Conopeptide characterization and classifications: an analysis using
        ConoServer.'
    - doi: 10.1152/physrev.00020.2003
      pubmed_id: 14715910
      title: 'Conus venoms: a rich source of novel ion channel-targeted peptides.'
    - doi: 10.1021/cb700091j
      pubmed_id: 17649970
      title: Chemical modification of conotoxins to improve stability and activity.
    - doi: 10.1093/bioinformatics/btm596
      pubmed_id: 18065428
      title: ConoServer, a database for conopeptide sequences and structures.
    subjects:
    - Neurophysiology
    - Statistics
    - Life Science
    - Synthetic Biology
  mappings:
    biocontext: CONOSERVER
    fairsharing: FAIRsharing.y00hz4
    miriam: conoserver
    n2t: conoserver
    uniprot: DB-0156
  miriam:
    deprecated: false
    description: ConoServer is a database specialized in the sequence and structures
      of conopeptides, which are peptides expressed by carnivorous marine cone snails.
    homepage: http://www.conoserver.org/
    id: '00000254'
    name: Conoserver
    namespaceEmbeddedInLui: false
    pattern: ^\d+$
    prefix: conoserver
    sampleId: '2639'
    uri_format: http://www.conoserver.org/?page=card&table=protein&id=$1
  n2t:
    description: ConoServer is a database specialized in the sequence and structures
      of conopeptides, which are peptides expressed by carnivorous marine cone snails.
    example: '2639'
    homepage: http://www.conoserver.org/
    name: ConoServer at University of Queensland
    namespaceEmbeddedInLui: false
    pattern: ^\d+$
    prefix: conoserver
    uri_format: http://www.conoserver.org/?page=card&table=protein&id=$1
  name: ConoServer
  prefix: conoserver
  publications:
  - doi: 10.1093/nar/gkr886
    pmc: PMC3245185
    pubmed: '22058133'
    title: 'ConoServer: updated content, knowledge, and discovery tools in the conopeptide
      database'
    year: 2011
  - doi: 10.1016/j.toxicon.2010.03.002
    pmc: null
    pubmed: '20211197'
    title: 'Conopeptide characterization and classifications: an analysis using ConoServer'
    year: 2010
  - doi: 10.1021/cb700091j
    pmc: null
    pubmed: '17649970'
    title: Chemical modification of conotoxins to improve stability and activity
    year: 2007
  - doi: 10.1093/bioinformatics/btm596
    pmc: null
    pubmed: '18065428'
    title: ConoServer, a database for conopeptide sequences and structures
    year: 2007
  - doi: 10.1152/physrev.00020.2003
    pmc: null
    pubmed: '14715910'
    title: 'Conus venoms: a rich source of novel ion channel-targeted peptides'
    year: 2004
  uniprot:
    abbreviation: ConoServer
    category: Organism-specific databases
    homepage: https://www.conoserver.org/
    name: ConoServer
    prefix: DB-0156
    publications:
    - doi: 10.1093/nar/gkr886
      pubmed: '22058133'
    uri_format: https://www.conoserver.org/?page=card&table=protein&id=$1
conso:
  contact:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: An ontology describing phenomena encountered in the literature surrounding
    neurodegenerative diseases such as Alzheimer's disease, Parkinson's disease, Huntington's
    disease, tauopathies, and related protein aggregation diseases.
  domain: multiple
  example: CONSO00010
  homepage: https://pharmacome.github.io/conso/
  keywords:
  - biology
  - life science
  - neurodegeneration
  - neuroscience
  - ontology
  name: Curation of Neurodegeneration Supporting Ontology
  pattern: ^CONSO\d{5}$
  prefix: conso
  uri_format: https://pharmacome.github.io/conso/$1
cora:
  example: -bare#CollectiveRoboticSystem
  mappings:
    tib: cora
  name: Core Ontology for Robotics and Automation
  prefix: cora
  tib:
    description: This is the OWL implementation of CORA in IEEE 1872-2015. It only
      includes  the taxonomy of concepts and relations, with some few axioms reggarding
      disjointness, property characteristics and property ranges/domains. The OWL
      implementation is an underspecified version of the SUO-KIF implementation in
      IEEE 1872-2015. That is, the set of allowed models of the SUO-KIF implementation
      is a proper subset of the allowed models by the OWL implementation. Concept
      definitions in natural language and othe clarifications can be found in the  IEEE
      1872-2015 standard.
    download_owl: https://raw.githubusercontent.com/srfiorini/IEEE1872-owl/master/cora.owl
    homepage: https://github.com/srfiorini/IEEE1872-owl
    keywords:
    - NFDI4ING
    - engineering
    name: Core Ontology for Robotics and Automation (CORA)
    prefix: cora
    tracker: https://github.com/srfiorini/IEEE1872-owl/issues
    uri_format: http://purl.org/ieee1872-owl/cora$1
coral.como:
  contact:
    email: JMChandonia@lbl.gov
    github: jmchandonia
    name: John-Marc Chandonia
    orcid: 0000-0002-5153-9079
  contributor:
    email: JMChandonia@lbl.gov
    github: jmchandonia
    name: John-Marc Chandonia
    orcid: 0000-0002-5153-9079
  description: The Context and Measurement Ontology (COMO) contains ontological terms
    to describe the context for various types of experimental data and measurements.  It
    is useful in its current state for several different environmental microbiology
    projects. This ontology is used in multiple CORAL (Contextual Ontology-based Repository
    Analysis Library) deployments.
  download_obo: https://raw.githubusercontent.com/jmchandonia/CORAL/refs/heads/main/example/pedometer/ontologies/context_measurement_ontology.obo
  example: '0000001'
  github_request_issue: 1360
  homepage: https://github.com/jmchandonia/CORAL
  license: AGPL-3.0-only
  name: Contextual Ontology-based Repository Analysis Library - Context and Measurement
    Ontology
  pattern: ^\d+$
  prefix: coral.como
  publications:
  - doi: 10.1093/gigascience/giac089
    pmc: PMC9575582
    pubmed: '36251274'
    title: 'CORAL: A framework for rigorous self-validated data modeling and integrative,
      reproducible data analysis'
    year: 2022
  repository: https://github.com/jmchandonia/CORAL
  reviewer:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
cordis.article:
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: The Community Research and Development Information Service (CORDIS)
    is the European Commission's primary source of results from the projects funded
    by the EU's framework programmes for research and innovation (FP1 to Horizon 2020).
  example: '436605'
  homepage: https://cordis.europa.eu/
  name: CORDIS Article
  pattern: ^\d+$
  prefix: cordis.article
  uri_format: https://cordis.europa.eu/article/id/$1
cordis.project:
  contributor:
    email: benjamin_gyori@hms.harvard.edu
    github: bgyori
    name: Benjamin M. Gyori
    orcid: 0000-0001-9439-5346
  description: The Community Research and Development Information Service (CORDIS)
    is the European Commission's primary source of results from the projects funded
    by the EU's framework programmes for research and innovation (FP1 to Horizon 2020).
  example: '817732'
  github_request_issue: 450
  homepage: https://cordis.europa.eu/
  name: CORDIS Project
  pattern: ^\d+$
  prefix: cordis.project
  reviewer:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  uri_format: https://cordis.europa.eu/project/id/$1
coriell:
  biocontext:
    prefix: Coriell
    uri_format: https://catalog.coriell.org/0/Sections/Search/Sample_Detail.aspx?Ref=$1
  cellosaurus:
    category: Cell line collections (Providers)
    homepage: https://catalog.coriell.org
    name: Coriell Institute Biorepositories
    prefix: Coriell
    uri_format: https://catalog.coriell.org/0/Sections/Search/Sample_Detail.aspx?Ref=$1&Product=CC
  go:
    description: The Coriell Cell Repositories provide essential research reagents
      to the scientific community by establishing, verifying, maintaining, and distributing
      cell cultures and DNA derived from cell cultures. These collections, supported
      by funds from the National Institutes of Health (NIH) and several foundations,
      are extensively utilized by research scientists around the world.
    homepage: http://ccr.coriell.org/
    name: Coriell Institute for Medical Research
    prefix: CORIELL
    uri_format: http://ccr.coriell.org/Sections/Search/Sample_Detail.aspx?Ref=$1
  mappings:
    biocontext: Coriell
    cellosaurus: Coriell
    go: CORIELL
    miriam: coriell
    n2t: coriell
  miriam:
    deprecated: false
    description: The Coriell Cell Repositories provide essential research reagents
      to the scientific community by establishing, verifying, maintaining, and distributing
      cell cultures and DNA derived from cell cultures. These collections, supported
      by funds from the National Institutes of Health (NIH) and several foundations,
      are extensively utilized by research scientists around the world.
    homepage: http://ccr.coriell.org/
    id: 00000439
    name: Coriell Cell Repositories
    namespaceEmbeddedInLui: false
    pattern: ^[A-Z]{2}\d+$
    prefix: coriell
    sampleId: GM17027
    uri_format: http://ccr.coriell.org/Sections/Search/Sample_Detail.aspx?Ref=$1
  n2t:
    description: The Coriell Cell Repositories provide essential research reagents
      to the scientific community by establishing, verifying, maintaining, and distributing
      cell cultures and DNA derived from cell cultures. These collections, supported
      by funds from the National Institutes of Health (NIH) and several foundations,
      are extensively utilized by research scientists around the world.
    example: GM17027
    homepage: http://ccr.coriell.org/
    name: Coriell Cell Repositories at Coriell Institute
    namespaceEmbeddedInLui: false
    pattern: ^[A-Z]{2}\d+$
    prefix: coriell
    uri_format: http://ccr.coriell.org/Sections/Search/Sample_Detail.aspx?Ref=$1
  prefix: coriell
corrdb:
  fairsharing:
    abbreviation: CorrDB
    contact:
      email: zhu@iastate.edu
      name: Zhiliang Hu
      orcid: 0000-0002-6704-7538
    description: A genetic correlation is the proportion of shared variance between
      two traits that is due to genetic causes; a phenotypic correlation is the degree
      to which two traits co-vary among individuals in a population. In the genomics
      era, while gene expression, genetic association, and network analysis provide
      unprecedented means to decode the genetic basis of complex phenotypes, it is
      important to recognize the possible effects genetic progress in one trait can
      have on other traits. This database is designed to collect all published livestock
      genetic/phenotypic trait correlation data, aimed at facilitating genetic network
      analysis or systems biology studies
    homepage: https://www.animalgenome.org/cgi-bin/CorrDB/index
    name: Animal Trait Correlation Database
    prefix: FAIRsharing.IziuCK
    publications: []
    subjects:
    - Animal Genetics
    - Genetics
    - Life Science
    - Systems Biology
  mappings:
    fairsharing: FAIRsharing.IziuCK
    miriam: corrdb
    re3data: r3d100011496
  miriam:
    deprecated: false
    description: A genetic correlation is the proportion of shared variance between
      two traits that is due to genetic causes; a phenotypic correlation is the degree
      to which two traits co-vary among individuals in a population. In the genomics
      era, while gene expression, genetic association, and network analysis provide
      unprecedented means to decode the genetic basis of complex phenotypes, it is
      important to recognize the possible effects genetic progress in one trait can
      have on other traits. This database is designed to collect all published livestock
      genetic/phenotypic trait correlation data, aimed at facilitating genetic network
      analysis or systems biology studies.
    homepage: https://www.animalgenome.org
    id: 00000831
    name: CorrDB
    namespaceEmbeddedInLui: false
    pattern: ^[0-9]+$
    prefix: corrdb
    sampleId: '37232'
    uri_format: https://www.animalgenome.org/CorrDB/q/?id=CorrID:$1
  prefix: corrdb
  re3data:
    description: CorrDB has data of cattle, relating to meat production, milk production,
      growth, health, and others. This database is designed to collect all published
      livestock genetic/phenotypic trait correlation data, aimed at facilitating genetic
      network analysis or systems biology studies.
    doi: 10.17616/R3TW6G
    homepage: https://www.animalgenome.org/cgi-bin/CorrDB/index
    name: CorrDB
    prefix: r3d100011496
    synonyms:
    - Animal Trait Correlation Database
corum:
  biocontext:
    prefix: CORUM
  fairsharing:
    abbreviation: CORUM
    contact:
      email: andreas.ruepp@helmholtz-muenchen.de
      name: Andreas Ruepp
      orcid: 0000-0003-1705-3515
    description: CORUM is a database that provides a manually curated repository of
      experimentally characterized protein complexes from mammalian organisms, mainly
      human (64%), mouse (16%) and rat (12%). Each protein complex is described by
      a protein complex name, subunit composition, function as well as the literature
      reference that characterizes the respective protein complex.
    homepage: https://mips.helmholtz-muenchen.de/corum/
    name: ' Comprehensive Resource of Mammalian protein complexes'
    prefix: FAIRsharing.ohbpNw
    publications:
    - doi: 10.1093/nar/gky973
      pubmed_id: 30357367
      title: 'CORUM: the comprehensive resource of mammalian protein complexes-2019.'
    subjects:
    - Bioinformatics
    - Biology
  go:
    homepage: https://mips.helmholtz-muenchen.de/corum/
    name: CORUM - the Comprehensive Resource of Mammalian protein complexes
    prefix: CORUM
    uri_format: https://mips.helmholtz-muenchen.de/corum/?id=$1
  homepage: https://mips.helmholtz-muenchen.de/corum
  mappings:
    biocontext: CORUM
    fairsharing: FAIRsharing.ohbpNw
    go: CORUM
    miriam: corum
    n2t: corum
    pathguide: '322'
    prefixcommons: corum
    uniprot: DB-0224
  miriam:
    deprecated: false
    description: The CORUM database provides a resource of manually annotated protein
      complexes from mammalian organisms. Annotation includes protein complex function,
      localization, subunit composition, literature references and more. All information
      is obtained from individual experiments published in scientific articles, data
      from high-throughput experiments is excluded.
    homepage: https://mips.helmholtz-muenchen.de/genre/proj/corum/
    id: '00000440'
    name: CORUM
    namespaceEmbeddedInLui: false
    pattern: ^\d+$
    prefix: corum
    sampleId: '100'
    uri_format: https://mips.helmholtz-muenchen.de/corum/?id=$1
  n2t:
    description: The CORUM database provides a resource of manually annotated protein
      complexes from mammalian organisms. Annotation includes protein complex function,
      localization, subunit composition, literature references and more. All information
      is obtained from individual experiments published in scientific articles, data
      from high-throughput experiments is excluded.
    example: '100'
    homepage: https://mips.helmholtz-muenchen.de/genre/proj/corum/
    name: CORUM at Institute for Bioinformatics and Systems Biology (Germany)
    namespaceEmbeddedInLui: false
    pattern: ^\d+$
    prefix: corum
    uri_format: https://mips.helmholtz-muenchen.de/corum/?id=$1
  name: Comprehensive Resource of Mammalian protein complexes
  pathguide:
    abbreviation: CORUM
    homepage: http://mips.helmholtz-muenchen.de/corum/#
    keywords:
    - PSI-MI
    name: Comprehensive resource of mammalian protein complexes
    prefix: '322'
  prefix: corum
  prefixcommons:
    description: The CORUM database provides a resource of manually annotated protein
      complexes from mammalian organisms. Annotation includes protein complex function,
      localization, subunit composition, literature references and more.
    example: '56'
    homepage: http://mips.gsf.de/genre/proj/corum
    keywords:
    - protein
    name: the Comprehensive Resource of Mammalian protein complexes
    pattern: ^\d+$
    prefix: corum
    uri_format: http://mips.helmholtz-muenchen.de/genre/proj/corum/complexdetails.html?id=$1
  publications:
  - doi: 10.1093/nar/gkae1033
    pmc: null
    pubmed: '39526397'
    title: 'CORUM in 2024: protein complexes as drug targets'
    year: 2024
  - doi: 10.1093/nar/gky973
    pmc: PMC6323970
    pubmed: '30357367'
    title: 'CORUM: the comprehensive resource of mammalian protein complexes-2019'
    year: 2019
  - doi: 10.1093/nar/gky973
    pmc: null
    pubmed: null
    title: 'CORUM: the comprehensive resource of mammalian protein complexes-2019.'
    year: null
  - doi: 10.1093/nar/gkac1015
    pmc: null
    pubmed: '36382402'
    title: null
    year: null
  uniprot:
    abbreviation: CORUM
    category: Protein-protein interaction databases
    homepage: https://mips.helmholtz-muenchen.de/corum/
    name: CORUM comprehensive resource of mammalian protein complexes
    prefix: DB-0224
    publications:
    - doi: 10.1093/nar/gkac1015
      pubmed: '36382402'
    uri_format: https://mips.helmholtz-muenchen.de/corum/#?uniprotID=$1
  uri_format: https://mips.helmholtz-muenchen.de/corum/?complex_id=$1
cosmic.cell:
  cellosaurus:
    category: Polymorphism and mutation databases
    homepage: https://cancer.sanger.ac.uk/cosmic
    name: Catalogue of somatic mutations in cancer
    prefix: Cosmic
    uri_format: https://cancer.sanger.ac.uk/cosmic/sample/overview?id=$1
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: COSMIC, the Catalogue Of Somatic Mutations In Cancer, is the world's
    largest and most comprehensive resource for exploring the impact of somatic mutations
    in human cancer
  example: '906801'
  homepage: https://cancer.sanger.ac.uk/cell_lines/
  mappings:
    cellosaurus: Cosmic
  name: COSMIC Cell Lines
  part_of_database: cosmic
  pattern: ^\d+$
  prefix: cosmic.cell
  uri_format: https://cancer.sanger.ac.uk/cell_lines/sample/overview?id=$1
cosmic.gene:
  biocontext:
    prefix: COSMIC
    uri_format: http://cancer.sanger.ac.uk/cosmic/mutation/overview?id=$1
  contact:
    email: jt6@sanger.ac.uk
    github: jgtate
    name: John G Tate
    orcid: 0000-0002-8315-6574
  edam:
    description: Identifier of a COSMIC database entry.
    name: COSMIC
    obsolete: false
    prefix: '3264'
  fairsharing:
    abbreviation: COSMIC
    description: The Catalogue of Somatic Mutations in Cancer (COSMIC) is a database
      of manually-curated somatic mutation information relating to human cancers.
      The COSMIC database combines manually-curated data and genome-wide screen data.
    homepage: http://cancer.sanger.ac.uk
    name: Catalogue of Somatic Mutations in Cancer
    prefix: FAIRsharing.s5zmbp
    publications:
    - doi: 10.1093/nar/gku1075
      pubmed_id: 25355519
      title: 'COSMIC: exploring the world''s knowledge of somatic mutations in human
        cancer.'
    - doi: 10.1093/nar/gkq929
      pubmed_id: 20952405
      title: 'COSMIC: mining complete cancer genomes in the Catalogue of Somatic Mutations
        in Cancer.'
    - doi: 10.1038/sj.bjc.6601894
      pubmed_id: 15188009
      title: The COSMIC (Catalogue of Somatic Mutations in Cancer) database and website.
    - doi: 10.1093/nar/gky1015
      pubmed_id: 30371878
      title: 'COSMIC: the Catalogue Of Somatic Mutations In Cancer.'
    subjects:
    - Genetics
    - Biomedical Science
  mappings:
    biocontext: COSMIC
    edam: '3264'
    fairsharing: FAIRsharing.s5zmbp
    miriam: cosmic
    n2t: cosmic
  miriam:
    deprecated: false
    description: COSMIC is a comprehensive global resource for information on somatic
      mutations in human cancer, combining curation of the scientific literature with
      tumor resequencing data from the Cancer Genome Project at the Sanger Institute,
      U.K. This collection references genes.
    homepage: http://cancer.sanger.ac.uk/cosmic/
    id: '00000601'
    name: COSMIC Gene
    namespaceEmbeddedInLui: false
    pattern: ^[A-Z0-9]+$
    prefix: cosmic
    sampleId: BRAF
    uri_format: http://cancer.sanger.ac.uk/cosmic/gene/overview?ln=$1
  n2t:
    description: COSMIC is a comprehensive global resource for information on somatic
      mutations in human cancer, combining curation of the scientific literature with
      tumor resequencing data from the Cancer Genome Project at the Sanger Institute,
      U.K. This collection references genes.
    example: BRAF
    homepage: http://cancer.sanger.ac.uk/cosmic/
    name: COSMIC Gene at Sanger
    namespaceEmbeddedInLui: false
    pattern: ^[A-Z0-9]+$
    prefix: cosmic
    uri_format: http://cancer.sanger.ac.uk/cosmic/gene/overview?ln=$1
  name: COSMIC Gene
  part_of_database: cosmic
  pattern: ^[A-Z0-9][A-Z0-9-]*$
  prefix: cosmic.gene
  provides: hgnc.symbol
  publications:
  - doi: 10.1093/nar/gky1015
    pmc: PMC6323903
    pubmed: '30371878'
    title: 'COSMIC: the Catalogue Of Somatic Mutations In Cancer'
    year: 2019
  - doi: 10.1093/nar/gku1075
    pmc: PMC4383913
    pubmed: '25355519'
    title: 'COSMIC: exploring the world''s knowledge of somatic mutations in human
      cancer'
    year: 2014
  - doi: 10.1093/nar/gkq929
    pmc: PMC3013785
    pubmed: '20952405'
    title: 'COSMIC: mining complete cancer genomes in the Catalogue of Somatic Mutations
      in Cancer'
    year: 2010
  - doi: 10.1038/sj.bjc.6601894
    pmc: PMC2409828
    pubmed: '15188009'
    title: The COSMIC (Catalogue of Somatic Mutations in Cancer) database and website
    year: 2004
  synonyms:
  - cosmic
covid19:
  aberowl:
    description: The COVID-19 Surveillance Ontology is an application ontology used
      to support SARS-CoV-2 (severe acute respiratory syndrome coronavirus 2) surveillance
      in primary care. The ontology facilitates monitoring of COVID-19 cases and related
      respiratory conditions using data from multiple brands of computerised medical
      record systems.
    download_owl: http://aber-owl.net/media/ontologies/COVID19/3/covid19.owl
    homepage: https://orchid.phc.ox.ac.uk/index.php/cov-19/
    name: COVID-19 Surveillance Ontology
    prefix: COVID19
    version: V1.0
  bioportal:
    contact:
      email: john.williams@phc.ox.ac.uk
      name: John Williams
    description: The COVID-19 Surveillance Ontology is an application ontology used
      to support SARS-CoV-2 (severe acute respiratory syndrome coronavirus 2) surveillance
      in primary care. The ontology facilitates monitoring of COVID-19 cases and related
      respiratory conditions using data from multiple brands of computerised medical
      record systems.
    homepage: https://orchid.phc.ox.ac.uk/index.php/cov-19/
    name: COVID-19 Surveillance Ontology
    prefix: COVID19
    publications:
    - https://publichealth.jmir.org/2020/4/e21434/
    version: V1.0
  contact:
    email: dylan.mcgagh@magd.ox.ac.uk
    github: null
    name: Dylan McGagh
    orcid: 0000-0002-6772-2775
  mappings:
    aberowl: COVID19
    bioportal: COVID19
    miriam: covid19
  miriam:
    deprecated: false
    description: Curated contextual database gathering samples related to SARS-CoV-2
      virus and covid-19 disease.
    homepage: https://covid19.sfb.uit.no
    id: 00000789
    name: SARS-CoV-2
    namespaceEmbeddedInLui: false
    pattern: ^\w+_COVID19_[-\w]+$
    prefix: covid19
    sampleId: SFB_COVID19_MW286762
    uri_format: https://covid19.sfb.uit.no/api/records/$1
  prefix: covid19
covoc:
  contact:
    email: zmp@ebi.ac.uk
    github: zoependlington
    name: Zoë May Pendlington
    orcid: 0000-0002-4071-8397
  download_json: https://github.com/EBISPOT/covoc/releases/download/current/covoc.json
  download_obo: https://github.com/EBISPOT/covoc/releases/download/current/covoc.obo
  download_owl: https://github.com/EBISPOT/covoc/releases/download/current/covoc.owl
  example: '0010034'
  homepage: https://github.com/EBISPOT/covoc
  mappings:
    ols: covoc
  ols:
    description: The COVID-19 Vocabulary (COVoc) is an ontology containing terms related
      to the research of the COVID-19 pandemic. This includes host organisms, pathogenicity,
      gene and gene products, barrier gestures, treatments and more.
    download_owl: https://github.com/EBISPOT/covoc/releases/download/current/covoc.owl
    homepage: https://github.com/EBISPOT/covoc
    name: CoVoc Coronavirus Vocabulary
    prefix: covoc
    uri_format: http://purl.obolibrary.org/obo/COVOC_$1
    version: '2022-10-26'
    version.iri: http://purl.obolibrary.org/obo/covoc/releases/2022-10-26/covoc.owl
  pattern: ^\d{7}$
  prefix: covoc
  repository: https://github.com/EBISPOT/covoc
  uri_format: http://purl.obolibrary.org/obo/COVOC_$1
coypu:
  example: AbductionOrForcedDisappearance
  mappings:
    tib: coy
  prefix: coypu
  tib:
    description: Ontology to describe companies and their supply network, employees,
      products, production materials, industries, events and relations.
    download_rdf: https://gitlab.com/coypu-project/coy-ontology/-/raw/main/ontology/global/coy.ttl
    homepage: https://gitlab.com/coypu-project/coy-ontology
    keywords:
    - CoyPu
    - economics
    name: CoyPu Ontology
    prefix: coy
    uri_format: https://schema.coypu.org/global#$1
    version.iri: https://schema.coypu.org/global/2.3
coypu.emdat:
  example: Air
  mappings:
    tib: emdat
  prefix: coypu.emdat
  tib:
    description: Crisis and hazard related taxonomy developed by CRED for disaster
      preparedness and humanitarian actions at national and international level.
    download_rdf: https://gitlab.com/coypu-project/coy-ontology/-/raw/main/ontology/events/em-dat.ttl
    homepage: https://schema.coypu.org/em-dat/1.0
    keywords:
    - CoyPu
    - earth sciences
    - life sciences, biology
    name: EM-DAT Disaster Classification Ontology
    prefix: emdat
    uri_format: https://schema.coypu.org/em-dat#$1
    version.iri: https://schema.coypu.org/em-dat/1.0
coypu.gta:
  example: AffectedCommercialFlow
  mappings:
    tib: gta
  prefix: coypu.gta
  tib:
    description: An ontology for modeling global trade alerts, mainly inspired by
      the Global Trade Alerts repository.
    download_rdf: https://gitlab.com/coypu-project/coy-ontology/-/raw/main/ontology/events/gta.ttl
    homepage: https://schema.coypu.org/gta/1.0
    keywords:
    - CoyPu
    - economics
    name: Global Trade Alerts Ontology
    prefix: gta
    uri_format: https://schema.coypu.org/gta#$1
    version.iri: https://schema.coypu.org/gta/1.0
coypu.ta:
  example: CustomsUnion
  mappings:
    tib: ta
  prefix: coypu.ta
  tib:
    description: An ontology for modeling trade agreements
    download_rdf: https://gitlab.com/coypu-project/coy-ontology/-/raw/main/ontology/events/rta.ttl
    homepage: https://schema.coypu.org/ta/1.0
    keywords:
    - CoyPu
    - economics
    name: Trade Agreement Ontology
    prefix: ta
    uri_format: https://schema.coypu.org/ta#$1
    version.iri: https://schema.coypu.org/ta/1.0
coypu.tiva:
  example: hasExport
  mappings:
    tib: tiva
  prefix: coypu.tiva
  tib:
    description: An ontology for modeling international trade flows.
    download_rdf: https://gitlab.com/coypu-project/coy-ontology/-/raw/main/ontology/indicators/valueandtradeflows.ttl
    homepage: https://gitlab.com/coypu-project/coy-ontology/
    keywords:
    - CoyPu
    - economics
    name: OECD TIVA Ontology
    prefix: tiva
    uri_format: https://schema.coypu.org/vtf#$1
    version.iri: https://schema.coypu.org/vtf/1.4
cp:
  appears_in:
  - cl
  comment: Part of cell ontology but deprecated, see https://github.com/obophenotype/cell-ontology/issues/572
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  deprecated: true
  name: Cellular Phenotypes
  prefix: cp
cpc:
  biocontext:
    prefix: CPC
  fairsharing:
    abbreviation: CPC
    description: The Climate Prediction Center (CPC) produces operational predictions
      of climate variability, real-time monitoring of climate and the required data
      bases, and assessments of the origins of major climate anomalies. These cover
      time scales from a week to seasons, extending into the future as far as technically
      feasible, and cover the land, the ocean, and the atmosphere, extending into
      the stratosphere.
    homepage: https://www.cpc.ncep.noaa.gov/
    name: Climate Prediction Center
    prefix: FAIRsharing.e08886
    publications: []
    subjects:
    - Hydrogeology
    - Geography
    - Meteorology
    - Geodesy
    - Earth Science
    - Atmospheric Science
  mappings:
    biocontext: CPC
    fairsharing: FAIRsharing.e08886
    miriam: cpc
    n2t: cpc
  miriam:
    deprecated: false
    description: The Cooperative Patent Classification (CPC) is a patent classification
      system, developed jointly by the European Patent Office (EPO) and the United
      States Patent and Trademark Office (USPTO). It is based on the previous European
      classification system (ECLA), which itself was a version of the International
      Patent Classification (IPC) system. The CPC patent classification system has
      been used by EPO and USPTO since 1st January, 2013.
    homepage: https://worldwide.espacenet.com/classification
    id: 00000539
    name: Cooperative Patent Classification
    namespaceEmbeddedInLui: false
    pattern: ^([A-H,Y]|[A-H, Y]\d{2}|[A-H, Y]\d{2}[A-Z]|[A-H, Y]\d{2}[A-Z]\d{1,3}|[A-H,
      Y]\d{2}[A-Z]\d{1,3}(\/)?\d{2,})$
    prefix: cpc
    sampleId: A01M1/026
    uri_format: https://worldwide.espacenet.com/classification?locale=en_EP#!/CPC=$1
  n2t:
    description: The Cooperative Patent Classification (CPC) is a patent classification
      system, developed jointly by the European Patent Office (EPO) and the United
      States Patent and Trademark Office (USPTO). It is based on the previous European
      classification system (ECLA), which itself was a version of the International
      Patent Classification (IPC) system. The CPC patent classification system has
      been used by EPO and USPTO since 1st January, 2013.
    example: A01M1/026
    homepage: https://worldwide.espacenet.com/classification
    name: Cooperative Patent Classification at Espace
    namespaceEmbeddedInLui: false
    pattern: ^([A-H,Y]|[A-H, Y]\d{2}|[A-H, Y]\d{2}[A-Z]|[A-H, Y]\d{2}[A-Z]\d{1,3}|[A-H,
      Y]\d{2}[A-Z]\d{1,3}(\/)?\d{2,})$
    prefix: cpc
    uri_format: https://worldwide.espacenet.com/classification?locale=en_EP#!/CPC=$1
  prefix: cpc
cpt:
  aberowl:
    description: Current Procedural Terminology
    homepage: http://www.ama-assn.org/ama/pub/category/3113.html
    name: Current Procedural Terminology
    prefix: CPT
    version: 2016AB
  biolink:
    is_identifiers: false
    is_obo: false
    prefix: CPT
    uri_format: https://www.ama-assn.org/practice-management/cpt/$1
  bioportal:
    contact:
      email: Intellectual.PropertyServices@ama-assn.org
      name: American Medical Association
    description: CPT is a list of descriptive terms and identifying numeric codes
      for medical services and procedures that are provided by physicians and health
      care professionals.
    homepage: https://www.ama-assn.org/practice-management/cpt-current-procedural-terminology
    name: CPT - Current Procedural Terminology
    prefix: CPT
    version: 2020AB
  contributor:
    email: smoxon@lbl.gov
    github: sierra-moxon
    name: Sierra Moxon
    orcid: 0000-0002-8719-7760
  contributor_extras:
  - email: null
    github: colleenXu
    name: Colleen Xu
    orcid: 0000-0003-2975-882X
  description: Current Procedural Terminology, more commonly known as CPT®, refers
    to a medical code set created and maintained by the American Medical Association
    — and used by physicians, allied health professionals, nonphysician practitioners,
    hospitals, outpatient facilities, and laboratories to represent the services and
    procedures they perform. No provider of outpatient services gets paid without
    reporting the proper CPT® codes. [Description taken from this site](https://www.aapc.com/codes/cpt-codes-range/)]
  domain: vaccine
  example: '00103'
  fairsharing:
    abbreviation: CPT
    description: Current Procedural Terminology is a medical nomenclature used to
      report medical procedures and services under public and private health insurance
      programs.
    homepage: https://www.ama-assn.org/practice-management/cpt/ama-cpt-licensing-overview
    name: Current Procedural Terminology
    prefix: FAIRsharing.wpxab1
    publications:
    - doi: 10.1136/neurintsurg-2014-011156
      pubmed: '24589819'
      title: Current procedural terminology; a primer
      year: 2014
    - doi: 10.1016/j.jacr.2007.10.004
      pubmed: '18359442'
      title: 'CPT: an open system that describes all that you do'
      year: 2008
    subjects:
    - Biomedical Science
    - Health Science
    - Medicine
  github_request_issue: 357
  homepage: https://www.aapc.com
  logo: https://edhub.ama-assn.org/ImageLibrary/Ed-Hub-Self-Serve/CPT-monogram.png
  mappings:
    aberowl: CPT
    biolink: CPT
    bioportal: CPT
    fairsharing: FAIRsharing.wpxab1
  name: Current Procedural Terminology
  pattern: ^\d+$
  prefix: cpt
  providers:
  - code: bioportal.purl
    description: null
    example: null
    first_party: null
    homepage: null
    name: null
    publications: null
    status: null
    uri_format: http://purl.bioontology.org/ontology/CPT/$1
  publications:
  - doi: 10.1136/neurintsurg-2014-011156
    pmc: null
    pubmed: '24589819'
    title: Current procedural terminology; a primer
    year: 2014
  - doi: 10.1016/j.jacr.2007.10.004
    pmc: null
    pubmed: '18359442'
    title: 'CPT: an open system that describes all that you do'
    year: 2008
  - doi: 10.1136/neurintsurg-2014-011156
    pmc: null
    pubmed: '24589819'
    title: Current procedural terminology; a primer
    year: 2014
  - doi: 10.1016/j.jacr.2007.10.004
    pmc: null
    pubmed: '18359442'
    title: 'CPT: an open system that describes all that you do'
    year: 2008
  - doi: 10.1136/neurintsurg-2014-011156
    pmc: null
    pubmed: '24589819'
    title: Current procedural terminology; a primer
    year: 2014
  - doi: 10.1016/j.jacr.2007.10.004
    pmc: null
    pubmed: '18359442'
    title: 'CPT: an open system that describes all that you do'
    year: 2008
  - doi: 10.1136/neurintsurg-2014-011156
    pmc: null
    pubmed: '24589819'
    title: Current procedural terminology; a primer
    year: 2014
  - doi: 10.1016/j.jacr.2007.10.004
    pmc: null
    pubmed: '18359442'
    title: 'CPT: an open system that describes all that you do'
    year: 2008
  references:
  - https://github.com/biopragmatics/bioregistry/pull/358
  - https://github.com/biolink/biolink-model/pull/993
  reviewer:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  synonyms:
  - ama-cpt
  uri_format: https://www.aapc.com/codes/cpt-codes/$1
cran:
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: Repository of packages for the R programming language
  example: ggplot2
  homepage: https://cran.r-project.org/
  mappings:
    wikidata: P5565
  name: The Comprehensive R Archive Network
  prefix: cran
  uri_format: https://cran.r-project.org/web/packages/$1
  wikidata:
    description: name of a project in CRAN
    example:
    - RGtk2
    - knitr
    - qdap
    name: CRAN project
    prefix: P5565
    uri_format: https://CRAN.R-project.org/package=$1
crates:
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: A repository of software packages written in Rust.
  example: curies
  homepage: https://crates.io
  name: Crates.io
  prefix: crates
  uri_format: https://crates.io/crates/$1
creativebiolabs.antibody:
  contributor:
    email: m.naguthana@hotmail.com
    github: nagutm
    name: Mufaddal Naguthanawala
    orcid: 0009-0009-5240-7463
  description: Creative Biolabs Antigen provides identifiers  for antibody-based entities
    such as recombinant, functional, engineered, and format-specific antibodies as
    well as antibody processing tools, which are essential for applications in diagnostics,
    therapeutics, and immunology.
  domain: antibody
  example: TAB-884
  github_request_issue: 1257
  homepage: https://www.creativebiolabs.net
  name: Creative Biolabs antibody
  pattern: ^[a-zA-Z]+-[a-zA-Z0-9()]+(-[a-zA-Z0-9]*)?$
  prefix: creativebiolabs.antibody
  reviewer:
    email: b.gyori@northeastern.edu
    github: bgyori
    name: Benjamin M. Gyori
    orcid: 0000-0001-9439-5346
creativebiolabs.protein:
  contributor:
    email: m.naguthana@hotmail.com
    github: nagutm
    name: Mufaddal Naguthanawala
    orcid: 0009-0009-5240-7463
  description: Creative Biolabs Protein provides identifiers for protein-related entities,
    including therapeutic proteins, proteolytic enzymes, antibody-like scaffold proteins,
    soluble T cell receptors, and tetramers.
  example: VS-0724-CJ1
  github_request_issue: 1257
  homepage: https://www.creativebiolabs.net
  name: Creative Biolabs protein
  pattern: ^[a-zA-Z]+-[a-zA-Z0-9()]+(-[a-zA-Z0-9]*)?$
  prefix: creativebiolabs.protein
  reviewer:
    email: b.gyori@northeastern.edu
    github: bgyori
    name: Benjamin M. Gyori
    orcid: 0000-0001-9439-5346
credit:
  contact:
    email: liz.allen@f1000.com
    github: null
    name: Liz Allen
    orcid: 0000-0002-9298-3168
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: CRediT (Contributor Roles Taxonomy) is high-level taxonomy, including
    14 roles, that can be used to represent the roles typically played by contributors
    to scientific scholarly output. The roles describe each contributor’s specific
    contribution to the scholarly output.
  domain: bibliometrics
  example: software
  fairsharing:
    abbreviation: CRediT
    description: CRediT (Contributor Roles Taxonomy) is a high-level taxonomy, including
      14 roles, that can be used to represent the roles typically played by contributors
      to scientific scholarly output. The roles describe each contributor’s specific
      contribution to the scholarly output.
    domains:
    - Resource metadata
    - Classification
    homepage: https://credit.niso.org/
    license: CC-BY-4.0
    logo: https://api.fairsharing.org/rails/active_storage/blobs/redirect/eyJfcmFpbHMiOnsibWVzc2FnZSI6IkJBaHBBaUFCIiwiZXhwIjpudWxsLCJwdXIiOiJibG9iX2lkIn19--af4f02374db4f42007e6674ea2055ccaa36aa830/credit-icon-499x500-1.png?disposition=inline
    name: Contributor Roles Taxonomy
    prefix: FAIRsharing.fe4816
    publications:
    - doi: 10.1038/508312a
      title: 'Publishing: Credit where credit is due'
      year: 2014
    - doi: 10.3789/ansi.niso.z39.104-2022
      title: ANSI/NISO Z39.104-2022, CRediT, Contributor Roles Taxonomy
      year: 2022
    - doi: 10.1002/leap.1210
      title: How can we ensure visibility and diversity in research contributions?
        How the Contributor Role Taxonomy (CRediT) is helping the shift from authorship
        to contributorship
      year: 2019
    - doi: 10.1087/20150211
      title: 'Beyond authorship: attribution, contribution, collaboration, and credit'
      year: 2015
    - doi: 10.1038/d41586-019-01715-4
      title: Credit data generators for data reuse
      year: 2019
    subjects:
    - Omics
    - Data Quality
    - Subject Agnostic
    twitter: contrib_roles
  homepage: https://credit.niso.org/
  keywords:
  - attribution
  - contributor roles
  license: CC-BY-4.0
  mappings:
    fairsharing: FAIRsharing.fe4816
    ols: credit
    tib: credit
  name: Contributor Roles Taxonomy
  ols:
    description: CRediT (Contributor Roles Taxonomy) is high-level taxonomy, including
      14 roles, that can be used to represent the roles typically played by contributors
      to scientific scholarly output. The roles describe each contributor’s specific
      contribution to the scholarly output.
    download_owl: https://w3id.org/biopragmatics/resources/credit/credit.owl
    homepage: https://credit.niso.org/
    name: Contributor Roles Taxonomy
    prefix: credit
    uri_format: https://credit.niso.org/contributor-roles/$1
    version.iri: https://w3id.org/biopragmatics/resources/credit/2022/credit.ofn
  pattern: ^(conceptualization|data-curation|formal-analysis|funding-acquisition|investigation|methodology|project-administration|resources|software|supervision|validation|visualization|writing-original-draft|writing-review-editing)$
  prefix: credit
  publications:
  - doi: 10.1038/d41586-019-01715-4
    pmc: null
    pubmed: '31164773'
    title: Credit data generators for data reuse
    year: 2019
  - doi: 10.1002/leap.1210
    pmc: null
    pubmed: null
    title: How can we ensure visibility and diversity in research contributions? How
      the Contributor Role Taxonomy (CRediT) is helping the shift from authorship
      to contributorship
    year: 2019
  - doi: 10.1087/20150211
    pmc: null
    pubmed: null
    title: 'Beyond authorship: attribution, contribution, collaboration, and credit'
    year: 2015
  - doi: 10.1038/508312a
    pmc: null
    pubmed: '24745070'
    title: 'Publishing: Credit where credit is due'
    year: 2014
  - doi: 10.3789/ansi.niso.z39.104-2022
    pmc: null
    pubmed: null
    title: ANSI/NISO Z39.104-2022, CRediT, Contributor Roles Taxonomy
    year: null
  - doi: 10.1038/508312a
    pmc: null
    pubmed: null
    title: 'Publishing: Credit where credit is due'
    year: 2014
  - doi: 10.3789/ansi.niso.z39.104-2022
    pmc: null
    pubmed: null
    title: ANSI/NISO Z39.104-2022, CRediT, Contributor Roles Taxonomy
    year: 2022
  - doi: 10.1002/leap.1210
    pmc: null
    pubmed: null
    title: How can we ensure visibility and diversity in research contributions? How
      the Contributor Role Taxonomy (CRediT) is helping the shift from authorship
      to contributorship
    year: 2019
  - doi: 10.1087/20150211
    pmc: null
    pubmed: null
    title: 'Beyond authorship: attribution, contribution, collaboration, and credit'
    year: 2015
  - doi: 10.1038/d41586-019-01715-4
    pmc: null
    pubmed: null
    title: Credit data generators for data reuse
    year: 2019
  - doi: 10.1038/508312a
    pmc: null
    pubmed: null
    title: 'Publishing: Credit where credit is due'
    year: 2014
  - doi: 10.3789/ansi.niso.z39.104-2022
    pmc: null
    pubmed: null
    title: ANSI/NISO Z39.104-2022, CRediT, Contributor Roles Taxonomy
    year: 2022
  - doi: 10.1002/leap.1210
    pmc: null
    pubmed: null
    title: How can we ensure visibility and diversity in research contributions? How
      the Contributor Role Taxonomy (CRediT) is helping the shift from authorship
      to contributorship
    year: 2019
  - doi: 10.1087/20150211
    pmc: null
    pubmed: null
    title: 'Beyond authorship: attribution, contribution, collaboration, and credit'
    year: 2015
  - doi: 10.1038/d41586-019-01715-4
    pmc: null
    pubmed: null
    title: Credit data generators for data reuse
    year: 2019
  references:
  - https://casrai.org/credit/
  tib:
    description: CRediT (Contributor Roles Taxonomy) is a high-level taxonomy, including
      14 roles, that can be used to represent the roles typically played by contributors
      to scientific scholarly output. The roles describe each contributor's specific
      contribution to the scholarly output.
    download_owl: https://w3id.org/biopragmatics/resources/credit/credit.owl
    homepage: https://credit.niso.org/
    keywords:
    - NFDI4ING
    - TIB
    - Digital Planning and Construction
    - FID BAUdigital
    - FID move
    name: Contributor Roles Taxonomy
    prefix: credit
    tracker: https://github.com/biopragmatics/obo-db-ingest/issues
    uri_format: https://credit.niso.org/contributor-roles/$1
    version.iri: https://w3id.org/biopragmatics/resources/credit/2022/credit.ofn
  uri_format: https://credit.niso.org/contributor-roles/$1
crisprdb:
  biocontext:
    prefix: CRISPRDB
  fairsharing:
    abbreviation: CRISPRdb
    contact:
      email: Christine.Pourcel@u-psud.fr
      name: Christine Pourcel
      orcid: 0000-0002-8951-466X
    description: CRISPRdb acts as a gateway to a publicly accessible database and
      software. It enables the easy detection of CRISPR sequences in locally-produced
      data and the consultation of CRISPR sequence data present in the database. It
      also gives information on the presence of CRISPR-associated (cas) genes when
      they have been annotated as such.
    homepage: http://crispr.i2bc.paris-saclay.fr/
    name: CRISPRdb
    prefix: FAIRsharing.7sfedh
    publications:
    - doi: 10.1186/1471-2105-8-172
      pubmed_id: 17521438
      title: The CRISPRdb database and tools to display CRISPRs and to generate dictionaries
        of spacers and repeats.
    - doi: 10.1093/nar/gkm360
      pubmed_id: 17537822
      title: 'CRISPRFinder: a web tool to identify clustered regularly interspaced
        short palindromic repeats.'
    - doi: 10.1093/nar/gkn228
      pubmed_id: 18442988
      title: 'CRISPRcompar: a website to compare clustered regularly interspaced short
        palindromic repeats.'
    subjects:
    - Life Science
  integbio:
    description: CRISPRdb acts as a gateway to a publicly accessible database and
      software. It enables the easy detection of CRISPR sequences in locally-produced
      data and the consultation of CRISPR sequence data present in the database. It
      also gives information on the presence of CRISPR-associated (cas) genes when
      they have been annotated as such.
    fairsharing: FAIRsharing.7sfedh
    homepage: http://crispr.i2bc.paris-saclay.fr/
    information_keywords:
    - Sequence
    maintainer: Universitè Paris-Sud 11, CNRS
    name: CRISPRdb
    prefix: nbdc02213
    pubmeds:
    - '17537822'
    - '17521438'
    - '18442988'
    target_keywords:
    - Genome/Gene
  mappings:
    biocontext: CRISPRDB
    fairsharing: FAIRsharing.7sfedh
    integbio: nbdc02213
    miriam: crisprdb
    n2t: crisprdb
  miriam:
    deprecated: false
    description: Repeated CRISPR ("clustered regularly interspaced short palindromic
      repeats") elements found in archaebacteria and eubacteria are believed to defend
      against viral infection, potentially targeting invading DNA for degradation.
      CRISPRdb is a database that stores information on CRISPRs that are automatically
      extracted from newly released genome sequence data.
    homepage: http://crispr.i2bc.paris-saclay.fr/
    id: '00000626'
    name: CRISPRdb
    namespaceEmbeddedInLui: false
    pattern: ^[0-9]+$
    prefix: crisprdb
    sampleId: '551115'
    uri_format: http://crispr.i2bc.paris-saclay.fr/cgi-bin/crispr/SpecieProperties_db.cgi?Taxon_id[]=$1
  n2t:
    description: Repeated CRISPR ("clustered regularly interspaced short palindromic
      repeats") elements found in archaebacteria and eubacteria are believed to defend
      against viral infection, potentially targeting invading DNA for degradation.
      CRISPRdb is a database that stores information on CRISPRs that are automatically
      extracted from newly released genome sequence data.
    example: '551115'
    homepage: http://crispr.i2bc.paris-saclay.fr/
    name: CRISPRdb
    namespaceEmbeddedInLui: false
    pattern: ^[0-9]+$
    prefix: crisprdb
    uri_format: http://crispr.i2bc.paris-saclay.fr/cgi-bin/crispr/SpecieProperties_db.cgi?Taxon_id[]=$1
  prefix: crisprdb
  publications:
  - doi: 10.1093/nar/gkn228
    pmc: PMC2447796
    pubmed: '18442988'
    title: 'CRISPRcompar: a website to compare clustered regularly interspaced short
      palindromic repeats'
    year: 2008
  - doi: 10.1093/nar/gkm360
    pmc: PMC1933234
    pubmed: '17537822'
    title: 'CRISPRFinder: a web tool to identify clustered regularly interspaced short
      palindromic repeats'
    year: 2007
  - doi: 10.1186/1471-2105-8-172
    pmc: PMC1892036
    pubmed: '17521438'
    title: The CRISPRdb database and tools to display CRISPRs and to generate dictionaries
      of spacers and repeats
    year: 2007
cro:
  aberowl:
    description: A classification of the diverse roles performed in the work leading
      to a published research output in the sciences. Its purpose to provide transparency
      in contributions to scholarly published work, to enable improved systems of
      attribution, credit, and accountability.
    download_owl: http://aber-owl.net/media/ontologies/CRO/5/cro.owl
    homepage: https://github.com/data2health/contributor-role-ontology
    name: Contributor Role Ontology
    prefix: CRO
  biocontext:
    prefix: CRO
  bioportal:
    contact:
      email: whimar@ohsu.edu
      name: Marijane White
    description: The Contributor Role Ontology (CRO) is an extension of the CASRAI
      Contributor Roles Taxonomy (CRediT).
    homepage: https://github.com/data2health/contributor-role-ontology
    name: Contributor Role Ontology
    prefix: CRO
    publications:
    - https://github.com/data2health/contributor-role-ontology
    version: v2019-08-16
  download_obo: https://raw.githubusercontent.com/data2health/contributor-role-ontology/master/cro.obo
  example: 0000038
  keywords:
  - attribution
  - contributor roles
  mappings:
    aberowl: CRO
    biocontext: CRO
    bioportal: CRO
    obofoundry: cro
    ols: cro
    ontobee: CRO
    wikidata.entity: Q70987840
  obofoundry:
    contact: whimar@ohsu.edu
    contact.github: marijane
    contact.label: Marijane White
    contact.orcid: 0000-0001-5059-4132
    deprecated: false
    description: A classification of the diverse roles performed in the work leading
      to a published research output in the sciences. Its purpose to provide transparency
      in contributions to scholarly published work, to enable improved systems of
      attribution, credit, and accountability.
    domain: information
    download.owl: http://purl.obolibrary.org/obo/cro.owl
    homepage: https://github.com/data2health/contributor-role-ontology
    license: CC BY 2.0
    license.url: https://creativecommons.org/licenses/by/2.0/
    name: Contributor Role Ontology
    preferredPrefix: CRO
    prefix: cro
    repository: https://github.com/data2health/contributor-role-ontology
  ols:
    description: A classification of the diverse roles performed in the work leading
      to a published research output in the sciences. Its purpose to provide transparency
      in contributions to scholarly published work, to enable improved systems of
      attribution, credit, and accountability.
    download_owl: http://purl.obolibrary.org/obo/cro.owl
    homepage: https://github.com/data2health/contributor-role-ontology
    name: Contributor Role Ontology
    prefix: cro
    tracker: https://github.com/data2health/contributor-role-ontology/issues
    version: '2019-12-11'
    version.iri: http://purl.obolibrary.org/obo/cro/releases/2019-12-11/cro.owl
  ontobee:
    library: Library
    name: Contributor Role Ontology
    prefix: CRO
  pattern: ^\d{7}$
  prefix: cro
  uri_format: http://purl.obolibrary.org/obo/CRO_$1
croissant:
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: A data model describing machine learning experiments
  domain: data model
  example: FileObject
  github_request_issue: 1726
  homepage: http://mlcommons.org/croissant/
  keywords:
  - artificial intelligence
  - machine learning
  name: Croissant Format Specification
  prefix: croissant
  uri_format: http://mlcommons.org/croissant/$1
crop2ml:
  mappings:
    miriam: crop2ml
  miriam:
    deprecated: false
    description: CropMRespository is a database of soil and crop biophysical process
      models.
    homepage: http://www.crop2ml.org
    id: '00001015'
    name: CropMRepository
    namespaceEmbeddedInLui: false
    pattern: ^[0-9]{9}$
    prefix: crop2ml
    sampleId: '000000001'
    uri_format: http://www.crop2ml.org/cropmdb/$1
  prefix: crop2ml
cryoem:
  aberowl:
    description: Ontology that describes data types and image processing operations
      in Cryo Electron Microscopy of Single Particles
    download_owl: http://aber-owl.net/media/ontologies/CRYOEM/4/cryoem.owl
    homepage: http://scipion.i2pc.es/ontology/cryoem
    name: Cryo Electron Microscopy
    prefix: CRYOEM
    version: '2021-03-09'
  bioportal:
    contact:
      email: coss@cnb.csic.es
      name: Carlos Oscar Sorzano
    description: Ontology that describes data types and image processing operations
      in Cryo Electron Microscopy of Single Particles
    homepage: http://scipion.i2pc.es/ontology/cryoem
    name: Cryo Electron Microscopy
    prefix: CRYOEM
    version: '2021-03-09'
  example: '0000052'
  fairsharing:
    abbreviation: CryoEM Ontology
    contact:
      email: coss@cnb.csic.es
      name: Carlos Oscar S. Sorzano
      orcid: 0000-0002-9473-283X
    description: The CryoEM Ontology for describing objects and workflows in Single
      Particle Analysis by Cryo Electron Microscopy.
    domains:
    - Bioimaging
    - electron microscopy
    homepage: http://scipion.i2pc.es/ontology/cryoem
    license: CC-BY-3.0
    name: CryoEM Ontology
    prefix: FAIRsharing.q47I0t
    repository: https://github.com/I2PC/cryoem
    subjects:
    - Structural Biology
  mappings:
    aberowl: CRYOEM
    bioportal: CRYOEM
    fairsharing: FAIRsharing.q47I0t
    ols: cryoem
  ols:
    contact: isanchez@cnb.csic.es
    description: Ontology that describes data types and image processing operations
      in Cryo Electron Microscopy of Single Particles
    download_owl: http://scipion.i2pc.es/ontology/cryoem.owl
    homepage: http://scipion.i2pc.es/ontology/cryoem
    name: Cryo Electron Microscopy ontology
    prefix: cryoem
    version: '2021-03-09'
    version.iri: http://scipion.i2pc.es/ontology/cryoem/releases/2021-03-09/cryoem.owl
  pattern: ^\d{7}$
  prefix: cryoem
  uri_format: http://scipion.i2pc.es/ontology/CRYOEM_$1
cryptodb:
  biocontext:
    prefix: CRYPTODB
  fairsharing:
    abbreviation: CryptoDB
    contact:
      email: jkissing@uga.edu
      name: Jessica Kissinger
      orcid: 0000-0003-4446-6200
    description: CryptoDB serves as the functional genomics database for Cryptosporidium
      and related species. CryptoDB is a free, online resource for accessing and exploring
      genome sequence and annotation, functional genomics data, isolate sequences,
      and orthology profiles across organisms. It also includes supplemental bioinformatics
      analyses and a web interface for data-mining.
    homepage: https://cryptodb.org/cryptodb/app
    name: CryptoDB
    prefix: FAIRsharing.t3nprm
    publications:
    - doi: 10.1093/nar/gkj078
      pubmed_id: 16381902
      title: 'CryptoDB: a Cryptosporidium bioinformatics resource update.'
    - doi: 10.1007/978-1-4939-9748-0_10
      pubmed_id: 31452162
      title: Accessing Cryptosporidium Omic and Isolate Data via CryptoDB.org.
    subjects:
    - Functional Genomics
    - Genomics
    - Parasitology
    twitter: VEuPathDB
  integbio:
    description: CryptoDB serves as the functional genomics database for Cryptosporidium
      and related species. CryptoDB is a free, online resource for accessing and exploring
      genome sequence and annotation, functional genomics data, isolate sequences,
      and orthology profiles across organisms. It also includes supplemental bioinformatics
      analyses and a web interface for data-mining.
    fairsharing: FAIRsharing.t3nprm
    homepage: https://cryptodb.org/cryptodb/app
    information_keywords:
    - Sequence
    - Expression
    - Ontology/Terminology/Nomenclature
    maintainer: CBIL (Computational Biology and Informatics Laboratory, University
      of Pennsylvania)||Center for Tropical & Emerging Global Diseases, University
      of Georgia
    name: CryptoDB
    prefix: nbdc01780
    pubmeds:
    - '16381902'
    status: Active
    target_keywords:
    - Genome/Gene
    - cDNA/EST
    - DNA
    - Organism
  mappings:
    biocontext: CRYPTODB
    fairsharing: FAIRsharing.t3nprm
    integbio: nbdc01780
    miriam: cryptodb
    n2t: cryptodb
    prefixcommons: cryptodb
    re3data: r3d100012265
  miriam:
    deprecated: false
    description: CryptoDB is one of the databases that can be accessed through the
      EuPathDB (http://EuPathDB.org; formerly ApiDB) portal, covering eukaryotic pathogens
      of the genera Cryptosporidium, Giardia, Leishmania, Neospora, Plasmodium, Toxoplasma,
      Trichomonas and Trypanosoma. While each of these groups is supported by a taxon-specific
      database built upon the same infrastructure, the EuPathDB portal offers an entry
      point to all these resources, and the opportunity to leverage orthology for
      searches across genera.
    homepage: https://cryptodb.org/cryptodb/
    id: 00000149
    name: CryptoDB
    namespaceEmbeddedInLui: false
    pattern: ^\w+$
    prefix: cryptodb
    sampleId: cgd7_230
    uri_format: https://cryptodb.org/cryptodb/app/record/gene/$1
  n2t:
    description: CryptoDB is one of the databases that can be accessed through the
      EuPathDB (http://EuPathDB.org; formerly ApiDB) portal, covering eukaryotic pathogens
      of the genera Cryptosporidium, Giardia, Leishmania, Neospora, Plasmodium, Toxoplasma,
      Trichomonas and Trypanosoma. While each of these groups is supported by a taxon-specific
      database built upon the same infrastructure, the EuPathDB portal offers an entry
      point to all these resources, and the opportunity to leverage orthology for
      searches across genera.
    example: cgd7_230
    homepage: https://cryptodb.org/cryptodb/
    name: CryptoDB at EuPathDB
    namespaceEmbeddedInLui: false
    pattern: ^\w+
    prefix: cryptodb
    uri_format: https://cryptodb.org/cryptodb/app/record/gene/$1
  prefix: cryptodb
  prefixcommons:
    description: CryptoDB is an integrated genomic and functional genomic database
      for the parasite Cryptosporidium. CryptoDB integrates whole genome sequence
      and annotation along with experimental data and environmental isolate sequences
      provided by community researchers, it also includes supplemental bioinformatics
      analyses and a web interface for data-mining.
    example: cgd7_230
    homepage: http://cryptodb.org/cryptodb/
    keywords:
    - genome
    name: Cryptosporidum Genomics Resource
    pattern: ^\w+$
    prefix: cryptodb
    pubmed_ids:
    - '16381902'
    uri_format: http://cryptodb.org/cryptodb/showRecord.do?name=GeneRecordClasses.GeneRecordClass&source_id=$1
  publications:
  - doi: 10.1007/978-1-4939-9748-0_10
    pmc: null
    pubmed: '31452162'
    title: Accessing Cryptosporidium Omic and Isolate Data via CryptoDB.org
    year: 2020
  - doi: 10.1093/nar/gkj078
    pmc: PMC1347441
    pubmed: '16381902'
    title: 'CryptoDB: a Cryptosporidium bioinformatics resource update'
    year: 2006
  - doi: 10.1093/nar/gkj078
    pmc: null
    pubmed: null
    title: 'CryptoDB: a Cryptosporidium bioinformatics resource update.'
    year: null
  - doi: 10.1007/978-1-4939-9748-0_10
    pmc: null
    pubmed: null
    title: Accessing Cryptosporidium Omic and Isolate Data via CryptoDB.org.
    year: null
  - doi: null
    pmc: null
    pubmed: '16381902'
    title: null
    year: null
  re3data:
    description: CryptoDB is an integrated genomic and functional genomic database
      for the parasite Cryptosporidium and other related genera. CryptoDB integrates
      whole genome sequence and annotation along with experimental data and environmental
      isolate sequences provided by community researchers. The database includes supplemental
      bioinformatics analyses and a web interface for data-mining.
    doi: 10.17616/R35M1X
    homepage: https://cryptodb.org/cryptodb/app
    name: CryptoDB
    prefix: r3d100012265
csa:
  biocontext:
    prefix: CSA
  fairsharing:
    abbreviation: CSA
    contact:
      email: nickf@ebi.ac.uk
      name: Nicholas Furnham
      orcid: 0000-0002-7532-1269
    description: The Catalytic Site Atlas (CSA) is a database documenting enzyme active
      sites and catalytic residues in enzymes of 3D structure. It uses a defined classification
      for catalytic residues which includes only those residues thought to be directly
      involved in some aspect of the reaction catalysed by an enzyme.
    homepage: http://www.ebi.ac.uk/thornton-srv/databases/CSA/
    license: http://opendatacommons.org/licenses/pddl/1.0
    name: Catalytic Site Atlas
    prefix: FAIRsharing.2ajtcf
    publications:
    - doi: 10.1093/nar/gkh028
      pubmed_id: 14681376
      title: 'The Catalytic Site Atlas: a resource of catalytic sites and residues
        identified in enzymes using structural data.'
    - doi: 10.1093/nar/gkt1243
      pubmed_id: 24319146
      title: 'The Catalytic Site Atlas 2.0: cataloging catalytic sites and residues
        identified in enzymes.'
    subjects:
    - Life Science
  mappings:
    biocontext: CSA
    fairsharing: FAIRsharing.2ajtcf
    miriam: csa
    n2t: csa
    prefixcommons: csa
  miriam:
    deprecated: true
    description: The Catalytic Site Atlas (CSA) is a database documenting enzyme active
      sites and catalytic residues in enzymes of 3D structure. It uses a defined classification
      for catalytic residues which includes only those residues thought to be directly
      involved in some aspect of the reaction catalysed by an enzyme.
    homepage: https://www.ebi.ac.uk/thornton-srv/databases/CSA/
    id: '00000144'
    name: CSA
    namespaceEmbeddedInLui: false
    pattern: ^[0-9][A-Za-z0-9]{3}$
    prefix: csa
    sampleId: 1a05
    uri_format: https://www.ebi.ac.uk/thornton-srv/databases/CSA/SearchResults.php?PDBID=$1
  n2t:
    description: The Catalytic Site Atlas (CSA) is a database documenting enzyme active
      sites and catalytic residues in enzymes of 3D structure. It uses a defined classification
      for catalytic residues which includes only those residues thought to be directly
      involved in some aspect of the reaction catalysed by an enzyme.
    example: 1a05
    homepage: https://www.ebi.ac.uk/thornton-srv/databases/CSA/
    name: CSA at EBI
    namespaceEmbeddedInLui: false
    pattern: ^[0-9][A-Za-z0-9]{3}$
    prefix: csa
    uri_format: https://www.ebi.ac.uk/thornton-srv/databases/CSA/SearchResults.php?PDBID=$1
  name: Catalytic Site Atlas
  prefix: csa
  prefixcommons:
    description: The Catalytic Site Atlas (CSA) is a database documenting enzyme active
      sites and catalytic residues in enzymes of 3D structure. It uses a defined classification
      for catalytic residues which includes only those residues thought to be directly
      involved in some aspect of the reaction catalysed by an enzyme.
    example: 1a05
    homepage: http://www.ebi.ac.uk/thornton-srv/databases/CSA/
    keywords:
    - enzyme
    - structure
    name: Catalytic Site Atlas
    pattern: ^[0-9][A-Za-z0-9]{3}$
    prefix: csa
    pubmed_ids:
    - '14681376'
    uri_format: http://www.ebi.ac.uk/thornton-srv/databases/cgi-bin/CSA/CSA_Site_Wrapper.pl?pdb=$1
  publications:
  - doi: 10.1093/nar/gkt1243
    pmc: PMC3964973
    pubmed: '24319146'
    title: 'The Catalytic Site Atlas 2.0: cataloging catalytic sites and residues
      identified in enzymes'
    year: 2013
  - doi: 10.1093/nar/gkh028
    pmc: PMC308762
    pubmed: '14681376'
    title: 'The Catalytic Site Atlas: a resource of catalytic sites and residues identified
      in enzymes using structural data'
    year: 2004
  - doi: 10.1093/nar/gkh028
    pmc: null
    pubmed: null
    title: 'The Catalytic Site Atlas: a resource of catalytic sites and residues identified
      in enzymes using structural data.'
    year: null
  - doi: 10.1093/nar/gkt1243
    pmc: null
    pubmed: null
    title: 'The Catalytic Site Atlas 2.0: cataloging catalytic sites and residues
      identified in enzymes.'
    year: null
  - doi: null
    pmc: null
    pubmed: '14681376'
    title: null
    year: null
csd:
  contact:
    email: groom@ccdc.cam.ac.uk
    github: null
    name: Colin Groom
    orcid: 0000-0001-8921-9575
  contact_group_email: support@ccdc.cam.ac.uk
  fairsharing:
    abbreviation: CSD
    contact:
      email: support@ccdc.cam.ac.uk
      name: Support Email
      orcid: 0000-0002-6062-7492
    description: Established in 1965, the Cambridge Structural Database (CSD) is the
      a repository for small-molecule organic and metal-organic crystal 3D structures.
      Database records are automatically checked and manually curated by one of our
      expert in-house scientific editors. Every structure is enriched with chemical
      representations, as well as bibliographic, chemical and physical property information,
      adding further value to the raw structural data.
    homepage: http://www.ccdc.cam.ac.uk/solutions/csd-system/components/csd/
    license: https://www.ccdc.cam.ac.uk/access-structures-terms
    name: The Cambridge Structural Database
    prefix: FAIRsharing.vs7865
    publications:
    - doi: 10.1107/S0108768102003890
      pubmed_id: 12037359
      title: 'The Cambridge Structural Database: a quarter of a million crystal structures
        and rising'
    - doi: 10.1107/S2052520616003954
      pubmed_id: 27048719
      title: The Cambridge Structural Database.
    subjects:
    - Organic Chemistry
    - Biochemistry
    - Organic Molecular Chemistry
    - Chemistry
    twitter: ccdc_cambridge
  mappings:
    fairsharing: FAIRsharing.vs7865
    miriam: csd
    re3data: r3d100010197
  miriam:
    deprecated: false
    description: The Cambridge Stuctural Database (CSD) is the world's most comprehensive
      collection of small-molecule crystal structures. Entries curated into the CSD
      are identified by a CSD Refcode.
    homepage: https://www.ccdc.cam.ac.uk/
    id: 00000820
    name: Cambridge Structural Database
    namespaceEmbeddedInLui: false
    pattern: ^[A-Z]{6}(\d{2})?$
    prefix: csd
    sampleId: PELNAW
    uri_format: https://www.ccdc.cam.ac.uk/services/structures?pid=csd:$1&sid=IDORG
  prefix: csd
  publications:
  - doi: 10.1107/s2052520616003954
    pmc: PMC4822653
    pubmed: '27048719'
    title: The Cambridge Structural Database
    year: 2016
  - doi: 10.1107/s0108768102003890
    pmc: null
    pubmed: '12037359'
    title: 'The Cambridge Structural Database: a quarter of a million crystal structures
      and rising'
    year: 2002
  - doi: 10.1107/S0108768102003890
    pmc: null
    pubmed: null
    title: 'The Cambridge Structural Database: a quarter of a million crystal structures
      and rising'
    year: null
  - doi: 10.1107/S2052520616003954
    pmc: null
    pubmed: null
    title: The Cambridge Structural Database.
    year: null
  re3data:
    description: "Established in 1965, the CSD is the world’s repository for small-molecule\
      \ organic and metal-organic crystal structures. Containing the results of over\
      \ one million x-ray and neutron diffraction analyses this unique database of\
      \ accurate 3D structures has become an essential resource to scientists around\
      \ the world. The CSD records bibliographic, chemical and crystallographic information\
      \ for:organic molecules, metal-organic compounds whose 3D structures have been\
      \ determined using X-ray diffraction, neutron diffraction. The CSD records results\
      \ of: single crystal studies, powder diffraction studies which yield 3D atomic\
      \ coordinate data for at least all non-H atoms. In some cases the CCDC is unable\
      \ to obtain coordinates, and incomplete entries are archived to the CSD. \n\
      The CSD includes crystal structure data arising from: publications in the open\
      \ literature and Private Communications to the CSD (via direct data deposition).\
      \ \nThe CSD contains directly deposited data that are not available anywhere\
      \ else, known as CSD Communications."
    doi: 10.17616/R36011
    homepage: https://www.ccdc.cam.ac.uk/solutions/software/csd/
    name: Cambridge Structural Database
    prefix: r3d100010197
    synonyms:
    - CSD
    - Cambridge Crystallographic Data Centre
    xrefs:
      nif: 0000-00174
csp:
  aberowl:
    description: Computer Retrieval of Information on Scientific Projects (CRISP)
    name: Computer Retrieval of Information on Scientific Projects Thesaurus
    prefix: CRISP
    version: 2016AB
  bioportal:
    contact:
      email: af8d@nih.gov
      name: Anita Ghebeles
    description: 'The Computer Retrieval of Information on Scientific Projects (CRISP)
      Thesaurus was developed by the National Institutes of Health for use in the
      CRISP database of research projects funded by the U.S. Public Health Service
      (PHS). CRISP contains over 8,000 preferred terms that are grouped hierarchically
      into 11 domains. The 11 domains are: - anatomy - behavioral/social science -
      biology - chemical - disease/disorder - food science/technology - medicine -
      named group - organism - physical science technology/technique'
    homepage: https://www.nlm.nih.gov/research/umls/sourcereleasedocs/current/CSP/index.html
    name: Computer Retrieval of Information on Scientific Projects Thesaurus
    prefix: CRISP
    publications:
    - http://www.ncbi.nlm.nih.gov/pubmed/8718842
    version: CSP2006
  deprecated: true
  example: 2004-2820
  fairsharing:
    abbreviation: CRISP
    description: CRISP is a terminology used for indexing biomedical information.
      CRISP contains over 8,000 preferred terms that are grouped hierarchically into
      11 domains. Note that while still available and included in Unified Medical
      Language System (UMLS), it has not been updated since 2006.
    domains:
    - food
    - disease
    homepage: https://www.nlm.nih.gov/research/umls/sourcereleasedocs/current/CSP/index.html
    name: Computer Retrieval of Information on Scientific Projects Thesaurus
    prefix: FAIRsharing.1evfpc
    publications:
    - pubmed: '8718842'
      title: Taking a bite out of CRISP. Strategies on using and conducting searches
        in the Computer Retrieval of Information on Scientific Projects database
      year: 1996
    subjects:
    - Anatomy
    - Chemical Biology
    - Biomedical Science
    - Biology
    - Social Science
    - Medicine
  hl7:
    description: 'Computer Retrieval of Information on Scientific Projects (CRISP).
      Bethesda (MD): National Institutes of Health, Division of Research Grants, Research
      Documentation Section, 2004.   http://crisp.cit.nih.gov/The CRISP system has
      been replaced by the RePORT Expenditures and Results (RePORTER) query tool.'
    homepage: http://www.nih.gov/
    name: CRISP Thesaurus
    organization: National Institutes of Health
    preferred_prefix: csp
    prefix: 2.16.840.1.113883.6.120
    status: Complete
  homepage: https://web.archive.org/web/20091223034048/http://crisp.cit.nih.gov/Thesaurus/index.htm
  mappings:
    aberowl: CRISP
    bioportal: CRISP
    fairsharing: FAIRsharing.1evfpc
    hl7: 2.16.840.1.113883.6.120
    pathguide: '192'
  name: Computer Retrieval of Information on Science Projects Thesaurus
  pathguide:
    abbreviation: CSP
    homepage: http://csp.medic.kumamoto-u.ac.jp/
    name: Cytokine Signaling Pathway Database
    prefix: '192'
  prefix: csp
  publications:
  - doi: null
    pmc: null
    pubmed: '8718842'
    title: Taking a bite out of CRISP. Strategies on using and conducting searches
      in the Computer Retrieval of Information on Scientific Projects database
    year: 1996
  - doi: null
    pmc: null
    pubmed: '8718842'
    title: Taking a bite out of CRISP. Strategies on using and conducting searches
      in the Computer Retrieval of Information on Scientific Projects database
    year: 1996
  synonyms:
  - CRISP
  - CRISP Thesaurus
  - CRISP Thesaurus, 2006
  - CSP2005
  uri_format: http://purl.bioontology.org/ontology/CSP/$1
cst.antibody:
  biocontext:
    prefix: CST.AB
  mappings:
    biocontext: CST.AB
    miriam: cst.ab
    n2t: cst.ab
    prefixcommons: cst
  miriam:
    deprecated: false
    description: Cell Signaling Technology is a commercial organisation which provides
      a pathway portal to showcase their phospho-antibody products. This collection
      references antibody products.
    homepage: http://www.cellsignal.com/catalog/index.html
    id: '00000430'
    name: Cell Signaling Technology Antibody
    namespaceEmbeddedInLui: false
    pattern: ^\d+$
    prefix: cst.ab
    sampleId: '3305'
    uri_format: http://www.cellsignal.com/products/$1.html
  n2t:
    description: Cell Signaling Technology is a commercial organisation which provides
      a pathway portal to showcase their phospho-antibody products. This collection
      references antibody products.
    example: '3305'
    homepage: http://www.cellsignal.com/catalog/index.html
    name: CST Antibody at Cell Signaling Technology
    namespaceEmbeddedInLui: false
    pattern: ^\d+$
    prefix: cst.ab
    uri_format: http://www.cellsignal.com/products/$1.html
  part_of_database: cst
  prefix: cst.antibody
  prefixcommons:
    description: A small pathway portal for showcasing Cell Signaling Technology phospho-antibody
      products.  Contains pathway diagrams that are clickable and link to more information
      about each protein and the commercial products that are available for that protein.
    example: '3762'
    homepage: http://www.cellsignal.com/
    keywords:
    - pathway
    name: Cell Signaling Technology Pathway Database
    pattern: ^\d+$
    prefix: cst
    uri_format: http://www.cellsignal.com/products/$1.html
  synonyms:
  - cst.ab
cst.pathway:
  biocontext:
    prefix: CST
  domain: antibody
  fairsharing:
    abbreviation: CST
    description: A small pathway portal for showcasing Cell Signaling Technology phospho-antibody
      products. Contains pathway diagrams that are clickable and link to more information
      about each protein and the commercial products that are available for that protein.
    homepage: http://www.cellsignal.com/
    name: Cell Signaling Technology Pathway Database
    prefix: FAIRsharing.n8pxvx
    publications: []
    subjects:
    - Life Science
    - Biomedical Science
  mappings:
    biocontext: CST
    fairsharing: FAIRsharing.n8pxvx
    miriam: cst
    n2t: cst
    pathguide: '193'
  miriam:
    deprecated: false
    description: Cell Signaling Technology is a commercial organisation which provides
      a pathway portal to showcase their phospho-antibody products. This collection
      references pathways.
    homepage: http://www.cellsignal.com/pathways/index.html
    id: 00000429
    name: Cell Signaling Technology Pathways
    namespaceEmbeddedInLui: false
    pattern: ^[A-Za-z0-9_-]+$
    prefix: cst
    sampleId: Akt_PKB
    uri_format: http://www.cellsignal.com/reference/pathway/$1.html
  n2t:
    description: Cell Signaling Technology is a commercial organisation which provides
      a pathway portal to showcase their phospho-antibody products. This collection
      references pathways.
    example: Akt_PKB
    homepage: http://www.cellsignal.com/pathways/index.html
    name: CST Pathways at Cell Signaling Technology
    namespaceEmbeddedInLui: false
    pattern: ^[A-Za-z0-9_-]+$
    prefix: cst
    uri_format: http://www.cellsignal.com/reference/pathway/$1.html
  part_of_database: cst
  pathguide:
    abbreviation: CST
    homepage: https://www.cellsignal.com/common/content/content.jsp?id=science-pathways
    name: Cell Signaling Technology Pathway Database
    prefix: '193'
  prefix: cst.pathway
  synonyms:
  - cst
cstr:
  fairsharing:
    abbreviation: CSTR
    description: The Common Science and Technology Resource Identifier ("CSTR") is
      a persistent identifier schema for locating, accessing, and manipulating science
      and technology resources. CSTR aims to promote the interconnection among various
      science and technology resources, to promote the openness and sharing of science
      and technology resources.
    domains:
    - centrally registered identifier
    homepage: https://www.cstr.cn/doc/specification
    name: Common Science and Technology Resource Identifier
    prefix: FAIRsharing.f0d465
    subjects:
    - Subject Agnostic
    user_defined_tags:
    - Open Science
  mappings:
    fairsharing: FAIRsharing.f0d465
    miriam: cstr
  miriam:
    deprecated: false
    description: 'CSTR is an identifier for Common Science and Technology Resources,
      to provide persistent identification services for the positioning, traceability,
      citation, statistics and evaluation of science and technology resources. '
    homepage: https://www.cstr.cn/en/
    id: 00000998
    name: CSTR
    namespaceEmbeddedInLui: false
    pattern: ^\w{5}\.\d{2}\..*$
    prefix: cstr
    sampleId: 31253.11.sciencedb.j00001.00123
    uri_format: https://cstr.cn/$1
  name: Common Science and Technology Resources
  prefix: cstr
csvw:
  example: uriTemplate
  lov:
    description: This document describes the RDFS vocabulary description used in the
      Metadata Vocabulary for Tabular Data along with the default JSON-LD Context.
    homepage: http://www.w3.org/ns/csvw#
    keywords:
    - Vocabularies
    - W3C Rec
    modified: '2015-12-17'
    name: CSV on the Web Vocabulary
    prefix: csvw
    uri_prefix: http://www.w3.org/ns/csvw#$1
  mappings:
    lov: csvw
    zazuko: csvw
  prefix: csvw
  zazuko:
    prefix: csvw
    uri_format: http://www.w3.org/ns/csvw#$1
ctcae:
  aberowl:
    description: A coding system for reporting adverse events that occur in the course
      of cancer therapy. It was derived from the Common Toxicity Criteria (CTC) v2.0
      and is maintained by the Cancer Therapy Evaluation Program (CTEP) at the National
      Cancer Institution (NCI).
    download_owl: http://aber-owl.net/media/ontologies/CTCAE/2/ctcae.owl
    name: Common Terminology Criteria for Adverse Events
    prefix: CTCAE
    version: '4.03'
  appears_in:
  - oae
  bioportal:
    contact:
      email: ncictcaehelp@mail.nih.gov
      name: CTCAE Help
    description: Common Terminology Criteria for Adverse Events (CTCAE) is widely
      accepted throughout the oncology community as the standard classification and
      severity grading scale for adverse events in cancer therapy clinical trials
      and other oncology settings. Version 5 was published by the NCI Cancer Therapy
      Evaluation Program (CTEP) in November 2017. It is organized by MedDRA System
      Organ Class and mapped to MedDRA LLTs with corresponding MedDRA codes, and harmonized
      with MedDRA at the Adverse Event (AE) level including revised AE terms and severity
      indicators to reflect clinical effects identified with current oncology interventions.Severity
      grades are assigned and most are defined to clarify the meaning of the term.
      CTCAE is designed to integrate into information networks for safety data exchange,
      and is the primary standard for data management for AE data collection, analysis,
      and patient outcomes associated with cancer research and care.
    homepage: https://nciterms.nci.nih.gov/ncitbrowser/pages/vocabulary.jsf?dictionary=CTCAE_v5&version=5.0
    name: Common Terminology Criteria for Adverse Events
    prefix: CTCAE
    version: '5.0'
  contact:
    email: yongqunh@med.umich.edu
    github: yongqunh
    name: Yongqun Oliver He
    orcid: 0000-0001-9189-9661
  contact_group_email: ncictcaehelp@mail.nih.gov
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: The Common Terminology Criteria for Adverse Events (CTCAE),[1] formerly
    called the Common Toxicity Criteria (CTC or NCI-CTC), are a set of criteria for
    the standardized classification of adverse effects of drugs used in cancer therapy.
    The CTCAE system is a product of the US National Cancer Institute (NCI).
  example: E12768
  fairsharing:
    abbreviation: CTCAE
    description: A coding system for reporting adverse events that occur in the course
      of cancer therapy. It was derived from the Common Toxicity Criteria (CTC) v2.0
      and is maintained by the Cancer Therapy Evaluation Program (CTEP) at the National
      Cancer Institution (NCI).
    domains:
    - cancer
    - disease
    homepage: http://ctep.cancer.gov/protocolDevelopment/electronic_applications/ctc.htm
    name: Common Terminology Criteria for Adverse Events
    prefix: FAIRsharing.dcsw6j
    publications:
    - doi: 10.1111/j.1476-5810.2004.0053b.x
      pubmed: '19379294'
      title: Veterinary Co-operative Oncology Group - Common Terminology Criteria
        for Adverse Events (VCOG-CTCAE) following chemotherapy or biological antineoplastic
        therapy in dogs and cats v1.0
      year: 2004
    subjects:
    - Biomedical Science
  homepage: https://evs.nci.nih.gov/ftp1/CTCAE/About.html
  mappings:
    aberowl: CTCAE
    bioportal: CTCAE
    fairsharing: FAIRsharing.dcsw6j
  name: Common Terminology Criteria for Adverse Events
  pattern: ^E\d+$
  prefix: ctcae
  publications:
  - doi: null
    pmc: PMC5977606
    pubmed: '29854250'
    title: 'Towards precision informatics of pharmacovigilance: OAE-CTCAE mapping
      and OAE-based representation and analysis of adverse events in patients treated
      with cancer drugs'
    year: 2018
  - doi: 10.1111/j.1476-5810.2004.0053b.x
    pmc: null
    pubmed: '19379294'
    title: Veterinary Co-operative Oncology Group - Common Terminology Criteria for
      Adverse Events (VCOG-CTCAE) following chemotherapy or biological antineoplastic
      therapy in dogs and cats v1.0
    year: 2004
  references:
  - https://github.com/OAE-ontology/OAE/issues/8
  - https://en.wikipedia.org/wiki/Common_Terminology_Criteria_for_Adverse_Events
  synonyms:
  - CTCAE
  uri_format: http://ncicb.nci.nih.gov/xml/owl/EVS/ctcae5.owl#$1
ctd.chemical:
  biocontext:
    prefix: CTD.CHEMICAL
  biolink:
    is_identifiers: false
    is_obo: false
    prefix: CTD.CHEMICAL
    uri_format: http://ctdbase.org/detail.go?type=chem&acc=$1
  mappings:
    biocontext: CTD.CHEMICAL
    biolink: CTD.CHEMICAL
    miriam: ctd.chemical
    n2t: ctd.chemical
  miriam:
    deprecated: false
    description: The Comparative Toxicogenomics Database (CTD) presents scientifically
      reviewed and curated information on chemicals, relevant genes and proteins,
      and their interactions in vertebrates and invertebrates. It integrates sequence,
      reference, species, microarray, and general toxicology information to provide
      a unique centralized resource for toxicogenomic research. The database also
      provides visualization capabilities that enable cross-species comparisons of
      gene and protein sequences.
    homepage: http://ctdbase.org/
    id: 00000098
    name: CTD Chemical
    namespaceEmbeddedInLui: false
    pattern: ^[CD]\d+$
    prefix: ctd.chemical
    sampleId: D001151
    uri_format: http://ctdbase.org/detail.go?type=chem&acc=$1
  n2t:
    description: The Comparative Toxicogenomics Database (CTD) presents scientifically
      reviewed and curated information on chemicals, relevant genes and proteins,
      and their interactions in vertebrates and invertebrates. It integrates sequence,
      reference, species, microarray, and general toxicology information to provide
      a unique centralized resource for toxicogenomic research. The database also
      provides visualization capabilities that enable cross-species comparisons of
      gene and protein sequences.
    example: D001151
    homepage: http://ctdbase.org/
    name: Comparative Toxicogenomics Database (Chemical)
    namespaceEmbeddedInLui: false
    pattern: ^[CD]\d+$
    prefix: ctd.chemical
    uri_format: http://ctdbase.org/detail.go?type=chem&acc=$1
  part_of_database: ctd
  prefix: ctd.chemical
  provides: mesh
ctd.disease:
  biocontext:
    prefix: CTD.DISEASE
  biolink:
    is_identifiers: false
    is_obo: false
    prefix: CTD.DISEASE
    uri_format: http://ctdbase.org/detail.go?type=disease&db=MESH&acc=$1
  mappings:
    biocontext: CTD.DISEASE
    biolink: CTD.DISEASE
    miriam: ctd.disease
    n2t: ctd.disease
  miriam:
    deprecated: false
    description: The Comparative Toxicogenomics Database (CTD) presents scientifically
      reviewed and curated information on chemicals, relevant genes and proteins,
      and their interactions in vertebrates and invertebrates. It integrates sequence,
      reference, species, microarray, and general toxicology information to provide
      a unique centralized resource for toxicogenomic research. The database also
      provides visualization capabilities that enable cross-species comparisons of
      gene and protein sequences.
    homepage: http://ctdbase.org/
    id: 00000099
    name: CTD Disease
    namespaceEmbeddedInLui: false
    pattern: ^D\d+$
    prefix: ctd.disease
    sampleId: D053716
    uri_format: http://ctdbase.org/detail.go?type=disease&db=MESH&acc=$1
  n2t:
    description: The Comparative Toxicogenomics Database (CTD) presents scientifically
      reviewed and curated information on chemicals, relevant genes and proteins,
      and their interactions in vertebrates and invertebrates. It integrates sequence,
      reference, species, microarray, and general toxicology information to provide
      a unique centralized resource for toxicogenomic research. The database also
      provides visualization capabilities that enable cross-species comparisons of
      gene and protein sequences.
    example: D053716
    homepage: http://ctdbase.org/
    name: Comparative Toxicogenomics Database (Disease)
    namespaceEmbeddedInLui: false
    pattern: ^D\d+$
    prefix: ctd.disease
    uri_format: http://ctdbase.org/detail.go?type=disease&db=MESH&acc=$1
  part_of_database: ctd
  prefix: ctd.disease
  provides: mesh
ctd.gene:
  biocontext:
    prefix: CTD.GENE
  biolink:
    is_identifiers: false
    is_obo: false
    prefix: CTD.GENE
    uri_format: http://ctdbase.org/detail.go?type=gene&acc=$1
  contact:
    email: apdavis3@ncsu.edu
    github: null
    name: Allan Peter Davis
    orcid: 0000-0002-5741-7128
  mappings:
    biocontext: CTD.GENE
    biolink: CTD.GENE
    miriam: ctd.gene
    n2t: ctd.gene
    uniprot: DB-0140
  miriam:
    deprecated: false
    description: The Comparative Toxicogenomics Database (CTD) presents scientifically
      reviewed and curated information on chemicals, relevant genes and proteins,
      and their interactions in vertebrates and invertebrates. It integrates sequence,
      reference, species, microarray, and general toxicology information to provide
      a unique centralized resource for toxicogenomic research. The database also
      provides visualization capabilities that enable cross-species comparisons of
      gene and protein sequences.
    homepage: http://ctdbase.org/
    id: '00000100'
    name: CTD Gene
    namespaceEmbeddedInLui: false
    pattern: ^\d+$
    prefix: ctd.gene
    sampleId: '101'
    uri_format: http://ctdbase.org/detail.go?type=gene&acc=$1
  n2t:
    description: The Comparative Toxicogenomics Database (CTD) presents scientifically
      reviewed and curated information on chemicals, relevant genes and proteins,
      and their interactions in vertebrates and invertebrates. It integrates sequence,
      reference, species, microarray, and general toxicology information to provide
      a unique centralized resource for toxicogenomic research. The database also
      provides visualization capabilities that enable cross-species comparisons of
      gene and protein sequences.
    example: '101'
    homepage: http://ctdbase.org/
    name: Comparative Toxicogenomics Database (Gene)
    namespaceEmbeddedInLui: false
    pattern: ^\d+$
    prefix: ctd.gene
    uri_format: http://ctdbase.org/detail.go?type=gene&acc=$1
  part_of_database: ctd
  prefix: ctd.gene
  provides: ncbigene
  publications:
  - doi: 10.1093/nar/gkaa891
    pmc: PMC7779006
    pubmed: '33068428'
    title: 'Comparative Toxicogenomics Database (CTD): update 2021'
    year: 2021
  - doi: 10.1093/nar/gkaa891
    pmc: null
    pubmed: '33068428'
    title: null
    year: null
  uniprot:
    abbreviation: CTD
    category: Organism-specific databases
    homepage: https://ctdbase.org/
    name: Comparative Toxicogenomics Database
    prefix: DB-0140
    publications:
    - doi: 10.1093/nar/gkaa891
      pubmed: '33068428'
    uri_format: https://ctdbase.org/detail.go?type=gene&db=GENE&acc=$1
cteno:
  aberowl:
    description: An anatomical and developmental ontology for ctenophores (Comb Jellies)
    download_owl: http://aber-owl.net/media/ontologies/CTENO/2/cteno.owl
    homepage: https://github.com/obophenotype/ctenophore-ontology
    name: Ctenophore Ontology
    prefix: CTENO
  biocontext:
    prefix: CTENO
  bioportal:
    contact:
      email: cjmungall@lbl.gov
      name: Chris Mungall
    description: An anatomical and developmental ontology for ctenophores (Comb Jellies)
    homepage: https://github.com/obophenotype/ctenophore-ontology
    name: Ctenophore Ontology
    prefix: CTENO
  download_obo: https://raw.githubusercontent.com/obophenotype/ctenophore-ontology/master/cteno.obo
  example: '0000047'
  fairsharing:
    abbreviation: CTENO
    description: An anatomical and developmental ontology for ctenophores (Comb Jellies).
      Please note that, while available, this ontology has not been updated since
      2016.
    homepage: https://github.com/obophenotype/ctenophore-ontology
    license: CC-BY-3.0
    name: Ctenophore Ontology
    prefix: FAIRsharing.mgxgza
    subjects:
    - Anatomy
    - Developmental Biology
  mappings:
    aberowl: CTENO
    biocontext: CTENO
    bioportal: CTENO
    fairsharing: FAIRsharing.mgxgza
    obofoundry: cteno
    ols: cteno
    ontobee: CTENO
    wikidata.entity: Q81661576
  obofoundry:
    contact: cjmungall@lbl.gov
    contact.github: cmungall
    contact.label: Chris Mungall
    contact.orcid: 0000-0002-6601-2165
    depends_on:
    - ro
    - uberon
    deprecated: false
    description: An anatomical and developmental ontology for ctenophores (Comb Jellies)
    domain: anatomy and development
    download.owl: http://purl.obolibrary.org/obo/cteno.owl
    homepage: https://github.com/obophenotype/ctenophore-ontology
    license: CC BY 3.0
    license.url: http://creativecommons.org/licenses/by/3.0/
    name: Ctenophore Ontology
    preferredPrefix: CTENO
    prefix: cteno
    repository: https://github.com/obophenotype/ctenophore-ontology
  ols:
    description: An anatomical and developmental ontology for ctenophores (Comb Jellies)
    download_owl: http://purl.obolibrary.org/obo/cteno.owl
    homepage: https://github.com/obophenotype/ctenophore-ontology
    name: Ctenophore Ontology
    prefix: cteno
    tracker: https://github.com/obophenotype/ctenophore-ontology/issues
    version: '2016-10-19'
    version.iri: http://purl.obolibrary.org/obo/cteno/releases/2016-10-19/cteno.owl
  ontobee:
    library: Library
    name: Ctenophore Ontology
    prefix: CTENO
  pattern: ^\d{7}$
  prefix: cteno
  uri_format: http://purl.obolibrary.org/obo/CTENO_$1
ctis:
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: This website supports the undertaking and oversight of clinical trials
    in the European Union (EU) and European Economic Area (EEA). It is part of a broad
    initiative to transform the EU/EEA clinical trials environment in support of large
    clinical trials in multiple European countries, to the benefit of medical innovation
    and patients. (from homepage)
  example: 2023-503698-40-00
  homepage: https://euclinicaltrials.eu/
  name: Clinical Trials Information System
  pattern: ^\d{4}-\d+-\d+-\d+$
  prefix: ctis
  uri_format: https://euclinicaltrials.eu/app/#/view/$1
cto:
  aberowl:
    description: The core Ontology of Clinical Trials (CTO) will serve as a structured
      resource integrating basic terms and concepts in the context of clinical trials.
      Thereby covering clinicaltrails.gov. CoreCTO will serve as a basic ontology
      to generate extended versions for specific applications such as annotation of
      variables in study documents from clinical trials.
    download_owl: http://aber-owl.net/media/ontologies/CTO/5/cto.owl
    homepage: https://github.com/ClinicalTrialOntology/CTO/
    name: 'CTO: Core Ontology of Clinical Trials'
    prefix: CTO
  bioportal:
    contact:
      email: alpha.tom.kodamullil@scai.fraunhofer.de
      name: Alpha Tom Kodamullil
    description: 'Clinical Trial Ontology (CTO) is designed to formally represent
      and integrate all terms used to describe and register the clinical trials. The
      development of CTO was done as a collaborative project among Fraunhofer SCAI,
      Germany; University of Michigan; Center for Devices and Radiological Health,
      FDA; and National Center for Biotechnology Information, National Library of
      Medicine, National Institutes of Health, Bethesda. Respective related projects
      are described below: At Fraunhofer SCAI, the work was supported and funded from
      the EU’s Horizon 2020 Framework Programme for Research and Innovation under
      the Specific Grant Agreement No. 785907 (Human Brain Project SGA2 by the HBP
      Medical Informatics Platform) and No. 826421 (VirtualBrainCloud), and a Fraunhofer
      internal funding MAVO project "Human Brain Pharmacome". At University of Michigan,
      the work was supported by the NIH-NIDDK U2C Project (1U2CDK114886) and a grant
      from the Michigan Medicine–Peking University Health Sciences Center Joint Institute
      for Clinical and Translational Research (U063430). At NCBI side, thhe work of
      QL and EB was supported by the Intramural Research Program of the National Library
      of Medicine, National Institutes of Health.'
    name: Clinical Trials Ontology
    prefix: CTO
    version: 'Version Release: 1.0.0'
  example: '0000022'
  fairsharing:
    abbreviation: CTO
    contact:
      email: alpha.tom.kodamullil@scai.fraunhofer.de
      name: Alpha Tom Kodamullil
      orcid: 0000-0001-9896-3531
    description: The core Ontology of Clinical Trials (CTO) will serve as a structured
      resource integrating basic terms and concepts in the context of clinical trials,
      and as a basic ontology to generate extended versions for specific applications
      such as annotation of variables in study documents from clinical trials. The
      small set of terms were primarily based on the WHO/ICMJE – ClinicalTrials.gov
      Cross Reference selected from ClinicalTrials.gov and WHO clinical trial terms.
      Please note that, while the repository remains active, the ontology has not
      been updated since 2021.
    domains:
    - disease
    homepage: https://github.com/ClinicalTrialOntology/CTO/
    license: CC-BY-4.0
    name: Clinical Trials Ontology
    prefix: FAIRsharing.qp211a
    publications:
    - pubmed: '35992013'
      title: 'CTO: a Community-Based Clinical Trial Ontology and its Applications
        in PubChemRDF and SCAIView'
      year: 2020
    subjects:
    - Neurobiology
    - Preclinical Studies
    - Biomedical Science
  mappings:
    aberowl: CTO
    bioportal: CTO
    fairsharing: FAIRsharing.qp211a
    obofoundry: cto
    ols: cto
    ontobee: CTO
    wikidata.entity: Q113009139
  name: Clinical Trials Ontology
  obofoundry:
    contact: alpha.tom.kodamullil@scai.fraunhofer.de
    contact.github: akodamullil
    contact.label: Dr. Alpha Tom Kodamullil
    contact.orcid: 0000-0001-9896-3531
    deprecated: false
    description: The core Ontology of Clinical Trials (CTO) will serve as a structured
      resource integrating basic terms and concepts in the context of clinical trials.
      Thereby covering clinicaltrails.gov. CoreCTO will serve as a basic ontology
      to generate extended versions for specific applications such as annotation of
      variables in study documents from clinical trials.
    domain: health
    download.owl: http://purl.obolibrary.org/obo/cto.owl
    homepage: https://github.com/ClinicalTrialOntology/CTO/
    license: CC BY 4.0
    license.url: http://creativecommons.org/licenses/by/4.0/
    name: 'CTO: Core Ontology of Clinical Trials'
    preferredPrefix: CTO
    prefix: cto
    repository: https://github.com/ClinicalTrialOntology/CTO
  ols:
    description: The core Ontology of Clinical Trials (CTO) will serve as a structured
      resource integrating basic terms and concepts in the context of clinical trials.
      Thereby covering clinicaltrails.gov. CoreCTO will serve as a basic ontology
      to generate extended versions for specific applications such as annotation of
      variables in study documents from clinical trials.
    download: http://purl.obolibrary.org/obo/cto.owl
    homepage: https://github.com/BFO-ontology/BFO
    name: 'CTO: Core Ontology of Clinical Trials'
    prefix: cto
    version: 1.0.0
  ontobee:
    library: Library
    name: 'CTO: Core Ontology of Clinical Trials'
    prefix: CTO
  pattern: ^\d{7}$
  prefix: cto
  uri_format: http://purl.obolibrary.org/obo/CTO_$1
ctri:
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: 'The mission of the Clinical Trials Registry-India (CTRI) is to ensure
    that all clinical trials conducted in India are prospectively registered, i.e.
    before the enrolment of the first participant. Additionally, post-marketing surveillance
    studies, BA/BE studies as well as clinical studies as part of PG thesis are also
    expected to be registered in the CTRI. (from homepage)


    Note that the identifier in this semantic space is not the one used in the webpages'
  example: CTRI/2023/04/052053
  homepage: https://ctri.nic.in
  name: India Clinical Trials Registry
  pattern: ^CTRI/\d{4}/\d{2,3}/\d+$
  prefix: ctri
  references:
  - https://www.ctri.nic.in/Clinicaltrials/pmaindet2.php?trialid=82487
  uri_format: https://trialsearch.who.int/Trial2.aspx?TrialID=$1
cubedb:
  biocontext:
    prefix: CUBEDB
  comment: website down as of 2021-10-04
  deprecated: true
  integbio:
    description: Detection of functional divergence in human protein families. Cube-DB
      is a database of pre-evaluated conservation and specialization scores for residues
      in paralogous proteins belonging to multi-member families of human proteins.
      Protein family classification follows (largely) the classification suggested
      by HUGO Gene Nomenclature Committee. Sets of orthologous protein sequences were
      generated by mutual-best-hit strategy using full vertebrate genomes available
      in Ensembl. The scores, described on documentation page, are assigned to each
      individual residue in a protein, and presented in the form of a table (html
      or downloadable xls formats) and mapped, when appropriate, onto the related
      structure (Jmol, Pymol, Chimera).
    fairsharing: FAIRsharing.aqb4ne
    homepage: http://epsf.bmad.bii.a-star.edu.sg/cube/db/html/home.html
    information_keywords:
    - Sequence
    maintainer: Evolution of Protein Structure and Function Group, Biomolecular Modelling
      and Design Division, Bioinformatics Institute
    name: CUBE-DB
    prefix: nbdc02094
    pubmeds:
    - '21931701'
    - '22139934'
    status: Inactive
    target_keywords:
    - Genome/Gene
  mappings:
    biocontext: CUBEDB
    integbio: nbdc02094
    miriam: cubedb
    n2t: cubedb
  miriam:
    deprecated: true
    description: Cube-DB is a database of pre-evaluated results for detection of functional
      divergence in human/vertebrate protein families. It analyzes comparable taxonomical
      samples for all paralogues under consideration, storing functional specialisation
      at the level of residues. The data are presented as a table of per-residue scores,
      and mapped onto related structures where available.
    homepage: http://epsf.bmad.bii.a-star.edu.sg/cube/db/html/home.html
    id: 00000397
    name: Cube db
    namespaceEmbeddedInLui: false
    pattern: ^[A-Za-z_0-9]+$
    prefix: cubedb
    sampleId: AKR
    uri_format: http://epsf.bmad.bii.a-star.edu.sg/cube/db/data/$1/
  n2t:
    description: Cube-DB is a database of pre-evaluated results for detection of functional
      divergence in human/vertebrate protein families. It analyzes comparable taxonomical
      samples for all paralogues under consideration, storing functional specialisation
      at the level of residues. The data are presented as a table of per-residue scores,
      and mapped onto related structures where available.
    example: AKR
    homepage: http://epsf.bmad.bii.a-star.edu.sg/cube/db/html/home.html
    name: Cube db at Bioinformatics Institute (Singapore)
    namespaceEmbeddedInLui: false
    pattern: ^[A-Za-z_0-9]+$
    prefix: cubedb
    uri_format: http://epsf.bmad.bii.a-star.edu.sg/cube/db/data/$1/
  prefix: cubedb
cutg:
  mappings:
    prefixcommons: cutg
  prefix: cutg
  prefixcommons:
    description: Codon usage in individual genes has been calculated using the nucleotide
      sequence data obtained from the GenBank Genetic Sequence Database.  The compilation
      of codon usage is synchronized with each major release of GenBank.
    example: '9606'
    homepage: http://www.kazusa.or.jp/codon/
    keywords:
    - gene
    - DNA
    name: Codon Usage Tabulated from GenBank
    pattern: ^\d+$
    prefix: cutg
    uri_format: http://www.kazusa.or.jp/codon/cgi-bin/showcodon.cgi?species=$1
  provides: ncbitaxon
  reviewer:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
cvdo:
  aberowl:
    description: An ontology to describe entities related to cardiovascular diseases
    download_owl: http://aber-owl.net/media/ontologies/CVDO/6/cvdo.owl
    homepage: https://github.com/OpenLHS/CVDO
    name: Cardiovascular Disease Ontology
    prefix: CVDO
  biocontext:
    prefix: CVDO
  bioportal:
    contact:
      email: adrien.barton@gmail.com
      name: Adrien Barton
    description: CVDO is an ontology based on the OGMS model of disease, designed
      to describe entities related to cardiovascular diseases (including the diseases
      themselves, the underlying disorders, and the related pathological processes).
      It is being developed at Sherbrooke University (Canada) and the INSERM research
      institute (Institut National de la Santé et de la Recherche Médicale).
    homepage: https://github.com/OpenLHS/CVDO
    name: Cardiovascular Disease Ontology
    prefix: CVDO
    version: '2024-05-17'
  example: '0000546'
  fairsharing:
    abbreviation: CVDO
    description: CVDO is an ontology based on the OGMS model of disease, designed
      to describe entities related to cardiovascular diseases (including the diseases
      themselves, the underlying disorders, and the related pathological processes).
    domains:
    - cardiovascular disease
    homepage: https://github.com/OpenLHS/CVDO
    license: CC-BY-4.0
    name: Cardiovascular Disease Ontology
    prefix: FAIRsharing.2basyz
    subjects:
    - Cardiology
  mappings:
    aberowl: CVDO
    biocontext: CVDO
    bioportal: CVDO
    fairsharing: FAIRsharing.2basyz
    obofoundry: cvdo
    ols: cvdo
    ontobee: CVDO
    wikidata.entity: Q55118269
  obofoundry:
    contact: paul.fabry@usherbrooke.ca
    contact.github: pfabry
    contact.label: Paul Fabry
    contact.orcid: 0000-0002-3336-2476
    deprecated: false
    description: An ontology to describe entities related to cardiovascular diseases
    domain: health
    download.owl: http://purl.obolibrary.org/obo/cvdo.owl
    homepage: https://github.com/OpenLHS/CVDO
    license: CC BY 4.0
    license.url: https://creativecommons.org/licenses/by/4.0/
    name: Cardiovascular Disease Ontology
    preferredPrefix: CVDO
    prefix: cvdo
    repository: https://github.com/OpenLHS/CVDO
  ols:
    description: An ontology to describe entities related to cardiovascular diseases
    download_owl: http://purl.obolibrary.org/obo/cvdo.owl
    homepage: https://github.com/OpenLHS/CVDO
    name: Cardiovascular Disease Ontology
    prefix: cvdo
    tracker: https://github.com/OpenLHS/CVDO/issues
    version: '2024-05-17'
    version.iri: http://purl.obolibrary.org/obo/cvdo/2024-05-17/cvdo.owl
  ontobee:
    library: Library
    name: Cardiovascular Disease Ontology
    prefix: CVDO
  pattern: ^\d{7}$
  prefix: cvdo
  uri_format: http://purl.obolibrary.org/obo/CVDO_$1
cvx:
  contact:
    email: iisinfo@cdc.gov
    github: null
    name: IIS Helpdesk
    orcid: null
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: The CDC's National Center of Immunization and Respiratory Diseases
    (NCIRD) developed and maintains the CVX (vaccine administered) code set. The table
    below has the most up to date values. It includes both active and inactive vaccines
    available in the US. CVX codes for inactive vaccines allow transmission of historical
    immunization records.
  domain: vaccine
  example: '54'
  hl7:
    description: CDC Vaccine Codes used in the 1999 RRF research project at HL7.DO
      NOT USEThis OID has been retired as it only identifies the set of codes used
      in the RRF research project.
    name: CVX
    preferred_prefix: cvx
    prefix: 2.16.840.1.113883.6.59
    status: Retired
  homepage: https://www2a.cdc.gov/vaccines/iis/iisstandards/vaccines.asp?rpt=cvx
  keywords:
  - vaccine
  logo: https://www2.cdc.gov/TemplatePackage/4.0/assets/imgs/logo/logo-notext.svg
  mappings:
    hl7: 2.16.840.1.113883.6.59
  name: Vaccine administered code set
  pattern: ^\d+$
  prefix: cvx
  uri_format: https://biopragmatics.github.io/providers/cvx/$1
d1id:
  biocontext:
    prefix: D1ID
  mappings:
    biocontext: D1ID
    miriam: d1id
    n2t: d1id
  miriam:
    deprecated: false
    description: DataONE provides infrastructure facilitating long-term access to
      scientific research data of relevance to the earth sciences.
    homepage: https://www.dataone.org
    id: '00000611'
    name: DataONE
    namespaceEmbeddedInLui: false
    pattern: ^\S+$
    prefix: d1id
    sampleId: 00030692-0FE1-4A1B-955E-A2E55D659267
    uri_format: https://cn.dataone.org/cn/v2/resolve/%7B$1%7D
  n2t:
    description: DataONE provides infrastructure facilitating long-term access to
      scientific research data of relevance to the earth sciences.
    example: 00030692-0FE1-4A1B-955E-A2E55D659267
    homepage: https://www.dataone.org
    name: DataONE
    namespaceEmbeddedInLui: false
    pattern: \S+
    prefix: d1id
    uri_format: https://cn.dataone.org/cn/v2/resolve/{$1}
  prefix: d1id
dai.thesauri:
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: A thesaurus of terms useful for digital archaeology
  example: _fe65f286
  homepage: http://thesauri.dainst.org/en.html
  name: German Archaeological Institute Thesaurus
  prefix: dai.thesauri
  uri_format: http://thesauri.dainst.org/en/concepts/$1
dailymed:
  biocontext:
    prefix: DAILYMED
  mappings:
    biocontext: DAILYMED
    miriam: dailymed
    n2t: dailymed
    prefixcommons: dailymed
  miriam:
    deprecated: false
    description: DailyMed provides information about marketed drugs. This information
      includes FDA labels (package inserts). The Web site provides a standard, comprehensive,
      up-to-date, look-up and download resource of medication content and labeling
      as found in medication package inserts. Drug labeling is the most recent submitted
      to the Food and Drug Administration (FDA) and currently in use; it may include,
      for example, strengthened warnings undergoing FDA review or minor editorial
      changes. These labels have been reformatted to make them easier to read.
    homepage: https://dailymed.nlm.nih.gov/dailymed/
    id: '00000434'
    name: DailyMed
    namespaceEmbeddedInLui: false
    pattern: ^[A-Za-z0-9-]+$
    prefix: dailymed
    sampleId: 973a9333-fec7-46dd-8eb5-25738f06ee54
    uri_format: https://dailymed.nlm.nih.gov/dailymed/drugInfo.cfm?setid=$1
  n2t:
    description: DailyMed provides information about marketed drugs. This information
      includes FDA labels (package inserts). The Web site provides a standard, comprehensive,
      up-to-date, look-up and download resource of medication content and labeling
      as found in medication package inserts. Drug labeling is the most recent submitted
      to the Food and Drug Administration (FDA) and currently in use; it may include,
      for example, strengthened warnings undergoing FDA review or minor editorial
      changes. These labels have been reformatted to make them easier to read.
    example: 973a9333-fec7-46dd-8eb5-25738f06ee54
    homepage: https://dailymed.nlm.nih.gov/dailymed/
    name: DailyMed at NLM
    namespaceEmbeddedInLui: false
    pattern: ^[A-Za-z0-9-]+
    prefix: dailymed
    uri_format: https://dailymed.nlm.nih.gov/dailymed/drugInfo.cfm?setid=$1
  prefix: dailymed
  prefixcommons:
    description: DailyMed provides high quality information about marketed drugs including
      FDA labels (package inserts).
    example: 3be94523-f6d6-4b25-82b0-3e0d021594c5
    homepage: http://dailymed.nlm.nih.gov/dailymed/
    name: Dailymed
    pattern: ^[A-Za-z0-9]{8}-[A-Za-z0-9]{4}-[A-Za-z0-9]{4}-[A-Za-z0-9]{4}-[A-Za-z0-9]{12}$
    prefix: dailymed
    uri_format: http://dailymed.nlm.nih.gov/dailymed/lookup.cfm?setid=$1
dalia.community:
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: A UUID for a community indexed in the Data Liteacy Alliance (DALIA)
    web application
  example: bead62a8-c3c2-46d6-9eb1-ffeaba38d5bf
  github_request_issue: 1616
  homepage: https://search.dalia.education
  name: DALIA Community
  part_of_database: dalia
  pattern: ^[A-Za-z0-9]{8}-[A-Za-z0-9]{4}-[A-Za-z0-9]{4}-[A-Za-z0-9]{4}-[A-Za-z0-9]{12}$
  prefix: dalia.community
  uri_format: https://search.dalia.education/communities/$1
dalia.oer:
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: A UUID for an open educational resource indexed in the Data Liteacy
    Alliance (DALIA) web application
  example: 69aebdfe-73f6-4bac-85d7-047dd8cec076
  github_request_issue: 1616
  homepage: https://search.dalia.education
  name: DALIA Open Educational Resource
  part_of_database: dalia
  pattern: ^[A-Za-z0-9]{8}-[A-Za-z0-9]{4}-[A-Za-z0-9]{4}-[A-Za-z0-9]{4}-[A-Za-z0-9]{12}$
  prefix: dalia.oer
  uri_format: https://search.dalia.education/items/$1
daml.pt:
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: A representation of the periodic table of the elements in OWL, with
    both elements and a hierarchical classification. This is from the DARPA Agent
    Markup Language (DAML) project, which has been inactive since the mid 2000's.
  download_owl: https://www.daml.org/2003/01/periodictable/PeriodicTable.owl
  example: Be
  example_extras:
  - Metallic
  - Non-metallic
  github_request_issue: 1419
  homepage: https://www.daml.org/2003/01/periodictable/
  name: DAML Periodic Table of the Elements
  prefix: daml.pt
  uri_format: http://www.daml.org/2003/01/periodictable/PeriodicTable#$1
dandi:
  fairsharing:
    abbreviation: DANDI
    contact:
      email: yoh@dartmouth.edu
      name: Yaroslav Halchenko
      orcid: 0000-0003-3456-2493
    description: The Distributed Archives for Neurophysiology Data Integration (DANDI)
      is a platform for publishing, sharing, and processing neurophysiology data funded
      by the BRAIN Initiative. The archive accepts cellular neurophysiology data including
      electrophysiology, optophysiology, and behavioral time-series, and images from
      immunostaining experiments.
    homepage: https://www.dandiarchive.org
    license: CC0-1.0
    name: Distributed Archives for Neurophysiology Data Integration
    prefix: FAIRsharing.f2c119
    publications: []
    repository: https://github.com/dandi/dandiarchive
    subjects:
    - Neurophysiology
    twitter: dandiarchive
  mappings:
    fairsharing: FAIRsharing.f2c119
    miriam: dandi
    re3data: r3d100013638
  miriam:
    deprecated: false
    description: 'DANDI works with BICCN and other BRAIN Initiative awardees to curate
      data using community data standards such as NWB and BIDS, and to make data and
      software for cellular neurophysiology FAIR (Findable, Accessible, Interoperable,
      and Reusable).

      DANDI references electrical and optical cellular neurophysiology recordings
      and associated MRI and/or optical imaging data.

      These data will help scientists uncover and understand cellular level mechanisms
      of brain function. Scientists will study the formation of neural networks, how
      cells and networks enable functions such as learning and memory, and how these
      functions are disrupted in neurological disorders.'
    homepage: https://dandiarchive.org/
    id: 00000786
    name: 'DANDI: Distributed Archives for Neurophysiology Data Integration'
    namespaceEmbeddedInLui: false
    pattern: ^\d{6}(\/\d+\.\d+\.\d+)?$
    prefix: dandi
    sampleId: '000017'
    uri_format: https://dandiarchive.org/dandiset/$1
  name: Distributed Archives for Neurophysiology Data Integration
  prefix: dandi
  re3data:
    description: The US BRAIN Initiative archive for publishing and sharing neurophysiology
      data including electrophysiology, optophysiology, and behavioral time-series,
      and images from immunostaining experiments.
    doi: 10.17616/R31NJN0M
    homepage: https://dandiarchive.org/
    name: DANDI
    prefix: r3d100013638
    synonyms:
    - DANDI Archive
    - Distributed Archives for Neurophysiology Data Integration
darc:
  biocontext:
    prefix: DARC
  contact:
    email: daniel.wilson@uni-hamburg.de
    github: null
    name: Daniel N. Wilson
    orcid: 0000-0003-3816-3828
  fairsharing:
    abbreviation: DARC
    description: The Database for Aligned Ribosomal Complexes (DARC) site provides
      a resource for directly comparing the structures of available ribosomal complexes.
    homepage: http://darcsite.genzentrum.lmu.de/darc/
    name: Database of Aligned Ribosomal Complexes
    prefix: FAIRsharing.evfe2s
    publications:
    - doi: 10.1093/nar/gkr824
      pubmed_id: 22009674
      title: 'The DARC site: a database of aligned ribosomal complexes.'
    subjects:
    - Life Science
  mappings:
    biocontext: DARC
    fairsharing: FAIRsharing.evfe2s
    miriam: darc
    n2t: darc
  miriam:
    deprecated: true
    description: DARC (Database of Aligned Ribosomal Complexes) stores available cryo-EM
      (electron microscopy) data and atomic coordinates of ribosomal particles from
      the PDB, which are aligned within a common coordinate system. The aligned coordinate
      system simplifies direct visualization of conformational changes in the ribosome,
      such as subunit rotation and head-swiveling, as well as direct comparison of
      bound ligands, such as antibiotics or translation factors.
    homepage: http://darcsite.genzentrum.lmu.de/darc/index.php
    id: '00000366'
    name: DARC
    namespaceEmbeddedInLui: false
    pattern: ^\d+$
    prefix: darc
    sampleId: '1250'
    uri_format: http://darcsite.genzentrum.lmu.de/darc/view.php?id=$1
  n2t:
    description: DARC (Database of Aligned Ribosomal Complexes) stores available cryo-EM
      (electron microscopy) data and atomic coordinates of ribosomal particles from
      the PDB, which are aligned within a common coordinate system. The aligned coordinate
      system simplifies direct visualization of conformational changes in the ribosome,
      such as subunit rotation and head-swiveling, as well as direct comparison of
      bound ligands, such as antibiotics or translation factors.
    example: '1250'
    homepage: http://darcsite.genzentrum.lmu.de/darc/index.php
    name: DARC at University of Munich
    namespaceEmbeddedInLui: false
    pattern: ^\d+$
    prefix: darc
    uri_format: http://darcsite.genzentrum.lmu.de/darc/view.php?id=$1
  name: Database of Aligned Ribosomal Complexes
  prefix: darc
  publications:
  - doi: 10.1093/nar/gkr824
    pmc: PMC3245104
    pubmed: '22009674'
    title: 'The DARC site: a database of aligned ribosomal complexes'
    year: 2011
  - doi: 10.1093/nar/gkr824
    pmc: null
    pubmed: null
    title: 'The DARC site: a database of aligned ribosomal complexes.'
    year: null
dashr.expression:
  biocontext:
    prefix: DASHR.EXPRESSION
  mappings:
    biocontext: DASHR.EXPRESSION
    miriam: dashr.expression
    n2t: dashr.expression
  miriam:
    deprecated: false
    description: DASHR reports the annotation, expression and evidence for specific
      RNA processing (cleavage specificity scores/entropy) of human sncRNA genes,
      precursor and mature sncRNA products across different human tissues and cell
      types. DASHR integrates information from multiple existing annotation resources
      for small non-coding RNAs, including microRNAs (miRNAs), Piwi-interacting (piRNAs),
      small nuclear (snRNAs), nucleolar (snoRNAs), cytoplasmic (scRNAs), transfer
      (tRNAs), tRNA fragments (tRFs), and ribosomal RNAs (rRNAs). These datasets were
      obtained from non-diseased human tissues and cell types and were generated for
      studying or profiling small non-coding RNAs. This collection references RNA
      expression.
    homepage: https://dashr1.lisanwanglab.org/show-expression-table.php?start=0
    id: '00000565'
    name: DASHR expression
    namespaceEmbeddedInLui: false
    pattern: ^(hsa-(let|mir)-\w+(-\w+)?)|(piR-\d+)|(chr\w+.tRNA\d+-\w+)|(chr\w+.tRNA\d+-\w+-tRF\d)|((SNORD|SNORA|ACA|HBII|HBI|U)(-)?\w+)|(HY\d\+(-L\d+)?)|((LSU|SSU|5S)(-rRNA_Hsa)?(-L\d+)?)$
    prefix: dashr.expression
    sampleId: hsa-mir-200a
    uri_format: https://dashr1.lisanwanglab.org/entry/hsa-mir-200a#$1#exprPerTissueTable
  n2t:
    description: DASHR reports the annotation, expression and evidence for specific
      RNA processing (cleavage specificity scores/entropy) of human sncRNA genes,
      precursor and mature sncRNA products across different human tissues and cell
      types. DASHR integrates information from multiple existing annotation resources
      for small non-coding RNAs, including microRNAs (miRNAs), Piwi-interacting (piRNAs),
      small nuclear (snRNAs), nucleolar (snoRNAs), cytoplasmic (scRNAs), transfer
      (tRNAs), tRNA fragments (tRFs), and ribosomal RNAs (rRNAs). These datasets were
      obtained from non-diseased human tissues and cell types and were generated for
      studying or profiling small non-coding RNAs. This collection references RNA
      expression.
    example: hsa-mir-200a
    homepage: https://dashr1.lisanwanglab.org/show-expression-table.php?start=0
    name: DASHR expression at University of Pennsylvania
    namespaceEmbeddedInLui: false
    pattern: ^(hsa-(let|mir)-\w+(-\w+)?)|(piR-\d+)|(chr\w+.tRNA\d+-\w+)|(chr\w+.tRNA\d+-\w+-tRF\d)|((SNORD|SNORA|ACA|HBII|HBI|U)(-)?\w+)|(HY\d\+(-L\d+)?)|((LSU|SSU|5S)(-rRNA_Hsa)?(-L\d+)?)$
    prefix: dashr.expression
    uri_format: https://dashr1.lisanwanglab.org/entry/hsa-mir-200a#$1#exprPerTissueTable
  part_of_database: dashr
  prefix: dashr.expression
dashr.rna:
  biocontext:
    prefix: DASHR
  fairsharing:
    abbreviation: DASHR
    contact:
      email: dashr@lisanwanglab.org
      name: Li-San Wang
      orcid: 0000-0002-3684-0031
    description: Integrated annotation and sequencing-based expression data for all
      major classes of human small non-coding RNAs (sncRNAs) for both full sncRNA
      transcripts and mature sncRNA products derived from these larger RNAs.
    homepage: http://lisanwanglab.org/DASHR
    name: Database of small human non-coding RNAs
    prefix: FAIRsharing.ztvs34
    publications:
    - doi: 10.1093/nar/gkv1188
      pubmed_id: 26553799
      title: 'DASHR: database of small human noncoding RNAs.'
    subjects:
    - Life Science
  mappings:
    biocontext: DASHR
    fairsharing: FAIRsharing.ztvs34
    miriam: dashr
    n2t: dashr
  miriam:
    deprecated: false
    description: DASHR reports the annotation, expression and evidence for specific
      RNA processing (cleavage specificity scores/entropy) of human sncRNA genes,
      precursor and mature sncRNA products across different human tissues and cell
      types. DASHR integrates information from multiple existing annotation resources
      for small non-coding RNAs, including microRNAs (miRNAs), Piwi-interacting (piRNAs),
      small nuclear (snRNAs), nucleolar (snoRNAs), cytoplasmic (scRNAs), transfer
      (tRNAs), tRNA fragments (tRFs), and ribosomal RNAs (rRNAs). These datasets were
      obtained from non-diseased human tissues and cell types and were generated for
      studying or profiling small non-coding RNAs. This collection references RNA
      records.
    homepage: http://lisanwanglab.org/DASHR/
    id: '00000564'
    name: DASHR
    namespaceEmbeddedInLui: false
    pattern: ^(hsa-(let|mir)-\w+(-\w+)?)|(piR-\d+)|(chr\w+.tRNA\d+-\w+)|(chr\w+.tRNA\d+-\w+-tRF\d)|((SNORD|SNORA|ACA|HBII|HBI|U)(-)?\w+)|(HY\d\+(-L\d+)?)|((LSU|SSU|5S)(-rRNA_Hsa)?(-L\d+)?)$
    prefix: dashr
    sampleId: hsa-mir-200a
    uri_format: http://lisanwanglab.org/DASHR/entry/$1
  n2t:
    description: DASHR reports the annotation, expression and evidence for specific
      RNA processing (cleavage specificity scores/entropy) of human sncRNA genes,
      precursor and mature sncRNA products across different human tissues and cell
      types. DASHR integrates information from multiple existing annotation resources
      for small non-coding RNAs, including microRNAs (miRNAs), Piwi-interacting (piRNAs),
      small nuclear (snRNAs), nucleolar (snoRNAs), cytoplasmic (scRNAs), transfer
      (tRNAs), tRNA fragments (tRFs), and ribosomal RNAs (rRNAs). These datasets were
      obtained from non-diseased human tissues and cell types and were generated for
      studying or profiling small non-coding RNAs. This collection references RNA
      records.
    example: hsa-mir-200a
    homepage: http://lisanwanglab.org/DASHR/
    name: DASHR at  University of Pennsylvania
    namespaceEmbeddedInLui: false
    pattern: ^(hsa-(let|mir)-\w+(-\w+)?)|(piR-\d+)|(chr\w+.tRNA\d+-\w+)|(chr\w+.tRNA\d+-\w+-tRF\d)|((SNORD|SNORA|ACA|HBII|HBI|U)(-)?\w+)|(HY\d\+(-L\d+)?)|((LSU|SSU|5S)(-rRNA_Hsa)?(-L\d+)?)$
    prefix: dashr
    uri_format: http://lisanwanglab.org/DASHR/entry/$1
  name: Database of small human noncoding RNAs
  part_of_database: dashr
  prefix: dashr.rna
  publications:
  - doi: 10.1093/nar/gkv1188
    pmc: PMC4702848
    pubmed: '26553799'
    title: 'DASHR: database of small human noncoding RNAs'
    year: 2015
  - doi: 10.1093/nar/gkv1188
    pmc: null
    pubmed: null
    title: 'DASHR: database of small human noncoding RNAs.'
    year: null
  synonyms:
  - dashr
datacite:
  aberowl:
    description: The DataCite Ontology (DataCite) is an ontology that enables the
      metadata properties of the DataCite Metadata Schema Specification (i.e., a list
      of metadata properties for the accurate and consistent identification of a resource
      for citation and retrieval purposes) to be described in RDF., The DataCite Ontology
      is an ontology written in OWL 2 DL to enable the metadata properties of the
      [DataCite Metadata Kernel Specification version 3.1](https://www.datacite.org/sites/default/files/document/DataCite-MetadataSchema_V31_Final_8-24-2015_0.pdf)
      to be described in RDF.  This version of the DataCite Ontology has been completely
      revised and significantly expanded to permit accurate mapping of this new version
      of the DataCite Metadata Kernel Specification to RDF., http://purl.org/spar/datacite/datacite.png
    download_owl: http://aber-owl.net/media/ontologies/DATACITE/3/datacite.owl
    homepage: http://www.sparontologies.net/ontologies/datacite
    name: SPAR DataCite Ontology
    prefix: DATACITE
    version: 1.2.1
  bioportal:
    contact:
      email: sparontologies@gmail.com
      name: SPAR Ontologies
    description: "The DataCite Ontology (DataCite) is an ontology that enables the\
      \ metadata properties of the DataCite Metadata Schema Specification (i.e., a\
      \ list of metadata properties for the accurate and consistent identification\
      \ of a resource for citation and retrieval purposes) to be described in RDF.,\
      \ The DataCite Ontology is an ontology written in OWL 2 DL to enable the metadata\
      \ properties of the [DataCite Metadata Kernel Specification version 3.1](https://www.datacite.org/sites/default/files/document/DataCite-MetadataSchema_V31_Final_8-24-2015_0.pdf)\
      \ to be described in RDF. \n\nThis version of the DataCite Ontology has been\
      \ completely revised and significantly expanded to permit accurate mapping of\
      \ this new version of the DataCite Metadata Kernel Specification to RDF., http://purl.org/spar/datacite/datacite.png"
    homepage: http://www.sparontologies.net/ontologies/datacite
    name: SPAR DataCite Ontology
    prefix: DATACITE
    publications:
    - http://dx.doi.org/10.6084/m9.figshare.2075356
    version: 1.2.1
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: An ontology that enables the metadata properties of the DataCite Metadata
    Schema Specification (i.e., a list of metadata properties for the accurate and
    consistent identification of a resource for citation and retrieval purposes) to
    be described in RDF.
  example: AgentIdentifierScheme
  fairsharing:
    abbreviation: DataCite
    contact:
      email: silvio.peroni@unibo.it
      name: Silvio Peroni
      orcid: 0000-0003-0530-4305
    description: The DataCite Ontology (DataCite) is an ontology that enables the
      metadata properties of the DataCite Metadata Schema Specification (i.e., a list
      of metadata properties for the accurate and consistent identification of a resource
      for citation and retrieval purposes) to be described in RDF.
    homepage: http://www.sparontologies.net/ontologies/datacite
    license: CC-BY-4.0
    name: 'DataCite Ontology '
    prefix: FAIRsharing.c06f1e
    repository: https://github.com/sparontologies/datacite
    subjects:
    - Subject Agnostic
    twitter: sparontologies
  homepage: http://www.sparontologies.net/ontologies/datacite
  mappings:
    aberowl: DATACITE
    bioportal: DATACITE
    fairsharing: FAIRsharing.c06f1e
  name: DataCite Ontology
  preferred_prefix: DataCite
  prefix: datacite
  repository: https://github.com/sparontologies/datacite
  twitter: datacite
  uri_format: http://purl.org/spar/datacite/$1
datacommons:
  biolink:
    is_identifiers: false
    is_obo: false
    prefix: dcid
    uri_format: https://datacommons.org/browser/$1
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: A large RDF store built from American governmental data. This semantic
    space has a mixture of direct terms and subspaces.
  example: Gene
  homepage: https://datacommons.org
  mappings:
    biolink: dcid
  name: Data Commons
  prefix: datacommons
  repository: https://github.com/datacommonsorg/website
  synonyms:
  - dcid
  uri_format: https://datacommons.org/browser/$1
datanator.gene:
  mappings:
    miriam: datanator.gene
  miriam:
    deprecated: false
    description: Datanator is an integrated database of genomic and biochemical data
      designed to help investigators find data about specific molecules and reactions
      in specific organisms and specific environments for meta-analyses and mechanistic
      models. Datanator currently includes metabolite concentrations, RNA modifications
      and half-lives, protein abundances and modifications, and reaction kinetics
      integrated from several databases and numerous publications. The Datanator website
      and REST API provide tools for extracting clouds of data about specific molecules
      and reactions in specific organisms and specific environments, as well as data
      about similar molecules and reactions in taxonomically similar organisms.
    homepage: https://datanator.info/
    id: '00000720'
    name: Datanator Gene
    namespaceEmbeddedInLui: false
    pattern: ^K[0-9]+$
    prefix: datanator.gene
    sampleId: K00973
    uri_format: https://www.datanator.info/gene/$1
  part_of_database: datanator
  prefix: datanator.gene
datanator.metabolite:
  mappings:
    miriam: datanator.metabolite
  miriam:
    deprecated: false
    description: Datanator is an integrated database of genomic and biochemical data
      designed to help investigators find data about specific molecules and reactions
      in specific organisms and specific environments for meta-analyses and mechanistic
      models. Datanator currently includes metabolite concentrations, RNA modifications
      and half-lives, protein abundances and modifications, and reaction kinetics
      integrated from several databases and numerous publications. The Datanator website
      and REST API provide tools for extracting clouds of data about specific molecules
      and reactions in specific organisms and specific environments, as well as data
      about similar molecules and reactions in taxonomically similar organisms.
    homepage: https://datanator.info/
    id: 00000718
    name: Datanator Metabolite
    namespaceEmbeddedInLui: false
    pattern: ^[A-Z\-]+$
    prefix: datanator.metabolite
    sampleId: OUYCCCASQSFEME-MRVPVSSYSA-N
    uri_format: https://www.datanator.info/metabolite/$1
  part_of_database: datanator
  prefix: datanator.metabolite
datanator.reaction:
  mappings:
    miriam: datanator.reaction
  miriam:
    deprecated: false
    description: "\tDatanator is an integrated database of genomic and biochemical\
      \ data designed to help investigators find data about specific molecules and\
      \ reactions in specific organisms and specific environments for meta-analyses\
      \ and mechanistic models. Datanator currently includes metabolite concentrations,\
      \ RNA modifications and half-lives, protein abundances and modifications, and\
      \ reaction kinetics integrated from several databases and numerous publications.\
      \ The Datanator website and REST API provide tools for extracting clouds of\
      \ data about specific molecules and reactions in specific organisms and specific\
      \ environments, as well as data about similar molecules and reactions in taxonomically\
      \ similar organisms."
    homepage: https://icahn.mssm.edu/
    id: 00000855
    name: Datanator Reaction
    namespaceEmbeddedInLui: false
    pattern: ^.*?--%3E.*?$
    prefix: datanator.reaction
    sampleId: XLYOFNOQVPJJNP-UHFFFAOYSA-N,NBSCHQHZLSJFNQ-GASJEMHNSA-N--%3ENBIIXXVUZAFLBC-UHFFFAOYSA-N,WQZGKKKJIJFFOK-GASJEMHNSA-N
    uri_format: https://datanator.info/reaction/$1
  prefix: datanator.reaction
datf:
  biocontext:
    prefix: DATF
  deprecated: true
  mappings:
    biocontext: DATF
    miriam: datf
    n2t: datf
    pathguide: '518'
    prefixcommons: datf
  miriam:
    deprecated: true
    description: DATF contains known and predicted Arabidopsis transcription factors
      (1827 genes in 56 families) with the unique information of 1177 cloned sequences
      and many other features including 3D structure templates, EST expression information,
      transcription factor binding sites and nuclear location signals.
    homepage: http://datf.cbi.pku.edu.cn/
    id: '00000456'
    name: DATF
    namespaceEmbeddedInLui: false
    pattern: ^AT[1-5]G\d{5}(\.\d+)?$
    prefix: datf
    sampleId: AT1G01030.1
    uri_format: http://planttfdb.cbi.pku.edu.cn/tf.php?sp=Ath&did=$1
  n2t:
    description: DATF contains known and predicted Arabidopsis transcription factors
      (1827 genes in 56 families) with the unique information of 1177 cloned sequences
      and many other features including 3D structure templates, EST expression information,
      transcription factor binding sites and nuclear location signals.
    example: AT1G01030.1
    homepage: http://datf.cbi.pku.edu.cn/
    name: DATF through PlantTFDB
    namespaceEmbeddedInLui: false
    pattern: ^AT[1-5]G\d{5}(\.\d+)?$
    prefix: datf
    uri_format: http://planttfdb.cbi.pku.edu.cn/tf.php?sp=Ath&did=$1
  name: Database of Arabidopsis Transcription Factors
  pathguide:
    abbreviation: DATF
    homepage: http://datf.cbi.pku.edu.cn/
    name: Database of Arabidopsis Transcription Factors
    prefix: '518'
  prefix: datf
  prefixcommons:
    description: The Database of Arabidopsis Transcription Factors (DATF) collects
      all Arabidopsis transcription factors (totally 1922 Loci; 2290 Gene Models)
      and classifies them into 64 families.The Version 2 of DATF was updated at July
      2006. It is based on the Arabidopsis Sequence of TAIR http://www.pdb.org, predicted
      Nuclear Location Signals, UniGene information, as well as links to literature
      reference.
    example: AT1G08970.3
    homepage: http://datf.cbi.pku.edu.cn
    keywords:
    - regulation
    name: Database of Arabidopsis Transcription Factors
    pattern: ^AT\d[A-Z]\d+$
    prefix: datf
    uri_format: http://datf.cbi.pku.edu.cn/entry-display.php?id=$1
dbamp:
  banana: dbAMP
  banana_peel: _
  contact:
    email: leetzongyi@nycu.edu.tw
    github: null
    name: Tzong-Yi Lee
    orcid: 0000-0001-8475-7868
  contributor:
    email: ji.kang@northeastern.edu
    github: kanghosaeyo
    name: Kangho Ji
    orcid: 0009-0009-3402-8013
  description: Identifiers represent antimicrobial peptides in the Database of Antimicrobial
    Peptides (dbAMP) which is an open-access, manually curated database of antimicrobial
    peptides (AMPs).
  domain: peptide
  example: '28463'
  github_request_issue: 1714
  homepage: https://awi.cuhk.edu.cn/dbAMP/
  integbio:
    description: 'dbAMP is a database of anti-microbial peptides (AMPs) which are
      naturally encoded by genes and generally containing 12-100 amino acids. It provides
      information of antibacterial activities, physical-chemical properties, target
      species, structures, interacting proteins, links to external databases etc.
      It includes two categories of AMPs: experimental AMPs from published articles
      or public databases and predicted AMPs from public databases. Users can browse
      using following keys; peptide sequences, organisms, structures, targets and
      references.'
    homepage: http://140.138.77.240/~dbamp/index.php
    information_keywords:
    - Sequence
    - 3D structure
    - Interaction/Pathway
    maintainer: Arieh Warshel Institute of Computational Biology, The Chinese University
      of Hong Kong
    name: dbAMP
    prefix: nbdc02467
    pubmeds:
    - '30380085'
    status: Inactive
    target_keywords:
    - Protein
    - Drug
    - Health/Disease
  keywords:
  - antimicrobial peptides
  logo: https://awi.cuhk.edu.cn/dbAMP/assets/img/dbAMPv2.svg
  mappings:
    integbio: nbdc02467
  name: Database of Anti-Microbial Peptides
  pattern: ^\d{5}$
  prefix: dbamp
  providers:
  - code: abpdb
    description: Antimicrobial Peptide Database (ABPDB) is a comprehensive database
      that aggregates antimicrobial peptide data from DRAMP and dbAMP.
    example: null
    first_party: null
    homepage: http://www.acdb.plus/ABPDB/
    name: AntiBacterial Peptides DataBase
    publications:
    - doi: 10.1109/tcbbio.2025.3582844
      pmc: null
      pubmed: '40811252'
      title: 'ABPDB: a Database of Antibacterial Peptides'
      year: 2025
    status: null
    uri_format: http://www.acdb.plus/ABPDB/abp-search.php?keywords=dbAMP$1
  publications:
  - doi: 10.1093/nar/gkae1019
    pmc: PMC11701527
    pubmed: '39540425'
    title: 'dbAMP 3.0: updated resource of antimicrobial activity and structural annotation
      of peptides in the post-pandemic era'
    year: 2025
  - doi: 10.1093/nar/gkab1080
    pmc: PMC8690246
    pubmed: '34850155'
    title: 'dbAMP 2.0: updated resource for antimicrobial peptides with an enhanced
      scanning method for genomic and proteomic data'
    year: 2022
  - doi: 10.1093/nar/gky1030
    pmc: PMC6323920
    pubmed: '30380085'
    title: 'dbAMP: an integrated resource for exploring antimicrobial peptides with
      functional activities and physicochemical properties on transcriptome and proteome
      data'
    year: 2019
  - doi: 10.1109/tcbbio.2025.3582844
    pmc: null
    pubmed: '40811252'
    title: 'ABPDB: a Database of Antibacterial Peptides'
    year: 2025
  - doi: 10.1109/tcbbio.2025.3582844
    pmc: null
    pubmed: '40811252'
    title: 'ABPDB: a Database of Antibacterial Peptides'
    year: 2025
  reviewer:
    email: b.gyori@northeastern.edu
    github: bgyori
    name: Benjamin M. Gyori
    orcid: 0000-0001-9439-5346
  reviewer_extras:
  - email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  uri_format: https://awi.cuhk.edu.cn/dbAMP/information.php?db=dbamp_$1
dbd:
  biocontext:
    prefix: DBD
  edam:
    description: Identifier of a predicted transcription factor from the DBD database.
    name: DBD
    obsolete: false
    prefix: '2716'
  mappings:
    biocontext: DBD
    edam: '2716'
    miriam: dbd
    n2t: dbd
    pathguide: '496'
    prefixcommons: dbd
  miriam:
    deprecated: false
    description: The DBD (transcription factor database) provides genome-wide transcription
      factor predictions for organisms across the tree of life. The prediction method
      identifies sequence-specific DNA-binding transcription factors through homology
      using profile hidden Markov models (HMMs) of domains from Pfam and SUPERFAMILY.
      It does not include basal transcription factors or chromatin-associated proteins.
    homepage: http://www.transcriptionfactor.org/
    id: '00000455'
    name: DBD
    namespaceEmbeddedInLui: false
    pattern: ^\d+$
    prefix: dbd
    sampleId: '0045310'
    uri_format: http://www.transcriptionfactor.org/index.cgi?Search/Domain+domain:$1+cat:DBD
  n2t:
    description: The DBD (transcription factor database) provides genome-wide transcription
      factor predictions for organisms across the tree of life. The prediction method
      identifies sequence-specific DNA-binding transcription factors through homology
      using profile hidden Markov models (HMMs) of domains from Pfam and SUPERFAMILY.
      It does not include basal transcription factors or chromatin-associated proteins.
    example: '0045310'
    homepage: http://www.transcriptionfactor.org/
    name: DBD at MRC Laboratory of Molecular Biology
    namespaceEmbeddedInLui: false
    pattern: ^\d+$
    prefix: dbd
    uri_format: http://www.transcriptionfactor.org/index.cgi?Search/Domain+domain:$1+cat:DBD
  name: Transcription Factor Database
  pathguide:
    abbreviation: DBD
    homepage: http://www.transcriptionfactor.org/index.cgi?Home
    name: 'DNA-Binding Domain: Transcription Factor Predictor Database'
    prefix: '496'
  prefix: dbd
  prefixcommons:
    description: DBD provides transcription factor predictions for more than 150 completely
      sequenced genomes available for browsing and download. Predictions are based
      on presence of sequence specific DNA binding domain assignments using hidden
      Markov models from the SUPERFAMILY and PFAM databases
    example: '0035306'
    homepage: http://www.transcriptionfactor.org
    keywords:
    - regulation
    - genome
    name: DBD
    pattern: ^\d+$
    prefix: dbd
    uri_format: http://dbd.mrc-lmb.cam.ac.uk/DBD/index.cgi?Search/Domain+domain:$1
dbest:
  biocontext:
    prefix: DBEST
  contact:
    email: tmjlowe@ucsc.edu
    github: null
    name: Todd M Lowe
    orcid: 0000-0003-3253-6021
  edam:
    description: Identifier of a dbEST database entry.
    name: dbEST
    obsolete: false
    prefix: '1105'
  fairsharing:
    abbreviation: dbEST
    description: The dbEST contains sequence data and other information on "single-pass"
      cDNA sequences, or "Expressed Sequence Tags", from a number of organisms. NCBI
      is in the process of merging EST and GSS records into the Nucleotide database,
      and the process is expected to be completed 2019. Accession.version and GI identifiers
      will not change during this process. For more information please see https://ncbiinsights.ncbi.nlm.nih.gov/2018/07/30/upcoming-changes-est-gss-databases/
    homepage: https://www.ncbi.nlm.nih.gov/genbank/dbest/
    license: http://opendatacommons.org/licenses/pddl/1.0
    name: Expressed Sequence Tags database
    prefix: FAIRsharing.v9fya8
    publications:
    - doi: 10.1038/ng0893-332
      pubmed_id: 8401577
      title: dbEST--database for "expressed sequence tags".
    subjects:
    - Bioinformatics
    - Life Science
  integbio:
    alt_name: Expressed Sequence Tags database
    description: This is one of the world's largest repository for EST with information
      on multiple species. Users can also submit their own data.
    fairsharing: biodbcore-000435
    homepage: https://www.ncbi.nlm.nih.gov/genbank/dbest/
    information_keywords:
    - Sequence
    - Repository
    maintainer: NCBI (National Center for Biotechnology Information)
    name: dbEST
    prefix: nbdc00413
    pubmeds:
    - '8401577'
    status: Active
    target_keywords:
    - cDNA/EST
  mappings:
    biocontext: DBEST
    edam: '1105'
    fairsharing: FAIRsharing.v9fya8
    integbio: nbdc00413
    miriam: dbest
    n2t: dbest
    ncbi: dbEST
    prefixcommons: dbest
    re3data: r3d100010648
  miriam:
    deprecated: false
    description: The dbEST contains sequence data and other information on "single-pass"
      cDNA sequences, or "Expressed Sequence Tags", from a number of organisms.
    homepage: https://www.ncbi.nlm.nih.gov/nucest
    id: 00000159
    name: dbEST
    namespaceEmbeddedInLui: false
    pattern: ^([A-Z]+)?\d+(\.\d+)?$
    prefix: dbest
    providers:
    - code: ebi
      description: dbEST through European Nucleotide Archive (ENA)
      homepage: https://www.ebi.ac.uk/ena
      name: dbEST through European Nucleotide Archive (ENA)
      uri_format: https://www.ebi.ac.uk/ena/data/view/$1
    - code: ''
      description: dbEST through DNA Data Bank of Japan (DDBJ)
      homepage: http://www.ddbj.nig.ac.jp/
      name: dbEST through DNA Data Bank of Japan (DDBJ)
      uri_format: https://getentry.ddbj.nig.ac.jp/getentry/na/$1
    sampleId: BP100000
    uri_format: https://www.ncbi.nlm.nih.gov/nucest/$1
  n2t:
    description: The dbEST contains sequence data and other information on "single-pass"
      cDNA sequences, or "Expressed Sequence Tags", from a number of organisms.
    example: BP100000
    homepage: https://www.ncbi.nlm.nih.gov/nucest
    name: dbEST at NCBI
    namespaceEmbeddedInLui: false
    pattern: ^([A-Z]+)?\d+(\.\d+)?$
    prefix: dbest
    uri_format: https://www.ncbi.nlm.nih.gov/nucest/$1
  ncbi:
    example: '123456'
    homepage: https://www.ncbi.nlm.nih.gov/genbank/dbest
    name: EST database maintained at the NCBI.
    prefix: dbEST
  prefix: dbest
  prefixcommons:
    description: The dbEST contains sequence data and other information on "single-pass"
      cDNA sequences, or "Expressed Sequence Tags", from a number of organisms.
    example: BP100000.1
    homepage: http://www.ncbi.nlm.nih.gov/dbEST/index.html
    keywords:
    - DNA
    name: EST database maintained at the NCBI.
    pattern: ^BP\d+(\.\d+)?$
    prefix: dbest
    uri_format: http://www.ncbi.nlm.nih.gov/nucest/$1
  publications:
  - doi: 10.1038/ng0893-332
    pmc: null
    pubmed: '8401577'
    title: dbEST--database for "expressed sequence tags"
    year: 1993
  - doi: 10.1038/ng0893-332
    pmc: null
    pubmed: null
    title: dbEST--database for "expressed sequence tags".
    year: null
  - doi: 10.1038/ng0893-332
    pmc: null
    pubmed: null
    title: dbEST--database for "expressed sequence tags".
    year: null
  re3data:
    description: 'dbEST is a division of GenBank that contains sequence data and other
      information on "single-pass" cDNA sequences, or "Expressed Sequence Tags", from
      a number of organisms.  Expressed Sequence Tags (ESTs) are short (usually about
      300-500 bp), single-pass sequence reads from mRNA (cDNA). Typically they are
      produced in large batches. They represent a snapshot of genes expressed in a
      given tissue and/or at a given developmental stage. They are tags (some coding,
      others not) of expression for a given cDNA library.

      Most EST projects develop large numbers of sequences. These are commonly submitted
      to GenBank and dbEST as batches of dozens to thousands of entries, with a great
      deal of redundancy in the citation, submitter and library information. To improve
      the efficiency of the submission process for this type of data, we have designed
      a special streamlined submission process and data format.

      dbEST also includes sequences that are longer than the traditional ESTs, or
      are produced as single sequences or in small batches. Among these sequences
      are products of differential display experiments and RACE experiments. The thing
      that these sequences have in common with traditional ESTs, regardless of length,
      quality, or quantity, is that there is little information that can be annotated
      in the record.

      If a sequence is later characterized and annotated with biological features
      such as a coding region, 5''UTR, or 3''UTR, it should be submitted through the
      regular GenBank submissions procedure (via BankIt or Sequin), even if part of
      the sequence is already in dbEST.

      dbEST is reserved for single-pass reads. Assembled sequences should not be submitted
      to dbEST. GenBank will accept assembled EST submissions for the forthcoming
      TSA (Transcriptome Shotgun Assembly) division.  The individual reads which make
      up the assembly should be submitted to dbEST, the Trace archive or the Short
      Read Archive (SRA) prior to the submission of the assemblies.'
    doi: 10.17616/R3FG8P
    homepage: https://www.ncbi.nlm.nih.gov/genbank/dbest/
    name: Expressed Sequence Tags database
    prefix: r3d100010648
    synonyms:
    - NCBI EST
    - dbEST
dbg2introns:
  biocontext:
    prefix: DBG2INTRONS
  contact:
    email: zimmerly@ucalgary.ca
    github: null
    name: Steven John Zimmerly
    orcid: null
  mappings:
    biocontext: DBG2INTRONS
    miriam: dbg2introns
    n2t: dbg2introns
    prefixcommons: mgiid
  miriam:
    deprecated: true
    description: The Database for Bacterial Group II Introns  provides a catalogue
      of full-length, non-redundant group II introns present in bacterial DNA sequences
      in GenBank.
    homepage: http://webapps2.ucalgary.ca/~groupii/
    id: 00000318
    name: DBG2 Introns
    namespaceEmbeddedInLui: false
    pattern: ^\w{1,2}\.(\w{1,2}\.)?[A-Za-z0-9]+$
    prefix: dbg2introns
    sampleId: Cu.me.I1
    uri_format: http://webapps2.ucalgary.ca/~groupii/cgi-bin/intron.cgi?name=$1
  n2t:
    description: The Database for Bacterial Group II Introns  provides a catalogue
      of full-length, non-redundant group II introns present in bacterial DNA sequences
      in GenBank.
    example: Cu.me.I1
    homepage: http://webapps2.ucalgary.ca/~groupii/
    name: Bacterial Group II Introns at University of Calgary
    namespaceEmbeddedInLui: false
    pattern: ^\w{1,2}\.(\w{1,2}\.)?[A-Za-z0-9]+$
    prefix: dbg2introns
    uri_format: http://webapps2.ucalgary.ca/~groupii/cgi-bin/intron.cgi?name=$1
  prefix: dbg2introns
  prefixcommons:
    description: Many newly sequenced bacterial group II introns are incorrectly identified
      or annotated. A major goal of this database is to be a resource in helping to
      identify and catalog group II introns in the databases.
    example: Cu.me.I1
    homepage: http://www.fp.ucalgary.ca/group2introns/
    keywords:
    - DNA
    name: Mobile group II introns database
    pattern: ^\w{1,2}\.(\w{1,2}\.)?[A-Za-z0-9]+$
    prefix: mgiid
    pubmed_ids:
    - '22080509'
    synonyms:
    - dbg2introns
    uri_format: http://www.fp.ucalgary.ca/group2introns/$1.htm
  publications:
  - doi: 10.1093/nar/gkr1043
    pmc: PMC3245105
    pubmed: '22080509'
    title: Database for bacterial group II introns
    year: 2011
  - doi: null
    pmc: null
    pubmed: '22080509'
    title: null
    year: null
  - doi: null
    pmc: null
    pubmed: '22080509'
    title: null
    year: null
dbgap:
  biocontext:
    prefix: DBGAP
  cellosaurus:
    category: Sequence databases
    homepage: https://www.ncbi.nlm.nih.gov/gap/
    name: Database of Genotypes and Phenotypes
    prefix: dbGAP
    uri_format: https://www.ncbi.nlm.nih.gov/projects/gap/cgi-bin/study.cgi?study_id=$1
  contact:
    email: feolo@ncbi.nlm.nih.gov
    github: mfeolo
    name: Michael Feolo
    orcid: 0000-0002-1650-5156
  fairsharing:
    abbreviation: dbGaP
    description: The Database of Genotypes and Phenotypes (dbGaP) archives and distributes
      the results of studies that have investigated the interaction of genotype and
      phenotype. Such studies include genome-wide association studies, medical sequencing,
      molecular diagnostic assays, as well as association between genotype and non-clinical
      traits.
    homepage: https://www.ncbi.nlm.nih.gov/gap/
    name: Database of Genotypes and Phenotypes
    prefix: FAIRsharing.88v2k0
    publications:
    - doi: 10.1038/ng1007-1181
      pubmed_id: 17898773
      title: The NCBI dbGaP database of genotypes and phenotypes.
    - doi: 10.1093/nar/gkt1211
      pubmed_id: 24297256
      title: 'NCBI''s Database of Genotypes and Phenotypes: dbGaP.'
    subjects:
    - Epigenetics
    - Genetics
    - Biomedical Science
  integbio:
    alt_name: Genotypes and Phenotypes
    description: This is a database for research on genotypes and phenotypes in humans,
      including genome-wide association studies (GWAS), medical sequencing, and molecular
      diagnostic assays. The dataset is classified into public data and controlled-access
      data, and an application procedure is required for access to controlled-access
      data.
    fairsharing: biodbcore-000462
    homepage: http://www.ncbi.nlm.nih.gov/gap
    information_keywords:
    - Phenotype
    - Bibliography/Documents
    - Repository
    maintainer: NCBI (National Center for Biotechnology Information)
    name: dbGaP
    prefix: nbdc00414
    status: Active
    target_keywords:
    - Genome/Gene
    - Health/Disease
  mappings:
    biocontext: DBGAP
    cellosaurus: dbGAP
    fairsharing: FAIRsharing.88v2k0
    integbio: nbdc00414
    miriam: dbgap
    n2t: dbgap
  miriam:
    deprecated: false
    description: The database of Genotypes and Phenotypes (dbGaP) archives and distributes
      the results of studies that have investigated the interaction of genotype and
      phenotype.
    homepage: https://www.ncbi.nlm.nih.gov/gap/
    id: '00000602'
    name: dbGaP
    namespaceEmbeddedInLui: false
    pattern: ^phs[0-9]{6}(.v\d+.p\d+)?$
    prefix: dbgap
    sampleId: phs000768.v2.p1
    uri_format: https://www.ncbi.nlm.nih.gov/projects/gap/cgi-bin/study.cgi?study_id=$1
  n2t:
    description: The database of Genotypes and Phenotypes (dbGaP) archives and distributes
      the results of studies that have investigated the interaction of genotype and
      phenotype.
    example: phs000768.v2.p1
    homepage: https://www.ncbi.nlm.nih.gov/projects/gap
    name: dbGaP through NCBI
    namespaceEmbeddedInLui: false
    pattern: ^phs[0-9]{6}(.v\d+.p\d+)?$
    prefix: dbgap
    uri_format: https://www.ncbi.nlm.nih.gov/projects/gap/cgi-bin/study.cgi?study_id=$1
  name: Database of Genotypes and Phenotypes
  prefix: dbgap
  publications:
  - doi: 10.1093/nar/gkt1211
    pmc: PMC3965052
    pubmed: '24297256'
    title: 'NCBI''s Database of Genotypes and Phenotypes: dbGaP'
    year: 2013
  - doi: 10.1038/ng1007-1181
    pmc: PMC2031016
    pubmed: '17898773'
    title: The NCBI dbGaP database of genotypes and phenotypes
    year: 2007
dblp.author:
  example: 199/2168
  mappings:
    wikidata: P2456
  prefix: dblp.author
  wikidata:
    description: identifier for author entries in the DBLP computer science bibliography
      (use portion of DBLP person key after pid/)
    example:
    - 181/8944
    - d/JeffreyDean
    - z/LixiaZhang1
    homepage: https://dblp.org/
    name: DBLP author ID
    prefix: P2456
    uri_format: https://dblp.org/pid/$1
    uri_format_rdf: https://dblp.org/pid/$1
dbmhc:
  appears_in:
  - cellosaurus
  cellosaurus:
    category: Cell line databases/resources
    homepage: https://www.ncbi.nlm.nih.gov/gv/mhc/
    name: dbMHC database
    prefix: dbMHC
  deprecated: true
  example: '48439'
  integbio:
    description: dbMHC provides access to HLA sequences, tools to support genetic
      testing of HLA loci, HLA allele and haplotype frequencies of over 90 populations
      worldwide, as well as clinical datasets on nematopoietic stem cell transplantation,
      and insulin dependant diabetes mellitus (IDDM), Rheumatoid Arthritis (RA), Narcolepsy
      and Spondyloarthropathy. All clinical datasets housed at the dbMHC provide access
      to genotypic and phenotypic data on anonimyzed samples with aggregate query
      functions, and complete download capability.
    fairsharing: FAIRsharing.r90425
    homepage: http://www.ncbi.nlm.nih.gov/mhc/
    information_keywords:
    - Sequence
    - Expression
    name: dbMHC
    prefix: nbdc01831
    status: Closed
    target_keywords:
    - Genome/Gene
    - Health/Disease
    - Protein
  mappings:
    cellosaurus: dbMHC
    integbio: nbdc01831
  name: Database of human Major Histocompatibility Complex
  pattern: ^\d+$
  prefix: dbmhc
dbo:
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: This ontology is generated from the manually created specifications
    in the dbpedia mappings wiki. each release of this ontology corresponds to a new
    release of the dbpedia data set which contains instance data extracted from the
    different language versions of wikipedia. for information regarding changes in
    this ontology, please refer to the dbpedia mappings wiki.
  example: careerPrizeMoney
  github_request_issue: 515
  homepage: https://dbpedia.org/ontology
  keywords:
  - dbpedia
  - ontology
  mappings:
    zazuko: dbo
  name: DBPedia Ontology
  prefix: dbo
  uri_format: https://dbpedia.org/ontology/$1
  zazuko:
    prefix: dbo
    uri_format: http://dbpedia.org/ontology/$1
dbpedia.property:
  appears_in:
  - fovt
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: Properties in DBPedia.
  example: insertion
  github_request_issue: 1420
  homepage: http://dbpedia.org/property
  name: DBPedia Property
  part_of_database: dbpedia
  prefix: dbpedia.property
  uri_format: http://dbpedia.org/property/$1
dbpedia.resource:
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: A semi-automatically generated knowledgebase
  example: Grenada
  github_request_issue: 1315
  homepage: https://dbpedia.org
  mappings:
    re3data: r3d100011713
  name: DBPedia Resource
  part_of_database: dbpedia
  prefix: dbpedia.resource
  re3data:
    description: DBpedia is a crowd-sourced community effort to extract structured
      information from Wikipedia and make this information available on the Web. DBpedia
      allows you to ask sophisticated queries against Wikipedia, and to link the different
      data sets on the Web to Wikipedia data. We hope that this work will make it
      easier for the huge amount of information in Wikipedia to be used in some new
      interesting ways. Furthermore, it might inspire new mechanisms for navigating,
      linking, and improving the encyclopedia itself.
    doi: 10.17616/R3R92G
    homepage: https://www.dbpedia.org/
    license: other
    name: DBpedia
    prefix: r3d100011713
  synonyms:
  - dbpedia
  - dbr
  uri_format: http://dbpedia.org/resource/$1
dbprobe:
  biocontext:
    prefix: DBPROBE
  edam:
    description: Identifier of an oligonucleotide probe from the dbProbe database.
    name: dbProbe
    obsolete: false
    prefix: '2719'
  mappings:
    biocontext: DBPROBE
    edam: '2719'
    miriam: dbprobe
    n2t: dbprobe
    ncbi: dbProbe
    prefixcommons: dbprobe
  miriam:
    deprecated: true
    description: The NCBI Probe Database is a public registry of nucleic acid reagents
      designed for use in a wide variety of biomedical research applications, together
      with information on reagent distributors, probe effectiveness, and computed
      sequence similarities.
    homepage: https://www.ncbi.nlm.nih.gov/sites/entrez?db=probe
    id: '00000160'
    name: dbProbe
    namespaceEmbeddedInLui: false
    pattern: ^\d+$
    prefix: dbprobe
    sampleId: '1000000'
    uri_format: https://www.ncbi.nlm.nih.gov/probe/?term=$1
  n2t:
    description: The NCBI Probe Database is a public registry of nucleic acid reagents
      designed for use in a wide variety of biomedical research applications, together
      with information on reagent distributors, probe effectiveness, and computed
      sequence similarities.
    example: '1000000'
    homepage: https://www.ncbi.nlm.nih.gov/sites/entrez?db=probe
    name: dbProbe at NCBI
    namespaceEmbeddedInLui: false
    pattern: ^\d+$
    prefix: dbprobe
    uri_format: https://www.ncbi.nlm.nih.gov/probe/?term=$1
  ncbi:
    example: '38'
    homepage: https://www.ncbi.nlm.nih.gov/sites/entrez?db=probe
    name: NCBI Probe database Public registry of nucleic acid reagents
    prefix: dbProbe
  prefix: dbprobe
  prefixcommons:
    description: The NCBI Probe Database is a public registry of nucleic acid reagents
      designed for use in a wide variety of biomedical research applications, together
      with information on reagent distributors, probe effectiveness, and computed
      sequence similarities.
    example: '1000000'
    homepage: http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=probe
    keywords:
    - nucleotide
    name: NCBI Probe database Public registry of nucleic acid reagents
    pattern: ^\d+$
    prefix: dbprobe
    uri_format: http://www.ncbi.nlm.nih.gov/genome/probe/reports/probereport.cgi?uid=$1
dbsnp:
  biocontext:
    prefix: dbSNP
    uri_format: http://www.ncbi.nlm.nih.gov/projects/SNP/snp_ref.cgi?rs=$1
  cellosaurus:
    category: Polymorphism and mutation databases
    homepage: https://www.ncbi.nlm.nih.gov/snp/
    name: Single Nucleotide Polymorphism database
    prefix: dbSNP
    uri_format: https://www.ncbi.nlm.nih.gov/snp/$1
  contact:
    email: pruitt@ncbi.nlm.nih.gov
    github: null
    name: Kim Dixon Pruitt
    orcid: 0000-0001-7950-1374
  domain: variant
  edam:
    description: Identifier of a dbSNP database entry.
    name: dbSNP
    obsolete: false
    prefix: '1106'
  fairsharing:
    abbreviation: dbSNP
    description: dbSNP contains human single nucleotide variations, microsatellites,
      and small-scale insertions and deletions along with publication, population
      frequency, molecular consequence, and genomic and RefSeq mapping information
      for both common variations and clinical mutations.
    homepage: https://www.ncbi.nlm.nih.gov/snp/
    license: http://opendatacommons.org/licenses/pddl/1.0
    name: Database of Single Nucleotide Polymorphism
    prefix: FAIRsharing.edxb58
    publications:
    - doi: 10.1093/nar/29.1.308
      pubmed_id: 11125122
      title: 'dbSNP: the NCBI database of genetic variation.'
    repository: https://github.com/ncbi/dbsnp/tree/master/tutorials
    subjects:
    - Life Science
  go:
    homepage: http://www.ncbi.nlm.nih.gov/projects/SNP
    name: NCBI dbSNP
    prefix: dbSNP
    uri_format: http://www.ncbi.nlm.nih.gov/projects/SNP/snp_ref.cgi?rs=$1
  hl7:
    description: 'In collaboration with the National Human Genome Research Institute,
      The National Center for Biotechnology Information has established the dbSNP
      database to serve as a central repository for both single base nucleotide substitutions
      and short deletion and insertion polymorphisms.  The entries in the dbSNP database
      can be used with the HL7 coded data type.  For example, in the HL7 messages
      specified according to the HL7 V2 Clinical Genomics Fully LOINC-Qualified Genetic
      Variation Model, dbSNP entries can be used to as the observation values for
      DNA sequence variation identifiers.  For example, OBX|1|CWE|48004-6^DNA Sequence
      Variation Identifier^LN||rs55538123^^dbSNPVersioning is identified by the build
      id.  A new build is released approximately every six months or every year. The
      latest build id is 130, and the dbSNP web query for built 130 was available
      on Apr 30, 2009.dbSNP is a database that can be used freely by the public.More
      information may be fouond at: http://www.ncbi.nlm.nih.gov/projects/SNP/'
    homepage: https://lhncbc.nlm.nih.gov/
    name: The Short Genetic Variations database
    organization: National Center for Biotechnology Information,National Center for
      Biotechnology Information
    preferred_prefix: dbSNP
    prefix: 2.16.840.1.113883.6.284
    status: Complete
  integbio:
    alt_name: The Single Nucleotide Polymorphism Database (dbSNP)
    description: dbSNP collects information on polymorphisms based on single and small-scale
      multi-base substitutions, including insertions and deletions, microsatelites,
      and non-polymorphic variants. Differences in the frequency of polymorphisms
      in a population can be visually compared for each SNP.
    fairsharing: biodbcore-000438
    homepage: http://www.ncbi.nlm.nih.gov/snp/
    information_keywords:
    - Sequence
    - Repository
    maintainer: NCBI (National Center for Biotechnology Information)
    name: dbSNP
    prefix: nbdc00206
    pubmeds:
    - '11125122'
    - '10592272'
    status: Active
    target_keywords:
    - Genetic variation
  mappings:
    biocontext: dbSNP
    cellosaurus: dbSNP
    edam: '1106'
    fairsharing: FAIRsharing.edxb58
    go: dbSNP
    hl7: 2.16.840.1.113883.6.284
    integbio: nbdc00206
    miriam: dbsnp
    n2t: dbsnp
    ncbi: dbSNP
    prefixcommons: dbsnp
    re3data: r3d100010652
    togoid: Dbsnp
    uniprot: DB-0013
    wikidata: P6861
  miriam:
    deprecated: false
    description: The dbSNP database is a repository for both single base nucleotide
      subsitutions and short deletion and insertion polymorphisms.
    homepage: https://www.ncbi.nlm.nih.gov/snp/
    id: '00000161'
    name: dbSNP
    namespaceEmbeddedInLui: false
    pattern: ^rs\d+$
    prefix: dbsnp
    providers:
    - code: sib
      description: SNP2TFBS
      homepage: https://epd.expasy.org/
      name: SNP2TFBS
      uri_format: https://epd.expasy.org/cgi-bin/snp2tfbs/snpviewer_form_parser.cgi?snpid=$1
    sampleId: rs121909098
    uri_format: https://www.ncbi.nlm.nih.gov/snp/$1
  n2t:
    description: The dbSNP database is a repository for both single base nucleotide
      subsitutions and short deletion and insertion polymorphisms.
    example: rs121909098
    homepage: https://www.ncbi.nlm.nih.gov/snp/
    name: dbSNP at NCBI
    namespaceEmbeddedInLui: false
    pattern: ^rs\d+$
    prefix: dbsnp
    uri_format: https://www.ncbi.nlm.nih.gov/snp/$1
  ncbi:
    example: '4647'
    homepage: https://www.ncbi.nlm.nih.gov/snp
    name: Variation database maintained at the NCBI.
    prefix: dbSNP
  prefix: dbsnp
  prefixcommons:
    description: The dbSNP database is a repository for both single base nucleotide
      subsitutions and short deletion and insertion polymorphisms.
    example: rs199422184
    homepage: http://www.ncbi.nlm.nih.gov/SNP/
    keywords:
    - genome
    name: Database of single nucleotide polymorphism
    pattern: ^rs\d+$
    prefix: dbsnp
    pubmed_ids:
    - '11125122'
    uri_format: http://www.ncbi.nlm.nih.gov/projects/SNP/snp_ref.cgi?rs=$1
  publications:
  - doi: 10.1093/nar/gkl1031
    pmc: PMC1781113
    pubmed: '17170002'
    title: Database resources of the National Center for Biotechnology Information
    year: 2006
  - doi: 10.1093/nar/29.1.308
    pmc: PMC29783
    pubmed: '11125122'
    title: 'dbSNP: the NCBI database of genetic variation'
    year: 2001
  re3data:
    description: 'The NCBI Short Genetic Variations database, commonly known as dbSNP,
      catalogs short variations in nucleotide sequences from a wide range of organisms.
      These variations include single nucleotide variations, short nucleotide insertions
      and deletions, short tandem repeats and microsatellites. Short Genetic Variations
      may be common, thus representing true polymorphisms, or they may be rare. Some
      rare human entries have additional information associated withthem, including
      disease associations, genotype information and allele origin, as some variations
      are somatic rather than germline events.

      ***NCBI will phase out support for non-human organism data in dbSNP and dbVar
      beginning on September 1, 2017***'
    doi: 10.17616/R3XG81
    homepage: https://www.ncbi.nlm.nih.gov/snp/
    name: dbSNP
    prefix: r3d100010652
    synonyms:
    - Database for short genetic variations
    - SNV
    xrefs:
      nif: 0000-02734
      omics: '00264'
  togoid:
    catalog: nbdc00206
    description: dbSNP collects information on polymorphisms based on single and small-scale
      multi-base substitutions, including insertions and deletions, microsatelites,
      and non-polymorphic variants. Differences in the frequency of polymorphisms
      in a population can be visually compared for each SNP.
    examples:
    - rs746303788
    - rs1407020249
    - rs374003162
    - rs4647297
    - rs549539526
    - rs1387864740
    - rs1177577242
    - rs769848663
    - rs16961655
    - rs79135400
    keywords:
    - Variant
    name: dbSNP
    pattern: ^(?rs\d+)$
    prefix: Dbsnp
    uri_format: http://identifiers.org/dbsnp/$1
  uniprot:
    abbreviation: dbSNP
    category: Genetic variation databases
    homepage: https://www.ncbi.nlm.nih.gov/snp/
    name: Database of single nucleotide polymorphism
    prefix: DB-0013
    publications:
    - doi: 10.1093/nar/gkaa892
      pubmed: '33095870'
    uri_format: https://www.ncbi.nlm.nih.gov/snp/$1
  wikidata:
    description: identifier used in dbSNP to uniquely identify a genetic variant
    example:
    - rs113488022
    - rs121913355
    - rs1488384581
    homepage: https://civicdb.org/home
    miriam: dbsnp
    name: dbSNP Reference SNP number
    prefix: P6861
    uri_format: https://www.ncbi.nlm.nih.gov/snp/$1
dbvar.study:
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: Studies in dbVar.
  example: nstd102
  homepage: https://www.ncbi.nlm.nih.gov/dbvar
  name: Database of Genomic Structural Variation - Study
  prefix: dbvar.study
  synonyms:
  - dbvar.studies
  uri_format: https://www.ncbi.nlm.nih.gov/dbvar/studies/$1
dbvar.variant:
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: Variants in dbVar.
  example: nsv3875336
  homepage: https://www.ncbi.nlm.nih.gov/dbvar
  name: Database of Genomic Structural Variation - Variant
  prefix: dbvar.variant
  synonyms:
  - dbvar.variants
  uri_format: https://www.ncbi.nlm.nih.gov/dbvar/variants/$1
dc:
  aberowl:
    description: "This file is imported by vivo-core-public-1.5.owl. It contains selected\
      \ terms from the \thttp://purl.org/dc/elements/1.1/ namespace that are included\
      \ in the vivo core ontology."
    download_owl: http://aber-owl.net/media/ontologies/dcelements/1/dcelements.owl
    homepage: http://sourceforge.net/apps/mediawiki/vivo/index.php?title=Ontology
    name: dcelements
    prefix: dcelements
    version: '1.5'
  biocontext:
    prefix: dc
    uri_format: http://purl.org/dc/elements/1.1/$1
  bioportal:
    contact:
      email: kdurante@stanford.edu
      name: Kim Durante
    description: The Dublin Core Schema is a small set of vocabulary terms that can
      be used to describe several kinds of resources. Dublin Core Metadata may be
      used for multiple purposes, from simple resource description, to combining metadata
      vocabularies of different metadata standards, to providing interoperability
      for metadata vocabularies in the Linked Data cloud and Semantic Web implementations.
    homepage: http://dublincore.org
    name: Dublin Core
    prefix: DC
  contact:
    email: kdurante@stanford.edu
    github: null
    name: Kim Durante
    orcid: 0000-0001-9052-2854
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  deprecated: true
  description: 'Metadata terms maintained by the Dublin Core Metadata Initiative,
    including properties, vocabulary encoding schemes, syntax encoding schemes, and
    classes.


    **Deprecation Notice**: While the `/elements/1.1/` namespace will be supported
    indefinitely, DCMI gently encourages use of the `/terms/` namespace (i.e., `dcterms`)
    ([source](https://www.dublincore.org/specifications/dublin-core/dcmi-terms/#section-3)).'
  example: contributor
  fairsharing:
    abbreviation: DCES
    description: 'The Dublin Metadata Element Set, which is often called Dublin Core
      (DC), is a standardized metadata scheme for description of any kind of resource
      such as documents in electronic and non-electronic form, digital materials (such
      as video, sound, images, etc) and composite media like web pages. Dublin Core
      Metadata may be used for multiple purposes, from simple resource description,
      to combining metadata vocabularies of different metadata standards, to providing
      interoperability for metadata vocabularies in the Linked Data cloud and Semantic
      Web implementations. Please note that this version of the specification for
      the Dublin Core Element Set 1.1 is somewhat out of date, although it is not
      officially deprecated. The DCMI Metadata Terms specification is linked to this
      record and is the current documentation that should be used for the Dublin Core
      Element Set 1.1. This document, an excerpt from the more comprehensive document
      "DCMI Metadata Terms" [DCTERMS] provides an abbreviated reference version of
      the fifteen element descriptions that have been formally endorsed in the following
      standards: ISO Standard 15836:2009 of February 2009 [ISO15836], ANSI/NISO Standard
      Z39.85-2012 of February 2013 [NISOZ3985], and IETF RFC 5013 of August 2007 [RFC5013].'
    domains:
    - Resource metadata
    - Annotation
    homepage: https://www.dublincore.org/specifications/dublin-core/dces/
    license: CC-BY-3.0
    name: Dublin Core Metadata Element Set
    prefix: FAIRsharing.3nx7t
    subjects:
    - Life Science
    - Biomedical Science
    - Subject Agnostic
    user_defined_tags:
    - Metadata standardization
  homepage: https://www.dublincore.org/specifications/dublin-core/dcmi-terms/
  lov:
    description: The Dublin Core Metadata Element Set is a vocabulary of fifteen properties
      for use in resource description. The name "Dublin" is due to its origin at a
      1995 invitational workshop in Dublin, Ohio; "core" because its elements are
      broad and generic, usable for describing a wide range of resources.
    homepage: http://dublincore.org/documents/dces
    keywords:
    - Metadata
    modified: '2012-06-14'
    name: Dublin Core Metadata Element Set
    prefix: dce
    uri_prefix: http://purl.org/dc/elements/1.1/$1
  mappings:
    aberowl: dcelements
    biocontext: dc
    bioportal: DC
    fairsharing: FAIRsharing.3nx7t
    lov: dce
    ols: dc
    zazuko: dc11
  name: Dublin Core Elements (1.1)
  ols:
    download_rdf: https://www.dublincore.org/specifications/dublin-core/dcmi-terms/dublin_core_elements.rdf
    prefix: dc
    uri_format: http://purl.org/dc/elements/1.1/$1
  preferred_prefix: dc
  prefix: dc
  synonyms:
  - dc.elements
  - dc11
  - dce
  - dcelem
  - elements
  uri_format: http://purl.org/dc/elements/1.1/$1
  zazuko:
    prefix: dc11
    uri_format: http://purl.org/dc/elements/1.1/$1
dc_cl:
  biocontext:
    prefix: DC_CL
  example: '0000003'
  mappings:
    biocontext: DC_CL
    obofoundry: dc_cl
  obofoundry:
    contact: Lindsay.Cowell@utsouthwestern.edu
    contact.label: Lindsay Cowell
    contact.orcid: 0000-0003-1617-8244
    deprecated: true
    domain: anatomy and development
    homepage: http://www.dukeontologygroup.org/Projects.html
    name: Dendritic cell
    prefix: dc_cl
  pattern: ^\d{7}$
  prefix: dc_cl
dcam:
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: A metadata model for Dublin Core metadata
  example: domainIncludes
  github_request_issue: 1677
  homepage: https://www.dublincore.org/specifications/dublin-core/abstract-model/2007-06-04/
  keywords:
  - metadata model
  - schema
  - semantic web
  logo: https://www.dublincore.org/images/dcmi_logo_v802.svg
  lov:
    description: An abstract model for Dublin Core metadata
    homepage: http://dublincore.org/documents/abstract-model/
    keywords:
    - General & Upper
    modified: '2012-06-14'
    name: DCMI Abstract Model
    prefix: dcam
    uri_prefix: http://purl.org/dc/dcam/$1
  mappings:
    lov: dcam
    zazuko: dcam
  name: Dublin Core Metadata Initiative Abstract Model
  part_of_database: dc
  prefix: dcam
  rdf_uri_format: http://purl.org/dc/dcam/$1
  uri_format: http://purl.org/dc/dcam/$1
  zazuko:
    prefix: dcam
    uri_format: http://purl.org/dc/dcam/$1
dcat:
  aberowl:
    description: DCAT is an RDF vocabulary designed to facilitate interoperability
      between data catalogs published on the Web.
    download_owl: http://aber-owl.net/media/ontologies/DCAT/2/dcat.owl
    homepage: https://www.w3.org/TR/vocab-dcat/
    name: Data Catalog Vocabulary
    prefix: DCAT
  biocontext:
    prefix: dcat
    uri_format: http://www.w3.org/ns/dcat#$1
  biolink:
    is_identifiers: false
    is_obo: false
    prefix: dcat
    uri_format: http://www.w3.org/ns/dcat#$1
  bioportal:
    contact:
      email: kdurante@stanford.edu
      name: kdurante
    description: DCAT is an RDF vocabulary designed to facilitate interoperability
      between data catalogs published on the Web.
    homepage: https://www.w3.org/TR/vocab-dcat/
    name: Data Catalog Vocabulary
    prefix: DCAT
  contact:
    email: kdurante@stanford.edu
    github: null
    name: Kim Durante
    orcid: 0000-0001-9052-2854
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: DCAT is an RDF vocabulary designed to facilitate interoperability between
    data catalogs published on the Web
  example: Dataset
  fairsharing:
    abbreviation: DCAT
    contact:
      email: phila@w3.org
      name: Phil Archer
      orcid: 0000-0002-4989-0601
    description: An RDF vocabulary designed to facilitate interoperability between
      data catalogs published on the Web. By using DCAT to describe datasets in data
      catalogs, publishers increase discoverability and enable applications easily
      to consume metadata from multiple catalogs. It further enables decentralized
      publishing of catalogs and facilitates federated dataset search across sites.
      Aggregated DCAT metadata can serve as a manifest file to facilitate digital
      preservation.
    homepage: https://www.w3.org/TR/vocab-dcat/
    name: Data Catalog Vocabulary
    prefix: FAIRsharing.h4j3qm
    publications: []
    repository: https://github.com/w3c/dxwg/
    subjects:
    - Data Management
    - Subject Agnostic
  homepage: https://www.w3.org/ns/dcat
  lov:
    description: DCAT is an RDF vocabulary designed to facilitate interoperability
      between data catalogs published on the Web
    homepage: http://www.w3.org/TR/vocab-dcat/
    keywords:
    - W3C Rec
    modified: '2020-02-04'
    name: Data Catalog Vocabulary
    prefix: dcat
    uri_prefix: http://www.w3.org/ns/dcat#$1
  mappings:
    aberowl: DCAT
    biocontext: dcat
    biolink: dcat
    bioportal: DCAT
    fairsharing: FAIRsharing.h4j3qm
    lov: dcat
    ols: dcat
    tib: dcat3
    zazuko: dcat
  name: Data Catalog
  ols:
    download_rdf: https://www.w3.org/ns/dcat.ttl
    prefix: dcat
    version: '3'
    version.iri: http://www.w3.org/ns/dcat3
  preferred_prefix: dcat
  prefix: dcat
  tib:
    description: DCAT is an RDF vocabulary designed to facilitate interoperability
      between data catalogs published on the Web. By using DCAT to describe datasets
      in data catalogs, publishers increase discoverability and enable applications
      easily to consume metadata from multiple catalogs. It further enables decentralized
      publishing of catalogs and facilitates federated dataset search across sites.
      Aggregated DCAT metadata can serve as a manifest file to facilitate digital
      preservation. DCAT is defined at http://www.w3.org/TR/vocab-dcat/. Any variance
      between that normative document and this schema is an error in this schema.
    download_rdf: https://www.w3.org/ns/dcat3.ttl
    homepage: https://www.w3.org/TR/vocab-dcat-3/
    keywords:
    - TIB
    - ESS
    - computer science
    name: The data catalog vocabulary
    prefix: dcat3
    tracker: https://github.com/w3c/dxwg/issues
    uri_format: http://www.w3.org/ns/dcat#$1
    version.iri: http://www.w3.org/ns/dcat3
  uri_format: http://www.w3.org/ns/dcat#$1
  zazuko:
    prefix: dcat
    uri_format: http://www.w3.org/ns/dcat#$1
dcterms:
  aberowl:
    description: This file is imported by vivo-core-public-1.5.owl. It contains terms
      from the http://purl.org/dc/terms/ namespace that are included in the vivo ontology.
    download_owl: http://aber-owl.net/media/ontologies/dcterms/1/dcterms.owl
    homepage: http://sourceforge.net/apps/mediawiki/vivo/index.php?title=Ontology
    name: dcterms
    prefix: dcterms
    version: '1.5'
  biocontext:
    prefix: dcterms
    uri_format: http://purl.org/dc/terms/$1
  biolink:
    is_identifiers: false
    is_obo: false
    prefix: dct
    uri_format: http://purl.org/dc/terms/$1
  bioportal:
    contact:
      email: futo@stanford.edu
      name: Michelle Futornick
    description: DCMI properties in the /terms/ namespace
    homepage: http://dublincore.org/documents/dcmi-terms/
    name: 'DCMI Metadata Terms: properties in /terms/ namespace'
    prefix: DCTERMS
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: This document is an up-to-date specification of all metadata terms
    maintained by the Dublin Core Metadata Initiative, including properties, vocabulary
    encoding schemes, syntax encoding schemes, and classes.
  download_rdf: https://www.dublincore.org/specifications/dublin-core/dcmi-terms/dublin_core_terms.ttl
  example: title
  fairsharing:
    abbreviation: DCMI Metadata Terms
    description: This document is an up-to-date, authoritative specification of all
      metadata terms maintained by the Dublin Core Metadata Initiative, including
      properties, vocabulary encoding schemes, syntax encoding schemes, and classes.
      Included are the fifteen terms of the Dublin Core Metadata Element Set, which
      have also been published as a separate specification.
    domains:
    - Resource metadata
    homepage: https://www.dublincore.org/specifications/dublin-core/dcmi-terms/
    license: CC-BY-3.0
    name: Dublin Core Metadata Initiative Terms
    prefix: FAIRsharing.9vtwjs
    subjects:
    - Subject Agnostic
    user_defined_tags:
    - Metadata standardization
  homepage: https://www.dublincore.org/specifications/dublin-core/dcmi-terms/
  lov:
    description: an up-to-date specification of all metadata terms maintained by the
      Dublin Core Metadata Initiative, including properties, vocabulary encoding schemes,
      syntax encoding schemes, and classes.
    homepage: http://dublincore.org/documents/dcmi-terms
    keywords:
    - Metadata
    modified: '2012-06-14'
    name: DCMI Metadata Terms
    prefix: dcterms
    uri_prefix: http://purl.org/dc/terms/$1
  mappings:
    aberowl: dcterms
    biocontext: dcterms
    biolink: dct
    bioportal: DCTERMS
    fairsharing: FAIRsharing.9vtwjs
    lov: dcterms
    ols: dcterms
    tib: dcterms
    zazuko: dcterms
  name: Dublin Core Metadata Initiative Terms
  ols:
    download_rdf: https://www.dublincore.org/specifications/dublin-core/dcmi-terms/dublin_core_terms.rdf
    prefix: dcterms
    uri_format: http://purl.org/dc/terms/$1
  preferred_prefix: dcterms
  prefix: dcterms
  synonyms:
  - dc.terms
  - dct
  - terms
  tib:
    description: This document is an up-to-date specification of all metadata terms
      maintained by the Dublin Core Metadata Initiative, including properties, vocabulary
      encoding schemes, syntax encoding schemes, and classes.
    homepage: http://dublincore.org/specifications/dublin-core/dcmi-terms/2020-01-20/
    keywords:
    - NFDI4ING
    - Digital Planning and Construction
    - FID BAUdigital
    - ESS
    name: DCMI Metadata Terms
    prefix: dcterms
    uri_format: http://purl.org/dc/terms/$1
  uri_format: http://purl.org/dc/terms/$1
  zazuko:
    prefix: dcterms
    uri_format: http://purl.org/dc/terms/$1
dctypes:
  aberowl:
    description: The DCMI Type Vocabulary provides a general, cross-domain list of
      approved terms that may be used as values for the Resource Type element to identify
      the genre of a resource
    download_owl: http://aber-owl.net/media/ontologies/DCMITYPE/4/dcmitype.owl
    homepage: http://dublincore.org/documents/dcmi-type-vocabulary
    name: DCMI Type Vocabulary
    prefix: DCMITYPE
  biocontext:
    prefix: dctypes
    uri_format: http://purl.org/dc/dcmitype/$1
  bioportal:
    contact:
      email: kdurante@stanford.edu
      name: Kim Durante
    description: The DCMI Type Vocabulary provides a general, cross-domain list of
      approved terms that may be used as values for the Resource Type element to identify
      the genre of a resource
    homepage: http://dublincore.org/documents/dcmi-type-vocabulary
    name: DCMI Type Vocabulary
    prefix: DCMITYPE
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: This document is an up-to-date specification of all metadata terms
    maintained by the Dublin Core Metadata Initiative, including properties, vocabulary
    encoding schemes, syntax encoding schemes, and classes.
  example: Collection
  homepage: https://dublincore.org/specifications/dublin-core/dcmi-terms/
  mappings:
    aberowl: DCMITYPE
    biocontext: dctypes
    bioportal: DCMITYPE
    zazuko: dcmitype
  name: Dublin Core Types
  part_of_database: dc
  preferred_prefix: dctypes
  prefix: dctypes
  synonyms:
  - dcmitype
  - dcmitypes
  uri_format: http://purl.org/dc/dcmitype/$1
  zazuko:
    prefix: dcmitype
    uri_format: http://purl.org/dc/dcmitype/$1
ddanat:
  aberowl:
    description: A structured controlled vocabulary of the anatomy of the slime-mold
      Dictyostelium discoideum
    download_owl: http://aber-owl.net/media/ontologies/DDANAT/134/ddanat.owl
    homepage: http://dictybase.org/
    name: Dictyostelium discoideum anatomy
    prefix: DDANAT
  biocontext:
    prefix: DDANAT
  bioportal:
    contact:
      email: pfey@northwestern.edu
      name: Petra Fey
    description: A structured controlled vocabulary of the anatomy of the slime-mould
      <i>Dictyostelium discoideum</i>.
    homepage: http://dictybase.org/
    name: Dictyostelium Discoideum Anatomy Ontology
    prefix: DDANAT
    publications:
    - http://www.biomedcentral.com/1471-2164/9/130
    version: '1.19'
  example: '0000006'
  fairsharing:
    abbreviation: DDANAT
    contact:
      email: pgaudet@northwestern.edu
      name: Pascale Gaudet
      orcid: 0000-0003-1813-6857
    description: 'The Dictyostelium Anatomy Ontology ontology describes the anatomy
      of the slime mold. It defines the structural makeup of Dictyostelium and its
      composing parts including the different cell types, throughout its life cycle.
      It has two main goals: (1) promote the consistent annotation of Dictyostelium-specific
      events, such as phenotypes and gene expression information; and (2) encourage
      researchers to use the same terms with the same intended meaning.'
    domains:
    - cell
    homepage: http://dictybase.org/Dicty_Info/dicty_anatomy_ontology.html
    name: Dictyostelium Anatomy Ontology
    prefix: FAIRsharing.z656ab
    publications:
    - doi: 10.1186/1471-2164-9-130
      pubmed: '18366659'
      title: An anatomy ontology to represent biological knowledge in Dictyostelium
        discoideum
      year: 2008
    repository: https://github.com/dictyBase
    subjects:
    - Life Science
    - Anatomy
  go:
    homepage: http://dictybase.org/Dicty_Info/dicty_anatomy_ontology.html
    name: Dictyostelium discoideum anatomy
    prefix: DDANAT
  logo: http://dictybase.org/inc/images/logo.gif
  mappings:
    aberowl: DDANAT
    biocontext: DDANAT
    bioportal: DDANAT
    fairsharing: FAIRsharing.z656ab
    go: DDANAT
    obofoundry: ddanat
    ols: ddanat
    ontobee: DDANAT
    prefixcommons: ddanat
    wikidata.entity: Q81661582
  obofoundry:
    contact: pfey@northwestern.edu
    contact.github: pfey03
    contact.label: Petra Fey
    contact.orcid: 0000-0002-4532-2703
    deprecated: false
    description: A structured controlled vocabulary of the anatomy of the slime-mold
      Dictyostelium discoideum
    domain: anatomy and development
    download.obo: http://purl.obolibrary.org/obo/ddanat.obo
    download.owl: http://purl.obolibrary.org/obo/ddanat.owl
    homepage: http://dictybase.org/
    license: CC0 1.0
    license.url: https://creativecommons.org/publicdomain/zero/1.0/
    name: Dictyostelium discoideum anatomy
    preferredPrefix: DDANAT
    prefix: ddanat
    publications:
    - id: https://www.ncbi.nlm.nih.gov/pubmed/18366659
      title: An anatomy ontology to represent biological knowledge in Dictyostelium
        discoideum
    repository: https://github.com/dictyBase/migration-data
    twitter: dictybase
  ols:
    description: A structured controlled vocabulary of anatomies of the slime-mold
      Dictyostelium discoideum.
    download_owl: http://purl.obolibrary.org/obo/ddanat.owl
    homepage: http://dictybase.org/
    name: Dicty Anatomy Ontology (DDANAT)
    prefix: ddanat
    tracker: https://github.com/dictyBase/migration-data/issues
  ontobee:
    library: Library
    name: Dictyostelium discoideum anatomy
    prefix: DDANAT
  pattern: ^\d{7}$
  prefix: ddanat
  prefixcommons:
    bioportal: '1008'
    description: A structured controlled vocabulary of the anatomy of the slime-mould
      <i>Dictyostelium discoideum</i>.
    example: DDANAT_0010081
    homepage: http://dictybase.org/
    keywords:
    - obo
    - anatomy
    - slime-mould
    name: Dictyostelium discoideum anatomy
    pattern: ^DDANAT_\d+$
    prefix: ddanat
    synonyms:
    - ddana
  publications:
  - doi: 10.1186/1471-2164-9-130
    pmc: PMC2323390
    pubmed: '18366659'
    title: An anatomy ontology to represent biological knowledge in Dictyostelium
      discoideum
    year: 2008
  uri_format: http://purl.obolibrary.org/obo/DDANAT_$1
ddc:
  bartoc:
    abbreviation: DDC
    description: The Dewey Decimal Classification (DDC) system, devised by library
      pioneer Melvil Dewey in the 1870s and owned by OCLC since 1988, provides a dynamic
      structure for the organization of library collections. Now in its 23rd edition,
      and available in print and Web versions, the DDC is the world's most widely
      used library classification system.
    homepage: http://www.oclc.org/dewey/
    license: http://rightsstatements.org/vocab/InC/1.0
    name: Dewey Decimal Classification
    pattern: ^(([0-9][0-9]?|[0-9]{3}(-[0-9]{3})?|[0-9]{3}(-[0-9]{3}(:[0-9]+)?)?|[0-9]{3}\.[0-9]+(-[0-9]{3}\.[0-9]+(:[0-9]+)?)?|T[1-9][A-Z]?--[0-9]+(-T[1-9][A-Z]?--[0-9]+(:[0-9]+)?)?|[1-9][A-Z]?--[0-9]+(-[1-9][A-Z]?--[0-9]+(:[0-9]+)?)?)?)$
    prefix: '241'
    uri_format: http://dewey.info/class/$1/e23/
    wikidata_database: Q48460
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  example: '325.4'
  example_extras:
  - 325.4-325.9
  - '325'
  - '32'
  - '3'
  mappings:
    bartoc: '241'
    wikidata.entity: Q48460
  prefix: ddc
ddi:
  aberowl:
    description: The goal of DDI project is to develop an ontology for the description
      of drug discovery investigations. DDI aims to follow to the OBO (Open Biomedical
      Ontologies) Foundry principles, uses relations laid down in the OBO Relation
      Ontology, and be compliant with Ontology for biomedical investigations (OBI).
    download_owl: http://aber-owl.net/media/ontologies/DDI/2/ddi.owl
    homepage: http://purl.org/ddi/home
    name: Ontology for Drug Discovery Investigations
    prefix: DDI
    version: $Revision$
  bioportal:
    contact:
      email: soldatova.larisa@gmail.com
      name: Larisa Soldatova; Da Qi (ddq@aber.ac.uk)
    description: The goal of DDI project is to develop an ontology for the description
      of drug discovery investigations. DDI aims to follow to the OBO (Open Biomedical
      Ontologies) Foundry principles, uses relations laid down in the OBO Relation
      Ontology, and be compliant with Ontology for biomedical investigations (OBI).
    homepage: http://purl.org/ddi/home
    name: Ontology for Drug Discovery Investigations
    prefix: DDI
    version: $Revision$
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: A set of controlled vocabularies in the Data Documentation Initiative,
    each of which has its own code.
  example: Instrument
  fairsharing:
    abbreviation: DDI
    contact:
      email: soldatova.larisa@gmail.com
      name: Larisa Soldatova
      orcid: 0000-0001-6489-3029
    description: The goal of DDI project is to develop an ontology for the description
      of drug discovery investigations. The Pharmaceutical industry is an information
      based industry. The aim of DDI is to add value to the information generated
      in the drug pipeline by making the information easier to reuse, integrate, curate,
      retrieve, and reason with. DDI aims to follow to the Open Biomedical Ontologies
      Foundry (OBO) principles, to use relations laid down in the OBO Relation Ontology,
      and to be compliant with the Ontology for biomedical investigations (OBI).
    homepage: https://code.google.com/p/ddi-ontology/
    name: Ontology for Drug Discovery Investigations
    prefix: FAIRsharing.pf2qyq
    subjects:
    - Drug Discovery
    - Biomedical Science
  github_request_issue: 1632
  homepage: https://rdf-vocabulary.ddialliance.org/
  keywords:
  - registry
  mappings:
    aberowl: DDI
    bioportal: DDI
    fairsharing: FAIRsharing.pf2qyq
  name: Data Documentation Initiative Vocabulary
  prefix: ddi
  uri_format: http://rdf-vocabulary.ddialliance.org/lifecycle#$1
ddi.aggregationmethod:
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: 'Identifies the type of aggregation used to combine related categories,
    usually within a common branch of a hierarchy, to provide information at a broader
    level than the level at which detailed observations are taken. (From: The OECD
    Glossary of Statistical Terms)'
  example: Sum
  homepage: https://vocabularies.cessda.eu/vocabulary/AggregationMethod
  license: CC-BY-4.0
  name: Aggregation Method
  owners:
  - name: Data Documentation Initiative Alliance
    partnered: false
    ror: 015em2733
    wikidata: null
  part_of_database: ddi
  prefix: ddi.aggregationmethod
  uri_format: https://vocabularies.cessda.eu/vocabulary/AggregationMethod?lang=en#code_$1
  version: 1.1.2
ddi.analysisunit:
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: Describes the entity being analyzed in the study or variable. This
    vocabulary can also be used to describe the unit of observation, which is the
    unit being observed, or from which data are collected. The unit of observation
    can be the same as, or different from the unit of analysis.
  example: Individual
  homepage: https://vocabularies.cessda.eu/vocabulary/AnalysisUnit
  license: CC-BY-4.0
  name: Analysis Unit
  owners:
  - name: Data Documentation Initiative Alliance
    partnered: false
    ror: 015em2733
    wikidata: null
  part_of_database: ddi
  prefix: ddi.analysisunit
  uri_format: https://vocabularies.cessda.eu/vocabulary/AnalysisUnit?lang=en#code_$1
  version: 2.1.3
ddi.characterset:
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: Standard set of characters upon which many character encodings are
    based (Wikipedia).
  example: ASCII
  homepage: https://vocabularies.cessda.eu/vocabulary/CharacterSet
  license: CC-BY-4.0
  name: Character Set
  owners:
  - name: Data Documentation Initiative Alliance
    partnered: false
    ror: 015em2733
    wikidata: null
  part_of_database: ddi
  prefix: ddi.characterset
  uri_format: https://vocabularies.cessda.eu/vocabulary/CharacterSet?lang=en#code_$1
  version: 1.0.0
ddi.commonalitytype:
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: Describes the degree of similarity between two items or schemes (collections
    of items).
  example: Identical
  homepage: https://vocabularies.cessda.eu/vocabulary/CommonalityType
  license: CC-BY-4.0
  name: Commonality Type
  owners:
  - name: Data Documentation Initiative Alliance
    partnered: false
    ror: 015em2733
    wikidata: null
  part_of_database: ddi
  prefix: ddi.commonalitytype
  uri_format: https://vocabularies.cessda.eu/vocabulary/CommonalityType?lang=en#code_$1
  version: 1.0.2
ddi.contributorrole:
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: A classification of contributor roles.
  example: ProjectOrStudyDesign
  homepage: https://vocabularies.cessda.eu/vocabulary/ContributorRole
  license: CC-BY-4.0
  name: Contributor Role
  owners:
  - name: Data Documentation Initiative Alliance
    partnered: false
    ror: 015em2733
    wikidata: null
  part_of_database: ddi
  prefix: ddi.contributorrole
  uri_format: https://vocabularies.cessda.eu/vocabulary/ContributorRole?lang=en#code_$1
  version: 1.0.3
ddi.datasourcetype:
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: Includes a typology of data sources.
  example: RegistersRecordsAccounts
  homepage: https://vocabularies.cessda.eu/vocabulary/DataSourceType
  license: CC-BY-4.0
  name: Data Source Type
  owners:
  - name: Data Documentation Initiative Alliance
    partnered: false
    ror: 015em2733
    wikidata: null
  part_of_database: ddi
  prefix: ddi.datasourcetype
  uri_format: https://vocabularies.cessda.eu/vocabulary/DataSourceType?lang=en#code_$1
  version: 1.0.2
ddi.datatype:
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: Identifies the type of data, which has a bearing on the acceptable
    data values, the operations that can be performed with the data, and the ways
    in which the data are stored.
  example: String
  homepage: https://vocabularies.cessda.eu/vocabulary/DataType
  license: CC-BY-4.0
  name: Data Type
  owners:
  - name: Data Documentation Initiative Alliance
    partnered: false
    ror: 015em2733
    wikidata: null
  part_of_database: ddi
  prefix: ddi.datatype
  uri_format: https://vocabularies.cessda.eu/vocabulary/DataType?lang=en#code_$1
  version: 1.1.2
ddi.datetype:
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: Specifies the type of date.
  example: DateTime
  homepage: https://vocabularies.cessda.eu/vocabulary/DateType
  license: CC-BY-4.0
  name: Date Type
  owners:
  - name: Data Documentation Initiative Alliance
    partnered: false
    ror: 015em2733
    wikidata: null
  part_of_database: ddi
  prefix: ddi.datetype
  uri_format: https://vocabularies.cessda.eu/vocabulary/DateType?lang=en#code_$1
  version: 1.1.2
ddi.generaldataformat:
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: Describes the physical format(s) of the data documented in the logical
    product(s) of a study unit.
  example: Numeric
  homepage: https://vocabularies.cessda.eu/vocabulary/GeneralDataFormat
  license: CC-BY-4.0
  name: General Data Format
  owners:
  - name: Data Documentation Initiative Alliance
    partnered: false
    ror: 015em2733
    wikidata: null
  part_of_database: ddi
  prefix: ddi.generaldataformat
  uri_format: https://vocabularies.cessda.eu/vocabulary/GeneralDataFormat?lang=en#code_$1
  version: 2.0.3
ddi.languageproficiency:
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: Describes the level of proficiency of an individual in a natural language.
  example: Native
  homepage: https://vocabularies.cessda.eu/vocabulary/LanguageProficiency
  license: CC-BY-4.0
  name: Language Proficiency
  owners:
  - name: Data Documentation Initiative Alliance
    partnered: false
    ror: 015em2733
    wikidata: null
  part_of_database: ddi
  prefix: ddi.languageproficiency
  uri_format: https://vocabularies.cessda.eu/vocabulary/LanguageProficiency?lang=en#code_$1
  version: 1.0.2
ddi.lifecycleeventtype:
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: Specifies the event happening over the data life cycle that is considered
    significant enough to document.
  example: StudyProposal
  homepage: https://vocabularies.cessda.eu/vocabulary/LifecycleEventType
  license: CC-BY-4.0
  name: Lifecycle Event Type
  owners:
  - name: Data Documentation Initiative Alliance
    partnered: false
    ror: 015em2733
    wikidata: null
  part_of_database: ddi
  prefix: ddi.lifecycleeventtype
  uri_format: https://vocabularies.cessda.eu/vocabulary/LifecycleEventType?lang=en#code_$1
  version: 1.0.2
ddi.modeofcollection:
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: The procedure, technique, or mode of inquiry used to attain the data.
  example: Interview
  homepage: https://vocabularies.cessda.eu/vocabulary/ModeOfCollection
  license: CC-BY-4.0
  name: Mode Of Collection
  owners:
  - name: Data Documentation Initiative Alliance
    partnered: false
    ror: 015em2733
    wikidata: null
  part_of_database: ddi
  prefix: ddi.modeofcollection
  uri_format: https://vocabularies.cessda.eu/vocabulary/ModeOfCollection?lang=en#code_$1
  version: 5.0.0
ddi.numerictype:
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: Specifies the type of numeric data.
  example: Integer
  homepage: https://vocabularies.cessda.eu/vocabulary/NumericType
  license: CC-BY-4.0
  name: Numeric Type
  owners:
  - name: Data Documentation Initiative Alliance
    partnered: false
    ror: 015em2733
    wikidata: null
  part_of_database: ddi
  prefix: ddi.numerictype
  uri_format: https://vocabularies.cessda.eu/vocabulary/NumericType?lang=en#code_$1
  version: 1.1.0
ddi.responseunit:
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: Indicates the entity that provided the information carried by the variable.
  example: Self
  homepage: https://vocabularies.cessda.eu/vocabulary/ResponseUnit
  license: CC-BY-4.0
  name: Response Unit
  owners:
  - name: Data Documentation Initiative Alliance
    partnered: false
    ror: 015em2733
    wikidata: null
  part_of_database: ddi
  prefix: ddi.responseunit
  uri_format: https://vocabularies.cessda.eu/vocabulary/ResponseUnit?lang=en#code_$1
  version: 1.0.2
ddi.samplingprocedure:
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: A typology of sampling methods.
  example: TotalUniverseCompleteEnumeration
  homepage: https://vocabularies.cessda.eu/vocabulary/SamplingProcedure
  license: CC-BY-4.0
  name: Sampling Procedure
  owners:
  - name: Data Documentation Initiative Alliance
    partnered: false
    ror: 015em2733
    wikidata: null
  part_of_database: ddi
  prefix: ddi.samplingprocedure
  uri_format: https://vocabularies.cessda.eu/vocabulary/SamplingProcedure?lang=en#code_$1
  version: 2.0.1
ddi.softwarepackage:
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: Indicates the statistical software package used in the production/processing/dissemination
    of the data. Data collection software is not covered in this list.
  example: AcaStat
  homepage: https://vocabularies.cessda.eu/vocabulary/SoftwarePackage
  license: CC-BY-4.0
  name: Software Package
  owners:
  - name: Data Documentation Initiative Alliance
    partnered: false
    ror: 015em2733
    wikidata: null
  part_of_database: ddi
  prefix: ddi.softwarepackage
  uri_format: https://vocabularies.cessda.eu/vocabulary/SoftwarePackage?lang=en#code_$1
  version: 1.0.1
ddi.summarystatistictype:
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: Specifies the type of summary statistic. Summary statistics are a single
    number representation of the characteristics of a set of values.
  example: ArithmeticMean
  homepage: https://vocabularies.cessda.eu/vocabulary/SummaryStatisticType
  license: CC-BY-4.0
  name: Summary Statistic Type
  owners:
  - name: Data Documentation Initiative Alliance
    partnered: false
    ror: 015em2733
    wikidata: null
  part_of_database: ddi
  prefix: ddi.summarystatistictype
  uri_format: https://vocabularies.cessda.eu/vocabulary/SummaryStatisticType?lang=en#code_$1
  version: 2.1.2
ddi.timemethod:
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: Describes the time dimension of the data collection.
  example: Longitudinal
  homepage: https://vocabularies.cessda.eu/vocabulary/TimeMethod
  license: CC-BY-4.0
  name: Time Method
  owners:
  - name: Data Documentation Initiative Alliance
    partnered: false
    ror: 015em2733
    wikidata: null
  part_of_database: ddi
  prefix: ddi.timemethod
  uri_format: https://vocabularies.cessda.eu/vocabulary/TimeMethod?lang=en#code_$1
  version: 1.2.3
ddi.timezone:
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: Time zone specification as an offset from UTC (Coordinated Universal
    Time) in terms of hours and minutes.
  example: '-12:00'
  homepage: https://vocabularies.cessda.eu/vocabulary/TimeZone
  license: CC-BY-4.0
  name: Time Zone
  owners:
  - name: Data Documentation Initiative Alliance
    partnered: false
    ror: 015em2733
    wikidata: null
  part_of_database: ddi
  prefix: ddi.timezone
  uri_format: https://vocabularies.cessda.eu/vocabulary/TimeZone?lang=en#code_$1
  version: 1.0.0
ddi.typeofaddress:
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: Identifies the type of address entered as contact information for an
    individual or an organization.
  example: Mailing
  homepage: https://vocabularies.cessda.eu/vocabulary/TypeOfAddress
  license: CC-BY-4.0
  name: Type of Address
  owners:
  - name: Data Documentation Initiative Alliance
    partnered: false
    ror: 015em2733
    wikidata: null
  part_of_database: ddi
  prefix: ddi.typeofaddress
  uri_format: https://vocabularies.cessda.eu/vocabulary/TypeOfAddress?lang=en#code_$1
  version: 1.1.0
ddi.typeofconceptgroup:
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: Specifies the rationale for creating a concept group.
  example: Administrative
  homepage: https://vocabularies.cessda.eu/vocabulary/TypeOfConceptGroup
  license: CC-BY-4.0
  name: Type of Concept Group
  owners:
  - name: Data Documentation Initiative Alliance
    partnered: false
    ror: 015em2733
    wikidata: null
  part_of_database: ddi
  prefix: ddi.typeofconceptgroup
  uri_format: https://vocabularies.cessda.eu/vocabulary/TypeOfConceptGroup?lang=en#code_$1
  version: 1.0.2
ddi.typeoffrequency:
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: Indicates the frequency of data collection events.
  example: Continuous
  homepage: https://vocabularies.cessda.eu/vocabulary/TypeOfFrequency
  license: CC-BY-4.0
  name: Type of Frequency
  owners:
  - name: Data Documentation Initiative Alliance
    partnered: false
    ror: 015em2733
    wikidata: null
  part_of_database: ddi
  prefix: ddi.typeoffrequency
  uri_format: https://vocabularies.cessda.eu/vocabulary/TypeOfFrequency?lang=en#code_$1
  version: 1.0.2
ddi.typeofinstrument:
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: Includes a typology of data collection instruments.
  example: Questionnaire
  homepage: https://vocabularies.cessda.eu/vocabulary/TypeOfInstrument
  license: CC-BY-4.0
  name: Type of Instrument
  owners:
  - name: Data Documentation Initiative Alliance
    partnered: false
    ror: 015em2733
    wikidata: null
  part_of_database: ddi
  prefix: ddi.typeofinstrument
  uri_format: https://vocabularies.cessda.eu/vocabulary/TypeOfInstrument?lang=en#code_$1
  version: 1.1.2
ddi.typeofnote:
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: Includes a typology of notes.
  example: Processing
  homepage: https://vocabularies.cessda.eu/vocabulary/TypeOfNote
  license: CC-BY-4.0
  name: Type of Note
  owners:
  - name: Data Documentation Initiative Alliance
    partnered: false
    ror: 015em2733
    wikidata: null
  part_of_database: ddi
  prefix: ddi.typeofnote
  uri_format: https://vocabularies.cessda.eu/vocabulary/TypeOfNote?lang=en#code_$1
  version: 1.1.1
ddi.typeoftelephone:
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: Identifies the type of telephone entered as contact information for
    an individual or an organization.
  example: Fixed
  homepage: https://vocabularies.cessda.eu/vocabulary/TypeOfTelephone
  license: CC-BY-4.0
  name: Type of Telephone
  owners:
  - name: Data Documentation Initiative Alliance
    partnered: false
    ror: 015em2733
    wikidata: null
  part_of_database: ddi
  prefix: ddi.typeoftelephone
  uri_format: https://vocabularies.cessda.eu/vocabulary/TypeOfTelephone?lang=en#code_$1
  version: 1.0.0
ddi.typeoftranslationmethod:
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: A typology of methods used to translate data collection instruments,
    including questionnaires, individual questions, measurements, data capture flows,
    etc.
  example: SingleTranslation
  homepage: https://vocabularies.cessda.eu/vocabulary/TypeOfTranslationMethod
  license: CC-BY-4.0
  name: Type of Translation Method
  owners:
  - name: Data Documentation Initiative Alliance
    partnered: false
    ror: 015em2733
    wikidata: null
  part_of_database: ddi
  prefix: ddi.typeoftranslationmethod
  uri_format: https://vocabularies.cessda.eu/vocabulary/TypeOfTranslationMethod?lang=en#code_$1
  version: 1.0.0
ddinter.drug:
  contact:
    email: oriental-cds@163.com
    github: null
    name: Dongsheng Cao
    orcid: 0000-0003-3604-3785
  contributor:
    email: smoxon@lbl.gov
    github: sierra-moxon
    name: Sierra Moxon
    orcid: 0000-0002-8719-7760
  description: Ddinter is a comprehensive, professional, and open-access database
    specific to drug-drug interactions. it provides abundant annotations for each
    ddi association including mechanism description, risk levels, management strategies,
    alternative medications, etc. to improve clinical decision-making and patient
    safety.
  example: DDInter20
  github_request_issue: 492
  homepage: http://ddinter.scbdd.com
  keywords:
  - chemistry
  - drugs
  - relationships
  license: CC BY-NC-SA 4.0
  name: Curated Drug-Drug Interactions Database - Drug
  pattern: ^DDInter\d+$
  prefix: ddinter.drug
  reviewer:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  uri_format: http://ddinter.scbdd.com/ddinter/drug-detail/$1
ddinter.interaction:
  contact:
    email: oriental-cds@163.com
    github: null
    name: Dongsheng Cao
    orcid: 0000-0003-3604-3785
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: Ddinter is a comprehensive, professional, and open-access database
    specific to drug-drug interactions. it provides abundant annotations for each
    ddi association including mechanism description, risk levels, management strategies,
    alternative medications, etc. to improve clinical decision-making and patient
    safety.
  example: '1122888'
  github_request_issue: 492
  homepage: http://ddinter.scbdd.com
  keywords:
  - chemistry
  - drug-drug interactions
  - drugs
  - relationships
  license: CC BY-NC-SA 4.0
  name: Curated Drug-Drug Interactions Database - Interaction
  pattern: ^\d+$
  prefix: ddinter.interaction
  uri_format: http://ddinter.scbdd.com/ddinter/interact/$1
ddpheno:
  aberowl:
    description: A structured controlled vocabulary of phenotypes of the slime-mould
      <i>Dictyostelium discoideum</i>.
    download_owl: http://aber-owl.net/media/ontologies/DDPHENO/165/ddpheno.owl
    homepage: http://dictybase.org/
    name: Dictyostelium discoideum phenotype ontology
    prefix: DDPHENO
  biocontext:
    prefix: DDPHENO
  bioportal:
    contact:
      email: pfey@northwestern.edu
      name: Petra Fey
    description: A structured controlled vocabulary of phenotypes of the slime-mould
      Dictyostelium discoideum.
    homepage: http://dictybase.org/
    name: Dictyostelium Discoideum Phenotype Ontology
    prefix: DDPHENO
  download_json: http://purl.obolibrary.org/obo/ddpheno.json
  download_obo: https://raw.githubusercontent.com/obophenotype/dicty-phenotype-ontology/master/ddpheno.obo
  example: '0001417'
  fairsharing:
    abbreviation: DDPHENO
    contact:
      email: pfey@northwestern.edu
      name: Petra Fey
      orcid: 0000-0002-4532-2703
    description: 'The Dictyostelium Phenotype Ontology (DDPHENO) is a structured controlled
      vocabulary of phenotypes of the slime-mould Dictyostelium discoideum. DDPHENO
      is a hierarchical controlled vocabulary used for annotating strains with phenotypes,
      and are required when annotating phenotypes within the dictyBase. The phenotype
      ontology consists of two composite terms: (1) the anatomical part or the biological
      process changed in the mutant, and (2) a quality describing that modification.
      For example, a ‘delayed aggregation’ phenotype qualifies the ‘aggregation’ (biological
      process) as being ‘delayed’, or the ‘decreased spore size’ qualifies the ‘spore’
      to be of ‘decreased size’.'
    domains:
    - phenotype
    - microbe-host interaction phenotype
    homepage: https://github.com/obophenotype/dicty-phenotype-ontology
    license: https://creativecommons.org/licenses/by/1.0
    name: Dictyostelium Phenotype Ontology
    prefix: FAIRsharing.9c1p18
    publications:
    - doi: 10.1007/978-1-62703-302-2_4
      pubmed: '23494302'
      title: 'One stop shop for everything Dictyostelium: dictyBase and the Dicty
        Stock Center in 2012'
      year: 2013
    repository: https://github.com/obophenotype/dicty-phenotype-ontology/issues
    subjects:
    - Life Science
    - Soil Science
    - Anatomy
    - Phenomics
    - Microbial Ecology
    - Developmental Biology
  mappings:
    aberowl: DDPHENO
    biocontext: DDPHENO
    bioportal: DDPHENO
    fairsharing: FAIRsharing.9c1p18
    obofoundry: ddpheno
    ols: ddpheno
    ontobee: DDPHENO
    wikidata.entity: Q81661585
  obofoundry:
    contact: pfey@northwestern.edu
    contact.github: pfey03
    contact.label: Petra Fey
    contact.orcid: 0000-0002-4532-2703
    deprecated: false
    description: A structured controlled vocabulary of phenotypes of the slime-mould
      <i>Dictyostelium discoideum</i>.
    domain: anatomy and development
    download.obo: http://purl.obolibrary.org/obo/ddpheno.obo
    download.owl: http://purl.obolibrary.org/obo/ddpheno.owl
    homepage: http://dictybase.org/
    license: CC0 1.0
    license.url: http://creativecommons.org/publicdomain/zero/1.0/
    name: Dictyostelium discoideum phenotype ontology
    preferredPrefix: DDPHENO
    prefix: ddpheno
    publications:
    - id: https://www.ncbi.nlm.nih.gov/pubmed/31840793
      title: dictyBase and the Dicty Stock Center (version 2.0) - a progress report
    repository: https://github.com/obophenotype/dicty-phenotype-ontology
    twitter: dictybase
  ols:
    description: A structured controlled vocabulary of phenotypes of the slime-mould
      Dictyostelium discoideum.
    download_owl: http://purl.obolibrary.org/obo/ddpheno.owl
    homepage: http://dictybase.org/
    name: Dicty Phenotype Ontology (DDPHENO)
    prefix: ddpheno
    tracker: https://github.com/obophenotype/dicty-phenotype-ontology/issues
    version: '2023-08-26'
    version.iri: http://purl.obolibrary.org/obo/ddpheno/releases/2023-08-26/ddpheno.owl
  ontobee:
    library: Library
    name: Dictyostelium discoideum phenotype ontology
    prefix: DDPHENO
  pattern: ^\d{7}$
  prefix: ddpheno
  publications:
  - doi: 10.1387/ijdb.190226pf
    pmc: PMC7409682
    pubmed: '31840793'
    title: dictyBase and the Dicty Stock Center (version 2.0) - a progress report
    year: 2019
  - doi: 10.1007/978-1-62703-302-2_4
    pmc: PMC3762881
    pubmed: '23494302'
    title: 'One stop shop for everything Dictyostelium: dictyBase and the Dicty Stock
      Center in 2012'
    year: 2013
  uri_format: http://purl.obolibrary.org/obo/DDPHENO_$1
debio:
  contact:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: A repository for the TSV-based, decentralized, community-curated curation
    of terms, properties, and relations that get turned into OBO, OWL, and OBO Graph
    JSON.
  download_json: https://raw.githubusercontent.com/biopragmatics/debio/main/releases/current/debio.json
  download_obo: https://raw.githubusercontent.com/biopragmatics/debio/main/releases/current/debio.obo
  download_owl: https://raw.githubusercontent.com/biopragmatics/debio/main/releases/current/debio.owl
  example: '0000001'
  homepage: https://biopragmatics.github.io/debio
  name: Decentralized Biomedical Ontology
  pattern: ^\d{7}$
  prefix: debio
  providers:
  - code: obo2
    description: Because it's not possible to configure the base URI with ROBOT/OWLAPI,
      this pops out
    example: null
    first_party: null
    homepage: http://purl.obolibrary.org
    name: Placeholder OBO PURL
    publications: null
    status: null
    uri_format: http://purl.obolibrary.org/obo/debio_$1
  synonyms:
  - DeBiO
  uri_format: https://biopragmatics.github.io/debio/$1
decipher:
  biocontext:
    prefix: DECIPHER
  contact:
    email: ganesh.swaminathan@sanger.ac.uk
    github: null
    name: Jawahar Swaminathan
    orcid: 0000-0002-0215-4084
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: CNV syndromes in the DECIPHER genomics database that are linked to
    Human Phenotype Ontology terms
  example: '1'
  fairsharing:
    abbreviation: DECIPHER
    description: DECIPHER (Database of Chromosomal Imbalance and Phenotype in Humans
      Using Ensembl Resources) is an interactive web-based resource that incorporates
      a suite of tools designed to aid the interpretation of submicroscopic chromosomal
      imbalance, inversions, and translocations.
    homepage: https://decipher.sanger.ac.uk/
    name: DatabasE of genomiC varIation and Phenotype in Humans using Ensembl Resources
    prefix: FAIRsharing.l8Sf5x
    publications:
    - doi: 10.1093/nar/gkt937
      pubmed_id: 24150940
      title: 'DECIPHER: database for the interpretation of phenotype-linked plausibly
        pathogenic sequence and copy-number variation.'
    - doi: 10.1016/j.ajhg.2009.03.010
      pubmed_id: 19344873
      title: 'DECIPHER: Database of Chromosomal Imbalance and Phenotype in Humans
        Using Ensembl Resources.'
    subjects:
    - Life Science
    - Biomedical Science
  homepage: https://www.deciphergenomics.org/
  mappings:
    biocontext: DECIPHER
    fairsharing: FAIRsharing.l8Sf5x
  name: DECIPHER CNV Syndromes
  pattern: ^\d+$
  prefix: decipher
  publications:
  - doi: 10.1093/nar/gkt937
    pmc: PMC3965078
    pubmed: '24150940'
    title: 'DECIPHER: database for the interpretation of phenotype-linked plausibly
      pathogenic sequence and copy-number variation'
    year: 2013
  - doi: 10.1016/j.ajhg.2009.03.010
    pmc: PMC2667985
    pubmed: '19344873'
    title: 'DECIPHER: Database of Chromosomal Imbalance and Phenotype in Humans Using
      Ensembl Resources'
    year: 2009
  - doi: 10.1093/nar/gkt937
    pmc: null
    pubmed: null
    title: 'DECIPHER: database for the interpretation of phenotype-linked plausibly
      pathogenic sequence and copy-number variation.'
    year: null
  - doi: 10.1016/j.ajhg.2009.03.010
    pmc: null
    pubmed: null
    title: 'DECIPHER: Database of Chromosomal Imbalance and Phenotype in Humans Using
      Ensembl Resources.'
    year: null
  - doi: 10.1093/nar/gkt937
    pmc: null
    pubmed: null
    title: 'DECIPHER: database for the interpretation of phenotype-linked plausibly
      pathogenic sequence and copy-number variation.'
    year: null
  - doi: 10.1016/j.ajhg.2009.03.010
    pmc: null
    pubmed: null
    title: 'DECIPHER: Database of Chromosomal Imbalance and Phenotype in Humans Using
      Ensembl Resources.'
    year: null
  uri_format: https://www.deciphergenomics.org/syndrome/$1
degradome:
  biocontext:
    prefix: DEGRADOME
  mappings:
    biocontext: DEGRADOME
    miriam: degradome
    n2t: degradome
  miriam:
    deprecated: false
    description: The Degradome Database contains information on the complete set of
      predicted proteases present in a a variety of mammalian species that have been
      subjected to whole genome sequencing. Each protease sequence is curated and,
      when necessary, cloned and sequenced.
    homepage: http://degradome.uniovi.es/
    id: '00000454'
    name: Degradome Database
    namespaceEmbeddedInLui: false
    pattern: ^[AMCST][0-9x][0-9]$
    prefix: degradome
    sampleId: Ax1
    uri_format: http://degradome.uniovi.es/cgi-bin/protease/$1
  n2t:
    description: The Degradome Database contains information on the complete set of
      predicted proteases present in a a variety of mammalian species that have been
      subjected to whole genome sequencing. Each protease sequence is curated and,
      when necessary, cloned and sequenced.
    example: Ax1
    homepage: http://degradome.uniovi.es/
    name: Degradome Database at
    namespaceEmbeddedInLui: false
    pattern: ^[AMCST][0-9x][0-9]$
    prefix: degradome
    uri_format: http://degradome.uniovi.es/cgi-bin/protease/$1
  prefix: degradome
deims.activity:
  contact:
    email: christoph.wohner@umweltbundesamt.at
    github: stopopol
    name: Christoph Wohner
    orcid: 0000-0002-0655-3699
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: Activities in DEIMS SDR
  example: 7dfd3f10-d410-45a4-983d-8fbd6dfbc374
  github_request_issue: 1381
  homepage: https://deims.org
  license: CC-BY-NC-4.0
  name: Dynamic Ecological Information Management System - Site and Dataset Registry
    - Activity
  part_of_database: deims
  pattern: ^[0-9a-f\-]+$
  prefix: deims.activity
  providers:
  - code: api
    description: A first-party API endpoint for an activity in DEIMS-SDR
    example: null
    first_party: null
    homepage: https://deims.org/api
    name: DEIMS-SDR API
    publications: null
    status: null
    uri_format: https://deims.org/api/activities/$1
  publications:
  - doi: 10.1016/j.ecoinf.2022.101708
    pmc: PMC9461184
    pubmed: '36105745'
    title: Designing and implementing a data model for describing environmental monitoring
      and research sites
    year: 2022
  - doi: 10.1016/j.ecoinf.2020.101158
    pmc: null
    pubmed: null
    title: Towards interoperable research site documentation – Recommendations for
      information models and data provision
    year: 2020
  - doi: 10.1016/j.ecoinf.2019.01.005
    pmc: null
    pubmed: null
    title: DEIMS-SDR – A web portal to document research sites and their associated
      data
    year: 2019
  uri_format: https://deims.org/activity/$1
deims.dataset:
  contact:
    email: christoph.wohner@umweltbundesamt.at
    github: stopopol
    name: Christoph Wohner
    orcid: 0000-0002-0655-3699
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: Datasets in DEIMS SDR
  example: bb0754dd-7e69-4b29-b348-3f8017f73d6b
  github_request_issue: 1381
  homepage: https://deims.org
  license: CC-BY-NC-4.0
  name: Dynamic Ecological Information Management System - Site and Dataset Registry
    - Dataset
  part_of_database: deims
  pattern: ^[0-9a-f\-]+$
  prefix: deims.dataset
  providers:
  - code: api
    description: A first-party API endpoint for a dataset in DEIMS-SDR
    example: null
    first_party: null
    homepage: https://deims.org/api
    name: DEIMS-SDR API
    publications: null
    status: null
    uri_format: https://deims.org/api/datasets/$1
  publications:
  - doi: 10.1016/j.ecoinf.2022.101708
    pmc: PMC9461184
    pubmed: '36105745'
    title: Designing and implementing a data model for describing environmental monitoring
      and research sites
    year: 2022
  - doi: 10.1016/j.ecoinf.2020.101158
    pmc: null
    pubmed: null
    title: Towards interoperable research site documentation – Recommendations for
      information models and data provision
    year: 2020
  - doi: 10.1016/j.ecoinf.2019.01.005
    pmc: null
    pubmed: null
    title: DEIMS-SDR – A web portal to document research sites and their associated
      data
    year: 2019
  uri_format: https://deims.org/dataset/$1
deims.location:
  contact:
    email: christoph.wohner@umweltbundesamt.at
    github: stopopol
    name: Christoph Wohner
    orcid: 0000-0002-0655-3699
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: Locations in DEIMS SDR
  example: 85dc6019-9654-4ba0-8338-08c4ffe8fe47
  github_request_issue: 1381
  homepage: https://deims.org
  license: CC-BY-NC-4.0
  name: Dynamic Ecological Information Management System - Site and Dataset Registry
    - Locations
  part_of_database: deims
  pattern: ^[0-9a-f\-]+$
  prefix: deims.location
  providers:
  - code: api
    description: A first-party API endpoint for a location in DEIMS-SDR
    example: null
    first_party: null
    homepage: https://deims.org/api
    name: DEIMS-SDR API
    publications: null
    status: null
    uri_format: https://deims.org/api/locations/$1
  publications:
  - doi: 10.1016/j.ecoinf.2022.101708
    pmc: PMC9461184
    pubmed: '36105745'
    title: Designing and implementing a data model for describing environmental monitoring
      and research sites
    year: 2022
  - doi: 10.1016/j.ecoinf.2020.101158
    pmc: null
    pubmed: null
    title: Towards interoperable research site documentation – Recommendations for
      information models and data provision
    year: 2020
  - doi: 10.1016/j.ecoinf.2019.01.005
    pmc: null
    pubmed: null
    title: DEIMS-SDR – A web portal to document research sites and their associated
      data
    year: 2019
  uri_format: https://deims.org/locations/$1
deims.network:
  contact:
    email: christoph.wohner@umweltbundesamt.at
    github: stopopol
    name: Christoph Wohner
    orcid: 0000-0002-0655-3699
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: Networks in DEIMS SDR
  example: c3abdc60-49f1-49db-81fe-863b7dbb21d3
  github_request_issue: 1381
  homepage: https://deims.org
  license: CC-BY-NC-4.0
  name: Dynamic Ecological Information Management System - Site and Dataset Registry
    - Network
  part_of_database: deims
  pattern: ^[0-9a-f\-]+$
  prefix: deims.network
  publications:
  - doi: 10.1016/j.ecoinf.2022.101708
    pmc: PMC9461184
    pubmed: '36105745'
    title: Designing and implementing a data model for describing environmental monitoring
      and research sites
    year: 2022
  - doi: 10.1016/j.ecoinf.2020.101158
    pmc: null
    pubmed: null
    title: Towards interoperable research site documentation – Recommendations for
      information models and data provision
    year: 2020
  - doi: 10.1016/j.ecoinf.2019.01.005
    pmc: null
    pubmed: null
    title: DEIMS-SDR – A web portal to document research sites and their associated
      data
    year: 2019
  uri_format: https://deims.org/networks/$1
deims.sensor:
  contact:
    email: christoph.wohner@umweltbundesamt.at
    github: stopopol
    name: Christoph Wohner
    orcid: 0000-0002-0655-3699
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: Sensors in DEIMS SDR
  example: 2af339dd-a956-471f-9406-b0f74bacd579
  github_request_issue: 1381
  homepage: https://deims.org
  license: CC-BY-NC-4.0
  name: Dynamic Ecological Information Management System - Site and Dataset Registry
    - Sensor
  part_of_database: deims
  pattern: ^[0-9a-f\-]+$
  prefix: deims.sensor
  providers:
  - code: api
    description: A first-party API endpoint for a sensor in DEIMS-SDR
    example: null
    first_party: null
    homepage: https://deims.org/api
    name: DEIMS-SDR API
    publications: null
    status: null
    uri_format: https://deims.org/api/sensors/$1
  publications:
  - doi: 10.1016/j.ecoinf.2022.101708
    pmc: PMC9461184
    pubmed: '36105745'
    title: Designing and implementing a data model for describing environmental monitoring
      and research sites
    year: 2022
  - doi: 10.1016/j.ecoinf.2020.101158
    pmc: null
    pubmed: null
    title: Towards interoperable research site documentation – Recommendations for
      information models and data provision
    year: 2020
  - doi: 10.1016/j.ecoinf.2019.01.005
    pmc: null
    pubmed: null
    title: DEIMS-SDR – A web portal to document research sites and their associated
      data
    year: 2019
  uri_format: https://deims.org/sensors/$1
deims.site:
  comment: This is an important resource for us in fields like environmental genomics.
    We frequently want to link metagenome samples to sites to make it easier to pull
    in environmental data to explore connections between environments, gene functions,
    community structure, etc. I will try and reach out to establish contacts with
    them
  contact:
    email: christoph.wohner@umweltbundesamt.at
    github: stopopol
    name: Christoph Wohner
    orcid: 0000-0002-0655-3699
  contributor:
    email: cjmungall@lbl.gov
    github: cmungall
    name: Chris Mungall
    orcid: 0000-0002-6601-2165
  description: DEIMS-SDR (Dynamic Ecological Information Management System - Site
    and dataset registry) is an information management system powered by eLTER. It
    allows you to discover long-term ecosystem research sites around the globe, along
    with the data gathered at those sites and the people and networks associated with
    them. DEIMS-SDR describes a wide range of sites, providing a wealth of information,
    including each site’s location, ecosystems, facilities, parameters measured and
    research themes. It is also possible to access a growing number of datasets and
    data products associated with the sites.
  example: 0e39569d-ff81-4b78-9c34-b07309504d80
  github_request_issue: 1381
  homepage: https://deims.org/
  license: CC-BY-NC-4.0
  name: Dynamic Ecological Information Management System - Site and dataset registry
  part_of_database: deims
  pattern: ^[0-9a-f\-]+$
  prefix: deims.site
  providers:
  - code: api
    description: A first-party API endpoint for a site in DEIMS-SDR
    example: null
    first_party: null
    homepage: https://deims.org/api
    name: DEIMS-SDR API
    publications: null
    status: null
    uri_format: https://deims.org/api/sites/$1
  publications:
  - doi: 10.1016/j.ecoinf.2022.101708
    pmc: PMC9461184
    pubmed: '36105745'
    title: Designing and implementing a data model for describing environmental monitoring
      and research sites
    year: 2022
  - doi: 10.1016/j.ecoinf.2020.101158
    pmc: null
    pubmed: null
    title: Towards interoperable research site documentation – Recommendations for
      information models and data provision
    year: 2020
  - doi: 10.1016/j.ecoinf.2019.01.005
    pmc: null
    pubmed: null
    title: DEIMS-SDR – A web portal to document research sites and their associated
      data
    year: 2019
  reviewer:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  synonyms:
  - deims.id
  uri_format: https://deims.org/$1
deims.taxonomy:
  contact:
    email: christoph.wohner@umweltbundesamt.at
    github: stopopol
    name: Christoph Wohner
    orcid: 0000-0002-0655-3699
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: Taxonomy in DEIMS SDR
  example: '21157'
  github_request_issue: 1381
  homepage: https://deims.org
  license: CC-BY-NC-4.0
  name: Dynamic Ecological Information Management System - Site and Dataset Registry
    - Taxonomy
  part_of_database: deims
  pattern: ^\d+$
  prefix: deims.taxonomy
  publications:
  - doi: 10.1016/j.ecoinf.2022.101708
    pmc: PMC9461184
    pubmed: '36105745'
    title: Designing and implementing a data model for describing environmental monitoring
      and research sites
    year: 2022
  - doi: 10.1016/j.ecoinf.2020.101158
    pmc: null
    pubmed: null
    title: Towards interoperable research site documentation – Recommendations for
      information models and data provision
    year: 2020
  - doi: 10.1016/j.ecoinf.2019.01.005
    pmc: null
    pubmed: null
    title: DEIMS-SDR – A web portal to document research sites and their associated
      data
    year: 2019
  uri_format: https://deims.org/taxonomy/term/$1
deo:
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: An ontology that provides a structured vocabulary for rhetorical elements
    within documents (e.g., Introduction, Discussion, Acknowledgements, Reference
    List, Figures, Appendix). It is imported by DoCO.
  example: Reference
  fairsharing:
    abbreviation: DEO
    contact:
      email: silvio.peroni@unibo.it
      name: Silvio Peroni
      orcid: 0000-0003-0530-4305
    description: The Discourse Elements Ontology (DEO) is an ontology that provides
      a structured vocabulary for rhetorical elements within documents (e.g., Introduction,
      Discussion, Acknowledgements, Reference List, Figures, Appendix). It is imported
      by DoCO.
    homepage: http://www.sparontologies.net/ontologies/deo
    license: CC-BY-4.0
    name: Discourse Elements Ontology
    prefix: FAIRsharing.39fd58
    publications:
    - doi: 10.3233/sw-150177
      title: The Document Components Ontology (DoCO)
      year: 2016
    repository: https://github.com/sparontologies/deo
    subjects:
    - Subject Agnostic
    twitter: sparontologies
  homepage: http://www.sparontologies.net/ontologies/deo
  lov:
    description: The Discourse Elements Ontology is an ontology for describing the
      major rhetorical elements of a document such as a journal article. It is a subsidiary
      ontology that is imported into the Document Components Ontology, itself part
      of SPAR, the Semantic Publishing and Referencing Ontologies
    homepage: http://www.essepuntato.it/lode/http://purl.org/spar/deo
    keywords:
    - SPAR
    modified: '2015-07-03'
    name: The Discourse Elements Ontology
    prefix: deo
    uri_prefix: http://purl.org/spar/deo/$1
  mappings:
    fairsharing: FAIRsharing.39fd58
    lov: deo
  name: Discourse Elements Ontology
  preferred_prefix: DEO
  prefix: deo
  publications:
  - doi: 10.3233/sw-150177
    pmc: null
    pubmed: null
    title: The Document Components Ontology (DoCO)
    year: 2016
  - doi: 10.3233/sw-150177
    pmc: null
    pubmed: null
    title: The Document Components Ontology (DoCO)
    year: 2016
  repository: https://github.com/sparontologies/deo
  uri_format: http://purl.org/spar/deo/$1
depmap:
  cellosaurus:
    category: Cell line databases/resources
    homepage: https://depmap.org/portal/
    name: Cancer Dependency Map
    prefix: DepMap
    uri_format: https://depmap.org/portal/cell_line/$1
  contact:
    email: vazquez@broadinstitute.org
    github: null
    name: Francisca Vazquez
    orcid: 0000-0002-2857-4685
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: Cell lines used in the Dependency Map (DepMap). Highly related to CCLE
    Cells.
  domain: cell and cell line
  example: ACH-000001
  homepage: https://depmap.org/portal
  keywords:
  - cancer cell line
  - cell
  - cell line
  license: CC-BY-4.0
  logo: https://target-discovery.depmap.org/img/depmaplogo.png
  mappings:
    cellosaurus: DepMap
  name: DepMap Cell Lines
  pattern: ^ACH-\d+$
  prefix: depmap
  publications:
  - doi: 10.1038/s41568-024-00763-x
    pmc: null
    pubmed: '39468210'
    title: The present and future of the Cancer Dependency Map
    year: 2025
  uri_format: https://depmap.org/portal/cell_line/$1
depod:
  biocontext:
    prefix: DEPOD
  fairsharing:
    abbreviation: DEPOD
    contact:
      email: depod@embl.de
      name: General Enquiries
      orcid: 0000-0003-3562-7869
    description: DEPOD - the human DEPhOsphorylation Database is a manually curated
      database collecting human active and inactive phosphatases, their experimentally
      verified protein and non-protein substrates, and dephosphorylation site information,
      and pathways in which they are involved. It also provides links to popular kinase
      databases and protein-protein interaction databases for these phosphatases and
      substrates.
    homepage: http://www.depod.org/
    name: The human DEPhOsphorylation Database
    prefix: FAIRsharing.q9j2e3
    publications:
    - doi: 10.1093/nar/gku1009
      pubmed_id: 25332398
      title: 'The human DEPhOsphorylation database DEPOD: a 2015 update.'
    - doi: 10.1126/scisignal.2003203
      pubmed_id: 23674824
      title: Elucidating human phosphatase-substrate networks.
    subjects:
    - Life Science
  mappings:
    biocontext: DEPOD
    fairsharing: FAIRsharing.q9j2e3
    miriam: depod
    n2t: depod
    pathguide: '584'
    re3data: r3d100011936
    uniprot: DB-0190
  miriam:
    deprecated: false
    description: The human DEPhOsphorylation Database (DEPOD) contains information
      on known human active phosphatases and their experimentally verified protein
      and nonprotein substrates. Reliability scores are provided for dephosphorylation
      interactions, according to the type of assay used, as well as the number of
      laboratories that have confirmed such interaction. Phosphatase and substrate
      entries are listed along with the dephosphorylation site, bioassay type, and
      original literature, and contain links to other resources.
    homepage: http://www.depod.bioss.uni-freiburg.de
    id: 00000428
    name: DEPOD
    namespaceEmbeddedInLui: false
    pattern: ^[A-Z0-9]+$
    prefix: depod
    sampleId: PTPN1
    uri_format: http://www.depod.bioss.uni-freiburg.de/showp.php?gene=$1
  n2t:
    description: The human DEPhOsphorylation Database (DEPOD) contains information
      on known human active phosphatases and their experimentally verified protein
      and nonprotein substrates. Reliability scores are provided for dephosphorylation
      interactions, according to the type of assay used, as well as the number of
      laboratories that have confirmed such interaction. Phosphatase and substrate
      entries are listed along with the dephosphorylation site, bioassay type, and
      original literature, and contain links to other resources.
    example: PTPN1
    homepage: http://www.depod.bioss.uni-freiburg.de
    name: DEPOD at EMBL
    namespaceEmbeddedInLui: false
    pattern: ^[A-Z0-9]+$
    prefix: depod
    uri_format: http://www.depod.bioss.uni-freiburg.de/showp.php?gene=$1
  name: Human Dephosphorylation Database
  pathguide:
    abbreviation: DEPOD
    homepage: http://depod.bioss.uni-freiburg.de/
    keywords:
    - PSI-MI
    name: the human DEPhOsphorylation Database
    prefix: '584'
  prefix: depod
  provides: hgnc.symbol
  publications:
  - doi: 10.1093/database/baz133
    pmc: PMC6911163
    pubmed: '31836896'
    title: 'The human DEPhOsphorylation Database DEPOD: 2019 update'
    year: 2019
  - doi: 10.1093/nar/gku1009
    pmc: PMC4383878
    pubmed: '25332398'
    title: 'The human DEPhOsphorylation database DEPOD: a 2015 update'
    year: 2014
  - doi: 10.1126/scisignal.2003203
    pmc: null
    pubmed: '23674824'
    title: Elucidating human phosphatase-substrate networks
    year: 2013
  - doi: 10.1093/nar/gku1009
    pmc: null
    pubmed: null
    title: 'The human DEPhOsphorylation database DEPOD: a 2015 update.'
    year: null
  - doi: 10.1126/scisignal.2003203
    pmc: null
    pubmed: null
    title: Elucidating human phosphatase-substrate networks.
    year: null
  - doi: null
    pmc: null
    pubmed: '31836896'
    title: null
    year: null
  - doi: 10.1093/nar/gku1009
    pmc: null
    pubmed: null
    title: 'The human DEPhOsphorylation database DEPOD: a 2015 update.'
    year: null
  - doi: 10.1126/scisignal.2003203
    pmc: null
    pubmed: null
    title: Elucidating human phosphatase-substrate networks.
    year: null
  - doi: null
    pmc: null
    pubmed: '31836896'
    title: null
    year: null
  - doi: 10.1093/nar/gku1009
    pmc: null
    pubmed: null
    title: 'The human DEPhOsphorylation database DEPOD: a 2015 update.'
    year: null
  - doi: 10.1126/scisignal.2003203
    pmc: null
    pubmed: null
    title: Elucidating human phosphatase-substrate networks.
    year: null
  - doi: null
    pmc: null
    pubmed: '31836896'
    title: null
    year: null
  re3data:
    description: DEPOD - the human DEPhOsphorylation Database (version 1.1) is a manually
      curated database collecting human active phosphatases, their experimentally
      verified protein and non-protein substrates and dephosphorylation site information,
      and pathways in which they are involved. It also provides links to popular kinase
      databases and protein-protein interaction databases for these phosphatases and
      substrates. DEPOD aims to be a valuable resource for studying human phosphatases
      and their substrate specificities and molecular mechanisms; phosphatase-targeted
      drug discovery and development; connecting phosphatases with kinases through
      their common substrates; completing the human phosphorylation/dephosphorylation
      network.
    doi: 10.17616/R3GP9F
    homepage: https://depod.bioss.uni-freiburg.de/
    name: DEPOD
    prefix: r3d100011936
    synonyms:
    - DEPhOsphorylation Database
  uniprot:
    abbreviation: DEPOD
    category: PTM databases
    homepage: https://depod.bioss.uni-freiburg.de
    name: DEPOD human dephosphorylation database
    prefix: DB-0190
    publications:
    - pubmed: '31836896'
    uri_format: https://depod.bioss.uni-freiburg.de/showp.php?name=$1
dermo:
  aberowl:
    description: Ontology of human dermatologic disease
    download_obo: http://aber-owl.net/media/ontologies/DERMO/10/dermo.obo
    name: Human Dermatological Disease Ontology
    prefix: DERMO
    version: '1.19'
  bioportal:
    contact:
      email: pns12@cam.ac.uk
      name: Paul Schofield
    description: Ontology of human dermatologic disease
    name: Human Dermatological Disease Ontology
    prefix: DERMO
    version: '1.19'
  contact:
    email: pns12@hermes.cam.ac.uk
    github: PaulNSchofield
    name: Paul Schofield
    orcid: 0000-0002-5111-7263
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: DermO is an ontology with broad coverage of the domain of dermatologic
    disease and we demonstrate here its utility for text mining and investigation
    of phenotypic relationships between dermatologic disorders
  example: '0000000'
  fairsharing:
    abbreviation: DERMO
    description: DermO is an Ontology of cutaneous disease, constructed manually by
      domain experts. With more than 3000 terms, DermO represents the most comprehensive
      formal dermatological disease terminology available. The disease entities are
      categorized in 20 upper level terms, which use a variety of features such as
      anatomical location, heritability, affected cell or tissue type, or etiology,
      as the features for classification, in line with professional practice and nosology
      in dermatology.
    domains:
    - disease
    homepage: http://bioportal.bioontology.org/ontologies/DERMO
    name: Human Dermatological Disease Ontology
    prefix: FAIRsharing.k008w7
    publications:
    - doi: 10.1186/s13326-016-0085-x
      pubmed: '27296450'
      title: DermO; an ontology for the description of dermatologic disease
      year: 2016
    subjects:
    - Dermatology
  homepage: https://jbiomedsem.biomedcentral.com/articles/10.1186/s13326-016-0085-x
  mappings:
    aberowl: DERMO
    bioportal: DERMO
    fairsharing: FAIRsharing.k008w7
  name: Human Dermatological Disease Ontology
  pattern: ^\d{7}$
  prefix: dermo
  publications:
  - doi: 10.1186/s13326-016-0085-x
    pmc: PMC4907256
    pubmed: '27296450'
    title: DermO; an ontology for the description of dermatologic disease
    year: 2016
  repository: https://github.com/dermatology-ontology/dermatology
  uri_format: http://purl.obolibrary.org/obo/DERMO_$1
destatis.subject:
  description: A vocabulary of university course subjects
  example: '01'
  homepage: https://github.com/VIVO-DE/destatis_faecherklassifikation
  keywords:
  - subject
  mappings:
    tib: destf
  name: Destatis subject classification
  prefix: destatis.subject
  repository: https://github.com/VIVO-DE/destatis_faecherklassifikation
  tib:
    description: 'Diese Ontologie basiert auf "Statistisches Bundesamt (2018): Anhang
      Übersicht 1 - Fächergruppen, Lehr- und Forschungsbereiche, Fachgebiete - Stand
      2017. In: Statistisches Bundesamt: Bildung und Kultur - Personal an Hochschulen.
      Fachserie 11 Reihe 4.4. S. 351. URL: https://www.statistischebibliothek.de/mir/servlets/MCRFileNodeServlet/DEHeft_derivate_00041050/2110440177004.pdf#%5B%7B%22num%22%3A1748%2C%22gen%22%3A0%7D%2C%7B%22name%22%3A%22Fit%22%7D%5D
      (letzter Zugriff: 2022-10-12)." In SKOS konvertiert von Tatiana Walther unter
      Mitwirkung von Christian Hauschke (Technische Informationsbibliothek (TIB) Hannover).
      Die Bezeichnungen und Inhalte der Fächersystematik sind unverändert.'
    download_rdf: https://raw.githubusercontent.com/VIVO-DE/destatis_faecherklassifikation/master/faecherklassifikation.rdf
    keywords:
    - TIB
    - educational science
    name: Destatis-Fächerklassifikation "Personal an Hochschulen - Fächersystematik"
    prefix: destf
    tracker: https://github.com/VIVO-DE/destatis_faecherklassifikation/issues
    uri_format: https://onto.tib.eu/destf/cs/$1
dev.ga4ghdos:
  biocontext:
    prefix: DEV.GA4GHDOS
  mappings:
    biocontext: DEV.GA4GHDOS
    miriam: dev.ga4ghdos
    n2t: dev.ga4ghdos
  miriam:
    deprecated: false
    description: Assists in resolving data across cloud resources.
    homepage: http://github.com/ga4gh/data-object-service-schemas
    id: '00000656'
    name: Development Data Object Service
    namespaceEmbeddedInLui: false
    pattern: ^[a-zA-Z0-9\-:#\.]+$
    prefix: dev.ga4ghdos
    sampleId: 23fa7b4b-9d68-429b-aece-658b11124bb3#2017-03-24T18:43:16.886826-05:00
    uri_format: https://dos-gdc.ucsc-cgp-dev.org/ga4gh/dos/v1/dataobjects/$1
  n2t:
    description: Assists in resolving data across cloud resources.
    example: 23fa7b4b-9d68-429b-aece-658b11124bb3#2017-03-24T18:43:16.886826-05:00
    homepage: http://github.com/ga4gh/data-object-service-schemas
    name: Data Object Service
    namespaceEmbeddedInLui: false
    pattern: ^[a-zA-Z0-9\-:#\.]+$
    prefix: dev.ga4ghdos
    uri_format: https://dos-gdc.ucsc-cgp-dev.org/ga4gh/dos/v1/dataobjects/$1
  prefix: dev.ga4ghdos
devtox:
  contact:
    email: rupert.kellner@item.fraunhofer.de
    github: null
    name: Rupert Kellner
    orcid: 0000-0002-6807-8731
  contributor:
    email: null
    github: bgyori
    name: Benjamin M. Gyori
    orcid: 0000-0001-9439-5346
  description: The DevTox Project harmonizes the nomenclature used to describe developmental
    anomalies in laboratory animals, assists in the visual recognition of developmental
    anomalies with the aid of photographs, and provides a historical control database
    of developmental effects in laboratory animals.
  example: '311935300'
  github_request_issue: 989
  homepage: https://www.devtox.org/
  name: DevTox
  pattern: ^\d+$
  prefix: devtox
  publications:
  - doi: 10.1016/j.reprotox.2019.07.003
    pmc: PMC8865445
    pubmed: '31288076'
    title: 'Update of the DevTox data database for harmonized risk assessment and
      alternative methodologies in developmental toxicology: Report of the 9th Berlin
      Workshop on Developmental Toxicity'
    year: 2019
  reviewer:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  uri_format: https://www.devtox.org/nomenclature/ml_manus.php?mno=$1
dfg.fo:
  example: 101-01
  homepage: https://github.com/tibonto/DFG-Fachsystematik-Ontology
  keywords:
  - educational resources
  - open educational resource
  - open educational resources
  mappings:
    tib: dfgfo
  prefix: dfg.fo
  repository: https://github.com/tibonto/DFG-Fachsystematik-Ontology
  tib:
    description: DFG Fachsystematik Ontology / DFG Classification of Subject Areas
      Ontology (DFGFO) encodes the DFG Classification of Subject Areas into an ontology,
      where each subject number are is enconded into a Class with subclass statements
      following the DFG Classification of Subject Areas hierarchy. Labels are provide
      German and English.
    download_rdf: https://raw.githubusercontent.com/tibonto/DFG-Fachsystematik-Ontology/refs/tags/2020-2025-06-01/dfgfo.ttl
    keywords:
    - NFDI4ING
    - FID move
    - Digital Planning and Construction
    - FID BAUdigital
    - ESS
    - educational science
    name: DFG Classification of Subject Areas Ontology - 2020-2024
    prefix: dfgfo
    tracker: https://github.com/tibonto/DFG-Fachsystematik-Ontology/issues
    uri_format: https://w3id.org/dfgfo/2020/$1
    version.iri: https://w3id.org/dfgfo/2020
dg.4503:
  mappings:
    miriam: dg.4503
  miriam:
    deprecated: false
    description: Full implementation of the DRS 1.1 standard with support for persistent
      identifiers. Open source DRS server that follows the Gen3 implementation. Gen3
      is a GA4GH compliant open source platform for developing framework services
      and data commons. Data commons accelerate and democratize the process of scientific
      discovery, especially over large or complex datasets. Gen3 is maintained by
      the Center for Translational Data Science at the University of Chicago. https://gen3.org
    homepage: https://gen3.biodatacatalyst.nhlbi.nih.gov
    id: 00000869
    name: BioData Catalyst
    namespaceEmbeddedInLui: false
    pattern: '[0-9a-fA-F]{8}-[0-9a-fA-F]{4}-[0-9a-fA-F]{4}-[0-9a-fA-F]{4}\-[0-9a-fA-F]{12}'
    prefix: dg.4503
    sampleId: 0000ffeb-36e0-4a29-b21d-84423bda979d
    uri_format: https://gen3.biodatacatalyst.nhlbi.nih.gov/ga4gh/drs/v1/objects/$1
  prefix: dg.4503
dg.4dfc:
  mappings:
    miriam: dg.4dfc
  miriam:
    deprecated: false
    description: DRS server that follows the Gen3 implementation. Gen3 is a GA4GH
      compliant open source platform for developing framework services and data commons.
      Data commons accelerate and democratize the process of scientific discovery,
      especially over large or complex datasets. Gen3 is maintained by the Center
      for Translational Data Science at the University of Chicago. https://gen3.org
    homepage: https://nci-crdc.datacommons.io/
    id: 00000857
    name: NCI Data Commons Framework Services
    namespaceEmbeddedInLui: false
    pattern: '[0-9a-fA-F]{8}\-[0-9a-fA-F]{4}\-[0-9a-fA-F]{4}\-[0-9a-fA-F]{4}\-[0-9a-fA-F]{12}'
    prefix: dg.4dfc
    sampleId: 81944ba1-81d0-436e-8552-33d77a27834b
    uri_format: https://nci-crdc.datacommons.io/ga4gh/drs/v1/objects/$1
  prefix: dg.4dfc
dg.6vts:
  mappings:
    miriam: dg.6vts
  miriam:
    deprecated: false
    description: Full implementation of the DRS 1.1 standard with support for persistent
      identifiers. Open source DRS server that follows the Gen3 implementation. Gen3
      is a GA4GH compliant open source platform for developing framework services
      and data commons. Data commons accelerate and democratize the process of scientific
      discovery, especially over large or complex datasets. Gen3 is maintained by
      the Center for Translational Data Science at the University of Chicago. https://gen3.org
    homepage: https://jcoin.datacommons.io
    id: 00000876
    name: JCOIN
    namespaceEmbeddedInLui: false
    pattern: '[0-9a-fA-F]{8}\-[0-9a-fA-F]{4}\-[0-9a-fA-F]{4}\-[0-9a-fA-F]{4}\-[0-9a-fA-F]{12}'
    prefix: dg.6vts
    sampleId: 2afacf00-9a1d-4d80-8c32-69d3923d3913
    uri_format: https://jcoin.datacommons.io/ga4gh/drs/v1/objects/$1
  prefix: dg.6vts
dg.anv0:
  mappings:
    miriam: dg.anv0
  miriam:
    deprecated: false
    description: DRS server that follows the Gen3 implementation. Gen3 is a GA4GH
      compliant open source platform for developing framework services and data commons.
      Data commons accelerate and democratize the process of scientific discovery,
      especially over large or complex datasets. Gen3 is maintained by the Center
      for Translational Data Science at the University of Chicago. https://gen3.org
    homepage: https://gen3.theanvil.io
    id: 00000871
    name: Anvil
    namespaceEmbeddedInLui: false
    pattern: '[0-9a-fA-F]{8}-[0-9a-fA-F]{4}-[0-9a-fA-F]{4}-[0-9a-fA-F]{4}-[0-9a-fA-F]{12}'
    prefix: dg.anv0
    sampleId: 00077f1c-c45a-47ba-8e6c-1bf6b6b43fce
    uri_format: https://gen3.theanvil.io/ga4gh/drs/v1/objects/$1
  prefix: dg.anv0
dg.f82a1a:
  mappings:
    miriam: dg.f82a1a
  miriam:
    deprecated: false
    description: Full implementation of the DRS 1.1 standard with support for persistent
      identifiers. Open source DRS server that follows the Gen3 implementation. Gen3
      is a GA4GH compliant open source platform for developing framework services
      and data commons. Data commons accelerate and democratize the process of scientific
      discovery, especially over large or complex datasets. Gen3 is maintained by
      the Center for Translational Data Science at the University of Chicago. https://gen3.org
    homepage: https://kidsfirstdrc.org
    id: 00000887
    name: Kids First
    namespaceEmbeddedInLui: false
    pattern: '[0-9a-fA-F]{8}\-[0-9a-fA-F]{4}\-[0-9a-fA-F]{4}\-[0-9a-fA-F]{4}\-[0-9a-fA-F]{12}'
    prefix: dg.f82a1a
    sampleId: 00026f50-858a-446b-8ed9-b0e3ecd7b20e
    uri_format: https://data.kidsfirstdrc.org/ga4gh/drs/v1/objects/$1
  prefix: dg.f82a1a
dg5b0d:
  mappings:
    miriam: dg.5b0d
  miriam:
    deprecated: false
    description: The Blood Profiling Atlas in Cancer (BloodPAC) supports the management,
      analysis and sharing of liquid biopsy data for the oncology research community
      and aims to accelerate discovery and development of therapies, diagnostic tests,
      and other technologies for cancer treatment and prevention. The data commons
      supports cross-project analyses by harmonizing data from different projects
      through the collaborative development of a data dictionary, providing an API
      for data queries and download, and providing a cloud-based analysis workspace
      with rich tools and resources.
    homepage: https://data.bloodpac.org/.
    id: 00000895
    name: BloodPAC
    namespaceEmbeddedInLui: false
    pattern: '[0-9a-fA-F]{8}\-[0-9a-fA-F]{4}\-[0-9a-fA-F]{4}\-[0-9a-fA-F]{4}\-[0-9a-fA-F]{12}'
    prefix: dg.5b0d
    sampleId: 00000d53-99bc-4d3e-8ed7-6dc358baccb7
    uri_format: https://data.bloodpac.org/ga4gh/drs/v1/objects/$1
  prefix: dg5b0d
dggr:
  description: Organism supplier which collects Drosophila stocks from laboratories
    all over the world, maintains them, and provides them to researchers upon request.
    [from RRID]
  example: '918902'
  mappings:
    rrid: DGGR
  pattern: ^\d+$
  prefix: dggr
  rrid:
    homepage: http://kyotofly.kit.jp/cgi-bin/stocks/data_search.cgi
    keywords:
    - drosophila
    - genetic resource
    - genomics
    - organism supplier
    name: Kyoto Stock Center
    prefix: DGGR
    scr: 008469
    twitter: kyotofly
  uri_format: https://kyotofly.kit.jp/cgi-bin/stocks/search_res_det.cgi?DB_NUM=1&DG_NUM=$1
dgrc:
  cellosaurus:
    category: Cell line collections (Providers)
    homepage: https://dgrc.bio.indiana.edu/cells/Catalog
    name: Drosophila Genomics Resource Center
    prefix: DGRC
    uri_format: https://dgrc.bio.indiana.edu/product/View?product=$1
  example: '215'
  integbio:
    alt_name: Drosophila Genetic Resource Center
    description: DGRC is the integrated retrieval system for Drosophila strains collected
      and maintained by NBRP 'Drosophila'. DGRC provides strain search system to input
      information such as genotypes, cytolocations, names of a species and phenotypes.
      This database also supplies chromosome maps that strains are mapped. Requests
      for Drosophila strains are available by using online contact form.
    homepage: http://fruitfly.jp/flystock/index_e.html
    information_keywords:
    - Bioresource
    - Sequence
    maintainer: Kyoto Institute of Technology Drosophila Genetic Resource Center
    name: DGRC
    prefix: nbdc00048
    status: Active
    target_keywords:
    - Genome/Gene
    - Organism
  mappings:
    cellosaurus: DGRC
    integbio: nbdc00048
  pattern: ^\d+$
  prefix: dgrc
dhba:
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: A controlled vocabulary to support the study of transcription in the
    developing human brain
  download_obo: https://raw.githubusercontent.com/obophenotype/uberon/master/source-ontologies/allen-dhba.obo
  example: '10153'
  homepage: https://www.brainspan.org/
  mappings:
    ols: dhba
  name: Developing Human Brain Atlas
  ols:
    description: An application ontology built by combining ontologised versions of
      the Allen Institute Developing Human Brain Atlas (DHBA) Structure Graph mapped
      to Uberon.
    download_owl: https://purl.brain-bican.org/ontology/dhbao/dhbao.owl
    homepage: https://purl.brain-bican.org/ontology/dhbao
    name: Developing Human Brain Atlas Ontology
    prefix: dhba
    uri_format: https://purl.brain-bican.org/ontology/dhbao/DHBA_$1
    version: '2025-11-13'
    version.iri: https://purl.brain-bican.org/ontology/dhbao/releases/2025-11-13/dhbao.owl
  pattern: ^\d+$
  preferred_prefix: DHBA
  prefix: dhba
  providers:
  - code: biopragmatics
    description: A static site generated for the DHBA resource
    example: null
    first_party: null
    homepage: https://biopragmatics.github.io/providers
    name: Biopragmatics Browser
    publications: null
    status: null
    uri_format: https://biopragmatics.github.io/providers/dhba/$1
  repository: https://github.com/brain-bican/developing_human_brain_atlas_ontology
  uri_format: https://purl.brain-bican.org/ontology/dhbao/DHBA_$1
diabetesomic:
  contact:
    email: liujianghua@usc.edu.cn
    github: null
    name: Jiang-hua Liu
    orcid: 0000-0003-0344-3168
  contributor:
    email: maaya.m466@gmail.com
    github: maayamanoj466
    name: Maaya Manoj
    orcid: 0009-0000-6974-6386
  description: DiabetesOmic is a multi-omics database designed to collect and analyze
    transcriptional regulatory information across five high-throughput sequencing
    modalities, including ChIP-seq, RNA-seq, ATAC-seq, scATAC-seq, and scRNA-seq.
    This database's identifiers each represent a single sample. It contains clinical
    complication annotations including diabetic nephropathy, retinopathy, and atherosclerosis
    to enhance translational relevance. It enables the identification of disease-associated
    regulatory elements, epigenetic modifications, and cell type-specific molecular
    signatures, providing valuable insights into the molecular mechanisms of diabetes
    and its complications.
  example: sample_002
  github_request_issue: 1628
  homepage: https://bio.liclab.net/diabetesOmicdb/
  keywords:
  - diabetes
  - omics
  - sample
  name: DiabetesOmic
  pattern: ^sample_\d{3}$
  prefix: diabetesomic
  publications:
  - doi: 10.1016/j.csbj.2025.05.008
    pmc: PMC12158550
    pubmed: '40502930'
    title: 'DiabetesOmic: A comprehensive multi-omics diabetes database'
    year: 2025
  reviewer:
    email: b.gyori@northeastern.edu
    github: bgyori
    name: Benjamin M. Gyori
    orcid: 0000-0001-9439-5346
  uri_format: https://bio.liclab.net/diabetesOmicdb/RNA-seq?sampleId=$1
dialnet.article:
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  mappings:
    wikidata: P1610
  prefix: dialnet.article
  references:
  - https://github.com/biopragmatics/bioregistry/pull/1171
  wikidata:
    description: identifier of an article in Dialnet
    example:
    - '262393'
    - '263241'
    - '3635829'
    homepage: https://dialnet.unirioja.es
    name: Dialnet article ID
    prefix: P1610
    uri_format: https://dialnet.unirioja.es/servlet/articulo?codigo=$1
dialnet.author:
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  keywords:
  - person
  - researcher
  mappings:
    wikidata: P1607
  prefix: dialnet.author
  references:
  - https://github.com/biopragmatics/bioregistry/pull/1171
  wikidata:
    description: identifier of an author in Dialnet
    example:
    - '241889'
    - '3073901'
    homepage: https://dialnet.unirioja.es
    name: Dialnet author ID
    pattern: ^[1-9]\d*$
    prefix: P1607
    uri_format: https://dialnet.unirioja.es/servlet/autor?codigo=$1
dialnet.book:
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  mappings:
    wikidata: P1608
  prefix: dialnet.book
  references:
  - https://github.com/biopragmatics/bioregistry/pull/1171
  wikidata:
    description: identifier of a book in Dialnet
    example:
    - '187021'
    - '190555'
    - '3555'
    homepage: https://dialnet.unirioja.es
    name: Dialnet book ID
    prefix: P1608
    uri_format: https://dialnet.unirioja.es/servlet/libro?codigo=$1
dialnet.journal:
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  mappings:
    wikidata: P1609
  prefix: dialnet.journal
  references:
  - https://github.com/biopragmatics/bioregistry/pull/1171
  wikidata:
    description: identifier of a journal in Dialnet
    example:
    - '1119'
    - '206'
    - '8911'
    homepage: http://dialnet.unirioja.es
    name: Dialnet journal ID
    pattern: ^[1-9]\d{0,6}$
    prefix: P1609
    uri_format: https://dialnet.unirioja.es/servlet/revista?codigo=$1
dicom:
  aberowl:
    description: DICOM Controlled Terminology (PS3.16 2017d Annex D)
    download_owl: http://aber-owl.net/media/ontologies/DCM/12/dcm.owl
    homepage: http://dicom.nema.org/medical/dicom/current/output/chtml/part16/chapter_D.html
    name: DICOM Controlled Terminology
    prefix: DCM
    version: 2017d_20170924
  bioportal:
    contact:
      email: dclunie@dclunie.com
      name: David Clunie
    description: DICOM Controlled Terminology (PS3.16 2025e Annex D)
    name: DICOM Controlled Terminology
    prefix: DCM
    version: 2025e_20251115
  contact:
    email: dclunie@dclunie.com
    github: null
    name: David Clunie
    orcid: 0000-0002-2406-1145
  example: '109082'
  fairsharing:
    abbreviation: DICOM
    description: DICOM — Digital Imaging and Communications in Medicine — is the international
      standard for medical images and related information (ISO 12052). It defines
      the formats for medical images that can be exchanged with the data and quality
      necessary for clinical use. DICOM is implemented in almost every radiology,
      cardiology imaging, and radiotherapy device (X-ray, CT, MRI, ultrasound, etc.),
      and increasingly in devices in other medical domains such as ophthalmology and
      dentistry. With tens of thousands of imaging devices in use, DICOM is one of
      the most widely deployed healthcare messaging standards in the world. There
      are literally billions of DICOM images currently in use for clinical care. Since
      its first publication in 1993, DICOM has revolutionized the practice of radiology,
      allowing the replacement of X-ray film with a fully digital workflow. Much as
      the Internet has become the platform for new consumer information applications,
      DICOM has enabled advanced medical imaging applications that have “changed the
      face of clinical medicine”. From the emergency department, to cardiac stress
      testing, to breast cancer detection, DICOM is the standard that makes medical
      imaging work — for doctors and for patients.
    homepage: http://medical.nema.org/
    name: Digital Imaging and COmmunications in Medicine
    prefix: FAIRsharing.b7z8by
    publications:
    - doi: 10.1007/s10278-013-9577-8
      pubmed_id: 23404629
      title: 'Multi-series DICOM: an extension of DICOM that stores a whole study
        in a single object.'
    - doi: 10.1016/j.crad.2005.07.003
      pubmed_id: 16223609
      title: 'DICOM demystified: a review of digital file formats and their use in
        radiological practice.'
    subjects:
    - Anatomy
    - Medicine
    - Biomedical Science
  hl7:
    description: 'Coded concepts defined in PS 3.16 Digital Imaging andCommunications
      in Medicine (DICOM): Part 16: Content Mapping Resource,Annex D: DICOM Controlled
      Terminology Definition'
    homepage: http://medical.nema.org/
    name: DICOM Controlled Terminology
    organization: DICOM Standards Committee
    preferred_prefix: DCM
    prefix: 1.2.840.10008.2.16.4
    status: Complete
  mappings:
    aberowl: DCM
    bioportal: DCM
    fairsharing: FAIRsharing.b7z8by
    hl7: 1.2.840.10008.2.16.4
    ols: dicom
  ols:
    contact: dclunie@dclunie.com
    description: DICOM Controlled Terminology
    download_owl: ftp://medical.nema.org/MEDICAL/Dicom/Resources/Ontology/DCM/dcm.owl
    homepage: http://dicom.nema.org/medical/dicom/current/output/chtml/part16/chapter_D.html
    name: DICOM Controlled Terminology
    prefix: dicom
    version: 2025b_20250411
  pattern: ^\d+$
  prefix: dicom
  publications:
  - doi: 10.1007/s10278-013-9577-8
    pmc: PMC3705029
    pubmed: '23404629'
    title: 'Multi-series DICOM: an extension of DICOM that stores a whole study in
      a single object'
    year: 2013
  - doi: 10.1016/j.crad.2005.07.003
    pmc: null
    pubmed: '16223609'
    title: 'DICOM demystified: a review of digital file formats and their use in radiological
      practice'
    year: 2005
  uri_format: http://dicom.nema.org/resources/ontology/DCM/$1
dictybase:
  biocontext:
    prefix: dictyBase
    uri_format: http://dictybase.org/gene/$1
  contact:
    email: pfey@northwestern.edu
    github: pfey03
    name: Petra Fey
    orcid: 0000-0002-4532-2703
  description: A resource for Dictyostelid discoideum (a soil-dwelling amoeba) genomics
  fairsharing:
    abbreviation: dictyBase
    description: dictyBase is a single-access database for the complete genome sequence
      and expression data of four Dictyostelid species providing information on research,
      genome and annotations. There is also a repository of plasmids and strains held
      at the Dicty Stock Centre. Relevant literature is integrated into the database,
      and gene models and functional annotation are manually curated from experimental
      results and comparative multigenome analyses.
    homepage: http://www.dictybase.org
    name: dictyBase
    prefix: FAIRsharing.4shj9c
    publications:
    - doi: 10.1007/978-1-62703-302-2_4
      pubmed_id: 23494302
      title: 'One stop shop for everything Dictyostelium: dictyBase and the Dicty
        Stock Center in 2012.'
    - doi: 10.1093/nar/gks1064
      pubmed_id: 23172289
      title: 'DictyBase 2013: integrating multiple Dictyostelid species.'
    - doi: 10.1093/nar/gkh138
      pubmed_id: 14681427
      title: 'dictyBase: a new Dictyostelium discoideum genome database.'
    subjects:
    - Anatomy
    - Life Science
    - Comparative Genomics
  go:
    homepage: http://dictybase.org
    name: dictyBase
    prefix: dictyBase
    synonyms:
    - DDB
    - DictyBase
    uri_format: http://dictybase.org/gene/$1
  integbio:
    description: This site contains information related to the ameboid protozoan Dictyostelium
      discoideum, including information of genomes and genes, conferences, experimental
      protocols, tools for analysis, and distribution of strains.
    fairsharing: biodbcore-000767
    homepage: http://dictybase.org/
    information_keywords:
    - Bioresource
    - Method
    - Ontology/Terminology/Nomenclature
    - Sequence
    - Image/Movie
    - Bibliography/Documents
    maintainer: Northwestern University
    name: dictyBase
    prefix: nbdc00420
    pubmeds:
    - '21087999'
    - '18974179'
    - '16381903'
    - '16957284'
    - '14681427'
    status: Active
    target_keywords:
    - Genome/Gene
    - DNA
    - Protein
    - Organism
  license: CC-BY-SA-4.0
  logo: https://dictybase-docker.github.io/developer-docs/static/4eeedc37c188406acdddc392200815a7/logo-nav-light.png
  mappings:
    biocontext: dictyBase
    fairsharing: FAIRsharing.4shj9c
    go: dictyBase
    integbio: nbdc00420
    ncbi: dictyBase
    prefixcommons: dictybase
    re3data: r3d100010586
    uniprot: DB-0015
  name: dictyBase
  ncbi:
    example: DDB0191090
    homepage: http://dictybase.org/
    name: Dictyostelium genome database
    prefix: dictyBase
  prefix: dictybase
  prefixcommons:
    description: Genome information, literature and experimental resources for Dictyostelium
      discoideum
    example: DBS0237308
    homepage: http://dictybase.org/
    keywords:
    - genome
    name: Dictyostelium discoideum online informatics resource
    pattern: ^DBS\d{7}$
    prefix: dictybase
  publications:
  - doi: 10.1007/978-1-62703-302-2_4
    pmc: PMC3762881
    pubmed: '23494302'
    title: 'One stop shop for everything Dictyostelium: dictyBase and the Dicty Stock
      Center in 2012'
    year: 2013
  - doi: 10.1093/nar/gks1064
    pmc: PMC3531180
    pubmed: '23172289'
    title: 'DictyBase 2013: integrating multiple Dictyostelid species'
    year: 2012
  - doi: 10.1093/nar/gkh138
    pmc: PMC308872
    pubmed: '14681427'
    title: 'dictyBase: a new Dictyostelium discoideum genome database'
    year: 2004
  re3data:
    description: dictyBase is an integrated genetic and literature database that contains
      published Dictyostelium discoideum literature, genes, expressed sequence tags
      (ESTs), as well as the chromosomal and mitochondrial genome sequences. Direct
      access to the genome browser, a Blast search tool, the Dictyostelium Stock Center,
      research tools, colleague databases, and much much more are just a mouse click
      away. Dictybase is a genome portal for the Amoebozoa. dictyBase is funded by
      a grant from the National Institute for General Medical Sciences.
    doi: 10.17616/R3XS50
    homepage: http://dictybase.org/
    license: other
    name: dictybase
    prefix: r3d100010586
    synonyms:
    - Dictyostelium discoideum
    xrefs:
      nif: 0000-02751
      omics: 03158
  synonyms:
  - dictyBase
  uniprot:
    abbreviation: dictyBase
    category: Organism-specific databases
    homepage: http://dictybase.org/
    name: Dictyostelium discoideum online informatics resource
    prefix: DB-0015
    publications:
    - doi: 10.1093/nar/gks1064
      pubmed: '23172289'
    uri_format: http://dictybase.org/db/cgi-bin/gene_page.pl?primary_id=$1
dictybase.est:
  biocontext:
    prefix: DICTYBASE.EST
  license: CC-BY-SA-4.0
  logo: https://dictybase-docker.github.io/developer-docs/static/4eeedc37c188406acdddc392200815a7/logo-nav-light.png
  mappings:
    biocontext: DICTYBASE.EST
    miriam: dictybase.est
    n2t: dictybase.est
  miriam:
    deprecated: false
    description: The dictyBase database provides data on the model organism Dictyostelium
      discoideum and related species. It contains the complete genome sequence, ESTs,
      gene models and functional annotations. This collection references expressed
      sequence tag (EST) information.
    homepage: http://dictybase.org/
    id: '00000330'
    name: Dictybase EST
    namespaceEmbeddedInLui: false
    pattern: ^DDB\d+$
    prefix: dictybase.est
    sampleId: DDB0016567
    uri_format: http://dictybase.org/db/cgi-bin/feature_page.pl?primary_id=$1
  n2t:
    description: The dictyBase database provides data on the model organism Dictyostelium
      discoideum and related species. It contains the complete genome sequence, ESTs,
      gene models and functional annotations. This collection references expressed
      sequence tag (EST) information.
    example: DDB0016567
    homepage: http://dictybase.org/
    name: Dictybase Gene at Northwestern University
    namespaceEmbeddedInLui: false
    pattern: ^DDB\d+$
    prefix: dictybase.est
    uri_format: http://dictybase.org/db/cgi-bin/feature_page.pl?primary_id=$1
  name: dictyBase Expressed Sequence Tag
  part_of_database: dictybase
  prefix: dictybase.est
dictybase.gene:
  biocontext:
    prefix: DICTYBASE.GENE
  contact:
    email: pfey@northwestern.edu
    github: pfey03
    name: Petra Fey
    orcid: 0000-0002-4532-2703
  domain: gene
  keywords:
  - gene
  license: CC-BY-SA-4.0
  logo: https://dictybase-docker.github.io/developer-docs/static/4eeedc37c188406acdddc392200815a7/logo-nav-light.png
  mappings:
    biocontext: DICTYBASE.GENE
    miriam: dictybase.gene
    n2t: dictybase.gene
  miriam:
    deprecated: false
    description: The dictyBase database provides data on the model organism Dictyostelium
      discoideum and related species. It contains the complete genome sequence, ESTs,
      gene models and functional annotations. This collection references gene information.
    homepage: http://dictybase.org/
    id: 00000286
    name: Dictybase Gene
    namespaceEmbeddedInLui: false
    pattern: ^DDB_G\d+$
    prefix: dictybase.gene
    sampleId: DDB_G0267522
    uri_format: http://dictybase.org/gene/$1
  n2t:
    description: The dictyBase database provides data on the model organism Dictyostelium
      discoideum and related species. It contains the complete genome sequence, ESTs,
      gene models and functional annotations. This collection references gene information.
    example: DDB_G0267522
    homepage: http://dictybase.org/
    name: Dictybase Gene at Northwestern University
    namespaceEmbeddedInLui: false
    pattern: ^DDB_G\d+$
    prefix: dictybase.gene
    uri_format: http://dictybase.org/gene/$1
  part_of: dictybase
  prefix: dictybase.gene
did:
  banana: did
  mappings:
    miriam: did
    n2t: did
  miriam:
    deprecated: false
    description: DIDs are an effort by the W3C Credentials Community Group and the
      wider Internet identity community to define identifiers that can be registered,
      updated, resolved, and revoked without any dependency on a central authority
      or intermediary.
    homepage: https://w3c-ccg.github.io/did-spec/
    id: 00000691
    name: Decentralized Identifiers (DIDs)
    namespaceEmbeddedInLui: true
    pattern: ^did:[a-z0-9]+:[A-Za-z0-9.\-:]+$
    prefix: did
    sampleId: sov:WRfXPg8dantKVubE3HX8pw
    uri_format: https://uniresolver.io/#did:$1
  n2t:
    description: DIDs are an effort by the W3C Credentials Community Group and the
      wider Internet identity community to define identifiers that can be registered,
      updated, resolved, and revoked without any dependency on a central authority
      or intermediary.
    example: sov:WRfXPg8dantKVubE3HX8pw
    homepage: https://w3c-ccg.github.io/did-spec/
    name: Decentralized Identifiers (DIDs)
    namespaceEmbeddedInLui: true
    pattern: ^did:[a-z0-9]+:[A-Za-z0-9.\-:]+$
    prefix: did
    uri_format: https://uniresolver.io/#did:$1
  name: Decentralized Identifier
  pattern: ^[a-z0-9]+:[A-Za-z0-9.\-:]+$
  prefix: did
dideo:
  aberowl:
    description: The Potential Drug-drug Interaction and Potential Drug-drug Interaction
      Evidence Ontology
    download_owl: http://aber-owl.net/media/ontologies/DIDEO/54/dideo.owl
    homepage: https://github.com/DIDEO/DIDEO
    name: Drug-drug Interaction and Drug-drug Interaction Evidence Ontology
    prefix: DIDEO
  biocontext:
    prefix: DIDEO
  bioportal:
    contact:
      email: mbrochhausen@gmail.com
      name: Mathias Brochhausen
    description: The Potential Drug-drug Interaction and Potential Drug-drug Interaction
      Evidence Ontology. DIDEO is created as part of an NIH-funded project aiming
      towards developing a new knowledge base for potential drug drug interaction
      information. In DIDEO we represent PDDIs as information content entities and
      we aim to also provide the evidence for those entities using nano- and micro
      publication approaches.
    homepage: https://github.com/DIDEO/DIDEO
    name: Drug Interaction and Evidence Ontology
    prefix: DIDEO
    publications:
    - https://dikb.org
    version: release version 2017-11-17
  example: 00000180
  fairsharing:
    abbreviation: DIDEO
    contact:
      email: rdb20@pitt.edu
      name: Richard D. Boyce
      orcid: 0000-0002-2993-2085
    description: 'A domain ontology for potential drug-drug interactions (PDDIs) that
      covers the material entities and processes in the domain of discourse for PDDI
      evidence and knowledge claims. The representation enables the integration of
      drug interaction mechanisms, effects, risk factors, severity, and management
      options with the chemical and pharmacological properties (e.g., chemical structure,
      function, pharmacokinetic and pharmacodynamic properties) of the interacting
      drugs. It also has a rich and detailed set evidence entities related to pharmacology.  See
      below for publications about DIDEO. A description of the goals of the project
      can be found in the following workshop paper located in the docs/DIDEO-discussion-ICBO-Brochhausen-2014.pdf:
      Brochhausen, M., Schneider, J., Malone, D., Empey, PE., Hogan WR., and Boyce,
      RD. Towards a foundational representation of potential drug-drug interaction
      knowledge. The 1st International Drug-Drug Interaction Knowledge Representation
      Workshop (DIKR 2014). Collocated with the 2014 International Conference on Biomedical
      Ontology (ICBO 2014). October 6th, Houston, Texas. United States.'
    domains:
    - Evidence
    - Natural Product
    - drug interaction
    homepage: https://github.com/DIDEO/DIDEO
    license: CC-BY-4.0
    name: The Potential Drug-drug Interaction and Potential Drug-drug Interaction
      Evidence Ontology
    prefix: FAIRsharing.9y8f0n
    publications:
    - doi: 10.1016/j.knosys.2016.10.006
      title: 'Conceptual models of drug-drug interactions : A summary of recent efforts'
      year: 2016
    - doi: 10.1186/s13326-018-0183-z
      pubmed: '29743102'
      title: Extending the DIDEO ontology to include entities from the natural product
        drug interaction domain of discourse
      year: 2018
    - pubmed: '29295242'
      title: Formalizing Evidence Type Definitions for Drug-Drug Interaction Studies
        to Improve Evidence Base Curation
      year: 2018
    subjects:
    - Biochemistry
  mappings:
    aberowl: DIDEO
    biocontext: DIDEO
    bioportal: DIDEO
    fairsharing: FAIRsharing.9y8f0n
    obofoundry: dideo
    ols: dideo
    ontobee: DIDEO
    wikidata.entity: Q81661586
  obofoundry:
    contact: mbrochhausen@gmail.com
    contact.github: mbrochhausen
    contact.label: Mathias Brochhausen
    contact.orcid: 0000-0003-1834-3856
    deprecated: false
    description: The Potential Drug-drug Interaction and Potential Drug-drug Interaction
      Evidence Ontology
    domain: chemistry and biochemistry
    download.owl: http://purl.obolibrary.org/obo/dideo.owl
    homepage: https://github.com/DIDEO/DIDEO
    license: CC BY 4.0
    license.url: https://creativecommons.org/licenses/by/4.0/
    name: Drug-drug Interaction and Drug-drug Interaction Evidence Ontology
    preferredPrefix: DIDEO
    prefix: dideo
    repository: https://github.com/DIDEO/DIDEO
  ols:
    description: The Potential Drug-drug Interaction and Potential Drug-drug Interaction
      Evidence Ontology
    download_owl: http://purl.obolibrary.org/obo/dideo.owl
    homepage: https://github.com/DIDEO/DIDEO
    name: Drug-drug Interaction and Drug-drug Interaction Evidence Ontology
    prefix: dideo
    tracker: https://github.com/DIDEO/DIDEO/issues
    version: '2023-10-16'
    version.iri: http://purl.obolibrary.org/obo/dideo/release/2023-10-16/dideo.owl
  ontobee:
    library: Library
    name: Drug-drug Interaction and Drug-drug Interaction Evidence Ontology
    prefix: DIDEO
  pattern: ^\d{8}$
  prefix: dideo
  publications:
  - doi: 10.1186/s13326-018-0183-z
    pmc: PMC5944177
    pubmed: '29743102'
    title: Extending the DIDEO ontology to include entities from the natural product
      drug interaction domain of discourse
    year: 2018
  - doi: null
    pmc: PMC5765984
    pubmed: '29295242'
    title: Formalizing Evidence Type Definitions for Drug-Drug Interaction Studies
      to Improve Evidence Base Curation
    year: 2017
  - doi: 10.1016/j.knosys.2016.10.006
    pmc: null
    pubmed: null
    title: 'Conceptual models of drug-drug interactions: A summary of recent efforts'
    year: 2016
  uri_format: http://purl.obolibrary.org/obo/DIDEO_$1
digitalconstruction.energy:
  example: EnergyProperty
  mappings:
    tib: dices
  part_of_database: digitalconstruction
  prefix: digitalconstruction.energy
  tib:
    description: An ontology for energy systems and energy efficiency in the construction
      and renovation domain
    download_rdf: https://digitalconstruction.github.io/Energy/v/0.5/energy.ttl
    homepage: https://digitalconstruction.github.io/v/0.5/index.html
    keywords:
    - NFDI4ING
    - Digital Planning and Construction
    - FID BAUdigital
    - NFDI4Energy
    - civil engineering
    name: Digital Construction Energy (dices)
    prefix: dices
    uri_format: https://w3id.org/digitalconstruction/0.5/Energy#$1
digitalconstruction.lifecycle:
  example: BLCS_Framework
  mappings:
    tib: dicl
  part_of_database: digitalconstruction
  prefix: digitalconstruction.lifecycle
  tib:
    description: An ontology to represent the enhancement of building data throughout
      the construction lifecycle stages
    download_rdf: https://digitalconstruction.github.io/Lifecycle/v/0.5/lifecycle.ttl
    homepage: https://digitalconstruction.github.io/Lifecycle/v/0.5/
    keywords:
    - NFDI4ING
    - Digital Planning and Construction
    - FID BAUdigital
    - civil engineering
    name: Digital Construction Lifecycle (dicl)
    prefix: dicl
    uri_format: https://w3id.org/digitalconstruction/0.5/Lifecycle#$1
digitalconstruction.occupancy:
  example: AcousticComfort
  mappings:
    tib: dicob
  part_of_database: digitalconstruction
  prefix: digitalconstruction.occupancy
  tib:
    description: Digital Construction Occupancy ontology represents those aspects
      of construction and renovation projects that concern the comfort, safety and
      health of occupants, including visual and thermal comfort, indoor air quality
      and building acoustics, as well as related sensor observations.
    download_rdf: https://digitalconstruction.github.io/Occupancy/v/0.5/occupancy.ttl
    homepage: https://digitalconstruction.github.io/Occupancy/v/0.5/
    keywords:
    - NFDI4ING
    - Digital Planning and Construction
    - FID BAUdigital
    - civil engineering
    name: Digital Construction Occupancy
    prefix: dicob
    uri_format: https://w3id.org/digitalconstruction/0.5/Occupancy#$1
digitrubber:
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: An ontology demonstrating rich ontology for rubber extrusion.
  download_json: https://github.com/TIBHannover/DIGIT-RUBBER/raw/refs/heads/main/digitrubber.json
  download_obo: https://github.com/TIBHannover/DIGIT-RUBBER/raw/refs/heads/main/digitrubber.obo
  download_owl: https://github.com/TIBHannover/DIGIT-RUBBER/raw/refs/heads/main/digitrubber.owl
  example: '000040'
  homepage: https://tibhannover.github.io/DIGIT-RUBBER/
  name: DigitRubber Ontology
  prefix: digitrubber
  repository: https://github.com/TIBHannover/DIGIT-RUBBER
  uri_format: https://www.tib.eu/digitrubber#DIGITRUBBER_$1
dinto:
  aberowl:
    description: DINTO is an OWL ontology that systematically organizes all drug-drug
      interaction (DDI) related information. Drug-drug interactions (DDIs) form a
      significant risk group for adverse effects associated with pharmaceutical treatment.
      These interactions are often reported in the literature, however, they are sparsely
      represented in machine-readable resources, such as online databases, thesauri
      or ontologies. DINTO is an ontology that describes and categorizes DDIs and
      all the possible mechanisms that can lead to them (including both pharmacodynamic
      and pharmacokinetic DDI mechanisms).
    download_owl: http://aber-owl.net/media/ontologies/DINTO/5/dinto.owl
    homepage: http://labda.inf.uc3m.es/doku.php?id=es:labda_dinto
    name: The Drug-Drug Interactions Ontology
    prefix: DINTO
    version: '1.3'
  biocontext:
    prefix: DINTO
  bioportal:
    contact:
      email: maria.herrero@kcl.ac.uk
      name: Maria Herrero
    description: DINTO is an OWL ontology that systematically organizes all drug-drug
      interaction (DDI) related information. Drug-drug interactions (DDIs) form a
      significant risk group for adverse effects associated with pharmaceutical treatment.
      These interactions are often reported in the literature, however, they are sparsely
      represented in machine-readable resources, such as online databases, thesauri
      or ontologies. DINTO is an ontology that describes and categorizes DDIs and
      all the possible mechanisms that can lead to them (including both pharmacodynamic
      and pharmacokinetic DDI mechanisms).
    homepage: http://labda.inf.uc3m.es/doku.php?id=es:labda_dinto
    name: The Drug-Drug Interactions Ontology
    prefix: DINTO
    version: '1.3'
  mappings:
    aberowl: DINTO
    biocontext: DINTO
    bioportal: DINTO
    obofoundry: dinto
    ontobee: DINTO
  obofoundry:
    contact: maria.herrero@kcl.ac.uk
    contact.label: Maria Herrero
    deprecated: true
    description: A formal represention for drug-drug interactions knowledge.
    domain: health
    download.owl: http://purl.obolibrary.org/obo/dinto.owl
    homepage: http://labda.inf.uc3m.es/doku.php?id=es:labda_dinto
    license: CC BY 3.0
    license.url: https://creativecommons.org/licenses/by/3.0/
    name: The Drug-Drug Interactions Ontology
    prefix: dinto
    publications:
    - id: https://www.ncbi.nlm.nih.gov/pubmed/26147071
      title: 'DINTO: Using OWL Ontologies and SWRL Rules to Infer Drug–Drug Interactions
        and Their Mechanisms.'
    repository: https://github.com/labda/DINTO
  ontobee:
    library: Library
    name: The Drug-Drug Interactions Ontology
    prefix: DINTO
  prefix: dinto
  publications:
  - doi: 10.1021/acs.jcim.5b00119
    pmc: null
    pubmed: '26147071'
    title: 'DINTO: Using OWL Ontologies and SWRL Rules to Infer Drug-Drug Interactions
      and Their Mechanisms'
    year: 2015
dip:
  biocontext:
    prefix: DIP
  contact:
    email: david@mbi.ucla.edu
    github: null
    name: David Eisenberg
    orcid: 0000-0003-2432-5419
  edam:
    description: Unique identifier of an entry from the DIP database of protein-protein
      interactions.
    name: DIP
    obsolete: false
    prefix: '2616'
  fairsharing:
    abbreviation: DIP
    description: The database of interacting protein (DIP) database stores experimentally
      determined interactions between proteins. It combines information from a variety
      of sources to create a single, consistent set of protein-protein interactions.
      The data stored within the DIP database were curated, both manually by expert
      curators and automatically using computational approaches that utilize the the
      knowledge about the protein-protein interaction networks extracted from the
      core DIP data.
    homepage: https://dip.doe-mbi.ucla.edu/dip/Main.cgi
    license: CC BY-ND 3.0
    name: Database of Interacting Proteins
    prefix: FAIRsharing.qje0v8
    publications:
    - doi: 10.1093/nar/29.1.239
      pubmed_id: 11125102
      title: 'DIP: The Database of Interacting Proteins: 2001 update.'
    - doi: 10.1093/nar/28.1.289
      pubmed_id: 10592249
      title: 'DIP: the database of interacting proteins.'
    - doi: 10.1093/nar/30.1.303
      pubmed_id: 11752321
      title: 'DIP, the Database of Interacting Proteins: a research tool for studying
        cellular networks of protein interactions.'
    - doi: 10.1093/nar/gkh086
      pubmed_id: 14681454
      title: 'The Database of Interacting Proteins: 2004 update.'
    subjects:
    - Biology
  integbio:
    alt_name: Database of Interacting Proteins
    description: The DIP is a database of experimentally determined interactions between
      proteins. It contains protein pairs that are known to bind with each other at
      two amino acid chains. Each entry is curated, both, manually by expert curators
      and also automatically using computational approaches that utilize the the knowledge
      about the protein-protein interaction networks extracted from the most reliable,
      core subset of the DIP data. Each protein participating in a DIP interaction
      cross-references to, at least, one of the major protein databases - PIR, SWISSPROT
      and/or GENBANK. This database can be searched with node, BLAST, or text searches.
    fairsharing: biodbcore-000558
    homepage: http://dip.doe-mbi.ucla.edu/dip/Main.cgi
    information_keywords:
    - Sequence
    - Interaction/Pathway
    - Repository
    maintainer: University of California
    name: DIP
    prefix: nbdc00049
    pubmeds:
    - '14681454'
    - '1175232'
    - '11125102'
    - '10592249'
    status: Active
    target_keywords:
    - Protein
  logo: https://dip.doe-mbi.ucla.edu/dip/img/dip_logo.png
  mappings:
    biocontext: DIP
    edam: '2616'
    fairsharing: FAIRsharing.qje0v8
    integbio: nbdc00049
    miriam: dip
    n2t: dip
    pathguide: '3'
    prefixcommons: dip
    re3data: r3d100010670
    uniprot: DB-0016
  miriam:
    deprecated: false
    description: The database of interacting protein (DIP) database stores experimentally
      determined interactions between proteins. It combines information from a variety
      of sources to create a single, consistent set of protein-protein interactions
    homepage: https://dip.doe-mbi.ucla.edu/
    id: '00000044'
    name: Database of Interacting Proteins
    namespaceEmbeddedInLui: false
    pattern: ^DIP(\:)?\-\d{1,}[ENXS]$
    prefix: dip
    sampleId: DIP-743N
    uri_format: https://dip.doe-mbi.ucla.edu/dip/DIPview.cgi?ID=$1
  n2t:
    description: The database of interacting protein (DIP) database stores experimentally
      determined interactions between proteins. It combines information from a variety
      of sources to create a single, consistent set of protein-protein interactions
    example: DIP-743N
    homepage: https://dip.doe-mbi.ucla.edu/
    name: Database of interacting proteins
    namespaceEmbeddedInLui: false
    pattern: ^DIP(\:)?\-\d{1,}[ENXS]$
    prefix: dip
    uri_format: https://dip.doe-mbi.ucla.edu/dip/DIPview.cgi?ID=$1
  pathguide:
    abbreviation: DIP
    homepage: http://dip.doe-mbi.ucla.edu/dip/Main.cgi
    keywords:
    - PSI-MI
    name: Database of Interacting Proteins
    prefix: '3'
  prefix: dip
  prefixcommons:
    description: The database of interacting protein (DIP) database stores experimentally
      determined interactions between proteins. It combines information from a variety
      of sources to create a single, consistent set of protein-protein interactions
    example: DIP-743N
    homepage: http://dip.doe-mbi.ucla.edu
    keywords:
    - interaction
    - protein
    license: http://dip.doe-mbi.ucla.edu/dip/termsofuse.html
    name: Database of Interacting Proteins
    pattern: ^DIP[\:\-]\d{3}[EN]$
    prefix: dip
    pubmed_ids:
    - '14681454'
    uri_format: http://dip.doe-mbi.ucla.edu/dip/DIPview.cgi?ID=$1
  publications:
  - doi: 10.1093/nar/gkh086
    pmc: PMC308820
    pubmed: '14681454'
    title: 'The Database of Interacting Proteins: 2004 update'
    year: 2004
  - doi: 10.1093/nar/30.1.303
    pmc: PMC99070
    pubmed: '11752321'
    title: 'DIP, the Database of Interacting Proteins: a research tool for studying
      cellular networks of protein interactions'
    year: 2002
  - doi: 10.1093/nar/29.1.239
    pmc: PMC29798
    pubmed: '11125102'
    title: 'DIP: The Database of Interacting Proteins: 2001 update'
    year: 2001
  - doi: 10.1093/nar/28.1.289
    pmc: PMC102387
    pubmed: '10592249'
    title: 'DIP: the database of interacting proteins'
    year: 2000
  re3data:
    description: The DIP database catalogs experimentally determined interactions
      between proteins. It combines information from a variety of sources to create
      a single, consistent set of protein-protein interactions. The data stored within
      the DIP database were curated, both, manually by expert curators and also automatically
      using computational approaches that utilize the the knowledge about the protein-protein
      interaction networks extracted from the most reliable, core subset of the DIP
      data. Please, check the reference page to find articles describing the DIP database
      in greater detail. The Database of Ligand-Receptor Partners (DLRP) is a subset
      of DIP (Database of Interacting Proteins). The DLRP is a database of protein
      ligand and protein receptor pairs that are known to interact with each other.
      By interact we mean that the ligand and receptor are members of a ligand-receptor
      complex and, unless otherwise noted, transduce a signal. In some instances the
      ligand and/or receptor may form a heterocomplex with other ligands/receptors
      in order to be functional. We have entered the majority of interactions in DLRP
      as full DIP entries, with links to references and additional information
    doi: 10.17616/R3VG8D
    homepage: https://dip.doe-mbi.ucla.edu/dip/Main.cgi
    name: Database of Interacting Proteins
    prefix: r3d100010670
    synonyms:
    - DIP
    xrefs:
      nif: 0000-00569
      omics: 01905
  uniprot:
    abbreviation: DIP
    category: Protein-protein interaction databases
    homepage: https://dip.doe-mbi.ucla.edu/
    name: Database of interacting proteins
    prefix: DB-0016
    publications:
    - doi: 10.1093/nar/gkh086
      pubmed: '14681454'
    uri_format: https://dip.doe-mbi.ucla.edu/dip/Browse.cgi?ID=$1
discoverx:
  cellosaurus:
    category: Cell line collections (Providers)
    homepage: https://emea.discoverx.com/product_types/cell-lines-primary-cells
    name: DiscoverX cell line products
    prefix: DiscoverX
    uri_format: https://emea.discoverx.com/catalog/$1
  example: 95-0166C6
  mappings:
    cellosaurus: DiscoverX
  prefix: discoverx
disdriv:
  aberowl:
    description: Ontology for drivers and triggers of human diseases, built to classify
      ExO ontology exposure stressors. An application ontology. Built in collaboration
      with EnvO, ExO, ECTO and ChEBI.
    download_owl: http://aber-owl.net/media/ontologies/DISDRIV/3/disdriv.owl
    homepage: http://www.disease-ontology.org
    name: Disease Drivers Ontology
    prefix: DISDRIV
  bioportal:
    contact:
      email: lynn.schriml@gmail.com
      name: Lynn Schriml
    description: Ontology for drivers and triggers of human diseases, built to classify
      ExO ontology exposure stressors. An application ontology. Built in collaboration
      with EnvO, ExO, ECTO and ChEBI.
    homepage: https://disease-ontology.org/
    name: Disease Drivers Ontology
    prefix: DISDRIV
    version: '2025-03-20'
  example: '0000000'
  mappings:
    aberowl: DISDRIV
    bioportal: DISDRIV
    obofoundry: disdriv
    ols: disdriv
    ontobee: DISDRIV
    wikidata.entity: Q113009148
  obofoundry:
    contact: lynn.schriml@gmail.com
    contact.github: lschriml
    contact.label: Lynn Schriml
    contact.orcid: 0000-0001-8910-9851
    deprecated: false
    description: Ontology for drivers and triggers of human diseases, built to classify
      ExO ontology exposure stressors. An application ontology. Built in collaboration
      with EnvO, ExO, ECTO and ChEBI.
    domain: health
    download.owl: http://purl.obolibrary.org/obo/disdriv.owl
    homepage: https://disease-ontology.org/
    license: CC0 1.0
    license.url: https://creativecommons.org/publicdomain/zero/1.0/
    name: Disease Drivers Ontology
    preferredPrefix: DISDRIV
    prefix: disdriv
    repository: https://github.com/DiseaseOntology/DiseaseDriversOntology
    twitter: diseaseontology
  ols:
    description: Drivers of human diseases including environmental, maternal and social
      exposures.
    download_owl: http://purl.obolibrary.org/obo/disdriv.owl
    homepage: https://disease-ontology.org/
    name: Disease Drivers
    prefix: disdriv
    tracker: https://github.com/DiseaseOntology/DiseaseDriversOntology/issues
    version: '2025-03-20'
    version.iri: http://purl.obolibrary.org/obo/disdriv/releases/2025-03-20/disdriv.owl
  ontobee:
    library: Library
    name: Disease Drivers Ontology
    prefix: DISDRIV
  pattern: ^\d+$
  prefix: disdriv
  uri_format: http://purl.obolibrary.org/obo/DISDRIV_$1
diseaseclass:
  appears_in:
  - efo
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  deprecated: true
  description: Legacy disease classes that later became MONDO
  download_obo: https://github.com/obophenotype/human-disease-ontology/raw/master/src/experimental/missing-omc.obo
  example: 0000598
  name: Disease Class
  pattern: ^\d{7}$
  prefix: diseaseclass
  uri_format: https://biopragmatics.github.io/providers/diseaseclass/$1
diseasesdb:
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: 'The Diseases Database is a cross-referenced index of human disease,
    medications, symptoms, signs, abnormal investigation findings etc. This site provides
    a medical textbook-like index and search portal covering areas including: internal
    medical disorders, symptoms and signs, congenital and inherited disorders, infectious
    diseases and organisms, drugs and medications, common haematology and biochemistry
    investigation abnormalities.'
  example: '1784'
  homepage: http://www.diseasesdatabase.com/
  mappings:
    wikidata: P557
  name: Diseases Database
  pattern: ^\d+$
  prefix: diseasesdb
  uri_format: https://www.diseasesdatabase.com/ddb$1.htm
  wikidata:
    description: identifier sourced on the Diseases Database
    example:
    - '10166'
    - '8664'
    homepage: http://www.diseasesdatabase.com
    name: DiseasesDB
    pattern: ^\d{2,5}$
    prefix: P557
    uri_format: http://www.diseasesdatabase.com/ddb$1.htm
disprot:
  biocontext:
    prefix: DISPROT
  edam:
    description: Unique identifier for a protein from the DisProt database.
    name: Protein ID (DisProt)
    obsolete: false
    prefix: '2723'
  fairsharing:
    abbreviation: DisProt
    contact:
      email: silvio.tosatto@unipd.it
      name: Silvio C.E. Tosatto
      orcid: 0000-0003-4525-7793
    description: The Database of Protein Disorder (DisProt) is a curated database
      that provides information about intrinsically disordered proteins that lack
      fixed 3D structure in their putatively native states, either in their entirety
      or in part. Disordered regions are manually curated from literature. DisProt
      annotations cover both structural and functional aspects of disorder detected
      by specific experimental methods.
    homepage: https://disprot.org/
    license: CC-BY-4.0
    name: DisProt
    prefix: FAIRsharing.dt9z89
    publications:
    - doi: 10.1093/nar/gkl893
      pubmed_id: 17145717
      title: 'DisProt: the Database of Disordered Proteins.'
    - doi: 10.1093/nar/gkw1056
      pubmed_id: 27899601
      title: 'DisProt 7.0: a major update of the database of disordered proteins.'
    - doi: 10.1093/nar/gkz975
      pubmed_id: 31713636
      title: 'DisProt: intrinsic protein disorder annotation in 2020.'
    - doi: 10.1093/nar/gkab1082
      pubmed_id: null
      title: 'DisProt in 2022: improved quality and accessibility of protein intrinsic
        disorder annotation'
    repository: https://disprot.github.io/
    subjects:
    - Structural Biology
    - Biomedical Science
    - Biology
    twitter: disprot_db
  go:
    description: Database of intrinsically disordered proteins
    homepage: https://www.disprot.org
    name: DisProt
    prefix: DisProt
    uri_format: https://www.disprot.org/$1
  integbio:
    description: The Database of Protein Disorder (DisProt) is a curated database
      that provides information about intrinsically disordered proteins that lack
      fixed 3D structure in their putatively native states, either in their entirety
      or in part. Disordered regions are manually curated from literature. DisProt
      annotations cover both structural and functional aspects of disorder detected
      by specific experimental methods.
    fairsharing: FAIRsharing.dt9z89
    homepage: https://disprot.org/
    information_keywords:
    - Sequence
    - 3D structure
    - Chemical structure
    - Interaction/Pathway
    maintainer: BioComputing laboratory, University of Padua
    name: DisProt
    prefix: nbdc01798
    pubmeds:
    - '17145717'
    status: Active
    target_keywords:
    - Protein
    - Health/Disease
  logo: https://disprot.org/assets/DisProt_prot_vect_brownonly.svg
  mappings:
    biocontext: DISPROT
    edam: '2723'
    fairsharing: FAIRsharing.dt9z89
    go: DisProt
    integbio: nbdc01798
    miriam: disprot
    n2t: disprot
    prefixcommons: disprot
    re3data: r3d100010561
    uniprot: DB-0017
  miriam:
    deprecated: false
    description: DisProt is a database of intrinsically disordered proteins and protein
      disordered regions, manually curated from literature.
    homepage: https://disprot.org/
    id: 00000199
    name: DisProt
    namespaceEmbeddedInLui: false
    pattern: ^DP\d{5}$
    prefix: disprot
    sampleId: DP00003
    uri_format: https://disprot.org/$1
  n2t:
    description: The Database of Protein Disorder (DisProt) is a curated database
      that provides information about proteins that lack fixed 3D structure in their
      putatively native states, either in their entirety or in part.
    example: DP00003
    homepage: http://www.disprot.org/
    name: DisProt at Indiana University
    namespaceEmbeddedInLui: false
    pattern: ^DP\d{5}$
    prefix: disprot
    uri_format: http://www.disprot.org/$1
  prefix: disprot
  prefixcommons:
    description: The Database of Protein Disorder (DisProt) is a curated database
      that provides information about proteins that lack fixed 3D structure in their
      putatively native states, either in their entirety or in part.
    example: DP00001
    homepage: http://www.disprot.org/
    keywords:
    - protein
    - structure
    name: Database of protein disorder
    pattern: ^DP\d{5}$
    prefix: disprot
    pubmed_ids:
    - '17145717'
    uri_format: http://www.disprot.org/protein.php?id=$1
  publications:
  - doi: 10.1093/nar/gkab1082
    pmc: PMC8728214
    pubmed: '34850135'
    title: 'DisProt in 2022: improved quality and accessibility of protein intrinsic
      disorder annotation'
    year: 2022
  - doi: 10.1093/nar/gkz975
    pmc: PMC7145575
    pubmed: '31713636'
    title: 'DisProt: intrinsic protein disorder annotation in 2020'
    year: 2020
  - doi: 10.1093/nar/gkw1056
    pmc: PMC5210544
    pubmed: '27899601'
    title: 'DisProt 7.0: a major update of the database of disordered proteins'
    year: 2016
  - doi: 10.1093/nar/gkl893
    pmc: PMC1751543
    pubmed: '17145717'
    title: 'DisProt: the Database of Disordered Proteins'
    year: 2006
  - doi: 10.1093/bioinformatics/bth476
    pmc: null
    pubmed: '15310560'
    title: 'DisProt: a database of protein disorder'
    year: 2004
  re3data:
    description: 'The Database of Protein Disorder (DisProt) is a curated database
      that provides information about proteins that lack fixed 3D structure in their
      putatively native states, either in their entirety or in part.  DisProt is a
      community resource annotating protein sequences for intrinsically disorder regions
      from the literature.

      It classifies intrinsic disorder based on experimental methods and three ontologies
      for molecular function, transition and binding partner.'
    doi: 10.17616/R3NG75
    homepage: https://www.disprot.org/
    name: DisProt
    prefix: r3d100010561
    synonyms:
    - Database of Protein Disorder
    xrefs:
      nif: 0000-02754
  uniprot:
    abbreviation: DisProt
    category: Family and domain databases
    homepage: https://disprot.org
    name: Database of protein disorder
    prefix: DB-0017
    publications:
    - doi: 10.1093/nar/gkab1082
      pubmed: '34850135'
    uri_format: https://disprot.org/$1
disprot.region:
  mappings:
    miriam: disprot.region
  miriam:
    deprecated: false
    description: DisProt is a database of intrisically disordered proteins and protein
      disordered regions, manually curated from literature.
    homepage: https://www.disprot.org
    id: '00000745'
    name: DisProt region
    namespaceEmbeddedInLui: false
    pattern: ^DP\d{5}r\d{3}$
    prefix: disprot.region
    sampleId: DP00086r013
    uri_format: https://www.disprot.org/$1
  part_of: disprot
  prefix: disprot.region
dlxb:
  mappings:
    miriam: dlxb
  miriam:
    deprecated: false
    description: DOULIX lab-tested standard biological parts, in this case linear
      double stranded DNA sequences.
    homepage: https://doulix.com
    id: '00000747'
    name: Linear double stranded DNA sequences
    namespaceEmbeddedInLui: false
    pattern: ^[A-Z0-9]{6,7}$
    prefix: dlxb
    sampleId: 6VDC956
    uri_format: https://doulix.com/biomodules/$1/
  part_of_database: dlx
  prefix: dlxb
  uri_format: https://doulix.com/biomodules/$1
dlxc:
  mappings:
    miriam: dlxc
  miriam:
    deprecated: false
    description: DOULIX lab-tested standard biological parts, in this case, full length
      constructs.
    homepage: https://doulix.com
    id: '00000742'
    name: Circular double stranded DNA sequences composed
    namespaceEmbeddedInLui: false
    pattern: ^[A-Z0-9]{6,7}$
    prefix: dlxc
    sampleId: M77F7JM
    uri_format: https://doulix.com/constructs/$1/
  part_of_database: dlx
  prefix: dlxc
  uri_format: https://doulix.com/constructs/$1
dmba:
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: A controlled vocabulary to support the study of transcription in the
    developing mouse brain
  download_obo: https://raw.githubusercontent.com/obophenotype/uberon/master/source-ontologies/allen-dmba.obo
  example: '15567'
  homepage: https://developingmouse.brain-map.org/
  mappings:
    ols: dmba
  name: Developing Mouse Brain Atlas
  ols:
    contact: cellsemantics@gmail.com
    description: An application ontology built by combining ontologised versions of
      the Allen Institute Developing Mouse Brain Atlas (DMBA) StructureGraph mapped
      to Uberon.
    download_owl: https://purl.brain-bican.org/ontology/dmbao/dmbao.owl
    homepage: https://purl.brain-bican.org/ontology/dmbao
    name: Developing Mouse Brain Atlas Ontology
    prefix: dmba
    uri_format: https://purl.brain-bican.org/ontology/dmbao/DMBA_$1
    version: '2025-02-10'
    version.iri: https://purl.brain-bican.org/ontology/dmbao/releases/2025-02-10/dmbao.owl
  pattern: ^\d+$
  preferred_prefix: DMBA
  prefix: dmba
  providers:
  - code: biopragmatics
    description: Biopragmatics provider for DMBA
    example: null
    first_party: null
    homepage: https://biopragmatics.github.io/providers/dmba
    name: DMBA from Biopragmatics
    publications: null
    status: null
    uri_format: https://biopragmatics.github.io/providers/dmba/$1
  repository: https://github.com/brain-bican/developing_mouse_brain_atlas_ontology
  uri_format: https://purl.brain-bican.org/ontology/dmbao/DMBA_$1
doap:
  contact:
    email: edd@usefulinc.com
    github: ewilderj
    name: Edd Wilder-James
    orcid: null
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: DOAP is a project to create an XML/RDF vocabulary to describe software
    projects, and in particular open source projects.
  download_rdf: http://usefulinc.com/ns/doap
  example: Project
  homepage: https://github.com/ewilderj/doap/wiki
  keywords:
  - metadata
  - rdf
  - semantic web
  lov:
    description: The Description of a Project (DOAP) vocabulary, described using W3C
      RDF Schema and the Web Ontology Language.
    homepage: https://github.com/edumbill/doap/wiki
    keywords:
    - Society
    modified: '2012-01-04'
    name: Description of a Project vocabulary
    prefix: doap
    uri_prefix: http://usefulinc.com/ns/doap#$1
  mappings:
    lov: doap
    zazuko: doap
  name: Description of a Project
  preferred_prefix: doap
  prefix: doap
  references:
  - https://en.wikipedia.org/wiki/DOAP
  repository: https://github.com/ewilderj/doap
  uri_format: http://usefulinc.com/ns/doap#$1
  zazuko:
    prefix: doap
    uri_format: http://usefulinc.com/ns/doap#$1
docid:
  contact:
    email: null
    github: Africa-PID-Alliance
    name: Joy Owango
    orcid: 0000-0002-3910-2691
  contact_group_email: info@africapidalliance.org
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: Assigns persistent identifiers to multidisciplinary research outputs
    with focus on research originating in Africa, such as in cultural heritage and
    indigenous knowledge.
  example: 20.500.14351/5a7cdd09d9b65bc39697
  github_request_issue: 1692
  homepage: https://docid.africapidalliance.org/
  keywords:
  - bibliometrics
  - cultural heritage
  - digital humanities
  - publishing
  name: Digical Object Container Identifier
  owners:
  - name: University of Nairobi
    partnered: false
    ror: 02y9nww90
    wikidata: null
  prefix: docid
  synonyms:
  - DOCiD
  uri_format: https://docid.africapidalliance.org/docid/$1
dockerhub.repo:
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  mappings:
    wikidata: P8778
  prefix: dockerhub.repo
  references:
  - https://github.com/biopragmatics/bioregistry/pull/1171
  wikidata:
    description: Docker repository hosted on Docker Hub
    example:
    - gitea/gitea
    - library/nginx
    - library/redis
    homepage: https://hub.docker.com/
    name: Docker Hub repository
    prefix: P8778
    uri_format: https://hub.docker.com/r/$1
dockerhub.user:
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: A user in DockerHub
  example: cthoyt
  homepage: https://hub.docker.com/
  name: DockerHub User
  prefix: dockerhub.user
  uri_format: https://hub.docker.com/u/$1
doco:
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: An ontology that provides a structured vocabulary written of document
    components, both structural (e.g., block, inline, paragraph, section, chapter)
    and rhetorical (e.g., introduction, discussion, acknowledgements, reference list,
    figure, appendix).
  example: Paragraph
  fairsharing:
    abbreviation: DoCO
    contact:
      email: silvio.peroni@unibo.it
      name: Silvio Peroni
      orcid: 0000-0003-0530-4305
    description: The Document Components Ontology (DoCO) is an ontology that provides
      a structured vocabulary written of document components, both structural (e.g.,
      block, inline, paragraph, section, chapter) and rhetorical (e.g., introduction,
      discussion, acknowledgements, reference list, figure, appendix).
    homepage: http://www.sparontologies.net/ontologies/doco
    license: CC-BY-4.0
    name: 'Document Components Ontology '
    prefix: FAIRsharing.162003
    publications:
    - doi: 10.3233/sw-150177
      title: The Document Components Ontology (DoCO)
      year: 2016
    repository: https://github.com/sparontologies/doco
    subjects:
    - Subject Agnostic
    twitter: sparontologies
  homepage: http://www.sparontologies.net/ontologies/doco
  lov:
    description: An ontology for describing the component parts of a bibliographic
      document
    homepage: https://sparontologies.github.io/doco/current/doco.html
    keywords:
    - SPAR
    modified: '2015-07-03'
    name: DoCO, the Document Components Ontology
    prefix: doco
    uri_prefix: http://purl.org/spar/doco/$1
  mappings:
    fairsharing: FAIRsharing.162003
    lov: doco
  name: Document Components Ontology
  preferred_prefix: DoCO
  prefix: doco
  publications:
  - doi: 10.3233/sw-150177
    pmc: null
    pubmed: null
    title: The Document Components Ontology (DoCO)
    year: 2016
  repository: https://github.com/sparontologies/doco
  uri_format: http://purl.org/spar/doco/$1
dogont:
  example: AccelerationStateValue
  lov:
    description: The DogOnt ontology supports device/network independent description
      of houses, including both controllable and architectural elements.
    homepage: http://iot-ontologies.github.io/dogont/
    keywords:
    - Environment
    - IoT
    modified: '2015-01-11'
    name: Ontology Modeling for Intelligent Domotic Environments
    prefix: dogont
    uri_prefix: http://elite.polito.it/ontologies/dogont$1
  mappings:
    lov: dogont
    tib: dogont
  prefix: dogont
  tib:
    description: DogOnt is a modeling language for IEs (Intelligent Environments),
      based on Semantic Web technologies. By adopting well known representations such
      as ontologies and by providing suitable reasoning facilities,
    download_owl: https://raw.githubusercontent.com/iot-ontologies/dogont/master/dogont.owl
    homepage: http://iot-ontologies.github.io/dogont/
    keywords:
    - NFDI4ING
    - NFDI4Energy
    - engineering
    name: DogOnt Ontology Modeling for Intelligent Domotic Environments
    prefix: dogont
    tracker: https://github.com/iot-ontologies/dogont/issues
    uri_format: http://elite.polito.it/ontologies/dogont.owl#$1
doi:
  banana: doi
  bartoc:
    abbreviation: DOI
    description: 'A DOI is a digital identifier of an object, any object — physical,
      digital, or abstract. DOIs solve a common problem: keeping track of things.
      Things can be matter, material, content, or activities.'
    homepage: https://www.doi.org/
    license: CC-BY-4.0
    name: Digital Object Identifier
    prefix: '20716'
  biocontext:
    prefix: DOI
    uri_format: http://dx.doi.org/$1
  biolink:
    is_identifiers: false
    is_obo: false
    prefix: doi
    uri_format: https://doi.org/$1
  cellosaurus:
    category: Reference resources
    homepage: https://doi.org
    name: Digital Object Identifier
    prefix: DOI
    uri_format: https://doi.org/$1
  comment: 'The [DOI resolution factsheet](https://www.doi.org/factsheets/DOIProxy.html)
    specifies that `https://doi.org/DOI` is the preferred format:


    > Users may resolve DOI names that are structured to use the DOI system Proxy
    Server (https://doi.org (preferred)). The resolution of the DOI name in this case
    depends on the use of URL syntax: the example DOI name doi:10.10.123/456 would
    be resolved from the address: "https://doi.org/10.123/456". Any standard browser
    encountering a DOI name in this form will be able to resolve it. The proxy service
    (both doi.org and the **earlier but no longer preferred** dx.doi.org) is accessible
    over IPv6, and supports DNSSEC. The proxy servers respond to HTTPS (**preferred**)
    as well as HTTP requests.'
  contributor_extras:
  - email: cjmungall@lbl.gov
    github: cmungall
    name: Chris Mungall
    orcid: 0000-0002-6601-2165
  - email: null
    github: dhimmel
    name: Daniel Himmelstein
    orcid: 0000-0002-3012-7446
  edam:
    description: Digital Object Identifier (DOI) of a published article.
    name: DOI
    obsolete: false
    prefix: '1188'
  example: 10.1038/s41597-022-01807-3
  example_extras:
  - 10.21/FQSQT4T3
  - 10.1333/s00897980202a
  - 10.1139/z02-135
  - 10.1016/j.foodchem.2008.11.065
  - 10.1093/acprof:oso/9780195159561.001.1
  fairsharing:
    abbreviation: DOI
    contact:
      email: jonathanmtclark@gmail.com
      name: Jonathan Clark
      orcid: 0000-0001-9551-9662
    description: The digital object identifier (DOI) system originated in a joint
      initiative of three trade associations in the publishing industry (International
      Publishers Association; International Association of Scientific, Technical and
      Medical Publishers; Association of American Publishers). The system was announced
      at the Frankfurt Book Fair 1997. The International DOI® Foundation (IDF) was
      created to develop and manage the DOI system, also in 1997. The DOI system was
      adopted as International Standard ISO 26324 in 2012. The DOI system implements
      the Handle System and adds a number of new features. The DOI system provides
      an infrastructure for persistent unique identification of objects of any type.
      The DOI system is designed to work over the Internet. A DOI name is permanently
      assigned to an object to provide a resolvable persistent network link to current
      information about that object, including where the object, or information about
      it, can be found on the Internet. While information about an object can change
      over time, its DOI name will not change. A DOI name can be resolved within the
      DOI system to values of one or more types of data relating to the object identified
      by that DOI name, such as a URL, an e-mail address, other identifiers and descriptive
      metadata. The DOI system enables the construction of automated services and
      transactions. Applications of the DOI system include but are not limited to
      managing information and documentation location and access; managing metadata;
      facilitating electronic transactions; persistent unique identification of any
      form of any data; and commercial and non-commercial transactions. The content
      of an object associated with a DOI name is described unambiguously by DOI metadata,
      based on a structured extensible data model that enables the object to be associated
      with metadata of any desired degree of precision and granularity to support
      description and services. The data model supports interoperability between DOI
      applications. The scope of the DOI system is not defined by reference to the
      type of content (format, etc.) of the referent, but by reference to the functionalities
      it provides and the context of use. The DOI system provides, within networks
      of DOI applications, for unique identification, persistence, resolution, metadata
      and semantic interoperability.
    domains:
    - centrally registered identifier
    homepage: https://www.doi.org
    name: Digital Object Identifier
    prefix: FAIRsharing.hFLKCn
    publications:
    - doi: 10.1000/292
      title: DOI URI Scheme
      year: 2024
    subjects:
    - Subject Agnostic
  go:
    homepage: http://dx.doi.org/
    name: Digital Object Identifier
    prefix: DOI
    uri_format: http://dx.doi.org/$1
  logo: https://upload.wikimedia.org/wikipedia/commons/1/11/DOI_logo.svg
  mappings:
    bartoc: '20716'
    biocontext: DOI
    biolink: doi
    cellosaurus: DOI
    edam: '1188'
    fairsharing: FAIRsharing.hFLKCn
    go: DOI
    miriam: doi
    n2t: doi
    prefixcommons: doi
    wikidata: P356
    wikidata.entity: Q25670
  miriam:
    deprecated: false
    description: The Digital Object Identifier System is for identifying content objects
      in the digital environment.
    homepage: https://www.doi.org/
    id: 00000019
    name: DOI
    namespaceEmbeddedInLui: false
    pattern: ^(doi\:)?10\.\d+/.*$
    prefix: doi
    providers:
    - code: scholia
      description: Scholia is a service that creates visual scholarly profiles for
        topic, people, organizations, species, chemicals, etc using bibliographic
        and other information in Wikidata.
      homepage: https://scholia.toolforge.org/
      name: Scholia
      uri_format: https://scholia.toolforge.org/doi/$1
    sampleId: 10.1038/nbt1156
    uri_format: https://doi.org/$1
  n2t:
    description: The Digital Object Identifier System is for identifying content objects
      in the digital environment.
    example: 10.1038/nbt1156
    homepage: https://www.doi.org/
    name: Digital Object Identifier
    namespaceEmbeddedInLui: false
    pattern: ^(doi\:)?\d{2}\.\d{4}.*$
    prefix: doi
    uri_format: https://doi.org/$1
  name: Digital Object Identifier
  pattern: ^10.\d{2,9}/.*$
  prefix: doi
  prefixcommons:
    alt_uri_formats:
    - http://hdl.handle.net/#$1
    description: The Digital Object Identifier System is for identifying content objects
      in the digital environment.
    example: 10.1038/nbt1156
    homepage: http://www.doi.org/
    keywords:
    - bibliography
    name: Digital Object Identifier
    pattern: ^(doi\:)?\d{2}\.\d{4}.*$
    prefix: doi
    uri_format: http://dx.doi.org/$1
  providers:
  - code: dx_doi_http
    description: An alternate provider from the DOI website using HTTP
    example: null
    first_party: null
    homepage: https://www.doi.org
    name: Digital Object Identifier
    publications: null
    status: null
    uri_format: http://dx.doi.org/$1
  - code: dx_doi_https
    description: An alternate provider from the DOI website using HTTPS
    example: null
    first_party: null
    homepage: https://www.doi.org
    name: Digital Object Identifier
    publications: null
    status: null
    uri_format: https://dx.doi.org/$1
  - code: doi_http
    description: An alternate provider from the DOI website using HTTP
    example: null
    first_party: null
    homepage: https://www.doi.org
    name: Digital Object Identifier
    publications: null
    status: null
    uri_format: http://doi.org/$1
  - code: miriam_legacy
    description: A legacy MIRIAM URI that does not follow the standard pattern
    example: null
    first_party: null
    homepage: https://identifiers.org
    name: Legacy MIRIAM URI
    publications: null
    status: null
    uri_format: http://identifiers.org/DOI/$1
  references:
  - https://github.com/biopragmatics/bioregistry/issues/287
  - https://github.com/biopragmatics/bioregistry/pull/316
  uri_format: https://doi.org/$1
  wikidata:
    database: Q25670
    description: serial code used to uniquely identify digital objects like academic
      papers (use upper case letters only)
    example:
    - 10.12987/YALE/9780300197051.003.0010
    - 10.1371/JOURNAL.PONE.0029797
    name: DOI
    pattern: ^(?i)10.\d{4,9}/[^\s]+$
    prefix: P356
    uri_format: https://doi.org/$1
    uri_format_rdf: http://dx.doi.org/$1
doid:
  aberowl:
    description: An ontology for describing the classification of human diseases organized
      by etiology.
    download_owl: http://aber-owl.net/media/ontologies/DOID/701/doid.owl
    homepage: https://disease-ontology.org
    name: Human Disease Ontology
    prefix: DOID
  bartoc:
    abbreviation: DO
    description: 'The Disease Ontology has been developed as a standardized ontology
      for human disease with the purpose of providing the biomedical community with
      consistent, reusable and sustainable descriptions of human disease terms, phenotype
      characteristics and related medical vocabulary disease concepts through collaborative
      efforts of researchers at Northwestern University, Center for Genetic Medicine
      and the University of Maryland School of Medicine, Institute for Genome Sciences.


      The Disease Ontology semantically integrates disease and medical vocabularies
      through extensive cross mapping of DO terms to MeSH, ICD, NCI’s thesaurus, SNOMED
      and OMIM.'
    homepage: http://disease-ontology.org/
    license: CC0-1.0
    name: Disease Ontology
    prefix: '576'
    wikidata_database: Q5282129
  biocontext:
    prefix: DOID
  bioportal:
    contact:
      email: lynn.schriml@gmail.com
      name: Lynn Schriml
    description: Creating a comprehensive classification of human diseases organized
      by etiology., The Disease Ontology has been developed as a standardized ontology
      for human disease with the purpose of providing the biomedical community with
      consistent, reusable and sustainable descriptions of human disease terms, phenotype
      characteristics and related medical vocabulary disease concepts.
    homepage: https://disease-ontology.org/
    license: CC0-1.0
    name: Human Disease Ontology
    prefix: DOID
    publications:
    - https://disease-ontology.org/community/publications
    version: '2025-11-25'
  download_json: http://purl.obolibrary.org/obo/doid.json
  download_obo: https://github.com/DiseaseOntology/HumanDiseaseOntology/raw/main/src/ontology/doid.obo
  example: 0110974
  fairsharing:
    abbreviation: DOID
    contact:
      email: lynn.schriml@gmail.com
      name: Lynn Schriml
      orcid: 0000-0001-8910-9851
    description: The Disease Ontology has been developed as a standardized ontology
      for human disease with the purpose of providing the biomedical community with
      consistent, reusable and sustainable descriptions of human disease terms, phenotype
      characteristics, underlying mechanisms and related medical vocabulary disease
      concepts.
    domains:
    - infection process
    - disease phenotype
    - disease
    - disease course
    - Classification
    - genetic disorder
    - mental health
    homepage: http://www.disease-ontology.org
    license: CC0-1.0
    logo: https://api.fairsharing.org/rails/active_storage/blobs/redirect/eyJfcmFpbHMiOnsibWVzc2FnZSI6IkJBaHBBWkU9IiwiZXhwIjpudWxsLCJwdXIiOiJibG9iX2lkIn19--cfd1eca9383fe170c6035a80aa48bff273f7607c/DO_blue_logo.png?disposition=inline
    name: Disease Ontology
    prefix: FAIRsharing.8b6wfq
    publications:
    - doi: 10.1093/nar/gky1036
      pubmed: '30407590'
      title: 'ECO, the Evidence & Conclusion Ontology: community standard for evidence
        information'
      year: 2018
    - doi: 10.1093/nar/gkr972
      pubmed: '22080554'
      title: 'Disease Ontology: a backbone for disease semantic integration'
      year: 2011
    - doi: 10.1093/database/baw015
      pubmed: '26989148'
      title: Wikidata as a semantic framework for the Gene Wiki initiative
      year: 2016
    - doi: 10.1093/nar/gku1011
      pubmed: '25348409'
      title: 'Disease Ontology 2015 update: an expanded and updated database of human
        diseases for linking biomedical knowledge through disease data'
      year: 2014
    - doi: 10.1093/bioinformatics/btp193
      pubmed: '19478018'
      title: 'From disease ontology to disease-ontology lite: statistical methods
        to adapt a general-purpose ontology for the test of gene-ontology associations'
      year: 2009
    - doi: 10.1093/nar/gkab1063
      pubmed: '34755882'
      title: The Human Disease Ontology 2022 update
      year: 2022
    - doi: 10.1093/nar/gky1032
      pubmed: '30407550'
      title: 'Human Disease Ontology 2018 update: classification, content and workflow
        expansion'
      year: 2019
    - doi: 10.1242/dmm.032839
      pubmed: '29590633'
      title: 'Disease Ontology: improving and unifying disease annotations across
        species'
      year: 2018
    - doi: 10.1007/s00335-015-9576-9
      pubmed: '26093607'
      title: 'The Disease Ontology: fostering interoperability between biological
        and clinical human disease-related data'
      year: 2015
    - doi: 10.1093/database/bav032
      pubmed: '25841438'
      title: Generating a focused view of disease ontology cancer terms for pan-cancer
        data integration and analysis
      year: 2015
    - doi: 10.1186/1471-2164-10-s1-s6
      pubmed: '19594883'
      title: Annotating the human genome with Disease Ontology
      year: 2009
    - doi: 10.1093/bib/bbab191
      pubmed: '34015823'
      title: COVID-19 biomarkers and their overlap with comorbidities in a disease
        biomarker data model
      year: 2021
    - doi: 10.7554/elife.52614
      pubmed: '32180547'
      title: Wikidata as a knowledge graph for the life sciences
      year: 2020
    - doi: 10.1016/j.ajhg.2015.05.020
      pubmed: '26119816'
      title: 'The Human Phenotype Ontology: Semantic Unification of Common and Rare
        Disease'
      year: 2015
    - doi: 10.1093/nar/gkad1051
      pubmed: '37953304'
      title: 'The DO-KB Knowledgebase: a 20-year journey developing the disease open
        science ecosystem'
      year: 2023
    repository: https://github.com/DiseaseOntology/HumanDiseaseOntology
    subjects:
    - Life Science
    - Biomedical Science
    twitter: diseaseontology
  integbio:
    alt_name: Disease Ontology
    description: This site provides a Disease Ontology, which is a standardized ontology
      organized by human disease terms and related medical concepts. The DO terms
      are associated with MeSH, ICD, NCI's thesaurus, SNOMED and OMIM to integrate
      disease and medical vocabularies.
    fairsharing: FAIRsharing.8b6wfq
    homepage: https://disease-ontology.org/
    information_keywords:
    - Ontology/Terminology/Nomenclature
    maintainer: Institute of Genome Sciences, University of Maryland School of Medicine
    name: DO
    prefix: nbdc00261
    pubmeds:
    - '30407550'
    status: Active
    target_keywords:
    - Health/Disease
  mappings:
    aberowl: DOID
    bartoc: '576'
    biocontext: DOID
    bioportal: DOID
    fairsharing: FAIRsharing.8b6wfq
    integbio: nbdc00261
    miriam: doid
    n2t: doid
    obofoundry: doid
    ols: doid
    ontobee: DOID
    prefixcommons: do
    togoid: Doid
    wikidata: P699
    wikidata.entity: Q5282129
  miriam:
    deprecated: false
    description: The Disease Ontology has been developed as a standardized ontology
      for human disease with the purpose of providing the biomedical community with
      consistent, reusable and sustainable descriptions of human disease terms, phenotype
      characteristics and related medical vocabulary disease concepts.
    homepage: https://www.ebi.ac.uk/ols4/ontologies/doid
    id: '00000233'
    name: Human Disease Ontology
    namespaceEmbeddedInLui: true
    pattern: ^DOID:\d+$
    prefix: doid
    providers:
    - code: hdo
      description: Human Disease Ontology at Northwestern University
      homepage: http://disease-ontology.org/
      name: Human Disease Ontology at Northwestern University
      uri_format: http://disease-ontology.org/term/DOID:$1
    sampleId: '11337'
    uri_format: https://www.ebi.ac.uk/ols4/ontologies/doid/terms?obo_id=DOID:$1
  n2t:
    description: The Disease Ontology has been developed as a standardized ontology
      for human disease with the purpose of providing the biomedical community with
      consistent, reusable and sustainable descriptions of human disease terms, phenotype
      characteristics and related medical vocabulary disease concepts.
    example: '11337'
    homepage: http://disease-ontology.org/
    name: Human Disease Ontology at Northwestern University
    namespaceEmbeddedInLui: true
    pattern: ^DOID\:\d+$
    prefix: doid
    uri_format: http://disease-ontology.org/term/DOID:$1
  obofoundry:
    appears_in:
    - clo
    - scdo
    contact: lynn.schriml@gmail.com
    contact.github: lschriml
    contact.label: Lynn Schriml
    contact.orcid: 0000-0001-8910-9851
    deprecated: false
    description: An ontology for describing the classification of human diseases organized
      by etiology.
    domain: health
    download.obo: http://purl.obolibrary.org/obo/doid.obo
    download.owl: http://purl.obolibrary.org/obo/doid.owl
    homepage: https://disease-ontology.org
    license: CC0 1.0
    license.url: https://creativecommons.org/publicdomain/zero/1.0/
    logo: https://disease-ontology.org/media/images/DO_logo_teal.png
    name: Human Disease Ontology
    preferredPrefix: DOID
    prefix: doid
    publications:
    - id: https://www.ncbi.nlm.nih.gov/pubmed/25348409
      title: 'Disease Ontology 2015 update: an expanded and updated database of human
        diseases for linking biomedical knowledge through disease data'
    - id: https://www.ncbi.nlm.nih.gov/pubmed/34755882
      title: The Human Disease Ontology 2022 update
    repository: https://github.com/DiseaseOntology/HumanDiseaseOntology
    twitter: diseaseontology
  ols:
    description: The Disease Ontology has been developed as a standardized ontology
      for human disease with the purpose of providing the biomedical community with
      consistent, reusable and sustainable descriptions of human disease terms, phenotype
      characteristics and related medical vocabulary disease concepts.
    download_owl: https://purl.obolibrary.org/obo/doid/translations/doid-international.owl
    homepage: https://disease-ontology.org
    name: Human Disease Ontology
    prefix: doid
    tracker: https://github.com/DiseaseOntology/HumanDiseaseOntology/issues
    version: '2025-11-25'
    version.iri: http://purl.obolibrary.org/obo/doid/releases/2025-11-25/translations/doid-international.owl
  ontobee:
    library: Foundry
    name: Human Disease Ontology
    prefix: DOID
  pattern: ^\d+$
  prefix: doid
  prefixcommons:
    alt_uri_formats:
    - http://purl.org/obo/owl/DOID#$1
    - http://www.loria.fr/~coulet/ontology/sopharm/version2.1/disease_ontology.owl#$1
    - http://purl.org/obo/owl/DO#$1
    - http://www.owl-ontologies.com/NPOntology.owl#DOID_$1
    bioportal: '1009'
    description: The Disease Ontology has been developed as a standardized ontology
      for human disease with the purpose of providing the biomedical community with
      consistent, reusable and sustainable descriptions of human disease terms, phenotype
      characteristics and related medical vocabulary disease concepts.
    example: DOID:11337
    homepage: http://diseaseontology.sourceforge.net/
    keywords:
    - obo
    - disease
    - human
    - ontology
    name: Human disease ontology
    pattern: ^DOID\:\d+$
    prefix: do
    synonyms:
    - doid
    - diseaseontology
    - obo.do
    uri_format: http://disease-ontology.org/term/$1
  providers:
  - code: purl
    description: Legacy PURLs for DOID, including the redundant DOID_
    example: null
    first_party: null
    homepage: http://purl.org/obo/owl/
    name: Legacy PURL
    publications: null
    status: null
    uri_format: http://purl.org/obo/owl/DOID#DOID_$1
  - code: purl2
    description: Legacy PURLs for DOID, not including the redundant DOID_
    example: null
    first_party: null
    homepage: http://purl.org/obo/owl/
    name: Legacy PURL
    publications: null
    status: null
    uri_format: http://purl.org/obo/owl/DOID#$1
  publications:
  - doi: 10.1093/nar/gkab1063
    pmc: PMC8728220
    pubmed: '34755882'
    title: The Human Disease Ontology 2022 update
    year: 2022
  - doi: 10.1093/bib/bbab191
    pmc: PMC8195003
    pubmed: '34015823'
    title: COVID-19 biomarkers and their overlap with comorbidities in a disease biomarker
      data model
    year: 2021
  - doi: 10.7554/elife.52614
    pmc: PMC7077981
    pubmed: '32180547'
    title: Wikidata as a knowledge graph for the life sciences
    year: 2020
  - doi: 10.1093/nar/gky1036
    pmc: PMC6323956
    pubmed: '30407590'
    title: 'ECO, the Evidence & Conclusion Ontology: community standard for evidence
      information'
    year: 2019
  - doi: 10.1093/nar/gky1032
    pmc: PMC6323977
    pubmed: '30407550'
    title: 'Human Disease Ontology 2018 update: classification, content and workflow
      expansion'
    year: 2019
  - doi: 10.1242/dmm.032839
    pmc: PMC5897730
    pubmed: '29590633'
    title: 'Disease Ontology: improving and unifying disease annotations across species'
    year: 2018
  - doi: 10.1093/database/baw015
    pmc: PMC4795929
    pubmed: '26989148'
    title: Wikidata as a semantic framework for the Gene Wiki initiative
    year: 2016
  - doi: 10.1093/database/bav032
    pmc: PMC4385274
    pubmed: '25841438'
    title: Generating a focused view of disease ontology cancer terms for pan-cancer
      data integration and analysis
    year: 2015
  - doi: 10.1007/s00335-015-9576-9
    pmc: PMC4602048
    pubmed: '26093607'
    title: 'The Disease Ontology: fostering interoperability between biological and
      clinical human disease-related data'
    year: 2015
  - doi: 10.1016/j.ajhg.2015.05.020
    pmc: PMC4572507
    pubmed: '26119816'
    title: 'The Human Phenotype Ontology: Semantic Unification of Common and Rare
      Disease'
    year: 2015
  - doi: 10.1093/nar/gku1011
    pmc: PMC4383880
    pubmed: '25348409'
    title: 'Disease Ontology 2015 update: an expanded and updated database of human
      diseases for linking biomedical knowledge through disease data'
    year: 2014
  - doi: 10.1093/nar/gkr972
    pmc: PMC3245088
    pubmed: '22080554'
    title: 'Disease Ontology: a backbone for disease semantic integration'
    year: 2011
  - doi: 10.1186/1471-2164-10-s1-s6
    pmc: PMC2709267
    pubmed: '19594883'
    title: Annotating the human genome with Disease Ontology
    year: 2009
  - doi: 10.1093/bioinformatics/btp193
    pmc: PMC2687947
    pubmed: '19478018'
    title: 'From disease ontology to disease-ontology lite: statistical methods to
      adapt a general-purpose ontology for the test of gene-ontology associations'
    year: 2009
  - doi: null
    pmc: null
    pubmed: '25348409'
    title: 'Disease Ontology 2015 update: an expanded and updated database of human
      diseases for linking biomedical knowledge through disease data'
    year: null
  - doi: null
    pmc: null
    pubmed: '34755882'
    title: The Human Disease Ontology 2022 update
    year: null
  - doi: 10.1093/nar/gky1036
    pmc: null
    pubmed: '30407590'
    title: 'ECO, the Evidence & Conclusion Ontology: community standard for evidence
      information'
    year: 2018
  - doi: 10.1093/nar/gkr972
    pmc: null
    pubmed: '22080554'
    title: 'Disease Ontology: a backbone for disease semantic integration'
    year: 2011
  - doi: 10.1093/database/baw015
    pmc: null
    pubmed: '26989148'
    title: Wikidata as a semantic framework for the Gene Wiki initiative
    year: 2016
  - doi: 10.1093/nar/gku1011
    pmc: null
    pubmed: '25348409'
    title: 'Disease Ontology 2015 update: an expanded and updated database of human
      diseases for linking biomedical knowledge through disease data'
    year: 2014
  - doi: 10.1093/bioinformatics/btp193
    pmc: null
    pubmed: '19478018'
    title: 'From disease ontology to disease-ontology lite: statistical methods to
      adapt a general-purpose ontology for the test of gene-ontology associations'
    year: 2009
  - doi: 10.1093/nar/gkab1063
    pmc: null
    pubmed: '34755882'
    title: The Human Disease Ontology 2022 update
    year: 2022
  - doi: 10.1093/nar/gky1032
    pmc: null
    pubmed: '30407550'
    title: 'Human Disease Ontology 2018 update: classification, content and workflow
      expansion'
    year: 2019
  - doi: 10.1242/dmm.032839
    pmc: null
    pubmed: '29590633'
    title: 'Disease Ontology: improving and unifying disease annotations across species'
    year: 2018
  - doi: 10.1007/s00335-015-9576-9
    pmc: null
    pubmed: '26093607'
    title: 'The Disease Ontology: fostering interoperability between biological and
      clinical human disease-related data'
    year: 2015
  - doi: 10.1093/database/bav032
    pmc: null
    pubmed: '25841438'
    title: Generating a focused view of disease ontology cancer terms for pan-cancer
      data integration and analysis
    year: 2015
  - doi: 10.1186/1471-2164-10-s1-s6
    pmc: null
    pubmed: '19594883'
    title: Annotating the human genome with Disease Ontology
    year: 2009
  - doi: 10.1093/bib/bbab191
    pmc: null
    pubmed: '34015823'
    title: COVID-19 biomarkers and their overlap with comorbidities in a disease biomarker
      data model
    year: 2021
  - doi: 10.7554/elife.52614
    pmc: null
    pubmed: '32180547'
    title: Wikidata as a knowledge graph for the life sciences
    year: 2020
  - doi: 10.1016/j.ajhg.2015.05.020
    pmc: null
    pubmed: '26119816'
    title: 'The Human Phenotype Ontology: Semantic Unification of Common and Rare
      Disease'
    year: 2015
  - doi: 10.1093/nar/gkad1051
    pmc: null
    pubmed: '37953304'
    title: 'The DO-KB Knowledgebase: a 20-year journey developing the disease open
      science ecosystem'
    year: 2023
  synonyms:
  - do
  togoid:
    catalog: nbdc00261
    description: This site provides a Disease Ontology, which is a standardized ontology
      organized by human disease terms and related medical concepts. The DO terms
      are associated with MeSH, ICD, NCI's thesaurus, SNOMED and OMIM to integrate
      disease and medical vocabularies.
    examples:
    - DO:9036
    - DO:3159
    - DO:10964
    - DO:12698
    - DO:0060459
    - DO:11840
    - DO:11339
    - DO:914
    - DO:9945
    - DO:1407
    keywords:
    - Phenotype
    name: Disease ontology
    pattern: ^DO(?:ID)?[:_](?\d+)$
    prefix: Doid
    uri_format: http://purl.obolibrary.org/obo/DOID_$1
  uri_format: http://purl.obolibrary.org/obo/DOID_$1
  wikidata:
    description: identifier in the Disease Ontology database
    example:
    - DOID:769
    - DOID:8778
    homepage: http://disease-ontology.org
    miriam: doid
    name: Disease Ontology ID
    pattern: ^DOID:([0-9]{7}|[1-9][0-9]{0,4})$
    prefix: P699
    uri_format: http://www.disease-ontology.org/?id=$1
    uri_format_rdf: http://purl.obolibrary.org/obo/DOID_$1
dolce:
  comment: This resource doesn't exist anymore
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  deprecated: true
  fairsharing:
    abbreviation: DOLCE
    description: DOLCE (Descriptive Ontology for Linguistic and Cognitive Engineering)
      is a foundational ontology developed as part of the WonderWeb Foundational Ontologies
      Library (WFOL).  The development of this library has been guided by the need
      of a reliable set of foundational ontologies that can serve as 1) astarting
      point for building other ontologies, 2) a reference point for easy and rigorous
      comparisons among different ontological approaches, and 3) a rigorous basis
      for analyzing, harmonizing and integrating existing ontologies and metadata
      standards (by manually mapping them into some general module(s) in the library).
      DOLCE is the first module of WFOL and it is not a candidate for a universal
      standard ontology. Rather, it is intended as a starting point for comparing
      and elucidating the relationships with the other modules of the library, and
      also for clarifying the hidden assumptions underlying existing ontologies or
      linguistic resources such as WordNet.  As reflected by its acronym, DOLCE has
      a clear cognitive bias, in the sense that it aims at capturing the ontological
      categories underlying natural language and human commonsense. DOLCE is an ontology
      that focuses on particulars in the sense that its domain of discourse is restricted
      to them. The project is complete, though the ontology remains available for
      use.
    domains:
    - Classification
    homepage: http://www.loa.istc.cnr.it/dolce/overview.html
    name: Descriptive Ontology for Linguistic and Cognitive Engineering
    prefix: FAIRsharing.ae8hpt
    subjects:
    - Linguistics
    - Knowledge and Information Systems
    - Computer Science
    - Subject Agnostic
  mappings:
    fairsharing: FAIRsharing.ae8hpt
  name: Descriptive Ontology for Linguistic and Cognitive Engineering
  prefix: dolce
dome:
  contact:
    email: silvio.tosatto@unipd.it
    github: silvio-tosatto
    name: Silvio Tosatto
    orcid: 0000-0003-4525-7793
  contributor:
    email: palayoor.n@northeastern.edu
    github: nalikapalayoor
    name: Nalika Palayoor
    orcid: 0009-0008-8406-631X
  description: The DOME registry is a curated set of papers related to machine learning
    methods in biology, each with its own unique DOME identifier.
  example: dfyn1yvtz3
  github_request_issue: 1374
  homepage: https://registry.dome-ml.org
  mappings:
    miriam: dome
  miriam:
    deprecated: false
    description: A database of annotations for published papers describing machine
      learning methods in biology
    homepage: https://registry.dome-ml.org/
    id: 00001086
    name: DOME Registry
    namespaceEmbeddedInLui: false
    pattern: ^[a-z0-9]{10}$
    prefix: dome
    sampleId: 88n4lxv68p
    uri_format: https://registry.dome-ml.org/review/$1
  name: DOME Registry
  pattern: ^[a-z0-9]{10}$
  prefix: dome
  publications:
  - doi: 10.1093/gigascience/giae094
    pmc: PMC11633452
    pubmed: '39661723'
    title: 'DOME Registry: implementing community-wide recommendations for reporting
      supervised machine learning in biology'
    year: 2024
  reviewer:
    email: b.gyori@northeastern.edu
    github: bgyori
    name: Benjamin M. Gyori
    orcid: 0000-0001-9439-5346
  uri_format: https://registry.dome-ml.org/review/$1
dommino:
  biocontext:
    prefix: DOMMINO
  homepage: http://korkinlab.org/dommino
  mappings:
    biocontext: DOMMINO
    miriam: dommino
    n2t: dommino
    pathguide: '423'
  miriam:
    deprecated: true
    description: DOMMINO is a database of macromolecular interactions that includes
      the interactions between protein domains, interdomain linkers, N- and C-terminal
      regions and protein peptides.
    homepage: http://dommino.org/
    id: '00000373'
    name: DOMMINO
    namespaceEmbeddedInLui: false
    pattern: ^[0-9][A-Za-z0-9]{3}$
    prefix: dommino
    sampleId: 2GC4
    uri_format: http://orion.rnet.missouri.edu/~nz953/DOMMINO/index.php/result/show_network/$1
  n2t:
    description: DOMMINO is a database of macromolecular interactions that includes
      the interactions between protein domains, interdomain linkers, N- and C-terminal
      regions and protein peptides.
    example: 2GC4
    homepage: http://dommino.org/
    name: DOMMINO at University of Missouri
    namespaceEmbeddedInLui: false
    pattern: ^[0-9][A-Za-z0-9]{3}$
    prefix: dommino
    uri_format: http://orion.rnet.missouri.edu/~nz953/DOMMINO/index.php/result/show_network/$1
  name: Database of Macromolecular Interactions
  pathguide:
    abbreviation: DOMMINO
    homepage: http://orion.rnet.missouri.edu/~nz953/DOMMINO/
    name: Database of MacroMolecular Interactions
    prefix: '423'
  prefix: dommino
door:
  biocontext:
    prefix: DOOR
  mappings:
    biocontext: DOOR
    miriam: door
    n2t: door
    prefixcommons: door
    re3data: r3d100014113
  miriam:
    deprecated: true
    description: DOOR (Database for prOkaryotic OpeRons) contains computationally
      predicted operons of all the sequenced prokaryotic genomes. It includes operons
      for RNA genes.
    homepage: http://csbl.bmb.uga.edu/DOOR/operon.php
    id: '00000453'
    name: DOOR
    namespaceEmbeddedInLui: false
    pattern: ^\d+$
    prefix: door
    sampleId: '1398574'
    uri_format: http://csbl.bmb.uga.edu/DOOR/operon.php?id=$1
  n2t:
    description: DOOR (Database for prOkaryotic OpeRons) contains computationally
      predicted operons of all the sequenced prokaryotic genomes. It includes operons
      for RNA genes.
    example: '1398574'
    homepage: http://csbl.bmb.uga.edu/DOOR/operon.php
    name: DOOR v1 at University of Georgia
    namespaceEmbeddedInLui: false
    pattern: ^\d+$
    prefix: door
    uri_format: http://csbl.bmb.uga.edu/DOOR/operon.php?id=$1
  name: Database for Prokaryotic Operons
  prefix: door
  prefixcommons:
    description: DOOR (Database of prOkaryotic OpeRons) is an operon database developed
      by Computational Systems Biology Lab (CSBL) at University of Georgia. The operons
      in the database are based on prediction.
    example: '607986'
    homepage: http://csbl1.bmb.uga.edu/OperonDB/
    keywords:
    - DNA
    name: Database of prOkaryotic OpeRons
    pattern: ^\d+$
    prefix: door
    uri_format: http://csbl1.bmb.uga.edu/OperonDB/genedetail.php?id=$1
  re3data:
    description: DOOR is the open institutional repository of the University for Continuing
      Education Krems, formerly known as Danube University Krems. DOOR runs on the
      fedora Software and is a partner repository of Phaidra Vienna and other fedora
      users in Austria. We provide access to OA publications, scientific data and
      much more for interested users and support our scientists and co-workers in
      their publication processis.
    doi: 10.17616/R31NJNDT
    homepage: https://door.donau-uni.ac.at/
    name: DOOR
    prefix: r3d100014113
    synonyms:
    - DOOR University for Continuing Education Krems
    - DOOR Universität für Weiterbildung Krems
    - Danube University Open Online Repository
doqcs.model:
  biocontext:
    prefix: DOQCS.MODEL
  contact:
    email: bhalla@ncbs.res.in
    github: upibhalla
    name: Upinder S. Bhalla
    orcid: 0000-0003-1722-5188
  mappings:
    biocontext: DOQCS.MODEL
    miriam: doqcs.model
    n2t: doqcs.model
    prefixcommons: doqcs.model
  miriam:
    deprecated: false
    description: The Database of Quantitative Cellular Signaling is a repository of
      models of signaling pathways. It includes reaction schemes, concentrations,
      rate constants, as well as annotations on the models. The database provides
      a range of search, navigation, and comparison functions. This datatype provides
      access to specific models.
    homepage: http://doqcs.ncbs.res.in/
    id: '00000134'
    name: 'Database of Quantitative Cellular Signaling: Model'
    namespaceEmbeddedInLui: false
    pattern: ^\d+$
    prefix: doqcs.model
    sampleId: '57'
    uri_format: http://doqcs.ncbs.res.in/template.php?&y=accessiondetails&an=$1
  n2t:
    description: The Database of Quantitative Cellular Signaling is a repository of
      models of signaling pathways. It includes reaction schemes, concentrations,
      rate constants, as well as annotations on the models. The database provides
      a range of search, navigation, and comparison functions. This datatype provides
      access to specific models.
    example: '57'
    homepage: http://doqcs.ncbs.res.in/
    name: Database of Quantitative Cellular Signaling (DOQCS) - Model Access
    namespaceEmbeddedInLui: false
    pattern: ^\d+$
    prefix: doqcs.model
    uri_format: http://doqcs.ncbs.res.in/template.php?&y=accessiondetails&an=$1
  part_of_database: doqcs
  prefix: doqcs.model
  prefixcommons:
    description: The Database of Quantitative Cellular Signaling is a repository of
      models of signaling pathways. It includes reaction schemes, concentrations,
      rate constants, as well as annotations on the models. The database provides
      a range of search, navigation, and comparison functions. This datatype provides
      access to specific models.
    example: '57'
    homepage: http://doqcs.ncbs.res.in/
    keywords:
    - model
    license: http://doqcs.ncbs.res.in/template.php?&y=faq#q2
    name: 'Database of Quantitative Cellular Signaling: Model'
    pattern: ^\d+$
    prefix: doqcs.model
    pubmed_ids:
    - '12584128'
    uri_format: http://doqcs.ncbs.res.in/template.php?&y=accessiondetails&an=$1
  publications:
  - doi: 10.1093/bioinformatics/btf860
    pmc: null
    pubmed: '12584128'
    title: 'The Database of Quantitative Cellular Signaling: management and analysis
      of chemical kinetic models of signaling networks'
    year: 2003
doqcs.pathway:
  biocontext:
    prefix: DOQCS.PATHWAY
  contact:
    email: bhalla@ncbs.res.in
    github: upibhalla
    name: Upinder S. Bhalla
    orcid: 0000-0003-1722-5188
  mappings:
    biocontext: DOQCS.PATHWAY
    miriam: doqcs.pathway
    n2t: doqcs.pathway
    prefixcommons: doqcs.pathway
  miriam:
    deprecated: false
    description: The Database of Quantitative Cellular Signaling is a repository of
      models of signaling pathways. It includes reaction schemes, concentrations,
      rate constants, as well as annotations on the models. The database provides
      a range of search, navigation, and comparison functions. This datatype provides
      access to pathways.
    homepage: http://doqcs.ncbs.res.in/
    id: '00000135'
    name: 'Database of Quantitative Cellular Signaling: Pathway'
    namespaceEmbeddedInLui: false
    pattern: ^\d+$
    prefix: doqcs.pathway
    sampleId: '131'
    uri_format: http://doqcs.ncbs.res.in/template.php?&y=pathwaydetails&pn=$1
  n2t:
    description: The Database of Quantitative Cellular Signaling is a repository of
      models of signaling pathways. It includes reaction schemes, concentrations,
      rate constants, as well as annotations on the models. The database provides
      a range of search, navigation, and comparison functions. This datatype provides
      access to pathways.
    example: '131'
    homepage: http://doqcs.ncbs.res.in/
    name: Database of Quantitative Cellular Signaling (DOQCS) - Pathway Access
    namespaceEmbeddedInLui: false
    pattern: ^\d+$
    prefix: doqcs.pathway
    uri_format: http://doqcs.ncbs.res.in/template.php?&y=pathwaydetails&pn=$1
  part_of_database: doqcs
  prefix: doqcs.pathway
  prefixcommons:
    description: The Database of Quantitative Cellular Signaling is a repository of
      models of signaling pathways. It includes reaction schemes, concentrations,
      rate constants, as well as annotations on the models. The database provides
      a range of search, navigation, and comparison functions.
    example: '38'
    homepage: http://doqcs.ncbs.res.in/
    keywords:
    - pathway
    license: http://doqcs.ncbs.res.in/template.php?&y=faq#q2
    name: 'Database of Quantitative Cellular Signaling: Pathway'
    pattern: ^\d+$
    prefix: doqcs.pathway
    pubmed_ids:
    - '12584128'
    uri_format: http://doqcs.ncbs.res.in/template.php?&y=pathwaydetails&pn=$1
  publications:
  - doi: 10.1093/bioinformatics/btf860
    pmc: null
    pubmed: '12584128'
    title: 'The Database of Quantitative Cellular Signaling: management and analysis
      of chemical kinetic models of signaling networks'
    year: 2003
dpbo:
  contact:
    email: k.dumschott@fz-juelich.de
    github: kdumschott
    name: Kathryn Dumschott
    orcid: 0000-0002-9905-4011
  contact_extras:
  - email: a.kranz@fz-juelich.de
    github: AngelaKranz
    name: Angela Kranz
    orcid: 0000-0002-8000-0400
  contributor:
    email: h.doerpholz@fz-juelich.de
    github: Hannah-Doerpholz
    name: Hannah Dörpholz
    orcid: 0000-0002-0476-9699
  description: With the DataPLANT biology ontology (DPBO), DataPLANT provides an intermediate
    ontology that acts as a broker and bridge between the individual researcher/domain
    experts and main ontology providers. DPBO enables easy and agile collection of
    missing vocabulary as well as relationships between terms for (meta)data annotation
    using DataPLANT’s Swate tool.
  download_obo: https://raw.githubusercontent.com/nfdi4plants/nfdi4plants_ontology/refs/heads/main/dpbo.obo
  example: '0010015'
  github_request_issue: 1466
  homepage: https://www.nfdi4plants.org/
  license: CC-BY-4.0
  mappings:
    tib: dpbo
  name: DataPLANT Biology Ontology
  pattern: ^\d+$
  prefix: dpbo
  publications:
  - doi: 10.11588/heibooks.1288.c18067
    pmc: null
    pubmed: null
    title: DataPLANT - Harnessing the Power of Ontologies for FAIR Research Data Management
    year: 2023
  repository: https://github.com/nfdi4plants/nfdi4plants_ontology
  reviewer:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  tib:
    description: With the DataPLANT biology ontology (DPBO), DataPLANT provides an
      intermediate ontology that acts as a broker and bridge between the individual
      researcher/domain experts and main ontology providers. DPBO enables easy and
      agile collection of missing vocabulary as well as relationships between terms
      for (meta)data annotation using DataPLANT’s Swate tool.
    homepage: https://www.nfdi4plants.org/
    keywords:
    - DataPLANT
    - life sciences, biology
    name: DataPLANT Biology Ontology
    prefix: dpbo
    tracker: https://github.com/nfdi4plants/nfdi4plants_ontology/issues/
    uri_format: https://purl.org/nfdi4plants/ontology/dpbo$1
    version.iri: http://purl.obolibrary.org/obo/dpbo/init/2020-12-01/dpbo.owl
  uri_format: https://purl.org/nfdi4plants/ontology/dpbo/DPBO_$1
dpo:
  aberowl:
    description: An ontology of commonly encountered and/or high level Drosophila
      phenotypes.
    download_owl: http://aber-owl.net/media/ontologies/DPO/41/dpo.owl
    homepage: http://purl.obolibrary.org/obo/fbcv
    name: Drosophila Phenotype Ontology
    prefix: DPO
  bioportal:
    contact:
      email: cp390@cam.ac.uk
      name: Clare Pilgrim
    description: An ontology of commonly encountered and/or high level Drosophila
      phenotypes. It has significant formalisation - utilising terms from GO, CL,
      PATO and the Drosophila anatomy ontology. It has been used by FlyBase for >
      159000 annotations of phenotype., An ontology for the description of Drosophila
      melanogaster phenotypes.
    homepage: http://dx.doi.org/10.1186/2041-1480-4-30
    license: CC-BY-4.0
    name: Drosophila Phenotype Ontology
    prefix: DPO
    version: '2025-10-17'
  comment: DPO is a subset of terms from FBcv
  mappings:
    aberowl: DPO
    bioportal: DPO
    obofoundry: dpo
    ols: dpo
    ontobee: DPO
  no_own_terms: true
  obofoundry:
    contact: cp390@cam.ac.uk
    contact.github: Clare72
    contact.label: Clare Pilgrim
    contact.orcid: 0000-0002-1373-1705
    deprecated: false
    description: An ontology of commonly encountered and/or high level Drosophila
      phenotypes.
    domain: phenotype
    download.json: http://purl.obolibrary.org/obo/dpo.json
    download.obo: http://purl.obolibrary.org/obo/dpo.obo
    download.owl: http://purl.obolibrary.org/obo/dpo.owl
    homepage: http://purl.obolibrary.org/obo/fbcv
    license: CC BY 4.0
    license.url: http://creativecommons.org/licenses/by/4.0/
    name: Drosophila Phenotype Ontology
    preferredPrefix: FBcv
    prefix: dpo
    publications:
    - id: https://www.ncbi.nlm.nih.gov/pubmed/24138933
      title: The Drosophila phenotype ontology.
    repository: https://github.com/FlyBase/drosophila-phenotype-ontology
  ols:
    description: An ontology of commonly encountered and/or high level Drosophila
      phenotypes.
    download_owl: http://purl.obolibrary.org/obo/dpo.owl
    homepage: http://purl.obolibrary.org/obo/fbcv
    name: Drosophila Phenotype Ontology
    prefix: dpo
    tracker: https://github.com/FlyBase/drosophila-phenotype-ontology/issues
    version: '2025-10-17'
    version.iri: http://purl.obolibrary.org/obo/dpo/releases/2025-10-17/dpo.owl
  ontobee:
    library: Library
    name: Drosophila Phenotype Ontology
    prefix: DPO
  part_of: fbcv
  preferred_prefix: DPO
  prefix: dpo
  publications:
  - doi: 10.1186/2041-1480-4-30
    pmc: PMC3816596
    pubmed: '24138933'
    title: The Drosophila phenotype ontology
    year: 2013
dpv:
  biocontext:
    prefix: DPV
  contact:
    email: mike.adams@bbsrc.ac.uk
    github: null
    name: Michael J. Adams
    orcid: null
  integbio:
    alt_name: Database of Pathogenic Variants
    description: DPV provides information on germline pathogenic mutations in the
      Japanese population. The data of mutations were curated from published papers
      regarding Japanese patients with rare diseases and research activities in Japan.
      All registered variants can be downloaded as an aggregated single VCF file to
      use in laboratories.
    homepage: http://dpv.cmg.med.keio.ac.jp/dpv-pub/top
    information_keywords:
    - Phenotype
    - Sequence
    - Bibliography/Documents
    maintainer: Center for Medical Genetics, Keio University School of Medicine
    name: DPV
    prefix: nbdc02410
    status: Active
    target_keywords:
    - Genome/Gene
    - Genetic variation
    - Health/Disease
  lov:
    description: The Data Privacy Vocabulary (DPV) provides terms (classes and properties)
      to represent information about processing of personal data, for example - purposes,
      processing operations, personal data, technical and organisational measures.
    homepage: https://github.com/w3c/dpv/
    keywords:
    - People
    - Security
    modified: '2025-08-01'
    name: Data Privacy Vocabulary (DPV)
    prefix: dpv
    uri_prefix: https://w3id.org/dpv#$1
  mappings:
    biocontext: DPV
    integbio: nbdc02410
    lov: dpv
    miriam: dpv
    n2t: dpv
    prefixcommons: dpvweb
  miriam:
    deprecated: false
    description: Description of Plant Viruses (DPV) provides information about viruses,
      viroids and satellites of plants, fungi and protozoa. It provides taxonomic
      information, including brief descriptions of each family and genus, and classified
      lists of virus sequences. The database also holds detailed information for all
      sequences of viruses, viroids and satellites of plants, fungi and protozoa that
      are complete or that contain at least one complete gene.
    homepage: http://www.dpvweb.net/
    id: 00000280
    name: DPV
    namespaceEmbeddedInLui: false
    pattern: ^\d+$
    prefix: dpv
    sampleId: '100'
    uri_format: https://www.dpvweb.net/dpv/showdpv/?dpvno=$1
  n2t:
    description: Description of Plant Viruses (DPV) provides information about viruses,
      viroids and satellites of plants, fungi and protozoa. It provides taxonomic
      information, including brief descriptions of each family and genus, and classified
      lists of virus sequences. The database also holds detailed information for all
      sequences of viruses, viroids and satellites of plants, fungi and protozoa that
      are complete or that contain at least one complete gene.
    example: '100'
    homepage: http://www.dpvweb.net/
    name: DPV at Rothamsted
    namespaceEmbeddedInLui: false
    pattern: ^\d+$
    prefix: dpv
    uri_format: http://www.dpvweb.net/dpv/showdpv.php?dpvno=$1
  name: Description of Plant Viruses
  prefix: dpv
  prefixcommons:
    description: DPVweb provides a central source of information about viruses, viroids
      and satellites of plants, fungi and protozoa. Comprehensive taxonomic information,
      including brief descriptions of each family and genus, and classified lists
      of virus sequences are provided. The database also holds detailed, curated,
      information for all sequences of viruses, viroids and satellites of plants,
      fungi and protozoa that are complete or that contain at least one complete gene
      (currently, n~9000).
    example: '100'
    homepage: http://www.dpvweb.net
    keywords:
    - classification
    - gene
    name: Description of Plant Viruses
    pattern: ^\d+$
    prefix: dpvweb
    pubmed_ids:
    - '16381892'
    uri_format: http://www.dpvweb.net/dpv/showdpv.php?dpvno=$1
  publications:
  - doi: 10.1093/nar/gkj023
    pmc: PMC1347386
    pubmed: '16381892'
    title: 'DPVweb: a comprehensive database of plant and fungal virus genes and genomes'
    year: 2006
dpvocab:
  comment: The resource itself specifies a preferred prefix of `dpv` but this is already
    claimed in Bioregistry by the Description of Plant Viruses (https://bioregistry.io/registry/dpv).
    See also license discussion at https://github.com/w3c/dpv/issues/195.
  contact:
    email: me@harshp.com
    github: coolharsh55
    name: Harshvardhan J. Pandit
    orcid: 0000-0002-5068-3714
  contributor:
    email: jhc@lbl.gov
    github: caufieldjh
    name: Harry Caufield
    orcid: 0000-0001-5705-7831
  contributor_extras:
  - email: b.gyori@northeastern.edu
    github: bgyori
    name: Benjamin M. Gyori
    orcid: 0000-0001-9439-5346
  - email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  - email: m.naguthana@hotmail.com
    github: nagutm
    name: Mufaddal Naguthanawala
    orcid: 0009-0009-5240-7463
  - email: arthit@gmail.com
    github: bact
    name: Arthit Suriyawongkul
    orcid: 0000-0002-9698-1899
  description: The Data Privacy Vocabulary provides an ontology (classes and properties)
    and taxonomies of concepts to represent information regarding how personal data
    is processed in the form of an ontology or a knowledge graph.
  example: Duration
  github_request_issue: 1241
  homepage: https://w3c.github.io/dpv/2.0/dpv
  license: W3C-20150513
  mappings:
    tib: dpv
  name: Data Privacy Vocabulary
  prefix: dpvocab
  publications:
  - doi: 10.48550/arxiv.2404.13426
    pmc: null
    pubmed: null
    title: Data Privacy Vocabulary (DPV) -- Version 2
    year: 2024
  - doi: 10.1007/978-3-030-33246-4_44
    pmc: null
    pubmed: null
    title: Creating a Vocabulary for Data Privacy
    year: 2019
  references:
  - https://github.com/biopragmatics/bioregistry/pull/1250
  repository: https://github.com/w3c/dpv
  reviewer:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  tib:
    description: The Data Privacy Vocabulary (DPV) provides terms (classes and properties)
      to describe and represent information related to processing of personal data
      based on established requirements such as for the EU General Data Protection
      Regulation (GDPR). The DPV is structured as a top-down hierarchical vocabulary
      with the core or base concepts of personal data categories, purposes of processing
      and types of processing, data controller(s) associated, recipients of personal
      data, legal bases or justifications used, technical and organisational measures
      and restrictions (e.g. storage locations and storage durations), applicable
      rights, and the risks involved.
    homepage: https://www.w3.org/community/dpvcg/
    keywords:
    - NFDI4ING
    - ESS
    - law
    name: Data Privacy Vocabulary (DPV)
    prefix: dpv
    uri_format: https://w3id.org/dpv/$1
    version.iri: https://w3id.org/dpv/2.2
  uri_format: https://w3id.org/dpv#$1
dqv:
  example: QualityAnnotation
  lov:
    description: The Data Quality Vocabulary (DQV) is seen as an extension to DCAT
      to cover the quality of the data, how frequently is it updated, whether it accepts
      user corrections, persistence commitments etc. When used by publishers, this
      vocabulary will foster trust in the data amongst developers.
    homepage: https://www.w3.org/TR/vocab-dqv/
    keywords:
    - Quality
    modified: '2016-08-26'
    name: Data Quality Vocabulary
    prefix: dqv
    uri_prefix: http://www.w3.org/ns/dqv#$1
  mappings:
    lov: dqv
    zazuko: dqv
  prefix: dqv
  zazuko:
    prefix: dqv
    uri_format: http://www.w3.org/ns/dqv#$1
dragondb.allele:
  biocontext:
    prefix: DRAGONDB.ALLELE
  comment: Deprecated because the website is dead
  deprecated: true
  mappings:
    biocontext: DRAGONDB.ALLELE
    miriam: dragondb.allele
    n2t: dragondb.allele
  miriam:
    deprecated: true
    description: DragonDB is a genetic and genomic database for Antirrhinum majus
      (Snapdragon). This collection refers to allele information.
    homepage: http://www.antirrhinum.net/
    id: '00000300'
    name: DragonDB Allele
    namespaceEmbeddedInLui: false
    pattern: ^\w+$
    prefix: dragondb.allele
    sampleId: cho
    uri_format: http://antirrhinum.net/cgi-bin/ace/generic/tree/DragonDB?name=$1&amp;class=Allele
  n2t:
    description: DragonDB is a genetic and genomic database for Antirrhinum majus
      (Snapdragon). This collection refers to allele information.
    example: cho
    homepage: http://www.antirrhinum.net/
    name: DragonDB Allele at University of British Columbia
    namespaceEmbeddedInLui: false
    pattern: ^\w+$
    prefix: dragondb.allele
    uri_format: http://antirrhinum.net/cgi-bin/ace/generic/tree/DragonDB?name=$1&amp;class=Allele
  part_of_database: dragondb
  prefix: dragondb.allele
dragondb.dna:
  biocontext:
    prefix: DRAGONDB.DNA
  comment: Deprecated because the website is dead
  deprecated: true
  mappings:
    biocontext: DRAGONDB.DNA
    miriam: dragondb.dna
    n2t: dragondb.dna
  miriam:
    deprecated: true
    description: DragonDB is a genetic and genomic database for Antirrhinum majus
      (Snapdragon). This collection refers to DNA sequence information.
    homepage: http://www.antirrhinum.net/
    id: 00000297
    name: DragonDB DNA
    namespaceEmbeddedInLui: false
    pattern: ^\d\w+$
    prefix: dragondb.dna
    sampleId: 3hB06
    uri_format: http://antirrhinum.net/cgi-bin/ace/generic/tree/DragonDB?name=$1;class=DNA
  n2t:
    description: DragonDB is a genetic and genomic database for Antirrhinum majus
      (Snapdragon). This collection refers to DNA sequence information.
    example: 3hB06
    homepage: http://www.antirrhinum.net/
    name: DragonDB DNA at University of British Columbia
    namespaceEmbeddedInLui: false
    pattern: ^\d\w+$
    prefix: dragondb.dna
    uri_format: http://antirrhinum.net/cgi-bin/ace/generic/tree/DragonDB?name=$1;class=DNA
  part_of_database: dragondb
  prefix: dragondb.dna
dragondb.locus:
  biocontext:
    prefix: DRAGONDB.LOCUS
  comment: Deprecated because the website is dead
  deprecated: true
  mappings:
    biocontext: DRAGONDB.LOCUS
    miriam: dragondb.locus
    n2t: dragondb.locus
  miriam:
    deprecated: true
    description: DragonDB is a genetic and genomic database for Antirrhinum majus
      (Snapdragon). This collection refers to Locus information.
    homepage: http://www.antirrhinum.net/
    id: 00000299
    name: DragonDB Locus
    namespaceEmbeddedInLui: false
    pattern: ^\w+$
    prefix: dragondb.locus
    sampleId: DEF
    uri_format: http://antirrhinum.net/cgi-bin/ace/generic/tree/DragonDB?name=$1&amp;class=Locus
  n2t:
    description: DragonDB is a genetic and genomic database for Antirrhinum majus
      (Snapdragon). This collection refers to Locus information.
    example: DEF
    homepage: http://www.antirrhinum.net/
    name: DragonDB Locus at University of British Columbia
    namespaceEmbeddedInLui: false
    pattern: ^\w+$
    prefix: dragondb.locus
    uri_format: http://antirrhinum.net/cgi-bin/ace/generic/tree/DragonDB?name=$1&amp;class=Locus
  part_of_database: dragondb
  prefix: dragondb.locus
dragondb.protein:
  biocontext:
    prefix: DRAGONDB.PROTEIN
  comment: Deprecated because the website is dead
  deprecated: true
  mappings:
    biocontext: DRAGONDB.PROTEIN
    miriam: dragondb.protein
    n2t: dragondb.protein
  miriam:
    deprecated: true
    description: DragonDB is a genetic and genomic database for Antirrhinum majus
      (Snapdragon). This collection refers to protein sequence information.
    homepage: http://www.antirrhinum.net/
    id: 00000298
    name: DragonDB Protein
    namespaceEmbeddedInLui: false
    pattern: ^\w+$
    prefix: dragondb.protein
    sampleId: AMDEFA
    uri_format: http://antirrhinum.net/cgi-bin/ace/generic/tree/DragonDB?name=$1;class=Peptide
  n2t:
    description: DragonDB is a genetic and genomic database for Antirrhinum majus
      (Snapdragon). This collection refers to protein sequence information.
    example: AMDEFA
    homepage: http://www.antirrhinum.net/
    name: DragonDB Protein at University of British Columbia
    namespaceEmbeddedInLui: false
    pattern: ^\w+$
    prefix: dragondb.protein
    uri_format: http://antirrhinum.net/cgi-bin/ace/generic/tree/DragonDB?name=$1;class=Peptide
  part_of_database: dragondb
  prefix: dragondb.protein
dramp:
  contact:
    email: zhengh18@hotmail.com
    github: null
    name: Heng Zheng
    orcid: 0000-0002-1810-5842
  contributor:
    email: b.gyori@northeastern.edu
    github: bgyori
    name: Benjamin M. Gyori
    orcid: 0000-0001-9439-5346
  description: Identifiers repesent antimicrobial peptides in the Data Repository
    of Antimicrobial Peptides (DRAMP) database which is an open-access, manually curated
    database of antimicrobial peptides (AMPs).
  domain: peptide
  example: DRAMP00005
  github_request_issue: 1705
  homepage: http://dramp.cpu-bioinfor.org
  keywords:
  - antimicrobial peptides
  name: Data Repository of Antimicrobial Peptides
  pattern: ^DRAMP\d{5}$
  prefix: dramp
  providers:
  - code: abpdb
    description: Antimicrobial Peptide Database (ABPDB) is a comprehensive database
      that aggregates antimicrobial peptide data from multiple sources including DRAMP,
      providing streamlined access to antimicrobial peptide information.
    example: null
    first_party: null
    homepage: http://www.acdb.plus/ABPDB/
    name: AntiBacterial Peptides DataBase
    publications:
    - doi: 10.1109/tcbbio.2025.3582844
      pmc: null
      pubmed: '40811252'
      title: 'ABPDB: a Database of Antibacterial Peptides'
      year: 2025
    status: null
    uri_format: http://www.acdb.plus/ABPDB/abp-search.php?keywords=$1
  publications:
  - doi: 10.1093/nar/gkae1046
    pmc: PMC11701585
    pubmed: '39526377'
    title: 'DRAMP 4.0: an open-access data repository dedicated to the clinical translation
      of antimicrobial peptides'
    year: 2025
  - doi: 10.1093/nar/gkab651
    pmc: PMC8728287
    pubmed: '34390348'
    title: 'DRAMP 3.0: an enhanced comprehensive data repository of antimicrobial
      peptides'
    year: 2022
  - doi: 10.1038/s41597-019-0154-y
    pmc: PMC6692298
    pubmed: '31409791'
    title: DRAMP 2.0, an updated data repository of antimicrobial peptides
    year: 2019
  - doi: 10.1038/srep24482
    pmc: PMC4830929
    pubmed: '27075512'
    title: 'DRAMP: a comprehensive data repository of antimicrobial peptides'
    year: 2016
  reviewer:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  uri_format: http://dramp.cpu-bioinfor.org/browse/All_Information.php?id=$1
drao:
  contact:
    email: allyson.lister@oerc.ox.ac.uk
    github: allysonlister
    name: Allyson Lister
    orcid: 0000-0002-7702-4495
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: A project supporting the DRAO application ontology, a hierarchy of
    specific research domains and descriptors which imports subsets of terms from
    over 40 publicly-available terminologies. (from repository)
  download_obo: https://github.com/FAIRsharing/domain-ontology/raw/refs/heads/master/DRAO.obo
  download_owl: https://github.com/FAIRsharing/domain-ontology/raw/refs/heads/master/DRAO.owl
  example: '0000001'
  fairsharing:
    abbreviation: DRAO
    description: The Domain Resource Application Ontology (DRAO) is an application
      ontology describing cross-discipline research domains used within FAIRsharing
      records by curators and the user community (see also the DRAO FAIRsharing record).
      It is built in conjunction with the Subject Resource Application Ontology (SRAO),
      which describes higher-level subject areas / disciplines. All classes within
      DRAO come from publicly-available terminologies. The full list of terminologies
      used to develop DRAO is available in the relationship graph of this record,
      with further information available on our github pages.
    domains:
    - Resource metadata
    - Classification
    - FAIR
    homepage: https://github.com/FAIRsharing/domain-ontology
    license: CC BY-SA 4.0
    name: Domain Resource Application Ontology
    prefix: FAIRsharing.FSIfv8
    repository: https://github.com/FAIRsharing/domain-ontology/blob/master/Development.md
    subjects:
    - Agriculture
    - Environmental Science
    - Life Science
    - Computer Science
    - Biomedical Science
    - Humanities
    - Natural Science
    - Earth Science
    user_defined_tags:
    - Metadata standardization
  homepage: http://www.fairsharing.org
  license: CC-BY-4.0
  mappings:
    fairsharing: FAIRsharing.FSIfv8
  name: Domain Resource Application Ontology
  part_of_database: fairsharing
  pattern: ^\d{7}$
  prefix: drao
  repository: https://github.com/FAIRsharing/domain-ontology
  uri_format: http://www.fairsharing.org/ontology/domain/DRAO_$1
drc.filenumber:
  contributor:
    email: egon.willighagen@maastrichtuniversity.nl
    github: egonw
    name: Egon Willighagen
    orcid: 0000-0001-7542-0286
  description: Dutch Research Council file numbers are used for approved grants.
  example: osf232097
  github_request_issue: 1460
  homepage: https://www.nwo.nl/en/
  name: Dutch Research Council File Number
  prefix: drc.filenumber
  reviewer:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  uri_format: https://www.nwo.nl/en/projects/$1
drduke:
  mappings:
    wikidata: P10074
  name: Dr. Duke's Phytochemical and Ethnobotanical Databases chemical
  prefix: drduke
  wikidata:
    description: identifier for chemicals linked to information on occurrence in plants
    example:
    - '19'
    - '32'
    homepage: https://phytochem.nal.usda.gov/phytochem/search/list
    name: Dr. Duke's Phytochemical and Ethnobotanical Databases chemical ID
    prefix: P10074
    uri_format: https://phytochem.nal.usda.gov/phytochem/chemicals/show/$1
drks:
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: The German Clinical Trials Register (DRKS) is the German WHO primary
    registry. It is competent for the registration of all patient-oriented clinical
    trials conducted in Germany. The DRKS now contains well over 14,000 studies. Currently,
    around 2,000 studies are added annually. (from website)
  example: DRKS00031815
  homepage: http://drks.de
  name: German Clinical Trials Register
  pattern: ^DRKS\d+$
  prefix: drks
  providers:
  - code: alt1
    description: German Language Provider
    example: null
    first_party: true
    homepage: http://drks.de
    name: German Language Provider
    publications: null
    status: null
    uri_format: https://drks.de/search/de/trial/$1
  - code: alt2
    description: Legacy Provider
    example: null
    first_party: true
    homepage: http://drks.de
    name: Legacy Provider
    publications: null
    status: null
    uri_format: http://drks.de/en/trial/$1
  uri_format: https://drks.de/search/en/trial/$1
dron:
  aberowl:
    description: An ontology to support comparative effectiveness researchers studying
      claims data.
    download_owl: http://aber-owl.net/media/ontologies/DRON/33/dron.owl
    homepage: https://github.com/ufbmi/dron
    name: The Drug Ontology
    prefix: DRON
  biocontext:
    prefix: DRON
  bioportal:
    contact:
      email: hoganwr@gmail.com
      name: William Hogan
    description: We built this ontology primarily to support comparative effectiveness
      researchers studying claims data. They need to be able to query U.S. National
      Drug Codes (NDCs) by ingredient, mechanism of action (beta-adrenergic blockade),
      physiological effect (diuresis), and therapeutic intent (anti-hypertensive).
    homepage: https://github.com/ufbmi/dron
    license: CC-BY-3.0
    name: The Drug Ontology
    prefix: DRON
    version: '2025-11-20'
  download_json: http://purl.obolibrary.org/obo/dron.json
  download_obo: http://purl.obolibrary.org/obo/dron.obo
  example: '00023232'
  fairsharing:
    abbreviation: DrOn
    contact:
      email: hoganwr@gmail.com
      name: William Hogan
      orcid: 0000-0002-9881-1017
    description: An ontology of drug products and packaged drug products.
    domains:
    - drug
    - small molecule
    - Approved drug
    homepage: https://github.com/mcwdsi/dron
    license: CC-BY-4.0
    name: The Drug Ontology
    prefix: FAIRsharing.w5ntfd
    publications:
    - doi: 10.1186/s13326-016-0048-2
      pubmed: '27096073'
      title: An accurate and precise representation of drug ingredients
      year: 2016
    - doi: 10.1186/s13326-017-0121-5
      pubmed: '28253937'
      title: 'Therapeutic indications and other use-case-driven updates in the drug
        ontology: anti-malarials, anti-hypertensives, opioid analgesics, and a large
        term request'
      year: 2017
    - doi: 10.1186/2041-1480-4-44
      pubmed: '24345026'
      title: Building a drug ontology based on RxNorm and other sources
      year: 2013
    subjects:
    - Biomedical Science
  mappings:
    aberowl: DRON
    biocontext: DRON
    bioportal: DRON
    fairsharing: FAIRsharing.w5ntfd
    obofoundry: dron
    ols: dron
    ontobee: DRON
    wikidata.entity: Q81661592
  obofoundry:
    appears_in:
    - scdo
    contact: hoganwr@gmail.com
    contact.github: hoganwr
    contact.label: William Hogan
    contact.orcid: 0000-0002-9881-1017
    deprecated: false
    description: An ontology to support comparative effectiveness researchers studying
      claims data.
    domain: health
    download.owl: http://purl.obolibrary.org/obo/dron.owl
    homepage: https://github.com/ufbmi/dron
    license: CC BY 3.0
    license.url: http://creativecommons.org/licenses/by/3.0/
    name: The Drug Ontology
    preferredPrefix: DRON
    prefix: dron
    publications:
    - id: https://doi.org/10.1186/s13326-017-0121-5
      title: 'Therapeutic indications and other use-case-driven updates in the drug
        ontology: anti-malarials, anti-hypertensives, opioid analgesics, and a large
        term request'
    repository: https://github.com/ufbmi/dron
  ols:
    description: An ontology to support comparative effectiveness researchers studying
      claims data.
    download_owl: http://purl.obolibrary.org/obo/dron.owl
    homepage: https://github.com/ufbmi/dron
    name: The Drug Ontology
    prefix: dron
    tracker: https://github.com/ufbmi/dron/issues
    version: '2025-11-20'
    version.iri: http://purl.obolibrary.org/obo/dron/releases/2025-11-20/dron.owl
  ontobee:
    library: Library
    name: The Drug Ontology
    prefix: DRON
  pattern: ^\d{8}$
  prefix: dron
  publications:
  - doi: 10.1186/s13326-017-0121-5
    pmc: PMC5335794
    pubmed: '28253937'
    title: 'Therapeutic indications and other use-case-driven updates in the drug
      ontology: anti-malarials, anti-hypertensives, opioid analgesics, and a large
      term request'
    year: 2017
  - doi: 10.1186/s13326-016-0048-2
    pmc: PMC4836073
    pubmed: '27096073'
    title: An accurate and precise representation of drug ingredients
    year: 2016
  - doi: 10.1186/2041-1480-4-44
    pmc: PMC3931349
    pubmed: '24345026'
    title: Building a drug ontology based on RxNorm and other sources
    year: 2013
  repository: https://github.com/mcwdsi/dron
  uri_format: http://purl.obolibrary.org/obo/DRON_$1
drsanv0:
  mappings:
    miriam: drs.anv0
  miriam:
    deprecated: false
    description: 'This namespace is used for GA4GH Data Repository Service (DRS) access
      to the USA National Institutes of Health (NIH), National Human Genome Research
      Institute (NHGRI), Genomic Analysis, Visualization and Informatics Lab-space
      (AnVIL) program data. AnVIL is a cloud-based genomic data sharing and analysis
      platform which facilitates integration and computing on and across large datasets
      generated by NHGRI programs, as well as initiatives funded by the National Institutes
      of Health (NIH) or by other agencies that support human genomics research.   '
    homepage: https://www.genome.gov/
    id: '00001014'
    name: AnVIL DRS
    namespaceEmbeddedInLui: false
    pattern: ^v2_[0-9a-fA-F]{8}-[0-9a-fA-F]{4}-[0-9a-fA-F]{4}-[0-9a-fA-F]{4}-[0-9a-fA-F]{12}$
    prefix: drs.anv0
    sampleId: v2_1b0f158a-86e2-3887-b990-89e3cf2d9082
    uri_format: https://data.terra.bio/ga4gh/drs/v1/objects/$1
  prefix: drsanv0
drsc:
  biocontext:
    prefix: DRSC
  mappings:
    biocontext: DRSC
    miriam: drsc
    n2t: drsc
  miriam:
    deprecated: false
    description: The DRSC (Drosophila RNAi Screening Cente) tracks both production
      of reagents for RNA interference (RNAi) screening in Drosophila cells and RNAi
      screen results. It maintains a list of Drosophila gene names, identifiers, symbols
      and synonyms and provides  information for cell-based or in vivo RNAi reagents,
      other types of reagents, screen results, etc. corresponding for a given gene.
    homepage: http://flyrnai.org/
    id: '00000367'
    name: DRSC
    namespaceEmbeddedInLui: false
    pattern: ^DRSC\d+$
    prefix: drsc
    sampleId: DRSC05221
    uri_format: http://www.flyrnai.org/cgi-bin/RNAi_gene_lookup_public.pl?gname=$1
  n2t:
    description: The DRSC (Drosophila RNAi Screening Cente) tracks both production
      of reagents for RNA interference (RNAi) screening in Drosophila cells and RNAi
      screen results. It maintains a list of Drosophila gene names, identifiers, symbols
      and synonyms and provides  information for cell-based or in vivo RNAi reagents,
      other types of reagents, screen results, etc. corresponding for a given gene.
    example: DRSC05221
    homepage: http://flyrnai.org/
    name: DRSC at Harvard Medical School
    namespaceEmbeddedInLui: false
    pattern: ^DRSC\d+$
    prefix: drsc
    uri_format: http://www.flyrnai.org/cgi-bin/RNAi_gene_lookup_public.pl?gname=$1
  name: Drosophila RNAi Screening Center
  prefix: drsc
drugbank:
  bartoc:
    description: The DrugBank database is a unique bioinformatics and cheminformatics
      resource that combines detailed drug (i.e. chemical, pharmacological and pharmaceutical)
      data with comprehensive drug target (i.e. sequence, structure, and pathway)
      information. The database contains 8246 drug entries including 2012 FDA-approved
      small molecule drugs, 229 FDA-approved biotech (protein/peptide) drugs, 94 nutraceuticals
      and over 6000 experimental drugs. Additionally, 4344 non-redundant protein (i.e.
      drug target/enzyme/transporter/carrier) sequences are linked to these drug entries.
      Each DrugCard entry contains more than 200 data fields with half of the information
      being devoted to drug/chemical data and the other half devoted to drug target
      or protein data.
    homepage: http://www.drugbank.ca/
    license: CC BY-NC 3.0
    name: DrugBank
    prefix: '18377'
    wikidata_database: Q1122544
  biocontext:
    prefix: DrugBank
    uri_format: http://www.drugbank.ca/drugs/$1
  cellosaurus:
    category: Chemistry resources
    homepage: https://go.drugbank.com/
    name: DrugBank database
    prefix: DrugBank
    uri_format: https://go.drugbank.com/drugs/$1
  cheminf:
    description: Database identifier used by DrugBank.
    name: DrugBank
    obsolete: false
    prefix: '000406'
  contact:
    email: david.wishart@ualberta.ca
    github: DavidWishartLab
    name: David S. Wishart
    orcid: 0000-0002-3207-2434
  domain: chemical
  edam:
    description: Unique identifier of a drug from the DrugBank database.
    name: DrugBank
    obsolete: false
    prefix: '2326'
  example: DB14938
  fairsharing:
    abbreviation: DrugBank
    contact:
      email: david.wishart@ualberta.ca
      name: David Wishart
      orcid: 0000-0002-3207-2434
    description: The DrugBank database is a freely available bioinformatics and chemoinformatics
      resource that combines detailed drug (i.e. chemical, pharmacological and pharmaceutical)
      data with comprehensive drug target (i.e. sequence, structure, and pathway)
      information.
    homepage: http://www.drugbank.ca/
    name: DrugBank
    prefix: FAIRsharing.353yat
    publications:
    - doi: 10.1093/nar/gkt1068
      pubmed_id: 24203711
      title: 'DrugBank 4.0: shedding new light on drug metabolism.'
    - doi: 10.1093/nar/gkq1126
      pubmed_id: 21059682
      title: 'DrugBank 3.0: a comprehensive resource for ''omics'' research on drugs.'
    - doi: 10.1093/nar/gkm958
      pubmed_id: 18048412
      title: 'DrugBank: a knowledgebase for drugs, drug actions and drug targets.'
    - doi: 10.1093/nar/gkj067
      pubmed_id: 16381955
      title: 'DrugBank: a comprehensive resource for in silico drug discovery and
        exploration.'
    subjects:
    - Life Science
    - Biomedical Science
    twitter: DrugBankDB
  homepage: http://www.drugbank.ca
  integbio:
    description: DrugBank is a database of detailed informatics resources on approved
      and experimental drugs. The database contains informaiton on drug targets as
      well as the results of experiments resulting in extensive bioinformatics and
      chemoinformatics data. Users can browse or search by drug or target. Data is
      available for download.
    fairsharing: biodbcore-000304
    homepage: http://www.drugbank.ca/
    information_keywords:
    - Sequence
    - Interaction/Pathway
    - Chemical structure
    maintainer: University of Alberta/Department of Computing Science
    name: DrugBank
    prefix: nbdc01071
    pubmeds:
    - '18048412'
    - '16381955'
    status: Active
    target_keywords:
    - Protein
    - Drug
  logo: https://upload.wikimedia.org/wikipedia/commons/thumb/f/fd/Drugbank_logo.svg/1280px-Drugbank_logo.svg.png
  mappings:
    bartoc: '18377'
    biocontext: DrugBank
    cellosaurus: DrugBank
    cheminf: '000406'
    edam: '2326'
    fairsharing: FAIRsharing.353yat
    integbio: nbdc01071
    miriam: drugbank
    n2t: drugbank
    pathguide: '221'
    prefixcommons: drugbank
    re3data: r3d100010544
    togoid: Drugbank
    uniprot: DB-0019
    wikidata: P715
    wikidata.entity: Q1122544
  miriam:
    deprecated: false
    description: The DrugBank database is a bioinformatics and chemoinformatics resource
      that combines detailed drug (i.e. chemical, pharmacological and pharmaceutical)
      data with comprehensive drug target (i.e. sequence, structure, and pathway)
      information. This collection references drug information.
    homepage: https://www.drugbank.com
    id: '00000102'
    name: DrugBank
    namespaceEmbeddedInLui: false
    pattern: ^DB\d{5}$
    prefix: drugbank
    sampleId: DB00001
    uri_format: https://go.drugbank.com/drugs/$1
  n2t:
    description: The DrugBank database is a bioinformatics and chemoinformatics resource
      that combines detailed drug (i.e. chemical, pharmacological and pharmaceutical)
      data with comprehensive drug target (i.e. sequence, structure, and pathway)
      information. This collection references drug information.
    example: DB00001
    homepage: http://www.drugbank.ca/
    name: DrugBank drug information
    namespaceEmbeddedInLui: false
    pattern: ^DB\d{5}$
    prefix: drugbank
    uri_format: http://www.drugbank.ca/drugs/$1
  name: DrugBank
  pathguide:
    abbreviation: DrugBank
    homepage: http://www.drugbank.ca/
    name: DrugBank
    prefix: '221'
  prefix: drugbank
  prefixcommons:
    description: The DrugBank database is a bioinformatics and chemoinformatics resource
      that combines detailed drug (i.e. chemical, pharmacological and pharmaceutical)
      data with comprehensive drug target (i.e. sequence, structure, and pathway)
      information.
    example: DB00001
    homepage: http://www.drugbank.ca/
    keywords:
    - drug
    - protein
    license: http://www.drugbank.ca/about
    name: DrugBank
    pattern: ^DB\d{5}$
    prefix: drugbank
    pubmed_ids:
    - '24203711'
    - '21059682'
    - '18048412'
    - '16381955'
    uri_format: http://www.drugbank.ca/drugs/$1
  publications:
  - doi: 10.1093/nar/gkt1068
    pmc: PMC3965102
    pubmed: '24203711'
    title: 'DrugBank 4.0: shedding new light on drug metabolism'
    year: 2013
  - doi: 10.1093/nar/gkq1126
    pmc: PMC3013709
    pubmed: '21059682'
    title: 'DrugBank 3.0: a comprehensive resource for ''omics'' research on drugs'
    year: 2010
  - doi: 10.1093/nar/gkm958
    pmc: PMC2238889
    pubmed: '18048412'
    title: 'DrugBank: a knowledgebase for drugs, drug actions and drug targets'
    year: 2007
  - doi: 10.1093/nar/gkj067
    pmc: PMC1347430
    pubmed: '16381955'
    title: 'DrugBank: a comprehensive resource for in silico drug discovery and exploration'
    year: 2006
  - doi: 10.1093/nar/gkt1068
    pmc: null
    pubmed: null
    title: 'DrugBank 4.0: shedding new light on drug metabolism.'
    year: null
  - doi: 10.1093/nar/gkq1126
    pmc: null
    pubmed: null
    title: 'DrugBank 3.0: a comprehensive resource for ''omics'' research on drugs.'
    year: null
  - doi: 10.1093/nar/gkm958
    pmc: null
    pubmed: null
    title: 'DrugBank: a knowledgebase for drugs, drug actions and drug targets.'
    year: null
  - doi: 10.1093/nar/gkj067
    pmc: null
    pubmed: null
    title: 'DrugBank: a comprehensive resource for in silico drug discovery and exploration.'
    year: null
  - doi: null
    pmc: null
    pubmed: '24203711'
    title: null
    year: null
  - doi: null
    pmc: null
    pubmed: '21059682'
    title: null
    year: null
  - doi: null
    pmc: null
    pubmed: '18048412'
    title: null
    year: null
  - doi: null
    pmc: null
    pubmed: '16381955'
    title: null
    year: null
  - doi: 10.1093/nar/gkad976
    pmc: null
    pubmed: '37953279'
    title: null
    year: null
  re3data:
    description: The DrugBank database is a unique bioinformatics and cheminformatics
      resource that combines detailed drug (i.e. chemical, pharmacological and pharmaceutical)
      data with comprehensive drug target (i.e. sequence, structure, and pathway)
      information. The latest release of DrugBank Online (version 5.1.12, released
      2024-03-14) contains 17,423 drug entries including 2,800 approved small molecule
      drugs, 1,671 approved biologics (proteins, peptides, vaccines, and allergenics),
      135 nutraceuticals and over 6,726 experimental (discovery-phase) drugs. Additionally,
      5,429 non-redundant protein (i.e. drug target/enzyme/transporter/carrier) sequences
      are linked to these drug entries. Each entry contains more than 200 data fields
      with half of the information being devoted to drug/chemical data and the other
      half devoted to drug target or protein data.
    doi: 10.17616/R3V60M
    homepage: https://go.drugbank.com/
    name: DrugBank
    prefix: r3d100010544
    synonyms:
    - DrugBank Online
    - Open Data Drug & Drug Target Database
    xrefs:
      nif: 0000-00417
  synonyms:
  - DRUGBANK_ID
  - DrugBank
  togoid:
    catalog: nbdc01071
    description: DrugBank is a database of detailed informatics resources on approved
      and experimental drugs. The database contains informaiton on drug targets as
      well as the results of experiments resulting in extensive bioinformatics and
      chemoinformatics data. Users can browse or search by drug or target. Data is
      available for download.
    examples:
    - DB15589
    - DB13471
    - DB05830
    - DB07423
    - DB07074
    - DB08912
    - DB02908
    - DB05088
    - DB05229
    - DB08910
    keywords:
    - Drug
    name: DrugBank
    pattern: ^(?DB\d{5})$
    prefix: Drugbank
    uri_format: http://identifiers.org/drugbank/$1
  uniprot:
    abbreviation: DrugBank
    category: Chemistry databases
    homepage: https://go.drugbank.com
    name: Drug and drug target database
    prefix: DB-0019
    publications:
    - doi: 10.1093/nar/gkad976
      pubmed: '37953279'
    uri_format: https://go.drugbank.com/drugs/$1
  wikidata:
    description: identifier in the bioinformatics and cheminformatics database from
      the University of Alberta
    example:
    - DB00126
    - DB09145
    homepage: https://www.drugbank.ca
    name: DrugBank ID
    pattern: ^DB(SALT\d|CAT\d)?\d{5}$
    prefix: P715
    uri_format: https://go.drugbank.com/drugs/$1
drugbank.bioentity:
  biocontext:
    prefix: DRUGBANKV4.TARGET
  contact:
    email: david.wishart@ualberta.ca
    github: DavidWishartLab
    name: David S. Wishart
    orcid: 0000-0002-3207-2434
  logo: https://upload.wikimedia.org/wikipedia/commons/thumb/f/fd/Drugbank_logo.svg/1280px-Drugbank_logo.svg.png
  mappings:
    biocontext: DRUGBANKV4.TARGET
    miriam: drugbankv4.target
    n2t: drugbankv4.target
  miriam:
    deprecated: false
    description: The DrugBank database is a bioinformatics and chemoinformatics resource
      that combines detailed drug (i.e. chemical, pharmacological and pharmaceutical)
      data with comprehensive drug target (i.e. sequence, structure, and pathway)
      information. This collection references target information from version 4 of
      the database.
    homepage: http://www.drugbank.ca/targets
    id: 00000528
    name: DrugBank Target v4
    namespaceEmbeddedInLui: false
    pattern: ^BE\d{7}$
    prefix: drugbankv4.target
    sampleId: BE0000048
    uri_format: http://www.drugbank.ca/biodb/bio_entities/$1
  n2t:
    description: The DrugBank database is a bioinformatics and chemoinformatics resource
      that combines detailed drug (i.e. chemical, pharmacological and pharmaceutical)
      data with comprehensive drug target (i.e. sequence, structure, and pathway)
      information. This collection references target information from version 4 of
      the database.
    example: BE0000048
    homepage: http://www.drugbank.ca/targets
    name: DrugBank Target information version 4
    namespaceEmbeddedInLui: false
    pattern: ^BE\d{7}$
    prefix: drugbankv4.target
    uri_format: http://www.drugbank.ca/biodb/bio_entities/$1
  part_of_database: drugbank
  prefix: drugbank.bioentity
  synonyms:
  - drugbank.target
  - drugbankv4.target
  uri_format: https://go.drugbank.com/bio_entities/$1
drugbank.category:
  contact:
    email: david.wishart@ualberta.ca
    github: DavidWishartLab
    name: David S. Wishart
    orcid: 0000-0002-3207-2434
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: Close to 5K Categorizations for drugs, similar to ATCC.
  example: DBCAT000600
  homepage: https://go.drugbank.com/categories
  keywords:
  - chemistry
  - drugs
  - metascience
  - topics
  logo: https://upload.wikimedia.org/wikipedia/commons/thumb/f/fd/Drugbank_logo.svg/1280px-Drugbank_logo.svg.png
  name: DrugBank Drug Category
  part_of_database: drugbank
  pattern: ^DBCAT\d+$
  prefix: drugbank.category
  uri_format: https://www.drugbank.ca/categories/$1
drugbank.condition:
  contact:
    email: david.wishart@ualberta.ca
    github: DavidWishartLab
    name: David S. Wishart
    orcid: 0000-0002-3207-2434
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: Indications and other conditions in drugbank
  example: DBCOND0066902
  homepage: https://go.drugbank.com
  logo: https://upload.wikimedia.org/wikipedia/commons/thumb/f/fd/Drugbank_logo.svg/1280px-Drugbank_logo.svg.png
  name: DrugBank Condition
  part_of_database: drugbank
  pattern: ^DBCOND\d+$
  prefix: drugbank.condition
  uri_format: https://go.drugbank.com/indications/$1
drugbank.metabolite:
  contact:
    email: david.wishart@ualberta.ca
    github: DavidWishartLab
    name: David S. Wishart
    orcid: 0000-0002-3207-2434
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: Metabolites in drugbank
  example: DBMET02292
  homepage: https://go.drugbank.com
  logo: https://upload.wikimedia.org/wikipedia/commons/thumb/f/fd/Drugbank_logo.svg/1280px-Drugbank_logo.svg.png
  name: DrugBank Metabolite
  part_of_database: drugbank
  pattern: ^DBMET\d+$
  prefix: drugbank.metabolite
  uri_format: https://go.drugbank.com/metabolites/$1
drugbank.reaction:
  contact:
    email: david.wishart@ualberta.ca
    github: DavidWishartLab
    name: David S. Wishart
    orcid: 0000-0002-3207-2434
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: Reactions in drugbank
  example: '1537'
  homepage: https://go.drugbank.com
  logo: https://upload.wikimedia.org/wikipedia/commons/thumb/f/fd/Drugbank_logo.svg/1280px-Drugbank_logo.svg.png
  name: DrugBank Reaction
  part_of_database: drugbank
  pattern: ^\d+$
  prefix: drugbank.reaction
  uri_format: https://go.drugbank.com/reactions/$1
drugbank.salt:
  contact:
    email: david.wishart@ualberta.ca
    github: DavidWishartLab
    name: David S. Wishart
    orcid: 0000-0002-3207-2434
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: DrugBank is a web-enabled database containing comprehensive molecular
    information about drugs, their mechanisms, their interactions and their targets.
  domain: chemical
  example: DBSALT001211
  homepage: http://www.drugbank.ca
  keywords:
  - chemical
  - compound
  - salt
  - small molecule
  logo: https://upload.wikimedia.org/wikipedia/commons/thumb/f/fd/Drugbank_logo.svg/1280px-Drugbank_logo.svg.png
  name: DrugBank Salts
  part_of_database: drugbank
  pattern: ^DBSALT\d{6}$
  prefix: drugbank.salt
  uri_format: https://go.drugbank.com/salts/$1
drugcentral:
  biolink:
    is_identifiers: false
    is_obo: false
    prefix: DrugCentral
    uri_format: http://drugcentral.org/drugcard/$1
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: DrugCentral  provides information on active ingredients chemical entities,
    pharmaceutical products, drug mode of action, indications, pharmacologic action.
  domain: chemical
  example: '307'
  fairsharing:
    abbreviation: DrugCentral
    contact:
      email: toprea@salud.unm.edu
      name: Tudor Oprea
      orcid: 0000-0002-6195-6976
    description: DrugCentral is online drug information that provides information
      on active ingredients, chemical entities, pharmaceutical products, drug mode
      of action, indications, and pharmacologic mode of action. DrugCentral monitors
      FDA, EMA, and PMDA for new drug approval on regular basis to ensure currency
      of the resource. This resource was created and is maintained by the Division
      of Translational Informatics at the University of New Mexico School of Medicine.
    homepage: http://drugcentral.org/
    license: CC BY-SA 4.0
    name: DrugCentral
    prefix: FAIRsharing.3me82d
    publications:
    - doi: 10.1093/nar/gkw993
      pubmed_id: 27789690
      title: 'DrugCentral: online drug compendium.'
    subjects:
    - Drug Discovery
    - Drug Repositioning
    - Drug Development
    - Pharmacy
    - Pharmacology
    - Biomedical Science
  homepage: http://drugcentral.org
  integbio:
    description: DrugCentral is online drug information that provides information
      on active ingredients, chemical entities, pharmaceutical products, drug mode
      of action, indications, and pharmacologic mode of action. DrugCentral monitors
      FDA, EMA, and PMDA for new drug approval on regular basis to ensure currency
      of the resource. This resource was created and is maintained by the Division
      of Translational Informatics at the University of New Mexico School of Medicine.
    fairsharing: FAIRsharing.3me82d
    homepage: http://drugcentral.org/
    information_keywords:
    - Ontology/Terminology/Nomenclature
    - Chemical structure
    - Interaction/Pathway
    - Phenotype
    maintainer: UNM School of Medicine
    name: DrugCentral
    prefix: nbdc02192
    pubmeds:
    - '27789690'
    status: Active
    target_keywords:
    - Chemical compound
    - Drug
  license: CC-BY-SA-4.0
  logo: https://encrypted-tbn0.gstatic.com/images?q=tbn:ANd9GcTV8USVHMzllhzTb3yLIUbEA9qKRR4Sub2QDA&s
  mappings:
    biolink: DrugCentral
    fairsharing: FAIRsharing.3me82d
    integbio: nbdc02192
    miriam: drugcentral
    uniprot: DB-0239
    wikidata: P11198
  miriam:
    deprecated: false
    description: DrugCentral (http://drugcentral.org) is an open-access online drug
      compendium. DrugCentral integrates structure, bioactivity, regulatory, pharmacologic
      actions and indications for active pharmaceutical ingredients approved by FDA
      and other regulatory agencies. Monitoring of regulatory agencies for new drugs
      approvals ensures the resource is up-to-date. DrugCentral integrates content
      for active ingredients with pharmaceutical formulations, indexing drugs and
      drug label annotations, complementing similar resources available online. Its
      complementarity with other online resources is facilitated by cross referencing
      to external resources. At the molecular level, DrugCentral bridges drug-target
      interactions with pharmacological action and indications. The integration with
      FDA drug labels enables text mining applications for drug adverse events and
      clinical trial information. Chemical structure overlap between DrugCentral and
      five online drug resources, and the overlap between DrugCentral FDA-approved
      drugs and their presence in four different chemical collections, are discussed.
      DrugCentral can be accessed via the web application or downloaded in relational
      database format.
    homepage: http://www.unm.edu/
    id: 00000966
    name: DrugCentral
    namespaceEmbeddedInLui: false
    pattern: ^[0-9]+$
    prefix: drugcentral
    sampleId: '257'
    uri_format: https://drugcentral.org/drugcard/$1
  name: Drug Central
  pattern: ^\d+$
  prefix: drugcentral
  publications:
  - doi: 10.1093/nar/gky963
    pmc: PMC6323925
    pubmed: '30371892'
    title: 'DrugCentral 2018: an update'
    year: 2019
  - doi: 10.1093/nar/gkw993
    pmc: PMC5210665
    pubmed: '27789690'
    title: 'DrugCentral: online drug compendium'
    year: 2016
  - doi: 10.1093/nar/gkw993
    pmc: null
    pubmed: null
    title: 'DrugCentral: online drug compendium.'
    year: null
  - doi: 10.1093/nar/gkac1085
    pmc: null
    pubmed: '36484092'
    title: null
    year: null
  - doi: 10.1093/nar/gkw993
    pmc: null
    pubmed: null
    title: 'DrugCentral: online drug compendium.'
    year: null
  - doi: 10.1093/nar/gkac1085
    pmc: null
    pubmed: '36484092'
    title: null
    year: null
  - doi: 10.1093/nar/gkw993
    pmc: null
    pubmed: null
    title: 'DrugCentral: online drug compendium.'
    year: null
  - doi: 10.1093/nar/gkac1085
    pmc: null
    pubmed: '36484092'
    title: null
    year: null
  - doi: 10.1093/nar/gkw993
    pmc: null
    pubmed: null
    title: 'DrugCentral: online drug compendium.'
    year: null
  - doi: 10.1093/nar/gkac1085
    pmc: null
    pubmed: '36484092'
    title: null
    year: null
  - doi: 10.1093/nar/gkw993
    pmc: null
    pubmed: null
    title: 'DrugCentral: online drug compendium.'
    year: null
  - doi: 10.1093/nar/gkac1085
    pmc: null
    pubmed: '36484092'
    title: null
    year: null
  synonyms:
  - Drug_Central
  uniprot:
    abbreviation: DrugCentral
    category: Chemistry databases
    homepage: https://drugcentral.org/
    name: DrugCentral
    prefix: DB-0239
    publications:
    - doi: 10.1093/nar/gkac1085
      pubmed: '36484092'
    uri_format: https://drugcentral.org?q=$1
  uri_format: http://drugcentral.org/drugcard/$1
  wikidata:
    description: ID of a chemical compound in DrugCentral
    example:
    - '158'
    - '21'
    - '947'
    homepage: https://drugcentral.org/
    name: DrugCentral ID
    pattern: ^\d+$
    prefix: P11198
    uri_format: https://drugcentral.org/drugcard/$1
dsm4:
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: A terminology published by the American Psychiatric Association (APA)
    for the classification of mental disorders using a common language and standard
    criteria. [wikipedia]
  example: '315.1'
  example_extras:
  - '291.89'
  hl7:
    description: 'Diagnostic and Statistical Manual of Mental Disorders (DSM-IV).
      4th ed. Washington (DC): American Psychiatric Association, 1994.'
    homepage: http://www.psych.org
    name: DSM-IV
    organization: American Psychiatric Association
    preferred_prefix: dsm4
    prefix: 2.16.840.1.113883.6.126
    status: Complete
  homepage: https://en.wikipedia.org/wiki/Diagnostic_and_Statistical_Manual_of_Mental_Disorders#DSM-IV-TR_(2000)
  mappings:
    hl7: 2.16.840.1.113883.6.126
    wikidata: P663
    wikidata.entity: Q3078495
  name: Diagnostic and Statistical Manual of Mental Disorders (4th Edition)
  pattern: ^\d+\.\d+$
  prefix: dsm4
  synonyms:
  - dsm-iv
  wikidata:
    database: Q3078495
    description: identifier for a mental disorder in the 4th edition of Diagnostic
      and Statistical Manual of Mental Disorders
    example:
    - '291.89'
    - '315.1'
    homepage: https://en.wikipedia.org/wiki/DSM-IV_codes
    name: DSM-IV classification
    pattern: ^\d+\.\d+$
    prefix: P663
dsm5:
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: A terminology published by the American Psychiatric Association (APA)
    for the classification of mental disorders using a common language and standard
    criteria. [wikipedia]
  example: '312.33'
  hl7:
    description: The Diagnostic and Statistical Manual of Mental Disorders, Fifth
      Edition (DSM-5) is the 2013 update to the Diagnostic and Statistical Manual
      of Mental Disorders, the taxonomic and diagnostic tool published by the American
      Psychiatric Association (APA). In the United States, the DSM serves as a universal
      authority for psychiatric diagnoses. Treatment recommendations, as well as payment
      by health care providers, are often determined by DSM classifications, so the
      appearance of a new version has significant practical importance.The DSM-5 was
      published on May 18, 2013, superseding the DSM-IV-TR, which was published in
      2000.
    homepage: https://www.psychiatry.org
    name: DSM-5
    organization: American Psychiatry Association
    preferred_prefix: dsm5
    prefix: 2.16.840.1.113883.6.344
    status: Complete
  homepage: https://en.wikipedia.org/wiki/DSM-5
  mappings:
    hl7: 2.16.840.1.113883.6.344
    wikidata: P1930
  name: Diagnostic and Statistical Manual of Mental Disorders (5th Edition)
  pattern: ^\d{3}\.\d{2}$
  prefix: dsm5
  references:
  - https://archive.org/details/diagnosticstatis0005unse
  synonyms:
  - dsm-v
  wikidata:
    database: Q3064664
    description: identifier for a mental disorder in the 5th edition of Diagnostic
      and Statistical Manual of Mental Disorders
    example:
    - '312.33'
    - '625.4'
    name: DSM-5 (identifier)
    pattern: ^\d\d\d\.\d\d?$
    prefix: P1930
dsmz:
  cellosaurus:
    category: Cell line databases/resources
    homepage: https://celldive.dsmz.de/
    name: DSMZ Tools for Diving into Cell Line Data
    prefix: DSMZCellDive
    uri_format: https://celldive.dsmz.de/celllines/$1
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: 'The Leibniz Institute DSMZ is the most diverse biological resource
    center in the world and one of the largest collections of microorganisms and cell
    cultures worldwide (bacteria, archaea, protists, yeasts, fungi, bacteriophages,
    plant viruses, genomic bacterial DNA as well as human and animal cell lines).
    The following designations are used as part of local unique identifiers:


    - `PC`: positive control

    - `NC`: negative control

    - `AS`: antiserum

    - `PV`: plant viruses

    - `RT`: recommended test

    - `ACC`: human or animal cell line

    - `DSM`: microorganism cell line'
  example: ACC-1
  example_extras:
  - DSM-2
  - RT-0753
  - PC-0754
  - AS-0753
  - PV-0998
  homepage: https://www.dsmz.de
  mappings:
    cellosaurus: DSMZCellDive
    re3data: r3d100010219
  name: Deutsche Sammlung von Mikroorganismen und Zellkulturen
  pattern: ^(ACC|DSM|NC|PC|RT|AS|PV)-\d+$
  prefix: dsmz
  re3data:
    description: The DSMZ is the most comprehensive biological resource center worldwide.
      Being one of the world's largest collections, the DSMZ currently comprises more
      than 73,700 items, including about 31,900 different bacterial and 6,600 fungal
      strains, 840 human and animal cell lines, 1,500 plant viruses and antisera,
      700 bacteriophages and 19,000 different types of bacterial genomic DNA. All
      biological materials accepted in the DSMZ collection are subject to extensive
      quality control and physiological and molecular characterization by our central
      services. In addition, DSMZ provides an extensive documentation and detailed
      diagnostic information on the biological materials. The unprecedented diversity
      and quality management of its bioresources render the DSMZ an internationally
      renowned supplier for science, diagnostic laboratories, national reference centers,
      as well as industrial partners.
    doi: 10.17616/R3G88X
    homepage: https://www.dsmz.de/
    license: Copyrights
    name: DSMZ
    prefix: r3d100010219
    synonyms:
    - Deutsche Sammlung von Mikroorganismen und Zellkulturen
    - Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures
    - Leibniz-Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen
    xrefs:
      nif: 0000-10209
  synonyms:
  - DSMZCellDive
  uri_format: https://www.dsmz.de/collection/catalogue/details/culture/$1
dso:
  contact:
    email: evan@epatters.org
    github: epatters
    name: Evan Patterson
    orcid: 0000-0002-8600-949X
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: The Data Science Ontology is a research project of IBM Research AI
    and Stanford University Statistics. Its long-term objective is to improve the
    efficiency and transparency of collaborative, data-driven science.
  example: classification-model
  homepage: https://www.datascienceontology.org/
  keywords:
  - data science
  - ontology
  name: Data Science Ontology
  prefix: dso
  repository: https://github.com/IBM/datascienceontology
  uri_format: https://www.datascienceontology.org/concept/$1
dsw:
  agroportal:
    contact:
      email: steve.baskauf@vanderbilt.edu
      name: Steve Baskauf
    description: 'Version 0.4 to 1.0 fixed reversed dsw:locates and dsw:locatedAt.
      Added labels. Changed comments and descriptions to conform to DC and DwC precedent.
      Added subClassOf relations to RO hasEvidence and isEvidenceFor. Specified preferred
      direction for inverse object property pairs., Changes from version 0.2.1 to
      version 0.3: removal of all functional and inverse function properties of object
      property terms, use of dwctype classes, deprecation of terms replaced by dwciri:
      terms, removal of references to TDWG Ontology., Changes from version 0.3 to
      0.4 change DwC class namespace from dwctype: to dwc: to follow class proposal,
      removed references to TDWG TaxonConcept ontology; deprecated terms that now
      have equivalent terms in Darwin Core., Change from version 1.0 to 1.0.1 Add
      CC0 license.'
    example_uri: http://xmlns.com/foaf/0.1/Agent
    homepage: https://github.com/darwin-sw/
    license: CC0-1.0
    name: Darwin-SW
    prefix: DSW
    repository: https://github.com/darwin-sw/dsw
    version: 1.0.1
  ecoportal:
    contact:
      email: steve.baskauf@vanderbilt.edu
      name: Steve Baskauf
    description: 'Version 0.4 to 1.0 fixed reversed dsw:locates and dsw:locatedAt.
      Added labels. Changed comments and descriptions to conform to DC and DwC precedent.
      Added subClassOf relations to RO hasEvidence and isEvidenceFor. Specified preferred
      direction for inverse object property pairs., Changes from version 0.2.1 to
      version 0.3: removal of all functional and inverse function properties of object
      property terms, use of dwctype classes, deprecation of terms replaced by dwciri:
      terms, removal of references to TDWG Ontology., Changes from version 0.3 to
      0.4 change DwC class namespace from dwctype: to dwc: to follow class proposal,
      removed references to TDWG TaxonConcept ontology; deprecated terms that now
      have equivalent terms in Darwin Core., Change from version 1.0 to 1.0.1 Add
      CC0 license., Version 0.4 to 1.0 fixed reversed dsw:locates and dsw:locatedAt.
      Added labels. Changed comments and descriptions to conform to DC and DwC precedent.
      Added subClassOf relations to RO hasEvidence and isEvidenceFor. Specified preferred
      direction for inverse object property pairs.'
    example_uri: http://xmlns.com/foaf/0.1/Agent
    homepage: https://github.com/darwin-sw/dsw
    license: CC0-1.0
    name: Darwin-SW
    prefix: DSW
    publications:
    - http://www.semantic-web-journal.net/content/darwin-sw-darwin-core-based-terms-expressing-biodiversity-data-rdf-1
    repository: https://github.com/darwin-sw/dsw
    version: 1.0.1
  example: DriedSpecimen
  homepage: https://github.com/darwin-sw/dsw
  mappings:
    agroportal: DSW
    ecoportal: DSW
    tib: dsw
  prefix: dsw
  repository: https://github.com/darwin-sw/dsw
  tib:
    description: Change from version 1.0 to 1.0.1 Add CC0 license.
    download_owl: https://raw.githubusercontent.com/darwin-sw/dsw/master/dsw.owl
    keywords:
    - FAIR Data Spaces
    - ESS
    - life sciences, biology
    - earth sciences
    name: Darwin Semantic Web
    prefix: dsw
    uri_format: http://purl.org/dsw/$1
dto:
  aberowl:
    description: Drug Target Ontology (DTO) is being developed at the University of
      Miami in the research group of Stephan Schürer. DTO is supported by grant U54CA189205
      (Illuminating the Druggable Genome Knowledge Management Center, Tudor Oprea,
      PI) awarded by the NCI through the NIH Common Fund. It is a component of the
      Illuminating the Druggable Genome (IDG) project (https://commonfund.nih.gov/idg).
      The DTO project develops a novel semantic framework to formalize knowledge about
      drug targets with a focus on the current IDG protein families. The DTO is developed
      as a reference for drug targets with the longer-term goal to create a community
      standard that will facilitate the integration of diverse drug discovery information
      from numerous heterogeneous resources. The first version of the DTO consists
      of asserted class hierarchies of the four IDG protein families, GPCRs, kinases,
      ion channels, and nuclear hormone receptors. Protein classes are linked to tissue
      and disease via different levels of confidence. DTO also contains drug target
      development level classifications developed in the IDG project (http://targetcentral.ws/),
      and functional and qualitative annotations and classifications for kinase proteins,
      GPCR ligands and ion channels. DTO is modeled in OWL2-DL to enable further classification
      by inference reasoning and SPARQL queries. DTO is implemented following a modularization
      approach. DTO is used as the organizational framework for drug targets in the
      IDG PHAROS User Interface Portal (https://pharos.nih.gov) and also the Tin-X
      Target Importance and Novelty Explorer (http://newdrugtargets.org).
    download_owl: http://aber-owl.net/media/ontologies/DTO/4/dto.owl
    homepage: http://drugtargetontology.org/
    name: Drug Target Ontology
    prefix: DTO
    version: '1.1'
  appears_in:
  - pr
  bioportal:
    contact:
      email: sschurer@med.miami.edu
      name: Stephan Schurer
    description: Drug Target Ontology (DTO) is being developed at the University of
      Miami in the research group of Stephan Schürer. DTO is supported by grant U54CA189205
      (Illuminating the Druggable Genome Knowledge Management Center, Tudor Oprea,
      PI) awarded by the NCI through the NIH Common Fund. It is a component of the
      Illuminating the Druggable Genome (IDG) project (https://commonfund.nih.gov/idg).
      The DTO project develops a novel semantic framework to formalize knowledge about
      drug targets with a focus on the current IDG protein families. The DTO is developed
      as a reference for drug targets with the longer-term goal to create a community
      standard that will facilitate the integration of diverse drug discovery information
      from numerous heterogeneous resources. The first version of the DTO consists
      of asserted class hierarchies of the four IDG protein families, GPCRs, kinases,
      ion channels, and nuclear hormone receptors. Protein classes are linked to tissue
      and disease via different levels of confidence. DTO also contains drug target
      development level classifications developed in the IDG project (http://targetcentral.ws/),
      and functional and qualitative annotations and classifications for kinase proteins,
      GPCR ligands and ion channels. DTO is modeled in OWL2-DL to enable further classification
      by inference reasoning and SPARQL queries. DTO is implemented following a modularization
      approach. DTO is used as the organizational framework for drug targets in the
      IDG PHAROS User Interface Portal (https://pharos.nih.gov) and also the Tin-X
      Target Importance and Novelty Explorer (http://newdrugtargets.org).
    homepage: http://drugtargetontology.org/
    name: Drug Target Ontology
    prefix: DTO
    publications:
    - http://drugtargetontology.org/
    version: 1.1.1
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: 'DTO integrates and harmonizes knowledge of the most important druggable
    protein families: kinases, GPCRs, ion channels and nuclear hormone receptors.'
  example: '90000018'
  fairsharing:
    abbreviation: DTO
    description: Drug Target Ontology (DTO) is developed as a reference for drug targets
      with the longer-term goal to create a community standard that will facilitate
      the integration of diverse drug discovery information from numerous heterogeneous
      resources. The first version of the DTO consists of asserted class hierarchies
      of the four IDG protein families, GPCRs, kinases, ion channels, and nuclear
      hormone receptors. Protein classes are linked to tissue and disease via different
      levels of confidence. DTO also contains drug target development classifications,
      a large collection of cell lines from the LINCS project and relevant cell-disease
      and cell-tissue relations. DTO is modeled in OWL2-DL to enable further classification
      by inference reasoning and SPARQL queries. DTO is implemented following a modularization
      approach. DTO will serve as the organizational framework for drug targets in
      the IDG PHAROS User Interface Portal (https://pharos.nih.gov).
    domains:
    - disease
    - protein
    homepage: http://drugtargetontology.org/
    license: CC-BY-3.0
    name: Drug Target Ontology
    prefix: FAIRsharing.tke3y2
    publications:
    - doi: 10.1186/s13326-017-0161-x
      pubmed: '29122012'
      title: Drug target ontology to classify and integrate drug discovery data
      year: 2017
    repository: https://github.com/DrugTargetOntology/DTO
    subjects:
    - Drug Discovery
    - Biomedical Science
    user_defined_tags:
    - Drug Target
  homepage: https://github.com/DrugTargetOntology/DTO
  mappings:
    aberowl: DTO
    bioportal: DTO
    fairsharing: FAIRsharing.tke3y2
  name: Drug Target Ontology
  pattern: ^\d+$
  prefix: dto
  publications:
  - doi: 10.1186/s13326-017-0161-x
    pmc: PMC5679337
    pubmed: '29122012'
    title: Drug target ontology to classify and integrate drug discovery data
    year: 2017
  - doi: 10.1186/s13326-017-0161-x
    pmc: null
    pubmed: '29122012'
    title: Drug target ontology to classify and integrate drug discovery data
    year: 2017
  - doi: 10.1186/s13326-017-0161-x
    pmc: null
    pubmed: '29122012'
    title: Drug target ontology to classify and integrate drug discovery data
    year: 2017
  repository: https://github.com/DrugTargetOntology/DTO
  uri_format: http://www.drugtargetontology.org/dto/DTO_$1
duo:
  aberowl:
    description: DUO is an ontology which represent data use conditions.
    download_owl: http://aber-owl.net/media/ontologies/DUO/9/duo.owl
    homepage: https://github.com/EBISPOT/DUO
    name: Data Use Ontology
    prefix: DUO
  biocontext:
    prefix: DUO
  bioportal:
    contact:
      email: mcourtot@ebi.ac.uk
      name: Melanie Courtot
    description: An ontology based on the consent codes decsription from the Dyke
      et al. paper at http://dx.doi.org/10.1371/journal.pgen.1005772. It allows to
      semantically tag datasets with restriction about their usage, making them discoverable
      automatically based on the authorization level of users, or intended usage.
      This resource is based on the OBO Foundry principles, and its use is under review
      by the Broad Institute ad the European Genome-phenome Archive (EGA) at EMBL-EBI.
    homepage: https://github.com/EBISPOT/DUO
    name: The Data Use Ontology
    prefix: DUO
  example: '0000046'
  fairsharing:
    abbreviation: DUO
    description: The Data Use Ontology (DUO) describes data use requirements and limitations.
      DUO allows to semantically tag datasets with restriction about their usage,
      making them discoverable automatically based on the authorization level of users,
      or intended usage. This resource is based on the OBO Foundry principles, and
      developed using the W3C Web Ontology Language. It is used in production by the
      European Genome-phenome Archive (EGA) at EMBL-EBI and CRG as well as the Broad
      Institute for the Data Use Oversight System (DUOS).
    homepage: https://raw.githubusercontent.com/EBISPOT/DUO/master/duo.owl
    license: CC-BY-3.0
    logo: https://api.fairsharing.org/rails/active_storage/blobs/redirect/eyJfcmFpbHMiOnsibWVzc2FnZSI6IkJBaHBBdmdCIiwiZXhwIjpudWxsLCJwdXIiOiJibG9iX2lkIn19--9a42083efa91d79ee5c7ed8e7868db0f7faf0b76/DUO_logo_white_background.png?disposition=inline
    name: The Data Use Ontology
    prefix: FAIRsharing.5dnjs2
    publications:
    - doi: 10.1016/j.xgen.2021.100028
      title: The Data Use Ontology to streamline responsible access to human biomedical
        datasets
      year: 2021
    repository: https://github.com/EBISPOT/duo/issues
    subjects:
    - Biomedical Science
    - Subject Agnostic
    user_defined_tags:
    - Metadata standardization
  mappings:
    aberowl: DUO
    biocontext: DUO
    bioportal: DUO
    fairsharing: FAIRsharing.5dnjs2
    obofoundry: duo
    ols: duo
    ontobee: DUO
    tib: duo
    wikidata.entity: Q113009193
  obofoundry:
    appears_in:
    - scdo
    contact: mcourtot@gmail.com
    contact.github: mcourtot
    contact.label: Melanie Courtot
    contact.orcid: 0000-0002-9551-6370
    depends_on:
    - bfo
    - iao
    deprecated: false
    description: DUO is an ontology which represent data use conditions.
    domain: information
    download.owl: http://purl.obolibrary.org/obo/duo.owl
    homepage: https://github.com/EBISPOT/DUO
    license: CC BY 4.0
    license.url: http://creativecommons.org/licenses/by/4.0/
    name: Data Use Ontology
    preferredPrefix: DUO
    prefix: duo
    repository: https://github.com/EBISPOT/DUO
  ols:
    description: DUO is an ontology which represent data use conditions.
    download_owl: http://purl.obolibrary.org/obo/duo.owl
    homepage: https://github.com/EBISPOT/DUO
    name: Data Use Ontology
    prefix: duo
    tracker: https://github.com/EBISPOT/DUO/issues
    version: '2021-02-23'
    version.iri: http://purl.obolibrary.org/obo/duo/releases/2021-02-23/duo.owl
  ontobee:
    library: Library
    name: Data Use Ontology
    prefix: DUO
  pattern: ^\d{7}$
  prefix: duo
  publications:
  - doi: 10.1016/j.xgen.2021.100028
    pmc: PMC8591903
    pubmed: '34820659'
    title: The Data Use Ontology to streamline responsible access to human biomedical
      datasets
    year: 2021
  repository: https://github.com/EBISPOT/DUO
  tib:
    description: DUO is an ontology which represent data use conditions.
    download_owl: http://purl.obolibrary.org/obo/duo.owl
    homepage: https://github.com/EBISPOT/DUO
    keywords:
    - NFDI4ING
    - NFDI4CHEM
    - ESS
    - computer science
    name: The Data Use Ontology
    prefix: duo
    tracker: https://github.com/EBISPOT/DUO/issues
    version.iri: http://purl.obolibrary.org/obo/duo/releases/2021-02-23/duo.owl
  uri_format: http://purl.obolibrary.org/obo/DUO_$1
dwc:
  contact:
    email: gtuco.btuco@gmail.com
    github: tucotuco
    name: John Wieczorek
    orcid: 0000-0003-1144-0290
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: Darwin Core is a vocabulary standard for transmitting information about
    biodiversity. This document lists all terms in namespaces currently used in the
    vocabulary.
  example: Dataset
  fairsharing:
    abbreviation: DwC
    description: 'Darwin Core (DwC) is a vocabulary that includes a glossary of terms
      (in other contexts these might be called properties, elements, fields, columns,
      attributes, or concepts) intended to facilitate the sharing of information about
      biological diversity by providing identifiers, labels, and definitions. The
      Darwin Core is primarily based on the observation, specimen and samples of taxa.
      The Darwin Core standard is comprised of one vocabulary (the Darwin Core vocabulary),
      and six associated documents. The vocabulary itself is composed of four term
      lists: Darwin Core terms borrowed from the Dublin Core legacy and terms namespace,
      Darwin Core IRI-value Term Analogs, and the core terms defined by Darwin Core.'
    domains:
    - Taxonomic classification
    - Sample annotation
    - Geographic location
    homepage: http://www.tdwg.org/standards/450
    license: https://creativecommons.org/licenses/by/3.0/us
    name: Darwin Core
    prefix: FAIRsharing.xvf5y3
    publications:
    - doi: 10.1371/journal.pone.0029715
      pubmed: '22238640'
      title: 'Darwin Core: an evolving community-developed biodiversity data standard'
      year: 2012
    - doi: 10.3897/bdj.2.e1039
      pubmed: '24723785'
      title: Linking multiple biodiversity informatics platforms with Darwin Core
        Archives
      year: 2014
    - doi: 10.1371/journal.pone.0102623
      pubmed: '25099149'
      title: 'The GBIF integrated publishing toolkit: facilitating the efficient publishing
        of biodiversity data on the internet'
      year: 2014
    repository: https://github.com/tdwg/dwc
    subjects:
    - Life Science
    - Biodiversity
  github_request_issue: 1316
  homepage: https://dwc.tdwg.org/list/
  mappings:
    fairsharing: FAIRsharing.xvf5y3
  name: Darwin Core Terms
  prefix: dwc
  uri_format: http://rs.tdwg.org/dwc/terms/$1
dwc.doe:
  ecoportal:
    contact:
      email: steve.baskauf@vanderbilt.edu
      name: Steve Baskauf
    description: The Darwin Core term degreeOfEstablishment provides information about
      degree to which an Organism survives, reproduces, and expands its range at the
      given place and time. The Degree of Establishment Controlled Vocabulary provides
      term that should be used as values for dwc:degreeOfEstablishment and dwciri:degreeOfEstablishment
    example_uri: http://xmlns.com/foaf/0.1/document
    homepage: https://dwc.tdwg.org/doe/
    license: CC-BY-4.0
    name: Darwin Core Degree Of Establishment Controlled Vocabulary
    prefix: DWCDOE
    publications:
    - https://doi.org/10.3897/biss.3.38084
    version: '1.0'
  example: d001
  mappings:
    ecoportal: DWCDOE
    tib: dwcdoe
  name: Degree of Establishment Controlled Vocabulary
  prefix: dwc.doe
  tib:
    description: Controlled vocabulary for the Darwin Core term degreeOfEstablishment
    download_rdf: http://rs.tdwg.org/dwcdoe.ttl
    homepage: http://rs.tdwg.org/dwcdoe.htm
    keywords:
    - FAIR Data Spaces
    - life sciences, biology
    name: degreeOfEstablishment controlled vocabulary
    prefix: dwcdoe
    uri_format: http://rs.tdwg.org/dwcdoe/$1
dwc.em:
  ecoportal:
    contact:
      email: tuco@berkeley.edu
      name: John Wieczorek
    description: The Darwin Core term establishmentMeans provides information about
      whether an organism or organisms have been introduced to a given place and time
      through the direct or indirect activity of modern humans. The Establishment
      Means Controlled Vocabulary provides terms that should be used as values for
      dwc:establishmentMeans and dwciri:establishmentMeans.
    homepage: http://rs.tdwg.org/dwc/doc/em/
    license: CC-BY-4.0
    name: Darwin Core Establishment Means Controlled Vocabulary
    prefix: DWCEM
    publications:
    - https://doi.org/10.3897/biss.3.38084
    version: '2021-09-01'
  example: e001
  mappings:
    ecoportal: DWCEM
    tib: dwcem
  name: Establishment Means Controlled Vocabulary
  prefix: dwc.em
  tib:
    description: Controlled vocabulary for the Darwin Core term establishmentMeans
    download_rdf: http://rs.tdwg.org/dwcem.ttl
    homepage: http://rs.tdwg.org/dwcem.htm
    keywords:
    - FAIR Data Spaces
    - life sciences, biology
    name: establishmentMeans controlled vocabulary
    prefix: dwcem
    uri_format: http://rs.tdwg.org/dwcem/$1
dwc.pw:
  ecoportal:
    contact:
      email: tuco@berkeley.edu
      name: John Wieczorek
    description: The Darwin Core term pathway provides information about the process
      by which an Organism came to be in a given place at a given time. The Pathway
      Controlled Vocabulary provides terms that should be used as values for dwc:pathway
      and dwciri:pathway.
    homepage: http://rs.tdwg.org/dwc/doc/pw/
    license: CC-BY-4.0
    name: Darwin Core Pathway Controlled Vocabulary
    prefix: DWCPW
    publications:
    - https://doi.org/10.3897/biss.3.38084
    version: '2021-09-01'
  example: p001
  mappings:
    ecoportal: DWCPW
    tib: dwcpw
  name: Darwin Core pathway controlled vocabulary
  prefix: dwc.pw
  tib:
    description: Controlled vocabulary for the Darwin Core term pathway
    download_rdf: http://rs.tdwg.org/dwcpw.ttl
    homepage: http://rs.tdwg.org/dwcpw.htm
    keywords:
    - FAIR Data Spaces
    - life sciences, biology
    name: pathway controlled vocabulary
    prefix: dwcpw
    uri_format: http://rs.tdwg.org/dwcpw/$1
eaglei:
  cellosaurus:
    category: Biological sample resources
    homepage: https://www.eagle-i.net/
    name: eagle-i resource discovery tool
    prefix: eagle-i
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  deprecated: true
  description: Discovery tool for biomedical research resources available at institutions
    throughout the U.S.
  example: 0000012b-5661-2f63-2f73-b43980000000
  homepage: https://hawaii.eagle-i.net
  mappings:
    cellosaurus: eagle-i
    re3data: r3d100011564
  name: eagle-i
  prefix: eaglei
  re3data:
    description: "<<<!!!<<<  The eagle-i National Network and eagle-i resource search\
      \ at www.eagle-.net was retired on November 4, 2021. \nThe repository is no\
      \ longer available. The data in eagle-i is contributed by Network member institutions.\
      \ This data can be freely searched using our central search application, but\
      \ it is also available three other ways https://open.catalyst.harvard.edu/wiki/display/eaglei/Get+Data\
      \  >>>!!!>>>"
    doi: 10.17616/R30S60
    homepage: https://open.catalyst.harvard.edu/products/eagle-i/
    name: eagle-i
    prefix: r3d100011564
  uri_format: http://hawaii.eagle-i.net/i/$1
earl:
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: EARL is a vocabulary, the terms of which are defined across a set of
    specifications and technical notes, and that is used to describe test results.
    The primary motivation for developing this vocabulary is to facilitate the exchange
    of test results between Web accessibility evaluation tools in a vendor-neutral
    and platform-independent format. It also provides reusable terms for generic quality
    assurance and validation purposes. [from homepage]
  example: Assertion
  homepage: https://www.w3.org/TR/EARL10/
  lov:
    description: EARL is a vocabulary, the terms of which are defined across a set
      of specifications and technical notes, and that is used to describe test results.
      The primary motivation for developing this vocabulary is to facilitate the exchange
      of test results between Web accessibility evaluation tools in a vendor-neutral
      and platform-independent format. It also provides reusable terms for generic
      quality assurance and validation purposes.
    homepage: http://www.w3.org/TR/EARL10/
    keywords:
    - Quality
    modified: '2011-05-10'
    name: Evaluation and Report Language
    prefix: earl
    uri_prefix: http://www.w3.org/ns/earl#$1
  mappings:
    lov: earl
    zazuko: earl
  name: Evaluation and Report Language
  prefix: earl
  rdf_uri_format: http://www.w3.org/ns/earl#$1
  uri_format: http://www.w3.org/ns/earl#$1
  zazuko:
    prefix: earl
    uri_format: http://www.w3.org/ns/earl#$1
earthcube.aut:
  contact:
    email: ruth.duerr3@gmail.com
    github: rduerr
    name: Ruth Duerr
    orcid: 0000-0003-4808-4736
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: The Audience Types Controlled Vocabulary was created for NSF's EarthCube
    program's Resource Registry. The vocabulary defines the types of audience each
    resource in the program is targeted to.  At this point the vocabulary is very
    bare - no term definitions even; however, the intention is to extend the vocabulary
    over time.  If you would like to assist with this or in extending any of the other
    controlled vocabularies/ontologies developed as part of the Resource Registry
    project, please see https://github.com/earthcubearchitecture-ecresourcereg.
  download_rdf: https://github.com/earthcubearchitecture-ecresourcereg/AUT/raw/refs/heads/master/aut.ttl
  example: '0000001'
  github_request_issue: 1627
  homepage: http://cor.esipfed.org/ont/earthcube/AUT
  keywords:
  - audience type
  - person
  - role
  name: Audience Types Controlled Vocabulary
  pattern: ^\d{7}$
  prefix: earthcube.aut
  repository: https://github.com/earthcubearchitecture-ecresourcereg/AUT
  uri_format: http://cor.esipfed.org/ont/earthcube/AUT_$1
earthcube.mola:
  contact:
    email: ruth.duerr3@gmail.com
    github: rduerr
    name: Ruth Duerr
    orcid: 0000-0003-4808-4736
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: The Data Model Language Controlled Vocabulary was created for NSF's
    EarthCube Program's Resource Registry.  At this point it merely lists a few of
    the languages used by data model resources in the registry.
  download_rdf: https://github.com/earthcubearchitecture-ecresourcereg/mola/raw/refs/heads/master/mola.ttl
  example: '000001'
  github_request_issue: 1627
  homepage: http://cor.esipfed.org/ont/earthcube/mola
  keywords:
  - metamodel
  name: Data Model Language Controlled Vocabulary
  pattern: ^\d+$
  prefix: earthcube.mola
  rdf_uri_format: http://cor.esipfed.org/ont/earthcube/MOLA_$1
  repository: https://github.com/earthcubearchitecture-ecresourcereg/mola
  uri_format: http://cor.esipfed.org/ont/earthcube/MOLA_$1
earthcube.sfo:
  contact:
    email: ruth.duerr3@gmail.com
    github: rduerr
    name: Ruth Duerr
    orcid: 0000-0003-4808-4736
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: This ontology defines a taxonomy of software functions based on the
    work of the NSF-funded EarthCube Resource Registry working group.  The functions
    are generally organized by their role in the research process.
  download_rdf: https://github.com/earthcubearchitecture-ecresourcereg/sfo/raw/refs/heads/master/sfo.ttl
  example: '0000001'
  github_request_issue: 1627
  homepage: http://cor.esipfed.org/ont/earthcube/sfo
  keywords:
  - software
  - software function
  name: Software Functions Ontology
  pattern: ^\d{7}$
  prefix: earthcube.sfo
  repository: https://github.com/earthcubearchitecture-ecresourcereg/sfo
  uri_format: http://cor.esipfed.org/ont/earthcube/SFO_$1
earthcube.srt:
  contact:
    email: ruth.duerr3@gmail.com
    github: rduerr
    name: Ruth Duerr
    orcid: 0000-0003-4808-4736
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: The Semantic Resource Types Vocabulary was created for NSF's EarthCube
    Program's Resource Repository. Includes entries for things like 'thesaurus', 'ontology',
    'controlled vocabulary', 'taxonomy'.
  download_rdf: https://github.com/earthcubearchitecture-ecresourcereg/srt/raw/refs/heads/master/srt.ttl
  example: '000001'
  github_request_issue: 1627
  homepage: http://cor.esipfed.org/ont/earthcube/srt
  keywords:
  - semantic resource
  name: Semantic Resource Types Vocabulary
  pattern: ^\d+$
  prefix: earthcube.srt
  rdf_uri_format: http://cor.esipfed.org/ont/earthcube/srt_$1
  repository: https://github.com/earthcubearchitecture-ecresourcereg/srt
  uri_format: http://cor.esipfed.org/ont/earthcube/srt_$1
earthcube.swl:
  contact:
    email: ruth.duerr3@gmail.com
    github: rduerr
    name: Ruth Duerr
    orcid: 0000-0003-4808-4736
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  deprecated: true
  description: This mini-ontology contains classes and instances for each version
    of the licenses that are commonly used in software projects, particularly open
    source software projects. The URI's for each are the canonical URI's for that
    license (where they exist).
  download_rdf: https://earthcubearchitecture-ecresourcereg.github.io/swl/ontology.ttl
  example: '0000013'
  github_request_issue: 1627
  homepage: https://earthcubearchitecture-ecresourcereg.github.io/swl/index-en.html
  keywords:
  - license
  license: CC0-1.0
  name: Software Licenses Ontology
  pattern: ^\d{7}$
  prefix: earthcube.swl
  providers:
  - code: earthcube
    description: It's not clear why some URIs have this earthcube subpath
    example: null
    first_party: null
    homepage: https://earthcubearchitecture-ecresourcereg.github.io/swl/index-en.html
    name: Earthcube URI
    publications: null
    status: null
    uri_format: http://cor.esipfed.org/ont/earthcube/swl/SWL_$1
  rdf_uri_format: http://cor.esipfed.org/ont/SWL_$1
  repository: https://github.com/earthcubearchitecture-ecresourcereg/swl
  uri_format: http://cor.esipfed.org/ont/SWL_$1
easychair.cfp:
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: Conferences in EasyChair
  example: SysBioCancer2022
  homepage: https://easychair.org/cfp/
  keywords:
  - conferences
  - metascience
  name: EasyChair Call for Paper
  prefix: easychair.cfp
  uri_format: https://easychair.org/cfp/$1
easychair.topic:
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: Call for paper topics in EasyChair
  example: '27106865'
  homepage: https://easychair.org/cfp/
  keywords:
  - metascience
  - topics
  name: EasyChair Topic
  pattern: ^\d+$
  prefix: easychair.topic
  uri_format: https://easychair.org/cfp/topic.cgi?tid=$1
ebisc:
  cellosaurus:
    category: Cell line collections (Providers)
    homepage: https://www.ebisc.org
    name: European Bank for induced pluripotent Stem Cells
    prefix: EBiSC
    uri_format: https://cells.ebisc.org/$1
  example: ESi007-A
  example_extras:
  - EDi008-B
  mappings:
    cellosaurus: EBiSC
  pattern: ^E(S|D)i\d+-\w$
  prefix: ebisc
ec:
  bartoc:
    description: By the late 1950's it had become evident that the nomenclature of
      enzymology, in the absence of any guiding authority, in a period when the number
      of known enzymes was increasing rapidly, was getting out of hand. The naming
      of enzymes by individual workers had proved far from satisfactory in practice.
      In many cases the same enzymes became known by several different names, while
      conversely the same name was sometimes given to different enzymes. Many of the
      names conveyed little or no idea of the nature of the reactions catalysed, and
      similar names were sometimes given to enzymes of quite different types. To meet
      this situation, various attempts to bring order into the general nomenclature
      of enzymes, or into that of particular groups of enzymes, were made by individuals
      or small groups of specialists, but none of the resulting nomenclatures met
      with general approval. (...) The Enzyme List in the sixth edition (1992) contains
      3540 entries, of which 178 record enzymes which are now transferred elsewhere
      in the list, and 166 have been deleted completely. Thus the number of enzymes
      actually listed is 3196, an increase of 29% on the 1984 edition.
    homepage: https://www.abbexa.com/enzyme-commission-number
    name: Enzyme Nomenclature
    prefix: '671'
    wikidata_database: Q741108
  biocontext:
    prefix: EC-CODE
  comment: The Nomenclature Committee website does not yet contain an official policy
    regarding the use of dashes in the hierarchical categorization of enzymes, so
    the Bioregistry's regular expression is permissive and accepts both EC identifiers
    with dashes (e.g. <code>2.3.-.-</code>) and without dashes (e.g., <code>2.3</code>).
    This means you may have to do post-processing of EC identifiers in data integration
    scenarios.
  contact:
    email: kristian.axelsen@sib.swiss
    github: kaxelsen
    name: Kristian Axelsen
    orcid: 0000-0003-3889-2879
  description: 'The Enzyme Nomenclature (also known as the Enzyme Commission Code)
    is a species-agnostic controlled vocabulary for specific enzymes and an associated
    hierarchical classification into 7 main categories.


    The Enzyme Nomenclature is maintained by the [Nomenclature Committee](https://iubmb.org/about/committees/nomenclature-committee/)
    of the International Union of Biochemistry and Molecular Biology (IUBMB). A detailed
    history of the nomenclature since the 1950s can be found [here](https://iubmb.qmul.ac.uk/enzyme/history.html).


    There are few notable resources providing access to the Enzyme Nomenclature:


    <table class="table table-striped"><thead><tr><th>Website</th><th>Homepage</td><th>Notes</td></tr></thead><tbody><tr><td>ExplorEnz</td><td><a
    href="https://www.enzyme-database.org">https://www.enzyme-database.org</a></td><td>This
    is the resource officially recommended by IUBMB</td></tr><tr><td>IUBMB (via by
    Queen Mary)</td><td><a href="https://iubmb.qmul.ac.uk/enzyme">https://iubmb.qmul.ac.uk/enzyme</a></td><td>This
    is a web-based version of the <a href="https://archive.org/details/enzymenomenclatu0000inte_d6c2">1992
    publication</a>.</td></tr><tr><td>IntEnz</td><td><a href="https://www.ebi.ac.uk/intenz">https://www.ebi.ac.uk/intenz</a></td><td>Shutdown
    in 2024</td></tr><tr><td>ExPaSy</td><td><a href="https://enzyme.expasy.org">https://enzyme.expasy.org</a></td></tr><tr><td>EnzymePortal</td><td><a
    href="https://www.ebi.ac.uk/enzymeportal">https://www.ebi.ac.uk/enzymeportal</a></td><td></td></tr></tbody></table>'
  domain: gene family
  edam:
    description: An Enzyme Commission (EC) number of an enzyme.
    name: EC number
    obsolete: false
    prefix: '1011'
  example_decoys:
  - '100'
  - '2.'
  - 2.n1
  - 2.3.
  - 2.3.n1
  - 2.3.1.
  - 2.3.1.n
  - 2.3.4.1.
  - 2.-.-
  - 2.-
  - 2.3.4.1.-
  example_extras:
  - '2'
  - '2.3'
  - 2.3.1
  - 2.-.-.-
  - 2.3.-.-
  - 2.3.1.-
  - 2.3.1.n12
  - 3.1.26.n2
  - 3.4.24.B15
  fairsharing:
    abbreviation: EC Number
    description: In its report in 1961, the first Enzyme Commission devised a system
      for enzyme classification that also serves as a basis for assigning code numbers.
      These code numbers, prefixed by EC, contain four elements separated by points
      / full stops and are now widely in use. The first number shows to which of the
      six main divisions (classes) the enzyme belongs and therefore identifies the
      class of reaction catalysed. The second number indicates the subclass, and generally
      contains information about the type of compound or group involved. The third
      figure gives the sub-subclass, which further specifies the type of reaction
      involved. The fourth figure is the serial number of the enzyme in its sub-subclass.
    domains:
    - Enzyme Commission number
    - centrally registered identifier
    - enzyme
    - Classification
    homepage: https://www.qmul.ac.uk/sbcs/iubmb/enzyme/rules.html
    name: Enzyme Commission Number
    prefix: FAIRsharing.rfLD2u
    subjects:
    - Biochemistry
    - Enzymology
  go:
    homepage: http://enzyme.expasy.org/
    name: Enzyme Commission
    prefix: EC
    uri_format: https://enzyme.expasy.org/EC/$1
  homepage: https://www.enzyme-database.org/
  integbio:
    alt_name: Integrated relational Enzyme database
    description: IntEnz is a resource for enzymatic nomenclature. The site contains
      information on naming conventions based on the interantional standards for enzyme
      classification. Users can browse classifications by type, access standard definitions,
      submit entries, and download entry data in several formats.
    fairsharing: biodbcore-000314
    homepage: http://www.ebi.ac.uk/intenz/index.jsp
    information_keywords:
    - Ontology/Terminology/Nomenclature
    - Repository
    maintainer: EMBL-EBI (European Bioinformatics Institute)
    name: IntEnz
    prefix: nbdc00508
    pubmeds:
    - '14681451'
    status: Active
    target_keywords:
    - RNA
    - Protein
  license: CC-BY-4.0
  logo: https://www.enzyme-database.org/images/banner_5.gif
  mappings:
    bartoc: '671'
    biocontext: EC-CODE
    edam: '1011'
    fairsharing: FAIRsharing.rfLD2u
    go: EC
    integbio: nbdc00508
    miriam: ec-code
    n2t: ec-code
    ols: ec
    pathguide: '106'
    prefixcommons: intenz
    re3data: r3d100010803
    togoid: Ec
    uniprot: DB-0024
    wikidata: P591
    wikidata.entity: Q741108
  miriam:
    deprecated: false
    description: The Enzyme Classification contains the recommendations of the Nomenclature
      Committee of the International Union of Biochemistry and Molecular Biology on
      the nomenclature and classification of enzyme-catalysed reactions.
    homepage: http://www.enzyme-database.org/
    id: '00000004'
    name: Enzyme Nomenclature
    namespaceEmbeddedInLui: false
    pattern: ^\d+\.-\.-\.-|\d+\.\d+\.-\.-|\d+\.\d+\.\d+\.-|\d+\.\d+\.\d+\.(n)?\d+$
    prefix: ec-code
    providers:
    - code: expasy
      description: Enzyme nomenclature database, ExPASy (Expert Protein Analysis System)
      homepage: https://enzyme.expasy.org/
      name: Enzyme nomenclature database, ExPASy (Expert Protein Analysis System)
      uri_format: https://enzyme.expasy.org/EC/$1
    - code: ''
      description: KEGG Ligand Database for Enzyme Nomenclature
      homepage: https://www.genome.jp/dbget-bin/www_bfind?enzyme
      name: KEGG Ligand Database for Enzyme Nomenclature
      uri_format: https://www.genome.jp/dbget-bin/www_bget?ec:$1
    sampleId: 1.1.1.1
    uri_format: http://www.enzyme-database.org/query.php?ec=$1
  n2t:
    description: The Enzyme Classification contains the recommendations of the Nomenclature
      Committee of the International Union of Biochemistry and Molecular Biology on
      the nomenclature and classification of enzyme-catalysed reactions.
    example: 1.1.1.1
    homepage: https://www.ebi.ac.uk/intenz/
    name: IntEnZ (Integrated relational Enzyme database)
    namespaceEmbeddedInLui: false
    pattern: ^\d+\.-\.-\.-|\d+\.\d+\.-\.-|\d+\.\d+\.\d+\.-|\d+\.\d+\.\d+\.(n)?\d+$
    prefix: ec-code
    uri_format: https://www.ebi.ac.uk/intenz/query?cmd=SearchEC&ec=$1
  name: Enzyme Nomenclature
  ols:
    contact: kristian.axelsen@sib.swiss
    description: 'The Enzyme Nomenclature (also known as the Enzyme Commission Code)
      is a species-agnostic controlled vocabulary for specific enzymes and an associated
      hierarchical classification into 7 main categories.


      The Enzyme Nomenclature is maintained by the [Nomenclature Committee](https://iubmb.org/about/committees/nomenclature-committee/)
      of the International Union of Biochemistry and Molecular Biology (IUBMB). A
      detailed history of the nomenclature since the 1950s can be found [here](https://iubmb.qmul.ac.uk/enzyme/history.html).


      There are few notable resources providing access to the Enzyme Nomenclature:


      <table class="table table-striped"><thead><tr><th>Website</th><th>Homepage</td><th>Notes</td></tr></thead><tbody><tr><td>ExplorEnz</td><td><a
      href="https://www.enzyme-database.org">https://www.enzyme-database.org</a></td><td>This
      is the resource officially recommended by IUBMB</td></tr><tr><td>IUBMB (via
      by Queen Mary)</td><td><a href="https://iubmb.qmul.ac.uk/enzyme">https://iubmb.qmul.ac.uk/enzyme</a></td><td>This
      is a web-based version of the <a href="https://archive.org/details/enzymenomenclatu0000inte_d6c2">1992
      publication</a>.</td></tr><tr><td>IntEnz</td><td><a href="https://www.ebi.ac.uk/intenz">https://www.ebi.ac.uk/intenz</a></td><td>Shutdown
      in 2024</td></tr><tr><td>ExPaSy</td><td><a href="https://enzyme.expasy.org">https://enzyme.expasy.org</a></td></tr><tr><td>EnzymePortal</td><td><a
      href="https://www.ebi.ac.uk/enzymeportal">https://www.ebi.ac.uk/enzymeportal</a></td><td></td></tr></tbody></table>
      Licensed under CC-BY-4.0.'
    download_owl: https://w3id.org/biopragmatics/resources/ec/ec.owl
    homepage: https://www.enzyme-database.org/
    name: Enzyme Nomenclature
    prefix: ec
    uri_format: https://www.enzyme-database.org/query.php?ec=$1
    version.iri: https://w3id.org/biopragmatics/resources/ec/2025-04-09/ec.ofn
  owners:
  - name: International Union of Biochemistry and Molecular Biology
    partnered: false
    ror: 00910ay07
    wikidata: null
  pathguide:
    abbreviation: IntEnz
    homepage: http://www.ebi.ac.uk/intenz/index.html
    keywords:
    - BioPAX
    name: Integrated relational Enzyme database
    prefix: '106'
  pattern: ^\d{1,2}(((\.\d{1,3}){1,3})|(\.\d+){2}\.[nB]\d{1,3}|\.-\.-\.-|\.\d{1,3}\.-\.-|\.\d{1,3}\.\d{1,3}\.-)?$
  preferred_prefix: EC
  prefix: ec
  prefixcommons:
    description: IntEnz is a freely available resource focused on enzyme nomenclature.
      IntEnz contains the recommendations of the Nomenclature Committee of the International
      Union of Biochemistry and Molecular Biology (NC-IUBMB) on the nomenclature and
      classification of enzyme-catalysed reactions.
    example: '17854'
    homepage: http://www.ebi.ac.uk/intenz
    keywords:
    - classification
    - enzyme
    license: http://www.ebi.ac.uk/Information/termsofuse.html
    name: Integrated relational Enzyme database
    pattern: ^\d+$
    prefix: intenz
    uri_format: http://www.ebi.ac.uk/intenz/query?cmd=SearchID&id=$1
  providers:
  - code: enzymeportal
    description: ' Enzyme Portal integrates publicly available information about enzymes,
      such as reaction mechanism, small-molecule chemistry, biochemical pathways and
      drug compounds.'
    example: null
    first_party: null
    homepage: https://www.ebi.ac.uk/enzymeportal
    name: EnzymePortal
    publications:
    - doi: 10.1093/protein/gzx008
      pmc: PMC5421622
      pubmed: '28158609'
      title: 'An update on the Enzyme Portal: an integrative approach for exploring
        enzyme knowledge'
      year: 2017
    status: null
    uri_format: https://www.ebi.ac.uk/enzymeportal/ec/$1
  publications:
  - doi: 10.1093/nar/28.1.304
    pmc: PMC102465
    pubmed: '10592255'
    title: The ENZYME database in 2000
    year: 2000
  - doi: 10.1093/nar/28.1.304
    pmc: null
    pubmed: '10592255'
    title: null
    year: null
  - doi: 10.1093/protein/gzx008
    pmc: PMC5421622
    pubmed: '28158609'
    title: 'An update on the Enzyme Portal: an integrative approach for exploring
      enzyme knowledge'
    year: 2017
  re3data:
    description: <<<!!!<<<IntEnz no longer exists>>>!!!>>>
    doi: 10.17616/R3XW4N
    homepage: https://www.ebi.ac.uk/intenz/
    name: Integrated Relational Enzyme database
    prefix: r3d100010803
    synonyms:
    - IntEnz
    xrefs:
      nif: 0000-03028
      omics: 02684
  references:
  - https://github.com/biopragmatics/bioregistry/issues/681
  - https://github.com/biopragmatics/bioregistry/pull/1611
  synonyms:
  - EC
  - EC number
  - EC-CODE
  - ECCODE
  - EC_CODE
  - ec-code
  - eccode
  - intenz
  togoid:
    catalog: nbdc01883
    examples:
    - 1.6.3.1
    - 2.4.1.353
    - 1.1.1.288
    - 1.5.1.2
    - 3.1.1.71
    - 1.3.1.31
    - 3.5.1.29
    - 1.16.1.1
    - 3.1.3.48
    - 2.3.1.138
    keywords:
    - Function
    name: Enzyme nomenclature
    pattern: ^(?:EC:)?(?\d+\.(?:(?:-\.-\.-)|\d+\.(?:(?:-\.-)|\d+\.(?:-|n?\d+))))$
    prefix: Ec
    uri_format: http://identifiers.org/ec-code/$1
  uniprot:
    abbreviation: ENZYME
    category: Enzyme and pathway databases
    homepage: https://enzyme.expasy.org/
    name: Enzyme nomenclature database
    prefix: DB-0024
    publications:
    - doi: 10.1093/nar/28.1.304
      pubmed: '10592255'
    uri_format: https://enzyme.expasy.org/EC/$1
  uri_format: https://www.enzyme-database.org/query.php?ec=$1
  wikidata:
    database: Q741108
    description: classification scheme for enzymes
    example:
    - 1.1.1.1
    - 2.7.3.2
    homepage: http://www.chem.qmul.ac.uk/iubmb/enzyme/
    name: EC enzyme number
    pattern: ^\d\.\d{1,2}\.\d{1,2}\.\d{1,3}$
    prefix: P591
    uri_format: http://enzyme.expasy.org/EC/$1
ecacc:
  cellosaurus:
    category: Cell line collections (Providers)
    homepage: https://www.culturecollections.org.uk/about-us/ecacc/
    name: European Collection of Cell Cultures
    prefix: ECACC
    uri_format: https://www.culturecollections.org.uk/products/celllines/detail.jsp?refId=$1
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: The European Collection of Authenticated Cell Cultures (ECACC) is one
    of four Culture Collections of Public Health England. We supply authenticated
    and quality controlled cell lines, nucleic acids and induced Pluripotent Stem
    Cells (iPSCs).
  example: '90062901'
  homepage: https://www.phe-culturecollections.org.uk/collections/ecacc.aspx
  mappings:
    cellosaurus: ECACC
  name: European Collection of Authenticated Cell Culture
  pattern: ^\d+$
  prefix: ecacc
  uri_format: https://www.phe-culturecollections.org.uk/products/celllines/generalcell/detail.jsp?collection=ecacc_gc&refId=$1
ecao:
  aberowl:
    description: An ontology for the development and anatomy of the different species
      of the phylum Echinodermata (NCBITaxon:7586).
    download_owl: http://aber-owl.net/media/ontologies/ECAO/5/ecao.owl
    homepage: https://github.com/echinoderm-ontology/ecao_ontology
    name: The Echinoderm Anatomy and Development Ontology
    prefix: ECAO
  bioportal:
    contact:
      email: ettensohn@cmu.edu
      name: Charles Ettensohn
    description: An ontology for the development and anatomy of the different species
      of the phylum Echinodermata (NCBITaxon:7586).
    homepage: https://github.com/echinoderm-ontology/ecao_ontology
    name: The Echinoderm Anatomy and Development Ontology
    prefix: ECAO
  example: 0107180
  mappings:
    aberowl: ECAO
    bioportal: ECAO
    obofoundry: ecao
    ols: ecao
    ontobee: ECAO
    wikidata.entity: Q113012596
  obofoundry:
    contact: ettensohn@cmu.edu
    contact.github: ettensohn
    contact.label: Charles Ettensohn
    contact.orcid: 0000-0002-3625-0955
    depends_on:
    - cl
    - ro
    - uberon
    deprecated: false
    description: An ontology for the development and anatomy of the different species
      of the phylum Echinodermata (NCBITaxon:7586).
    domain: anatomy and development
    download.obo: http://purl.obolibrary.org/obo/ecao.obo
    download.owl: http://purl.obolibrary.org/obo/ecao.owl
    homepage: https://github.com/echinoderm-ontology/ecao_ontology
    license: CC BY 3.0
    license.url: http://creativecommons.org/licenses/by/3.0/
    name: The Echinoderm Anatomy and Development Ontology
    preferredPrefix: ECAO
    prefix: ecao
    repository: https://github.com/echinoderm-ontology/ecao_ontology
  ols:
    description: None
    download_owl: http://purl.obolibrary.org/obo/ecao.owl
    homepage: https://github.com/echinoderm-ontology/ecao_ontology
    name: Echinoderm Anatomy and Development Ontology
    prefix: ecao
    tracker: https://github.com/echinoderm-ontology/ecao_ontology/issues
    version: '2025-05-15'
    version.iri: http://purl.obolibrary.org/obo/ecao/releases/2025-05-15/ecao.owl
  ontobee:
    library: Library
    name: The Echinoderm Anatomy and Development Ontology
    prefix: ECAO
  pattern: ^\d{7}$
  prefix: ecao
  uri_format: http://purl.obolibrary.org/obo/ECAO_$1
ecg:
  aberowl:
    description: The Electrocardiography (ECG) Ontology is a Driving Biological Project
      of the NCBO. The ECG Ontology will contain terms for describing electrocardiograms,
      their capture method(s) and their waveforms.
    download_owl: http://aber-owl.net/media/ontologies/ECG/12/ecg.owl
    homepage: http://www.cvrgrid.org
    name: Electrocardiography Ontology
    prefix: ECG
    version: '1'
  bioportal:
    contact:
      email: rwinslow@jhu.edu
      name: Raimond L. Winslow, PhD & Stephen Granite
    description: The Electrocardiography (ECG) Ontology is a Driving Biological Project
      of the NCBO. The ECG Ontology will contain terms for describing electrocardiograms,
      their capture method(s) and their waveforms.
    homepage: http://www.cvrgrid.org
    name: Electrocardiography Ontology
    prefix: ECG
    version: '1'
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: The Electrocardiography (ECG) Ontology is a Driving Biological Project
    of the NCBO. The ECG Ontology will contain terms for describing electrocardiograms,
    their capture method(s) and their waveforms.
  example: 000000159
  fairsharing:
    abbreviation: ECG
    contact:
      email: rwinslow@jhu.edu
      name: Raimond Winslow
      orcid: 0000-0003-1719-1651
    description: The Electrocardiography (ECG) Ontology is a Driving Biological Project
      of the NCBO. The ECG Ontology will contain terms for describing electrocardiograms,
      their capture method(s) and their waveforms. This ontology was developed and
      is being maintained by the CardioVascular Research Grid (www.cvrg.org).
    domains:
    - heart
    - electrocardiography
    homepage: http://wiki.cvrgrid.org/index.php/Ontology_Development
    name: ElectroCardioGraphy Ontology
    prefix: FAIRsharing.azr389
    publications:
    - doi: 10.1016/j.jbi.2010.08.007
      pubmed: '20800107'
      title: Using an ECG reference ontology for semantic interoperability of ECG
        data
      year: 2010
    subjects:
    - Biomedical Science
  homepage: https://bioportal.bioontology.org/ontologies/ECG
  mappings:
    aberowl: ECG
    bioportal: ECG
    fairsharing: FAIRsharing.azr389
  name: Electrocardiogram Ontology
  pattern: ^\d+$
  prefix: ecg
  publications:
  - doi: 10.1016/j.jbi.2010.08.007
    pmc: null
    pubmed: '20800107'
    title: Using an ECG reference ontology for semantic interoperability of ECG data
    year: 2010
  synonyms:
  - ECGOntology
  uri_format: http://www.cvrgrid.org/files/ECGOntologyv1.owl#ECG_$1
echinobase:
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: Echinobase supports the international research community by providing
    a centralized, integrated and easy to use web based resource to access the diverse
    and rich, functional genomics data of echinoderm species.
  example: '23159291'
  homepage: https://www.echinobase.org
  integbio:
    description: Echinobase is a comparative genomics platform for the echinoderm
      clade. It contains information on genomes of Strongylocentrotus purpuratus,
      Lytechinus variegatus, Patiria miniata, Parastichopus parvamensis and Ophiothrix
      spiculata. It also contains transcriptomes for these and other echinoderms.
      This database allows to browsing or searching using JBrowse (Genome Browser),
      BLAST tools, BAC Table, etc.
    homepage: https://www.echinobase.org/entry/
    information_keywords:
    - Sequence
    - Expression
    - Ontology/Terminology/Nomenclature
    maintainer: Center for Computational Regulatory Genomics, Beckman Institute
    name: Echinobase
    prefix: nbdc01512
    pubmeds:
    - '29761464'
    status: Active
    target_keywords:
    - Genome/Gene
    - Organism
  mappings:
    integbio: nbdc01512
  name: Echinobase
  pattern: ^\d+$
  prefix: echinobase
  uri_format: https://www.echinobase.org/entry/gene/showgene.do?method=display&geneId=$1
echobase:
  biocontext:
    prefix: ECHOBASE
  contact:
    email: gavin.thomas@york.ac.uk
    github: ghthomas
    name: Gavin H. Thomas
    orcid: 0000-0002-9763-1313
  go:
    homepage: https://www.york.ac.uk/res/thomas/
    name: EchoBASE post-genomic database for Escherichia coli
    prefix: EchoBASE
    uri_format: https://www.york.ac.uk/res/thomas/Gene.cfm?&recordID=$1
  mappings:
    biocontext: ECHOBASE
    go: EchoBASE
    miriam: echobase
    n2t: echobase
    prefixcommons: echobase
    re3data: r3d100011646
    uniprot: DB-0020
  miriam:
    deprecated: false
    description: EchoBASE is a database designed to contain and manipulate information
      from post-genomic experiments using the model bacterium Escherichia coli K-12.
      The database is built on an enhanced annotation of the updated genome sequence
      of strain MG1655 and the association of experimental data with the E.coli genes
      and their products.
    homepage: http://www.york.ac.uk/
    id: '00000200'
    name: EchoBASE
    namespaceEmbeddedInLui: false
    pattern: ^EB\d+$
    prefix: echobase
    sampleId: EB0170
    uri_format: http://www.york.ac.uk/res/thomas/Gene.cfm?recordID=$1
  n2t:
    description: EchoBASE is a database designed to contain and manipulate information
      from post-genomic experiments using the model bacterium Escherichia coli K-12.
      The database is built on an enhanced annotation of the updated genome sequence
      of strain MG1655 and the association of experimental data with the E.coli genes
      and their products.
    example: EB0170
    homepage: http://www.york.ac.uk/
    name: EchoBASE at the University of York
    namespaceEmbeddedInLui: false
    pattern: ^EB\d+$
    prefix: echobase
    uri_format: http://www.york.ac.uk/res/thomas/Gene.cfm?recordID=$1
  prefix: echobase
  prefixcommons:
    description: EchoBase is a database that curates new experimental and bioinformatic
      information about the genes and gene products of the model bacterium Escherichia
      coli K-12 strain MG1655.
    example: EB0170
    homepage: http://www.ecoli-york.org/
    keywords:
    - gene
    - gene expression
    name: EchoBASE - an integrated post-genomic database for E. coli
    pattern: ^EB\d+$
    prefix: echobase
    pubmed_ids:
    - '15608209'
    uri_format: http://www.york.ac.uk/res/thomas/Gene.cfm?recordID=$1
  publications:
  - doi: 10.1093/nar/gki028
    pmc: PMC539982
    pubmed: '15608209'
    title: 'EchoBASE: an integrated post-genomic database for Escherichia coli'
    year: 2005
  - doi: null
    pmc: null
    pubmed: '15608209'
    title: null
    year: null
  - doi: 10.1093/nar/gki028
    pmc: null
    pubmed: '15608209'
    title: null
    year: null
  - doi: null
    pmc: null
    pubmed: '15608209'
    title: null
    year: null
  - doi: 10.1093/nar/gki028
    pmc: null
    pubmed: '15608209'
    title: null
    year: null
  - doi: null
    pmc: null
    pubmed: '15608209'
    title: null
    year: null
  - doi: 10.1093/nar/gki028
    pmc: null
    pubmed: '15608209'
    title: null
    year: null
  re3data:
    description: EchoBase is a database that curates new experimental and bioinformatic
      information about the genes and gene products of the model bacterium Escherichia
      coli K-12 strain MG1655.
    doi: 10.17616/R38W6H
    homepage: https://www.york.ac.uk/res/thomas/index.cfm
    name: EchoBase
    prefix: r3d100011646
    synonyms:
    - an integrated post-genomic database for E.coli
    xrefs:
      nif: 0000-02781
  uniprot:
    abbreviation: EchoBASE
    category: Organism-specific databases
    homepage: https://www.york.ac.uk/res/thomas/
    name: EchoBASE - an integrated post-genomic database for E. coli
    prefix: DB-0020
    publications:
    - doi: 10.1093/nar/gki028
      pubmed: '15608209'
    uri_format: https://www.york.ac.uk/res/thomas/Gene.cfm?recordID=$1
eclas:
  example: 004.11.00.0100
  homepage: https://op.europa.eu
  mappings:
    tib: eclas
  name: European Commission Library Thesaurus
  prefix: eclas
  tib:
    description: Dating from 1978 when catalogues of the Central Library of the Commission
      of the European Communities (now the European Union) were computerised, ECLAS
      is a thesaurus created by the Central Library of the Commission of the European
      Communities for indexing the publications and documents acquired by the Central
      Library of the Commission. ECLAS was based on the Macrothesaurus of OECD and
      complemented by the ILO thesaurus. After creation of EUROVOC in 1984, convergence
      started in order to bring ECLAS in line with EUROVOC, but it was never complete.
      ECLAS contains nineteen areas of interest in a hierarchical tree structure consisting
      of four levels. ECLAS is fully available in English and in French. The OP COMM
      ECLAS is maintained by the Publications Office of the European Union on the
      EU Vocabularies website.
    homepage: https://op.europa.eu/de/home
    keywords:
    - Educational Resources
    - literature
    name: ECLAS
    prefix: eclas
    uri_format: http://data.europa.eu/bkc/notation_$1
ecmdb:
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: The ECMDB is an expertly curated database containing extensive metabolomic
    data and metabolic pathway diagrams about Escherichia coli (strain K12, MG1655).
    This database includes significant quantities of “original” data compiled by members
    of the Wishart laboratory as well as additional material derived from hundreds
    of textbooks, scientific journals, metabolic reconstructions and other electronic
    databases. Each metabolite is linked to more than 100 data fields describing the
    compound, its ontology, physical properties, reactions, pathways, references,
    external links and associated proteins or enzymes.
  example: ECMDB00005
  homepage: https://ecmdb.ca
  mappings:
    pathguide: '386'
    wikidata.entity: Q17052437
  name: E. coli Metabolite Database
  pathguide:
    abbreviation: ECMDB
    homepage: http://www.ecmdb.ca/
    name: E. Coli Metabolome Database
    prefix: '386'
  pattern: ^ECMDB\d+$
  prefix: ecmdb
  synonyms:
  - ECMDB
  uri_format: http://ecmdb.ca/compounds/$1
  wikidata:
    database: Q17052437
ecn:
  cheminf:
    description: A seven-digit identifier for chemical substances for regulatory purposes
      within the European Union.
    name: EC number
    obsolete: false
    prefix: '000447'
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  example: 200-003-9
  homepage: https://echa.europa.eu/information-on-chemicals
  mappings:
    cheminf: '000447'
    wikidata: P232
  pattern: ^\d{3}-\d{3}-\d$
  prefix: ecn
  references:
  - https://github.com/biopragmatics/bioregistry/issues/257
  - https://en.wikipedia.org/wiki/European_Community_number
  wikidata:
    description: identifier for a chemical compound per EINECS or ELINCS
    example:
    - 200-001-8
    - 200-578-6
    homepage: https://echa.europa.eu/information-on-chemicals/ec-inventory
    name: EC number
    pattern: ^(\d{3}-){2}\d$
    prefix: P232
    uri_format: https://www.echa.europa.eu/information-on-chemicals/ec-inventory/-/dislist/details/$1
eco:
  aberowl:
    description: An ontology for experimental and other evidence statements.
    download_owl: http://aber-owl.net/media/ontologies/ECO/115/eco.owl
    homepage: https://www.evidenceontology.org
    name: Evidence and Conclusion Ontology
    prefix: ECO
  bartoc:
    description: The Evidence Ontology (ECO) describes types of scientific evidence
      within the realm of biological research that can arise from laboratory experiments,
      computational methods, manual literature curation, and other means. Researchers
      can use these types of evidence to support assertions about things (such as
      scientific conclusions, gene annotations, or other statements of fact) that
      result from scientific research. ECO comprises two high-level classes, evidence
      and assertion method, where evidence is defined as “a type of information that
      is used to support an assertion,” and assertion method is defined as “a means
      by which a statement is made about an entity.” Together evidence and assertion
      method can be combined to describe both the support for an assertion and whether
      that assertion was made by a human being or a computer. However, ECO can not
      be used to make the assertion itself; for that, one would use another ontology,
      free text description, or other means. ECO was originally created around the
      year 2000 to support gene product annotation by the Gene Ontology.
    homepage: http://code.google.com/p/evidenceontology/
    name: Evidence Codes Ontology
    prefix: '1028'
  biocontext:
    prefix: ECO
  bioportal:
    contact:
      email: mgiglio@som.umaryland.edu
      name: Michelle Giglio
    description: An ontology of evidence types for supporting conclusions in scientific
      research
    homepage: https://github.com/evidenceontology/evidenceontology
    name: Evidence and Conclusion Ontology
    prefix: ECO
    publications:
    - https://github.com/evidenceontology/evidenceontology
    version: releases/2025-06-23
  contributor_extras:
  - email: null
    github: curtisim0
    name: Curtis Ross
    orcid: 0000-0003-3035-6940
  example: 0007807
  fairsharing:
    abbreviation: ECO
    contact:
      email: mchibucos@som.umaryland.edu
      name: Marcos Chibucos
      orcid: 0000-0001-9586-0780
    description: The Evidence and Conclusion Ontology (ECO) contains terms that describe
      types of evidence and assertion methods. ECO terms are used in the process of
      biocuration to capture the evidence that supports biological assertions (e.g.
      gene product X has function Y as supported by evidence Z). Capture of this information
      allows tracking of annotation provenance, establishment of quality control measures,
      and query of eviden
    domains:
    - Evidence
    - Resource metadata
    - Sample annotation
    - Text mining
    - assay
    - curated information
    - digital curation
    - study design
    - literature curation
    - Biocuration
    homepage: https://evidenceontology.org/
    license: CC0-1.0
    name: Evidence and Conclusion Ontology
    prefix: FAIRsharing.wvpgwn
    publications:
    - doi: 10.1142/9789812704856_0019
      pubmed: '14992503'
      title: An evidence ontology for use in pathway/genome databases
      year: 2004
    - doi: 10.1093/nar/gky1036
      pubmed: '30407590'
      title: 'ECO, the Evidence & Conclusion Ontology: community standard for evidence
        information'
      year: 2018
    - doi: 10.1007/978-1-4939-3743-1_18
      pubmed: '27812948'
      title: 'The Evidence and Conclusion Ontology (ECO): Supporting GO Annotations'
      year: 2016
    repository: https://github.com/evidenceontology/evidenceontology
    subjects:
    - Life Science
    - Computational Biology
  go:
    homepage: http://www.evidenceontology.org/
    name: Evidence Code Ontology
    prefix: ECO
    uri_format: http://www.evidenceontology.org/browse/#ECO_$1
  mappings:
    aberowl: ECO
    bartoc: '1028'
    biocontext: ECO
    bioportal: ECO
    fairsharing: FAIRsharing.wvpgwn
    go: ECO
    miriam: eco
    n2t: eco
    obofoundry: eco
    ols: eco
    ontobee: ECO
    prefixcommons: eco
    wikidata: P3811
    wikidata.entity: Q28445410
  miriam:
    deprecated: false
    description: Evidence codes can be used to specify the type of supporting evidence
      for a piece of knowledge. This allows inference of a 'level of support' between
      an entity and an annotation made to an entity.
    homepage: http://bioportal.bioontology.org/ontologies/ECO
    id: '00000055'
    name: Evidence Code Ontology
    namespaceEmbeddedInLui: true
    pattern: ^ECO:\d{7}$
    prefix: eco
    sampleId: '0000006'
    uri_format: http://purl.bioontology.org/ontology/ECO/ECO:$1
  n2t:
    description: Evidence codes can be used to specify the type of supporting evidence
      for a piece of knowledge. This allows inference of a 'level of support' between
      an entity and an annotation made to an entity.
    example: '0000006'
    homepage: http://bioportal.bioontology.org/ontologies/ECO
    name: Evidence Code Ontology through BioPortal
    namespaceEmbeddedInLui: true
    pattern: ECO:\d{7}$
    prefix: eco
    uri_format: http://purl.bioontology.org/ontology/ECO/ECO:$1
  obofoundry:
    contact: mgiglio@som.umaryland.edu
    contact.github: mgiglio99
    contact.label: Michelle Giglio
    contact.orcid: 0000-0001-7628-5565
    deprecated: false
    description: An ontology for experimental and other evidence statements.
    domain: investigations
    download.obo: http://purl.obolibrary.org/obo/eco.obo
    download.owl: http://purl.obolibrary.org/obo/eco.owl
    homepage: https://www.evidenceontology.org
    license: CC0 1.0
    license.url: https://creativecommons.org/publicdomain/zero/1.0/
    logo: https://avatars1.githubusercontent.com/u/12802432
    name: Evidence and Conclusion Ontology
    preferredPrefix: ECO
    prefix: eco
    publications:
    - id: https://www.ncbi.nlm.nih.gov/pubmed/34986598
      preferred: true
      title: 'ECO: the Evidence and Conclusion Ontology, an update for 2022.'
    - id: https://www.ncbi.nlm.nih.gov/pubmed/30407590
      title: 'ECO, the Evidence & Conclusion Ontology: community standard for evidence
        information.'
    - id: https://www.ncbi.nlm.nih.gov/pubmed/25052702
      title: Standardized description of scientific evidence using the Evidence Ontology
        (ECO)
    repository: https://github.com/evidenceontology/evidenceontology
  ols:
    description: The Evidence & Conclusion Ontology (ECO) describes types of scientific
      evidence within the biological research domain that arise from laboratory experiments,
      computational methods, literature curation, or other means.
    download_owl: http://purl.obolibrary.org/obo/eco.owl
    homepage: https://www.evidenceontology.org
    name: Evidence & Conclusion Ontology (ECO)
    prefix: eco
    tracker: https://github.com/evidenceontology/evidenceontology/issues
    version: '2025-06-23'
    version.iri: http://purl.obolibrary.org/obo/eco/releases/2025-06-23/eco.owl
  ontobee:
    library: Library
    name: Evidence and Conclusion Ontology
    prefix: ECO
  pattern: ^\d{7}$
  prefix: eco
  prefixcommons:
    alt_uri_formats:
    - http://purl.org/obo/owl/ECO#$1
    bioportal: '1012'
    description: Evidence codes can be used to specify the type of supporting evidence
      for a piece of knowledge. This allows inference of a 'level of support' between
      an entity and an annotation made to an entity.
    example: ECO:0000006
    keywords:
    - obo
    - ontology
    license: http://www.ebi.ac.uk/Information/termsofuse.html
    name: Evidence Code Ontology
    pattern: ^ECO:\d{7}$
    prefix: eco
    synonyms:
    - obo.eco
  providers:
  - code: quickgo
    description: QuickGO's portal includes ECO terms
    example: null
    first_party: null
    homepage: https://www.ebi.ac.uk/QuickGO
    name: QuickGO
    publications: null
    status: null
    uri_format: https://www.ebi.ac.uk/QuickGO/term/ECO:$1
  publications:
  - doi: 10.1093/nar/gkab1025
    pmc: PMC8728134
    pubmed: '34986598'
    title: 'ECO: the Evidence and Conclusion Ontology, an update for 2022'
    year: 2022
  - doi: 10.1093/nar/gky1036
    pmc: PMC6323956
    pubmed: '30407590'
    title: 'ECO, the Evidence & Conclusion Ontology: community standard for evidence
      information'
    year: 2019
  - doi: 10.1007/978-1-4939-3743-1_18
    pmc: PMC6377151
    pubmed: '27812948'
    title: 'The Evidence and Conclusion Ontology (ECO): Supporting GO Annotations'
    year: 2017
  - doi: 10.1093/database/bau075
    pmc: PMC4105709
    pubmed: '25052702'
    title: Standardized description of scientific evidence using the Evidence Ontology
      (ECO)
    year: 2014
  - doi: 10.1142/9789812704856_0019
    pmc: null
    pubmed: '14992503'
    title: An evidence ontology for use in pathway/genome databases
    year: 2004
  - doi: null
    pmc: null
    pubmed: '34986598'
    title: 'ECO: the Evidence and Conclusion Ontology, an update for 2022'
    year: null
  - doi: null
    pmc: null
    pubmed: '30407590'
    title: 'ECO, the Evidence & Conclusion Ontology: community standard for evidence
      information'
    year: null
  - doi: null
    pmc: null
    pubmed: '25052702'
    title: Standardized description of scientific evidence using the Evidence Ontology
      (ECO)
    year: null
  - doi: 10.1142/9789812704856_0019
    pmc: null
    pubmed: '14992503'
    title: An evidence ontology for use in pathway/genome databases
    year: 2004
  - doi: 10.1093/nar/gky1036
    pmc: null
    pubmed: '30407590'
    title: 'ECO, the Evidence & Conclusion Ontology: community standard for evidence
      information'
    year: 2018
  - doi: 10.1007/978-1-4939-3743-1_18
    pmc: null
    pubmed: '27812948'
    title: 'The Evidence and Conclusion Ontology (ECO): Supporting GO Annotations'
    year: 2016
  uri_format: http://purl.obolibrary.org/obo/ECO_$1
  wikidata:
    description: identifier in the Evidence & Conclusion Ontology for capturing evidence
      in biological research
    homepage: http://evidenceontology.org/
    name: Evidence & Conclusion Ontology ID
    pattern: ^ECO_[0-9]{7}$
    prefix: P3811
ecocore:
  aberowl:
    description: Ecocore is a community ontology for the concise and controlled description
      of ecological traits of organisms.
    download_owl: http://aber-owl.net/media/ontologies/ECOCORE/8/ecocore.owl
    homepage: https://github.com/EcologicalSemantics/ecocore
    name: An ontology of core ecological entities
    prefix: ECOCORE
  biocontext:
    prefix: ECOCORE
  bioportal:
    contact:
      email: noreply@bioontology.org
      name: Unknown
    homepage: https://github.com/EcologicalSemantics/ecocore
    name: An ontology of core ecological entities
    prefix: ECOCORE
    version: '2022-03-09'
  ecoportal:
    contact:
      email: pier.buttigieg@awi.de
      name: Pier Luigi Buttigieg
    description: This ontology aims to provide core semantics for ecological entities,
      such as ecological functions (for predators, prey, etc), food webs, and ecological
      interactions. The ontology, closely interoperates with existing OBO ontologies
      such as the Environment Ontology, the Population and Community Ontology (PCO),
      the Relations Ontology (RO), the Gene Ontology (for biological processes etc),
      the Phenotype and Quality Ontology (PATO), the Plant Ontology (PO), and many
      others. Ecocore is under active development.
    homepage: https://github.com/EcologicalSemantics/ecocore
    license: CC-BY-3.0
    name: An ontology of core ecological entities
    prefix: ECOCORE
    repository: https://github.com/EcologicalSemantics/ecocore
    version: '2022-03-09'
  example: '00000001'
  mappings:
    aberowl: ECOCORE
    biocontext: ECOCORE
    bioportal: ECOCORE
    ecoportal: ECOCORE
    obofoundry: ecocore
    ols: ecocore
    ontobee: ECOCORE
    wikidata.entity: Q81661598
  obofoundry:
    contact: p.buttigieg@gmail.com
    contact.github: pbuttigieg
    contact.label: Pier Luigi Buttigieg
    contact.orcid: 0000-0002-4366-3088
    depends_on:
    - bfo
    - chebi
    - envo
    - go
    - iao
    - pato
    - pco
    - po
    - ro
    - uberon
    deprecated: false
    description: Ecocore is a community ontology for the concise and controlled description
      of ecological traits of organisms.
    domain: environment
    download.obo: http://purl.obolibrary.org/obo/ecocore.obo
    download.owl: http://purl.obolibrary.org/obo/ecocore.owl
    homepage: https://github.com/EcologicalSemantics/ecocore
    license: CC BY 3.0
    license.url: http://creativecommons.org/licenses/by/3.0/
    name: An ontology of core ecological entities
    preferredPrefix: ECOCORE
    prefix: ecocore
    repository: https://github.com/EcologicalSemantics/ecocore
  ols:
    description: Ecocore is a community ontology for the concise and controlled description
      of ecological traits of organisms.
    download_owl: http://purl.obolibrary.org/obo/ecocore.owl
    homepage: https://github.com/EcologicalSemantics/ecocore
    name: An ontology of core ecological entities
    prefix: ecocore
    tracker: https://github.com/EcologicalSemantics/ecocore/issues
    version: '2022-03-09'
    version.iri: http://purl.obolibrary.org/obo/ecocore/releases/2022-03-09/ecocore.owl
  ontobee:
    library: Library
    name: An ontology of core ecological entities
    prefix: ECOCORE
  pattern: ^\d+$
  prefix: ecocore
  uri_format: http://purl.obolibrary.org/obo/ECOCORE_$1
ecocyc:
  contact:
    email: pkarp@ai.sri.com
    github: pkarp111
    name: Peter D. Karp
    orcid: 0000-0002-5876-6418
  contributor_extras:
  - email: cjmungall@lbl.gov
    github: cmungall
    name: Chris Mungall
    orcid: 0000-0002-6601-2165
  description: EcoCyc is a scientific database for the bacterium Escherichia coli
    K-12 MG1655. The EcoCyc project performs literature-based curation of its genome,
    and of transcriptional regulation, transporters, and metabolic pathways.
  example: AICARTRANSIMPCYCLO-CPLX
  fairsharing:
    abbreviation: EcoCyc
    description: EcoCyc is a model organism database for Escherichia coli K-12 MG1655.
      EcoCyc curation captures literature-based information on the functions of individual
      E. coli gene products, metabolic pathways, and regulation of E. coli gene expression.
      EcoCyc has been curated from 42,000 publications as of 2022. Updates to EcoCyc
      content continue to improve its comprehensive picture of E. coli biology. The
      utility of EcoCyc is enhanced by new tools available on the EcoCyc web site,
      and the development of EcoCyc as a teaching tool is increasing the impact of
      the knowledge collected in EcoCyc.
    homepage: https://ecocyc.org/
    name: EcoCyc E. coli Database
    prefix: FAIRsharing.65dmtr
    publications:
    - doi: 10.1093/nar/gks1027
      pubmed_id: 23143106
      title: 'EcoCyc: fusing model organism databases with systems biology.'
    - doi: 10.1093/nar/gkw1003
      pubmed_id: 27899573
      title: 'The EcoCyc database: reflecting new knowledge about Escherichia coli
        K-12.'
    - doi: 10.1128/ecosalplus.ESP-0009-2013
      pubmed_id: 26442933
      title: The EcoCyc Database.
    - doi: 10.3389/fmicb.2021.711077
      pubmed_id: 34394059
      title: The EcoCyc Database in 2021.
    subjects:
    - Biology
  go:
    homepage: https://ecocyc.org/
    name: Scientific database for the bacterium Escherichia coli K-12 MG1655
    prefix: EcoCyc
  integbio:
    description: This is a database provides information on genes, metabolites, reactions,
      operons and metabolic pathway of Escherichia coli. The data were curated based
      on literature. It is a member of the BioCyc database collections.
    fairsharing: biodbcore-000521
    homepage: http://ecocyc.org/
    information_keywords:
    - Sequence
    - Interaction/Pathway
    maintainer: SRI International
    name: EcoCyc
    prefix: nbdc00262
    pubmeds:
    - '21097882'
    status: Active
    target_keywords:
    - Genome/Gene
    - RNA
    - Protein
    - Metabolite
  mappings:
    fairsharing: FAIRsharing.65dmtr
    go: EcoCyc
    integbio: nbdc00262
    ncbi: ECOCYC
    pathguide: '9'
    re3data: r3d100011277
  name: EcoCyc
  ncbi:
    example: sroC
    homepage: https://ecocyc.org/
    name: E. coli database
    prefix: ECOCYC
  pathguide:
    abbreviation: EcoCyc
    homepage: http://ecocyc.org/
    keywords:
    - BioPAX
    - SBML
    name: Encyclopedia of E. coli Genes and Metabolism
    prefix: '9'
  prefix: ecocyc
  publications:
  - doi: 10.1128/ecosalplus.esp-0019-2024
    pmc: null
    pubmed: '40304522'
    title: The EcoCyc database (2025)
    year: 2025
  - doi: 10.3389/fmicb.2021.711077
    pmc: PMC8357350
    pubmed: '34394059'
    title: The EcoCyc Database in 2021
    year: 2021
  - doi: 10.1093/nar/gkw1003
    pmc: PMC5210515
    pubmed: '27899573'
    title: 'The EcoCyc database: reflecting new knowledge about Escherichia coli K-12'
    year: 2016
  - doi: 10.1128/ecosalplus.esp-0009-2013
    pmc: PMC4243172
    pubmed: '26442933'
    title: The EcoCyc Database
    year: 2014
  - doi: 10.1093/nar/gks1027
    pmc: PMC3531154
    pubmed: '23143106'
    title: 'EcoCyc: fusing model organism databases with systems biology'
    year: 2012
  - doi: 10.1093/nar/gks1027
    pmc: null
    pubmed: null
    title: 'EcoCyc: fusing model organism databases with systems biology.'
    year: null
  - doi: 10.1093/nar/gkw1003
    pmc: null
    pubmed: null
    title: 'The EcoCyc database: reflecting new knowledge about Escherichia coli K-12.'
    year: null
  - doi: 10.1128/ecosalplus.ESP-0009-2013
    pmc: null
    pubmed: null
    title: The EcoCyc Database.
    year: null
  - doi: 10.3389/fmicb.2021.711077
    pmc: null
    pubmed: null
    title: The EcoCyc Database in 2021.
    year: null
  - doi: 10.1093/nar/gks1027
    pmc: null
    pubmed: null
    title: 'EcoCyc: fusing model organism databases with systems biology.'
    year: null
  - doi: 10.1093/nar/gkw1003
    pmc: null
    pubmed: null
    title: 'The EcoCyc database: reflecting new knowledge about Escherichia coli K-12.'
    year: null
  - doi: 10.1128/ecosalplus.ESP-0009-2013
    pmc: null
    pubmed: null
    title: The EcoCyc Database.
    year: null
  - doi: 10.3389/fmicb.2021.711077
    pmc: null
    pubmed: null
    title: The EcoCyc Database in 2021.
    year: null
  re3data:
    description: EcoCyc is a scientific database for the bacterium Escherichia coli
      K-12 MG1655. The EcoCyc project performs literature-based curation of the entire
      genome, and of transcriptional regulation, transporters, and metabolic pathways.
    doi: 10.17616/R34K99
    homepage: https://ecocyc.org/
    license: other
    name: EcoCyc Database
    prefix: r3d100011277
    synonyms:
    - EcoCyc E. coli Database
    - Encyclopedia of E. coli Genes and Metabolism
    xrefs:
      nif: 0000-02783
  uri_format: https://ecocyc.org/gene?id=$1
ecogene:
  biocontext:
    prefix: EcoGene
    uri_format: http://ecogene.org/gene/$1
  fairsharing:
    abbreviation: EcoGene
    description: The EcoGene database contains updated information about the E. coli
      K-12 genome and proteome sequences, including extensive gene bibliographies.
      A major EcoGene focus has been the re-evaluation of translation start sites.
    homepage: http://ecogene.org/
    name: Escherichia coli strain K12 genome database
    prefix: FAIRsharing.3q3kvn
    publications:
    - doi: 10.1093/nar/28.1.60
      pubmed_id: 10592181
      title: 'EcoGene: a genome sequence database for Escherichia coli K-12.'
    subjects: []
  mappings:
    biocontext: EcoGene
    fairsharing: FAIRsharing.3q3kvn
    miriam: ecogene
    n2t: ecogene
    ncbi: EcoGene
    prefixcommons: ecogene
    re3data: r3d100010546
  miriam:
    deprecated: true
    description: The EcoGene database contains updated information about the E. coli
      K-12 genome and proteome sequences, including extensive gene bibliographies.
      A major EcoGene focus has been the re-evaluation of translation start sites.
    homepage: http://ecogene.org/
    id: '00000163'
    name: EcoGene
    namespaceEmbeddedInLui: false
    pattern: ^EG\d+$
    prefix: ecogene
    sampleId: EG10173
    uri_format: http://www.ecogene.org/gene/$1
  n2t:
    description: The EcoGene database contains updated information about the E. coli
      K-12 genome and proteome sequences, including extensive gene bibliographies.
      A major EcoGene focus has been the re-evaluation of translation start sites.
    example: EG10173
    homepage: http://ecogene.org/
    name: EcoGene at University of Miami
    namespaceEmbeddedInLui: false
    pattern: ^EG\d+$
    prefix: ecogene
    uri_format: http://www.ecogene.org/gene/$1
  ncbi:
    example: EG11277
    homepage: http://ecogene.org
    name: Database of Escherichia coli Sequence and Function
    prefix: EcoGene
  prefix: ecogene
  prefixcommons:
    description: The EcoGene database contains updated information about the E. coli
      K-12 genome and proteome sequences, including extensive gene bibliographies.
      A major EcoGene focus has been the re-evaluation of translation start sites.
    example: EG10173
    homepage: http://ecogene.org/
    keywords:
    - genome
    - protein
    name: Escherichia coli strain K12 genome database
    pattern: ^EG\d+$
    prefix: ecogene
    pubmed_ids:
    - '10592181'
    uri_format: http://ecogene.org/geneInfo.php?eg_id=$1
  publications:
  - doi: 10.1093/nar/28.1.60
    pmc: PMC102481
    pubmed: '10592181'
    title: 'EcoGene: a genome sequence database for Escherichia coli K-12'
    year: 2000
  re3data:
    description: '<<<!!!<<< The repository is no longer available.  2019-12-02: no
      more access to EcoGene >>>!!!>>>'
    doi: 10.17616/R3KP5V
    homepage: http://ecogene.org/
    name: EcoGene
    prefix: r3d100010546
    synonyms:
    - Escherichia coli strain K12 genome database
    xrefs:
      nif: 0000-02784
      omics: 03184
ecolexicon:
  comment: No resolution - everything is in a single page app
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: EcoLexicon represents the conceptual structure of the specialized domain
    of the Environment in the form of a visual thesaurus. This thesaurus has been
    elaborated according to the theoretical premises of Frame-Based Terminology.
  example: canal
  homepage: http://ecolexicon.ugr.es/en/index.htm
  keywords:
  - ecology
  - environmental science
  name: EcoLexicon
  prefix: ecolexicon
ecoliwiki:
  biocontext:
    prefix: ECOLIWIKI
  contact:
    email: pkarp@ai.sri.com
    github: pkarp111
    name: Peter D. Karp
    orcid: 0000-0002-5876-6418
  fairsharing:
    abbreviation: EcoliWiki
    description: EcoliWiki is a community-based resource for the annotation of all
      non-pathogenic E. coli, its phages, plasmids, and mobile genetic elements.
    homepage: https://ecoliwiki.org/colipedia/index.php/Welcome_to_EcoliWiki
    name: EcoliWiki
    prefix: FAIRsharing.tx95wa
    publications:
    - doi: 10.1016/j.tim.2009.04.004
      pubmed_id: 19576778
      title: What we can learn about Escherichia coli through application of Gene
        Ontology.
    subjects:
    - Genomics
    - Bioinformatics
    - Life Science
    - Ontology and Terminology
  go:
    description: EcoliHub\'s subsystem for community annotation of E. coli K-12
    homepage: http://ecoliwiki.net/
    name: EcoliWiki from EcoliHub
    prefix: EcoliWiki
  integbio:
    description: EcoliWiki is a community-based resource for the annotation of all
      non-pathogenic E. coli, its phages, plasmids, and mobile genetic elements.
    fairsharing: FAIRsharing.tx95wa
    homepage: https://ecoliwiki.org/colipedia/index.php/Welcome_to_EcoliWiki
    information_keywords:
    - Portal
    - Bibliography/Documents
    - Classification
    - Sequence
    - Ontology/Terminology/Nomenclature
    - Expression
    - Interaction/Pathway
    - Localization
    - Phenotype
    - Method
    - 3D structure
    maintainer: Texas A&M University
    name: EcoliWiki
    prefix: nbdc02041
    pubmeds:
    - '19576778'
    status: Active
    target_keywords:
    - Genome/Gene
    - Organism
  mappings:
    biocontext: ECOLIWIKI
    fairsharing: FAIRsharing.tx95wa
    go: EcoliWiki
    integbio: nbdc02041
    miriam: ecoliwiki
    n2t: ecoliwiki
  miriam:
    deprecated: false
    description: EcoliWiki is a wiki-based resource to store information related to
      non-pathogenic E. coli, its phages, plasmids, and mobile genetic elements. This
      collection references genes.
    homepage: http://ecoliwiki.net/colipedia/
    id: '00000442'
    name: EcoliWiki
    namespaceEmbeddedInLui: false
    pattern: ^[A-Za-z0-9-]+$
    prefix: ecoliwiki
    sampleId: aaeA
    uri_format: http://ecoliwiki.net/colipedia/index.php/$1:Gene
  n2t:
    description: EcoliWiki is a wiki-based resource to store information related to
      non-pathogenic E. coli, its phages, plasmids, and mobile genetic elements. This
      collection references genes.
    example: aaeA
    homepage: http://ecoliwiki.net/colipedia/
    name: EcoliWiki at Texas Agrilife Research
    namespaceEmbeddedInLui: false
    pattern: ^[A-Za-z0-9-]+$
    prefix: ecoliwiki
    uri_format: http://ecoliwiki.net/colipedia/index.php/$1:Gene
  prefix: ecoliwiki
  publications:
  - doi: 10.1016/j.tim.2009.04.004
    pmc: PMC3575750
    pubmed: '19576778'
    title: What we can learn about Escherichia coli through application of Gene Ontology
    year: 2009
ecso:
  aberowl:
    description: DataONE ontology of Carbon Flux measurements for MsTMIP and LTER
      Use Cases
    download_owl: http://aber-owl.net/media/ontologies/ECSO/51/ecso.owl
    name: The Ecosystem Ontology
    prefix: ECSO
    version: 0.9.1
  bioportal:
    contact:
      email: mecum@nceas.ucsb.edu
      name: Bryce Mecum
    description: DataONE ontology of Carbon Flux measurements for MsTMIP and LTER
      Use Cases
    homepage: https://github.com/DataONEorg/sem-prov-ontologies
    name: The Ecosystem Ontology
    prefix: ECSO
    version: '0.9'
  contact:
    email: brycemecum@gmail.com
    github: amoeba
    name: Bryce Mecum
    orcid: 0000-0002-0381-3766
  download_owl: https://raw.githubusercontent.com/DataONEorg/sem-prov-ontologies/run4/observation/d1-ECSO.owl
  ecoportal:
    contact:
      email: mecum@nceas.ucsb.edu
      name: Bryce Mecum
    description: DataONE ontology of Carbon Flux measurements for MsTMIP and LTER
      Use Cases
    homepage: https://bioportal.bioontology.org/ontologies/ECSO
    license: CC-BY-4.0
    name: The Ecosystem Ontology
    prefix: ECSO
    repository: https://github.com/DataONEorg/sem-prov-ontologies/tree/ECSO8-add_non-carbon_measurements
    version: 0.10.0
  example: '00000532'
  fairsharing:
    abbreviation: ECSO
    description: DataONE ontology of Carbon Flux measurements for MsTMIP and LTER
      Use Cases
    domains:
    - ecosystem
    homepage: http://bioportal.bioontology.org/ontologies/ECSO
    name: The Ecosystem Ontology
    prefix: FAIRsharing.a4ww64
    subjects:
    - Ecosystem Science
    - Earth Science
  mappings:
    aberowl: ECSO
    bioportal: ECSO
    ecoportal: ECSO
    fairsharing: FAIRsharing.a4ww64
    tib: ecso
  pattern: ^\d+$
  prefix: ecso
  repository: https://github.com/DataONEorg/sem-prov-ontologies
  tib:
    description: ECSO expresses 'Measurement Types' to describe measurements present
      in raw data. It uses the OBOÉ observation and measurements design pattern (OBOE
      https://github.com/NCEAS/oboe) to capture both the 'entity of interest' and
      'characteristic measured'. ECSO is intended to be used with terms in other OWL
      ontologies, including ENVO, PATO, CHEBI, BCO and PCO. It is currently focused
      on carbon and associated measurements.
    download_owl: https://raw.githubusercontent.com/DataONEorg/sem-prov-ontologies/ECSO8-add_non-carbon_measurements/observation/ECSO8.owl
    homepage: https://github.com/DataONEorg/sem-prov-ontologies
    keywords:
    - FAIR Data Spaces
    - ESS
    - chemical and environmental engineering
    - earth sciences
    name: The Ecosystems Ontology
    prefix: ecso
    tracker: https://github.com/DataONEorg/sem-prov-ontologies/issues
    uri_format: http://purl.dataone.org/odo/ECSO8.owl$1
  uri_format: http://purl.dataone.org/odo/ECSO_$1
ecto:
  aberowl:
    description: ECTO describes exposures to experimental treatments of plants and
      model organisms (e.g. exposures to modification of diet, lighting levels, temperature);
      exposures of humans or any other organisms to stressors through a variety of
      routes, for purposes of public health, environmental monitoring etc, stimuli,
      natural and experimental, any kind of environmental condition or change in condition
      that can be experienced by an organism or population of organisms on earth.
      The scope is very general and can include for example plant treatment regimens,
      as well as human clinical exposures (although these may better be handled by
      a more specialized ontology).
    download_owl: http://aber-owl.net/media/ontologies/ECTO/12/ecto.owl
    homepage: https://github.com/EnvironmentOntology/environmental-exposure-ontology
    name: Environmental conditions, treatments and exposures ontology
    prefix: ECTO
  agroportal:
    contact:
      email: cjmungall@lbl.gov
      name: Christopher J. Mungall
    description: ECTO describes exposures to experimental treatments of plants and
      model organisms (e.g. exposures to modification of diet, lighting levels, temperature);
      exposures of humans or any other organisms to stressors through a variety of
      routes, for purposes of public health, environmental monitoring etc, stimuli,
      natural and experimental, any kind of environmental condition or change in condition
      that can be experienced by an organism or population of organisms on earth.
      The scope is very general and can include for example plant treatment regimens,
      as well as human clinical exposures (although these may better be handled by
      a more specialized ontology).
    example_uri: http://purl.obolibrary.org/obo/ECTO_9000201
    homepage: https://github.com/EnvironmentOntology/environmental-exposure-ontology
    license: CC0-1.0
    name: Environmental Conditions, Treatments and Exposures Ontology
    prefix: ECTO
    publications:
    - https://doi.org/10.1186/s13326-023-00283-x
    repository: https://github.com/EnvironmentOntology/environmental-exposure-ontology
    version: '2023-02-14'
  biolink:
    is_identifiers: false
    is_obo: true
    prefix: ECTO
    uri_format: http://purl.obolibrary.org/obo/ECTO_$1
  bioportal:
    contact:
      email: annethessen@gmail.com
      name: Anne Thessen
    description: ECTO describes exposures to experimental treatments of plants and
      model organisms (e.g. exposures to modification of diet, lighting levels, temperature);
      exposures of humans or any other organisms to stressors through a variety of
      routes, for purposes of public health, environmental monitoring etc, stimuli,
      natural and experimental, any kind of environmental condition or change in condition
      that can be experienced by an organism or population of organisms on earth.
      The scope is very general and can include for example plant treatment regimens,
      as well as human clinical exposures (although these may better be handled by
      a more specialized ontology).
    homepage: https://github.com/EnvironmentOntology/environmental-exposure-ontology
    name: Environmental conditions, treatments and exposures ontology
    prefix: ECTO
    version: '2023-02-14'
  example: '0000001'
  fairsharing:
    abbreviation: ECTO
    description: The Environmental Conditions, Treatments, and Exposures Ontology
      (ECTO) is a species-agnostic ontology focused on exposure events that occur
      as a result of natural and experimental processes, such as diet, work, or research
      activities.
    domains:
    - exposure
    homepage: https://github.com/EnvironmentOntology/environmental-exposure-ontology
    license: CC0-1.0
    name: Environmental Conditions, Treatments, and exposures Ontology
    prefix: FAIRsharing.6b77ac
    publications:
    - doi: 10.1186/s13326-023-00283-x
      pubmed: '36823605'
      title: 'The Environmental Conditions, Treatments, and Exposures Ontology (ECTO):
        connecting toxicology and exposure to human health and beyond'
      year: 2023
    subjects:
    - Environmental Science
  mappings:
    aberowl: ECTO
    agroportal: ECTO
    biolink: ECTO
    bioportal: ECTO
    fairsharing: FAIRsharing.6b77ac
    obofoundry: ecto
    ols: ecto
    ontobee: ECTO
    wikidata.entity: Q113012651
  obofoundry:
    contact: annethessen@gmail.com
    contact.github: diatomsRcool
    contact.label: Anne Thessen
    contact.orcid: 0000-0002-2908-3327
    depends_on:
    - chebi
    - envo
    - exo
    - go
    - iao
    - maxo
    - nbo
    - ncbitaxon
    - ncit
    - pato
    - ro
    - uberon
    - xco
    deprecated: false
    description: ECTO describes exposures to experimental treatments of plants and
      model organisms (e.g. exposures to modification of diet, lighting levels, temperature);
      exposures of humans or any other organisms to stressors through a variety of
      routes, for purposes of public health, environmental monitoring etc, stimuli,
      natural and experimental, any kind of environmental condition or change in condition
      that can be experienced by an organism or population of organisms on earth.
      The scope is very general and can include for example plant treatment regimens,
      as well as human clinical exposures (although these may better be handled by
      a more specialized ontology).
    domain: environment
    download.json: http://purl.obolibrary.org/obo/ecto.json
    download.obo: http://purl.obolibrary.org/obo/ecto.obo
    download.owl: http://purl.obolibrary.org/obo/ecto.owl
    homepage: https://github.com/EnvironmentOntology/environmental-exposure-ontology
    license: CC0 1.0
    license.url: https://creativecommons.org/publicdomain/zero/1.0/
    logo: https://raw.githubusercontent.com/jmcmurry/closed-illustrations/master/logos/ecto-logos/ecto-logo_black-banner.png
    name: Environmental conditions, treatments and exposures ontology
    preferredPrefix: ECTO
    prefix: ecto
    repository: https://github.com/EnvironmentOntology/environmental-exposure-ontology
  ols:
    description: ECTO describes exposures to experimental treatments of plants and
      model organisms (e.g. exposures to modification of diet, lighting levels, temperature);
      exposures of humans or any other organisms to stressors through a variety of
      routes, for purposes of public health, environmental monitoring etc, stimuli,
      natural and experimental, any kind of environmental condition or change in condition
      that can be experienced by an organism or population of organisms on earth.
      The scope is very general and can include for example plant treatment regimens,
      as well as human clinical exposures (although these may better be handled by
      a more specialized ontology).
    download_owl: http://purl.obolibrary.org/obo/ecto.owl
    homepage: https://github.com/EnvironmentOntology/environmental-exposure-ontology
    name: Environment Exposure Ontology
    prefix: ecto
    tracker: https://github.com/EnvironmentOntology/environmental-exposure-ontology/issues
    version: '2023-02-14'
    version.iri: http://purl.obolibrary.org/obo/ecto/releases/2023-02-14/ecto.owl
  ontobee:
    library: Library
    name: Environmental conditions, treatments and exposures ontology
    prefix: ECTO
  pattern: ^\d{7}$
  prefix: ecto
  uri_format: http://purl.obolibrary.org/obo/ECTO_$1
ecyano.entity:
  biocontext:
    prefix: ECYANO.ENTITY
  mappings:
    biocontext: ECYANO.ENTITY
    miriam: ecyano.entity
    n2t: ecyano.entity
  miriam:
    deprecated: false
    description: E-cyanobacterium.org is a web-based platform for public sharing,
      annotation, analysis, and visualisation of dynamical models and wet-lab experiments
      related to cyanobacteria. It allows models to be represented at different levels
      of abstraction — as biochemical reaction networks or ordinary differential equations.It
      provides concise mappings of mathematical models to a formalised consortium-agreed
      biochemical description, with the aim of connecting the world of biological
      knowledge with benefits of mathematical description of dynamic processes. This
      collection references entities.
    homepage: http://www.e-cyanobacterium.org/bcs/entity/
    id: 00000585
    name: E-cyanobacterium entity
    namespaceEmbeddedInLui: false
    pattern: ^\d+$
    prefix: ecyano.entity
    sampleId: '23'
    uri_format: http://e-cyanobacterium.org/bcs/entity/$1/
  n2t:
    description: E-cyanobacterium.org is a web-based platform for public sharing,
      annotation, analysis, and visualisation of dynamical models and wet-lab experiments
      related to cyanobacteria. It allows models to be represented at different levels
      of abstraction &#x2014; as biochemical reaction networks or ordinary differential
      equations.It provides concise mappings of mathematical models to a formalised
      consortium-agreed biochemical description, with the aim of connecting the world
      of biological knowledge with benefits of mathematical description of dynamic
      processes. This collection references entities.
    example: '23'
    homepage: http://www.e-cyanobacterium.org/bcs/entity/
    name: e-cyanobacterium entity at Masaryk University Brno
    namespaceEmbeddedInLui: false
    pattern: ^\d+$
    prefix: ecyano.entity
    uri_format: http://e-cyanobacterium.org/bcs/entity/$1/
  part_of_database: ecyano
  prefix: ecyano.entity
  uri_format: https://www.e-cyanobacterium.org/bcs/entity/$1
ecyano.experiment:
  mappings:
    miriam: ecyano.experiment
  miriam:
    deprecated: false
    description: E-cyanobacterium experiments is a repository of wet-lab experiments
      related to cyanobacteria. The emphasis is placed on annotation via mapping to
      local database of biological knowledge and mathematical models along with the
      complete experimental setup supporting the reproducibility of the experiments.
    homepage: https://www.e-cyanobacterium.org/experiments-repository/
    id: '00000760'
    name: E-cyanobacterium Experimental Data
    namespaceEmbeddedInLui: false
    pattern: ^\d+$
    prefix: ecyano.experiment
    sampleId: '18'
    uri_format: https://www.e-cyanobacterium.org/experiments-repository/?action=detail&id=$1
  part_of_database: ecyano
  prefix: ecyano.experiment
ecyano.model:
  biocontext:
    prefix: ECYANO.MODEL
  mappings:
    biocontext: ECYANO.MODEL
    miriam: ecyano.model
    n2t: ecyano.model
  miriam:
    deprecated: false
    description: E-cyanobacterium.org is a web-based platform for public sharing,
      annotation, analysis, and visualisation of dynamical models and wet-lab experiments
      related to cyanobacteria. It allows models to be represented at different levels
      of abstraction — as biochemical reaction networks or ordinary differential equations.It
      provides concise mappings of mathematical models to a formalised consortium-agreed
      biochemical description, with the aim of connecting the world of biological
      knowledge with benefits of mathematical description of dynamic processes. This
      collection references models.
    homepage: http://e-cyanobacterium.org/models/
    id: 00000586
    name: E-cyanobacterium model
    namespaceEmbeddedInLui: false
    pattern: ^\d+$
    prefix: ecyano.model
    sampleId: '26'
    uri_format: http://e-cyanobacterium.org/models/model/$1/
  n2t:
    description: E-cyanobacterium.org is a web-based platform for public sharing,
      annotation, analysis, and visualisation of dynamical models and wet-lab experiments
      related to cyanobacteria. It allows models to be represented at different levels
      of abstraction &#x2014; as biochemical reaction networks or ordinary differential
      equations.It provides concise mappings of mathematical models to a formalised
      consortium-agreed biochemical description, with the aim of connecting the world
      of biological knowledge with benefits of mathematical description of dynamic
      processes. This collection references models.
    example: '26'
    homepage: http://e-cyanobacterium.org/models/
    name: e-cyanobacterium entity at Masaryk University Brno
    namespaceEmbeddedInLui: false
    pattern: ^\d+$
    prefix: ecyano.model
    uri_format: http://e-cyanobacterium.org/models/model/$1/
  prefix: ecyano.model
  uri_format: https://e-cyanobacterium.org/models/model/$1
ecyano.rule:
  biocontext:
    prefix: ECYANO.RULE
  mappings:
    biocontext: ECYANO.RULE
    miriam: ecyano.rule
    n2t: ecyano.rule
  miriam:
    deprecated: false
    description: E-cyanobacterium.org is a web-based platform for public sharing,
      annotation, analysis, and visualisation of dynamical models and wet-lab experiments
      related to cyanobacteria. It allows models to be represented at different levels
      of abstraction — as biochemical reaction networks or ordinary differential equations.It
      provides concise mappings of mathematical models to a formalised consortium-agreed
      biochemical description, with the aim of connecting the world of biological
      knowledge with benefits of mathematical description of dynamic processes. This
      collection references rules.
    homepage: http://www.e-cyanobacterium.org/bcs/rule/
    id: 00000587
    name: E-cyanobacterium rule
    namespaceEmbeddedInLui: false
    pattern: ^\d+$
    prefix: ecyano.rule
    sampleId: '56'
    uri_format: http://e-cyanobacterium.org/bcs/rule/$1/
  n2t:
    description: E-cyanobacterium.org is a web-based platform for public sharing,
      annotation, analysis, and visualisation of dynamical models and wet-lab experiments
      related to cyanobacteria. It allows models to be represented at different levels
      of abstraction &#x2014; as biochemical reaction networks or ordinary differential
      equations.It provides concise mappings of mathematical models to a formalised
      consortium-agreed biochemical description, with the aim of connecting the world
      of biological knowledge with benefits of mathematical description of dynamic
      processes. This collection references rules.
    example: '56'
    homepage: http://www.e-cyanobacterium.org/bcs/rule/
    name: e-cyanobacterium entity at Masaryk University Brno
    namespaceEmbeddedInLui: false
    pattern: ^\d+$
    prefix: ecyano.rule
    uri_format: http://e-cyanobacterium.org/bcs/rule/$1/
  part_of_database: ecyano
  prefix: ecyano.rule
  uri_format: https://e-cyanobacterium.org/bcs/rule/$1
edam:
  aberowl:
    description: EDAM is a comprehensive ontology of well-established, familiar concepts
      that are prevalent within bioinformatics and computational biology, including
      types of data and data identifiers, data formats, operations and topics. EDAM
      is a simply-structured ontology - essentially a set of concepts with preferred
      terms and synonyms, definitions, and some additional information - organised
      into a simple and intuitive hierarchy for convenient use by information curators,
      software developers and end-users. EDAM is suitable for large-scale semantic
      annotations and categorization of diverse bioinformatics resources. EDAM is
      also suitable for diverse application including for example within workbenches
      and workflow-management systems, software distributions, and resource registries.
    download_owl: http://aber-owl.net/media/ontologies/EDAM/36/edam.owl
    homepage: http://edamontology.org
    name: EDAM bioinformatics operations, types of data, data formats, identifiers,
      and topics
    prefix: EDAM
    version: '1.19'
  agroportal:
    contact:
      email: jison@bioinformatics.dtu.dk
      name: Jon Ison
    description: 'EDAM is a simple ontology of well established, familiar concepts
      that are prevalent within bioinformatics, including types of data and data identifiers,
      data formats, operations and topics. EDAM provides a set of terms with synonyms
      and definitions, organised into an intuitive hierarchy for convenient use.,
      EDAM is a domain ontology of data analysis and data management in bio- and other
      sciences, and science-based applications. It comprises concepts related to analysis,
      modelling, optimisation, and data life cycle. Targetting usability by diverse
      users, the structure of EDAM is relatively simple, divided into 4 main sections:
      Topic, Operation, Data (incl. Identifier), and Format.'
    example_uri: http://edamontology.org/topic_3519
    homepage: http://edamontology.org/page
    license: CC BY-SA 4.0
    name: Ontology of bioscientific data analysis and data management
    prefix: EDAM
    repository: https://github.com/edamontology/edamontology
    version: 1.25-20251112T1620Z-unstable(1.26)
  biocontext:
    prefix: EDAM
  bioportal:
    contact:
      email: herve.menager@pasteur.fr
      name: Hervé Ménager
    description: 'EDAM is a domain ontology of data analysis and data management in
      bio- and other sciences, and science-based applications. It comprises concepts
      related to analysis, modelling, optimisation, and data life cycle. Targetting
      usability by diverse users, the structure of EDAM is relatively simple, divided
      into 4 main sections: Topic, Operation, Data (incl. Identifier), and Format.
      EDAM is particularly suitable for semantic annotations and categorisation of
      diverse resources related to data analysis and management: e.g. tools, workflows,
      learning materials, or standards. EDAM is also useful in data management itself,
      for recording provenance metadata of processed data. As a reference citation,
      please use https://doi.org/10.7490/f1000research.1118900.1'
    homepage: http://edamontology.org
    license: CC BY-SA 4.0
    name: EDAM - The ontology of data analysis and management
    prefix: EDAM
    publications:
    - https://doi.org/10.7490/f1000research.1118900.1
    version: 1.25-20251112T1620Z-unstable(1.26)
  contact:
    email: matus.kalas@uib.no
    github: matuskalas
    name: Matúš Kalaš
    orcid: 0000-0002-1509-4981
  download_obo: https://github.com/edamontology/edamontology/raw/main/releases/EDAM.obo
  fairsharing:
    abbreviation: EDAM
    description: 'EDAM is a comprehensive ontology of well-established, familiar concepts
      that are prevalent within bioscientific data analysis and data management (including
      computational biology, bioinformatics, and bioimage informatics). EDAM includes
      topics, operations, types of data and data identifiers, and data formats, relevant
      in data analysis and data management in life sciences. EDAM provides a set of
      concepts with preferred terms and synonyms, related terms, definitions, and
      other information - organised into a simple and intuitive hierarchy for convenient
      use. EDAM is particularly suitable for semantic annotations and categorisation
      of diverse resources related to data analysis and management: e.g. tools, workflows,
      learning materials, or standards. EDAM is also useful in data management itself,
      for recording provenance metadata of processed bioscientific data.'
    domains:
    - Data analysis
    - Data acquisition
    - data transformation
    homepage: http://edamontology.org
    license: CC BY-SA 4.0
    name: The bioscientific data analysis and management ontology
    prefix: FAIRsharing.a6r7zs
    publications:
    - doi: 10.1093/bioinformatics/btt113
      pubmed: '23479348'
      title: 'EDAM: an ontology of bioinformatics operations, types of data and identifiers,
        topics and formats'
      year: 2013
    - doi: 10.7490/f1000research.1118900.1
      title: 'EDAM: the bioscientific data analysis ontology (update 2021)'
      year: 2021
    - doi: 10.5281/zenodo.3899895
      title: 'edamontology/edamontology: EDAM 1.25'
      year: 2020
    repository: https://github.com/edamontology/edamontology
    subjects:
    - Life Science
    - Omics
    - Bioinformatics
    twitter: edamontology
  mappings:
    aberowl: EDAM
    agroportal: EDAM
    biocontext: EDAM
    bioportal: EDAM
    fairsharing: FAIRsharing.a6r7zs
    miriam: edam
    n2t: edam
    ols: edam
    ontobee: EDAM
    prefixcommons: edam
    tib: edam
  miriam:
    deprecated: false
    description: 'EDAM is an ontology of general bioinformatics concepts, including
      topics, data types, formats, identifiers and operations. EDAM provides a controlled
      vocabulary for the description, in semantic terms, of things such as: web services
      (e.g. WSDL files), applications, tool collections and packages, work-benches
      and workflow software, databases and ontologies, XSD data schema and data objects,
      data syntax and file formats, web portals and pages, resource catalogues and
      documents (such as scientific publications).'
    homepage: http://bioportal.bioontology.org/ontologies/EDAM
    id: 00000189
    name: EDAM Ontology
    namespaceEmbeddedInLui: false
    pattern: ^(data|topic|operation|format)\_\d{4}$
    prefix: edam
    sampleId: data_1664
    uri_format: http://purl.bioontology.org/ontology/EDAM/$1
  n2t:
    description: 'EDAM is an ontology of general bioinformatics concepts, including
      topics, data types, formats, identifiers and operations. EDAM provides a controlled
      vocabulary for the description, in semantic terms, of things such as: web services
      (e.g. WSDL files), applications, tool collections and packages, work-benches
      and workflow software, databases and ontologies, XSD data schema and data objects,
      data syntax and file formats, web portals and pages, resource catalogues and
      documents (such as scientific publications).'
    example: data_1664
    homepage: http://bioportal.bioontology.org/ontologies/EDAM
    name: EDAM through BioPortal
    namespaceEmbeddedInLui: false
    pattern: ^(data|topic|operation|format)\_\d{4}$
    prefix: edam
    uri_format: http://purl.bioontology.org/ontology/EDAM/$1
  name: EDAM Ontology
  ols:
    contact: edam@elixir-dk.org
    description: 'EDAM is a domain ontology of data analysis and data management in
      bio- and other sciences, and science-based applications. It comprises concepts
      related to analysis, modelling, optimisation, and data life cycle. Targetting
      usability by diverse users, the structure of EDAM is relatively simple, divided
      into 4 main sections: Topic, Operation, Data (incl. Identifier), and Format.'
    download_owl: https://raw.githubusercontent.com/edamontology/edamontology/master/releases/EDAM.owl
    homepage: http://edamontology.org
    name: EDAM - The ontology of data analysis and management
    prefix: edam
    uri_format: http://edamontology.org/data_$1
    version: 1.25-20251112T1620Z-unstable(1.26)
    version.iri: http://edamontology.org/1.25-20251112T1620Z-unstable(1.26)
  ontobee:
    library: Not Specified/No
    name: EMBRACE Data and Methods
    prefix: EDAM
  prefix: edam
  prefixcommons:
    bioportal: '1498'
    description: EDAM (EMBRACE Data And Methods) is an ontology of bioinformatics
      operations (tool, application, or workflow functions), types of data, topics
      (application domains), and data formats. The applications of EDAM are within
      organising tools and data, finding suitable tools in catalogues, and integrating
      them into complex applications or workflows. Semantic annotations with EDAM
      are applicable to diverse entities such as for example Web services, databases,
      programmatic libraries, standalone tools and toolkits, interactive applications,
      data schemas, data sets, or publications within bioinformatics. Annotation with
      EDAM may also contribute to data provenance, and EDAM terms and synonyms can
      be used in text mining. EDAM - and in particular the EDAM Data sub-ontology
      - serves also as a markup vocabulary for bioinformatics data on the Semantic
      Web.
    example: EDAM_data:1664
    homepage: https://sourceforge.net/projects/edamontology/
    keywords:
    - obo
    - ontology
    name: Bioinformatics operations, types of data, data formats and topics
    pattern: ^EDAM_(data|topic)\:\d{4}$
    prefix: edam
  publications:
  - doi: 10.1093/bioinformatics/btt113
    pmc: PMC3654706
    pubmed: '23479348'
    title: 'EDAM: an ontology of bioinformatics operations, types of data and identifiers,
      topics and formats'
    year: 2013
  - doi: 10.1093/bioinformatics/btt113
    pmc: null
    pubmed: '23479348'
    title: 'EDAM: an ontology of bioinformatics operations, types of data and identifiers,
      topics and formats'
    year: 2013
  - doi: 10.7490/f1000research.1118900.1
    pmc: null
    pubmed: null
    title: 'EDAM: the bioscientific data analysis ontology (update 2021)'
    year: 2021
  - doi: 10.5281/zenodo.3899895
    pmc: null
    pubmed: null
    title: 'edamontology/edamontology: EDAM 1.25'
    year: 2020
  rdf_uri_format: http://edamontology.org/$1
  repository: https://github.com/edamontology/edamontology
  tib:
    description: 'EDAM is a domain ontology of data analysis and data management in
      bio- and other sciences, and science-based applications. It comprises concepts
      related to analysis, modelling, optimisation, and data life cycle. Targetting
      usability by diverse users, the structure of EDAM is relatively simple, divided
      into 4 main sections: Topic, Operation, Data (incl. Identifier), and Format.'
    download_owl: http://edamontology.org/EDAM.owl
    homepage: http://edamontology.org
    keywords:
    - NFDI4ING
    - NFDI4CHEM
    - ESS
    - NFDI4CAT
    - DataPLANT
    - life sciences, biology
    - computer science
    - earth sciences
    name: EDAM - The ontology of data analysis and management
    prefix: edam
    tracker: https://github.com/edamontology/edamontology/issues
    version.iri: http://edamontology.org/1.25-20240924T0027Z-unstable(1.26)
  twitter: edamontology
  uri_format: https://www.ebi.ac.uk/ols/ontologies/edam/terms?iri=http://edamontology.org/$1
edam.data:
  biolink:
    is_identifiers: false
    is_obo: false
    prefix: EDAM-DATA
    uri_format: http://edamontology.org/data_$1
  contact:
    email: matus.kalas@uib.no
    github: matuskalas
    name: Matúš Kalaš
    orcid: 0000-0002-1509-4981
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: Information, represented in an information artefact (data record) that
    is 'understandable' by dedicated computational tools that can use the data as
    input or produce it as output.
  download_obo: https://github.com/edamontology/edamontology/raw/main/releases/EDAM.obo
  example: '1664'
  homepage: http://edamontology.org
  mappings:
    biolink: EDAM-DATA
  name: EDAM Data
  pattern: ^\d+$
  prefix: edam.data
  repository: https://github.com/edamontology/edamontology
  twitter: edamontology
  uri_format: http://edamontology.org/data_$1
edam.format:
  biolink:
    is_identifiers: false
    is_obo: false
    prefix: EDAM-FORMAT
    uri_format: http://edamontology.org/format_$1
  contact:
    email: matus.kalas@uib.no
    github: matuskalas
    name: Matúš Kalaš
    orcid: 0000-0002-1509-4981
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: A defined way or layout of representing and structuring data in a computer
    file, blob, string, message, or elsewhere. The main focus in EDAM lies on formats
    as means of structuring data exchanged between different tools or resources. The
    serialisation, compression, or encoding of concrete data formats/models is not
    in scope of EDAM. Format 'is format of' Data.
  download_obo: https://github.com/edamontology/edamontology/raw/main/releases/EDAM.obo
  example: '1915'
  homepage: http://edamontology.org
  mappings:
    biolink: EDAM-FORMAT
  name: EDAM Format
  pattern: ^\d+$
  prefix: edam.format
  repository: https://github.com/edamontology/edamontology
  twitter: edamontology
  uri_format: http://edamontology.org/format_$1
edam.operation:
  biolink:
    is_identifiers: false
    is_obo: false
    prefix: EDAM-OPERATION
    uri_format: http://edamontology.org/operation_$1
  contact:
    email: matus.kalas@uib.no
    github: matuskalas
    name: Matúš Kalaš
    orcid: 0000-0002-1509-4981
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: 'A function that processes a set of inputs and results in a set of
    outputs, or associates arguments (inputs) with values (outputs). Special cases
    are: a) An operation that consumes no input (has no input arguments). Such operation
    is either a constant function, or an operation depending only on the underlying
    state. b) An operation that may modify the underlying state but has no output.
    c) The singular-case operation with no input or output, that still may modify
    the underlying state.'
  download_obo: https://github.com/edamontology/edamontology/raw/main/releases/EDAM.obo
  example: '0004'
  homepage: http://edamontology.org
  mappings:
    biolink: EDAM-OPERATION
  name: EDAM Operation
  pattern: ^\d+$
  prefix: edam.operation
  repository: https://github.com/edamontology/edamontology
  twitter: edamontology
  uri_format: http://edamontology.org/operation_$1
edam.topic:
  biolink:
    is_identifiers: false
    is_obo: false
    prefix: EDAM-TOPIC
    uri_format: http://edamontology.org/topic_$1
  contact:
    email: matus.kalas@uib.no
    github: matuskalas
    name: Matúš Kalaš
    orcid: 0000-0002-1509-4981
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: A category denoting a rather broad domain or field of interest, of
    study, application, work, data, or technology. Topics have no clearly defined
    borders between each other.
  download_obo: https://github.com/edamontology/edamontology/raw/main/releases/EDAM.obo
  example: '0003'
  homepage: http://edamontology.org
  mappings:
    biolink: EDAM-TOPIC
  name: EDAM Topic
  pattern: ^\d+$
  prefix: edam.topic
  repository: https://github.com/edamontology/edamontology
  twitter: edamontology
  uri_format: http://edamontology.org/topic_$1
edcc:
  example: 00098e55
  homepage: https://op.europa.eu
  mappings:
    tib: edcc
  prefix: edcc
  tib:
    description: EDCC Taxonomy contains the terms that are used to classify citizens'
      requests to the Europe Direct Contact Centre (EDCC). EDCC Taxonomy is maintained
      by the Directorate-General for Communication of the European Commission and
      published by the Publications Office of the European Union on the EU Vocabularies
      website.
    homepage: https://op.europa.eu/de/home
    keywords:
    - Educational Resources
    name: EDCC Taxonomy
    prefix: edcc
    uri_format: http://data.europa.eu/ett/kos/c_$1
edda:
  aberowl:
    description: 'The EDDA Study Designs Taxonomy (v2.0) was developed by the Evidence
      in Documents, Discovery, and Analytics (EDDA) Group: Tanja Bekhuis (Principal
      Scientist); Eugene Tseytlin (Systems Developer); Ashleigh Faith (Taxonomist);
      Faina Linkov (Epidemiologist). The EDDA Group is a division of TCB Research
      & Indexing LLC. This work was made possible, in part, by the US National Library
      of Medicine, National Institutes of Health, grant no. R00LM010943.  Foundational
      research is described in Bekhuis T, Demner Fushman D, Crowley RS. Comparative
      effectiveness research designs: an analysis of terms and coverage in Medical
      Subject Headings (MeSH) and Emtree. Journal of the Medical Library Association
      (JMLA). 2013 April;101(2):92-100. PMC3634392.  Coverage of the terminology appearing
      in JMLA was extended with terms from MeSH, NCI Thesaurus (NCI), Emtree, the
      HTA Database Canadian Repository [international repository for health technology
      assessment], and Robert Sandieson''s synonym ring for research synthesis. Collected
      terms were enriched with terms from the NCI Metathesaurus. Variants include
      synonyms for preferred terms, singular and plural forms, and American and British
      spellings. Definitions, if they exist, are mainly from MeSH, NCI, Emtree, and
      medical dictionaries. A PDF of this taxonomy is available in ResearchGate DOI:
      10.13140/RG.2.1.3769.2406/1. The EDDA Study Designs Taxonomy by Tanja Bekhuis
      and Eugene Tseytlin is licensed under a Creative Commons Attribution–NonCommercial–ShareAlike
      4.0 International License (CC BY-NC-SA 4.0). For information about this license,
      see https://creativecommons.org/licenses/by-nc-sa/4.0/.'
    download_owl: http://aber-owl.net/media/ontologies/EDDA/11/edda.owl
    name: EDDA Study Designs Taxonomy
    prefix: EDDA
    version: '2.0'
  bioportal:
    contact:
      email: tanja.bekhuis@tcbinfosci.com
      name: Tanja Bekhuis
    description: 'The EDDA Study Designs Taxonomy (v2.0) was developed by the Evidence
      in Documents, Discovery, and Analytics (EDDA) Group: Tanja Bekhuis (Principal
      Scientist); Eugene Tseytlin (Systems Developer); Ashleigh Faith (Taxonomist);
      Faina Linkov (Epidemiologist). The EDDA Group is a division of TCB Research
      & Indexing LLC. This work was made possible, in part, by the US National Library
      of Medicine, National Institutes of Health, grant no. R00LM010943. Foundational
      research is described in Bekhuis T, Demner Fushman D, Crowley RS. Comparative
      effectiveness research designs: an analysis of terms and coverage in Medical
      Subject Headings (MeSH) and Emtree. Journal of the Medical Library Association
      (JMLA). 2013 April;101(2):92-100. PMC3634392. Coverage of the terminology appearing
      in JMLA was extended with terms from MeSH, NCI Thesaurus (NCI), Emtree, the
      HTA Database Canadian Repository [international repository for health technology
      assessment], and Robert Sandieson''s synonym ring for research synthesis. Collected
      terms were enriched with terms from the NCI Metathesaurus. Variants include
      synonyms for preferred terms, singular and plural forms, and American and British
      spellings. Definitions, if they exist, are mainly from MeSH, NCI, Emtree, and
      medical dictionaries. A PDF of this taxonomy is available in ResearchGate DOI:
      10.13140/RG.2.1.3769.2406/1. The EDDA Study Designs Taxonomy by Tanja Bekhuis
      and Eugene Tseytlin is licensed under a Creative Commons Attribution–NonCommercial–ShareAlike
      4.0 International License (CC BY-NC-SA 4.0). For information about this license,
      see https://creativecommons.org/licenses/by-nc-sa/4.0/.'
    name: EDDA Study Designs Taxonomy
    prefix: EDDA
    version: '2.0'
  contact:
    email: tanja.bekhuis@tcbinfosci.com
    github: null
    name: Tanja Bekhuis
    orcid: 0000-0002-8537-9077
  description: Coverage of the terminology appearing in JMLA was extended with terms
    from MeSH, NCI Thesaurus (NCI), Emtree, the HTA Database Canadian Repository [international
    repository for health technology assessment], and Robert Sandieson's synonym ring
    for research synthesis. Collected terms were enriched with terms from the NCI
    Metathesaurus. Variants include synonyms for preferred terms, singular and plural
    forms, and American and British spellings. Definitions, if they exist, are mainly
    from MeSH, NCI, Emtree, and medical dictionaries.
  example: health_care_quality_assessment
  fairsharing:
    abbreviation: EDDA
    description: 'Terminology of study designs and publication types (beta version).
      Developed by the Evidence in Documents, Discovery, and Analysis (EDDA) Group.
      Tanja Bekhuis (PI); Eugene Tseytlin (Systems Developer); Ashleigh Faith (Taxonomist).
      Department of Biomedical Informatics, University of Pittsburgh School of Medicine,
      Pennsylvania, US. This work was made possible, in part, by the US National Library
      of Medicine, National Institutes of Health, grant no. R00LM010943. Based on
      research described in Bekhuis T, Demner-Fushman D, Crowley RS. Comparative effectiveness
      research designs: an analysis of terms and coverage in Medical Subject Headings
      (MeSH) and Emtree. Journal of the Medical Library Association (JMLA). 2013 April;101(2):92-100.
      PMC3634392. The terminology appearing in JMLA has been enriched with terms from
      MeSH, NCI Thesaurus (NCIT), and Emtree, the controlled vocabularies for MEDLINE,
      the National Cancer Institute, and Embase, respectively, as well as from published
      research literature. Variants include synonyms for preferred terms, singular
      and plural forms, and American and British spellings. Definitions, if they exist,
      are mainly from MeSH, NCIT, Emtree, and medical dictionaries. A class for Publication
      Type is included because investigators consider type and design when screening
      reports for inclusion in comparative effectiveness research. EDDA Study Designs
      and Publications by Tanja Bekhuis is licensed under a Creative Commons Attribution-NonCommercial-ShareAlike
      4.0 International License.'
    homepage: http://edda.dbmi.pitt.edu/
    name: EDDA Study Designs Taxonomy
    prefix: FAIRsharing.2ffmsb
    subjects:
    - Medicine
  homepage: https://bioportal.bioontology.org/ontologies/EDDA
  mappings:
    aberowl: EDDA
    bioportal: EDDA
    fairsharing: FAIRsharing.2ffmsb
  prefix: edda
  uri_format: http://ontologies.dbmi.pitt.edu/edda/StudyDesigns.owl#$1
edm:
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: The Europeana Data Model (EDM) is aimed at being an integration medium
    for collecting, connecting and enriching the descriptions provided by Europeana
    data providers. The RDF vocabulary for http://www.europeana.eu/schemas/edm/ defines
    the elements introduced by EDM (as opposed to the ones EDM re-uses from other
    namespaces).
  download_owl: https://github.com/europeana/metis-schema/raw/94c73a16320977fac121acfa366072e8e07e9158/src/main/resources/rdf_examples/edm.owl
  example: Event
  homepage: http://pro.europeana.eu/edm-documentation
  lov:
    description: The Europeana Data Model (EDM) is aimed at being an integration medium
      for collecting, connecting and enriching the descriptions provided by Europeana
      data providers.
    homepage: http://www.europeana.eu/schemas/edm/
    keywords:
    - Catalogs
    modified: '2013-05-20'
    name: Europeana Data Model vocabulary
    prefix: edm
    uri_prefix: http://www.europeana.eu/schemas/edm/$1
  mappings:
    lov: edm
  name: Europeana Data Model vocabulary
  prefix: edm
  repository: https://github.com/europeana/metis-schema
  uri_format: http://www.europeana.eu/schemas/edm/$1
edm.fibo:
  comment: FIBO is contructed as the union of many small ontologies, like sweetrealm,
    using hierarchical URIs based on the base URI prefix
  example: BE/MetadataBE/BEDomain
  mappings:
    tib: fibo
  prefix: edm.fibo
  repository: https://github.com/edmcouncil/fibo
  tib:
    description: FIBO defines the sets of things that are of interest in financial
      business applications and the ways that those things can relate to one another.
      In this way, FIBO can give meaning to any data (e.g., spreadsheets, relational
      databases, XML documents) that describe the business of finance
    download_rdf: https://raw.githubusercontent.com/edmcouncil/fibo/refs/heads/master/AboutFIBOProd.rdf
    homepage: https://github.com/edmcouncil/fibo
    keywords:
    - CoyPu
    - economics
    name: Financial Industry Business Ontology
    prefix: fibo
    tracker: https://github.com/edmcouncil/fibo/issues
    uri_format: https://spec.edmcouncil.org/fibo/ontology/AboutFIBOProd$1
    version.iri: https://spec.edmcouncil.org/fibo/ontology/20251001/AboutFIBOProd/
  uri_format: https://spec.edmcouncil.org/fibo/ontology/$1
educor:
  contact:
    email: ilkou@l3s.de
    github: eilkou
    name: Eleni Ilkou
    orcid: 0000-0002-4847-6177
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: An educational ontology for personalised recommendation learning systems
    that is based on learning path and user profile. It represents the key components
    for a personalised learning system based on our requirement analysis.
  download_rdf: https://github.com/tibonto/educor/raw/refs/heads/main/educor.ttl
  example: stri
  homepage: http://ontology.tib.eu/educor/
  license: CC0-1.0
  name: An Educational and Career-Oriented Recommendation Ontology
  prefix: educor
  publications:
  - doi: 10.1007/978-3-030-88361-4_32
    pmc: null
    pubmed: null
    title: 'EduCOR: An Educational and Career-Oriented Recommendation Ontology'
    year: 2021
  repository: https://github.com/tibonto/educor
  uri_format: https://github.com/tibonto/educor#$1
efo:
  aberowl:
    description: 'The Experimental Factor Ontology (EFO) is an application focused
      ontology modelling the experimental variables in multiple resources at the EBI
      and Open Targets. The ontology has been developed to increase the richness of
      the annotations that are currently made in resources and to promote consistent
      annotation, to facilitate automatic annotation and to integrate external data.
      The ontology pulls together classes from reference ontologies such as disease,
      cell line, cell type and anatomy and adds axiomatisation as necessary to connect
      areas such as disease to phenotype. Contact EFO users list for information:
      efo-users@lists.sourceforge.net'
    download_owl: http://aber-owl.net/media/ontologies/EFO/168/efo.owl
    homepage: http://www.ebi.ac.uk/efo
    name: Experimental Factor Ontology
    prefix: EFO
    version: '2.89'
  agroportal:
    contact:
      email: efo-users@lists.sourceforge.net
      name: EFO User List
    description: The Experimental Factor Ontology (EFO) provides a systematic description
      of many experimental variables available in EBI databases, and for projects
      such as the GWAS catalog. It combines parts of several biological ontologies,
      such as UBERON anatomy, ChEBI chemical compounds, and Cell Ontology. EFO is
      developed by the EMBL-EBI Samples, Phenotypes and Ontologies Team (SPOT). We
      also add terms for external users when requested., and for projects such as
      the NHGRI-EBI GWAS catalog. It combines parts of several biological ontologies,
      Cell Ontology and the Monarch Disease Ontology (MONDO). The scope of EFO is
      to support the annotation, analysis and visualization of data handled by many
      groups at the EBI and as the core ontology for Open Targets.
    example_uri: http://www.orpha.net/ORDO/Orphanet_1390
    homepage: http://www.ebi.ac.uk/efo/
    license: Apache 2.0 License
    name: Experimental Factor Ontology
    prefix: EFO
    repository: https://github.com/EBISPOT/efo
    version: 3.85.0
  biocontext:
    prefix: EFO
  biolink:
    is_identifiers: false
    is_obo: false
    prefix: EFO
    uri_format: http://www.ebi.ac.uk/efo/EFO_$1
  bioportal:
    contact:
      email: efo-users@ebi.ac.uk
      name: EFO User List
    description: 'The Experimental Factor Ontology (EFO) is an application focused
      ontology modelling the experimental variables in multiple resources at the EBI
      and Open Targets. The ontology has been developed to increase the richness of
      the annotations that are currently made in resources and to promote consistent
      annotation, to facilitate automatic annotation and to integrate external data.
      The ontology pulls together classes from reference ontologies such as disease,
      cell line, cell type and anatomy and adds axiomatisation as necessary to connect
      areas such as disease to phenotype. Contact EFO users list for information:
      efo-users@ebi.ac.uk.'
    homepage: http://www.ebi.ac.uk/efo
    name: Experimental Factor Ontology
    prefix: EFO
    version: 3.84.0
  cellosaurus:
    category: Experimental variables resources
    homepage: https://www.ebi.ac.uk/efo/
    name: Experimental Factor Ontology
    prefix: EFO
    uri_format: https://www.ebi.ac.uk/efo/$1
  contact:
    email: plwhetzel@gmail.com
    github: twhetzel
    name: Trish Whetzel
    orcid: 0000-0002-3458-4839
  download_obo: http://www.ebi.ac.uk/efo/efo.obo
  download_owl: http://www.ebi.ac.uk/efo/efo.owl
  example: '0005147'
  fairsharing:
    abbreviation: EFO
    contact:
      email: siiraa@ebi.ac.uk
      name: Sirarat Sarntivijai
      orcid: 0000-0002-2548-641X
    description: The Experimental Factor Ontology (EFO) is an application focused
      ontology modelling the experimental variables in multiple resources at the EBI
      and the Centre for Therapeutic Target Validation. The ontology has been developed
      to increase the richness of the annotations that are currently made in resources
      and to promote consistent annotation, to facilitate automatic annotation and
      to integrate external data. The ontology pulls together classes from reference
      ontologies such as disease, cell line, cell type and anatomy and adds axiomatisation
      as necessary to connect areas such as disease to phenotype.
    domains:
    - Experimental measurement
    - assay
    - study design independent variable
    - study design
    - genome-wide association study
    homepage: https://www.ebi.ac.uk/efo/
    license: Apache 2.0 License
    name: Experimental Factor Ontology
    prefix: FAIRsharing.1gr4tz
    publications:
    - doi: 10.1093/bioinformatics/btq099
      pubmed: '20200009'
      title: Modeling sample variables with an Experimental Factor Ontology
      year: 2010
    repository: https://github.com/EBISPOT/efo
    subjects:
    - Omics
    - Proteomics
    - Genomics
    user_defined_tags:
    - Experimental condition
  license: Apache-2.0
  logo: https://upload.wikimedia.org/wikipedia/en/d/d8/Logo_of_the_Experimental_Factor_Ontlogy.gif
  mappings:
    aberowl: EFO
    agroportal: EFO
    biocontext: EFO
    biolink: EFO
    bioportal: EFO
    cellosaurus: EFO
    fairsharing: FAIRsharing.1gr4tz
    miriam: efo
    n2t: efo
    ols: efo
    ontobee: EFO
    tib: efo
    wikidata: P11956
  miriam:
    deprecated: false
    description: The Experimental Factor Ontology (EFO) provides a systematic description
      of many experimental variables available in EBI databases. It combines parts
      of several biological ontologies, such as anatomy, disease and chemical compounds.
      The scope of EFO is to support the annotation, analysis and visualization of
      data handled by the EBI Functional Genomics Team.
    homepage: http://bioportal.bioontology.org/ontologies/EFO
    id: 00000391
    name: Experimental Factor Ontology
    namespaceEmbeddedInLui: false
    pattern: ^\d{7}$
    prefix: efo
    providers:
    - code: ebi
      description: EFO through Functional Genomics Group (EBI)
      homepage: https://www.ebi.ac.uk/efo/
      name: EFO through Functional Genomics Group (EBI)
      uri_format: https://www.ebi.ac.uk/efo/EFO_$1
    sampleId: 0004859
    uri_format: http://purl.bioontology.org/ontology/EFO/efo:EFO_$1
  n2t:
    description: The Experimental Factor Ontology (EFO) provides a systematic description
      of many experimental variables available in EBI databases. It combines parts
      of several biological ontologies, such as anatomy, disease and chemical compounds.
      The scope of EFO is to support the annotation, analysis and visualization of
      data handled by the EBI Functional Genomics Team.
    example: 0004859
    homepage: http://bioportal.bioontology.org/ontologies/EFO
    name: EFO through BioPortal
    namespaceEmbeddedInLui: false
    pattern: ^\d{7}$
    prefix: efo
    uri_format: http://purl.bioontology.org/ontology/EFO/efo:EFO_$1
  ols:
    contact: efo-users@lists.sourceforge.net
    description: The Experimental Factor Ontology (EFO) provides a systematic description
      of many experimental variables available in EBI databases, and for projects
      such as the NHGRI-EBI GWAS catalog. It combines parts of several biological
      ontologies, such as UBERON anatomy, ChEBI chemical compounds, Cell Ontology
      and the Monarch Disease Ontology (MONDO). The scope of EFO is to support the
      annotation, analysis and visualization of data handled by many groups at the
      EBI and as the core ontology for Open Targets.
    download_owl: http://www.ebi.ac.uk/efo/efo.owl
    homepage: http://www.ebi.ac.uk/efo
    name: Experimental Factor Ontology
    prefix: efo
    uri_format: http://www.ebi.ac.uk/efo/EFO_$1
    version: 3.85.0
    version.iri: http://www.ebi.ac.uk/efo/releases/v3.85.0/efo.owl
  ontobee:
    library: Not Specified/No
    name: Experimental Factor Ontology
    prefix: EFO
  owners:
  - name: European Bioinformatics Institute
    partnered: false
    ror: 02catss52
    wikidata: null
  preferred_prefix: EFO
  prefix: efo
  providers:
  - code: ols.curie
    description: OLS via CURIE
    example: null
    first_party: null
    homepage: https://www.ebi.ac.uk/ols
    name: OLS
    publications: null
    status: null
    uri_format: http://www.ebi.ac.uk/ols/ontologies/efo/terms?short_form=EFO_$1
  publications:
  - doi: 10.1093/bioinformatics/btq099
    pmc: PMC2853691
    pubmed: '20200009'
    title: Modeling sample variables with an Experimental Factor Ontology
    year: 2010
  - doi: 10.1093/bioinformatics/btq099
    pmc: null
    pubmed: '20200009'
    title: Modeling sample variables with an Experimental Factor Ontology
    year: 2010
  - doi: 10.1093/bioinformatics/btq099
    pmc: null
    pubmed: '20200009'
    title: Modeling sample variables with an Experimental Factor Ontology
    year: 2010
  repository: https://github.com/EBISPOT/efo
  tib:
    contact: efo-users@ebi.ac.uk
    description: The Experimental Factor Ontology (EFO) provides a systematic description
      of many experimental variables available in EBI databases, and for external
      projects such as the NHGRI GWAS catalogue. It combines parts of several biological
      ontologies, such as anatomy, disease and chemical compounds. The scope of EFO
      is to support the annotation, analysis and visualization of data handled by
      many groups at the EBI and as the core ontology for OpenTargets.org
    download_owl: http://www.ebi.ac.uk/efo/efo.owl
    homepage: https://www.ebi.ac.uk/efo/
    keywords:
    - NFDI4CHEM
    - ESS
    - DataPLANT
    - life sciences, biology
    - medicine
    - earth sciences
    name: Experimental Factor Ontology
    prefix: efo
    version.iri: http://www.ebi.ac.uk/efo/releases/v3.83.0/efo.owl
  uri_format: http://www.ebi.ac.uk/efo/EFO_$1
  wikidata:
    description: identifier for an experimental factor in the Experimental Factor
      Ontology
    example:
    - 0000408
    - 0003894
    - 0008559
    homepage: https://www.ebi.ac.uk/efo/
    name: Experimental Factor Ontology ID
    prefix: P11956
    uri_format: https://www.ebi.ac.uk/efo/EFO_$1
ega:
  cellosaurus:
    category: Sequence databases
    homepage: https://ega-archive.org/
    name: European Genome-Phenome Archive
    prefix: EGA
    uri_format: https://ega-archive.org/studies/$1
  edam:
    description: Identifier of an entry from the EGA database.
    name: EGA
    obsolete: false
    prefix: '2383'
  mappings:
    cellosaurus: EGA
    edam: '2383'
    miriam: ega
  miriam:
    deprecated: false
    description: The European Genome-phenome Archive (EGA) is a global network for
      permanent archiving and sharing of personally identifiable genetic, phenotypic,
      and clinical data generated for the purposes of biomedical research projects
      or in the context of research-focused healthcare systems. Jointly managed by
      the European Bioinformatics Institute (EMBL-EBI) in Cambridge (UK) and the Centre
      for Genomic Regulation (CRG) in Barcelona.
    homepage: https://ega-archive.org/
    id: '00001202'
    name: European Genome-phenome Archive
    namespaceEmbeddedInLui: false
    pattern: ^EGA[SCPNRXZDBF][0-9]{11}$
    prefix: ega
    sampleId: EGAD00001008392
    uri_format: https://ega-archive.org/identifiers/$1
  prefix: ega
ega.dataset:
  biocontext:
    prefix: EGA.DATASET
  contact:
    email: tk2@ebi.ac.uk
    github: tk2
    name: Thomas Keane
    orcid: 0000-0001-7532-6898
  fairsharing:
    abbreviation: EGA
    description: The European Genome-phenome Archive (EGA) is a service for permanent
      archiving and sharing of personally identifiable genetic, phenotypic, and clinical
      data generated for the purposes of biomedical research projects or in the context
      of research-focused healthcare systems. Access to data must be approved by the
      specified Data Access Committee (DAC).
    homepage: https://ega-archive.org/
    name: The European Genome-phenome Archive
    prefix: FAIRsharing.mya1ff
    publications:
    - doi: 10.1038/ng.3312
      pubmed_id: 26111507
      title: The European Genome-phenome Archive of human data consented for biomedical
        research.
    - doi: 10.1093/nar/gkab1059
      pubmed_id: null
      title: The European Genome-phenome Archive in 2021
    subjects:
    - Genomics
    - Clinical Studies
    - Phenomics
    - Biomedical Science
    - Biology
    twitter: EGAarchive
  homepage: https://ega-archive.org/
  mappings:
    biocontext: EGA.DATASET
    fairsharing: FAIRsharing.mya1ff
    miriam: ega.dataset
    n2t: ega.dataset
    re3data: r3d100011242
  miriam:
    deprecated: false
    description: The EGA is a service for permanent archiving and sharing of all types
      of personally identifiable genetic and phenotypic data resulting from biomedical
      research projects. The EGA contains exclusive data collected from individuals
      whose consent agreements authorize data release only for specific research use
      or to bona fide researchers. Strict protocols govern how information is managed,
      stored and distributed by the EGA project. This collection references 'Datasets'.
    homepage: https://www.ebi.ac.uk/ega/dataset
    id: '00000512'
    name: European Genome-phenome Archive Dataset
    namespaceEmbeddedInLui: false
    pattern: ^EGAD\d{11}$
    prefix: ega.dataset
    providers:
    - code: omicsdi
      description: EGA Dataset through OmicsDI
      homepage: https://www.omicsdi.org/
      name: EGA Dataset through OmicsDI
      uri_format: https://www.omicsdi.org/dataset/ega/$1
    sampleId: EGAD00000000001
    uri_format: https://www.ebi.ac.uk/ega/datasets/$1
  n2t:
    description: The EGA is a service for permanent archiving and sharing of all types
      of personally identifiable genetic and phenotypic data resulting from biomedical
      research projects. The EGA contains exclusive data collected from individuals
      whose consent agreements authorize data release only for specific research use
      or to bona fide researchers. Strict protocols govern how information is managed,
      stored and distributed by the EGA project. This collection references 'Datasets'.
    example: EGAD00000000001
    homepage: https://www.ebi.ac.uk/ega/dataset
    name: EGA Dataset at European Bioinformatics Institute
    namespaceEmbeddedInLui: false
    pattern: ^EGAD\d{11}$
    prefix: ega.dataset
    uri_format: https://www.ebi.ac.uk/ega/datasets/$1
  owners:
  - name: European Bioinformatics Institute
    partnered: false
    ror: 02catss52
    wikidata: null
  prefix: ega.dataset
  publications:
  - doi: 10.1093/nar/gkab1059
    pmc: PMC8728218
    pubmed: '34791407'
    title: The European Genome-phenome Archive in 2021
    year: 2022
  - doi: 10.1038/ng.3312
    pmc: PMC5426533
    pubmed: '26111507'
    title: The European Genome-phenome Archive of human data consented for biomedical
      research
    year: 2015
  - doi: 10.1038/ng.3312
    pmc: null
    pubmed: null
    title: The European Genome-phenome Archive of human data consented for biomedical
      research.
    year: null
  - doi: 10.1093/nar/gkab1059
    pmc: null
    pubmed: null
    title: The European Genome-phenome Archive in 2021
    year: null
  re3data:
    description: "The European Genome-phenome Archive (EGA) is designed to be a repository\
      \ for all types of sequence and genotype experiments, including case-control,\
      \ population, and family studies. We will include SNP and CNV genotypes from\
      \ array based methods and genotyping done with re-sequencing methods. \nThe\
      \ EGA will serve as a permanent archive that will archive several levels of\
      \ data including the raw data (which could, for example, be re-analysed in the\
      \ future by other algorithms) as well as the genotype calls provided by the\
      \ submitters. We are developing data mining and access tools for the database.\n\
      For controlled access data, the EGA will provide the necessary security required\
      \ to control access, and maintain patient confidentiality, while providing access\
      \ to those researchers and clinicians authorised to view the data. In all cases,\
      \ data access decisions will be made by the appropriate data access-granting\
      \ organisation (DAO) and not by the EGA. The DAO will normally be the same organisation\
      \ that approved and monitored the initial study protocol or a designate of this\
      \ approving organisation. The European Genome-phenome Archive (EGA) allows you\
      \ to explore datasets from genomic studies, provided by a range of data providers.\
      \ Access to datasets must be approved by the specified Data Access Committee\
      \ (DAC)."
    doi: 10.17616/R3W619
    homepage: https://ega-archive.org/
    name: The European Genome-phenome Archive
    prefix: r3d100011242
    synonyms:
    - EGA
ega.study:
  biocontext:
    prefix: EGA.STUDY
  mappings:
    biocontext: EGA.STUDY
    miriam: ega.study
    n2t: ega.study
  miriam:
    deprecated: false
    description: The EGA is a service for permanent archiving and sharing of all types
      of personally identifiable genetic and phenotypic data resulting from biomedical
      research projects. The EGA contains exclusive data collected from individuals
      whose consent agreements authorize data release only for specific research use
      or to bona fide researchers. Strict protocols govern how information is managed,
      stored and distributed by the EGA project. This collection references 'Studies'
      which are experimental investigations of a particular phenomenon, often drawn
      from different datasets.
    homepage: https://www.ebi.ac.uk/ega/studies
    id: '00000511'
    name: European Genome-phenome Archive Study
    namespaceEmbeddedInLui: false
    pattern: ^EGAS\d{11}$
    prefix: ega.study
    sampleId: EGAS00000000001
    uri_format: https://www.ebi.ac.uk/ega/studies/$1
  n2t:
    description: The EGA is a service for permanent archiving and sharing of all types
      of personally identifiable genetic and phenotypic data resulting from biomedical
      research projects. The EGA contains exclusive data collected from individuals
      whose consent agreements authorize data release only for specific research use
      or to bona fide researchers. Strict protocols govern how information is managed,
      stored and distributed by the EGA project. This collection references 'Studies'
      which are experimental investigations of a particular phenomenon, often drawn
      from different datasets.
    example: EGAS00000000001
    homepage: https://www.ebi.ac.uk/ega/studies
    name: EGA Study at European Bioinformatics Institute
    namespaceEmbeddedInLui: false
    pattern: ^EGAS\d{11}$
    prefix: ega.study
    uri_format: https://www.ebi.ac.uk/ega/studies/$1
  prefix: ega.study
eggnog:
  biocontext:
    prefix: EGGNOG
  contact:
    email: j.huerta@csic.es
    github: jhcepas
    name: Jaime Huerta-Cepas
    orcid: 0000-0003-4195-5025
  fairsharing:
    abbreviation: eggNOG
    description: 'eggNOG (evolutionary genealogy of genes: Non-supervised Orthologous
      Groups) is a database of orthologous groups of genes. The orthologous groups
      are annotated with functional description lines (derived by identifying a common
      denominator for the genes based on their various annotations), with functional
      categories (i.e derived from the original COG/KOG categories).'
    homepage: http://eggnog.embl.de
    name: 'Evolutionary Genealogy of Genes: Non-supervised Orthologous Groups'
    prefix: FAIRsharing.j1wj7d
    publications:
    - doi: 10.1093/nar/gkp951
      pubmed_id: 19900971
      title: 'eggNOG v2.0: extending the evolutionary genealogy of genes with enhanced
        non-supervised orthologous groups, species and functional annotations.'
    - doi: 10.1093/nar/gkm796
      pubmed_id: 17942413
      title: 'eggNOG: automated construction and annotation of orthologous groups
        of genes.'
    subjects:
    - Life Science
  mappings:
    biocontext: EGGNOG
    fairsharing: FAIRsharing.j1wj7d
    miriam: eggnog
    n2t: eggnog
    prefixcommons: eggnog
    uniprot: DB-0152
  miriam:
    deprecated: true
    description: 'eggNOG (evolutionary genealogy of genes: Non-supervised Orthologous
      Groups) is a database of orthologous groups of genes. The orthologous groups
      are annotated with functional description lines (derived by identifying a common
      denominator for the genes based on their various annotations), with functional
      categories (i.e derived from the original COG/KOG categories).'
    homepage: http://eggnog.embl.de/version_3.0/
    id: '00000201'
    name: eggNOG
    namespaceEmbeddedInLui: false
    pattern: ^\w+$
    prefix: eggnog
    sampleId: veNOG12876
    uri_format: http://eggnog.embl.de/version_3.0/cgi/search.py?search_term_0=$1
  n2t:
    description: 'eggNOG (evolutionary genealogy of genes: Non-supervised Orthologous
      Groups) is a database of orthologous groups of genes. The orthologous groups
      are annotated with functional description lines (derived by identifying a common
      denominator for the genes based on their various annotations), with functional
      categories (i.e derived from the original COG/KOG categories).'
    example: veNOG12876
    homepage: http://eggnog.embl.de/version_3.0/
    name: eggNOG Version 3 at European Molecular Biology Laboratory
    namespaceEmbeddedInLui: false
    pattern: ^\w+$
    prefix: eggnog
    uri_format: http://eggnog.embl.de/version_3.0/cgi/search.py?search_term_0=$1
  prefix: eggnog
  prefixcommons:
    description: 'eggNOG (evolutionary genealogy of genes: Non-supervised Orthologous
      Groups) is a database of orthologous groups of genes. The orthologous groups
      are annotated with functional description lines (derived by identifying a common
      denominator for the genes based on their various annotations), with functional
      categories (i.e derived from the original COG/KOG categories).'
    example: NOG80852
    homepage: http://eggnog.embl.de
    keywords:
    - gene
    name: 'Evolutionary Genealogy of Genes: Non-supervised Orthologous Groups'
    pattern: ^\w+$
    prefix: eggnog
    pubmed_ids:
    - '19900971'
    uri_format: http://eggnog.embl.de/version_3.0/cgi/search.py?search_term_0=$1
  publications:
  - doi: 10.1093/nar/gkp951
    pmc: PMC2808932
    pubmed: '19900971'
    title: 'eggNOG v2.0: extending the evolutionary genealogy of genes with enhanced
      non-supervised orthologous groups, species and functional annotations'
    year: 2009
  - doi: 10.1093/nar/gkm796
    pmc: PMC2238944
    pubmed: '17942413'
    title: 'eggNOG: automated construction and annotation of orthologous groups of
      genes'
    year: 2007
  uniprot:
    abbreviation: eggNOG
    category: Phylogenomic databases
    homepage: http://eggnogdb.embl.de/
    name: evolutionary genealogy of genes
    prefix: DB-0152
    publications:
    - doi: 10.1093/nar/gkac1022
      pubmed: '36399505'
    uri_format: http://eggnog.embl.de/search/ogs/$1
ehda:
  aberowl:
    description: A structured controlled vocabulary of stage-specific anatomical structures
      of the human. It has been designed to mesh with the mouse anatomy and incorporates
      each Carnegie stage of development (CS1-20). The timed version of the human
      developmental anatomy ontology gives all the tissues present at each Carnegie
      Stage (CS) of human development (1-20) linked by a part-of rule. Each term is
      mentioned only once so that the embryo at each stage can be seen as the simple
      sum of its parts. Users should note that tissues that are symmetric (e.g. eyes,
      ears, limbs) are only mentioned once.
    download_obo: http://aber-owl.net/media/ontologies/EHDA/6/ehda.obo
    homepage: http://genex.hgu.mrc.ac.uk/
    name: Human Developmental Anatomy Ontology, timed version
    prefix: EHDA
    version: unknown
  biocontext:
    prefix: EHDA
  bioportal:
    contact:
      email: J.Bard@ed.ac.uk
      name: Jonathan Bard
    description: A structured controlled vocabulary of stage-specific anatomical structures
      of the human. It has been designed to mesh with the mouse anatomy and incorporates
      each Carnegie stage of development (CS1-20). The timed version of the human
      developmental anatomy ontology gives all the tissues present at each Carnegie
      Stage (CS) of human development (1-20) linked by a part-of rule. Each term is
      mentioned only once so that the embryo at each stage can be seen as the simple
      sum of its parts. Users should note that tissues that are symmetric (e.g. eyes,
      ears, limbs) are only mentioned once.
    homepage: http://obofoundry.org/ontology/ehda.html
    name: Human Developmental Anatomy Ontology, timed version
    prefix: EHDA
    version: unknown
  example: '1'
  mappings:
    aberowl: EHDA
    biocontext: EHDA
    bioportal: EHDA
    obofoundry: ehda
    prefixcommons: ehda
    wikidata.entity: Q114677884
  obofoundry:
    contact: J.Bard@ed.ac.uk
    contact.label: Jonathan Bard
    deprecated: true
    domain: anatomy and development
    homepage: http://genex.hgu.mrc.ac.uk/
    name: Human developmental anatomy, timed version
    prefix: ehda
  pattern: ^\d+$
  prefix: ehda
  prefixcommons:
    bioportal: '1022'
    description: A structured controlled vocabulary of stage-specific anatomical structures
      of the human. It has been designed to mesh with the mouse anatomy and incorporates
      each Carnegie stage of development (CS1-20).
    example: EHDAA_1
    homepage: http://genex.hgu.mrc.ac.uk/
    keywords:
    - obo
    - anatomy
    - development
    - human
    name: Human developmental anatomy, timed version
    pattern: ^EHDA_\d+$
    prefix: ehda
ehdaa:
  aberowl:
    description: A structured controlled vocabulary of stage-specific anatomical structures
      of the human. It has been designed to mesh with the mouse anatomy and incorporates
      each Carnegie stage of development (CS1-20). The abstract version of the human
      developmental anatomy ontology compresses all the tissues present over Carnegie
      stages 1-20 into a single hierarchy. The heart, for example, is present from
      Carnegie Stage 9 onwards and is thus represented by 12 EHDA IDs (one for each
      stage). In the abstract mouse, it has a single ID so that the abstract term
      given as just <i>heart</i> really means <i>heart (CS 9-20)</i>. Timing details
      will be added to the abstract version of the ontology in a future release.
    download_obo: http://aber-owl.net/media/ontologies/EHDAA/6/ehdaa.obo
    homepage: http://genex.hgu.mrc.ac.uk/
    name: Human Developmental Anatomy Ontology, abstract version 1
    prefix: EHDAA
    version: unknown
  biocontext:
    prefix: EHDAA
  bioportal:
    contact:
      email: J.Bard@ed.ac.uk
      name: Jonathan Bard
    description: A structured controlled vocabulary of stage-specific anatomical structures
      of the human. It has been designed to mesh with the mouse anatomy and incorporates
      each Carnegie stage of development (CS1-20). The abstract version of the human
      developmental anatomy ontology compresses all the tissues present over Carnegie
      stages 1-20 into a single hierarchy. The heart, for example, is present from
      Carnegie Stage 9 onwards and is thus represented by 12 EHDA IDs (one for each
      stage). In the abstract mouse, it has a single ID so that the abstract term
      given as just <i>heart</i> really means <i>heart (CS 9-20)</i>. Timing details
      will be added to the abstract version of the ontology in a future release.
    homepage: http://obofoundry.org/ontology/ehdaa.html
    name: Human Developmental Anatomy Ontology, abstract version 1
    prefix: EHDAA
    version: unknown
  example: '1'
  mappings:
    aberowl: EHDAA
    biocontext: EHDAA
    bioportal: EHDAA
    obofoundry: ehdaa
    prefixcommons: ehdaa
    wikidata.entity: Q114677885
  obofoundry:
    contact: J.Bard@ed.ac.uk
    contact.label: Jonathan Bard
    deprecated: true
    domain: anatomy and development
    name: Human developmental anatomy, abstract version
    prefix: ehdaa
  pattern: ^\d+$
  prefix: ehdaa
  prefixcommons:
    bioportal: '1021'
    description: A structured controlled vocabulary of stage-specific anatomical structures
      of the human. It has been designed to mesh with the mouse anatomy and incorporates
      each Carnegie stage of development (CS1-20).
    example: EHDAA_573
    homepage: http://genex.hgu.mrc.ac.uk/
    keywords:
    - obo
    - anatomy
    - development
    - human
    name: Human developmental anatomy, abstract version
    pattern: ^EHDAA_\d+$
    prefix: ehdaa
    synonyms:
    - hdaa
ehdaa2:
  aberowl:
    description: A structured controlled vocabulary of stage-specific anatomical structures
      of the developing human.
    download_owl: http://aber-owl.net/media/ontologies/EHDAA2/33/ehdaa2.owl
    homepage: http://genex.hgu.mrc.ac.uk/
    name: Human developmental anatomy, abstract
    prefix: EHDAA2
  biocontext:
    prefix: EHDAA2
  bioportal:
    contact:
      email: J.Bard@ed.ac.uk
      name: EMAP Administrators
    description: A structured controlled vocabulary of stage-specific anatomical structures
      of the human. It has been designed to mesh with the mouse anatomy and incorporates
      each Carnegie stage of development (CS1-20). The abstract version of the human
      developmental anatomy ontology compresses all the tissues present over Carnegie
      stages 1-20 into a single hierarchy. The heart, for example, is present from
      Carnegie Stage 9 onwards and is thus represented by 12 EHDA IDs (one for each
      stage). In the abstract mouse, it has a single ID so that the abstract term
      given as just <i>heart</i> really means <i>heart (CS 9-20)</i>. Timing details
      will be added to the abstract version of the ontology in a future release.
    homepage: http://genex.hgu.mrc.ac.uk/
    name: Human Developmental Anatomy Ontology, abstract version 2
    prefix: EHDAA2
    version: releases/2024-01-11
  example: '0000000'
  fairsharing:
    abbreviation: EHDAA2
    description: 'The EHDAA2 ontology is a human developmental anatomy covering the
      first 49 days [Carnegie stages (CS)1–20], primarily structured around the parts
      of organ systems and their development. The ontology includes more than 2000
      anatomical entities (AEs) that range from the whole embryo, through organ systems
      and organ parts down to simple or leaf tissues (groups of cells with the same
      morphological phenotype), as well as features such as cavities. It represents
      a complete rebuilding of the EHDA intended to meet current standards. Please
      note that, while available, the OBO Foundry considers this resource to be inactive,
      therefore please take this into consideration when reviewing this resource.
      They state: "The intention has been to include as much information about human
      developmental anatomy as is practical and as is available in the literature.
      This ontology has been inactive for several years, as of 2022. As of yet there
      is no complete replacement ontology, but OBO users may want to consider potential
      alternatives: 1. HsapDv contains human-specific embryonic stage terms for Carnegie
      stages; 2. Uberon: includes embryonic anatomy and developmental stage relations,
      but is more taxonomically general than EHDAA2, and may be less complete and
      less precise. Uberon includes EHDAA2 in its composite metazoan build. 3. FMA:
      now includes some human embryonic anatomy, but is constructed on different principles
      than EHDAA2, and may be less complete and less precise in places."

      '
    domains:
    - animal organ development
    - life cycle stage
    homepage: http://obofoundry.org/ontology/ehdaa2.html
    name: Edinburgh human developmental anatomy abstract 2
    prefix: FAIRsharing.7zxrs6
    publications:
    - doi: 10.1111/j.1469-7580.2012.01566.x
      pubmed: '22973865'
      title: A new ontology (structured hierarchy) of human developmental anatomy
        for the first 7 weeks (Carnegie stages 1-20)
      year: 2012
    subjects:
    - Anatomy
    - Biomedical Science
  mappings:
    aberowl: EHDAA2
    biocontext: EHDAA2
    bioportal: EHDAA2
    fairsharing: FAIRsharing.7zxrs6
    obofoundry: ehdaa2
    ols: ehdaa2
    ontobee: EHDAA2
    wikidata.entity: Q114667913
  obofoundry:
    contact: J.Bard@ed.ac.uk
    contact.label: Jonathan Bard
    depends_on:
    - aeo
    - caro
    - cl
    deprecated: true
    description: A structured controlled vocabulary of stage-specific anatomical structures
      of the developing human.
    domain: anatomy and development
    download.obo: http://purl.obolibrary.org/obo/ehdaa2.obo
    download.owl: http://purl.obolibrary.org/obo/ehdaa2.owl
    homepage: https://github.com/obophenotype/human-developmental-anatomy-ontology
    license: CC BY 4.0
    license.url: https://creativecommons.org/licenses/by/4.0/
    name: Human developmental anatomy, abstract
    prefix: ehdaa2
    publications:
    - id: https://www.ncbi.nlm.nih.gov/pubmed/22973865
      title: A new ontology (structured hierarchy) of human developmental anatomy
        for the first 7 weeks (Carnegie stages 1-20).
    repository: https://github.com/obophenotype/human-developmental-anatomy-ontology
  ols:
    description: A structured controlled vocabulary of stage-specific anatomical structures
      of the developing human.
    download_owl: http://purl.obolibrary.org/obo/ehdaa2.owl
    homepage: https://github.com/obophenotype/human-developmental-anatomy-ontology
    name: Human developmental anatomy, abstract
    prefix: ehdaa2
    tracker: https://github.com/obophenotype/human-developmental-anatomy-ontology/issues
  ontobee:
    library: Library
    name: Human developmental anatomy, abstract
    prefix: EHDAA2
  pattern: ^\d{7}$
  prefix: ehdaa2
  publications:
  - doi: 10.1111/j.1469-7580.2012.01566.x
    pmc: PMC3482348
    pubmed: '22973865'
    title: A new ontology (structured hierarchy) of human developmental anatomy for
      the first 7 weeks (Carnegie stages 1-20)
    year: 2012
  - doi: null
    pmc: null
    pubmed: '22973865'
    title: A new ontology (structured hierarchy) of human developmental anatomy for
      the first 7 weeks (Carnegie stages 1-20)
    year: null
  - doi: 10.1111/j.1469-7580.2012.01566.x
    pmc: null
    pubmed: '22973865'
    title: A new ontology (structured hierarchy) of human developmental anatomy for
      the first 7 weeks (Carnegie stages 1-20)
    year: 2012
  synonyms:
  - EHDAA2_RETIRED
  - HDAA2
  - RETIRED_EHDAA2
ejprd:
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: This ontology is designed to support data search, retrieval and information
    identification in the EJP-RD catalogs which covers the registries and biobanks
    for rare diseases. (from repository)
  download_owl: https://github.com/EBISPOT/EJP-Ontology/raw/refs/heads/master/ejp-rd.owl
  example: alternative_term
  homepage: https://github.com/EBISPOT/EJP-Ontology
  logo: https://github.com/EBISPOT/EJP-Ontology/raw/master/docs/ejp.jpg
  name: European Joint Programme for Rare Disease Ontology
  prefix: ejprd
  repository: https://github.com/EBISPOT/EJP-Ontology
  uri_format: http://purl.org/ejp-rd/vocabulary/$1
eli:
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: An ontology to describe legislation, based on the FRBR model, that
    encodes the ELI metadata fields.
  example: InForce
  homepage: https://op.europa.eu/en/web/eu-vocabularies/eli
  lov:
    description: Transposition of the ELI metadata fields into an OWL ontology
    homepage: http://data.europa.eu/eli/ontology
    keywords:
    - Contracts
    - FRBR
    modified: '2018-05-23'
    name: The European Legislation Identifier
    prefix: eli
    uri_prefix: http://data.europa.eu/eli/ontology#$1
  mappings:
    lov: eli
  name: ELI Metadata Ontology
  prefix: eli
  uri_format: http://data.europa.eu/eli/ontology#$1
elm:
  biocontext:
    prefix: ELM
  contact:
    email: toby.gibson@embl.de
    github: null
    name: Toby J Gibson
    orcid: 0000-0003-0657-5166
  fairsharing:
    abbreviation: ELM
    description: This computational biology resource mainly focuses on annotation
      and detection of eukaryotic linear motifs (ELMs) by providing both a repository
      of annotated motif data and an exploratory tool for motif prediction. ELMs,
      or short linear motifs (SLiMs), are compact protein interaction sites composed
      of short stretches of adjacent amino acids.
    homepage: http://elm.eu.org
    name: Eukaryotic Linear Motifs
    prefix: FAIRsharing.rj3kj5
    publications:
    - doi: 10.1093/nar/gkg545
      pubmed_id: 12824381
      title: 'ELM server: A new resource for investigating short functional sites
        in modular eukaryotic proteins.'
    - doi: 10.1093/nar/gkr1064
      pubmed_id: 22110040
      title: ELM--the database of eukaryotic linear motifs.
    - doi: 10.1093/nar/gkv1291
      pubmed_id: 26615199
      title: ELM 2016--data update and new functionality of the eukaryotic linear
        motif resource.
    subjects:
    - Life Science
  mappings:
    biocontext: ELM
    fairsharing: FAIRsharing.rj3kj5
    miriam: elm
    n2t: elm
    uniprot: DB-0223
  miriam:
    deprecated: false
    description: Linear motifs are short, evolutionarily plastic components of regulatory
      proteins. Mainly focused on the eukaryotic sequences,the Eukaryotic Linear Motif
      resource (ELM) is a database of curated motif classes and instances.
    homepage: http://elm.eu.org/
    id: '00000250'
    name: ELM
    namespaceEmbeddedInLui: false
    pattern: ^[A-Za-z_0-9]+$
    prefix: elm
    sampleId: CLV_MEL_PAP_1
    uri_format: http://elm.eu.org/elms/elmPages/$1.html
  n2t:
    description: Linear motifs are short, evolutionarily plastic components of regulatory
      proteins. Mainly focused on the eukaryotic sequences,the Eukaryotic Linear Motif
      resource (ELM) is a database of curated motif classes and instances.
    example: CLV_MEL_PAP_1
    homepage: http://elm.eu.org/
    name: ELM at EMBL (Germany)
    namespaceEmbeddedInLui: false
    pattern: ^[A-Za-z_0-9]+$
    prefix: elm
    uri_format: http://elm.eu.org/elms/elmPages/$1.html
  name: Eukaryotic Linear Motif Resource
  prefix: elm
  publications:
  - doi: 10.1093/nar/gkz1030
    pmc: PMC7145657
    pubmed: '31680160'
    title: ELM-the eukaryotic linear motif resource in 2020
    year: 2020
  - doi: 10.1093/nar/gkv1291
    pmc: PMC4702912
    pubmed: '26615199'
    title: ELM 2016--data update and new functionality of the eukaryotic linear motif
      resource
    year: 2015
  - doi: 10.1093/nar/gkr1064
    pmc: PMC3245074
    pubmed: '22110040'
    title: ELM--the database of eukaryotic linear motifs
    year: 2011
  - doi: 10.1093/nar/gkg545
    pmc: PMC168952
    pubmed: '12824381'
    title: 'ELM server: A new resource for investigating short functional sites in
      modular eukaryotic proteins'
    year: 2003
  - doi: 10.1093/nar/gkg545
    pmc: null
    pubmed: null
    title: 'ELM server: A new resource for investigating short functional sites in
      modular eukaryotic proteins.'
    year: null
  - doi: 10.1093/nar/gkr1064
    pmc: null
    pubmed: null
    title: ELM--the database of eukaryotic linear motifs.
    year: null
  - doi: 10.1093/nar/gkv1291
    pmc: null
    pubmed: null
    title: ELM 2016--data update and new functionality of the eukaryotic linear motif
      resource.
    year: null
  - doi: 10.1093/nar/gkab975
    pmc: null
    pubmed: '34718738'
    title: null
    year: null
  - doi: 10.1093/nar/gkg545
    pmc: null
    pubmed: null
    title: 'ELM server: A new resource for investigating short functional sites in
      modular eukaryotic proteins.'
    year: null
  - doi: 10.1093/nar/gkr1064
    pmc: null
    pubmed: null
    title: ELM--the database of eukaryotic linear motifs.
    year: null
  - doi: 10.1093/nar/gkv1291
    pmc: null
    pubmed: null
    title: ELM 2016--data update and new functionality of the eukaryotic linear motif
      resource.
    year: null
  - doi: 10.1093/nar/gkab975
    pmc: null
    pubmed: '34718738'
    title: null
    year: null
  - doi: 10.1093/nar/gkg545
    pmc: null
    pubmed: null
    title: 'ELM server: A new resource for investigating short functional sites in
      modular eukaryotic proteins.'
    year: null
  - doi: 10.1093/nar/gkr1064
    pmc: null
    pubmed: null
    title: ELM--the database of eukaryotic linear motifs.
    year: null
  - doi: 10.1093/nar/gkv1291
    pmc: null
    pubmed: null
    title: ELM 2016--data update and new functionality of the eukaryotic linear motif
      resource.
    year: null
  - doi: 10.1093/nar/gkab975
    pmc: null
    pubmed: '34718738'
    title: null
    year: null
  uniprot:
    abbreviation: ELM
    category: Protein-protein interaction databases
    homepage: http://elm.eu.org/
    name: The Eukaryotic Linear Motif resource for Functional Sites in Proteins
    prefix: DB-0223
    publications:
    - doi: 10.1093/nar/gkab975
      pubmed: '34718738'
    uri_format: http://elm.eu.org/instances.html?q=$1
elsst:
  bartoc:
    abbreviation: ELSST
    description: 'The European Language Social Science Thesaurus (ELSST) is a broad-based,
      multilingual thesaurus for the social sciences. It is owned and published by
      the Consortium of European Social Science Data Archives (CESSDA) and its national
      Service Providers. The thesaurus consists of over 3,400 concepts and covers
      the core social science disciplines: politics, sociology, economics, education,
      law, crime, demography, health, employment, information and communication technology,
      and environmental science.

      ELSST is currently available in 15 languages: Czech, Dutch, English, Finnish,
      French, German, Greek, Hungarian, Icelandic, Lithuanian, Norwegian, Romanian,
      Slovenian, Spanish, and Swedish.

      Work for the latest release of ELSST (Release 6-2025) has focused on updating
      the DEMOGRAPHY hierarchy and related terms, in consultation with international
      demography experts. Changes include additional terms to improve coverage of
      vital statistics (such as births, marriages, cohabitation, civil partnerships
      and deaths) and updated definitions for existing terms.

      ELSST is also used for data discovery within CESSDA and facilitates access to
      data resources across Europe, independent of domain, resource, language or vocabulary.
      For ease of use, a bidirectional link has been established between ELSST and
      the CESSDA Data Catalogue (CDC), which contains descriptions of more than 40,000
      data collections held by CESSDA’s Service Providers, originating from over 20
      European countries.'
    homepage: https://elsst.cessda.eu/
    license: CC BY-SA 4.0
    name: European Language Social Science Thesaurus
    prefix: '14'
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: 'The European Language Social Science Thesaurus (ELSST) is a broad-based,
    multilingual thesaurus for the social sciences. It is owned and published by the
    Consortium of European Social Science Data Archives (CESSDA) and its national
    Service Providers. The thesaurus consists of over 3,000 concepts and covers the
    core social science disciplines: politics, sociology, economics, education, law,
    crime, demography, health, employment, information and communication technology
    and, increasingly, environmental science. [from homepage]'
  example: ffdd3a7e-f82e-4600-98b1-20402e74b0a6
  fairsharing:
    abbreviation: ELSST
    contact:
      email: alen.vodopijevec@cessda.eu
      name: Alen Vodopijevec
      orcid: 0000-0003-1003-0281
    description: 'The European Language Social Science Thesaurus (ELSST) is a broad-based,
      multilingual thesaurus for the social sciences. It is owned and published by
      the Consortium of European Social Science Data Archives (CESSDA) and its national
      Service Providers. The thesaurus consists of over 3,300 concepts and covers
      the core social science disciplines: politics, sociology, economics, education,
      law, crime, demography, health, employment, information, communication technology,
      and environmental science.

      ELSST is used for data discovery within CESSDA and facilitates access to data
      resources across Europe, independent of domain, resource, language, or vocabulary.


      ELSST is currently available in 16 languages: Danish, Dutch, Czech, English,
      Finnish, French, German, Greek, Hungarian, Icelandic, Lithuanian, Norwegian,
      Romanian, Slovenian, Spanish, and Swedish'
    homepage: https://thesauri.cessda.eu/en/
    license: CC BY-SA 4.0
    logo: https://api.fairsharing.org/rails/active_storage/blobs/redirect/eyJfcmFpbHMiOnsibWVzc2FnZSI6IkJBaHBBaFFDIiwiZXhwIjpudWxsLCJwdXIiOiJibG9iX2lkIn19--ee784912b873e09e9d907ebf15f37fb26c0ce50d/Screenshot%20from%202022-11-22%2021-00-34.png?disposition=inline
    name: European Language Social Science Thesaurus
    prefix: FAIRsharing.acd824
    subjects:
    - Economics
    - Social Science
    twitter: CESSDA_Data/
  github_request_issue: 1614
  homepage: https://elsst.cessda.eu/id/3/
  license: CC-BY-SA 4.0
  mappings:
    bartoc: '14'
    fairsharing: FAIRsharing.acd824
  name: European Language Social Science Thesaurus
  prefix: elsst
  uri_format: https://elsst.cessda.eu/id/3/$1
emap:
  biocontext:
    prefix: EMAP
  bioportal:
    contact:
      email: Terry.Hayamizu@jax.org
      name: Terry Hayamizu
    description: A structured controlled vocabulary of stage-specific anatomical structures
      of the mouse (Mus).
    homepage: http://emouseatlas.org/
    name: Mouse Gross Anatomy and Development Ontology
    prefix: EMAP
    version: unknown
  example: '1'
  mappings:
    biocontext: EMAP
    bioportal: EMAP
    obofoundry: emap
    ols: emap
    prefixcommons: emap.ontology
  obofoundry:
    contact: Terry.Hayamizu@jax.org
    contact.github: tfhayamizu
    contact.label: Terry Hayamizu
    contact.orcid: 0000-0002-0956-8634
    deprecated: true
    description: A structured controlled vocabulary of stage-specific anatomical structures
      of the mouse (Mus).
    domain: anatomy and development
    download.owl: http://purl.obolibrary.org/obo/emap.owl
    homepage: http://emouseatlas.org
    name: Mouse gross anatomy and development, timed
    prefix: emap
  ols:
    description: A structured controlled vocabulary of stage-specific anatomical structures
      of the mouse (Mus).
    homepage: http://emouseatlas.org
    name: Mouse gross anatomy and development, timed
    prefix: emap
    version: '2020-04-13'
    version.iri: http://purl.obolibrary.org/obo/emap/releases/2020-04-13/emap.owl
  pattern: ^\d+$
  prefix: emap
  prefixcommons:
    bioportal: '1010'
    description: A structured controlled vocabulary of stage-specific anatomical structures
      of the mouse (Mus).
    example: EMAP_3
    homepage: http://genex.hgu.mrc.ac.uk/
    keywords:
    - obo
    - anatomy
    - development
    - mouse
    name: Mouse gross anatomy and development
    pattern: ^EMAP_\d+$
    prefix: emap.ontology
emapa:
  aberowl:
    description: An ontology for mouse anatomy covering embryonic development and
      postnatal stages.
    download_owl: http://aber-owl.net/media/ontologies/EMAPA/24/emapa.owl
    homepage: http://www.informatics.jax.org/expression.shtml
    name: Mouse Developmental Anatomy Ontology
    prefix: EMAPA
  bartoc:
    abbreviation: EMAPA
    description: 'The ontology of mouse developmental anatomy was originally developed
      by Jonathan Bard and his colleagues as part of the Edinburgh Mouse Atlas Project
      (EMAP) (http://www.emouseatlas.org) in order to provide a structured controlled
      vocabulary of stage-specific anatomical structures for the developing laboratory
      mouse.


      The developmental mouse anatomy ontology has subsequently been substantially
      extended and refined in a collaborative effort between EMAP and the Gene Expression
      Database (GXD) project, part of the Mouse Genome Informatics (MGI) resource
      at The Jackson Laboratory. Both GXD and the Edinburgh Mouse Atlas of Gene Expression
      (EMAGE) database project currently use this anatomy ontology to describe patterns
      of gene expression in the mouse embryo.


      Previous versions, such as the one posted on the OBO Foundry site under the
      filename EMAP.obo, listed the anatomical entities for each developmental stage
      (Theiler Stages 1 through 26) separately. Stage-specific instances were presented
      as uniparental hierarchical trees organized using part-of relationships only
      (i.e. as a strict partonomy). These hierarchies have been used for annotation
      of expression in both the EMAGE and GXD databases, and the associated identifiers
      for the stage-specific instances are preserved.'
    homepage: https://obofoundry.org/ontology/emapa.html
    name: Ontology of Mouse Developmental Anatomy
    prefix: '549'
  biocontext:
    prefix: EMAPA
  bioportal:
    contact:
      email: Terry.Hayamizu@jax.org
      name: Terry Hayamizu
    description: Abstract (i.e. non-stage specific) stage-specific anatomical structures
      of the mouse.
    homepage: http://emouseatlas.org/
    name: Mouse gross anatomy and development, timed
    prefix: EMAPA
  example: '26753'
  fairsharing:
    abbreviation: EMAPA
    description: 'The ontology of mouse developmental anatomy was originally developed
      by Jonathan Bard and his colleagues as part of the Edinburgh Mouse Atlas Project
      (EMAP) in order to provide a structured controlled vocabulary of stage-specific
      anatomical structures for the developing laboratory mouse.


      Initial versions listed anatomical entities for each developmental stage (Theiler
      Stages 1 through 26) separately. Stage-specific instances were presented as
      uniparental hierarchies organized solely using part-of relationships (i.e. as
      a strict partonomy). An ‘abstract’ (i.e. non-stage-specific) representation
      of the mouse developmental anatomy ontology was subsequently developed.


      The mouse developmental anatomy ontology has been substantially extended and
      refined over many years in a collaborative effort between EMAP and the Gene
      Expression Database (GXD) project, part of the Mouse Genome Informatics (MGI)
      resource at The Jackson Laboratory. The ontology continues to be maintained
      and expanded by GXD.'
    domains:
    - gene expression
    - animal organ development
    homepage: https://www.informatics.jax.org/vocab/gxd/anatomy
    license: CC-BY-4.0
    name: Mouse Developmental Anatomy Ontology
    prefix: FAIRsharing.j0fa1d
    publications:
    - doi: 10.1186/2041-1480-4-15
      pubmed: '23972281'
      title: 'EMAP/EMAPA ontology of mouse developmental anatomy: 2013 update'
      year: 2013
    repository: https://github.com/obophenotype/mouse-anatomy-ontology
    subjects:
    - Anatomy
    - Developmental Biology
    - Bioinformatics
  go:
    description: A time-independent Mouse Anatomical Dictionary; part of Gene Expression
      Database
    homepage: http://emouseatlas.org/
    name: Mouse gross anatomy and development, abstract
    prefix: EMAPA
    uri_format: http://www.informatics.jax.org/vocab/gxd/anatomy/EMAPA:$1
  mappings:
    aberowl: EMAPA
    bartoc: '549'
    biocontext: EMAPA
    bioportal: EMAPA
    fairsharing: FAIRsharing.j0fa1d
    go: EMAPA
    obofoundry: emapa
    ols: emapa
    ontobee: EMAPA
    wikidata.entity: Q113012656
  obofoundry:
    contact: Terry.Hayamizu@jax.org
    contact.github: tfhayamizu
    contact.label: Terry Hayamizu
    contact.orcid: 0000-0002-0956-8634
    deprecated: false
    description: An ontology for mouse anatomy covering embryonic development and
      postnatal stages.
    domain: anatomy and development
    download.obo: http://purl.obolibrary.org/obo/emapa.obo
    download.owl: http://purl.obolibrary.org/obo/emapa.owl
    homepage: http://www.informatics.jax.org/expression.shtml
    license: CC BY 4.0
    license.url: https://creativecommons.org/licenses/by/4.0/
    name: Mouse Developmental Anatomy Ontology
    preferredPrefix: EMAPA
    prefix: emapa
    publications:
    - id: https://www.ncbi.nlm.nih.gov/pubmed/9651497
      title: An internet-accessible database of mouse developmental anatomy based
        on a systematic nomenclature
    - id: https://www.ncbi.nlm.nih.gov/pubmed/23972281
      title: 'EMAP/EMAPA ontology of mouse developmental anatomy: 2013 update'
    - id: https://www.ncbi.nlm.nih.gov/pubmed/26208972
      title: 'Mouse Anatomy Ontologies: Enhancements and Tools for Exploring and Integrating
        Biomedical Data'
    - id: https://doi.org/10.1016/B978-0-12-800043-4.00023-3
      title: 'Textual Anatomics: the Mouse Developmental Anatomy Ontology and the
        Gene Expression Database for Mouse Development (GXD)'
    repository: https://github.com/obophenotype/mouse-anatomy-ontology
  ols:
    description: An ontology for mouse anatomy covering embryonic development and
      postnatal stages.
    download_owl: http://purl.obolibrary.org/obo/emapa.owl
    homepage: http://www.informatics.jax.org/expression.shtml
    name: Mouse Developmental Anatomy Ontology
    prefix: emapa
    tracker: https://github.com/obophenotype/mouse-anatomy-ontology/issues
    version: '2023-11-14'
    version.iri: http://purl.obolibrary.org/obo/emapa/releases/2023-11-14/emapa.owl
  ontobee:
    library: Library
    name: Mouse Developmental Anatomy Ontology
    prefix: EMAPA
  pattern: ^\d+$
  prefix: emapa
  publications:
  - doi: 10.1016/b978-0-12-800043-4.00023-3
    pmc: null
    pubmed: null
    title: Textual Anatomics
    year: 2016
  - doi: 10.1007/s00335-015-9584-9
    pmc: PMC4602063
    pubmed: '26208972'
    title: 'Mouse anatomy ontologies: enhancements and tools for exploring and integrating
      biomedical data'
    year: 2015
  - doi: 10.1186/2041-1480-4-15
    pmc: PMC3851555
    pubmed: '23972281'
    title: 'EMAP/EMAPA ontology of mouse developmental anatomy: 2013 update'
    year: 2013
  - doi: 10.1016/s0925-4773(98)00069-0
    pmc: null
    pubmed: '9651497'
    title: An internet-accessible database of mouse developmental anatomy based on
      a systematic nomenclature
    year: 1998
  - doi: null
    pmc: null
    pubmed: '9651497'
    title: An internet-accessible database of mouse developmental anatomy based on
      a systematic nomenclature
    year: null
  - doi: null
    pmc: null
    pubmed: '23972281'
    title: 'EMAP/EMAPA ontology of mouse developmental anatomy: 2013 update'
    year: null
  - doi: null
    pmc: null
    pubmed: '26208972'
    title: 'Mouse Anatomy Ontologies: Enhancements and Tools for Exploring and Integrating
      Biomedical Data'
    year: null
  - doi: 10.1016/b978-0-12-800043-4.00023-3
    pmc: null
    pubmed: null
    title: 'Textual Anatomics: the Mouse Developmental Anatomy Ontology and the Gene
      Expression Database for Mouse Development (GXD)'
    year: null
  - doi: 10.1186/2041-1480-4-15
    pmc: null
    pubmed: '23972281'
    title: 'EMAP/EMAPA ontology of mouse developmental anatomy: 2013 update'
    year: 2013
  - doi: null
    pmc: null
    pubmed: '9651497'
    title: An internet-accessible database of mouse developmental anatomy based on
      a systematic nomenclature
    year: null
  - doi: null
    pmc: null
    pubmed: '23972281'
    title: 'EMAP/EMAPA ontology of mouse developmental anatomy: 2013 update'
    year: null
  - doi: null
    pmc: null
    pubmed: '26208972'
    title: 'Mouse Anatomy Ontologies: Enhancements and Tools for Exploring and Integrating
      Biomedical Data'
    year: null
  - doi: 10.1016/b978-0-12-800043-4.00023-3
    pmc: null
    pubmed: null
    title: 'Textual Anatomics: the Mouse Developmental Anatomy Ontology and the Gene
      Expression Database for Mouse Development (GXD)'
    year: null
  - doi: 10.1186/2041-1480-4-15
    pmc: null
    pubmed: '23972281'
    title: 'EMAP/EMAPA ontology of mouse developmental anatomy: 2013 update'
    year: 2013
  synonyms:
  - EMAPA_RETIRED
  uri_format: http://purl.obolibrary.org/obo/EMAPA_$1
emaps:
  contact:
    email: Terry.Hayamizu@jax.org
    github: tfhayamizu
    name: Terry Hayamizu
    orcid: 0000-0002-0956-8634
  contributor:
    email: benjamin_gyori@hms.harvard.edu
    github: bgyori
    name: Benjamin M. Gyori
    orcid: 0000-0001-9439-5346
  depends_on:
  - emapa
  description: EMAPA identifiers refer to developmental stage-independent mouse anatomical
    features, for instance, EMAPA:35178 resolves to the MGI's Mouse Developmental
    Anatomy Browser. EMAPS is an extension to EMAPA which introduces terms for different
    developmental stages of this generic EMAPA entry. EMAPS identifiers are constructed
    such that they are a concatenation of the EMAPA ID and a Theiler Stage (TS) number.
    For instance, EMAPA:35178 in TS 23 becomes EMAPS:3517823
  example: '3517823'
  github_request_issue: 747
  homepage: https://www.informatics.jax.org/vocab/gxd/anatomy/
  name: Mouse Developmental Anatomy Ontology with Theiler Stage
  pattern: ^\d+$
  preferred_prefix: EMAPS
  prefix: emaps
  reviewer:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  uri_format: https://www.informatics.jax.org/vocab/gxd/anatomy/EMAPS:$1
emdb:
  biocontext:
    prefix: EMDB
  edam:
    description: Identifier of an entry from the EMDB electron microscopy database.
    name: EMDB
    obsolete: false
    prefix: '1146'
  fairsharing:
    abbreviation: EMDB
    contact:
      email: help@emdatabank.org
      name: Ardan Patwardhan
      orcid: 0000-0001-7663-9028
    description: Cryo-electron microscopy reconstruction methods are uniquely able
      to reveal structures of many important macromolecules and macromolecular complexes.
      The Electron Microscopy Data Bank (EMDB) is a public repository for electron
      microscopy density maps of macromolecular complexes and subcellular structures.
      It covers a variety of techniques, including single-particle analysis, electron
      tomography, and electron (2D) crystallography. The EMDB was founded at EBI in
      2002, under the leadership of Kim Henrick. Since 2007 it has been operated jointly
      by the PDBe, and the Research Collaboratory for Structural Bioinformatics (RCSB
      PDB) as a part of EMDataBank which is funded by a joint NIH grant to PDBe, the
      RCSB and the National Center for Macromolecular Imaging (NCMI).
    homepage: https://www.ebi.ac.uk/emdb/
    license: CC0-1.0
    name: Electron Microscopy Data Bank
    prefix: FAIRsharing.651n9j
    publications:
    - doi: 10.1093/nar/gkq880
      pubmed_id: 20935055
      title: 'EMDataBank.org: unified data resource for CryoEM'
    - doi: 10.1016/S0968-0004(02)02176-X
      pubmed_id: 12417136
      title: New electron microscopy database and deposition system
    - doi: 10.1093/nar/gkv1126
      pubmed_id: 26578576
      title: EMDataBank unified data resource for 3DEM.
    subjects:
    - Structural Biology
    - Virology
    - Epidemiology
  mappings:
    biocontext: EMDB
    edam: '1146'
    fairsharing: FAIRsharing.651n9j
    miriam: emdb
    n2t: emdb
    re3data: r3d100010562
    uniprot: DB-0272
  miriam:
    deprecated: false
    description: The Electron Microscopy Data Bank (EMDB) is a public repository for
      electron microscopy density maps of macromolecular complexes and subcellular
      structures. It covers a variety of techniques, including single-particle analysis,
      electron tomography, and electron (2D) crystallography. The EMDB map distribution
      format follows the CCP4 definition, which is widely recognized by software packages
      used by the structural biology community.
    homepage: https://www.ebi.ac.uk/pdbe/emdb/
    id: '00000561'
    name: Electron Microscopy Data Bank
    namespaceEmbeddedInLui: false
    pattern: ^EMD-\d{4,5}$
    prefix: emdb
    sampleId: EMD-1001
    uri_format: https://www.ebi.ac.uk/pdbe/entry/emdb/$1
  n2t:
    description: The Electron Microscopy Data Bank (EMDB) is a public repository for
      electron microscopy density maps of macromolecular complexes and subcellular
      structures. It covers a variety of techniques, including single-particle analysis,
      electron tomography, and electron (2D) crystallography. The EMDB map distribution
      format follows the CCP4 definition, which is widely recognized by software packages
      used by the structural biology community.
    example: EMD-1001
    homepage: https://www.ebi.ac.uk/pdbe/emdb/
    name: EMDB at Protein Data Bank in Europe
    namespaceEmbeddedInLui: false
    pattern: ^EMD-\d{4}$
    prefix: emdb
    uri_format: https://www.ebi.ac.uk/pdbe/entry/emdb/$1
  owners:
  - name: European Bioinformatics Institute
    partnered: false
    ror: 02catss52
    wikidata: null
  prefix: emdb
  publications:
  - doi: 10.1093/nar/gkv1126
    pmc: PMC4702818
    pubmed: '26578576'
    title: EMDataBank unified data resource for 3DEM
    year: 2015
  - doi: 10.1093/nar/gkq880
    pmc: PMC3013769
    pubmed: '20935055'
    title: 'EMDataBank.org: unified data resource for CryoEM'
    year: 2010
  - doi: 10.1016/s0968-0004(02)02176-x
    pmc: null
    pubmed: '12417136'
    title: New electron microscopy database and deposition system
    year: 2002
  - doi: 10.1093/nar/gkq880
    pmc: null
    pubmed: null
    title: 'EMDataBank.org: unified data resource for CryoEM'
    year: null
  - doi: 10.1016/S0968-0004(02)02176-X
    pmc: null
    pubmed: null
    title: New electron microscopy database and deposition system
    year: null
  - doi: 10.1093/nar/gkv1126
    pmc: null
    pubmed: null
    title: EMDataBank unified data resource for 3DEM.
    year: null
  - doi: 10.1093/nar/gkv1126
    pmc: null
    pubmed: '26578576'
    title: null
    year: null
  re3data:
    description: The Electron Microscopy Data Bank (EMDB) is a public repository for
      electron microscopy density maps of macromolecular complexes and subcellular
      structures. It covers a variety of techniques, including single-particle analysis,
      electron tomography, and electron (2D) crystallography.
    doi: 10.17616/R3HP57
    homepage: https://www.ebi.ac.uk/emdb/
    name: Electron Microscopy Data Bank
    prefix: r3d100010562
    synonyms:
    - EMDB
    - EMDB at PDBe
    - The Electron Microscopy Data Bank at Protein Data Bank in Europe
  uniprot:
    abbreviation: EMDB
    category: 3D structure databases
    homepage: https://www.ebi.ac.uk/emdb
    name: Electron Microscopy Data Bank
    prefix: DB-0272
    publications:
    - doi: 10.1093/nar/gkv1126
      pubmed: '26578576'
    uri_format: https://www.ebi.ac.uk/emdb/$1
emea:
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: Product number for the European Medicines Agency
  example: EMEA/H/C/000181
  homepage: https://www.ema.europa.eu/en/medicines
  name: European Medicines Evaluation Agency
  prefix: emea
emg:
  contact:
    email: oonagh.mannix@helmholtz-berlin.de
    github: null
    name: Oonagh Brendike-Mannix
    orcid: 0000-0003-0575-2853
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: The Electron Microscopy (EM) Glossary is a widespread community effort
    to harmonize terminology in the electron and ion microscopies. It is created in
    a not-for profit collaboration between academic and non-university research institutions
    including domain and metadata experts. It provides harmonized terminology for
    application level semantic artifacts to source from and align with. [from homepage]
  download_owl: https://owl.emglossary.helmholtz-metadaten.de/ontology.owl
  download_rdf: https://owl.emglossary.helmholtz-metadaten.de/ontology.ttl
  example: '00000005'
  homepage: https://purls.helmholtz-metadaten.de/emg
  license: CC-BY-4.0
  logo: https://codebase.helmholtz.cloud/em_glossary/em_glossary/-/raw/main/EMGlossary.png
  name: Electron Microscopy Glossary
  pattern: ^\d{8}$
  prefix: emg
  rdf_uri_format: https://purls.helmholtz-metadaten.de/emg/EMG_$1
  repository: https://codebase.helmholtz.cloud/em_glossary/em_glossary
  uri_format: https://purls.helmholtz-metadaten.de/emg/EMG_$1
emi:
  contact:
    email: Tarcisio.Mendes@sib.swiss
    github: tarcisiotmf
    name: Tarcisio Mendes de Farias
    orcid: 0000-0002-3175-5372
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: The EMI ontology is used to structure spectrum annotation provenance
    by reusing the PROV-O ontology (a W3C recommendation) and sample and observation
    data by applying the SOSA ontology. EMI reuses the SOSA ontology as a data schema
    for struturing the Sample and Observation data. SOSA (Sensor, Observation, Sample,
    and Actuator) is a subset of SSN (Semantic Sensor Network Ontology) that is a
    W3C recommendation. [from homepage]
  download_rdf: https://github.com/digital-botanical-gardens-initiative/earth_metabolome_ontology/blob/main/emi.ttl
  example: ChemicalStructure
  github_request_issue: 1516
  homepage: https://www.dbgi.org/earth_metabolome_ontology/
  license: CC0-1.0
  mappings:
    ols: emi
  name: Earth Metabolome Ontology
  ols:
    contact: kru@sib.swiss
    description: The Earth Metabolome Initiative (EMI) ontology is designed to capture
      and structure the metabolic content of all currently known species on our planet.
    download_rdf: https://w3id.org/emi/ols.ttl
    homepage: https://w3id.org/emi
    name: The Earth Metabolome Initiative (EMI) ontology
    prefix: emi
    uri_format: https://w3id.org/emi#$1
    version: '1.0'
    version.iri: https://w3id.org/emi/version/1.0
  prefix: emi
  rdf_uri_format: ' https://purl.org/emi#$1'
  repository: https://github.com/digital-botanical-gardens-initiative/earth_metabolome_ontology
  uri_format: https://www.dbgi.org/earth_metabolome_ontology/#$1
emmo:
  banana: EMMO
  banana_peel: _
  bartoc:
    abbreviation: EMMO
    description: EMMO results from a multidisciplinary effort to develop a standard
      representational framework that is consistent with scientific principles and
      methodologies. It is based on physics, analytical philosophy and information
      and communication technologies. EMMO provides a framework for knowledge capture
      and interoperability in applied science and engineering, especially materials
      science and manufacturing. It is released under a Creative Commons CC BY 4.0
      license.
    homepage: https://github.com/emmo-repo/EMMO
    license: CC-BY-4.0
    name: European Materials & Modelling Ontology
    prefix: '20705'
  contact:
    email: jesper.friis@sintef.no
    github: jesper-friis
    name: Jesper Friis
    orcid: 0000-0002-1560-809X
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: EMMO is a multidisciplinary effort to develop a standard representational
    framework (the ontology) for applied sciences. It is based on physics, analytical
    philosophy and information and communication technologies. It has been instigated
    by materials science to provide a framework for knowledge capture that is consistent
    with scientific principles and methodologies. (from GitHub)
  download_rdf: https://raw.githubusercontent.com/emmo-repo/EMMO/master/emmo.ttl
  example: 03212fd7_abfd_4828_9c8e_62c293052d4b
  fairsharing:
    abbreviation: EMMO
    contact:
      email: gerhard@goldbeck-consulting.com
      name: Gerhard Goldbeck
      orcid: 0000-0002-4181-2852
    description: EMMO is a multidisciplinary effort to develop a standard representational
      framework (the ontology) for applied sciences. It is based on physics, analytical
      philosophy and information and communication technologies. It has been instigated
      by materials science to provide a framework for knowledge capture that is consistent
      with scientific principles and methodologies.
    homepage: https://emmo-repo.github.io/
    license: CC-BY-4.0
    logo: https://api.fairsharing.org/rails/active_storage/blobs/redirect/eyJfcmFpbHMiOnsibWVzc2FnZSI6IkJBaHBBdmtEIiwiZXhwIjpudWxsLCJwdXIiOiJibG9iX2lkIn19--69489934048fba98feded162d24a8e3b36c9d370/EMMO.jpg?disposition=inline
    name: 'Elementary Multiperspective Material Ontology '
    prefix: FAIRsharing.1bdf3c
    repository: https://github.com/emmo-repo/EMMO
    subjects:
    - Physics
    - Philosophy
    - Communication Science
  homepage: https://emmo-repo.github.io
  license: CC-BY-4.0
  lov:
    description: 'Elementary Multiperspective Material Ontology (EMMO)


      EMMO is a multidisciplinary effort to develop a standard representational framework
      (the ontology) based on current materials modelling knowledge, including physical
      sciences, analytical philosophy and information and communication technologies.


      It provides the connection between the physical world, materials characterisation
      world and materials modelling world.'
    homepage: https://w3id.org/emmo
    keywords:
    - Industry
    modified: '2024-07-04'
    name: Elementary Multiperspective Material Ontology (EMMO)
    prefix: emmo
    uri_prefix: https://w3id.org/emmo#$1
  mappings:
    bartoc: '20705'
    fairsharing: FAIRsharing.1bdf3c
    lov: emmo
    tib: emmo
  name: Elementary Multiperspective Material Ontology
  part_of_database: emmo
  prefix: emmo
  repository: https://github.com/emmo-repo/EMMO
  tib:
    description: EMMO is a multidisciplinary effort to develop a standard representational
      framework (the ontology) based on current materials modelling knowledge, including
      physical sciences, analytical philosophy and information and communication technologies.
      It provides the connection between the physical world, materials characterisation
      world and materials modelling world.
    download_owl: https://emmo-repo.github.io/versions/1.0.0-beta4/emmo-inferred.owl
    homepage: https://emmo-repo.github.io/
    keywords:
    - NFDI4ING
    - NFDI4CAT
    - material science
    name: The European Materials Modelling Ontology
    prefix: emmo
    tracker: https://github.com/emmo-repo/EMMO/issues
    uri_format: http://emmo.info/emmo#EMMO_$1
    version.iri: http://emmo.info/emmo/1.0.0-beta4
  uri_format: http://emmo.info/emmo#EMMO_$1
emmo.cif:
  contact:
    email: jesper.friis@sintef.no
    github: jesper-friis
    name: Jesper Friis
    orcid: 0000-0002-1560-809X
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: A crystallography domain ontology based on EMMO and the CIF core dictionary.
    It is implemented as a formal language. (from https://nfdi4cat.org/services/ontologie-sammlung/)
  download_rdf: https://raw.githubusercontent.com/emmo-repo/CIF-ontology/main/ontology/cif-core.ttl
  example: _space_group_symop.operation_xyz
  example_extras:
  - o12
  homepage: https://www.iucr.org/resources/cif
  mappings:
    tib: cif
  name: Crystallographic Information Framework
  part_of_database: emmo
  prefix: emmo.cif
  repository: https://github.com/emmo-repo/CIF-ontology
  tib:
    description: A toplevel crystallography ontology based on EMMO and the CIF core
      dictionary. It is implemented as a formal language.
    download_rdf: https://raw.githubusercontent.com/emmo-repo/domain-crystallography/master/crystallography.ttl
    keywords:
    - NFDI4CAT
    - material science
    - physics
    name: Crystallography domain ontology
    prefix: cif
    uri_format: http://emmo.info/domain-crystallography/crystallography#$1
    version.iri: http://emmo.info/domain-crystallography/0.0.1/crystallography
  uri_format: http://emmo.info/emmo/cif-core#$1
emolecules:
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: Catalog of purchasable reagents and building blocks
  example: '491187'
  homepage: https://reaxys.emolecules.com
  keywords:
  - chemistry
  - reagents
  - vendor
  name: Reaxys eMolecules
  pattern: ^\d+$
  prefix: emolecules
  uri_format: https://reaxys.emolecules.com/cgi-bin/more?vid=$1
empiar:
  banana: EMPIAR
  banana_peel: '-'
  contact:
    email: ardan@ebi.ac.uk
    github: null
    name: Ardan Patwardhan
    orcid: 0000-0001-7663-9028
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: EMPIAR, the Electron Microscopy Public Image Archive, is a public resource
    for raw, 2D electron microscopy images. Here, you can browse, upload and download
    the raw images used to build a 3D structure
  example: '10595'
  fairsharing:
    abbreviation: EMPIAR
    description: EMPIAR, the Electron Microscopy Public Image Archive, is a public
      resource for raw images underpinning 3D cryo-EM maps and tomograms (themselves
      archived in EMDB). EMPIAR also accommodates 3D datasets obtained with volume
      EM techniques and soft and hard X-ray tomography.
    homepage: https://www.ebi.ac.uk/empiar/
    license: CC0-1.0
    name: Electron Microscopy Public Image Archive
    prefix: FAIRsharing.dff3ef
    publications:
    - doi: 10.1038/nmeth.3806
      pubmed_id: 27067018
      title: 'EMPIAR: a public archive for raw electron microscopy image data.'
    subjects:
    - Bioinformatics
    - Biology
  homepage: https://www.ebi.ac.uk/pdbe/emdb
  mappings:
    fairsharing: FAIRsharing.dff3ef
    miriam: empiar
  miriam:
    deprecated: false
    description: EMPIAR, the Electron Microscopy Public Image Archive, is a public
      resource for raw images underpinning 3D cryo-EM maps and tomograms (themselves
      archived in EMDB). EMPIAR also accommodates 3D datasets obtained with volume
      EM techniques and soft and hard X-ray tomography.
    homepage: https://www.ebi.ac.uk
    id: 00000986
    name: EMPIAR
    namespaceEmbeddedInLui: false
    pattern: ^EMPIAR-\d{5,}$
    prefix: empiar
    sampleId: EMPIAR-10002
    uri_format: https://www.ebi.ac.uk/empiar/$1
  name: Electron Microscopy Public Image Archive
  owners:
  - name: European Bioinformatics Institute
    partnered: false
    ror: 02catss52
    wikidata: null
  pattern: ^\d+$
  prefix: empiar
  publications:
  - doi: 10.1038/nmeth.3806
    pmc: null
    pubmed: '27067018'
    title: 'EMPIAR: a public archive for raw electron microscopy image data'
    year: 2016
  uri_format: https://www.ebi.ac.uk/pdbe/emdb/empiar/entry/$1
empty:
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: The Experimental Measurements, Purposes, and Treatments ontologY (EMPTY)
    is a structured vocabulary designed to capture and standardize the scientific
    reasoning behind experimental measurements. It addresses a critical gap in existing
    metadata standards, which primarily focus on technical specifications rather than
    scientific intent. The ontology provides a common language to express why a measurement
    was taken and the conceptual conditions under which it should be interpreted.
    By focusing on experimental purposes and treatments, EMPTY is designed to significantly
    improve the findability, interoperability, and reusability of scientific data.
    This enables researchers to discover relevant datasets for meta-analyses and cross-disciplinary
    research based on shared scientific goals. (from https://github.com/OBOFoundry/OBOFoundry.github.io/issues/2753)
  download_json: https://github.com/Waltham-Data-Science/empty-ontology/raw/refs/heads/main/empty.json
  download_obo: https://github.com/Waltham-Data-Science/empty-ontology/raw/refs/heads/main/empty.obo
  download_owl: https://github.com/Waltham-Data-Science/empty-ontology/raw/refs/heads/main/empty.owl
  example: 00000085
  homepage: https://github.com/Waltham-Data-Science/empty-ontology
  name: Experimental Measurements Purposes and Treatments ontologY
  pattern: ^\d+$
  prefix: empty
  repository: https://github.com/Waltham-Data-Science/empty-ontology
  uri_format: http://purl.obolibrary.org/obo/EMPTY_$1
emsl.project:
  contact:
    email: montana.smith@pnnl.gov
    github: mslarae13
    name: Montana Smith
    orcid: 0000-0002-8683-0050
  contributor:
    email: cjmungall@lbl.gov
    github: cmungall
    name: Chris Mungall
    orcid: 0000-0002-6601-2165
  description: 'As a scientific user facility, the Environmental Molecular Sciences
    Laboratory (EMSL) provides expertise, instrumentation, and resources to 250 projects
    each year. Current and past projects supported through a variety of EMSL user
    proposal avenues are publicly searchable on the EMSL website. Project pages provide
    details including:

    - Research team and institution

    - The EMSL project DOI

    - Link to project data available in EMSLs Data Portal

    - Project type'
  example: '60141'
  github_request_issue: 835
  homepage: https://www.emsl.pnnl.gov/projects
  name: Environmental Molecular Sciences Laboratory Project
  pattern: ^\d+$
  prefix: emsl.project
  reviewer:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  uri_format: https://www.emsl.pnnl.gov/project/$1
ena.embl:
  biocontext:
    prefix: ENA.EMBL
  fairsharing:
    abbreviation: ENA
    contact:
      email: datasubs@ebi.ac.uk
      name: Guy Cochrane
      orcid: 0000-0001-7954-7057
    description: The European Nucleotide Archive (ENA) is a globally comprehensive
      data resource for nucleotide sequence, spanning raw data, alignments and assemblies,
      functional and taxonomic annotation and rich contextual data relating to sequenced
      samples and experimental design. Serving both as the database of record for
      the output of the world's sequencing activity and as a platform for the management,
      sharing and publication of sequence data, the ENA provides a portfolio of services
      for submission, data management, search and retrieval across web and programmatic
      interfaces. The ENA is part of the International Nucleotide Sequence Database
      Collaboration (INSDC), which comprises the DNA DataBank of Japan (DDBJ), the
      European Molecular Biology Laboratory (EMBL), and GenBank at the NCBI. These
      three organizations exchange data on a daily basis.
    homepage: http://www.ebi.ac.uk/ena
    license: Apache 2.0 License
    name: European Nucleotide Archive
    prefix: FAIRsharing.dj8nt8
    publications:
    - doi: 10.1093/nar/gkv1311
      pubmed_id: 26615190
      title: Biocuration of functional annotation at the European nucleotide archive.
    - doi: 10.1093/nar/gku1129
      pubmed_id: 25404130
      title: Content discovery and retrieval services at the European Nucleotide Archive.
    - doi: 10.1093/nar/gks1175
      pubmed_id: 23203883
      title: Facing growth in the European Nucleotide Archive.
    - doi: 10.1093/nar/gkv1323
      pubmed_id: 26657633
      title: The International Nucleotide Sequence Database Collaboration.
    - doi: 10.1093/nar/gkw1106
      pubmed_id: 27899630
      title: European Nucleotide Archive in 2016.
    - doi: 10.1093/nar/gkh120
      pubmed_id: 14681351
      title: The EMBL Nucleotide Sequence Database.
    subjects:
    - Functional Genomics
    - Metagenomics
    - Genomics
    - Bioinformatics
    - Data Management
    - Biodiversity
    - Transcriptomics
    twitter: enasequence
  go:
    description: ENA is made up of a number of distinct databases that includes EMBL-Bank,
      the newly established Sequence Read Archive (SRA) and the Trace Archive. International
      nucleotide sequence database collaboration, comprising ENA-EBI nucleotide sequence
      data library (EMBL-Bank), DNA DataBank of Japan (DDBJ), and NCBI GenBank
    homepage: http://www.ebi.ac.uk/ena/
    name: European Nucleotide Archive
    prefix: ENA
    uri_format: http://www.ebi.ac.uk/ena/data/view/$1
  has_canonical: insdc.run
  integbio:
    alt_name: European Nucleotide Archive
    description: ENA is a database of data from global nucleotide sequencing projects.
      The database contains information on projects from raw phases trhough complete
      functional annotation. Users can search by keyword or DNA sequence. Bulk data
      is available for download.
    fairsharing: biodbcore-000310
    homepage: https://www.ebi.ac.uk/ena/browser/home
    information_keywords:
    - Method
    - Sequence
    - Repository
    maintainer: EMBL-EBI (European Bioinformatics Institute)
    name: ENA
    prefix: nbdc00432
    pubmeds:
    - '20972220'
    status: Active
    target_keywords:
    - Genome/Gene
    - cDNA/EST
    - Genetic variation
    - DNA
  logo: https://www.ebi.ac.uk/ena/browser/assets/ENA_Logo_tagline.svg
  mappings:
    biocontext: ENA.EMBL
    fairsharing: FAIRsharing.dj8nt8
    go: ENA
    integbio: nbdc00432
    miriam: ena.embl
    n2t: ena.embl
    prefixcommons: ena
    re3data: r3d100010527
    uniprot: DB-0022
  miriam:
    deprecated: false
    description: The European Nucleotide Archive (ENA) captures and presents information
      relating to experimental workflows that are based around nucleotide sequencing.
      ENA is made up of a number of distinct databases that includes EMBL-Bank, the
      Sequence Read Archive (SRA) and the Trace Archive each with their own data formats
      and standards. This collection references Embl-Bank identifiers.
    homepage: https://www.ebi.ac.uk/ena/
    id: '00000372'
    name: ENA
    namespaceEmbeddedInLui: false
    pattern: ^[A-Z]+[0-9]+(\.\d+)?$
    prefix: ena.embl
    providers:
    - code: ''
      description: ENA through GenBank
      homepage: https://www.ncbi.nlm.nih.gov/Genbank/
      name: ENA through GenBank
      uri_format: https://www.ncbi.nlm.nih.gov/nuccore/$1
    sampleId: BN000065
    uri_format: https://www.ebi.ac.uk/ena/browser/view/$1
  n2t:
    description: The European Nucleotide Archive (ENA) captures and presents information
      relating to experimental workflows that are based around nucleotide sequencing.
      ENA is made up of a number of distinct databases that includes EMBL-Bank, the
      Sequence Read Archive (SRA) and the Trace Archive each with their own data formats
      and standards. This collection references Embl-Bank identifiers.
    example: BN000065
    homepage: https://www.ncbi.nlm.nih.gov/Genbank/
    name: ENA through GenBank
    namespaceEmbeddedInLui: false
    pattern: ^[A-Z]+[0-9]+(\.\d+)?$
    prefix: ena.embl
    uri_format: https://www.ncbi.nlm.nih.gov/nuccore/$1
  owners:
  - name: European Bioinformatics Institute
    partnered: false
    ror: 02catss52
    wikidata: null
  prefix: ena.embl
  prefixcommons:
    description: The European Nucleotide Archive (ENA) captures and presents information
      relating to experimental workflows that are based around nucleotide sequencing.
      A typical workflow includes the isolation and preparation of material for sequencing,
      a run of a sequencing machine in which sequencing data are produced and a subsequent
      bioinformatic analysis pipeline.
    example: BN000065
    homepage: http://www.ebi.ac.uk/ena/
    keywords:
    - DNA
    name: European Nucleotide Archive
    pattern: ^[A-Z]+[0-9]+$
    prefix: ena
    uri_format: http://www.ebi.ac.uk/ena/data/view/$1
  publications:
  - doi: 10.1093/nar/gkaa1028
    pmc: PMC7778925
    pubmed: '33175160'
    title: The European Nucleotide Archive in 2020
    year: 2021
  - doi: 10.1093/nar/gkw1106
    pmc: PMC5210577
    pubmed: '27899630'
    title: European Nucleotide Archive in 2016
    year: 2016
  - doi: 10.1093/nar/gkv1311
    pmc: PMC4702917
    pubmed: '26615190'
    title: Biocuration of functional annotation at the European nucleotide archive
    year: 2015
  - doi: 10.1093/nar/gkv1323
    pmc: PMC4702924
    pubmed: '26657633'
    title: The International Nucleotide Sequence Database Collaboration
    year: 2015
  - doi: 10.1093/nar/gku1129
    pmc: PMC4383942
    pubmed: '25404130'
    title: Content discovery and retrieval services at the European Nucleotide Archive
    year: 2014
  - doi: 10.1093/nar/gks1175
    pmc: PMC3531187
    pubmed: '23203883'
    title: Facing growth in the European Nucleotide Archive
    year: 2012
  - doi: 10.1093/nar/gkh120
    pmc: PMC308854
    pubmed: '14681351'
    title: The EMBL Nucleotide Sequence Database
    year: 2004
  - doi: 10.1093/nar/gkv1311
    pmc: null
    pubmed: null
    title: Biocuration of functional annotation at the European nucleotide archive.
    year: null
  - doi: 10.1093/nar/gku1129
    pmc: null
    pubmed: null
    title: Content discovery and retrieval services at the European Nucleotide Archive.
    year: null
  - doi: 10.1093/nar/gks1175
    pmc: null
    pubmed: null
    title: Facing growth in the European Nucleotide Archive.
    year: null
  - doi: 10.1093/nar/gkv1323
    pmc: null
    pubmed: null
    title: The International Nucleotide Sequence Database Collaboration.
    year: null
  - doi: 10.1093/nar/gkw1106
    pmc: null
    pubmed: null
    title: European Nucleotide Archive in 2016.
    year: null
  - doi: 10.1093/nar/gkh120
    pmc: null
    pubmed: null
    title: The EMBL Nucleotide Sequence Database.
    year: null
  - doi: 10.1093/nar/gkaa1028
    pmc: null
    pubmed: '33175160'
    title: null
    year: null
  - doi: 10.1093/nar/gkv1311
    pmc: null
    pubmed: null
    title: Biocuration of functional annotation at the European nucleotide archive.
    year: null
  - doi: 10.1093/nar/gku1129
    pmc: null
    pubmed: null
    title: Content discovery and retrieval services at the European Nucleotide Archive.
    year: null
  - doi: 10.1093/nar/gks1175
    pmc: null
    pubmed: null
    title: Facing growth in the European Nucleotide Archive.
    year: null
  - doi: 10.1093/nar/gkv1323
    pmc: null
    pubmed: null
    title: The International Nucleotide Sequence Database Collaboration.
    year: null
  - doi: 10.1093/nar/gkw1106
    pmc: null
    pubmed: null
    title: European Nucleotide Archive in 2016.
    year: null
  - doi: 10.1093/nar/gkh120
    pmc: null
    pubmed: null
    title: The EMBL Nucleotide Sequence Database.
    year: null
  - doi: 10.1093/nar/gkaa1028
    pmc: null
    pubmed: '33175160'
    title: null
    year: null
  re3data:
    description: "The European Nucleotide Archive (ENA) captures and presents information\
      \ relating to experimental workflows that are based around nucleotide sequencing.\
      \ A typical workflow includes the isolation and preparation of material for\
      \ sequencing, a run of a sequencing machine in which sequencing data are produced\
      \ and a subsequent bioinformatic analysis pipeline. ENA records this information\
      \ in a data model that covers input information (sample, experimental setup,\
      \ machine configuration), output machine data (sequence traces, reads and quality\
      \ scores) and interpreted information (assembly, mapping, functional annotation).\
      \ \nData arrive at ENA from a variety of sources. These include submissions\
      \ of raw data, assembled sequences and annotation from small-scale sequencing\
      \ efforts, data provision from the major European sequencing centres and routine\
      \ and comprehensive exchange with our partners in the International Nucleotide\
      \ Sequence Database Collaboration (INSDC).\nProvision of nucleotide sequence\
      \ data to ENA or its INSDC partners has become a central and mandatory step\
      \ in the dissemination of research findings to the scientific community. ENA\
      \ works with publishers of scientific literature and funding bodies to ensure\
      \ compliance with these principles and to provide optimal submission systems\
      \ and data access tools that work seamlessly with the published literature."
    doi: 10.17616/R3HW3J
    homepage: https://www.ebi.ac.uk/ena/browser/home
    license: Apache License 2.0
    name: European Nucleotide Archive
    prefix: r3d100010527
    synonyms:
    - ENA
    xrefs:
      nif: 0000-32981
      omics: 01029
  synonyms:
  - ena
  uniprot:
    abbreviation: EMBL
    category: Sequence databases
    homepage: https://www.ebi.ac.uk/ena/browser/home
    name: EMBL nucleotide sequence database
    prefix: DB-0022
    publications:
    - doi: 10.1093/nar/gkaa1028
      pubmed: '33175160'
    uri_format: https://www.ebi.ac.uk/ena/browser/view/$1
  uri_format: https://www.ebi.ac.uk/ena/browser/view/$1
encode:
  biocontext:
    prefix: ENCODE
  cellosaurus:
    category: Biological sample resources
    homepage: https://www.encodeproject.org
    name: Encyclopedia of DNA Elements
    prefix: ENCODE
    uri_format: https://www.encodeproject.org/biosamples/$1
  fairsharing:
    abbreviation: ENCODE
    contact:
      email: gabdank@stanford.edu
      name: Idan Gabdank
      orcid: 0000-0001-5025-5886
    description: The ENCODE (Encyclopedia of DNA Elements) Consortium is an international
      collaboration of research groups funded by the National Human Genome Research
      Institute (NHGRI). The goal of ENCODE is to build a comprehensive parts list
      of functional elements in the human genome including elements that act at the
      protein and RNA levels, and regulatory elements that control cells and circumstances
      in which a gene is active. ENCODE investigators employ a variety of assays and
      methods to identify functional elements. The discovery and annotation of gene
      elements is accomplished primarily by sequencing a diverse range of RNA sources,
      comparative genomics, integrative bioinformatic methods, and human curation.
      Regulatory elements are typically investigated through DNA hypersensitivity
      assays, assays of DNA methylation, and immunoprecipitation (IP) of proteins
      that interact with DNA and RNA, i.e., modified histones, transcription factors,
      chromatin regulators, and RNA-binding proteins, followed by sequencing.
    homepage: https://www.encodeproject.org/
    license: http://genome.ucsc.edu/ENCODE
    name: Encyclopedia of DNA Elements
    prefix: FAIRsharing.v0hbjs
    publications:
    - doi: 10.1093/database/bav010
      pubmed_id: 25776021
      title: Ontology application and use at the ENCODE DCC.
    - doi: 10.1093/nar/gks1172
      pubmed_id: 23193274
      title: 'ENCODE data in the UCSC Genome Browser: year 5 update'
    - doi: 10.1093/nar/gkq1017
      pubmed_id: 21037257
      title: ENCODE whole-genome data in the UCSC genome browser (2011 update)
    - doi: 10.1093/nar/gkv1160
      pubmed_id: 26527727
      title: ENCODE data at the ENCODE portal.
    - doi: 10.1093/database/baw001
      pubmed_id: 26980513
      title: Principles of metadata organization at the ENCODE data coordination center.
    - doi: 10.1093/nar/gkr1012
      pubmed_id: 22075998
      title: 'ENCODE whole-genome data in the UCSC Genome Browser: update 2012.'
    - doi: 10.1093/nar/gkp961
      pubmed_id: 19920125
      title: ENCODE whole-genome data in the UCSC Genome Browser
    - doi: 10.1093/nar/gkl1017
      pubmed_id: 17166863
      title: The ENCODE project at UC Santa Cruz
    - doi: 10.1093/nar/gkx1081
      pubmed_id: 29126249
      title: 'The Encyclopedia of DNA elements (ENCODE): data portal update.'
    - doi: null
      pubmed_id: 15499007
      title: The ENCODE (ENCyclopedia Of DNA Elements) Project.
    - doi: 10.1371/journal.pone.0175310
      pubmed_id: null
      title: 'SnoVault and encodeD: A novel object-based storage system and applications
        to ENCODE metadata'
    - doi: 10.1002/cpbi.89
      pubmed_id: 31751002
      title: The ENCODE Portal as an Epigenomics Resource.
    - doi: 10.1038/s41586-020-2493-4
      pubmed_id: null
      title: Expanded encyclopaedias of DNA elements in the human and mouse genomes
    - doi: 10.1038/s41586-020-2449-8
      pubmed_id: null
      title: Perspectives on ENCODE
    - doi: 10.1093/nar/gkz1062
      pubmed_id: 31713622
      title: New developments on the Encyclopedia of DNA Elements (ENCODE) data portal.
    subjects:
    - Functional Genomics
    - Epigenetics
  homepage: https://www.encodeproject.org
  mappings:
    biocontext: ENCODE
    cellosaurus: ENCODE
    fairsharing: FAIRsharing.v0hbjs
    miriam: encode
    n2t: encode
    re3data: r3d100013051
  miriam:
    deprecated: false
    description: The ENCODE Consortium is integrating multiple technologies and approaches
      in a collective effort to discover and define the functional elements encoded
      in the human genome, including genes, transcripts, and transcriptional regulatory
      regions, together with their attendant chromatin states and DNA methylation
      patterns.
    homepage: https://www.encodeproject.org
    id: '00000662'
    name: 'ENCODE: Encyclopedia of DNA Elements'
    namespaceEmbeddedInLui: false
    pattern: ^ENC[A-Za-z]{2}[0-9]{3}[A-Za-z]{3}$
    prefix: encode
    sampleId: ENCSR163RYW
    uri_format: https://www.encodeproject.org/$1
  n2t:
    description: The ENCODE Consortium is integrating multiple technologies and approaches
      in a collective effort to discover and define the functional elements encoded
      in the human genome, including genes, transcripts, and transcriptional regulatory
      regions, together with their attendant chromatin states and DNA methylation
      patterns.
    example: ENCSR163RYW
    homepage: www.encodeproject.org
    name: 'ENCODE: Encyclopedia of DNA Elements'
    namespaceEmbeddedInLui: false
    pattern: ^ENC[A-Za-z]{2}[0-9]{3}[A-Za-z]{3}$
    prefix: encode
    uri_format: https://www.encodeproject.org/$1
  name: Encyclopedia of DNA Elements
  prefix: encode
  publications:
  - doi: 10.1038/s41586-020-2493-4
    pmc: PMC7410828
    pubmed: '32728249'
    title: Expanded encyclopaedias of DNA elements in the human and mouse genomes
    year: 2020
  - doi: 10.1093/nar/gkz1062
    pmc: PMC7061942
    pubmed: '31713622'
    title: New developments on the Encyclopedia of DNA Elements (ENCODE) data portal
    year: 2020
  - doi: 10.1038/s41586-020-2449-8
    pmc: PMC7410827
    pubmed: '32728248'
    title: Perspectives on ENCODE
    year: 2020
  - doi: 10.1002/cpbi.89
    pmc: PMC7307447
    pubmed: '31751002'
    title: The ENCODE Portal as an Epigenomics Resource
    year: 2019
  - doi: 10.1093/nar/gkx1081
    pmc: PMC5753278
    pubmed: '29126249'
    title: 'The Encyclopedia of DNA elements (ENCODE): data portal update'
    year: 2018
  - doi: 10.1371/journal.pone.0175310
    pmc: PMC5389787
    pubmed: '28403240'
    title: 'SnoVault and encodeD: A novel object-based storage system and applications
      to ENCODE metadata'
    year: 2017
  - doi: 10.1093/database/baw001
    pmc: PMC4792520
    pubmed: '26980513'
    title: Principles of metadata organization at the ENCODE data coordination center
    year: 2016
  - doi: 10.1093/nar/gkv1160
    pmc: PMC4702836
    pubmed: '26527727'
    title: ENCODE data at the ENCODE portal
    year: 2015
  - doi: 10.1093/database/bav010
    pmc: PMC4360730
    pubmed: '25776021'
    title: Ontology application and use at the ENCODE DCC
    year: 2015
  - doi: 10.1093/nar/gks1172
    pmc: PMC3531152
    pubmed: '23193274'
    title: 'ENCODE data in the UCSC Genome Browser: year 5 update'
    year: 2012
  - doi: 10.1093/nar/gkr1012
    pmc: PMC3245183
    pubmed: '22075998'
    title: 'ENCODE whole-genome data in the UCSC Genome Browser: update 2012'
    year: 2011
  - doi: 10.1093/nar/gkq1017
    pmc: PMC3013645
    pubmed: '21037257'
    title: ENCODE whole-genome data in the UCSC genome browser (2011 update)
    year: 2010
  - doi: 10.1093/nar/gkp961
    pmc: PMC2808953
    pubmed: '19920125'
    title: ENCODE whole-genome data in the UCSC Genome Browser
    year: 2009
  - doi: 10.1093/nar/gkl1017
    pmc: PMC1781110
    pubmed: '17166863'
    title: The ENCODE Project at UC Santa Cruz
    year: 2006
  - doi: 10.1126/science.1105136
    pmc: null
    pubmed: '15499007'
    title: The ENCODE (ENCyclopedia Of DNA Elements) Project
    year: 2004
  re3data:
    description: "The ENCODE Encyclopedia organizes the most salient analysis products\
      \ into annotations, and provides tools to search and visualize them. The Encyclopedia\
      \ has two levels of annotations:\nIntegrative-level annotations integrate multiple\
      \ types of experimental data and ground level annotations. \nGround-level annotations\
      \ are derived directly from the experimental data, typically produced by uniform\
      \ processing pipelines."
    doi: 10.17616/R31NJMKB
    homepage: https://www.encodeproject.org/
    name: ENCODE
    prefix: r3d100013051
    synonyms:
    - ENCODE  Encyclopedia
    - Encyclopedia of DNA Elements
    xrefs:
      omics: '00532'
endlessforms.collection:
  contact:
    email: mclarkson@uky.edu
    github: null
    name: Melissa D Clarkson
    orcid: 0000-0001-9979-176X
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: Collections of images, based on topics, such as the human skull collection
  example: '2'
  homepage: https://images.endlessforms.info/
  name: EndlessForms Studio Image Collections
  part_of_database: endlessforms
  pattern: ^\d+$
  prefix: endlessforms.collection
  uri_format: https://images.endlessforms.info/collection/$1
endlessforms.element:
  contact:
    email: mclarkson@uky.edu
    github: null
    name: Melissa D Clarkson
    orcid: 0000-0001-9979-176X
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: A reusable element of a vector graphic for an anatomical entity useful
    for biological and biomedical informatics applications.
  example: HUMAN0000174
  homepage: https://graphics.endlessforms.info
  name: EndlessForms Studio Element
  part_of_database: endlessforms
  prefix: endlessforms.element
  uri_format: https://graphics.endlessforms.info/element?id=$1
endlessforms.graphic:
  contact:
    email: mclarkson@uky.edu
    github: null
    name: Melissa D Clarkson
    orcid: 0000-0001-9979-176X
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: A vector graphic for an anatomical entity useful for biological and
    biomedical informatics applications.
  example: HUMAN0000789
  homepage: https://endlessforms.info
  name: EndlessForms Studio Graphic
  part_of_database: endlessforms
  prefix: endlessforms.graphic
  uri_format: https://endlessforms.info/graphics/$1
endlessforms.image:
  contact:
    email: mclarkson@uky.edu
    github: null
    name: Melissa D Clarkson
    orcid: 0000-0001-9979-176X
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: Images used as reference
  example: '3'
  homepage: https://images.endlessforms.info/
  license: CC-BY-NC-4.0
  name: EndlessForms Studio Image
  part_of_database: endlessforms
  pattern: ^\d+$
  prefix: endlessforms.image
  uri_format: https://images.endlessforms.info/image/$1
endlessforms.library:
  contact:
    email: mclarkson@uky.edu
    github: null
    name: Melissa D Clarkson
    orcid: 0000-0001-9979-176X
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: A collection of graphics that relate to a theme
  example: HUMAN0000001
  homepage: https://graphics.endlessforms.info
  name: EndlessForms Studio Library
  part_of_database: endlessforms
  prefix: endlessforms.library
  uri_format: https://graphics.endlessforms.info/library?id=$1
endlessforms.unit:
  contact:
    email: mclarkson@uky.edu
    github: null
    name: Melissa D Clarkson
    orcid: 0000-0001-9979-176X
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: A unit of a vector graphic for an anatomical entity useful for biological
    and biomedical informatics applications.
  example: HUMAN0000304
  homepage: https://graphics.endlessforms.info
  name: EndlessForms Studio Unit
  part_of_database: endlessforms
  prefix: endlessforms.unit
  uri_format: https://graphics.endlessforms.info/unit?id=$1
energymarketroles:
  homepage: https://innoweb.mondragon.edu/ontologies/dabgeo/common-domain/energymarketroles/1.0/
  mappings:
    tib: energymarketroles
  no_own_terms: true
  prefix: energymarketroles
  tib:
    description: The 'Energy Market Roles' ontology module represents the energy market
      roles of energy agents. Additionally, it includes the consumer role, as it is
      reused in most of Smart Grid scenarios. This ontology module reuses the knowledge
      of the 'Actor' ontology module.
    download_rdf: https://innoweb.mondragon.edu/ontologies/dabgeo/common-domain/energymarketroles/1.0/ontology.ttl
    keywords:
    - NFDI4Energy
    name: Energy Market Roles ontology
    prefix: energymarketroles
    uri_format: http://www.purl.org/dabgeo/conceptual/energymarketroles#$1
enm:
  aberowl:
    download_owl: http://aber-owl.net/media/ontologies/ENM/17/enm.owl
    name: eNanoMapper
    prefix: ENM
    version: '6.0'
  bioportal:
    contact:
      email: hastings@ebi.ac.uk
      name: Janna Hastings
    description: The eNanoMapper ontology covers the full scope of terminology needed
      to support research into nanomaterial safety. It builds on multiple pre-existing
      external ontologies such as the NanoParticle Ontology.
    homepage: https://github.com/enanomapper/ontologies
    name: eNanoMapper
    prefix: ENM
    publications:
    - https://scholar.google.com/scholar?hl=nl&as_sdt=0%2C5&q=enanomapper+ontology&btnG=&oq=enano
    version: '10.0'
  example: '8000221'
  fairsharing:
    abbreviation: ENM
    contact:
      email: egon.willighagen@maastrichtuniversity.nl
      name: Egon Willighagen
      orcid: 0000-0001-7542-0286
    description: The eNanoMapper ontology covers the full scope of terminology needed
      to support research into nanomaterial safety. It builds on multiple pre-existing
      external ontologies such as the NanoParticle Ontology.
    domains:
    - chemical entity
    - nanoparticle
    homepage: https://github.com/enanomapper/ontologies
    license: CC-BY-3.0
    name: eNanoMapper Ontology
    prefix: FAIRsharing.2gpf81
    publications:
    - doi: 10.1186/s13326-015-0005-5
      pubmed: '25815161'
      title: 'eNanoMapper: harnessing ontologies to enable data integration for nanomaterial
        risk assessment'
      year: 2015
    subjects:
    - Health Science
    user_defined_tags:
    - Nanosafety
  mappings:
    aberowl: ENM
    bioportal: ENM
    fairsharing: FAIRsharing.2gpf81
    ols: enm
    tib: enm
  ols:
    description: The eNanoMapper project (https://www.enanomapper.net/), NanoCommons
      project (https://www.nanocommons.eu/) and ACEnano project (http://acenano-project.eu/)
      are creating a pan-European computational infrastructure for toxicological data
      management for ENMs, based on semantic web standards and ontologies. This ontology
      is an application ontology targeting the full domain of nanomaterial safety
      assessment. It re-uses several other ontologies including the NPO, CHEMINF,
      ChEBI, and ENVO.
    download_owl: http://enanomapper.github.io/ontologies/enanomapper.owl
    homepage: http://www.enanomapper.net/
    name: eNanoMapper ontology
    prefix: enm
    uri_format: http://purl.enanomapper.org/onto/ENM_$1
    version: '10.0'
    version.iri: http://enanomapper.github.io/ontologies/releases/10.0/enanomapper.owl
  pattern: ^\d+$
  prefix: enm
  publications:
  - doi: 10.1186/s13326-015-0005-5
    pmc: PMC4374589
    pubmed: '25815161'
    title: 'eNanoMapper: harnessing ontologies to enable data integration for nanomaterial
      risk assessment'
    year: 2015
  tib:
    description: The eNanoMapper project (https://www.enanomapper.net/), NanoCommons
      project (https://www.nanocommons.eu/) and ACEnano project (http://acenano-project.eu/)
      are creating a pan-European computational infrastructure for toxicological data
      management for ENMs, based on semantic web standards and ontologies. This ontology
      is an application ontology targeting the full domain of nanomaterial safety
      assessment. It re-uses several other ontologies including the NPO, CHEMINF,
      ChEBI, and ENVO.
    download_owl: http://enanomapper.github.io/ontologies/enanomapper.owl
    homepage: https://doi.org/10.1186/s13326-015-0005-5
    keywords:
    - NFDI4CHEM
    - chemistry
    license: CC-BY 3.0 https://creativecommons.org/licenses/by/3.0/
    name: eNanoMapper ontology
    prefix: enm
    tracker: https://github.com/enanomapper/ontologies/issues
    uri_format: http://purl.enanomapper.net/onto/ENM_$1
    version.iri: http://enanomapper.github.io/ontologies/releases/10.0/enanomapper.owl
  uri_format: http://purl.enanomapper.org/onto/ENM_$1
ensembl:
  biocontext:
    prefix: ENSEMBL
    uri_format: http://ensembl.org/id/$1
  contact:
    email: flicek@ebi.ac.uk
    github: null
    name: Paul Flicek
    orcid: 0000-0002-3897-7955
  edam:
    description: Identifier of an entry (exon, gene, transcript or protein) from the
      Ensembl database.
    name: Ensembl
    obsolete: false
    prefix: '2610'
  example_extras:
  - ENSG00000049246.14
  - ENSG00000109819.9
  - ENSG00000132326.12
  - ENSG00000179094.16
  - ENST00000264867.7
  fairsharing:
    abbreviation: Ensembl
    description: Ensembl creates, integrates and distributes reference datasets and
      analysis tools that enable genomics. Ensembl is a genome browser that supports
      research in comparative genomics, evolution, sequence variation and transcriptional
      regulation. Ensembl annotate genes, computes multiple alignments, predicts regulatory
      function and collects disease data.
    homepage: http://www.ensembl.org/
    license: Apache 2.0 License
    name: Ensembl
    prefix: FAIRsharing.fx0mw7
    publications:
    - doi: 10.1093/bioinformatics/btu613
      pubmed_id: 25236461
      title: 'The Ensembl REST API: Ensembl Data for Any Language.'
    - doi: 10.1186/s13059-016-0974-4
      pubmed_id: 27268795
      title: The Ensembl Variant Effect Predictor.
    - doi: 10.1101/gr.137901.112
      pubmed_id: 22798491
      title: Incorporating RNA-seq data into the zebrafish Ensembl genebuild.
    - doi: 10.1101/gr.1863004
      pubmed_id: 15123591
      title: 'The Ensembl Web site: mechanics of a genome browser.'
    - doi: 10.1101/gr.1857204
      pubmed_id: 15123588
      title: The Ensembl core software libraries.
    - doi: 10.1101/gr.135350.111
      pubmed_id: 22955987
      title: 'GENCODE: the reference human genome annotation for The ENCODE Project.'
    - doi: 10.1002/0471142905.hg0611s69
      pubmed_id: 21400687
      title: Disease and phenotype data at Ensembl.
    - doi: 10.1016/j.tig.2004.04.002
      pubmed_id: 15145580
      title: Genome information resources - developments at Ensembl.
    - doi: 10.1093/database/bar030
      pubmed_id: 21785142
      title: 'Ensembl BioMarts: a hub for data retrieval across taxonomic space.'
    - doi: doi:10.1093/nar/gku1010
      pubmed_id: 25352552
      title: Ensembl 2015
    - doi: 10.1093/nar/gkj133
      pubmed_id: 16381931
      title: Ensembl 2006.
    - doi: 10.1093/nar/gkt1196
      pubmed_id: 24316576
      title: Ensembl 2014.
    - doi: 10.1093/database/bav119
      pubmed_id: 26888907
      title: Ensembl regulation resources.
    - doi: 10.1093/database/baw093
      pubmed_id: 27337980
      title: The Ensembl gene annotation system.
    - doi: 10.1186/1471-2164-11-295
      pubmed_id: 20459808
      title: 'Touring Ensembl: a practical guide to genome browsing.'
    - doi: 10.1093/bfgp/elm025
      pubmed_id: 17967807
      title: 'Genome browsing with Ensembl: a practical overview.'
    - doi: 10.1093/nar/gkq1064
      pubmed_id: 21045057
      title: Ensembl 2011.
    - doi: 10.1093/nar/gkr991
      pubmed_id: 22086963
      title: Ensembl 2012.
    - doi: 10.1093/nar/gks1236
      pubmed_id: 23203987
      title: Ensembl 2013.
    - doi: 10.1093/database/bav127
      pubmed_id: 26980512
      title: ncRNA orthologies in the vertebrate lineage.
    - doi: 10.1093/database/baw053
      pubmed_id: 27141089
      title: Ensembl comparative genomics resources (Erratum)
    - doi: 10.1101/gr.1866304
      pubmed_id: 15123594
      title: The Ensembl computing architecture.
    - doi: 10.1093/nar/gki138
      pubmed_id: 15608235
      title: Ensembl 2005.
    - doi: 10.1101/gr.1862204
      pubmed_id: 15123595
      title: 'ESTGenes: alternative splicing from ESTs in Ensembl.'
    - doi: 10.1186/s13059-015-0621-5
      pubmed_id: 25887522
      title: The ensembl regulatory build.
    - doi: 10.1093/bioinformatics/btt737
      pubmed_id: 24363377
      title: 'WiggleTools: parallel processing of large collections of genome-wide
        datasets for visualization and statistical analysis.'
    - doi: 10.1093/nar/gkw1104
      pubmed_id: 27899575
      title: Ensembl 2017.
    - doi: 10.1038/ng0806-853a
      pubmed_id: 16874317
      title: 'TranscriptSNPView: a genome-wide catalog of mouse coding variation.'
    - doi: 10.1093/nar/gkv1157
      pubmed_id: 26687719
      title: Ensembl 2016.
    - doi: 10.1101/gr.076521.108
      pubmed_id: 18849525
      title: Genome-wide nucleotide-level mammalian ancestor reconstruction.
    - doi: 10.1093/nar/gkm988
      pubmed_id: 18000006
      title: Ensembl 2008.
    - doi: 10.1186/1471-2164-11-293
      pubmed_id: 20459805
      title: Ensembl variation resources.
    - doi: 10.1093/nar/gkg083
      pubmed_id: 12519943
      title: 'Ensembl 2002: accommodating comparative genomics.'
    - doi: 10.1101/gr.073585.107
      pubmed_id: 19029536
      title: 'EnsemblCompara GeneTrees: Complete, duplication-aware phylogenetic trees
        in vertebrates.'
    - doi: 10.1186/1471-2105-11-238
      pubmed_id: 20459810
      title: A database and API for variation, dense genotyping and resequencing data.
    - doi: 10.1093/nar/30.1.38
      pubmed_id: 11752248
      title: The Ensembl genome database project.
    - doi: 10.1093/nar/gkl996
      pubmed_id: 17148474
      title: Ensembl 2007.
    - doi: 10.1093/bioinformatics/btq330
      pubmed_id: 20562413
      title: Deriving the consequences of genomic variants with the Ensembl API and
        SNP Effect Predictor.
    - doi: 10.1093/nar/gkn828
      pubmed_id: 19033362
      title: Ensembl 2009.
    - doi: 10.1093/nar/gkp972
      pubmed_id: 19906699
      title: Ensembl's 10th year.
    - doi: 10.1093/database/bav096
      pubmed_id: 26896847
      title: Ensembl comparative genomics resources.
    - doi: 10.1101/gr.1859804
      pubmed_id: 15123589
      title: The Ensembl analysis pipeline.
    - doi: 10.1101/gr.1858004
      pubmed_id: 15123590
      title: The Ensembl automatic gene annotation system.
    - doi: 10.1093/nar/gky1113
      pubmed_id: 30407521
      title: Ensembl 2019.
    - doi: 10.1093/nar/gkz966
      pubmed_id: 31691826
      title: Ensembl 2020.
    - doi: 10.1186/1471-2105-11-240
      pubmed_id: 20459813
      title: 'eHive: an artificial intelligence workflow system for genomic analysis.'
    - doi: 10.1093/nar/gkab1049
      pubmed_id: null
      title: Ensembl 2022
    subjects:
    - Genomics
    - Biomedical Science
    - Comparative Genomics
    twitter: ensembl
  go:
    homepage: http://www.ensembl.org/
    name: Ensembl database of automatically annotated genomic data
    prefix: ENSEMBL
    synonyms:
    - Ensembl
    - ensembl
  integbio:
    description: "ENSEMBL is a collection of automatically annotated genome databases\
      \ for vertebrates and a number of eukaryotes, integrated with all other relevant\
      \ biological data available.\nThe repository covers data on gene annotation,\
      \ microarray probeset mapping and comparative genomics among many other topics.\n\
      Information may be downloaded by a variety of means: \nFor small amounts of\
      \ data, an export option is suggested.\nFor larger amounts of data, an FTP site\
      \ is provided from where a complete database may be downloaded in one of various\
      \ formats, from flat files to MySQL dumps."
    fairsharing: biodbcore-000330
    homepage: https://www.ensembl.org/index.html
    information_keywords:
    - Sequence
    maintainer: Wellcome Sanger Institute
    name: Ensembl
    prefix: nbdc00054
    pubmeds:
    - '11752248'
    - '28365736'
    status: Active
    target_keywords:
    - Genome/Gene
  logo: https://useast.ensembl.org/img/ebang-400dpi.png
  mappings:
    biocontext: ENSEMBL
    edam: '2610'
    fairsharing: FAIRsharing.fx0mw7
    go: ENSEMBL
    integbio: nbdc00054
    miriam: ensembl
    n2t: ensembl
    ncbi: ENSEMBL
    prefixcommons: ensembl
    re3data: r3d100010228
    uniprot: DB-0023
    wikidata: P594
    wikidata.entity: Q7187
  mastodon: ensembl@genomic.social
  miriam:
    deprecated: false
    description: Ensembl is a joint project between EMBL - EBI and the Sanger Institute  to
      develop a software system which produces and maintains automatic annotation
      on selected eukaryotic genomes. This collections also references outgroup organisms.
    homepage: https://www.ensembl.org/
    id: '00000003'
    name: Ensembl
    namespaceEmbeddedInLui: false
    pattern: ^((ENS[FPTG]\d{11}(\.\d+)?)|(FB\w{2}\d{7})|(Y[A-Z]{2}\d{3}[a-zA-Z](\-[A-Z])?)|([A-Z_a-z0-9]+(\.)?(t)?(\d+)?([a-z])?))$
    prefix: ensembl
    providers:
    - code: ''
      description: Ensembl US East mirror
      homepage: http://useast.ensembl.org/
      name: Ensembl US East mirror
      uri_format: http://useast.ensembl.org/id/$1
    - code: ''
      description: Ensembl Asia mirror
      homepage: http://asia.ensembl.org/
      name: Ensembl Asia mirror
      uri_format: http://asia.ensembl.org/id/$1
    sampleId: ENSG00000139618
    uri_format: https://www.ensembl.org/id/$1
  n2t:
    description: Ensembl is a joint project between EMBL - EBI and the Sanger Institute  to
      develop a software system which produces and maintains automatic annotation
      on selected eukaryotic genomes. This collections also references outgroup organisms.
    example: ENSG00000139618
    homepage: https://www.ensembl.org/
    name: Ensembl at Sanger/EMBL-EBI
    namespaceEmbeddedInLui: false
    pattern: ^((ENS[FPTG]\\d{11}(\\.\\d+)?)|(FB\\w{2}\\d{7})|(Y[A-Z]{2}\\d{3}[a-zA-Z](\\-[A-Z])?)|([A-Z_a-z0-9]+(\\.)?(t)?(\\d+)?([a-z])?))$
    prefix: ensembl
    uri_format: https://www.ensembl.org/id/$1
  name: Ensembl Gene
  ncbi:
    example: HUMAN-Clone-AC005612
    homepage: http://useast.ensembl.org/index.html
    name: Database of automatically annotated genomic data
    prefix: ENSEMBL
  pattern: ^((ENS[FPTG]\d{11}(\.\d+)?)|(FB\w{2}\d{7})|(Y[A-Z]{2}\d{3}[a-zA-Z](\-[A-Z])?)|([A-Z_a-z0-9]+(\.)?(t)?(\d+)?([a-z])?))$
  prefix: ensembl
  prefixcommons:
    description: Ensembl is a joint project between EMBL - EBI and the Sanger Institute
      to develop a software system which produces and maintains automatic annotation
      on selected eukaryotic genomes.
    example: ENSG00000139618
    homepage: http://www.ensembl.org/
    keywords:
    - genome
    license: http://www.ebi.ac.uk/Information/termsofuse.html
    name: Ensembl
    pattern: ^ENS[A-Z]*[FPTG]\d{11}(\.\d+)?$
    prefix: ensembl
    pubmed_ids:
    - '16381931'
    uri_format: http://www.ensembl.org/id/$1
  providers:
  - code: bgee
    description: Gene expression in various tissues
    example: null
    first_party: null
    homepage: https://bgee.org
    name: Bgee
    publications: null
    status: null
    uri_format: https://bgee.org/?page=gene&gene_id=$1
  - code: ciliogenics
    description: CilioGenics is an integrated and open source, community friendly
      database for ciliary genes.
    example: null
    first_party: null
    homepage: https://ciliogenics.com
    name: CilioGenics
    publications: null
    status: null
    uri_format: https://ciliogenics.com/?page=General%20info&query=$1
  - code: gnomad
    description: The Genome Aggregation Database (gnomAD) is a resource developed
      by an international coalition of investigators, with the goal of aggregating
      and harmonizing both exome and genome sequencing data from a wide variety of
      large-scale sequencing projects, and making summary data available for the wider
      scientific community.
    example: null
    first_party: null
    homepage: https://gnomad.broadinstitute.org
    name: Genome Aggregation database
    publications: null
    status: null
    uri_format: https://gnomad.broadinstitute.org/gene/$1
  - code: digger
    description: Digger integrates protein-protein interactions and domain-domain
      interactions into a joint graph and maps interacting residues to exons.
    example: null
    first_party: null
    homepage: https://exbio.wzw.tum.de/digger/
    name: Domain Interaction Graph Guided Explorer
    publications:
    - doi: 10.1093/nar/gkaf384
      pmc: PMC12230681
      pubmed: '40337913'
      title: 'DIGGER 2.0: digging into the functional impact of differential splicing
        on human and mouse disorders'
      year: 2025
    status: null
    uri_format: https://exbio.wzw.tum.de/digger/ID/gene/human/$1
  - code: opentargets.genetics
    description: Open Targets Genetics is a comprehensive tool highlighting variant-centric
      statistical evidence to allow both prioritisation of candidate causal variants
      at trait-associated loci and identification of potential drug targets.
    example: null
    first_party: null
    homepage: https://genetics.opentargets.org
    name: OpenTargets Genetics
    publications: null
    status: null
    uri_format: https://genetics.opentargets.org/gene/$1
  publications:
  - doi: 10.1093/nar/gkab1049
    pmc: PMC8728283
    pubmed: '34791404'
    title: Ensembl 2022
    year: 2022
  - doi: 10.1093/nar/gkz966
    pmc: PMC7145704
    pubmed: '31691826'
    title: Ensembl 2020
    year: 2020
  - doi: 10.1093/nar/gky1113
    pmc: PMC6323964
    pubmed: '30407521'
    title: Ensembl 2019
    year: 2019
  - doi: 10.1093/nar/gkw1104
    pmc: PMC5210575
    pubmed: '27899575'
    title: Ensembl 2017
    year: 2016
  - doi: 10.1093/database/bav096
    pmc: PMC4761110
    pubmed: '26896847'
    title: Ensembl comparative genomics resources
    year: 2016
  - doi: 10.1093/database/baw053
    pmc: PMC4852398
    pubmed: '27141089'
    title: Ensembl comparative genomics resources
    year: 2016
  - doi: 10.1093/database/bav119
    pmc: PMC4756621
    pubmed: '26888907'
    title: Ensembl regulation resources
    year: 2016
  - doi: 10.1093/database/bav127
    pmc: PMC4792531
    pubmed: '26980512'
    title: ncRNA orthologies in the vertebrate lineage
    year: 2016
  - doi: 10.1093/database/baw093
    pmc: PMC4919035
    pubmed: '27337980'
    title: The Ensembl gene annotation system
    year: 2016
  - doi: 10.1186/s13059-016-0974-4
    pmc: PMC4893825
    pubmed: '27268795'
    title: The Ensembl Variant Effect Predictor
    year: 2016
  - doi: 10.1093/nar/gkv1157
    pmc: PMC4702834
    pubmed: '26687719'
    title: Ensembl 2016
    year: 2015
  - doi: 10.1186/s13059-015-0621-5
    pmc: PMC4407537
    pubmed: '25887522'
    title: The ensembl regulatory build
    year: 2015
  - doi: 10.1093/nar/gku1010
    pmc: PMC4383879
    pubmed: '25352552'
    title: Ensembl 2015
    year: 2014
  - doi: 10.1093/bioinformatics/btu613
    pmc: PMC4271150
    pubmed: '25236461'
    title: 'The Ensembl REST API: Ensembl Data for Any Language'
    year: 2014
  - doi: 10.1093/nar/gkt1196
    pmc: PMC3964975
    pubmed: '24316576'
    title: Ensembl 2014
    year: 2013
  - doi: 10.1093/bioinformatics/btt737
    pmc: PMC3967112
    pubmed: '24363377'
    title: 'WiggleTools: parallel processing of large collections of genome-wide datasets
      for visualization and statistical analysis'
    year: 2013
  - doi: 10.1093/nar/gks1236
    pmc: PMC3531136
    pubmed: '23203987'
    title: Ensembl 2013
    year: 2012
  - doi: 10.1101/gr.135350.111
    pmc: PMC3431492
    pubmed: '22955987'
    title: 'GENCODE: the reference human genome annotation for The ENCODE Project'
    year: 2012
  - doi: 10.1101/gr.137901.112
    pmc: PMC3460200
    pubmed: '22798491'
    title: Incorporating RNA-seq data into the zebrafish Ensembl genebuild
    year: 2012
  - doi: 10.1002/0471142905.hg0611s69
    pmc: PMC3099348
    pubmed: '21400687'
    title: Disease and phenotype data at Ensembl
    year: 2011
  - doi: 10.1093/nar/gkr991
    pmc: PMC3245178
    pubmed: '22086963'
    title: Ensembl 2012
    year: 2011
  - doi: 10.1093/database/bar030
    pmc: PMC3170168
    pubmed: '21785142'
    title: 'Ensembl BioMarts: a hub for data retrieval across taxonomic space'
    year: 2011
  - doi: 10.1186/1471-2105-11-238
    pmc: PMC2882931
    pubmed: '20459810'
    title: A database and API for variation, dense genotyping and resequencing data
    year: 2010
  - doi: 10.1093/bioinformatics/btq330
    pmc: PMC2916720
    pubmed: '20562413'
    title: Deriving the consequences of genomic variants with the Ensembl API and
      SNP Effect Predictor
    year: 2010
  - doi: 10.1186/1471-2105-11-240
    pmc: PMC2885371
    pubmed: '20459813'
    title: 'eHive: an artificial intelligence workflow system for genomic analysis'
    year: 2010
  - doi: 10.1093/nar/gkq1064
    pmc: PMC3013672
    pubmed: '21045057'
    title: Ensembl 2011
    year: 2010
  - doi: 10.1186/1471-2164-11-293
    pmc: PMC2894800
    pubmed: '20459805'
    title: Ensembl variation resources
    year: 2010
  - doi: 10.1186/1471-2164-11-295
    pmc: PMC2894802
    pubmed: '20459808'
    title: 'Touring Ensembl: a practical guide to genome browsing'
    year: 2010
  - doi: 10.1093/nar/gkp972
    pmc: PMC2808936
    pubmed: '19906699'
    title: Ensembl's 10th year
    year: 2009
  - doi: 10.1093/nar/gkn828
    pmc: PMC2686571
    pubmed: '19033362'
    title: Ensembl 2009
    year: 2008
  - doi: 10.1101/gr.073585.107
    pmc: PMC2652215
    pubmed: '19029536'
    title: 'EnsemblCompara GeneTrees: Complete, duplication-aware phylogenetic trees
      in vertebrates'
    year: 2008
  - doi: 10.1101/gr.076521.108
    pmc: PMC2577868
    pubmed: '18849525'
    title: Genome-wide nucleotide-level mammalian ancestor reconstruction
    year: 2008
  - doi: 10.1093/nar/gkm988
    pmc: PMC2238821
    pubmed: '18000006'
    title: Ensembl 2008
    year: 2007
  - doi: 10.1093/bfgp/elm025
    pmc: null
    pubmed: '17967807'
    title: 'Genome browsing with Ensembl: a practical overview'
    year: 2007
  - doi: 10.1093/nar/gkj133
    pmc: PMC1347495
    pubmed: '16381931'
    title: Ensembl 2006
    year: 2006
  - doi: 10.1093/nar/gkl996
    pmc: PMC1761443
    pubmed: '17148474'
    title: Ensembl 2007
    year: 2006
  - doi: 10.1038/ng0806-853a
    pmc: PMC2610433
    pubmed: '16874317'
    title: 'TranscriptSNPView: a genome-wide catalog of mouse coding variation'
    year: 2006
  - doi: 10.1093/nar/gki138
    pmc: PMC540092
    pubmed: '15608235'
    title: Ensembl 2005
    year: 2005
  - doi: 10.1101/gr.1862204
    pmc: PMC479129
    pubmed: '15123595'
    title: 'ESTGenes: alternative splicing from ESTs in Ensembl'
    year: 2004
  - doi: 10.1016/j.tig.2004.04.002
    pmc: null
    pubmed: '15145580'
    title: Genome information resources - developments at Ensembl
    year: 2004
  - doi: 10.1101/gr.1859804
    pmc: PMC479123
    pubmed: '15123589'
    title: The Ensembl analysis pipeline
    year: 2004
  - doi: 10.1101/gr.1858004
    pmc: PMC479124
    pubmed: '15123590'
    title: The Ensembl automatic gene annotation system
    year: 2004
  - doi: 10.1101/gr.1866304
    pmc: PMC479128
    pubmed: '15123594'
    title: The Ensembl computing architecture
    year: 2004
  - doi: 10.1101/gr.1857204
    pmc: PMC479122
    pubmed: '15123588'
    title: The Ensembl core software libraries
    year: 2004
  - doi: 10.1101/gr.1863004
    pmc: PMC479125
    pubmed: '15123591'
    title: 'The Ensembl Web site: mechanics of a genome browser'
    year: 2004
  - doi: 10.1093/nar/gkg083
    pmc: PMC165530
    pubmed: '12519943'
    title: 'Ensembl 2002: accommodating comparative genomics'
    year: 2003
  - doi: 10.1093/nar/30.1.38
    pmc: PMC99161
    pubmed: '11752248'
    title: The Ensembl genome database project
    year: 2002
  - doi: 10.1093/bioinformatics/btu613
    pmc: null
    pubmed: null
    title: 'The Ensembl REST API: Ensembl Data for Any Language.'
    year: null
  - doi: 10.1186/s13059-016-0974-4
    pmc: null
    pubmed: null
    title: The Ensembl Variant Effect Predictor.
    year: null
  - doi: 10.1101/gr.137901.112
    pmc: null
    pubmed: null
    title: Incorporating RNA-seq data into the zebrafish Ensembl genebuild.
    year: null
  - doi: 10.1101/gr.1863004
    pmc: null
    pubmed: null
    title: 'The Ensembl Web site: mechanics of a genome browser.'
    year: null
  - doi: 10.1101/gr.1857204
    pmc: null
    pubmed: null
    title: The Ensembl core software libraries.
    year: null
  - doi: 10.1101/gr.135350.111
    pmc: null
    pubmed: null
    title: 'GENCODE: the reference human genome annotation for The ENCODE Project.'
    year: null
  - doi: 10.1002/0471142905.hg0611s69
    pmc: null
    pubmed: null
    title: Disease and phenotype data at Ensembl.
    year: null
  - doi: 10.1016/j.tig.2004.04.002
    pmc: null
    pubmed: null
    title: Genome information resources - developments at Ensembl.
    year: null
  - doi: 10.1093/database/bar030
    pmc: null
    pubmed: null
    title: 'Ensembl BioMarts: a hub for data retrieval across taxonomic space.'
    year: null
  - doi: doi:10.1093/nar/gku1010
    pmc: null
    pubmed: null
    title: Ensembl 2015
    year: null
  - doi: 10.1093/nar/gkj133
    pmc: null
    pubmed: null
    title: Ensembl 2006.
    year: null
  - doi: 10.1093/nar/gkt1196
    pmc: null
    pubmed: null
    title: Ensembl 2014.
    year: null
  - doi: 10.1093/database/bav119
    pmc: null
    pubmed: null
    title: Ensembl regulation resources.
    year: null
  - doi: 10.1093/database/baw093
    pmc: null
    pubmed: null
    title: The Ensembl gene annotation system.
    year: null
  - doi: 10.1186/1471-2164-11-295
    pmc: null
    pubmed: null
    title: 'Touring Ensembl: a practical guide to genome browsing.'
    year: null
  - doi: 10.1093/bfgp/elm025
    pmc: null
    pubmed: null
    title: 'Genome browsing with Ensembl: a practical overview.'
    year: null
  - doi: 10.1093/nar/gkq1064
    pmc: null
    pubmed: null
    title: Ensembl 2011.
    year: null
  - doi: 10.1093/nar/gkr991
    pmc: null
    pubmed: null
    title: Ensembl 2012.
    year: null
  - doi: 10.1093/nar/gks1236
    pmc: null
    pubmed: null
    title: Ensembl 2013.
    year: null
  - doi: 10.1093/database/bav127
    pmc: null
    pubmed: null
    title: ncRNA orthologies in the vertebrate lineage.
    year: null
  - doi: 10.1093/database/baw053
    pmc: null
    pubmed: null
    title: Ensembl comparative genomics resources (Erratum)
    year: null
  - doi: 10.1101/gr.1866304
    pmc: null
    pubmed: null
    title: The Ensembl computing architecture.
    year: null
  - doi: 10.1093/nar/gki138
    pmc: null
    pubmed: null
    title: Ensembl 2005.
    year: null
  - doi: 10.1101/gr.1862204
    pmc: null
    pubmed: null
    title: 'ESTGenes: alternative splicing from ESTs in Ensembl.'
    year: null
  - doi: 10.1186/s13059-015-0621-5
    pmc: null
    pubmed: null
    title: The ensembl regulatory build.
    year: null
  - doi: 10.1093/bioinformatics/btt737
    pmc: null
    pubmed: null
    title: 'WiggleTools: parallel processing of large collections of genome-wide datasets
      for visualization and statistical analysis.'
    year: null
  - doi: 10.1093/nar/gkw1104
    pmc: null
    pubmed: null
    title: Ensembl 2017.
    year: null
  - doi: 10.1038/ng0806-853a
    pmc: null
    pubmed: null
    title: 'TranscriptSNPView: a genome-wide catalog of mouse coding variation.'
    year: null
  - doi: 10.1093/nar/gkv1157
    pmc: null
    pubmed: null
    title: Ensembl 2016.
    year: null
  - doi: 10.1101/gr.076521.108
    pmc: null
    pubmed: null
    title: Genome-wide nucleotide-level mammalian ancestor reconstruction.
    year: null
  - doi: 10.1093/nar/gkm988
    pmc: null
    pubmed: null
    title: Ensembl 2008.
    year: null
  - doi: 10.1186/1471-2164-11-293
    pmc: null
    pubmed: null
    title: Ensembl variation resources.
    year: null
  - doi: 10.1093/nar/gkg083
    pmc: null
    pubmed: null
    title: 'Ensembl 2002: accommodating comparative genomics.'
    year: null
  - doi: 10.1101/gr.073585.107
    pmc: null
    pubmed: null
    title: 'EnsemblCompara GeneTrees: Complete, duplication-aware phylogenetic trees
      in vertebrates.'
    year: null
  - doi: 10.1186/1471-2105-11-238
    pmc: null
    pubmed: null
    title: A database and API for variation, dense genotyping and resequencing data.
    year: null
  - doi: 10.1093/nar/30.1.38
    pmc: null
    pubmed: null
    title: The Ensembl genome database project.
    year: null
  - doi: 10.1093/nar/gkl996
    pmc: null
    pubmed: null
    title: Ensembl 2007.
    year: null
  - doi: 10.1093/bioinformatics/btq330
    pmc: null
    pubmed: null
    title: Deriving the consequences of genomic variants with the Ensembl API and
      SNP Effect Predictor.
    year: null
  - doi: 10.1093/nar/gkn828
    pmc: null
    pubmed: null
    title: Ensembl 2009.
    year: null
  - doi: 10.1093/nar/gkp972
    pmc: null
    pubmed: null
    title: Ensembl's 10th year.
    year: null
  - doi: 10.1093/database/bav096
    pmc: null
    pubmed: null
    title: Ensembl comparative genomics resources.
    year: null
  - doi: 10.1101/gr.1859804
    pmc: null
    pubmed: null
    title: The Ensembl analysis pipeline.
    year: null
  - doi: 10.1101/gr.1858004
    pmc: null
    pubmed: null
    title: The Ensembl automatic gene annotation system.
    year: null
  - doi: 10.1093/nar/gky1113
    pmc: null
    pubmed: null
    title: Ensembl 2019.
    year: null
  - doi: 10.1093/nar/gkz966
    pmc: null
    pubmed: null
    title: Ensembl 2020.
    year: null
  - doi: 10.1186/1471-2105-11-240
    pmc: null
    pubmed: null
    title: 'eHive: an artificial intelligence workflow system for genomic analysis.'
    year: null
  - doi: 10.1093/nar/gkab1049
    pmc: null
    pubmed: null
    title: Ensembl 2022
    year: null
  - doi: null
    pmc: null
    pubmed: '16381931'
    title: null
    year: null
  - doi: 10.1093/nar/gkz966
    pmc: null
    pubmed: '31691826'
    title: null
    year: null
  - doi: 10.1093/nar/gkaf384
    pmc: PMC12230681
    pubmed: '40337913'
    title: 'DIGGER 2.0: digging into the functional impact of differential splicing
      on human and mouse disorders'
    year: 2025
  - doi: 10.1093/bioinformatics/btu613
    pmc: null
    pubmed: null
    title: 'The Ensembl REST API: Ensembl Data for Any Language.'
    year: null
  - doi: 10.1186/s13059-016-0974-4
    pmc: null
    pubmed: null
    title: The Ensembl Variant Effect Predictor.
    year: null
  - doi: 10.1101/gr.137901.112
    pmc: null
    pubmed: null
    title: Incorporating RNA-seq data into the zebrafish Ensembl genebuild.
    year: null
  - doi: 10.1101/gr.1863004
    pmc: null
    pubmed: null
    title: 'The Ensembl Web site: mechanics of a genome browser.'
    year: null
  - doi: 10.1101/gr.1857204
    pmc: null
    pubmed: null
    title: The Ensembl core software libraries.
    year: null
  - doi: 10.1101/gr.135350.111
    pmc: null
    pubmed: null
    title: 'GENCODE: the reference human genome annotation for The ENCODE Project.'
    year: null
  - doi: 10.1002/0471142905.hg0611s69
    pmc: null
    pubmed: null
    title: Disease and phenotype data at Ensembl.
    year: null
  - doi: 10.1016/j.tig.2004.04.002
    pmc: null
    pubmed: null
    title: Genome information resources - developments at Ensembl.
    year: null
  - doi: 10.1093/database/bar030
    pmc: null
    pubmed: null
    title: 'Ensembl BioMarts: a hub for data retrieval across taxonomic space.'
    year: null
  - doi: doi:10.1093/nar/gku1010
    pmc: null
    pubmed: null
    title: Ensembl 2015
    year: null
  - doi: 10.1093/nar/gkj133
    pmc: null
    pubmed: null
    title: Ensembl 2006.
    year: null
  - doi: 10.1093/nar/gkt1196
    pmc: null
    pubmed: null
    title: Ensembl 2014.
    year: null
  - doi: 10.1093/database/bav119
    pmc: null
    pubmed: null
    title: Ensembl regulation resources.
    year: null
  - doi: 10.1093/database/baw093
    pmc: null
    pubmed: null
    title: The Ensembl gene annotation system.
    year: null
  - doi: 10.1186/1471-2164-11-295
    pmc: null
    pubmed: null
    title: 'Touring Ensembl: a practical guide to genome browsing.'
    year: null
  - doi: 10.1093/bfgp/elm025
    pmc: null
    pubmed: null
    title: 'Genome browsing with Ensembl: a practical overview.'
    year: null
  - doi: 10.1093/nar/gkq1064
    pmc: null
    pubmed: null
    title: Ensembl 2011.
    year: null
  - doi: 10.1093/nar/gkr991
    pmc: null
    pubmed: null
    title: Ensembl 2012.
    year: null
  - doi: 10.1093/nar/gks1236
    pmc: null
    pubmed: null
    title: Ensembl 2013.
    year: null
  - doi: 10.1093/database/bav127
    pmc: null
    pubmed: null
    title: ncRNA orthologies in the vertebrate lineage.
    year: null
  - doi: 10.1093/database/baw053
    pmc: null
    pubmed: null
    title: Ensembl comparative genomics resources (Erratum)
    year: null
  - doi: 10.1101/gr.1866304
    pmc: null
    pubmed: null
    title: The Ensembl computing architecture.
    year: null
  - doi: 10.1093/nar/gki138
    pmc: null
    pubmed: null
    title: Ensembl 2005.
    year: null
  - doi: 10.1101/gr.1862204
    pmc: null
    pubmed: null
    title: 'ESTGenes: alternative splicing from ESTs in Ensembl.'
    year: null
  - doi: 10.1186/s13059-015-0621-5
    pmc: null
    pubmed: null
    title: The ensembl regulatory build.
    year: null
  - doi: 10.1093/bioinformatics/btt737
    pmc: null
    pubmed: null
    title: 'WiggleTools: parallel processing of large collections of genome-wide datasets
      for visualization and statistical analysis.'
    year: null
  - doi: 10.1093/nar/gkw1104
    pmc: null
    pubmed: null
    title: Ensembl 2017.
    year: null
  - doi: 10.1038/ng0806-853a
    pmc: null
    pubmed: null
    title: 'TranscriptSNPView: a genome-wide catalog of mouse coding variation.'
    year: null
  - doi: 10.1093/nar/gkv1157
    pmc: null
    pubmed: null
    title: Ensembl 2016.
    year: null
  - doi: 10.1101/gr.076521.108
    pmc: null
    pubmed: null
    title: Genome-wide nucleotide-level mammalian ancestor reconstruction.
    year: null
  - doi: 10.1093/nar/gkm988
    pmc: null
    pubmed: null
    title: Ensembl 2008.
    year: null
  - doi: 10.1186/1471-2164-11-293
    pmc: null
    pubmed: null
    title: Ensembl variation resources.
    year: null
  - doi: 10.1093/nar/gkg083
    pmc: null
    pubmed: null
    title: 'Ensembl 2002: accommodating comparative genomics.'
    year: null
  - doi: 10.1101/gr.073585.107
    pmc: null
    pubmed: null
    title: 'EnsemblCompara GeneTrees: Complete, duplication-aware phylogenetic trees
      in vertebrates.'
    year: null
  - doi: 10.1186/1471-2105-11-238
    pmc: null
    pubmed: null
    title: A database and API for variation, dense genotyping and resequencing data.
    year: null
  - doi: 10.1093/nar/30.1.38
    pmc: null
    pubmed: null
    title: The Ensembl genome database project.
    year: null
  - doi: 10.1093/nar/gkl996
    pmc: null
    pubmed: null
    title: Ensembl 2007.
    year: null
  - doi: 10.1093/bioinformatics/btq330
    pmc: null
    pubmed: null
    title: Deriving the consequences of genomic variants with the Ensembl API and
      SNP Effect Predictor.
    year: null
  - doi: 10.1093/nar/gkn828
    pmc: null
    pubmed: null
    title: Ensembl 2009.
    year: null
  - doi: 10.1093/nar/gkp972
    pmc: null
    pubmed: null
    title: Ensembl's 10th year.
    year: null
  - doi: 10.1093/database/bav096
    pmc: null
    pubmed: null
    title: Ensembl comparative genomics resources.
    year: null
  - doi: 10.1101/gr.1859804
    pmc: null
    pubmed: null
    title: The Ensembl analysis pipeline.
    year: null
  - doi: 10.1101/gr.1858004
    pmc: null
    pubmed: null
    title: The Ensembl automatic gene annotation system.
    year: null
  - doi: 10.1093/nar/gky1113
    pmc: null
    pubmed: null
    title: Ensembl 2019.
    year: null
  - doi: 10.1093/nar/gkz966
    pmc: null
    pubmed: null
    title: Ensembl 2020.
    year: null
  - doi: 10.1186/1471-2105-11-240
    pmc: null
    pubmed: null
    title: 'eHive: an artificial intelligence workflow system for genomic analysis.'
    year: null
  - doi: 10.1093/nar/gkab1049
    pmc: null
    pubmed: null
    title: Ensembl 2022
    year: null
  - doi: null
    pmc: null
    pubmed: '16381931'
    title: null
    year: null
  - doi: 10.1093/nar/gkz966
    pmc: null
    pubmed: '31691826'
    title: null
    year: null
  - doi: 10.1093/nar/gkaf384
    pmc: PMC12230681
    pubmed: '40337913'
    title: 'DIGGER 2.0: digging into the functional impact of differential splicing
      on human and mouse disorders'
    year: 2025
  - doi: 10.1093/bioinformatics/btu613
    pmc: null
    pubmed: null
    title: 'The Ensembl REST API: Ensembl Data for Any Language.'
    year: null
  - doi: 10.1186/s13059-016-0974-4
    pmc: null
    pubmed: null
    title: The Ensembl Variant Effect Predictor.
    year: null
  - doi: 10.1101/gr.137901.112
    pmc: null
    pubmed: null
    title: Incorporating RNA-seq data into the zebrafish Ensembl genebuild.
    year: null
  - doi: 10.1101/gr.1863004
    pmc: null
    pubmed: null
    title: 'The Ensembl Web site: mechanics of a genome browser.'
    year: null
  - doi: 10.1101/gr.1857204
    pmc: null
    pubmed: null
    title: The Ensembl core software libraries.
    year: null
  - doi: 10.1101/gr.135350.111
    pmc: null
    pubmed: null
    title: 'GENCODE: the reference human genome annotation for The ENCODE Project.'
    year: null
  - doi: 10.1002/0471142905.hg0611s69
    pmc: null
    pubmed: null
    title: Disease and phenotype data at Ensembl.
    year: null
  - doi: 10.1016/j.tig.2004.04.002
    pmc: null
    pubmed: null
    title: Genome information resources - developments at Ensembl.
    year: null
  - doi: 10.1093/database/bar030
    pmc: null
    pubmed: null
    title: 'Ensembl BioMarts: a hub for data retrieval across taxonomic space.'
    year: null
  - doi: doi:10.1093/nar/gku1010
    pmc: null
    pubmed: null
    title: Ensembl 2015
    year: null
  - doi: 10.1093/nar/gkj133
    pmc: null
    pubmed: null
    title: Ensembl 2006.
    year: null
  - doi: 10.1093/nar/gkt1196
    pmc: null
    pubmed: null
    title: Ensembl 2014.
    year: null
  - doi: 10.1093/database/bav119
    pmc: null
    pubmed: null
    title: Ensembl regulation resources.
    year: null
  - doi: 10.1093/database/baw093
    pmc: null
    pubmed: null
    title: The Ensembl gene annotation system.
    year: null
  - doi: 10.1186/1471-2164-11-295
    pmc: null
    pubmed: null
    title: 'Touring Ensembl: a practical guide to genome browsing.'
    year: null
  - doi: 10.1093/bfgp/elm025
    pmc: null
    pubmed: null
    title: 'Genome browsing with Ensembl: a practical overview.'
    year: null
  - doi: 10.1093/nar/gkq1064
    pmc: null
    pubmed: null
    title: Ensembl 2011.
    year: null
  - doi: 10.1093/nar/gkr991
    pmc: null
    pubmed: null
    title: Ensembl 2012.
    year: null
  - doi: 10.1093/nar/gks1236
    pmc: null
    pubmed: null
    title: Ensembl 2013.
    year: null
  - doi: 10.1093/database/bav127
    pmc: null
    pubmed: null
    title: ncRNA orthologies in the vertebrate lineage.
    year: null
  - doi: 10.1093/database/baw053
    pmc: null
    pubmed: null
    title: Ensembl comparative genomics resources (Erratum)
    year: null
  - doi: 10.1101/gr.1866304
    pmc: null
    pubmed: null
    title: The Ensembl computing architecture.
    year: null
  - doi: 10.1093/nar/gki138
    pmc: null
    pubmed: null
    title: Ensembl 2005.
    year: null
  - doi: 10.1101/gr.1862204
    pmc: null
    pubmed: null
    title: 'ESTGenes: alternative splicing from ESTs in Ensembl.'
    year: null
  - doi: 10.1186/s13059-015-0621-5
    pmc: null
    pubmed: null
    title: The ensembl regulatory build.
    year: null
  - doi: 10.1093/bioinformatics/btt737
    pmc: null
    pubmed: null
    title: 'WiggleTools: parallel processing of large collections of genome-wide datasets
      for visualization and statistical analysis.'
    year: null
  - doi: 10.1093/nar/gkw1104
    pmc: null
    pubmed: null
    title: Ensembl 2017.
    year: null
  - doi: 10.1038/ng0806-853a
    pmc: null
    pubmed: null
    title: 'TranscriptSNPView: a genome-wide catalog of mouse coding variation.'
    year: null
  - doi: 10.1093/nar/gkv1157
    pmc: null
    pubmed: null
    title: Ensembl 2016.
    year: null
  - doi: 10.1101/gr.076521.108
    pmc: null
    pubmed: null
    title: Genome-wide nucleotide-level mammalian ancestor reconstruction.
    year: null
  - doi: 10.1093/nar/gkm988
    pmc: null
    pubmed: null
    title: Ensembl 2008.
    year: null
  - doi: 10.1186/1471-2164-11-293
    pmc: null
    pubmed: null
    title: Ensembl variation resources.
    year: null
  - doi: 10.1093/nar/gkg083
    pmc: null
    pubmed: null
    title: 'Ensembl 2002: accommodating comparative genomics.'
    year: null
  - doi: 10.1101/gr.073585.107
    pmc: null
    pubmed: null
    title: 'EnsemblCompara GeneTrees: Complete, duplication-aware phylogenetic trees
      in vertebrates.'
    year: null
  - doi: 10.1186/1471-2105-11-238
    pmc: null
    pubmed: null
    title: A database and API for variation, dense genotyping and resequencing data.
    year: null
  - doi: 10.1093/nar/30.1.38
    pmc: null
    pubmed: null
    title: The Ensembl genome database project.
    year: null
  - doi: 10.1093/nar/gkl996
    pmc: null
    pubmed: null
    title: Ensembl 2007.
    year: null
  - doi: 10.1093/bioinformatics/btq330
    pmc: null
    pubmed: null
    title: Deriving the consequences of genomic variants with the Ensembl API and
      SNP Effect Predictor.
    year: null
  - doi: 10.1093/nar/gkn828
    pmc: null
    pubmed: null
    title: Ensembl 2009.
    year: null
  - doi: 10.1093/nar/gkp972
    pmc: null
    pubmed: null
    title: Ensembl's 10th year.
    year: null
  - doi: 10.1093/database/bav096
    pmc: null
    pubmed: null
    title: Ensembl comparative genomics resources.
    year: null
  - doi: 10.1101/gr.1859804
    pmc: null
    pubmed: null
    title: The Ensembl analysis pipeline.
    year: null
  - doi: 10.1101/gr.1858004
    pmc: null
    pubmed: null
    title: The Ensembl automatic gene annotation system.
    year: null
  - doi: 10.1093/nar/gky1113
    pmc: null
    pubmed: null
    title: Ensembl 2019.
    year: null
  - doi: 10.1093/nar/gkz966
    pmc: null
    pubmed: null
    title: Ensembl 2020.
    year: null
  - doi: 10.1186/1471-2105-11-240
    pmc: null
    pubmed: null
    title: 'eHive: an artificial intelligence workflow system for genomic analysis.'
    year: null
  - doi: 10.1093/nar/gkab1049
    pmc: null
    pubmed: null
    title: Ensembl 2022
    year: null
  - doi: null
    pmc: null
    pubmed: '16381931'
    title: null
    year: null
  - doi: 10.1093/nar/gkz966
    pmc: null
    pubmed: '31691826'
    title: null
    year: null
  - doi: 10.1093/nar/gkaf384
    pmc: PMC12230681
    pubmed: '40337913'
    title: 'DIGGER 2.0: digging into the functional impact of differential splicing
      on human and mouse disorders'
    year: 2025
  - doi: 10.1093/bioinformatics/btu613
    pmc: null
    pubmed: null
    title: 'The Ensembl REST API: Ensembl Data for Any Language.'
    year: null
  - doi: 10.1186/s13059-016-0974-4
    pmc: null
    pubmed: null
    title: The Ensembl Variant Effect Predictor.
    year: null
  - doi: 10.1101/gr.137901.112
    pmc: null
    pubmed: null
    title: Incorporating RNA-seq data into the zebrafish Ensembl genebuild.
    year: null
  - doi: 10.1101/gr.1863004
    pmc: null
    pubmed: null
    title: 'The Ensembl Web site: mechanics of a genome browser.'
    year: null
  - doi: 10.1101/gr.1857204
    pmc: null
    pubmed: null
    title: The Ensembl core software libraries.
    year: null
  - doi: 10.1101/gr.135350.111
    pmc: null
    pubmed: null
    title: 'GENCODE: the reference human genome annotation for The ENCODE Project.'
    year: null
  - doi: 10.1002/0471142905.hg0611s69
    pmc: null
    pubmed: null
    title: Disease and phenotype data at Ensembl.
    year: null
  - doi: 10.1016/j.tig.2004.04.002
    pmc: null
    pubmed: null
    title: Genome information resources - developments at Ensembl.
    year: null
  - doi: 10.1093/database/bar030
    pmc: null
    pubmed: null
    title: 'Ensembl BioMarts: a hub for data retrieval across taxonomic space.'
    year: null
  - doi: doi:10.1093/nar/gku1010
    pmc: null
    pubmed: null
    title: Ensembl 2015
    year: null
  - doi: 10.1093/nar/gkj133
    pmc: null
    pubmed: null
    title: Ensembl 2006.
    year: null
  - doi: 10.1093/nar/gkt1196
    pmc: null
    pubmed: null
    title: Ensembl 2014.
    year: null
  - doi: 10.1093/database/bav119
    pmc: null
    pubmed: null
    title: Ensembl regulation resources.
    year: null
  - doi: 10.1093/database/baw093
    pmc: null
    pubmed: null
    title: The Ensembl gene annotation system.
    year: null
  - doi: 10.1186/1471-2164-11-295
    pmc: null
    pubmed: null
    title: 'Touring Ensembl: a practical guide to genome browsing.'
    year: null
  - doi: 10.1093/bfgp/elm025
    pmc: null
    pubmed: null
    title: 'Genome browsing with Ensembl: a practical overview.'
    year: null
  - doi: 10.1093/nar/gkq1064
    pmc: null
    pubmed: null
    title: Ensembl 2011.
    year: null
  - doi: 10.1093/nar/gkr991
    pmc: null
    pubmed: null
    title: Ensembl 2012.
    year: null
  - doi: 10.1093/nar/gks1236
    pmc: null
    pubmed: null
    title: Ensembl 2013.
    year: null
  - doi: 10.1093/database/bav127
    pmc: null
    pubmed: null
    title: ncRNA orthologies in the vertebrate lineage.
    year: null
  - doi: 10.1093/database/baw053
    pmc: null
    pubmed: null
    title: Ensembl comparative genomics resources (Erratum)
    year: null
  - doi: 10.1101/gr.1866304
    pmc: null
    pubmed: null
    title: The Ensembl computing architecture.
    year: null
  - doi: 10.1093/nar/gki138
    pmc: null
    pubmed: null
    title: Ensembl 2005.
    year: null
  - doi: 10.1101/gr.1862204
    pmc: null
    pubmed: null
    title: 'ESTGenes: alternative splicing from ESTs in Ensembl.'
    year: null
  - doi: 10.1186/s13059-015-0621-5
    pmc: null
    pubmed: null
    title: The ensembl regulatory build.
    year: null
  - doi: 10.1093/bioinformatics/btt737
    pmc: null
    pubmed: null
    title: 'WiggleTools: parallel processing of large collections of genome-wide datasets
      for visualization and statistical analysis.'
    year: null
  - doi: 10.1093/nar/gkw1104
    pmc: null
    pubmed: null
    title: Ensembl 2017.
    year: null
  - doi: 10.1038/ng0806-853a
    pmc: null
    pubmed: null
    title: 'TranscriptSNPView: a genome-wide catalog of mouse coding variation.'
    year: null
  - doi: 10.1093/nar/gkv1157
    pmc: null
    pubmed: null
    title: Ensembl 2016.
    year: null
  - doi: 10.1101/gr.076521.108
    pmc: null
    pubmed: null
    title: Genome-wide nucleotide-level mammalian ancestor reconstruction.
    year: null
  - doi: 10.1093/nar/gkm988
    pmc: null
    pubmed: null
    title: Ensembl 2008.
    year: null
  - doi: 10.1186/1471-2164-11-293
    pmc: null
    pubmed: null
    title: Ensembl variation resources.
    year: null
  - doi: 10.1093/nar/gkg083
    pmc: null
    pubmed: null
    title: 'Ensembl 2002: accommodating comparative genomics.'
    year: null
  - doi: 10.1101/gr.073585.107
    pmc: null
    pubmed: null
    title: 'EnsemblCompara GeneTrees: Complete, duplication-aware phylogenetic trees
      in vertebrates.'
    year: null
  - doi: 10.1186/1471-2105-11-238
    pmc: null
    pubmed: null
    title: A database and API for variation, dense genotyping and resequencing data.
    year: null
  - doi: 10.1093/nar/30.1.38
    pmc: null
    pubmed: null
    title: The Ensembl genome database project.
    year: null
  - doi: 10.1093/nar/gkl996
    pmc: null
    pubmed: null
    title: Ensembl 2007.
    year: null
  - doi: 10.1093/bioinformatics/btq330
    pmc: null
    pubmed: null
    title: Deriving the consequences of genomic variants with the Ensembl API and
      SNP Effect Predictor.
    year: null
  - doi: 10.1093/nar/gkn828
    pmc: null
    pubmed: null
    title: Ensembl 2009.
    year: null
  - doi: 10.1093/nar/gkp972
    pmc: null
    pubmed: null
    title: Ensembl's 10th year.
    year: null
  - doi: 10.1093/database/bav096
    pmc: null
    pubmed: null
    title: Ensembl comparative genomics resources.
    year: null
  - doi: 10.1101/gr.1859804
    pmc: null
    pubmed: null
    title: The Ensembl analysis pipeline.
    year: null
  - doi: 10.1101/gr.1858004
    pmc: null
    pubmed: null
    title: The Ensembl automatic gene annotation system.
    year: null
  - doi: 10.1093/nar/gky1113
    pmc: null
    pubmed: null
    title: Ensembl 2019.
    year: null
  - doi: 10.1093/nar/gkz966
    pmc: null
    pubmed: null
    title: Ensembl 2020.
    year: null
  - doi: 10.1186/1471-2105-11-240
    pmc: null
    pubmed: null
    title: 'eHive: an artificial intelligence workflow system for genomic analysis.'
    year: null
  - doi: 10.1093/nar/gkab1049
    pmc: null
    pubmed: null
    title: Ensembl 2022
    year: null
  - doi: null
    pmc: null
    pubmed: '16381931'
    title: null
    year: null
  - doi: 10.1093/nar/gkz966
    pmc: null
    pubmed: '31691826'
    title: null
    year: null
  - doi: 10.1093/nar/gkaf384
    pmc: PMC12230681
    pubmed: '40337913'
    title: 'DIGGER 2.0: digging into the functional impact of differential splicing
      on human and mouse disorders'
    year: 2025
  re3data:
    description: The Ensembl project produces genome databases for vertebrates and
      other eukaryotic species. Ensembl is a joint project between the European Bioinformatics
      Institute (EBI) and the Wellcome Trust Sanger Institute (WTSI) to develop a
      software system that produces and maintains automatic annotation on selected
      genomes.The Ensembl project was started in 1999, some years before the draft
      human genome was completed. Even at that early stage it was clear that manual
      annotation of 3 billion base pairs of sequence would not be able to offer researchers
      timely access to the latest data. The goal of Ensembl was therefore to automatically
      annotate the genome, integrate this annotation with other available biological
      data and make all this publicly available via the web. Since the website's launch
      in July 2000, many more genomes have been added to Ensembl and the range of
      available data has also expanded to include comparative genomics, variation
      and regulatory data. Ensembl is a joint project between European Bioinformatics
      Institute (EBI), an outstation of the European Molecular Biology Laboratory
      (EMBL), and the Wellcome Trust Sanger Institute (WTSI). Both institutes are
      located on the Wellcome Trust Genome Campus in Hinxton, south of the city of
      Cambridge, United Kingdom.
    doi: 10.17616/R39K5B
    homepage: https://www.ensembl.org/index.html
    license: CC
    name: Ensembl
    prefix: r3d100010228
    synonyms:
    - e!
    xrefs:
      nif: 0000-21145
      omics: '01647'
  synonyms:
  - Ensembl
  uniprot:
    abbreviation: Ensembl
    category: Genome annotation databases
    homepage: https://www.ensembl.org/
    name: Ensembl eukaryotic genome annotation project
    prefix: DB-0023
    publications:
    - doi: 10.1093/nar/gkz966
      pubmed: '31691826'
    uri_format: https://www.ensembl.org/id/$1
  wikidata:
    database: Q7187
    description: identifier for a gene as per the Ensembl (European Bioinformatics
      Institute and the Wellcome Trust Sanger Institute) database
    example:
    - ENSG00000115414
    - ENSG00000198125
    - ENSMUSG00000018893
    - ENSMUSG00000026193
    - ENSRNOG00000014288
    homepage: https://www.ensembl.org
    name: Ensembl gene ID
    pattern: ^(ENS(|MUS|RNO)G\d{11})|(Y[A-P][LR]\d{3}[CW](-[A-G])?)$
    prefix: P594
    uri_format: https://identifiers.org/ensembl/$1
    uri_format_rdf: http://rdf.ebi.ac.uk/resource/ensembl/$1
ensembl.bacteria:
  biocontext:
    prefix: ENSEMBL.BACTERIA
  contact:
    email: flicek@ebi.ac.uk
    github: null
    name: Paul Flicek
    orcid: 0000-0002-3897-7955
  fairsharing:
    abbreviation: Ensembl Bacteria
    description: Ensembl Bacteria is a browser for bacterial and archaeal genomes.
      These are taken from the databases of the International Nucleotide Sequence
      Database Collaboration (the European Nucleotide Archive at the EBI, GenBank
      at the NCBI, and the DNA Database of Japan).
    homepage: https://bacteria.ensembl.org/index.html
    license: Apache 2.0 License
    name: Ensembl Bacteria
    prefix: FAIRsharing.zsgmvd
    publications:
    - doi: 10.1093/nar/gkz890
      pubmed_id: 31598706
      title: Ensembl Genomes 2020-enabling non-vertebrate genomic research.
    - doi: 10.1093/nar/gkv1209
      pubmed_id: 26578574
      title: 'Ensembl Genomes 2016: more genomes, more complexity.'
    subjects:
    - Genomics
    - Comparative Genomics
    twitter: ensemblgenomes
  integbio:
    description: EnsemblBacteria is a database of thousands of bacterial genomes.
      The database can be searched by gene, genome, or BLAST, and several tools are
      available. Data and ensembl software can also be downloaded.
    homepage: http://bacteria.ensembl.org/index.html
    information_keywords:
    - Sequence
    maintainer: Ensembl Project
    name: EnsemblBacteria
    prefix: nbdc00433
    pubmeds:
    - '19884133'
    status: Active
    target_keywords:
    - Genome/Gene
  mappings:
    biocontext: ENSEMBL.BACTERIA
    fairsharing: FAIRsharing.zsgmvd
    integbio: nbdc00433
    miriam: ensembl.bacteria
    n2t: ensembl.bacteria
    prefixcommons: ensembl.bacteria
    re3data: r3d100011195
    uniprot: DB-0147
  miriam:
    deprecated: false
    description: Ensembl Genomes consists of five sub-portals (for bacteria, protists,
      fungi, plants and invertebrate metazoa) designed to complement the availability
      of vertebrate genomes in Ensembl. This collection is concerned with bacterial
      genomes.
    homepage: https://bacteria.ensembl.org/
    id: '00000202'
    name: Ensembl Bacteria
    namespaceEmbeddedInLui: false
    pattern: ^((EB\w+)|([A-Z0-9]+\_[A-Z0-9]+))$
    prefix: ensembl.bacteria
    sampleId: MU9_3181
    uri_format: https://bacteria.ensembl.org/id/$1
  n2t:
    description: Ensembl Genomes consists of five sub-portals (for bacteria, protists,
      fungi, plants and invertebrate metazoa) designed to complement the availability
      of vertebrate genomes in Ensembl. This collection is concerned with bacterial
      genomes.
    example: MU9_3181
    homepage: https://bacteria.ensembl.org/
    name: Ensembl Bacteria at EBI
    namespaceEmbeddedInLui: false
    pattern: ^((EB\w+)|([A-Z0-9]+\_[A-Z0-9]+))$
    prefix: ensembl.bacteria
    uri_format: https://bacteria.ensembl.org/id/$1
  prefix: ensembl.bacteria
  prefixcommons:
    description: Ensembl Genomes consists of five sub-portals (for bacteria, protists,
      fungi, plants and invertebrate metazoa) designed to complement the availability
      of vertebrate genomes in Ensembl. This collection is concerned with bacterial
      genomes.
    example: EBESCT00000015660
    homepage: http://bacteria.ensembl.org/
    keywords:
    - genome
    name: Ensembl Bacteria
    pattern: ^EB\w+$
    prefix: ensembl.bacteria
    pubmed_ids:
    - '19884133'
    uri_format: http://bacteria.ensembl.org/[?species_name]/Gene/Summary?g=$1
  publications:
  - doi: 10.1093/nar/gkz890
    pmc: PMC6943047
    pubmed: '31598706'
    title: Ensembl Genomes 2020-enabling non-vertebrate genomic research
    year: 2020
  - doi: 10.1093/nar/gkv1209
    pmc: PMC4702859
    pubmed: '26578574'
    title: 'Ensembl Genomes 2016: more genomes, more complexity'
    year: 2015
  - doi: 10.1093/nar/gkp871
    pmc: PMC2808935
    pubmed: '19884133'
    title: 'Ensembl Genomes: extending Ensembl across the taxonomic space'
    year: 2009
  - doi: 10.1093/nar/gkz890
    pmc: null
    pubmed: null
    title: Ensembl Genomes 2020-enabling non-vertebrate genomic research.
    year: null
  - doi: 10.1093/nar/gkv1209
    pmc: null
    pubmed: null
    title: 'Ensembl Genomes 2016: more genomes, more complexity.'
    year: null
  - doi: null
    pmc: null
    pubmed: '19884133'
    title: null
    year: null
  - doi: 10.1093/nar/gkz890
    pmc: null
    pubmed: '31598706'
    title: null
    year: null
  - doi: 10.1093/nar/gkz890
    pmc: null
    pubmed: null
    title: Ensembl Genomes 2020-enabling non-vertebrate genomic research.
    year: null
  - doi: 10.1093/nar/gkv1209
    pmc: null
    pubmed: null
    title: 'Ensembl Genomes 2016: more genomes, more complexity.'
    year: null
  - doi: null
    pmc: null
    pubmed: '19884133'
    title: null
    year: null
  - doi: 10.1093/nar/gkz890
    pmc: null
    pubmed: '31598706'
    title: null
    year: null
  re3data:
    description: This site provides access to complete, annotated genomes from bacteria
      and archaea (present in the European Nucleotide Archive) through the Ensembl
      graphical user interface (genome browser). Ensembl Bacteria contains genomes
      from annotated INSDC records that are loaded into Ensembl multi-species databases,
      using the INSDC annotation import pipeline.
    doi: 10.17616/R3WD1C
    homepage: https://bacteria.ensembl.org/index.html
    license: other
    name: Ensembl Bacteria
    prefix: r3d100011195
    synonyms:
    - e!EnsemblBacteria
    xrefs:
      nif: 0000-33711
  uniprot:
    abbreviation: EnsemblBacteria
    category: Genome annotation databases
    homepage: https://bacteria.ensembl.org/
    name: Ensembl bacterial and archaeal genome annotation project
    prefix: DB-0147
    publications:
    - doi: 10.1093/nar/gkz890
      pubmed: '31598706'
ensembl.fungi:
  biocontext:
    prefix: ENSEMBL.FUNGI
  contact:
    email: flicek@ebi.ac.uk
    github: null
    name: Paul Flicek
    orcid: 0000-0002-3897-7955
  fairsharing:
    abbreviation: Ensembl Fungi
    description: Ensembl Fungi is a browser for fungal genomes. A majority of these
      are taken from the databases of the International Nucleotide Sequence Database
      Collaboration (the European Nucleotide Archive at the EBI, GenBank at the NCBI,
      and the DNA Database of Japan); in some cases, the annotation has been taken
      directly from the websites of the data generators.
    homepage: http://fungi.ensembl.org/index.html
    license: Apache 2.0 License
    name: Ensembl Fungi
    prefix: FAIRsharing.bg5xqs
    publications:
    - doi: 10.1093/nar/gkz890
      pubmed_id: 31598706
      title: Ensembl Genomes 2020-enabling non-vertebrate genomic research.
    - doi: 10.1093/nar/gkv1209
      pubmed_id: 26578574
      title: 'Ensembl Genomes 2016: more genomes, more complexity.'
    subjects:
    - Genomics
    - Comparative Genomics
    twitter: ensemblgenomes
  go:
    homepage: http://fungi.ensembl.org/
    name: Ensembl Fungi, the Ensembl database for accessing genome-scale data from
      fungi.
    prefix: EnsemblFungi
  integbio:
    description: EnsemblFungi is a database of fungal genomes. The database contains
      sequences from dozens of fungal species which can be searched by gene, genome,
      or BLAST. Tools for processing data are also available, as are bulk data downloads.
    homepage: http://fungi.ensembl.org/index.html
    information_keywords:
    - Sequence
    maintainer: Ensembl Project
    name: EnsemblFungi
    prefix: nbdc00434
    pubmeds:
    - '19884133'
    status: Active
    target_keywords:
    - Genome/Gene
  mappings:
    biocontext: ENSEMBL.FUNGI
    fairsharing: FAIRsharing.bg5xqs
    go: EnsemblFungi
    integbio: nbdc00434
    miriam: ensembl.fungi
    n2t: ensembl.fungi
    prefixcommons: ensembl.fungi
    re3data: r3d100011196
    uniprot: DB-0148
  miriam:
    deprecated: false
    description: Ensembl Genomes consists of five sub-portals (for bacteria, protists,
      fungi, plants and invertebrate metazoa) designed to complement the availability
      of vertebrate genomes in Ensembl. This collection is concerned with fungal genomes.
    homepage: https://fungi.ensembl.org/
    id: '00000206'
    name: Ensembl Fungi
    namespaceEmbeddedInLui: false
    pattern: ^[A-Z-a-z0-9]+$
    prefix: ensembl.fungi
    sampleId: CADAFLAT00006211
    uri_format: https://fungi.ensembl.org/id/$1
  n2t:
    description: Ensembl Genomes consists of five sub-portals (for bacteria, protists,
      fungi, plants and invertebrate metazoa) designed to complement the availability
      of vertebrate genomes in Ensembl. This collection is concerned with fungal genomes.
    example: CADAFLAT00006211
    homepage: https://fungi.ensembl.org/
    name: Enzembl Fungi at EBI
    namespaceEmbeddedInLui: false
    pattern: ^[A-Z-a-z0-9]+$
    prefix: ensembl.fungi
    uri_format: https://fungi.ensembl.org/id/$1
  prefix: ensembl.fungi
  prefixcommons:
    description: Ensembl Genomes consists of five sub-portals (for bacteria, protists,
      fungi, plants and invertebrate metazoa) designed to complement the availability
      of vertebrate genomes in Ensembl. This collection is concerned with bacterial
      genomes.
    example: CADAFLAT00006211
    homepage: http://fungi.ensembl.org/
    keywords:
    - genome
    name: Ensembl Fungi
    pattern: ^\w+$
    prefix: ensembl.fungi
    uri_format: http://fungi.ensembl.org/[?species_name]/Gene/Summary?g=$1
  publications:
  - doi: 10.1093/nar/gkz890
    pmc: PMC6943047
    pubmed: '31598706'
    title: Ensembl Genomes 2020-enabling non-vertebrate genomic research
    year: 2020
  - doi: 10.1093/nar/gkv1209
    pmc: PMC4702859
    pubmed: '26578574'
    title: 'Ensembl Genomes 2016: more genomes, more complexity'
    year: 2015
  re3data:
    description: EnsemblFungi is a genome-centric portal for fungal species. It is
      a project to maintain annotation on selected genomes.
    doi: 10.17616/R3RK74
    homepage: http://fungi.ensembl.org/index.html
    license: other
    name: Ensembl Fungi
    prefix: r3d100011196
    synonyms:
    - e!EnsemblFungi
    xrefs:
      nif: 0000-33718
  uniprot:
    abbreviation: EnsemblFungi
    category: Genome annotation databases
    homepage: https://fungi.ensembl.org/
    name: Ensembl fungal genome annotation project
    prefix: DB-0148
    publications:
    - doi: 10.1093/nar/gkz890
      pubmed: '31598706'
  uri_format: https://fungi.ensembl.org/id/$1
ensembl.metazoa:
  biocontext:
    prefix: ENSEMBL.METAZOA
  contact:
    email: flicek@ebi.ac.uk
    github: null
    name: Paul Flicek
    orcid: 0000-0002-3897-7955
  fairsharing:
    abbreviation: Ensembl Metazoa
    description: Ensembl Metazoa provides access to genomes of metazoans of interest
      in disease, environmental sciences, agriculture and economic concern. Extensive
      coverage exists of diptera, nematodes, lepidoptera and hymenoptera.
    homepage: https://metazoa.ensembl.org/index.html
    license: Apache 2.0 License
    name: Ensembl Metazoa
    prefix: FAIRsharing.c23cqq
    publications:
    - doi: 10.1093/nar/gkz890
      pubmed_id: 31598706
      title: Ensembl Genomes 2020-enabling non-vertebrate genomic research.
    - doi: 10.1093/nar/gkv1209
      pubmed_id: 26578574
      title: 'Ensembl Genomes 2016: more genomes, more complexity.'
    subjects:
    - Genomics
    - Comparative Genomics
    twitter: ensemblgenomes
  go:
    homepage: http://metazoa.ensembl.org/
    name: Ensembl Metazoa, the Ensembl database for accessing genome-scale data from
      non-vertebrate metazoa.
    prefix: EnsemblMetazoa
    uri_format: http://www.ensemblgenomes.org/id/$1
  integbio:
    description: EnsemblMetazoa is a database of metazoan genomes. The database contains
      sequences from dozens of metazoa which can be searched by gene, genome, or BLAST.
      Tools for processing data are also available, as are bulk data downloads.
    homepage: http://metazoa.ensembl.org/index.html
    information_keywords:
    - Sequence
    maintainer: Ensembl Project
    name: EnsemblMetazoa
    prefix: nbdc00435
    pubmeds:
    - '19884133'
    status: Active
    target_keywords:
    - Genome/Gene
  mappings:
    biocontext: ENSEMBL.METAZOA
    fairsharing: FAIRsharing.c23cqq
    go: EnsemblMetazoa
    integbio: nbdc00435
    miriam: ensembl.metazoa
    n2t: ensembl.metazoa
    prefixcommons: ensembl.metazoa
    re3data: r3d100011198
    uniprot: DB-0149
  miriam:
    deprecated: false
    description: Ensembl Genomes consists of five sub-portals (for bacteria, protists,
      fungi, plants and invertebrate metazoa) designed to complement the availability
      of vertebrate genomes in Ensembl. This collection is concerned with metazoa
      genomes.
    homepage: https://metazoa.ensembl.org/
    id: '00000204'
    name: Ensembl Metazoa
    namespaceEmbeddedInLui: false
    pattern: ^\w+(\.)?\d+$
    prefix: ensembl.metazoa
    sampleId: FBtr0084214
    uri_format: https://metazoa.ensembl.org/id/$1
  n2t:
    description: Ensembl Genomes consists of five sub-portals (for bacteria, protists,
      fungi, plants and invertebrate metazoa) designed to complement the availability
      of vertebrate genomes in Ensembl. This collection is concerned with metazoa
      genomes.
    example: FBtr0084214
    homepage: https://metazoa.ensembl.org/
    name: Enzembl Metazoa at EBI
    namespaceEmbeddedInLui: false
    pattern: ^\w+(\.)?\d+$
    prefix: ensembl.metazoa
    uri_format: https://metazoa.ensembl.org/id/$1
  prefix: ensembl.metazoa
  prefixcommons:
    description: Ensembl Genomes consists of five sub-portals (for bacteria, protists,
      fungi, plants and invertebrate metazoa) designed to complement the availability
      of vertebrate genomes in Ensembl. This collection is concerned with bacterial
      genomes.
    example: AGAP006864
    homepage: http://metazoa.ensembl.org/
    keywords:
    - genome
    name: Ensembl Metazoa
    pattern: ^\w+(\.)?\d+$
    prefix: ensembl.metazoa
    uri_format: http://metazoa.ensembl.org/[?species_name]/Gene/Summary?g=$1
  publications:
  - doi: 10.1093/nar/gkz890
    pmc: PMC6943047
    pubmed: '31598706'
    title: Ensembl Genomes 2020-enabling non-vertebrate genomic research
    year: 2020
  - doi: 10.1093/nar/gkv1209
    pmc: PMC4702859
    pubmed: '26578574'
    title: 'Ensembl Genomes 2016: more genomes, more complexity'
    year: 2015
  - doi: 10.1093/nar/gkz890
    pmc: null
    pubmed: null
    title: Ensembl Genomes 2020-enabling non-vertebrate genomic research.
    year: null
  - doi: 10.1093/nar/gkv1209
    pmc: null
    pubmed: null
    title: 'Ensembl Genomes 2016: more genomes, more complexity.'
    year: null
  - doi: 10.1093/nar/gkz890
    pmc: null
    pubmed: '31598706'
    title: null
    year: null
  re3data:
    description: Ensembl Metazoa is a genome-centric portal for metazoan species of
      scientific interest.
    doi: 10.17616/R3H33M
    homepage: https://metazoa.ensembl.org/index.html
    license: other
    name: Ensembl Metazoa
    prefix: r3d100011198
    synonyms:
    - e!EnsemblMetazoa
    xrefs:
      nif: 0000-33714
  uniprot:
    abbreviation: EnsemblMetazoa
    category: Genome annotation databases
    homepage: https://metazoa.ensembl.org/
    name: Ensembl metazoan genome annotation project
    prefix: DB-0149
    publications:
    - doi: 10.1093/nar/gkz890
      pubmed: '31598706'
    uri_format: https://www.ensemblgenomes.org/id/$1
ensembl.plant:
  biocontext:
    prefix: ENSEMBL.PLANT
  mappings:
    biocontext: ENSEMBL.PLANT
    miriam: ensembl.plant
    n2t: ensembl.plant
    prefixcommons: ensembl.plant
  miriam:
    deprecated: false
    description: Ensembl Genomes consists of five sub-portals (for bacteria, protists,
      fungi, plants and invertebrate metazoa) designed to complement the availability
      of vertebrate genomes in Ensembl. This collection is concerned with plant genomes.
    homepage: https://plants.ensembl.org/
    id: '00000205'
    name: Ensembl Plants
    namespaceEmbeddedInLui: false
    pattern: ^\w+(\.\d+)?(\.\d+)?$
    prefix: ensembl.plant
    sampleId: AT1G73965
    uri_format: https://plants.ensembl.org/id/$1
  n2t:
    description: Ensembl Genomes consists of five sub-portals (for bacteria, protists,
      fungi, plants and invertebrate metazoa) designed to complement the availability
      of vertebrate genomes in Ensembl. This collection is concerned with plant genomes.
    example: AT1G73965
    homepage: https://plants.ensembl.org/
    name: Enzembl Plants at EBI
    namespaceEmbeddedInLui: false
    pattern: ^\w+(\.\d+)?(\.\d+)?$
    prefix: ensembl.plant
    uri_format: https://plants.ensembl.org/id/$1
  prefix: ensembl.plant
  prefixcommons:
    description: Ensembl Genomes consists of five sub-portals (for bacteria, protists,
      fungi, plants and invertebrate metazoa) designed to complement the availability
      of vertebrate genomes in Ensembl. This collection is concerned with bacterial
      genomes.
    example: LOC_Os12g44300
    homepage: http://plants.ensembl.org/
    keywords:
    - genome
    name: Ensembl Plants
    pattern: ^\w+$
    prefix: ensembl.plant
    synonyms:
    - ensembl_plants
    uri_format: http://plants.ensembl.org/[?species_name]/Gene/Summary?g=$1
ensembl.protist:
  biocontext:
    prefix: ENSEMBL.PROTIST
  mappings:
    biocontext: ENSEMBL.PROTIST
    miriam: ensembl.protist
    n2t: ensembl.protist
    prefixcommons: ensembl.protist
  miriam:
    deprecated: false
    description: Ensembl Genomes consists of five sub-portals (for bacteria, protists,
      fungi, plants and invertebrate metazoa) designed to complement the availability
      of vertebrate genomes in Ensembl. This collection is concerned with protist
      genomes.
    homepage: https://protists.ensembl.org
    id: '00000203'
    name: Ensembl Protists
    namespaceEmbeddedInLui: false
    pattern: ^\w+$
    prefix: ensembl.protist
    sampleId: PF3D7_1328700
    uri_format: https://protists.ensembl.org/id/$1
  n2t:
    description: Ensembl Genomes consists of five sub-portals (for bacteria, protists,
      fungi, plants and invertebrate metazoa) designed to complement the availability
      of vertebrate genomes in Ensembl. This collection is concerned with protist
      genomes.
    example: PF3D7_1328700
    homepage: https://protists.ensembl.org
    name: Ensembl Protists at EBI
    namespaceEmbeddedInLui: false
    pattern: ^\w+$
    prefix: ensembl.protist
    uri_format: https://protists.ensembl.org/id/$1
  prefix: ensembl.protist
  prefixcommons:
    description: Ensembl Genomes consists of five sub-portals (for bacteria, protists,
      fungi, plants and invertebrate metazoa) designed to complement the availability
      of vertebrate genomes in Ensembl. This collection is concerned with bacterial
      genomes.
    example: PFC0120w
    homepage: http://protists.ensembl.org/
    keywords:
    - genome
    name: Ensembl Protists
    pattern: ^\w+$
    prefix: ensembl.protist
    synonyms:
    - ensembl_protists
    uri_format: http://protists.ensembl.org/[?species_name]/Gene/Summary?g=$1
ensemblglossary:
  example: 0000198
  mappings:
    ols: ensemblglossary
  ols:
    description: The Ensembl glossary lists the terms, data types and file types that
      are used in Ensembl and describes how they are used.
    download_owl: https://raw.githubusercontent.com/Ensembl/ensembl-glossary/master/ensembl-glossary.owl
    homepage: http://ensembl.org/glossary
    name: Ensembl Glossary
    prefix: ensemblglossary
    uri_format: http://ensembl.org/glossary/ENSGLOSS_$1
    version: '2023-01-04'
    version.iri: http://ensembl.org/glossary/ensembl-glossary/releases/2023-01-04/ensembl-glossary.owl
  pattern: ^\d{7}$
  prefix: ensemblglossary
  uri_format: http://ensembl.org/glossary/ENSGLOSSARY_$1
envipath:
  fairsharing:
    abbreviation: enviPath
    contact:
      email: admin@envipath.org
      name: Jörg Wicker
      orcid: 0000-0003-0533-3368
    description: enviPath is both a database and a prediction system, for the microbial
      biotransformation of organic environmental contaminants. The database provides
      the possibility to store and view experimentally observed biotransformation
      pathways, and supports the annotation of pathways with experimental and environmental
      conditions. The pathway prediction system provides different relative reasoning
      models to predict likely biotransformation pathways and products.
    homepage: https://envipath.org
    license: CC BY-NC 4.0
    name: enviPath
    prefix: FAIRsharing.g0c5qn
    publications:
    - doi: 10.1093/nar/gkv1229
      pubmed_id: 26582924
      title: enviPath - The environmental contaminant biotransformation pathway resource.
    - doi: 10.1186/s13321-021-00543-x
      pubmed_id: null
      title: 'Holistic Evaluation of Biodegradation Pathway Prediction: Assessing
        Multi-Step Reactions and Intermediate Products'
    - doi: 10.1039/C6EM00697C
      pubmed_id: null
      title: 'Eawag-Soil in enviPath: a new resource for exploring regulatory pesticide
        soil biodegradation pathways and half-life data'
    subjects:
    - Environmental Science
    twitter: envipath
  integbio:
    description: enviPath is both a database and a prediction system, for the microbial
      biotransformation of organic environmental contaminants. The database provides
      the possibility to store and view experimentally observed biotransformation
      pathways, and supports the annotation of pathways with experimental and environmental
      conditions. The pathway prediction system provides different relative reasoning
      models to predict likely biotransformation pathways and products.
    fairsharing: FAIRsharing.g0c5qn
    homepage: https://envipath.org
    information_keywords:
    - Method
    - Environment
    - Interaction/Pathway
    - Bibliography/Documents
    maintainer: Eawag||Johannes Gutenberg University
    name: enviPath
    prefix: nbdc02011
    pubmeds:
    - '26582924'
    status: Active
    target_keywords:
    - Chemical compound
  mappings:
    fairsharing: FAIRsharing.g0c5qn
    integbio: nbdc02011
    miriam: envipath
    re3data: r3d100012715
  miriam:
    deprecated: false
    description: enviPath is a database and prediction system for the microbial biotransformation
      of organic environmental contaminants. The database provides the possibility
      to store and view experimentally observed biotransformation pathways. The pathway
      prediction system provides different relative reasoning models to predict likely
      biotransformation pathways and products.
    homepage: https://envipath.org/
    id: '00000727'
    name: enviPath
    namespaceEmbeddedInLui: false
    pattern: ^[\w^_]{8}-[\w^_]{4}-[\w^_]{4}-[\w^_]{4}-[\w^_]{12}\/[\w-]+\/[\w^_]{8}-[\w^_]{4}-[\w^_]{4}-[\w^_]{4}-[\w^_]{12}$
    prefix: envipath
    sampleId: 32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/compound/b545cabc-8c9e-4b20-8848-efa015b481ea
    uri_format: https://envipath.org/package/$1
  prefix: envipath
  publications:
  - doi: 10.1186/s13321-021-00543-x
    pmc: PMC8414759
    pubmed: '34479624'
    title: 'Holistic evaluation of biodegradation pathway prediction: assessing multi-step
      reactions and intermediate products'
    year: 2021
  - doi: 10.1039/c6em00697c
    pmc: null
    pubmed: '28229138'
    title: 'Eawag-Soil in enviPath: a new resource for exploring regulatory pesticide
      soil biodegradation pathways and half-life data'
    year: 2017
  - doi: 10.1093/nar/gkv1229
    pmc: PMC4702869
    pubmed: '26582924'
    title: enviPath--The environmental contaminant biotransformation pathway resource
    year: 2015
  re3data:
    description: enviPath is a database and prediction system for the microbial biotransformation
      of organic environmental contaminants. The database provides the possibility
      to store and view experimentally observed biotransformation pathways. The pathway
      prediction system provides different relative reasoning models to predict likely
      biotransformation pathways and products.
    doi: 10.17616/R3WR3K
    homepage: https://envipath.org/
    name: enviPath
    prefix: r3d100012715
    synonyms:
    - The enironmental contaminant biotransormation pathway resource
    - 'including: Biocatalysis/Biodegradation Database EAWAG PPS Rules'
    xrefs:
      omics: '11129'
envo:
  aberowl:
    description: An ontology of environmental systems, components, and processes.
    download_owl: http://aber-owl.net/media/ontologies/ENVO/63/envo.owl
    homepage: http://environmentontology.org/
    name: Environment Ontology
    prefix: ENVO
  agroportal:
    contact:
      email: pier.buttigieg@awi.de
      name: Pier Luigi Buttigieg
    description: ENVO is an ontology which represents knowledge about environments,environmental
      processes, ecosystems, habitats, and related entities
    example_uri: http://purl.obolibrary.org/obo/ENVO_00005746
    homepage: http://environmentontology.org/
    license: CC0-1.0
    name: Environment Ontology
    prefix: ENVO
    publications:
    - https://doi.org/10.1186/s13326-016-0097-6
    repository: https://github.com/EnvironmentOntology/envo
    version: '2025-10-20'
  bartoc:
    abbreviation: ENVO
    description: The Environment Ontology (EnvO) provides a controlled, structured
      vocabulary that is designed to support the annotation of any organism or biological
      sample with environment descriptors. EnvO contains terms for biomes, environmental
      features, and environmental material." EnvO enables "a concise, standardised,
      and comprehensive description of environment that is key to the integration,
      archiving and federated searching of environmental data. As a tool for the life
      sciences, we see EnvO bringing benefits similar to those of the Gene Ontology
      (GO). Through promoting consistent annotation grounded in an ontological framework,
      we hope to facilitate the semantic retrieval of any biological record anchored
      to EnvO. Records contained in sequence databases, 'omic data repositories, tissue
      banks and museum collections are prime candidates for EnvO annotation. However,
      EnvO is also suitable for the annotation of any record that has an environmental
      component. For example, you can use EnvO terms to provide information on the
      environment of remote sensing devices or simply to tag a picture that you took
      at the weekend. Further, the EnvO project is closely tied with GAZ, a first
      step towards an open source gazetteer constructed on ontological principles.
      GAZ describes places and place names as well as the relations between them and,
      when linked with EnvO descriptors, provides a basis to infer environment from
      place names.
    homepage: http://www.environmentontology.org/
    name: Environment Ontology
    prefix: '562'
  biocontext:
    prefix: ENVO
  bioportal:
    description: 'Official PURL: http://purl.obolibrary.org/obo/envo.owl The most
      up-to-date information about ENVO is available here: http://www.obofoundry.org/ontology/envo.html
      EnvO is an OBO Foundry and Library ontology for the concise, controlled description
      of environmental entities such as ecosystems, environmental processes, and environmental
      qualities. It closely interoperates with a broad collection of other OBO ontologies
      and is used in a diverse range of projects. , ENVO is an ontology which represents
      knowledge about environments,environmental processes, ecosystems, habitats,
      and related entities'
    homepage: http://environmentontology.org/
    license: CC0-1.0
    name: Environment Ontology
    prefix: ENVO
    publications:
    - http://environmentontology.org/
    version: '2025-10-20'
  fairsharing:
    abbreviation: ENVO
    description: The Environment Ontology (EnvO) provides a controlled, structured
      vocabulary that is designed to support the annotation of any organism or biological
      sample with environment descriptors. EnvO contains terms ranging from astronomical
      objects, through planetary scale biomes, to nanomaterials. Further, these terms
      are interlinked with logical axioms describing their composition, colocalisation,
      and relationships to environmental and biological processes. Using ENVO terms
      for an environmental description allows a comprehensive description of environment
      that is key to machine-assisted integration, archiving and federated searching
      of environmental data.
    domains:
    - environmental material
    - marine metagenome
    - microbiome
    homepage: http://environmentontology.org/
    license: CC-BY-3.0
    name: Environment Ontology
    prefix: FAIRsharing.azqskx
    publications:
    - doi: 10.1186/s13326-016-0097-6
      pubmed: '27664130'
      title: 'The environment ontology in 2016: bridging domains with increased scope,
        semantic density, and interoperation'
      year: 2016
    - doi: 10.1186/2041-1480-4-43
      pubmed: '24330602'
      title: 'The environment ontology: contextualising biological and biomedical
        entities'
      year: 2013
    - doi: 10.1093/database/baw005
      pubmed: '26896844'
      title: 'EXTRACT: interactive extraction of environment metadata and term suggestion
        for metagenomic sample annotation'
      year: 2016
    - doi: 10.7717/peerj.1470
      pubmed: '26713234'
      title: Emerging semantics to link phenotype and environment
      year: 2015
    repository: https://github.com/EnvironmentOntology/envo
    subjects:
    - Environmental Science
    - Life Science
    - Nutritional Science
    - Ecology
    - Epidemiology
    twitter: envoTweets
  mappings:
    aberowl: ENVO
    agroportal: ENVO
    bartoc: '562'
    biocontext: ENVO
    bioportal: ENVO
    fairsharing: FAIRsharing.azqskx
    miriam: envo
    n2t: envo
    obofoundry: envo
    ols: envo
    ontobee: ENVO
    tib: envo
    wikidata.entity: Q31110555
  miriam:
    deprecated: false
    description: The Environment Ontology is a resource and research target for the
      semantically controlled description of environmental entities. The ontology's
      initial aim was the representation of the biomes, environmental features, and
      environmental materials pertinent to genomic and microbiome-related investigations.
    homepage: http://purl.bioontology.org/ontology/ENVO/
    id: 00000591
    name: Environment Ontology
    namespaceEmbeddedInLui: true
    pattern: ^ENVO:\d{7,8}$
    prefix: envo
    sampleId: 09200010
    uri_format: http://purl.bioontology.org/ontology/ENVO/ENVO:$1
  n2t:
    description: The Environment Ontology is a resource and research target for the
      semantically controlled description of environmental entities. The ontology's
      initial aim was the representation of the biomes, environmental features, and
      environmental materials pertinent to genomic and microbiome-related investigations.
    example: 09200010
    homepage: http://purl.bioontology.org/ontology/ENVO/
    name: The Environment Ontology through BioPortal
    namespaceEmbeddedInLui: true
    pattern: ^ENVO:\d{8}$
    prefix: envo
    uri_format: http://purl.bioontology.org/ontology/ENVO/ENVO:$1
  obofoundry:
    appears_in:
    - agro
    - cdno
    - ecocore
    - ecto
    - foodon
    - ons
    - pco
    - rbo
    - uberon
    - scdo
    contact: pier.buttigieg@awi.de
    contact.github: pbuttigieg
    contact.label: Pier Luigi Buttigieg
    contact.orcid: 0000-0002-4366-3088
    depends_on:
    - chebi
    - foodon
    - go
    - ncbitaxon
    - pco
    - po
    - ro
    - uberon
    deprecated: false
    description: An ontology of environmental systems, components, and processes.
    domain: environment
    download.json: http://purl.obolibrary.org/obo/envo.json
    download.obo: http://purl.obolibrary.org/obo/envo.obo
    download.owl: http://purl.obolibrary.org/obo/envo.owl
    homepage: http://environmentontology.org/
    license: CC0 1.0
    license.url: http://creativecommons.org/publicdomain/zero/1.0/
    logo: https://obofoundry.org/images/envo.png
    name: Environment Ontology
    preferredPrefix: ENVO
    prefix: envo
    publications:
    - id: https://doi.org/10.1186/2041-1480-4-43
      preferred: true
      title: 'The environment ontology: contextualising biological and biomedical
        entities'
    - id: https://doi.org/10.1186/s13326-016-0097-6
      title: 'The environment ontology in 2016: bridging domains with increased scope,
        semantic density, and interoperation'
    repository: https://github.com/EnvironmentOntology/envo
  ols:
    description: ENVO is an ontology which represents knowledge about environments,environmental
      processes, ecosystems, habitats, and related entities
    download_owl: http://purl.obolibrary.org/obo/envo.owl
    homepage: http://environmentontology.org/
    name: The Environment Ontology
    prefix: envo
    tracker: https://github.com/EnvironmentOntology/envo/issues/
    version: '2025-10-20'
    version.iri: http://purl.obolibrary.org/obo/envo/releases/2025-10-20/envo.owl
  ontobee:
    library: Library
    name: Environment Ontology
    prefix: ENVO
  pattern: ^\d{7,8}$
  prefix: envo
  publications:
  - doi: 10.1093/database/baw005
    pmc: PMC4761108
    pubmed: '26896844'
    title: 'EXTRACT: interactive extraction of environment metadata and term suggestion
      for metagenomic sample annotation'
    year: 2016
  - doi: 10.1186/s13326-016-0097-6
    pmc: PMC5035502
    pubmed: '27664130'
    title: 'The environment ontology in 2016: bridging domains with increased scope,
      semantic density, and interoperation'
    year: 2016
  - doi: 10.7717/peerj.1470
    pmc: PMC4690371
    pubmed: '26713234'
    title: Emerging semantics to link phenotype and environment
    year: 2015
  - doi: 10.1186/2041-1480-4-43
    pmc: PMC3904460
    pubmed: '24330602'
    title: 'The environment ontology: contextualising biological and biomedical entities'
    year: 2013
  - doi: 10.1186/2041-1480-4-43
    pmc: null
    pubmed: null
    title: 'The environment ontology: contextualising biological and biomedical entities'
    year: null
  - doi: 10.1186/s13326-016-0097-6
    pmc: null
    pubmed: null
    title: 'The environment ontology in 2016: bridging domains with increased scope,
      semantic density, and interoperation'
    year: null
  - doi: 10.1186/s13326-016-0097-6
    pmc: null
    pubmed: '27664130'
    title: 'The environment ontology in 2016: bridging domains with increased scope,
      semantic density, and interoperation'
    year: 2016
  - doi: 10.1186/2041-1480-4-43
    pmc: null
    pubmed: '24330602'
    title: 'The environment ontology: contextualising biological and biomedical entities'
    year: 2013
  - doi: 10.1093/database/baw005
    pmc: null
    pubmed: '26896844'
    title: 'EXTRACT: interactive extraction of environment metadata and term suggestion
      for metagenomic sample annotation'
    year: 2016
  - doi: 10.7717/peerj.1470
    pmc: null
    pubmed: '26713234'
    title: Emerging semantics to link phenotype and environment
    year: 2015
  tib:
    description: ENVO is an ontology which represents knowledge about environments,environmental
      processes, ecosystems, habitats, and related entities
    download_owl: http://purl.obolibrary.org/obo/envo.owl
    homepage: http://environmentontology.org/
    keywords:
    - FAIR Data Spaces
    - NFDI4CHEM
    - ESS
    - DataPLANT
    - NFDI4CAT
    - earth sciences
    - life sciences, biology
    name: The Environment Ontology
    prefix: envo
    tracker: https://github.com/EnvironmentOntology/envo/issues/
    version.iri: http://purl.obolibrary.org/obo/envo/releases/2025-10-20/envo.owl
  uri_format: http://purl.obolibrary.org/obo/ENVO_$1
envthes:
  aberowl:
    description: EnvThes, EnvThes compiles a set of terms in order to describe in
      a harmonised way data resulting from observations and measurements of ecosystem
      processes across different domain specific sciences. It is used by DEIMS-SDR
      for common keywords for annotation and quering metadata purposes.
    name: Thesaurus for long-term ecological research, monitoring, experiments
    prefix: ENVTHES
    version: 5.0.16
  bartoc:
    abbreviation: EnvThes
    description: EnvThes compiles a set of terms in order to describe in a harmonised
      way data resulting from observations and measurements of ecosystem processes
      across different domain specific sciences. It is used by DEIMS-SDR for common
      keywords for annotation and quering metadata purposes.
    homepage: https://vocabs.lter-europe.net/envthes/
    license: CC-BY-4.0
    name: Environmental Thesaurus
    prefix: '20684'
  bioportal:
    contact:
      email: barbara.magagna@gmail.com
      name: Barbara Magagna
    description: EnvThes, EnvThes compiles a set of terms in order to describe in
      a harmonised way data resulting from observations and measurements of ecosystem
      processes across different domain specific sciences. It is used by DEIMS-SDR
      for common keywords for annotation and quering metadata purposes.
    license: CC-BY-4.0
    name: Thesaurus for long-term ecological research, monitoring, experiments
    prefix: ENVTHES
    version: 5.0.16
  ecoportal:
    description: EnvThes compiles a set of terms in order to describe in a harmonised
      way data resulting from observations and measurements of ecosystem processes
      across different domain specific sciences. It is used by DEIMS-SDR for common
      keywords for annotation and quering metadata purposes.
    license: CC-BY-4.0
    name: Environmental Thesaurus
    prefix: ENVTHES
    publications:
    - https://www.w3.org/2013/share-psi/wiki/images/0/00/Schentz_et_al_SemanticDataIntegrationforLTER.pdf
    version: 5.0.15
  example: 03733596-c643-4c14-a7bc-3048591a3f2d
  fairsharing:
    abbreviation: EnvThes
    contact:
      email: barbara.magagna@umweltbundesamt.at
      name: Barbara Magagna
      orcid: 0000-0003-2195-3997
    description: The Environmental Thesaurus is a controlled vocabulary built to aid
      integration of the data resulting from long term ecological research and monitoring
      in Europe (eLTER). It provides described and semantically well defined terms
      for later analysis and it serves as harmonized specification of parameters in
      the observation and measurement of ecosystem processes.
    domains:
    - Geographic location
    - Monitoring
    homepage: https://github.com/LTER-Europe/EnvThes
    license: CC-BY-4.0
    name: Environmental Thesaurus
    prefix: FAIRsharing.dS2o69
    repository: https://github.com/LTER-Europe/EnvThes/issues
    subjects:
    - Geochemistry
    - Environmental Science
    - Ecology
    - Natural Science
    user_defined_tags:
    - Observations
  mappings:
    aberowl: ENVTHES
    bartoc: '20684'
    bioportal: ENVTHES
    ecoportal: ENVTHES
    fairsharing: FAIRsharing.dS2o69
    tib: et
  prefix: envthes
  tib:
    description: EnvThes compiles a set of terms in order to describe in a harmonised
      way data resulting from observations and measurements of ecosystem processes
      across different domain specific sciences. It is used by DEIMS-SDR for common
      keywords for annotation and quering metadata purposes.
    download_rdf: https://raw.githubusercontent.com/LTER-Europe/EnvThes/main/EnvThes.ttl
    homepage: https://vocabs.lter-europe.net/envthes/en/
    keywords:
    - ESS
    - earth sciences
    name: Environmental Thesaurus
    prefix: et
    tracker: https://github.com/LTER-Europe/EnvThes/issues
    uri_format: http://vocabs.lter-europe.net/EnvThes/$1
  uri_format: http://vocabs.lter-europe.net/EnvThes/$1
enzo:
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: Enzo Life Sciences is an antibody vendor.
  domain: antibody
  example: ALX-210-175
  homepage: https://www.enzolifesciences.com
  keywords:
  - antibodies
  - life sciences
  - vendor
  name: Enzo Life Sciences
  prefix: enzo
  synonyms:
  - Enzo Life Sciences
  uri_format: https://www.enzolifesciences.com/$1
eo:
  aberowl:
    description: The Ethnicity Ontology (EO) has been developed by extending the Basic
      Formal Ontology 2 standard in order to have a common reference for ethnicity
      concepts for semantic integration of datasets. It attempts to utilise iterated
      proxy markers for ethnicity such language spoken and interpreter requirements
      in order to support health care research studies.
    download_owl: http://aber-owl.net/media/ontologies/EO/1/eo.owl
    homepage: www.ClinInf.eu
    name: Ethnicity Ontoloy
    prefix: EO
    version: '1.0'
  agroportal:
    contact:
      email: jaiswalp@science.oregonstate.edu
      name: Pankaj Jaiswal
    description: The Plant Environment Ontology describes the treatments,growing conditions,
      and/or study types used in various types of plant biology experiments. The subjects
      of the studies may also include in vitro plant structures (PO:0000004). A plant
      treatment is the most specific,and may be a component of a plant growing condition,
      and the plant study type. The broadest classes are the plant study types where
      the terms can be used to identify the growth study facility. Each growth facility
      such as field study, growth chamber, green house etc is a environment on its
      own and it may also involve instances of biotic and abiotic treatments and different
      growing conditions.
    example_uri: http://purl.obolibrary.org/obo/EO_0007263
    homepage: http://planteome.org/
    license: CC-BY-4.0
    name: Plant Environment Ontology
    prefix: EO
    publications:
    - http://wiki.plantontology.org/index.php/Category:Publications
    repository: https://github.com/Planteome/plant-experimental-conditions-ontology
    version: releases/2023-11-10
  banana: EO
  biocontext:
    prefix: EO
  download_obo: https://github.com/Planteome/plant-experimental-conditions-ontology/raw/refs/heads/master/peco.obo
  download_owl: https://github.com/Planteome/plant-experimental-conditions-ontology/raw/refs/heads/master/peco.owl
  mappings:
    aberowl: EO
    agroportal: EO
    biocontext: EO
    miriam: eo
    n2t: eo
    obofoundry: eo
    prefixcommons: eo
  miriam:
    deprecated: false
    description: The Plant Environment Ontology is a set of standardized controlled
      vocabularies to describe various types of treatments given to an individual
      plant / a population or a cultured tissue and/or cell type sample to evaluate
      the response on its exposure. It also includes the study types, where the terms
      can be used to identify the growth study facility. Each growth facility such
      as field study, growth chamber, green house etc is a environment on its own
      it may also involve instances of biotic and abiotic environments as supplemental
      treatments used in these studies.
    homepage: http://bioportal.bioontology.org/ontologies/PECO
    id: 00000518
    name: Plant Environment Ontology
    namespaceEmbeddedInLui: true
    pattern: ^(P)?EO\:\d{7}$
    prefix: eo
    providers:
    - code: ''
      description: Plant Environment Ontology through Gramene
      homepage: http://archive.gramene.org/db/ontology/search_term?id=EO:0007359
      name: Plant Environment Ontology through Gramene
      uri_format: http://archive.gramene.org/db/ontology/search?query=EO:$1
    sampleId: '0007404'
    uri_format: http://purl.bioontology.org/ontology/PECO/EO:$1
  n2t:
    description: The Plant Environment Ontology is a set of standardized controlled
      vocabularies to describe various types of treatments given to an individual
      plant / a population or a cultured tissue and/or cell type sample to evaluate
      the response on its exposure. It also includes the study types, where the terms
      can be used to identify the growth study facility. Each growth facility such
      as field study, growth chamber, green house etc is a environment on its own
      it may also involve instances of biotic and abiotic environments as supplemental
      treatments used in these studies.
    example: '0007404'
    homepage: http://bioportal.bioontology.org/ontologies/PECO
    name: Plant Environment Ontology through BioPortal
    namespaceEmbeddedInLui: true
    pattern: ^(P)?EO\:\d{7}$
    prefix: eo
    uri_format: http://purl.bioontology.org/ontology/PECO/EO:$1
  obofoundry:
    appears_in:
    - foodon
    contact: jaiswalp@science.oregonstate.edu
    contact.github: jaiswalp
    contact.label: Pankaj Jaiswal
    contact.orcid: 0000-0002-1005-8383
    deprecated: true
    description: A structured, controlled vocabulary which describes the treatments,
      growing conditions, and/or study types used in plant biology experiments.
    domain: environment
    download.obo: http://purl.obolibrary.org/obo/eo.obo
    download.owl: http://purl.obolibrary.org/obo/eo.owl
    homepage: http://planteome.org/
    license: CC BY 4.0
    license.url: https://creativecommons.org/licenses/by/4.0/
    logo: http://planteome.org/sites/default/files/garland_logo.PNG
    name: Plant Environment Ontology
    prefix: eo
    publications:
    - id: https://www.ncbi.nlm.nih.gov/pubmed/22847540
      title: Ontologies as integrative tools for plant science.
    repository: https://github.com/Planteome/plant-environment-ontology
  pattern: ^\d{7}$
  prefix: eo
  prefixcommons:
    bioportal: '1036'
    description: A structured controlled vocabulary for the representation of plant
      environmental conditions.
    example: EO_0007191
    homepage: http://www.gramene.org/plant_ontology/ontology_browse.html#eo
    keywords:
    - obo
    - plant
    name: Plant environmental conditions
    pattern: ^EO_\d+$
    prefix: eo
  publications:
  - doi: 10.3732/ajb.1200222
    pmc: PMC3492881
    pubmed: '22847540'
    title: Ontologies as integrative tools for plant science
    year: 2012
eol:
  aberowl:
    description: L'ontologie EOL décrit les conditions d'environnement des élevages
      d'animaux domestiques. Elle décrit plus particulièrement les modalités de l'alimentation,
      de l'environnement, de la structure des élevages et des systèmes d'élevage
    download_owl: http://aber-owl.net/media/ontologies/EOL/1/eol.owl
    name: Environment Ontology for Livestock
    prefix: EOL
  agroportal:
    contact:
      email: jerome.bugeon@inrae.fr
      name: Jerome Bugeon
    description: L'ontologie EOL décrit les conditions d'environnement des élevages
      d'animaux domestiques. Elle décrit plus particulièrement les modalités de l'alimentation,
      de l'environnement, de la structure des élevages et des systèmes d'élevage.,
      The EOL ontology describes environmental conditions of livestock breeding. It
      includes feeding modalities, the structure of breeding systems and their environment.,
      the structure of breeding systems and their environment.
    example_uri: http://opendata.inra.fr/EOL/EOL_0000301
    homepage: http://www.atol-ontology.com/
    license: CC-BY-4.0
    name: Environment Ontology for Livestock
    prefix: EOL
    publications:
    - http://www.atol-ontology.com/rb/fr/6
    version: '1.2'
  bioportal:
    contact:
      email: matthieu.reichstadt@clermont.inra.fr
      name: Reichstadt Matthieu
    description: L'ontologie EOL décrit les conditions d'environnement des élevages
      d'animaux domestiques. Elle décrit plus particulièrement les modalités de l'alimentation,
      de l'environnement, de la structure des élevages et des systèmes d'élevage
    name: Environment Ontology for Livestock
    prefix: EOL
  contact:
    email: pylebail@rennes.inra.fr
    github: null
    name: Pierre-Yves LeBail
    orcid: 0000-0002-8310-5195
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: The EOL ontology describes environmental conditions of livestock farms.
    More specifically, it describes the feeding modalities, the environment, the structure
    of livestock farms and rearing systems.
  download_owl: http://sicpa-web.cati.inrae.fr/ontologies/visualisation/ontologie/atol/creation_fichier_owl.php?filename=eol.owl
  example: 0001927
  fairsharing:
    abbreviation: EOL
    description: The EOL ontology describes environmental conditions of livestock
      farms. More specifically, it describes the feeding modalities, the environment,
      the structure of livestock farms and rearing systems.
    homepage: http://www.atol-ontology.com/en/eol-2/
    license: CC-BY-4.0
    name: Environment Ontology for Livestock
    prefix: FAIRsharing.w7bw2y
    subjects:
    - Agriculture
    - Environmental Science
    - Animal Husbandry
    user_defined_tags:
    - Livestock
    - Species-environment interaction
  mappings:
    aberowl: EOL
    agroportal: EOL
    bioportal: EOL
    fairsharing: FAIRsharing.w7bw2y
    ols: eol
    re3data: r3d100011663
  ols:
    contact: pylebail@rennes.inra.fr
    description: L'ontologie EOL décrit les conditions d'environnement des élevages
      d'animaux domestiques. Elle décrit plus particulièrement les modalités de l'alimentation,
      de l'environnement, de la structure des élevages et des systèmes d'élevage
    download: http://www.atol-ontology.com/public/telechargement/eol.owl
    homepage: http://www.atol-ontology.com
    name: Environment Ontology for Livestock
    prefix: eol
    version: '2018-09-13'
  pattern: ^\d{7}$
  prefix: eol
  re3data:
    description: EOL’s platforms and instruments collect large and often unique data
      sets that must be validated, archived and made available to the research community.
      The goal of EOL data services is to advance science through delivering high-quality
      project data and metadata in ways that are as transparent, secure, and easily
      accessible as possible - today and into the future. By adhering to accepted
      standards in data formats and data services, EOL provides infrastructure to
      facilitate discovery and direct access to data and software from state-of-the-art
      commercial and locally-developed applications. EOL’s data services are committed
      to the highest standard of data stewardship from collection to validation to
      archival.
    doi: 10.17616/R3VK8F
    homepage: https://www.eol.ucar.edu/
    name: EOL
    prefix: r3d100011663
    synonyms:
    - Earth Observing Laboratory
  uri_format: http://purl.org/obo/owlEOL_$1
eol.schema:
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: Predicates in the Encyclopedia of Life data schema for describing animals,
    plants, and other organisms
  example: body_symmetry
  github_request_issue: 1421
  homepage: https://eol.org/terms/glossary/
  name: Encyclopedia of Life Schema
  prefix: eol.schema
  uri_format: http://eol.org/schema/terms/$1
eolife:
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: A collaborative project intended to create an encyclopedia documenting
    all living species known to science
  example: '1044544'
  fairsharing:
    abbreviation: EOL
    contact:
      email: secretariat@eol.org
      name: EOL Secretariat
      orcid: 0000-0002-9943-2342
    description: The Encyclopedia of Life (EOL) is a collaborative encyclopedia to
      describe all known living species. It identifies sources of biodiversity knowledge
      that are legally and practically shareable; integrates them with other sources
      and adds metadata; provides searching and other services; and collaborates with
      other projects to support data sharing.
    homepage: https://eol.org/
    license: https://creativecommons.org/licenses
    name: Encyclopedia of Life
    prefix: FAIRsharing.3J6NYn
    publications: []
    subjects:
    - Taxonomy
    - Ecology
    - Biodiversity
    - Biology
    twitter: eol
  homepage: https://eol.org
  mappings:
    fairsharing: FAIRsharing.3J6NYn
    re3data: r3d100010229
    wikidata: P830
  name: Encyclopedia of Life
  pattern: ^\d+$
  prefix: eolife
  re3data:
    description: Our knowledge of the many life-forms on Earth - of animals, plants,
      fungi, protists and bacteria - is scattered around the world in books, journals,
      databases, websites, specimen collections, and in the minds of people everywhere.
      Imagine what it would mean if this information could be gathered together and
      made available to everyone – anywhere – at a moment’s notice. This dream is
      becoming a reality through the Encyclopedia of Life.
    doi: 10.17616/R35S3D
    homepage: https://eol.org/
    license: CC
    name: Encyclopedia of Life
    prefix: r3d100010229
    synonyms:
    - Global access to knowledge about life on earth
    - eol
  uri_format: https://eol.org/pages/$1
  wikidata:
    description: eol.org item reference number
    example:
    - '1044544'
    - '110747'
    - '1174823'
    - '20831'
    - '327419'
    homepage: http://eol.org/api/docs/pages
    name: Encyclopedia of Life ID
    pattern: ^[1-9]\d{0,7}$
    prefix: P830
    uri_format: https://eol.org/pages/$1
epawaste:
  contact:
    email: brennan.thomas@epa.gov
    github: null
    name: Tom Brennan
    orcid: null
  contributor:
    email: m.naguthana@hotmail.com
    github: nagutm
    name: Mufaddal Naguthanawala
    orcid: 0009-0009-5240-7463
  description: This resource provides identifiers for listed hazardous wastes which
    are substances explicitly identified due to their potential harm to human health
    and the environment. These are categorized into four groups (F, K, P, and U) based
    on specific criteria, such as their source or inherent properties.
  example: F001
  example_extras:
  - K001
  - P001
  - U001
  github_request_issue: 1246
  homepage: https://www.ecfr.gov/current/title-40/chapter-I/subchapter-I/part-261
  name: EPA Hazardous Wastes
  pattern: ^[FKPU]\d{3}$
  prefix: epawaste
  reviewer:
    email: b.gyori@northeastern.edu
    github: bgyori
    name: Benjamin M. Gyori
    orcid: 0000-0001-9439-5346
epcc:
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: Collection of European paediatric cardiac coding files
  homepage: https://www.aepc.org/european-paediatric-cardiac-coding
  name: European Paediatric Cardiac Codes
  prefix: epcc
  proprietary: true
  references:
  - https://www.cambridge.org/core/journals/cardiology-in-the-young/article/abs/european-paediatric-cardiac-codes-the-long-list-with-icd9-icd10-crossmapping-and-crossmap-to-epcc-short-list/FCA4DFCCB661298294A3D113FC79D5BE
epd:
  biocontext:
    prefix: EPD
  contact:
    email: Philipp.Bucher@sib.swiss
    github: null
    name: Philipp Bucher
    orcid: 0000-0002-0816-7775
  contributor_extras:
  - email: sebastien.moretti@sib.swiss
    github: smoretti
    name: Sébastien Moretti
    orcid: 0000-0003-3947-488X
  edam:
    description: Identifier of an entry (promoter) from the EPD database.
    name: EPD
    obsolete: false
    prefix: '2386'
  fairsharing:
    abbreviation: EPD
    contact:
      email: ask-epd@googlegroups.com
      name: Philipp Bucher
      orcid: 0000-0002-0816-7775
    description: 'The Eukaryotic Promoter Database (EPD) provides accurate transcription
      start site (TSS) information for promoters of 15 model organisms, from human
      to yeast to the malaria parasite Plasmodium falciparum. While the original database
      was a manually curated database based on published experiments, new promoter
      collections are now produced entirely automatically (under the name “EPDnew”)
      based on high-throughput transcript mapping data and high-quality gene annotation
      resources. Corresponding functional genomics data can be viewed in a genome
      browser, queried or analyzed via web interfaces, or exported in standard formats
      like FASTA or BED for subsequent analysis with other tools; of note, EPD is
      tightly integrated with two tool suites developed by our group: ChIP-Seq and
      Signal Search Analysis, for analysis of chromatin context and sequence motif
      respectively. EPD provides promoter viewers, designed with the aim of integrating
      and displaying information from different sources about, for instance, histone
      marks, transcription factor-binding sites or SNPs with known phenotypes. These
      viewers rely upon the UCSC genome browser as a visualization platform, which
      enables users to view data tracks from EPD jointly with tracks from UCSC or
      public track hubs.'
    homepage: https://epd.epfl.ch/
    name: Eukaryotic Promoter Database
    prefix: FAIRsharing.yk1krv
    publications:
    - doi: 10.1093/nar/26.1.353
      pubmed_id: 9399872
      title: The Eukaryotic Promoter Database EPD.
    - doi: 10.1093/nar/28.1.302
      pubmed_id: 10592254
      title: The eukaryotic promoter database (EPD).
    - doi: 10.1093/nar/27.1.307
      pubmed_id: 9847211
      title: 'The Eukaryotic Promoter Database (EPD): recent developments.'
    - doi: 10.1093/nar/14.24.10009
      pubmed_id: 3808945
      title: Compilation and analysis of eukaryotic POL II promoter sequences
    - doi: 10.1093/nar/gku1111
      pubmed_id: 25378343
      title: 'The Eukaryotic Promoter Database: expansion of EPDnew and new promoter
        analysis tools.'
    - doi: 10.1093/nar/gks1233
      pubmed_id: 23193273
      title: EPD and EPDnew, high-quality promoter resources in the next-generation
        sequencing era.
    - doi: 10.1093/nar/gkj146
      pubmed_id: 16381980
      title: 'EPD in its twentieth year: towards complete promoter coverage of selected
        model organisms.'
    - doi: 10.1093/nar/gkh122
      pubmed_id: 14681364
      title: 'The Eukaryotic Promoter Database EPD: the impact of in silico primer
        extension.'
    - doi: 10.1093/nar/30.1.322
      pubmed_id: 11752326
      title: 'The Eukaryotic Promoter Database, EPD: new entry types and links to
        gene expression data.'
    - doi: 10.1093/nar/gkw1069
      pubmed_id: 27899657
      title: 'The eukaryotic promoter database in its 30th year: focus on non-vertebrate
        organisms.'
    subjects:
    - Bioinformatics
    - Biology
  homepage: https://epd.expasy.org/epd/
  integbio:
    alt_name: The Eukaryotic Promoter Database
    description: EPD is a satabase of unique gene promoters. The database contains
      non-redundant sequences of promoters for genes transcribed by RNA polymerase
      II. Users can search the database, browse promoter elements, or download sequences
      via HTTP or FTP.
    fairsharing: biodbcore-000653
    homepage: https://epd.expasy.org/epd/
    information_keywords:
    - Sequence
    maintainer: SIB (Swiss Institute of Bioinformatics)
    name: EPD
    prefix: nbdc00438
    pubmeds:
    - '16381980'
    - '14681364'
    - '11752326'
    - '10592254'
    - '9847211'
    - '9399872'
    status: Active
    target_keywords:
    - Genome/Gene
  mappings:
    biocontext: EPD
    edam: '2386'
    fairsharing: FAIRsharing.yk1krv
    integbio: nbdc00438
    miriam: epd
    n2t: epd
    ncbi: EPD
    uniprot: DB-0205
  miriam:
    deprecated: false
    description: The Eukaryotic Promoter Database (EPD) is an annotated non-redundant
      collection of eukaryotic POL II promoters, for which the transcription start
      site has been determined experimentally. Access to promoter sequences is provided
      by pointers to positions in nucleotide sequence entries. The annotation part
      of an entry includes description of the initiation site mapping data, cross-references
      to other databases, and bibliographic references. EPD is structured in a way
      that facilitates dynamic extraction of biologically meaningful promoter subsets
      for comparative sequence analysis.
    homepage: https://epd.expasy.org/epd
    id: 00000408
    name: EPD
    namespaceEmbeddedInLui: false
    pattern: ^[A-Z-_0-9]+$
    prefix: epd
    sampleId: TA_H3
    uri_format: https://epd.expasy.org/cgi-bin/epd/query_result.pl?out_format=NICE&Entry_0=$1
  n2t:
    description: The Eukaryotic Promoter Database (EPD) is an annotated non-redundant
      collection of eukaryotic POL II promoters, for which the transcription start
      site has been determined experimentally. Access to promoter sequences is provided
      by pointers to positions in nucleotide sequence entries. The annotation part
      of an entry includes description of the initiation site mapping data, cross-references
      to other databases, and bibliographic references. EPD is structured in a way
      that facilitates dynamic extraction of biologically meaningful promoter subsets
      for comparative sequence analysis.
    example: TA_H3
    homepage: http://epd.vital-it.ch/
    name: EPD at Swiss Institute of Bioinformatics
    namespaceEmbeddedInLui: false
    pattern: ^[A-Z-_0-9]+$
    prefix: epd
    uri_format: http://epd.vital-it.ch/cgi-bin/query_result.pl?out_format=NICE&Entry_0=$1
  ncbi:
    example: EP00576
    homepage: http://epd.vital-it.ch/
    name: Eukaryotic Promoter Database
    prefix: EPD
  prefix: epd
  publications:
  - doi: 10.1093/nar/gkx807
    pmc: PMC5753345
    pubmed: '28981707'
    title: 'The Encyclopedia of Proteome Dynamics: a big data ecosystem for (prote)omics'
    year: 2018
  - doi: 10.1093/nar/gkw1069
    pmc: PMC5210552
    pubmed: '27899657'
    title: 'The eukaryotic promoter database in its 30th year: focus on non-vertebrate
      organisms'
    year: 2016
  - doi: 10.1093/nar/gku1111
    pmc: PMC4383928
    pubmed: '25378343'
    title: 'The Eukaryotic Promoter Database: expansion of EPDnew and new promoter
      analysis tools'
    year: 2014
  - doi: 10.1093/nar/gks1233
    pmc: PMC3531148
    pubmed: '23193273'
    title: EPD and EPDnew, high-quality promoter resources in the next-generation
      sequencing era
    year: 2012
  - doi: 10.1093/nar/gkj146
    pmc: PMC1347508
    pubmed: '16381980'
    title: 'EPD in its twentieth year: towards complete promoter coverage of selected
      model organisms'
    year: 2006
  - doi: 10.1093/nar/gkh122
    pmc: PMC308856
    pubmed: '14681364'
    title: 'The Eukaryotic Promoter Database EPD: the impact of in silico primer extension'
    year: 2004
  - doi: 10.1093/nar/30.1.322
    pmc: PMC99099
    pubmed: '11752326'
    title: 'The Eukaryotic Promoter Database, EPD: new entry types and links to gene
      expression data'
    year: 2002
  - doi: 10.1093/nar/28.1.302
    pmc: PMC102462
    pubmed: '10592254'
    title: The eukaryotic promoter database (EPD)
    year: 2000
  - doi: 10.1093/nar/27.1.307
    pmc: PMC148166
    pubmed: '9847211'
    title: 'The Eukaryotic Promoter Database (EPD): recent developments'
    year: 1999
  - doi: 10.1093/nar/26.1.353
    pmc: PMC147208
    pubmed: '9399872'
    title: The Eukaryotic Promoter Database EPD
    year: 1998
  - doi: 10.1093/nar/14.24.10009
    pmc: PMC341352
    pubmed: '3808945'
    title: Compilation and analysis of eukaryotic POL II promoter sequences
    year: 1986
  - doi: 10.1093/nar/26.1.353
    pmc: null
    pubmed: null
    title: The Eukaryotic Promoter Database EPD.
    year: null
  - doi: 10.1093/nar/28.1.302
    pmc: null
    pubmed: null
    title: The eukaryotic promoter database (EPD).
    year: null
  - doi: 10.1093/nar/27.1.307
    pmc: null
    pubmed: null
    title: 'The Eukaryotic Promoter Database (EPD): recent developments.'
    year: null
  - doi: 10.1093/nar/14.24.10009
    pmc: null
    pubmed: null
    title: Compilation and analysis of eukaryotic POL II promoter sequences
    year: null
  - doi: 10.1093/nar/gku1111
    pmc: null
    pubmed: null
    title: 'The Eukaryotic Promoter Database: expansion of EPDnew and new promoter
      analysis tools.'
    year: null
  - doi: 10.1093/nar/gks1233
    pmc: null
    pubmed: null
    title: EPD and EPDnew, high-quality promoter resources in the next-generation
      sequencing era.
    year: null
  - doi: 10.1093/nar/gkj146
    pmc: null
    pubmed: null
    title: 'EPD in its twentieth year: towards complete promoter coverage of selected
      model organisms.'
    year: null
  - doi: 10.1093/nar/gkh122
    pmc: null
    pubmed: null
    title: 'The Eukaryotic Promoter Database EPD: the impact of in silico primer extension.'
    year: null
  - doi: 10.1093/nar/30.1.322
    pmc: null
    pubmed: null
    title: 'The Eukaryotic Promoter Database, EPD: new entry types and links to gene
      expression data.'
    year: null
  - doi: 10.1093/nar/gkw1069
    pmc: null
    pubmed: null
    title: 'The eukaryotic promoter database in its 30th year: focus on non-vertebrate
      organisms.'
    year: null
  - doi: 10.1093/nar/gkx807
    pmc: null
    pubmed: '28981707'
    title: null
    year: null
  - doi: 10.1093/nar/26.1.353
    pmc: null
    pubmed: null
    title: The Eukaryotic Promoter Database EPD.
    year: null
  - doi: 10.1093/nar/28.1.302
    pmc: null
    pubmed: null
    title: The eukaryotic promoter database (EPD).
    year: null
  - doi: 10.1093/nar/27.1.307
    pmc: null
    pubmed: null
    title: 'The Eukaryotic Promoter Database (EPD): recent developments.'
    year: null
  - doi: 10.1093/nar/14.24.10009
    pmc: null
    pubmed: null
    title: Compilation and analysis of eukaryotic POL II promoter sequences
    year: null
  - doi: 10.1093/nar/gku1111
    pmc: null
    pubmed: null
    title: 'The Eukaryotic Promoter Database: expansion of EPDnew and new promoter
      analysis tools.'
    year: null
  - doi: 10.1093/nar/gks1233
    pmc: null
    pubmed: null
    title: EPD and EPDnew, high-quality promoter resources in the next-generation
      sequencing era.
    year: null
  - doi: 10.1093/nar/gkj146
    pmc: null
    pubmed: null
    title: 'EPD in its twentieth year: towards complete promoter coverage of selected
      model organisms.'
    year: null
  - doi: 10.1093/nar/gkh122
    pmc: null
    pubmed: null
    title: 'The Eukaryotic Promoter Database EPD: the impact of in silico primer extension.'
    year: null
  - doi: 10.1093/nar/30.1.322
    pmc: null
    pubmed: null
    title: 'The Eukaryotic Promoter Database, EPD: new entry types and links to gene
      expression data.'
    year: null
  - doi: 10.1093/nar/gkw1069
    pmc: null
    pubmed: null
    title: 'The eukaryotic promoter database in its 30th year: focus on non-vertebrate
      organisms.'
    year: null
  - doi: 10.1093/nar/gkx807
    pmc: null
    pubmed: '28981707'
    title: null
    year: null
  - doi: 10.1093/nar/26.1.353
    pmc: null
    pubmed: null
    title: The Eukaryotic Promoter Database EPD.
    year: null
  - doi: 10.1093/nar/28.1.302
    pmc: null
    pubmed: null
    title: The eukaryotic promoter database (EPD).
    year: null
  - doi: 10.1093/nar/27.1.307
    pmc: null
    pubmed: null
    title: 'The Eukaryotic Promoter Database (EPD): recent developments.'
    year: null
  - doi: 10.1093/nar/14.24.10009
    pmc: null
    pubmed: null
    title: Compilation and analysis of eukaryotic POL II promoter sequences
    year: null
  - doi: 10.1093/nar/gku1111
    pmc: null
    pubmed: null
    title: 'The Eukaryotic Promoter Database: expansion of EPDnew and new promoter
      analysis tools.'
    year: null
  - doi: 10.1093/nar/gks1233
    pmc: null
    pubmed: null
    title: EPD and EPDnew, high-quality promoter resources in the next-generation
      sequencing era.
    year: null
  - doi: 10.1093/nar/gkj146
    pmc: null
    pubmed: null
    title: 'EPD in its twentieth year: towards complete promoter coverage of selected
      model organisms.'
    year: null
  - doi: 10.1093/nar/gkh122
    pmc: null
    pubmed: null
    title: 'The Eukaryotic Promoter Database EPD: the impact of in silico primer extension.'
    year: null
  - doi: 10.1093/nar/30.1.322
    pmc: null
    pubmed: null
    title: 'The Eukaryotic Promoter Database, EPD: new entry types and links to gene
      expression data.'
    year: null
  - doi: 10.1093/nar/gkw1069
    pmc: null
    pubmed: null
    title: 'The eukaryotic promoter database in its 30th year: focus on non-vertebrate
      organisms.'
    year: null
  - doi: 10.1093/nar/gkx807
    pmc: null
    pubmed: '28981707'
    title: null
    year: null
  uniprot:
    abbreviation: EPD
    category: Proteomic databases
    homepage: https://www.peptracker.com/epd/analytics/
    name: Encyclopedia of Proteome Dynamics
    prefix: DB-0205
    publications:
    - doi: 10.1093/nar/gkx807
      pubmed: '28981707'
    uri_format: https://www.peptracker.com/epd/analytics/?protein_id=$1
  uri_format: https://epd.expasy.org/cgi-bin/epd/query_result.pl?out_format=NICE&Entry_0=$1
epio:
  aberowl:
    description: A application driven Epilepsy Ontology with official terms from the
      ILAE.
    download_owl: http://aber-owl.net/media/ontologies/EPIO/3/epio.owl
    homepage: https://github.com/SCAI-BIO/EpilepsyOntology
    name: Epilepsy Ontology
    prefix: EPIO
  bioportal:
    contact:
      email: alpha.tom.kodamullil@scai.fraunhofer.de
      name: Alpha Tom Kodanullil
    description: The Epilepsy Ontology (EPO) is an assembly of structured knowledge
      on various aspects of epilepsy, developed according to basic formal ontology
      (BFO) and Open Biological and Biomedical Ontology (OBO) Foundry principles.
      Entities and definitions are collected from the latest International League
      against Epilepsy (ILAE) classification, as well as from domain-specific ontologies
      such as Epilepsy Ontology (EPILONT), Epilepsy Syndrome Seizure Ontology (ESSO),
      Epilepsy Semiology(EPISEM) and Epilepsy and Seizure Ontology (EPSO) and scientific
      literature. This ontology is intended to be used for data management and for
      text mining purposes. The current release of the ontology is publicly available
      and is a community based effort to assemble various facets of the complex disease
      Epilepsy.
    name: EpilepsyOntology
    prefix: EPIO
    version: 'Version Release: 1.0.0'
  example: '0000011'
  mappings:
    aberowl: EPIO
    bioportal: EPIO
    obofoundry: epio
    ontobee: EPIO
    wikidata.entity: Q113012657
  obofoundry:
    contact: alpha.tom.kodamullil@scai.fraunhofer.de
    contact.github: akodamullil
    contact.label: Alpha Tom Kodamullil
    contact.orcid: 0000-0001-9896-3531
    depends_on:
    - bfo
    deprecated: false
    description: A application driven Epilepsy Ontology with official terms from the
      ILAE.
    domain: health
    download.owl: http://purl.obolibrary.org/obo/epio.owl
    homepage: https://github.com/SCAI-BIO/EpilepsyOntology
    license: CC BY 4.0
    license.url: http://creativecommons.org/licenses/by/4.0/
    name: Epilepsy Ontology
    preferredPrefix: EPIO
    prefix: epio
    repository: https://github.com/SCAI-BIO/EpilepsyOntology
  ontobee:
    library: Library
    name: Epilepsy Ontology
    prefix: EPIO
  pattern: ^\d{7}$
  prefix: epio
  providers:
  - code: legacy
    description: Legacy internal URL before switching to OBO PURL
    example: null
    first_party: null
    homepage: https://bio.scai.fraunhofer.de/ontolog
    name: Legacy
    publications: null
    status: null
    uri_format: https://bio.scai.fraunhofer.de/ontology/epilepsy#$1
  uri_format: http://purl.obolibrary.org/obo/EPIO_$1
epo:
  biocontext:
    prefix: EPO
  contributor_extras:
  - email: null
    github: djinnome
    name: Jeremy Zucker
    orcid: 0000-0002-7276-9009
  download_owl: https://storage.googleapis.com/google-code-archive-downloads/v2/code.google.com/epidemiology-ontology/epo.owl
  mappings:
    biocontext: EPO
    obofoundry: epo
    ontobee: EPO
  obofoundry:
    deprecated: true
    description: An ontology designed to support the semantic annotation of epidemiology
      resources
    domain: health
    download.owl: http://purl.obolibrary.org/obo/epo.owl
    homepage: https://code.google.com/p/epidemiology-ontology/
    name: Epidemiology Ontology
    prefix: epo
  ontobee:
    library: Library
    name: Epidemiology Ontology
    prefix: EPO
  prefix: epo
epso:
  aberowl:
    description: A application driven Epilepsy Ontology sith official terms from the
      ILAE.
    download_owl: http://aber-owl.net/media/ontologies/EPSO/3/epso.owl
    name: Epilepsy Ontology
    prefix: EPSO
  bioportal:
    contact:
      email: satyasahoo@ieee.org
      name: Satya Sahoo
    description: The Epilepsy Ontology models seizure types, syndromes, etiology,
      electrophysiology, medication, neuropathology, including immunohistochemistry,
      microscopy, and anatomical description, together with terms describing preclinical
      model systems. The Epilepsy Ontology has been integrated with generative artificial
      intelligence (AI)/LLMs and machine learning models for natural language processing
      (NLP), drug efficacy analysis, and translational research.
    homepage: https://bmhinformatics.case.edu/
    name: Epilepsy and Seizure Ontology
    prefix: EPSO
    publications:
    - https://bmhinformatics.case.edu/
    version: '3.1'
  contact:
    email: satyasahoo@ieee.org
    github: null
    name: Satya S. Sahoo
    orcid: 0000-0001-9190-4256
  example: '0000400'
  fairsharing:
    abbreviation: EPSO
    description: 'The Epilepsy and Seizure Ontology (EpSO) is an application ontology
      developed to support epilepsy focused informatics tools for patient care and
      clinical research. '
    domains:
    - epilepsy
    - Patient Care
    homepage: https://bioportal.bioontology.org/ontologies/EPSO
    license: CC BY-SA 3.0
    name: Epilepsy and Seizure Ontology
    prefix: FAIRsharing.ttprgy
    publications:
    - doi: 10.1136/amiajnl-2013-001696
      title: 'Epilepsy and seizure ontology: towards an epilepsy informatics infrastructure
        for clinical research and patient care'
      year: 2013
    subjects:
    - Neurology
  homepage: http://prism.case.edu/prism/index.php/EpilepsyOntology
  mappings:
    aberowl: EPSO
    bioportal: EPSO
    fairsharing: FAIRsharing.ttprgy
    ontobee: EPSO
  ontobee:
    library: Library
    name: Epilepsy Ontology
    prefix: EPSO
  pattern: ^\d{7}$
  prefix: epso
  publications:
  - doi: 10.1136/amiajnl-2013-001696
    pmc: PMC3912711
    pubmed: '23686934'
    title: 'Epilepsy and seizure ontology: towards an epilepsy informatics infrastructure
      for clinical research and patient care'
    year: 2013
  uri_format: http://www.case.edu/EpilepsyOntology.owl#$1
erm:
  cheminf:
    description: Identifier used by the European Registry of Materials (https://nanocommons.github.io/identifiers/).
    name: European Registry of Materials
    obsolete: false
    prefix: 000569
  contact:
    email: egon.willighagen@gmail.com
    github: egonw
    name: Egon Willighagen
    orcid: 0000-0001-7542-0286
  download_rdf: https://nanocommons.github.io/identifiers/registry
  fairsharing:
    abbreviation: ERM Identifier
    contact:
      email: egon.willighagen@maastrichtuniversity.nl
      name: Egon Willighagen
      orcid: 0000-0001-7542-0286
    description: Identifier project to uniquely identify nanomaterials, allowing them
      to identify materials in experimental designs, data, reports, project deliverables,
      and scholarly publications.
    domains:
    - chemical entity
    homepage: https://nanocommons.github.io/identifiers/
    license: CC0-1.0
    name: European Registry of Materials Identifier
    prefix: FAIRsharing.c26a4e
    publications:
    - doi: 10.1186/s13321-022-00614-7
      title: 'European Registry of Materials: global, unique identifiers for (undisclosed)
        nanomaterials'
      year: 2022
    subjects:
    - Nanotechnology
    - Materials Science
    - Materials Informatics
  mappings:
    cheminf: 000569
    fairsharing: FAIRsharing.c26a4e
    miriam: erm
    n2t: erm
  miriam:
    deprecated: false
    description: The European Registry of Materials is a simple registry with the
      sole purpose to mint material identifiers to be used by research projects throughout
      the life cycle of their project.
    homepage: https://nanocommons.github.io/identifiers/
    id: '00000763'
    name: European Registry of Materials
    namespaceEmbeddedInLui: false
    pattern: ^ERM[0-9]{8}$
    prefix: erm
    sampleId: ERM00000044
    uri_format: https://nanocommons.github.io/identifiers/registry#$1
  n2t:
    description: The European Registry of Materials is a simple registry with the
      sole purpose to mint material identifiers to be used by research projects throughout
      the life cycle of their project.
    example: ERM00000044
    homepage: https://nanocommons.github.io/identifiers/
    name: European Registry of Materials
    namespaceEmbeddedInLui: false
    pattern: ^ERM[0-9]{8}$
    prefix: erm
    uri_format: https://nanocommons.github.io/identifiers/registry#$1
  prefix: erm
  providers:
  - code: erm.database
    description: Database that provides links to onlnie information about materials
      with an European Registry of Materials (ERM) identifier
    example: null
    first_party: null
    homepage: https://nanocommons.github.io/erm-database/
    name: ERM Identifier Database
    publications: null
    status: null
    uri_format: https://nanocommons.github.io/erm-database/substance/erm/$1
  publications:
  - doi: 10.1186/s13321-022-00614-7
    pmc: PMC9400299
    pubmed: '36002868'
    title: 'European Registry of Materials: global, unique identifiers for (undisclosed)
      nanomaterials'
    year: 2022
  - doi: 10.1186/s13321-022-00614-7
    pmc: null
    pubmed: null
    title: 'European Registry of Materials: global, unique identifiers for (undisclosed)
      nanomaterials'
    year: 2022
  twitter: nanocommons
ero:
  aberowl:
    description: An ontology of research resources such as instruments. protocols,
      reagents, animal models and biospecimens.
    download_owl: http://aber-owl.net/media/ontologies/ERO/15/ero.owl
    homepage: https://open.med.harvard.edu/wiki/display/eaglei/Ontology
    name: eagle-i resource ontology
    prefix: ERO
  biocontext:
    prefix: ERO
  bioportal:
    contact:
      email: carlotorniai@gmail.com
      name: Carlo Torniai
    description: This ontology models research resources such instruments. protocols,
      reagents, animal models and biospecimens. It has been developed in the context
      of the eagle-i project (http://eagle-i.net/).
    homepage: http://code.google.com/p/eagle-i/
    name: Eagle-I Research Resource Ontology
    prefix: ERO
    publications:
    - http://code.google.com/p/eagle-i/wiki/Publications
    version: '2013-08-02'
  example: '0001655'
  fairsharing:
    abbreviation: ERO
    contact:
      email: carlotorniai@gmail.com
      name: Carlo Torniai
      orcid: 0000-0002-3734-1859
    description: A unique feature of the eagle-i software is that the data collection
      and search tools are completely driven by ontologies. These ontologies are a
      set of modules that are written in the OWL language and edited and managed using
      Protégé. Beginning in 2009, the eagle-i Research Resource Ontology (ERO) was
      developed alongside the eagle-i applications to model various biomedical research
      resources such as instruments, Core Facilities, protocols, reagents, animal
      models and biospecimens. It has now been integrated into the VIVO-ISF Ontology,
      which leverages and expands upon both the eagle-i and VIVO ontologies to create
      a semantic framework that describes not only scientific resources but research
      activities and clinical activities.
    domains:
    - reagent
    - Biospecimen
    - study design
    homepage: https://open.catalyst.harvard.edu/wiki/display/eaglei/Ontology
    name: eagle-i Research Resource Ontology
    prefix: FAIRsharing.nwgynk
    publications:
    - doi: 10.1109/jcdl.2017.7991571
      pubmed: '29599662'
      title: 'Automating data citation: the eagle-i experience'
      year: 2018
    - doi: 10.1093/database/bar067
      pubmed: '22434835'
      title: 'Research resources: curating the new eagle-i discovery system'
      year: 2012
    subjects:
    - Life Science
    - Biomedical Science
  mappings:
    aberowl: ERO
    biocontext: ERO
    bioportal: ERO
    fairsharing: FAIRsharing.nwgynk
    obofoundry: ero
    ols: ero
    ontobee: ERO
  obofoundry:
    contact: Marc_Ciriello@hms.harvard.edu
    contact.label: Marc Ciriello
    deprecated: true
    description: An ontology of research resources such as instruments. protocols,
      reagents, animal models and biospecimens.
    domain: information
    download.owl: http://purl.obolibrary.org/obo/ero.owl
    homepage: https://open.med.harvard.edu/wiki/display/eaglei/Ontology
    license: CC BY 2.0
    license.url: https://creativecommons.org/licenses/by/2.0/
    name: eagle-i resource ontology
    prefix: ero
  ols:
    description: An ontology of research resources such as instruments. protocols,
      reagents, animal models and biospecimens.
    download: http://purl.obolibrary.org/obo/ero.owl
    homepage: https://open.med.harvard.edu/wiki/display/eaglei/Ontology
    name: eagle-i resource ontology
    prefix: ero
    version: '2016-07-27'
  ontobee:
    library: Library
    name: eagle-i resource ontology
    prefix: ERO
  pattern: ^\d{7}$
  prefix: ero
  publications:
  - doi: 10.1109/jcdl.2017.7991571
    pmc: PMC5868434
    pubmed: '29599662'
    title: 'Automating data citation: the eagle-i experience'
    year: 2017
  - doi: 10.1093/database/bar067
    pmc: PMC3308157
    pubmed: '22434835'
    title: 'Research resources: curating the new eagle-i discovery system'
    year: 2012
  - doi: 10.1109/jcdl.2017.7991571
    pmc: null
    pubmed: '29599662'
    title: 'Automating data citation: the eagle-i experience'
    year: 2018
  - doi: 10.1093/database/bar067
    pmc: null
    pubmed: '22434835'
    title: 'Research resources: curating the new eagle-i discovery system'
    year: 2012
eropmoscow:
  integbio:
    alt_name: Endogenous Regulatory OligoPeptide knowledgebase
    description: "EROP(Endogenous Regulatory OligoPeptide)-Moscow is a database that\
      \ provides information on a collection of oligopeptide sequences. \nThese sequences\
      \ contain any number of amino acid residues, from 2 to 50.\nAnnotations of a\
      \ high level of accuracy, such as an oligopeptide's source, function, structure\
      \ and post-translational modifications are provided.\nThis database contains\
      \ information on 10,229 sequences. \nInformation can be retrieved by entering\
      \ the EROP-accession ID, the name of the oligopeptide, its function, the family\
      \ name and/or the biological classification (oligopeptide source). \nThe database\
      \ may also be searched by entering physicochemical features, for instance, the\
      \ amino acid number, its sequence or molecular mass.\nThis version was released\
      \ on 21 August 2010."
    homepage: http://erop.inbi.ras.ru/
    information_keywords:
    - Sequence
    maintainer: SIB (Swiss Institute of Bioinformatics)
    name: EROP-Moscow
    prefix: nbdc00265
    pubmeds:
    - '16381860'
    status: Active
    target_keywords:
    - Protein
    - Carbohydrate
  mappings:
    integbio: nbdc00265
    prefixcommons: eropmoscow
  prefix: eropmoscow
  prefixcommons:
    description: EROP-Moscow is a curated oligopeptide (2-50 amino acid residues)
      sequence database which strives to provide a high level of annotations (such
      as descriptions of the structure of an oligopeptide, its source and function,
      post-translational modifications, etc.).
    example: E00002
    homepage: http://erop.inbi.ras.ru
    keywords:
    - protein
    name: Endogenous Regulatory OligoPeptide knowledgebase-Moscow
    pattern: ^E\d+$
    prefix: eropmoscow
    uri_format: http://erop.inbi.ras.ru/result2.php?PepName=$1
  reviewer:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
erudite:
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: A metadata stadnard to model data science training materials. Later,
    was replaced by Bioschemas' [training materials specification](http://bioschemas.org/specifications/TrainingMaterial/specification/).
  example: enables
  homepage: https://www.pagestudy.org/erudite-training-resource-standard
  keywords:
  - educational resource
  - learning material
  - open educational resource
  - schema
  name: Educational Resource Discovery Index Schema
  prefix: erudite
  uri_format: http://www.bigdatau.org/schema#$1
erv:
  biocontext:
    prefix: ERV
  mappings:
    biocontext: ERV
    miriam: erv
    n2t: erv
  miriam:
    deprecated: false
    description: Endogenous retroviruses (ERVs) are common in vertebrate genomes;
      a typical mammalian genome contains tens to hundreds of thousands of ERV elements.
      Most ERVs are evolutionarily old and have accumulated multiple mutations, playing
      important roles in physiology and disease processes. The Human Endogenous Retrovirus
      Database (hERV) is compiled from the human genome nucleotide sequences obtained
      from Human Genome Projects, and screens those sequences for hERVs, whilst continuously
      improving classification and characterization of retroviral families. It provides
      access to individual reconstructed HERV elements, their sequence, structure
      and features.
    homepage: https://herv.img.cas.cz/
    id: 00000619
    name: Human Endogenous Retrovirus Database
    namespaceEmbeddedInLui: false
    pattern: ^[A-Za-z0-9\-\_]+$
    prefix: erv
    sampleId: THE1B
    uri_format: https://herv.img.cas.cz/s/$1
  n2t:
    description: Endogenous retroviruses (ERVs) are common in vertebrate genomes;
      a typical mammalian genome contains tens to hundreds of thousands of ERV elements.
      Most ERVs are evolutionarily old and have accumulated multiple mutations, playing
      important roles in physiology and disease processes. The Human Endogenous Retrovirus
      Database (hERV) is compiled from the human genome nucleotide sequences obtained
      from Human Genome Projects, and screens those sequences for hERVs, whilst continuously
      improving classification and characterization of retroviral families. It provides
      access to individual reconstructed HERV elements, their sequence, structure
      and features.
    example: THE1B
    homepage: https://herv.img.cas.cz/
    name: Human Endogenous Retrovirus Database
    namespaceEmbeddedInLui: false
    pattern: ^[A-Za-z0-9\-\_]+$
    prefix: erv
    uri_format: https://herv.img.cas.cz/s/$1
  prefix: erv
esco.isco:
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: The European Skills, Competences, Qualifications and Occupations (ESCO)
    International Standard Classification of Occupations (ISCO).
  example: C4
  homepage: https://esco.ec.europa.eu/classification
  name: ESCO - International Standard Classification of Occupations
  prefix: esco.isco
  uri_format: http://data.europa.eu/esco/isco/$1
esco.model:
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: 'The ontology of the taxonomy "European Skills, Competences, qualifications
    and Occupations". The ontology considers three ESCO pillars (or taxonomy) and
    2 registers. The three pillars are: 1) Occupation, 2) Skill (and competences),
    and 3) Qualification'
  example: Occupation
  homepage: https://ec.europa.eu/esco/lod/static/model.html
  name: ESCO Ontology
  prefix: esco.model
  rdf_uri_format: http://data.europa.eu/esco/model#$1
  uri_format: https://ec.europa.eu/esco/lod/static/model.html#$1
esco.occupation:
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: The ESCO occupations pillar is built on ISCO-08 which serves as its
    hierarchical structure. ISCO-08 provides the top four levels for the occupations
    pillar and ESCO occupations are located at level 5 and lower. In ESCO, each occupation
    is mapped to exactly one ISCO-08 code. [from homepage]
  example: eea2b5c6-48d1-4612-957e-585783b3c7bb
  homepage: https://esco.ec.europa.eu/en/classification/occupation_main
  name: ESCO Occupation
  prefix: esco.occupation
  rdf_uri_format: http://data.europa.eu/esco/occupation/$1
  uri_format: http://data.europa.eu/esco/occupation/$1
esco.skill:
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: 'A vocabulary of knowledge, skills and competences relevant to the
    European labour market. In ESCO v1.2.0, the skills pillar is structured in a hierarchy
    which contains the following four sub-classifications: 1) Knowledge, 2) Language
    skills and knowledge, 3) Skills, and 4) Transversal skills. [adapted from homepage]'
  example: dc06de9f-dd3a-4f28-b58f-b01b5ae72ab8
  homepage: http://data.europa.eu/esco/skill
  name: ESCO Skill
  prefix: esco.skill
  uri_format: http://data.europa.eu/esco/skill/$1
esldb:
  mappings:
    prefixcommons: esldb
  prefix: esldb
  prefixcommons:
    description: eSLDB is a database of protein subcellular localization annotation
      for eukaryotic organisms. It contains experimental annotations derived from
      primary protein databases, homology based annotations and computational predictions.
    example: HS000015122
    homepage: http://gpcr.biocomp.unibo.it/esldb
    keywords:
    - protein
    name: eukaryotic Subcellular Localization database
    pattern: ^[A-Z]+\d+$
    prefix: esldb
    uri_format: http://gpcr.biocomp.unibo.it/cgi-bin/predictors/esldb/dettagli.cgi?codice=$1
  reviewer:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
estdab:
  cellosaurus:
    category: Cell line databases/resources
    homepage: https://www.ebi.ac.uk/ipd/estdab/
    name: European Searchable Tumour Line Database
    prefix: ESTDAB
  comment: Website is dead
  deprecated: true
  example: '046'
  mappings:
    cellosaurus: ESTDAB
  owners:
  - name: European Bioinformatics Institute
    partnered: false
    ror: 02catss52
    wikidata: null
  pattern: ^\d{3}$
  prefix: estdab
  uri_format: https://www.ebi.ac.uk/cgi-bin/ipd/estdab/print_cell.cgi?ESTDAB-$1
eu.publication:
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: Datasets published by the Publications Office of the European Union
  example: euvoc
  homepage: https://op.europa.eu
  name: European Union Publications Office dataset
  prefix: eu.publication
  uri_format: http://publications.europa.eu/resource/dataset/$1
eu89h:
  biocontext:
    prefix: EU89H
  mappings:
    biocontext: EU89H
    miriam: eu89h
    n2t: eu89h
  miriam:
    deprecated: false
    description: The JRC Data Catalogue gives access to the multidisciplinary data
      produced and maintained by the Joint Research Centre, the European Commission's
      in-house science service providing independent scientific advice and support
      to policies of the European Union.
    homepage: http://data.jrc.ec.europa.eu/
    id: '00000644'
    name: JRC Data Catalogue
    namespaceEmbeddedInLui: false
    pattern: ^[a-z0-9\-_]+$
    prefix: eu89h
    sampleId: jrc-eurl-ecvam-chemagora
    uri_format: http://data.europa.eu/89h/$1
  n2t:
    description: The JRC Data Catalogue gives access to the multidisciplinary data
      produced and maintained by the Joint Research Centre, the European Commission's
      in-house science service providing independent scientific advice and support
      to policies of the European Union.
    example: jrc-eurl-ecvam-chemagora
    homepage: http://data.jrc.ec.europa.eu/
    name: JRC Data Catalogue
    namespaceEmbeddedInLui: false
    pattern: ^[a-z0-9\-_]+$
    prefix: eu89h
    uri_format: http://data.europa.eu/89h/$1
  prefix: eu89h
eubopen:
  contact:
    email: tredup@pharmchem.uni-frankfurt.de
    github: null
    name: Claudia Tredup
    orcid: 0000-0001-6518-3344
  contributor:
    email: palayoor.n@northeastern.edu
    github: nalikapalayoor
    name: Nalika Palayoor
    orcid: 0009-0008-8406-631X
  description: EUbOPEN is a project focusing on organizing chemogenic library collections,
    advancing chemical probe discovery, profiling bioactive compounds, and making
    project data more accessible.
  example: EUB0000221
  github_request_issue: 1378
  homepage: https://gateway.eubopen.org
  name: Enabling and Unlocking Biology in the Open
  pattern: ^EUB\d{7}$
  prefix: eubopen
  publications:
  - doi: 10.1039/d4md00735b
    pmc: PMC11605244
    pubmed: '39618964'
    title: 'Toward target 2035: EUbOPEN - a public-private partnership to enable &
      unlock biology in the open'
    year: 2024
  reviewer:
    email: b.gyori@northeastern.edu
    github: bgyori
    name: Benjamin M. Gyori
    orcid: 0000-0001-9439-5346
  uri_format: https://gateway.eubopen.org/compound/$1
euclinicaltrials:
  biocontext:
    prefix: EUCLINICALTRIALS
  mappings:
    biocontext: EUCLINICALTRIALS
    miriam: euclinicaltrials
    n2t: euclinicaltrials
  miriam:
    deprecated: false
    description: "The EU Clinical Trials Register contains information on clinical\
      \ trials conducted in the European Union (EU), or the European Economic Area\
      \ (EEA) which started after 1 May 2004.\r\nIt also includes trials conducted\
      \ outside these areas if they form part of a paediatric investigation plan (PIP),\
      \ or are sponsored by a marketing authorisation holder, and involve the use\
      \ of a medicine in the paediatric population."
    homepage: https://www.clinicaltrialsregister.eu/
    id: '00000536'
    name: EU Clinical Trials
    namespaceEmbeddedInLui: false
    pattern: ^\d{4}\-\d{6}\-\d{2}$
    prefix: euclinicaltrials
    sampleId: 2008-005144-16
    uri_format: https://www.clinicaltrialsregister.eu/ctr-search/search?query=$1
  n2t:
    description: The EU Clinical Trials Register contains information on clinical
      trials conducted in the European Union (EU), or the European Economic Area (EEA)
      which started after 1 May 2004. It also includes trials conducted outside these
      areas if they form part of a paediatric investigation plan (PIP), or are sponsored
      by a marketing authorisation holder, and involve the use of a medicine in the
      paediatric population.
    example: 2008-005144-16
    homepage: https://www.clinicaltrialsregister.eu/
    name: EU Clinical Trials at  European Medicines Agency
    namespaceEmbeddedInLui: false
    pattern: ^\d{4}\-\d{6}\-\d{2}$
    prefix: euclinicaltrials
    uri_format: https://www.clinicaltrialsregister.eu/ctr-search/search?query=$1
  prefix: euclinicaltrials
  synonyms:
  - EUCTR
eugenes:
  fairsharing:
    abbreviation: euGenes
    contact:
      email: eugenes@iubio.bio.indiana.edu
      name: Don Gilbert
      orcid: 0000-0002-6646-7274
    description: euGenes provides a common summary of gene and genomic information
      from eukaryotic organism databases including gene symbol and full name, chromosome,
      genetic and molecular map information, Gene Ontology (Function/Location/Process)
      and gene homology, product information.
    homepage: http://eugenes.org/
    name: Eukaryotic Genes
    prefix: FAIRsharing.7fc5y6
    publications:
    - doi: 10.1093/nar/30.1.145
      pubmed_id: 11752277
      title: 'euGenes: a eukaryote genome information system.'
    subjects:
    - Life Science
  mappings:
    fairsharing: FAIRsharing.7fc5y6
    prefixcommons: eugenes
  prefix: eugenes
  prefixcommons:
    description: euGenes provides a common summary of gene and genomic information
      from eukaryotic organism databases including gene symbol and full name, chromosome,
      genetic and molecular map information, Gene Ontology (Function/Location/Process)
      and gene homology, product information.
    example: MGgn0008978
    homepage: http://eugenes.org/
    keywords:
    - genome
    - ontology
    name: Eukaryotic Genes
    pattern: ^[A-Z]+\d+$
    prefix: eugenes
    synonyms:
    - 'eugenes:'
    uri_format: http://eugenes.org:7072/.bin/fbidq.html?$1
  publications:
  - doi: 10.1093/nar/30.1.145
    pmc: PMC99146
    pubmed: '11752277'
    title: 'euGenes: a eukaryote genome information system'
    year: 2002
  - doi: 10.1093/nar/30.1.145
    pmc: null
    pubmed: null
    title: 'euGenes: a eukaryote genome information system.'
    year: null
  reviewer:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
eupath:
  aberowl:
    description: An ontology is developed to support Eukaryotic Pathogen, Host & Vector
      Genomics Resource (VEuPathDB; https://veupathdb.org).
    download_owl: http://aber-owl.net/media/ontologies/EUPATH/20/eupath.owl
    homepage: https://github.com/VEuPathDB-ontology/VEuPathDB-ontology
    name: VEuPathDB ontology
    prefix: EUPATH
  biocontext:
    prefix: EUPATH
  bioportal:
    contact:
      email: stoeckrt@pennmedicine.upenn.edu
      name: Chris Stoeckert
    description: The VEuPathDB ontology is an application ontology developed to encode
      our understanding of what data is about in the public resources developed and
      maintained by the Eukaryotic Pathogen, Host & Vector Genomics Resource (VEuPathDB;
      https://veupathdb.org). The VEuPathDB ontology was previously named the EuPathDB
      ontology prior to EuPathDB joining with VectorBase.The ontology was built based
      on the Ontology of Biomedical Investigations (OBI) with integration of other
      OBO ontologies such as PATO, OGMS, DO, etc. as needed for coverage. Currently
      the VEuPath ontology is primarily intended to be used for support of the VEuPathDB
      sites. Terms with VEuPathDB ontology IDs that are not specific to VEuPathDB
      will be submitted to OBO Foundry ontologies for subsequent import and replacement
      of those terms when they are available.
    homepage: https://github.com/EuPath-ontology/EuPath-ontology
    name: VEuPathDB Ontology
    prefix: EUPATH
    publications:
    - https://pdfs.semanticscholar.org/888e/a51dbb138122d39c42f863f2a1ada7976db4.pdf
    version: '2023-05-30'
  example: '0010316'
  fairsharing:
    abbreviation: VEuPathDB Ontology
    description: The VEuPathDB ontology is an application ontology developed to encode
      our understanding of what data is about in the public resources developed and
      maintained by the Eukaryotic Pathogen, Host and Vector Genomics Resource. The
      ontology was built based on the Ontology of Biomedical Investigations (OBI)
      with integration of other OBO ontologies such as PATO, OGMS, DO, etc. as needed
      for coverage. Currently the VEuPath ontology is primarily intended to be used
      for support of the VEuPathDB sites. Terms with VEuPathDB ontology IDs that are
      not specific to VEuPathDB will be submitted to OBO Foundry ontologies for subsequent
      import and replacement of those terms when they are available.
    domains:
    - microbiome
    homepage: https://github.com/VEuPathDB-ontology/VEuPathDB-ontology
    license: CC-BY-4.0
    name: Eukaryotic Pathogen, Host & Vector Genomics Resource Ontology
    prefix: FAIRsharing.9rhr9j
    repository: https://github.com/VEuPathDB-ontology/VEuPathDB-ontology
    subjects:
    - Functional Genomics
    - Population Genetics
    - Biomedical Science
    - Epidemiology
  mappings:
    aberowl: EUPATH
    biocontext: EUPATH
    bioportal: EUPATH
    fairsharing: FAIRsharing.9rhr9j
    obofoundry: eupath
    ols: eupath
    ontobee: EUPATH
    wikidata.entity: Q81661607
  obofoundry:
    appears_in:
    - scdo
    contact: jiezhen@med.umich.edu
    contact.github: zhengj2007
    contact.label: Jie Zheng
    contact.orcid: 0000-0002-2999-0103
    deprecated: true
    description: An ontology is developed to support Eukaryotic Pathogen, Host & Vector
      Genomics Resource (VEuPathDB; https://veupathdb.org).
    domain: organisms
    download.owl: http://purl.obolibrary.org/obo/eupath.owl
    homepage: https://github.com/VEuPathDB-ontology/VEuPathDB-ontology
    license: CC BY 4.0
    license.url: http://creativecommons.org/licenses/by/4.0/
    logo: https://raw.githubusercontent.com/EuPathDB/communitysite/master/assets/images/VEuPathDB-logo-s.png
    name: VEuPathDB ontology
    preferredPrefix: EUPATH
    prefix: eupath
    publications:
    - id: https://doi.org/10.5281/zenodo.6685957
      title: Malaria study data integration and information retrieval based on OBO
        Foundry ontologies.
    repository: https://github.com/VEuPathDB-ontology/VEuPathDB-ontology
  ols:
    description: The VEuPathDB ontology is an application ontology developed to encode
      our understanding of what data is about in the public resources developed and
      maintained by the Eukaryotic Pathogen, Host and Vector Genomics Resource (VEuPathDB;
      https://veupathdb.org). The VEuPathDB ontology was previously named the EuPathDB
      ontology prior to EuPathDB joining with VectorBase.The ontology was built based
      on the Ontology of Biomedical Investigations (OBI) with integration of other
      OBO ontologies such as PATO, OGMS, DO, etc. as needed for coverage. Currently
      the VEuPath ontology is primarily intended to be used for support of the VEuPathDB
      sites. Terms with VEuPathDB ontology IDs that are not specific to VEuPathDB
      will be submitted to OBO Foundry ontologies for subsequent import and replacement
      of those terms when they are available.
    download_owl: http://purl.obolibrary.org/obo/eupath.owl
    homepage: https://github.com/VEuPathDB-ontology/VEuPathDB-ontology
    name: VEuPathDB Ontology
    prefix: eupath
    tracker: https://github.com/VEuPathDB-ontology/VEuPathDB-ontology/issues
    version: '2023-05-30'
    version.iri: http://purl.obolibrary.org/obo/eupath/2023-05-30/eupath.owl
  ontobee:
    library: Library
    name: VEuPathDB ontology
    prefix: EUPATH
  pattern: ^\d{7}$
  prefix: eupath
  publications:
  - doi: 10.5281/zenodo.6685957
    pmc: null
    pubmed: null
    title: Malaria study data integration and information retrieval based on OBO Foundry
      ontologies
    year: 2016
  - doi: 10.5281/zenodo.6685957
    pmc: null
    pubmed: null
    title: Malaria study data integration and information retrieval based on OBO Foundry
      ontologies
    year: null
  uri_format: http://purl.obolibrary.org/obo/EUPATH_$1
eurofir:
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: EuroFir (European Food Information Resource Network), the world-leading
    European Network of Excellence on Food Composition Databank systems, is a partnership
    between 48 universities, research institutes and small-to-medium sized enterprises
    (SMEs) from 25 European countries.
  homepage: https://www.eurofir.org
  name: European Food Information Resource Network
  prefix: eurofir
  proprietary: true
europa.dcf:
  example: 00b51s9rc5
  mappings:
    tib: dcf
  prefix: europa.dcf
  tib:
    description: The Digital Competence Framework for Citizens standard list identifies
      the key components of digital competence in 5 broader, and a total of 21 narrower
      areas, with eight proficiency levels for each concept and a few contextualising
      examples of use. It is maintained by DG EMPL and published by the Publications
      Office of the European Union on the EU Vocabularies website.
    homepage: https://op.europa.eu/de/home
    keywords:
    - Educational Resources
    - literature
    - social sciences
    name: Digital Competence Framework
    prefix: dcf
    uri_format: http://data.europa.eu/snb/dcf/$1
europe.pic:
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: An identifier for an organization
  example: '881104060'
  homepage: https://ec.europa.eu/info/funding-tenders/opportunities/portal/screen/how-to-participate/participant-register-search?isExactMatch=true&type=ORGANISATION&order=DESC&pageNumber=1&pageSize=50&sortBy=lastModified
  name: European Commission Participant Identification Code (PIC)
  pattern: ^\d{9}$
  prefix: europe.pic
  references:
  - https://ec.europa.eu/info/funding-tenders/opportunities/portal/screen/how-to-participate/participant-register
  uri_format: https://ec.europa.eu/info/funding-tenders/opportunities/portal/screen/how-to-participate/org-details/$1
euroscivoc:
  bartoc:
    abbreviation: EuroSciVoc
    description: European Science Vocabulary (EuroSciVoc) is the taxonomy of fields
      of science based on OECD's 2015 Frascati Manual taxonomy. It was extended with
      fields of science categories extracted from CORDIS content through a semi-automatic
      process developed with Natural Language Processing (NLP) techniques.
    homepage: https://op.europa.eu/en/web/eu-vocabularies/dataset/-/resource?uri=http://publications.europa.eu/resource/dataset/euroscivoc
    name: European Science Vocabulary
    prefix: '20394'
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: European Science Vocabulary (EuroSciVoc) is the taxonomy of fields
    of science based on OECD's 2015 Frascati Manual taxonomy. It was extended with
    fields of science categories extracted from CORDIS content through a semi-automatic
    process developed with Natural Language Processing (NLP) techniques. (from homepage)
  download_rdf: https://op.europa.eu/o/opportal-service/euvoc-download-handler?cellarURI=http%3A%2F%2Fpublications.europa.eu%2Fresource%2Fdistribution%2Feuroscivoc%2F20250625-0%2Fttl%2Fskos_xl%2FEuroSciVoc.ttl&fileName=EuroSciVoc.ttl
  ecoportal:
    contact:
      email: OP-EU-VOCABULARIES@publications.europa.eu
      name: Publications Office of the European Union
    description: European Science Vocabulary (EuroSciVoc) is the taxonomy of fields
      of science based on OECD's 2015 Frascati Manual taxonomy. It was extended with
      fields of science categories extracted from CORDIS content through a semi-automatic
      process developed with Natural Language Processing (NLP) techniques.
    homepage: https://op.europa.eu/s/y4UK
    license: CC-BY-4.0
    name: EuroSciVoc
    prefix: EUROSCIVOC
    publications:
    - https://op.europa.eu/en/web/eu-vocabularies/dataset/-/resource?uri=http://publications.europa.eu/resource/dataset/euroscivoc
    version: '1.6'
  example: ceaf4ca0-9b09-4313-85a5-2edf1762e443
  homepage: https://op.europa.eu/en/web/eu-vocabularies/dataset/-/resource?uri=http://publications.europa.eu/resource/dataset/euroscivoc
  mappings:
    bartoc: '20394'
    ecoportal: EUROSCIVOC
    tib: euroscivoc
  name: European Science Vocabulary
  prefix: euroscivoc
  rdf_uri_format: http://data.europa.eu/8mn/euroscivoc/$1
  tib:
    description: European Science Vocabulary (EuroSciVoc) is the taxonomy of fields
      of science based on OECD's 2015 Frascati Manual taxonomy. It was extended with
      fields of science categories extracted from CORDIS content through a semi-automatic
      process developed with Natural Language Processing (NLP) techniques.
    homepage: https://op.europa.eu/de/home
    keywords:
    - Educational Resources
    - computer science
    name: European Science Vocabulary (EuroSciVoc)
    prefix: euroscivoc
    uri_format: http://data.europa.eu/8mn/euroscivoc/$1
  uri_format: http://data.europa.eu/8mn/euroscivoc/$1
euroscivoc.schema:
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: 'The Euvoc ontology, published by the Publications Office of the European
    Union, supports the development of authority tables (Name Authority Lists or NALs),
    Eurovoc and EU corporate datasets. It contains a set of classes and properties
    enabling all the information to be expressed in multilingual format. It helps
    define relationships between terms and concepts across multiple domains, supporting
    interoperability and standardization across European Union documentation and databases.
    It also defines a set a commonly use properties (i.e: start date, end dates, status),
    and supports the reusability on common data (currencies, languages, countries).


    The Euvoc ontology is maintained by the Publications Office of the European Union
    and disseminated on the EU Vocabularies website.'
  download_rdf: https://op.europa.eu/o/opportal-service/euvoc-download-handler?cellarURI=http%3A%2F%2Fpublications.europa.eu%2Fresource%2Fdistribution%2Feuvoc%2F20241211-0%2Fttl%2Fowl%2Feuvoc.ttl&fileName=euvoc.ttl
  example: isTextual
  homepage: https://op.europa.eu/en/web/eu-vocabularies/dataset/-/resource?uri=http://publications.europa.eu/resource/dataset/euvoc
  name: European Science Vocabulary Ontology
  prefix: euroscivoc.schema
eurovoc:
  bartoc:
    abbreviation: EuroVoc
    description: 'EuroVoc is a multilingual, multidisciplinary thesaurus covering
      the activities of the EU, the European Parliament in particular. It contains
      terms in 23 EU languages (Bulgarian, Croatian, Czech, Danish, Dutch, English,
      Estonian, Finnish, French, German, Greek, Hungarian, Italian, Latvian, Lithuanian,
      Maltese, Polish, Portuguese, Romanian, Slovak, Slovenian, Spanish and Swedish),
      plus in three languages of countries which are candidates for EU accession:
      македонски (mk), shqip (sq) and cрпски (sr).


      It is a multi-disciplinary thesaurus covering fields which are sufficiently
      wide-ranging to encompass both Community and national points of view, with a
      certain emphasis on parliamentary activities. EuroVoc is a controlled set of
      vocabulary which can be used outside the EU institutions, particularly by parliaments.


      The aim of the thesaurus is to provide the information management and dissemination
      services with a coherent indexing tool for the effective management of their
      documentary resources and to enable users to carry out documentary searches
      using controlled vocabulary.'
    homepage: https://op.europa.eu/en/web/eu-vocabularies/dataset/-/resource?uri=http://publications.europa.eu/resource/dataset/eurovoc
    license: CC0-1.0
    name: Multilingual Thesaurus of the European Union
    prefix: '15'
    wikidata_database: Q1370467
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: EuroVoc is the EU's multilingual and multidisciplinary thesaurus. It
    contains keywords, organized in 21 domains and 127 sub-domains, which are used
    to describe the content of documents in EUR-Lex. [from homepage]
  ecoportal:
    contact:
      email: OP-EU-VOCABULARIES@publications.europa.eu
      name: Publications Office of the European Union
    description: EuroVoc is a multilingual, multidisciplinary thesaurus covering the
      activities of the EU. It contains terms in 24 EU languages, plus in three languages
      of countries which are candidate for EU accession. EuroVoc is managed by the
      Publications Office of the European Union, which moved forward to ontology-based
      thesaurus management and semantic web technologies conformant to W3C recommendations
      as well as latest trends in thesaurus standards. EuroVoc users include the European
      Union institutions, the Publications Office of the EU, national and regional
      parliaments in Europe, plus national governments and private users around the
      world.
    homepage: https://op.europa.eu/s/y4TH
    license: CC-BY-4.0
    name: EuroVoc
    prefix: EUROVOC
    version: '4.21'
  example: '1837'
  fairsharing:
    abbreviation: EuroVoc
    description: EuroVoc is a multilingual, multidisciplinary thesaurus covering the
      activities of the EU, the European Parliament in particular. It contains terms
      in 23 official EU languages, plus in three languages of countries which are
      candidates for EU accession. The aim of the thesaurus is to provide the information
      management and dissemination services with a coherent indexing tool for the
      effective management of their documentary resources and to enable users to carry
      out documentary searches using a controlled vocabulary.
    domains:
    - food
    - transport
    homepage: https://op.europa.eu/en/web/eu-vocabularies/th-dataset/-/resource/dataset/eurovoc
    name: EuroVoc
    prefix: FAIRsharing.d0a681
    subjects:
    - Linguistics
    - Forest Management
    - Agriculture
    - Economics
    - Fisheries Science
    - Environmental Science
    - Public Finance
    - Social Policy
    - Geography
    - Social Science
    - Political Science
    - Business Administration
    - Energy Engineering
    - Transportation Planning
    user_defined_tags:
    - Employment
    - International Relations
    - Trade
  homepage: https://eur-lex.europa.eu/browse/eurovoc.html
  mappings:
    bartoc: '15'
    ecoportal: EUROVOC
    fairsharing: FAIRsharing.d0a681
  name: EuroVoc
  pattern: ^\d+$
  prefix: eurovoc
  rdf_uri_format: http://eurovoc.europa.eu/$1
  uri_format: http://eurovoc.europa.eu/$1
ev:
  appears_in:
  - cl
  biocontext:
    prefix: EV
  example: '0100011'
  mappings:
    biocontext: EV
    obofoundry: ev
    prefixcommons: evoc
    wikidata.entity: Q114677886
  obofoundry:
    contact: evoc@sanbi.ac.za
    contact.label: eVOC mailing list
    deprecated: true
    domain: anatomy and development
    name: eVOC (Expressed Sequence Annotation for Humans)
    prefix: ev
  pattern: ^\d{7}$
  prefix: ev
  prefixcommons:
    bioportal: '1013'
    description: Provides structured controlled vocabularies for the annotation of
      expressed sequences with respect to anatomical system, cell type, developmental
      stage, experimental technique, microarray platform, pathology, pooling, tissue
      preparation and treatment.
    example: EV_0100011
    homepage: http://www.evocontology.org/
    keywords:
    - obo
    - anatomy
    - cell
    - development
    - experiment
    name: eVOC (Expressed Sequence Annotation for Humans)
    pattern: ^EV_\d+$
    prefix: evoc
    synonyms:
    - ev
    uri_format: http://www.evocontology.org/site/Main/BrowseEvoc?x_termid=$1
  references:
  - https://twitter.com/Bgeedb/status/1350124337815281664
evm:
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  deprecated: true
  name: eVOC mouse development stage
  prefix: evm
  references:
  - https://genomebiology.biomedcentral.com/articles/10.1186/gb-2007-8-10-r229
evorao:
  aberowl:
    description: EVORAO is an ontology for standardized metadata supporting the sharing
      of pathogens as biological materials, their derived products, and associated
      services, organized into collections. While initially focused on virology, it
      is designed for interoperability and is extensible to other pathogens. EVORAO
      is compatible with DCAT, making it well-suited for efficiently cataloguing pathogen
      collections and related resources.
    download_owl: http://aber-owl.net/media/ontologies/EVORAO/18/evorao.owl
    homepage: https://w3id.org/evorao
    name: European Viral Outbreak Response Alliance Ontology
    prefix: EVORAO
    version: 1.0.10806
  bioportal:
    contact:
      email: evorao@evora-project.eu
      name: d3fk
    description: EVORAO is an ontology for standardized metadata supporting the sharing
      of pathogens as biological materials, their derived products, and associated
      services, organized into collections. While initially focused on virology, it
      is designed for interoperability and is extensible to other pathogens. EVORAO
      is compatible with DCAT, making it well-suited for efficiently cataloguing pathogen
      collections and related resources.
    homepage: https://w3id.org/evorao
    license: CC0-1.0
    name: European Viral Outbreak Response Alliance Ontology
    prefix: EVORAO
    version: 1.0.10769
  description: The EVORAO Ontology provides a structured and harmonized vocabulary
    for describing shareable pathogens as characterized biological materials, along
    with their derived products and associated services, organized into collections.
    Developed within the EVORA project, it supports consistent metadata annotation
    across research infrastructures, promoting findability, accessibility, interoperability,
    and reusability (FAIR). By aligning with relevant standards and ontologies, EVORAO
    facilitates cross-domain collaboration, integration, and sharing of pathogenic
    resources and services to enhance pandemic preparedness and response. While initially
    focused on virology, EVORAO is designed to be extensible and also supports metadata
    harmonization for other pathogens. [from repository]
  example: AlternateName
  homepage: https://github.com/EVORA-project/evora-ontology
  mappings:
    aberowl: EVORAO
    bioportal: EVORAO
    ols: evorao
  name: EVORA Ontology
  ols:
    download_rdf: https://raw.githubusercontent.com/EVORA-project/evora-ontology/refs/heads/main/models/owl/evora_ontology.owl.ttl
    prefix: evorao
    uri_format: https://w3id.org/evorao/$1
  prefix: evorao
  rdf_uri_format: https://w3id.org/evorao/$1
  repository: https://github.com/EVORA-project/evora-ontology
  uri_format: https://w3id.org/evorao/$1
evr:
  contact:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: 'An open, community-driven registry of conference and event venues.


    EVR assigns persistent identifiers (PIDs) to make referencing venues FAIR. This
    is similar to how ORCID assigns PIDs to researchers and ROR assigns PIDs to research
    organizations.


    This benefits researchers assembling information about in-person conferences and
    events by enabling them to refer in an unambiguous way to the venue where it takes
    place.


    This repository follows the [Open Data, Open Code, Open Infrastructure (O3) principles](https://www.nature.com/articles/s41597-024-03406-w),
    meaning that the data and code are all in one repository that anyone can contribute
    to.'
  example: '0000001'
  github_request_issue: 1363
  homepage: https://cthoyt.com/evr
  license: CC0-1.0
  name: Event Venue Registry
  pattern: ^\d{7}$
  prefix: evr
  repository: https://github.com/cthoyt/evr
  uri_format: https://cthoyt.com/evr/$1
exac.gene:
  biocontext:
    prefix: EXAC.GENE
  mappings:
    biocontext: EXAC.GENE
    miriam: exac.gene
    n2t: exac.gene
  miriam:
    deprecated: false
    description: The Exome Aggregation Consortium (ExAC) is a coalition of investigators
      seeking to aggregate and harmonize exome sequencing data from a variety of large-scale
      sequencing projects, and to make summary data available for the wider scientific
      community. The data pertains to unrelated individuals sequenced as part of various
      disease-specific and population genetic studies and serves as a reference set
      of allele frequencies for severe disease studies. This collection references
      gene information.
    homepage: http://exac.broadinstitute.org/
    id: 00000548
    name: ExAC Gene
    namespaceEmbeddedInLui: false
    pattern: ^ENSG\d{11}$
    prefix: exac.gene
    sampleId: ENSG00000169174
    uri_format: http://exac.broadinstitute.org/gene/$1
  n2t:
    description: The Exome Aggregation Consortium (ExAC) is a coalition of investigators
      seeking to aggregate and harmonize exome sequencing data from a variety of large-scale
      sequencing projects, and to make summary data available for the wider scientific
      community. The data pertains to unrelated individuals sequenced as part of various
      disease-specific and population genetic studies and serves as a reference set
      of allele frequencies for severe disease studies. This collection references
      gene information.
    example: ENSG00000169174
    homepage: http://exac.broadinstitute.org/
    name: ExAC Gene at Exome Aggregation Consortium
    namespaceEmbeddedInLui: false
    pattern: ^ENSG\d{11}$
    prefix: exac.gene
    uri_format: http://exac.broadinstitute.org/gene/$1
  prefix: exac.gene
exac.transcript:
  biocontext:
    prefix: EXAC.TRANSCRIPT
  mappings:
    biocontext: EXAC.TRANSCRIPT
    miriam: exac.transcript
    n2t: exac.transcript
  miriam:
    deprecated: false
    description: The Exome Aggregation Consortium (ExAC) is a coalition of investigators
      seeking to aggregate and harmonize exome sequencing data from a variety of large-scale
      sequencing projects, and to make summary data available for the wider scientific
      community. The data pertains to unrelated individuals sequenced as part of various
      disease-specific and population genetic studies and serves as a reference set
      of allele frequencies for severe disease studies. This collection references
      transcript information.
    homepage: http://exac.broadinstitute.org/
    id: '00000547'
    name: ExAC Transcript
    namespaceEmbeddedInLui: false
    pattern: ^ENST\d{11}$
    prefix: exac.transcript
    sampleId: ENST00000407236
    uri_format: http://exac.broadinstitute.org/transcript/$1
  n2t:
    description: The Exome Aggregation Consortium (ExAC) is a coalition of investigators
      seeking to aggregate and harmonize exome sequencing data from a variety of large-scale
      sequencing projects, and to make summary data available for the wider scientific
      community. The data pertains to unrelated individuals sequenced as part of various
      disease-specific and population genetic studies and serves as a reference set
      of allele frequencies for severe disease studies. This collection references
      transcript information.
    example: ENST00000407236
    homepage: http://exac.broadinstitute.org/
    name: ExAC Transcript at Exome Aggregation Consortium
    namespaceEmbeddedInLui: false
    pattern: ^ENST\d{11}$
    prefix: exac.transcript
    uri_format: http://exac.broadinstitute.org/transcript/$1
  prefix: exac.transcript
exac.variant:
  biocontext:
    prefix: EXAC.VARIANT
  mappings:
    biocontext: EXAC.VARIANT
    miriam: exac.variant
    n2t: exac.variant
  miriam:
    deprecated: false
    description: The Exome Aggregation Consortium (ExAC) is a coalition of investigators
      seeking to aggregate and harmonize exome sequencing data from a variety of large-scale
      sequencing projects, and to make summary data available for the wider scientific
      community. The data pertains to unrelated individuals sequenced as part of various
      disease-specific and population genetic studies and serves as a reference set
      of allele frequencies for severe disease studies. This collection references
      variant information.
    homepage: http://exac.broadinstitute.org/
    id: '00000541'
    name: ExAC Variant
    namespaceEmbeddedInLui: false
    pattern: ^\d{1,2}\-\d+\-[GATC]\-[GATC]$
    prefix: exac.variant
    sampleId: 22-46615880-T-C
    uri_format: http://exac.broadinstitute.org/variant/$1
  n2t:
    description: The Exome Aggregation Consortium (ExAC) is a coalition of investigators
      seeking to aggregate and harmonize exome sequencing data from a variety of large-scale
      sequencing projects, and to make summary data available for the wider scientific
      community. The data pertains to unrelated individuals sequenced as part of various
      disease-specific and population genetic studies and serves as a reference set
      of allele frequencies for severe disease studies. This collection references
      variant information.
    example: 22-46615880-T-C
    homepage: http://exac.broadinstitute.org/
    name: ExAC Variant at Exome Aggregation Consortium
    namespaceEmbeddedInLui: false
    pattern: ^\d{1,2}\-\d+\-[GATC]\-[GATC]$
    prefix: exac.variant
    uri_format: http://exac.broadinstitute.org/variant/$1
  prefix: exac.variant
exif:
  example: orientation
  lov:
    description: Vocabulary to describe an Exif format picture data. All Exif 2.2
      tags are defined as RDF properties, as well as several terms to help this schema.
    homepage: http://www.w3.org/2003/12/exif/
    keywords:
    - Image
    modified: '2003-08-19'
    name: Exif data description vocabulary
    prefix: exif
    uri_prefix: http://www.w3.org/2003/12/exif/ns#$1
  mappings:
    lov: exif
    zazuko: exif
  prefix: exif
  zazuko:
    prefix: exif
    uri_format: http://www.w3.org/2003/12/exif/ns#$1
exmo:
  aberowl:
    description: A core reference ontology built upon BFO about exercise medicine
      and it contains the related terms for healthy people, people with chronic conditions
      and people living with diability to exercise.
    download_owl: http://aber-owl.net/media/ontologies/EXMO/7/exmo.owl
    homepage: https://github.com/Exercise-Medicine-Ontology/EXMO
    name: Exercise Medicine Ontology
    prefix: EXMO
  bioportal:
    contact:
      email: xyz19940216@163.com
      name: Xingyun Liu
    description: A core reference ontology built upon BFO about exercise medicine.
      This ontology contains the related terms for healthy people, people with chronic
      conditions and people living with diability to exercise.
    homepage: https://github.com/Exercise-Medicine-Ontology/EXMO
    name: Exercise Medicine Ontology
    prefix: EXMO
    publications:
    - https://www.nature.com/articles/s41597-024-04217-9
    version: '2025-06-05'
  example: 0000008
  mappings:
    aberowl: EXMO
    bioportal: EXMO
    obofoundry: exmo
    ols: exmo
    ontobee: EXMO
  obofoundry:
    contact: xyz19940216@163.com
    contact.github: DarkKnight0-0
    contact.label: Xingyun Liu
    contact.orcid: 0000-0002-9295-2767
    deprecated: false
    description: A core reference ontology built upon BFO about exercise medicine
      and it contains the related terms for healthy people, people with chronic conditions
      and people living with diability to exercise.
    domain: health
    download.owl: http://purl.obolibrary.org/obo/exmo.owl
    homepage: https://github.com/Exercise-Medicine-Ontology/EXMO
    license: CC BY 4.0
    license.url: https://creativecommons.org/licenses/by/4.0/
    name: Exercise Medicine Ontology
    preferredPrefix: EXMO
    prefix: exmo
    publications:
    - id: https://www.ncbi.nlm.nih.gov/pubmed/39695140
      title: Core reference ontology for individualized exercise prescription
    repository: https://github.com/Exercise-Medicine-Ontology/EXMO
  ols:
    description: A core reference ontology built upon BFO about exercise medicine.
      This ontology contains the related terms for healthy people, people with chronic
      conditions and people living with diability to exercise.
    download_owl: http://purl.obolibrary.org/obo/exmo.owl
    homepage: https://github.com/Exercise-Medicine-Ontology/EXMO
    name: EXMO
    prefix: exmo
    tracker: https://github.com/Exercise-Medicine-Ontology/EXMO/issues
    version.iri: http://purl.obolibrary.org/obo/exmo/2025-06-05/exmo.owl
  ontobee:
    library: Library
    name: Exercise Medicine Ontology
    prefix: EXMO
  prefix: exmo
exo:
  aberowl:
    description: Vocabularies for describing exposure data to inform understanding
      of environmental health.
    download_owl: http://aber-owl.net/media/ontologies/EXO/16/exo.owl
    homepage: https://github.com/CTDbase/exposure-ontology
    name: Exposure ontology
    prefix: EXO
  biocontext:
    prefix: EXO
  biolink:
    is_identifiers: false
    is_obo: true
    prefix: ExO
    uri_format: http://purl.obolibrary.org/obo/ExO_$1
  bioportal:
    contact:
      email: annethessen@gmail.com
      name: Anne Thessen
    description: Significant progress has been made over the last several years in
      collecting and improving access to genomic, toxicology, and health data to promote
      understanding about environmental influences on human health. The resulting
      information resources, however, lack extensive and reliable exposure data, which
      are required to translate molecular insights, elucidate environmental contributions
      to diseases, and assess human health risks at the individual and population
      levels. We report our development of an Exposure Ontology, ExO, designed to
      address this information gap by facilitating centralization and integration
      of exposure data to inform understanding of environmental health. Like other
      widely used ontologies, ExO is intended to bridge the gap between exposure science
      and diverse environmental health disciplines including toxicology, epidemiology,
      disease surveillance, and epigenetics.
    homepage: https://github.com/CTDbase/exposure-ontology
    license: CC-BY-4.0
    name: Exposure Ontology
    prefix: EXO
    version: '2025-08-29'
  example: 0000078
  fairsharing:
    abbreviation: ExO
    description: Exposure Ontology (ExO) is designed to facilitate the centralization
      and integration of exposure data to inform understanding of environmental health.
      ExO is intended to bridge the gap between exposure science and diverse environmental
      health disciplines including toxicology, epidemiology, disease surveillance,
      and epigenetics.
    domains:
    - disease
    - exposure
    homepage: https://github.com/CTDbase/exposure-ontology
    license: CC-BY-4.0
    name: Exposure Ontology
    prefix: FAIRsharing.6hna78
    publications:
    - doi: 10.1021/es2033857
      pubmed: '22324457'
      title: 'Providing the missing link: the exposure science ontology ExO'
      year: 2012
    repository: https://github.com/CTDbase/exposure-ontology
    subjects:
    - Environmental Science
    - Toxicology
    - Epigenetics
  mappings:
    aberowl: EXO
    biocontext: EXO
    biolink: ExO
    bioportal: EXO
    fairsharing: FAIRsharing.6hna78
    obofoundry: exo
    ols: exo
    ontobee: ExO
    wikidata.entity: Q113012658
  obofoundry:
    appears_in:
    - ecto
    - scdo
    contact: annethessen@gmail.com
    contact.github: diatomsRcool
    contact.label: Anne Thessen
    contact.orcid: 0000-0002-2908-3327
    deprecated: false
    description: Vocabularies for describing exposure data to inform understanding
      of environmental health.
    domain: health
    download.obo: http://purl.obolibrary.org/obo/exo.obo
    download.owl: http://purl.obolibrary.org/obo/exo.owl
    homepage: https://github.com/CTDbase/exposure-ontology
    license: CC BY 4.0
    license.url: https://creativecommons.org/licenses/by/4.0/
    name: Exposure ontology
    preferredPrefix: ExO
    prefix: exo
    repository: https://github.com/CTDbase/exposure-ontology
  ols:
    description: ExO is intended to bridge the gap between exposure science and diverse
      environmental health disciplines including toxicology, epidemiology, disease
      surveillance, and epigenetics.
    download_owl: http://purl.obolibrary.org/obo/exo.owl
    homepage: https://github.com/CTDbase/exposure-ontology
    name: Exposure ontology (ExO)
    prefix: exo
    tracker: https://github.com/CTDbase/exposure-ontology/issues
    version: '2025-08-29'
    version.iri: http://purl.obolibrary.org/obo/exo/releases/2025-08-29/exo.owl
  ontobee:
    library: Library
    name: Exposure ontology
    prefix: ExO
  pattern: ^\d{7}$
  prefix: exo
  publications:
  - doi: 10.1021/es2033857
    pmc: PMC3314380
    pubmed: '22324457'
    title: 'Providing the missing link: the exposure science ontology ExO'
    year: 2012
  - doi: 10.1021/es2033857
    pmc: null
    pubmed: '22324457'
    title: 'Providing the missing link: the exposure science ontology ExO'
    year: 2012
  synonyms:
  - ExO
  uri_format: http://purl.obolibrary.org/obo/ExO_$1
fabio:
  aberowl:
    description: This file is imported by the vivo-core-public-1.5.owl file. It contains
      terms relating to documents from the http://purl.org/spar/fabio/ namespace that
      are included in the VIVO ontology. FaBiO is a FRBR-aligned Bibliographic Ontology
      that is part of the Semantic Publishing and Referencing (SPAR) suite of ontologies.
    download_owl: http://aber-owl.net/media/ontologies/FaBiO/1/fabio.owl
    homepage: http://sourceforge.net/apps/mediawiki/vivo/index.php?title=Ontology
    name: FaBiO (bibliographic)
    prefix: FaBiO
    version: '1.5'
  biolink:
    is_identifiers: false
    is_obo: false
    prefix: fabio
    uri_format: http://purl.org/spar/fabio/$1
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: The FRBR-aligned Bibliographic Ontology (FaBiO) is an ontology for
    describing entities that are published or potentially publishable (e.g., journal
    articles, conference papers, books), and that contain or are referred to by bibliographic
    references.
  ecoportal:
    contact:
      email: silvio.peroni@unibo.it
      name: Silvio Peroni
    description: "FaBiO, the FRBR-aligned Bibliographic Ontology, is an ontology for\
      \ recording and publishing on the Semantic Web descriptions of entities that\
      \ are published or potentially publishable, and that contain or are referred\
      \ to by bibliographic references, or entities used to define such bibliographic\
      \ references. FaBiO entities are primarily textual publications such as books,\
      \ magazines, newspapers and journals, and items of their content such as poems,\
      \ conference papers and editorials. However, they also include blogs, web pages,\
      \ datasets, computer algorithms, experimental protocols, formal specifications\
      \ and vocabularies, legal records, governmental papers, technical and commercial\
      \ reports and similar publications, and also anthologies, catalogues and similar\
      \ collections. FaBiO classes are structured according to the FRBR schema of\
      \ Works, Expressions, Manifestations and Items. Additional properties have been\
      \ added to extends the FRBR data model by linking Works and Manifestations (fabio:hasManifestation\
      \ and fabio:isManifestationOf), Works and Items (fabio:hasPortrayal and fabio:isPortrayedBy),\
      \ and Expressions and Items (fabio:hasRepresentation and fabio:isRepresentedBy).,\
      \ conference papers and editorials. However, catalogues and similar collections.\
      \ \n\nFaBiO classes are structured according to the FRBR schema of Works, http://purl.org/spar/fabio/FRBR%20diagram%20with%20new%20Fabio%20verbs.png"
    homepage: http://www.sparontologies.net/ontologies/fabio
    license: CC-BY-4.0
    name: FRBR-aligned Bibliographic Ontology
    prefix: FABIO
    publications:
    - http://speroni.web.cs.unibo.it/publications/peroni-2012-fabio-cito-ontologies.pdf
    version: '2.2'
  example: d4e2515
  fairsharing:
    abbreviation: FaBiO
    contact:
      email: silvio.peroni@unibo.it
      name: Silvio Peroni
      orcid: 0000-0003-0530-4305
    description: FaBiO, the FRBR-aligned Bibliographic Ontology, is an ontology for
      recording and publishing on the Semantic Web descriptions of entities that are
      published or potentially publishable, and that contain or are referred to by
      bibliographic references, or entities used to define such bibliographic references.
      FaBiO entities are primarily textual publications such as books, magazines,
      newspapers and journals, and items of their content such as poems, conference
      papers and editorials. However, they also include blogs, web pages, datasets,
      computer algorithms, experimental protocols, formal specifications and vocabularies,
      legal records, governmental papers, technical and commercial reports and similar
      publications, and also anthologies, catalogues and similar collections.
    homepage: http://www.sparontologies.net/ontologies/fabio
    license: CC-BY-4.0
    name: FRBR-aligned Bibliographic Ontology
    prefix: FAIRsharing.2f3180
    publications:
    - doi: 10.1016/j.websem.2012.08.001
      title: 'FaBiO and CiTO: Ontologies for describing bibliographic resources and
        citations'
      year: 2012
    repository: https://github.com/sparontologies/fabio
    subjects:
    - Subject Agnostic
    twitter: sparontologies
  homepage: https://github.com/sparontologies/fabio
  lov:
    description: FaBiO, the FRBR-aligned Bibliographic Ontology, is an ontology for
      recording and publishing on the Semantic Web bibliographic records of scholarly
      endeavours. It forms part of SPAR, a suite of Semantic Publishing and Referencing
      Ontologies.
    homepage: https://github.com/SPAROntologies/fabio
    keywords:
    - SPAR
    modified: '2019-02-19'
    name: FRBR-aligned Bibliographic Ontology
    prefix: fabio
    uri_prefix: http://purl.org/spar/fabio/$1
  mappings:
    aberowl: FaBiO
    biolink: fabio
    ecoportal: FABIO
    fairsharing: FAIRsharing.2f3180
    lov: fabio
    tib: fabio
  name: FaBiO, the FRBR-aligned Bibliographic Ontology
  prefix: fabio
  publications:
  - doi: 10.1016/j.websem.2012.08.001
    pmc: null
    pubmed: null
    title: 'FaBiO and CiTO: Ontologies for describing bibliographic resources and
      citations'
    year: 2012
  rdf_uri_format: http://purl.org/spar/fabio/$1
  repository: https://github.com/sparontologies/fabio
  tib:
    description: http://purl.org/spar/fabio/FRBR%20diagram%20with%20new%20Fabio%20verbs.png
    download_owl: https://raw.githubusercontent.com/SPAROntologies/fabio/master/docs/current/fabio.owl
    homepage: https://sparontologies.github.io/fabio/current/fabio.html
    keywords:
    - TIB
    - literature
    name: FaBiO, the FRBR-aligned Bibliographic Ontology
    prefix: fabio
    uri_format: http://purl.org/spar/fabio/$1
    version.iri: http://purl.org/spar/fabio/2019-02-19
  uri_format: https://sparontologies.github.io/fabio/current/fabio.html#$1
facebase:
  biocontext:
    prefix: FACEBASE
  contact:
    email: ychai@usc.edu
    github: null
    name: Yang Chai
    orcid: 0000-0003-2477-7247
  fairsharing:
    abbreviation: FaceBase
    description: FaceBase is a collaborative NIDCR-funded consortium to generate data
      in support of advancing research into craniofacial development and malformation.
      It serves as a community resource by generating large datasets of a variety
      of types and making them available to the wider research community via this
      website. Practices emphasize a comprehensive and multidisciplinary approach
      to understanding the developmental processes that create the face. The data
      offered spotlights high-throughput genetic, molecular, biological, imaging and
      computational techniques. One of the missions of this consortium is to facilitate
      cooperation and collaboration between projects.
    homepage: https://www.facebase.org/
    license: https://www.facebase.org/methods/policies
    name: FaceBase
    prefix: FAIRsharing.mqvqde
    publications:
    - doi: 10.1242/dev.191213
      pubmed_id: null
      title: 'FaceBase 3: analytical tools and FAIR resources for craniofacial and
        dental research'
    subjects:
    - Anatomy
    - Medicine
    - Epigenetics
    - Genetics
    - Developmental Biology
  integbio:
    description: FaceBase is a collaborative NIDCR-funded consortium to generate data
      in support of advancing research into craniofacial development and malformation.
      It serves as a community resource by generating large datasets of a variety
      of types and making them available to the wider research community via this
      website. Practices emphasize a comprehensive and multidisciplinary approach
      to understanding the developmental processes that create the face. The data
      offered spotlights high-throughput genetic, molecular, biological, imaging and
      computational techniques. One of the missions of this consortium is to facilitate
      cooperation and collaboration between projects.
    fairsharing: FAIRsharing.mqvqde
    homepage: https://www.facebase.org/
    information_keywords:
    - Interaction/Pathway
    - Expression
    - Phenotype
    - Image/Movie
    - Method
    - Bibliography/Documents
    maintainer: USC (University of Southern California)
    name: FaceBase
    prefix: nbdc02022
    status: Active
    target_keywords:
    - Protein
    - Genome/Gene
    - RNA
    - Health/Disease
  mappings:
    biocontext: FACEBASE
    fairsharing: FAIRsharing.mqvqde
    integbio: nbdc02022
    miriam: facebase
    n2t: facebase
    re3data: r3d100013263
  miriam:
    deprecated: false
    description: FaceBase is a collaborative NIDCR-funded consortium to generate data
      in support of advancing research into craniofacial development and malformation.
      It serves as a community resource by generating large datasets of a variety
      of types and making them available to the wider research community via this
      website. Practices emphasize a comprehensive and multidisciplinary approach
      to understanding the developmental processes that create the face. The data
      offered spotlights high-throughput genetic, molecular, biological, imaging and
      computational techniques. One of the missions of this consortium is to facilitate
      cooperation and collaboration between projects.
    homepage: https://www.facebase.org
    id: '00000642'
    name: FaceBase Data Repository
    namespaceEmbeddedInLui: false
    pattern: ^FB\d{8}$
    prefix: facebase
    sampleId: FB00000917
    uri_format: https://www.facebase.org/data/record/#1/isa:dataset/accession=$1
  n2t:
    description: FaceBase is a collaborative NIDCR-funded consortium to generate data
      in support of advancing research into craniofacial development and malformation.
      It serves as a community resource by generating large datasets of a variety
      of types and making them available to the wider research community via this
      website. Practices emphasize a comprehensive and multidisciplinary approach
      to understanding the developmental processes that create the face. The data
      offered spotlights high-throughput genetic, molecular, biological, imaging and
      computational techniques. One of the missions of this consortium is to facilitate
      cooperation and collaboration between projects.
    example: FB00000917
    homepage: https://www.facebase.org
    name: FaceBase Data Repository
    namespaceEmbeddedInLui: false
    pattern: ^FB\d{8}$
    prefix: facebase
    uri_format: https://www.facebase.org/data/record/#1/isa:dataset/accession=$1
  prefix: facebase
  publications:
  - doi: 10.1242/dev.191213
    pmc: PMC7522026
    pubmed: '32958507'
    title: 'FaceBase 3: analytical tools and FAIR resources for craniofacial and dental
      research'
    year: 2020
  re3data:
    description: FaceBase is a collaborative NIDCR-funded project that houses comprehensive
      data in support of advancing research into craniofacial development and malformation.
      It serves as a community resource by curating large datasets of a variety of
      types from the craniofacial research community and sharing them via this website.
      Practices emphasize a comprehensive and multidisciplinary approach to understanding
      the developmental processes that create the face. The data offered spotlights
      high-throughput genetic, molecular, biological, imaging and computational techniques.
      One of the missions of this project is to facilitate cooperation and collaboration
      between the central coordinating center (ie, the Hub) and the craniofacial research
      community.
    doi: 10.17616/R31NJMQ7
    homepage: https://www.facebase.org
    name: FaceBase
    prefix: r3d100013263
fair:
  example: FAIR
  mappings:
    tib: fair
  prefix: fair
  tib:
    description: This is the formal vocabulary (ontology) describing the FAIR principles.
    homepage: https://w3id.org/fair/principles/terms/FAIR-Vocabulary
    keywords:
    - NFDI4ING
    - FID move
    - Digital Planning and Construction
    - FID BAUdigital
    - NFDI4CHEM
    - computer science
    name: FAIR Vocabulary
    prefix: fair
    tracker: https://github.com/peta-pico/FAIR-nanopubs/issues
    uri_format: https://w3id.org/fair/principles/terms/$1
fairsharing:
  biocontext:
    prefix: FAIRSHARING
  example_extras:
  - FAIRsharing.CugtbQ
  fairsharing:
    abbreviation: FAIRsharing
    contact:
      email: allyson.lister@oerc.ox.ac.uk
      github: allysonlister
      name: Allyson Lister
      orcid: 0000-0002-7702-4495
    description: FAIRsharing is a FAIR-supporting resource that provides an informative
      and educational registry on data standards, databases, repositories and policy,
      alongside search and visualization tools and services that interoperate with
      other FAIR-enabling resources. FAIRsharing guides consumers to discover, select
      and use standards, databases, repositories and policy with confidence, and producers
      to make their resources more discoverable, more widely adopted and cited. Each
      record in FAIRsharing is curated in collaboration with the maintainers of the
      resource themselves, ensuring that the metadata in the FAIRsharing registry
      is accurate and timely. Every record is manually reviewed at least once a year.
      Records can be collated into collections, based on a project, society or organisation,
      or Recommendations, where they are collated around a policy, such as a journal
      or funder data policy.
    homepage: https://www.FAIRsharing.org
    license: CC-BY-4.0
    name: FAIRsharing
    prefix: FAIRsharing.2abjs5
    publications:
    - doi: 10.1038/s41587-019-0080-8
      pubmed_id: 30940948
      title: FAIRsharing as a community approach to standards, repositories and policies.
    - doi: 10.1093/database/baw075
      pubmed_id: 27189610
      title: 'BioSharing: curated and crowd-sourced metadata standards, databases
        and data policies in the life sciences.'
    - doi: 10.5281/zenodo.5106255
      pubmed_id: null
      title: FAIRsharing, a FAIR-enabling service for repositories, standards and
        policies
    repository: https://github.com/FAIRsharing
    subjects:
    - Environmental Science
    - Policy
    - Humanities
    - Data Governance
    - Natural Science
    - Earth Science
    - Agriculture
    - Life Science
    - Database Management
    - Biomedical Science
    - Ontology and Terminology
    twitter: fairsharing_org
  mappings:
    biocontext: FAIRSHARING
    fairsharing: FAIRsharing.2abjs5
    miriam: fairsharing
    n2t: fairsharing
    re3data: r3d100010142
  mastodon: fairsharing@fediscience.org
  miriam:
    deprecated: false
    description: The web-based FAIRSharing catalogues aim to centralize bioscience
      data policies, reporting standards and links to other related portals. This
      collection references bioinformatics data exchange standards, which includes
      'Reporting Guidelines', Format Specifications and Terminologies.
    homepage: https://fairsharing.org/
    id: '00000364'
    name: FAIRsharing
    namespaceEmbeddedInLui: false
    pattern: ^bsg-[dscp]?\d{6}$
    prefix: fairsharing
    sampleId: bsg-000052
    uri_format: https://fairsharing.org/$1
  n2t:
    description: The web-based FAIRSharing catalogues aim to centralize bioscience
      data policies, reporting standards and links to other related portals. This
      collection references bioinformatics data exchange standards, which includes
      'Reporting Guidelines', Format Specifications and Terminologies.
    example: bsg-000052
    homepage: https://fairsharing.org/
    name: FAIRSharing at University of Oxford
    namespaceEmbeddedInLui: false
    pattern: ^bsg-[dscp]?\d{6}$
    prefix: fairsharing
    uri_format: https://fairsharing.org/$1
  pattern: ^(bsg-[dscp]?\d{6})|(FAIRsharing\.\w+)$
  prefix: fairsharing
  publications:
  - doi: 10.5281/zenodo.5106255
    pmc: null
    pubmed: null
    title: FAIRsharing, a FAIR-enabling service for repositories, standards and policies
    year: 2021
  - doi: 10.1038/s41587-019-0080-8
    pmc: PMC6785156
    pubmed: '30940948'
    title: FAIRsharing as a community approach to standards, repositories and policies
    year: 2019
  - doi: 10.1093/database/baw075
    pmc: PMC4869797
    pubmed: '27189610'
    title: 'BioSharing: curated and crowd-sourced metadata standards, databases and
      data policies in the life sciences'
    year: 2016
  - doi: 10.1038/s41587-019-0080-8
    pmc: null
    pubmed: null
    title: FAIRsharing as a community approach to standards, repositories and policies.
    year: null
  - doi: 10.1093/database/baw075
    pmc: null
    pubmed: null
    title: 'BioSharing: curated and crowd-sourced metadata standards, databases and
      data policies in the life sciences.'
    year: null
  - doi: 10.5281/zenodo.5106255
    pmc: null
    pubmed: null
    title: FAIRsharing, a FAIR-enabling service for repositories, standards and policies
    year: null
  re3data:
    description: FAIRsharing is a web-based, searchable portal of three interlinked
      registries, containing both in-house and crowdsourced manually curated descriptions
      of standards, databases and data policies, combined with an integrated view
      across all three types of resource. By registering your resource on FAIRsharing,
      you not only gain credit for your work, but you increase its visibility outside
      of your direct domain, so reducing the potential for unnecessary reinvention
      and proliferation of standards and databases.
    doi: 10.17616/R3WS3X
    homepage: https://fairsharing.org/
    name: FAIRsharing
    prefix: r3d100010142
    synonyms:
    - 'formerly: biosharing'
    xrefs:
      omics: '17902'
fairsharing.organization:
  contact:
    email: allyson.lister@oerc.ox.ac.uk
    github: allysonlister
    name: Allyson Lister
    orcid: 0000-0002-7702-4495
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: An organization in FAIRsharing, including universities, labs, etc.
  example: '3851'
  homepage: https://fairsharing.org
  name: FAIRsharing Organization
  part_of_database: fairsharing
  pattern: ^\d+$
  prefix: fairsharing.organization
  uri_format: https://fairsharing.org/organisations/$1
fairsharing.user:
  contact:
    email: allyson.lister@oerc.ox.ac.uk
    github: allysonlister
    name: Allyson Lister
    orcid: 0000-0002-7702-4495
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: A user of FAIRsharing
  example: '5112'
  homepage: https://fairsharing.org
  name: FAIRsharing User
  part_of_database: fairsharing
  pattern: ^\d+$
  prefix: fairsharing.user
  uri_format: https://fairsharing.org/users/$1
faldo:
  aberowl:
    description: FALDO is the Feature Annotation Location Description Ontology. It
      is a simple ontology to describe sequence feature positions and regions as found
      in GFF3, DBBJ, EMBL, GenBank files, UniProt, and many other bioinformatics resources.
      The aim of this ontology is to describe the position of a sequence region or
      a feature. It does not aim to describe features or regions itself, but instead
      depends on resources such as the Sequence Ontology or the UniProt core ontolgy.
    download_owl: http://aber-owl.net/media/ontologies/FALDO/1/faldo.owl
    homepage: http://biohackathon.org/resource/faldo
    name: 'Feature Annotation Location Description Ontology '
    prefix: FALDO
    version: Created at the Biohackathon 2012 and 2013
  agroportal:
    contact:
      email: jerven.bolleman@isb-sib.ch
      name: Jerven Bolleman
    description: FALDO is the Feature Annotation Location Description Ontology. It
      is a simple ontology to describe sequence feature positions and regions as found
      in GFF3, DBBJ, EMBL, GenBank files, UniProt, and many other bioinformatics resources.
      The aim of this ontology is to describe the position of a sequence region or
      a feature. It does not aim to describe features or regions itself, but instead
      depends on resources such as the Sequence Ontology or the UniProt core ontolgy.
    example_uri: http://biohackathon.org/resource/faldo#CollectionOfRegions
    homepage: http://aber-owl.net/ontology/FALDO/#/
    license: CC0-1.0
    name: Feature Annotation Location Description Ontology
    prefix: FALDO
    repository: https://github.com/OBF/FALDO
    version: Created at the Biohackathon 2012 and 2013
  biocontext:
    prefix: faldo
    uri_format: http://biohackathon.org/resource/faldo#$1
  bioportal:
    contact:
      email: faldo@googlegroups.com
      name: FALDO group
    description: FALDO is the Feature Annotation Location Description Ontology. It
      is a simple ontology to describe sequence feature positions and regions as found
      in GFF3, DBBJ, EMBL, GenBank files, UniProt, and many other bioinformatics resources.
      The aim of this ontology is to describe the position of a sequence region or
      a feature. It does not aim to describe features or regions itself, but instead
      depends on resources such as the Sequence Ontology or the UniProt core ontolgy.
    homepage: http://biohackathon.org/resource/faldo
    name: Feature Annotation Location Description Ontology
    prefix: FALDO
    publications:
    - https://jbiomedsem.biomedcentral.com/articles/10.1186/s13326-016-0067-z
    version: Created at the Biohackathon 2012 and 2013
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: It is a simple ontology to describe sequence feature positions and
    regions as found in GFF3, DBBJ, EMBL, GenBank files, UniProt, and many other bioinformatics
    resources
  example: ForwardStrandPosition
  fairsharing:
    abbreviation: FALDO
    description: The Feature Annotation Location Description Ontology (FALDO), to
      describe the positions of annotated features on linear and circular sequences
      for data resources represented in RDF and/or OWL. FALDO can be used to describe
      nucleotide features in sequence records, protein annotations, and glycan binding
      sites, among other features in coordinate systems of the aforementioned “omics”
      areas. Using the same data format to represent sequence positions that are independent
      of file formats allows us to integrate sequence data from multiple sources and
      data types.
    domains:
    - Nucleic acid sequence
    - Sequence annotation
    - Gene Feature
    - sequence feature
    - binding site
    homepage: http://biohackathon.org/resource/faldo
    license: CC0-1.0
    name: Feature Annotation Location Description Ontology
    prefix: FAIRsharing.haxp7g
    publications:
    - doi: 10.1186/s13326-016-0067-z
      pubmed: '27296299'
      title: 'FALDO: a semantic standard for describing the location of nucleotide
        and protein feature annotation'
      year: 2016
    repository: https://github.com/OBF/FALDO
    subjects:
    - Genetics
  homepage: http://biohackathon.org/resource/faldo
  lov:
    description: Used to describe a location that consists of a number of Regions
      but where the order is not known. e.g. the oddly named order() keyword in a
      INSDC file.
    homepage: http://biohackathon.org/resource/faldo
    keywords:
    - Geography
    modified: '2012-09-07'
    name: Feature Annotation Location Description Ontology
    prefix: faldo
    uri_prefix: http://biohackathon.org/resource/faldo#$1
  mappings:
    aberowl: FALDO
    agroportal: FALDO
    biocontext: faldo
    bioportal: FALDO
    fairsharing: FAIRsharing.haxp7g
    lov: faldo
  name: Feature Annotation Location Description Ontology
  preferred_prefix: faldo
  prefix: faldo
  publications:
  - doi: 10.1186/s13326-016-0067-z
    pmc: PMC4907002
    pubmed: '27296299'
    title: 'FALDO: a semantic standard for describing the location of nucleotide and
      protein feature annotation'
    year: 2016
  uri_format: http://biohackathon.org/resource/faldo#$1
fanta:
  contact:
    email: takeya.kasukawa@riken.jp
    github: null
    name: Takeya Kasukawa
    orcid: null
  contributor:
    email: m.naguthana@hotmail.com
    github: nagutm
    name: Mufaddal Naguthanawala
    orcid: 0009-0009-5240-7463
  description: Functional annotations of genomes for studying gene regulation, with
    a primary focus on cis-regulatory elements (CREs) such as promoters and enhancers.
  example: FCHS_301358
  github_request_issue: 1328
  homepage: https://fanta.bio
  name: Functional Genome Annotations with Transcriptional Activities
  pattern: ^FC(HS|MM)_\d+$
  prefix: fanta
  publications:
  - doi: 10.1093/nar/gkae1047
    pmc: null
    pubmed: '39592010'
    title: 'Update of the FANTOM web resource: enhancement for studying noncoding
      genomes'
    year: 2024
  reviewer:
    email: b.gyori@northeastern.edu
    github: bgyori
    name: Benjamin M. Gyori
    orcid: 0000-0001-9439-5346
  uri_format: https://fanta.bio/cre/$1
fao:
  aberowl:
    description: A structured controlled vocabulary for the anatomy of fungi.
    download_owl: http://aber-owl.net/media/ontologies/FAO/29/fao.owl
    homepage: https://github.com/obophenotype/fungal-anatomy-ontology/
    name: Fungal gross anatomy
    prefix: FAO
  biocontext:
    prefix: FAO
  bioportal:
    contact:
      email: dinglis@stanford.edu
      name: Diane Inglis
    description: A structured controlled vocabulary for the anatomy of fungi.
    homepage: https://github.com/obophenotype/fungal-anatomy-ontology
    name: Fungal Gross Anatomy Ontology
    prefix: FAO
  example: '0000001'
  fairsharing:
    abbreviation: FAO
    contact:
      email: dinglis@stanford.edu
      name: Diane Inglis
      orcid: 0000-0003-3166-4638
    description: A structured controlled vocabulary for the anatomy of fungi.
    homepage: https://github.com/obophenotype/fungal-anatomy-ontology
    name: Fungal Gross Anatomy Ontology
    prefix: FAIRsharing.xs6t67
    repository: https://github.com/obophenotype/fungal-anatomy-ontology/issues
    subjects:
    - Life Science
    - Anatomy
    - Microbiology
  mappings:
    aberowl: FAO
    biocontext: FAO
    bioportal: FAO
    fairsharing: FAIRsharing.xs6t67
    obofoundry: fao
    ols: fao
    ontobee: FAO
    prefixcommons: fao
    wikidata.entity: Q81661616
  obofoundry:
    contact: vw253@cam.ac.uk
    contact.github: ValWood
    contact.label: Val Wood
    contact.orcid: 0000-0001-6330-7526
    deprecated: false
    description: A structured controlled vocabulary for the anatomy of fungi.
    domain: anatomy and development
    download.obo: http://purl.obolibrary.org/obo/fao.obo
    download.owl: http://purl.obolibrary.org/obo/fao.owl
    homepage: https://github.com/obophenotype/fungal-anatomy-ontology/
    license: CC0 1.0
    license.url: http://creativecommons.org/publicdomain/zero/1.0/
    name: Fungal gross anatomy
    preferredPrefix: FAO
    prefix: fao
    repository: https://github.com/obophenotype/fungal-anatomy-ontology
  ols:
    description: A structured controlled vocabulary for the anatomy of fungi.
    download_owl: http://purl.obolibrary.org/obo/fao.owl
    homepage: https://github.com/obophenotype/fungal-anatomy-ontology/
    name: Fungal gross anatomy
    prefix: fao
    tracker: https://github.com/obophenotype/fungal-anatomy-ontology/issues
    version: '2025-07-15'
    version.iri: http://purl.obolibrary.org/obo/fao/releases/2025-07-15/fao.owl
  ontobee:
    library: Library
    name: Fungal gross anatomy
    prefix: FAO
  pattern: ^\d{7}$
  prefix: fao
  prefixcommons:
    bioportal: '1019'
    description: The project aims to develop a controlled vocabulary to describe the
      'anatomy' of fungi and other microbes, called the fungal anatomy ontology (FAO).
    example: FAO_0000001
    homepage: http://www.yeastgenome.org/fungi/fungal_anatomy_ontology/
    keywords:
    - obo
    - anatomy
    - fungi
    name: Fungal Anatomy Ontology
    pattern: ^FAO_\d+$
    prefix: fao
  uri_format: http://purl.obolibrary.org/obo/FAO_$1
fao.asfis:
  comment: This resource is offered freely by FAO for download but no obvious licensing
    is indicated, and no caution about appropriate reuse.
  contributor:
    email: null
    github: ddooley
    name: Damion Dooley
    orcid: 0000-0002-8844-9165
  description: The FAO Statistics Team (NFISS) of Fisheries and Aquaculture Division
    collates world capture and aquaculture production statistics at either the species,
    genus, family, or higher taxonomic levels in 3,169 statistical categories (2022
    data release) referred to as species items. ASFIS list of species includes 13,417
    species items selected according to their interest or relation to fisheries and
    aquaculture. For each species item stored in a record, codes (ISSCAAP group, taxonomic
    and 3-alpha) and taxonomic information (scientific name, author(s), family, and
    higher taxonomic classification) are provided. An English name is available for
    most of the records, and about one third of them have also a French and Spanish
    name. Information is also provided about the availability of fishery production
    statistics on the species item in the FAO databases. (from homepage)
  example: '20560'
  github_request_issue: 872
  homepage: https://www.fao.org/fishery/en/collection/asfis/en
  name: Aquatic Sciences and Fisheries Information System
  pattern: ^\d+$
  prefix: fao.asfis
  reviewer:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  synonyms:
  - asfis
  uri_format: https://www.fao.org/fishery/en/species/$1
fbbi:
  aberowl:
    description: A structured controlled vocabulary of sample preparation, visualization
      and imaging methods used in biomedical research.
    download_obo: http://aber-owl.net/media/ontologies/FBbi/14/fbbi.obo
    homepage: http://cellimagelibrary.org/
    name: Biological Imaging Methods Ontology
    prefix: FBbi
    version: unknown
  biocontext:
    prefix: FBbi
  bioportal:
    contact:
      email: chris@bio.umass.edu
      name: Chris Woodcock
    description: A structured controlled vocabulary of sample preparation, visualization
      and imaging methods used in biomedical research.
    homepage: http://cellimagelibrary.org/
    name: Biological Imaging Methods Ontology
    prefix: FBbi
  example: 00000268
  fairsharing:
    abbreviation: FBbi
    description: A structured controlled vocabulary of sample preparation, visualization
      and imaging methods used in biomedical research.
    domains:
    - Imaging
    - assay
    homepage: http://flybase.org/vocabularies
    name: Biological Imaging methods Ontology
    prefix: FAIRsharing.ny3z9j
    subjects:
    - Life Science
    - Biomedical Science
  mappings:
    aberowl: FBbi
    biocontext: FBbi
    bioportal: FBbi
    fairsharing: FAIRsharing.ny3z9j
    obofoundry: fbbi
    ols: fbbi
    ontobee: FBbi
    prefixcommons: fbbi
    wikidata.entity: Q81661618
  obofoundry:
    contact: wawong@gmail.com
    contact.github: wawong
    contact.label: Willy Wong
    contact.orcid: 0000-0002-8841-5870
    deprecated: true
    description: A structured controlled vocabulary of sample preparation, visualization
      and imaging methods used in biomedical research.
    domain: investigations
    download.owl: http://purl.obolibrary.org/obo/fbbi.owl
    homepage: http://cellimagelibrary.org/
    license: CC BY 4.0
    license.url: https://creativecommons.org/licenses/by/4.0/
    name: Biological Imaging Methods Ontology
    preferredPrefix: FBbi
    prefix: fbbi
    repository: https://github.com/CRBS/Biological_Imaging_Methods_Ontology
  ols:
    description: A structured controlled vocabulary of sample preparation, visualization
      and imaging methods used in biomedical research.
    download_owl: http://purl.obolibrary.org/obo/fbbi.owl
    homepage: http://cellimagelibrary.org/
    name: Biological Imaging Methods Ontology
    prefix: fbbi
    tracker: https://github.com/CRBS/Biological_Imaging_Methods_Ontology/issues
    version: '2020-11-06'
    version.iri: http://purl.obolibrary.org/obo/fbbi/releases/2020-11-06/fbbi.owl
  ontobee:
    library: Library
    name: Biological Imaging Methods Ontology
    prefix: FBbi
  pattern: ^\d+$
  prefix: fbbi
  prefixcommons:
    bioportal: '1023'
    description: A structured controlled vocabulary of sample preparation, visualization
      and imaging methods used in biomedical research.
    example: FBbi_00000222
    homepage: http://cellimagelibrary.org/
    keywords:
    - obo
    - experiment
    - imaging
    name: Biological imaging methods
    pattern: ^FBbi_\d+$
    prefix: fbbi
    synonyms:
    - fbbi.root
  synonyms:
  - FBbi
  uri_format: http://purl.obolibrary.org/obo/FBbi_$1
fbbt:
  aberowl:
    description: An ontology representing the gross anatomy of Drosophila melanogaster.
    download_owl: http://aber-owl.net/media/ontologies/FBBT/49/fbbt.owl
    homepage: http://purl.obolibrary.org/obo/fbbt
    name: Drosophila gross anatomy
    prefix: FBBT
  biocontext:
    prefix: FBbt
  bioportal:
    contact:
      email: cp390@cam.ac.uk
      name: Claire Pilgrim
    description: An ontology representing the gross anatomy of Drosophila melanogaster
    homepage: http://purl.obolibrary.org/obo/fbbt
    name: Drosophila Gross Anatomy Ontology
    prefix: FB-BT
    version: '2025-10-16'
  example: 00007294
  fairsharing:
    abbreviation: FBbt
    contact:
      email: cp390@cam.ac.uk
      name: Clare Pilgrim
      orcid: 0000-0002-1373-1705
    description: An ontology of the anatomy of Drosophila melanogaster. It can be
      used for annotation and classification of data related to Drosophila anatomy,
      such as gene expression, phenotype and images. It was originally developed by
      FlyBase, who continue to maintain it and use it for curation.
    domains:
    - gene expression
    - phenotype
    - life cycle stage
    homepage: http://flybase.org/vocabularies
    license: CC-BY-4.0
    name: Drosophila anatomy ontology
    prefix: FAIRsharing.y2qkst
    publications:
    - doi: 10.1093/nar/gkj068
      pubmed: '16381917'
      title: 'FlyBase: anatomical data, images and queries'
      year: 2005
    - doi: 10.1186/2041-1480-4-32
      pubmed: '24139062'
      title: The Drosophila anatomy ontology
      year: 2013
    - doi: 10.1093/bioinformatics/bts113
      pubmed: '22402613'
      title: A strategy for building neuro-anatomy ontologies
      year: 2012
    - doi: 10.1093/bioinformatics/btr677
      pubmed: '22180411'
      title: The Virtual Fly Brain Browser and Query Interface
      year: 2011
    repository: https://github.com/FlyBase/drosophila-anatomy-developmental-ontology
    subjects:
    - Life Science
    - Anatomy
    - Developmental Biology
  go:
    homepage: http://flybase.org/
    name: Drosophila gross anatomy
    prefix: FBbt
  mappings:
    aberowl: FBBT
    biocontext: FBbt
    bioportal: FB-BT
    fairsharing: FAIRsharing.y2qkst
    go: FBbt
    obofoundry: fbbt
    ols: fbbt
    ontobee: FBbt
    prefixcommons: fbbt
    wikidata.entity: Q81661620
  obofoundry:
    contact: cp390@cam.ac.uk
    contact.github: Clare72
    contact.label: Clare Pilgrim
    contact.orcid: 0000-0002-1373-1705
    deprecated: false
    description: An ontology representing the gross anatomy of Drosophila melanogaster.
    domain: anatomy and development
    download.json: http://purl.obolibrary.org/obo/fbbt.json
    download.obo: http://purl.obolibrary.org/obo/fbbt.obo
    download.owl: http://purl.obolibrary.org/obo/fbbt.owl
    homepage: http://purl.obolibrary.org/obo/fbbt
    license: CC BY 4.0
    license.url: http://creativecommons.org/licenses/by/4.0/
    name: Drosophila gross anatomy
    preferredPrefix: FBbt
    prefix: fbbt
    publications:
    - id: https://www.ncbi.nlm.nih.gov/pubmed/24139062
      preferred: true
      title: The Drosophila anatomy ontology
    - id: https://www.ncbi.nlm.nih.gov/pubmed/22402613
      title: A strategy for building neuroanatomy ontologies
    - id: https://www.ncbi.nlm.nih.gov/pubmed/22180411
      title: The Virtual Fly Brain Browser and Query Interface
    - id: https://www.ncbi.nlm.nih.gov/pubmed/16381917
      title: 'FlyBase: anatomical data, images and queries'
    repository: https://github.com/FlyBase/drosophila-anatomy-developmental-ontology
  ols:
    description: An ontology representing the gross anatomy of Drosophila melanogaster.
    download_owl: http://purl.obolibrary.org/obo/fbbt.owl
    homepage: http://purl.obolibrary.org/obo/fbbt
    name: Drosophila gross anatomy
    prefix: fbbt
    tracker: http://purl.obolibrary.org/obo/fbbt/tracker
    version: '2025-10-16'
    version.iri: http://purl.obolibrary.org/obo/fbbt/releases/2025-10-16/fbbt.owl
  ontobee:
    library: Library
    name: Drosophila gross anatomy
    prefix: FBbt
  pattern: ^\d{8}$
  prefix: fbbt
  prefixcommons:
    bioportal: '1015'
    description: A structured controlled vocabulary of the anatomy of Drosophila melanogaster
    example: FBbt_00005835
    homepage: http://www.flybase.org/
    keywords:
    - obo
    - anatomy
    - fly
    name: Drosophila gross anatomy
    pattern: ^FBbt_\d{8}$
    prefix: fbbt
    synonyms:
    - fly_anatomy
    - fbbt_root
  publications:
  - doi: 10.1186/2041-1480-4-32
    pmc: PMC4015547
    pubmed: '24139062'
    title: The Drosophila anatomy ontology
    year: 2013
  - doi: 10.1093/bioinformatics/bts113
    pmc: null
    pubmed: '22402613'
    title: A strategy for building neuroanatomy ontologies
    year: 2012
  - doi: 10.1093/bioinformatics/btr677
    pmc: null
    pubmed: '22180411'
    title: The Virtual Fly Brain browser and query interface
    year: 2011
  - doi: 10.1093/nar/gkj068
    pmc: PMC1347431
    pubmed: '16381917'
    title: 'FlyBase: anatomical data, images and queries'
    year: 2006
  - doi: null
    pmc: null
    pubmed: '24139062'
    title: The Drosophila anatomy ontology
    year: null
  - doi: null
    pmc: null
    pubmed: '22402613'
    title: A strategy for building neuroanatomy ontologies
    year: null
  - doi: null
    pmc: null
    pubmed: '22180411'
    title: The Virtual Fly Brain Browser and Query Interface
    year: null
  - doi: null
    pmc: null
    pubmed: '16381917'
    title: 'FlyBase: anatomical data, images and queries'
    year: null
  - doi: 10.1093/nar/gkj068
    pmc: null
    pubmed: '16381917'
    title: 'FlyBase: anatomical data, images and queries'
    year: 2005
  - doi: 10.1186/2041-1480-4-32
    pmc: null
    pubmed: '24139062'
    title: The Drosophila anatomy ontology
    year: 2013
  - doi: 10.1093/bioinformatics/bts113
    pmc: null
    pubmed: '22402613'
    title: A strategy for building neuro-anatomy ontologies
    year: 2012
  - doi: 10.1093/bioinformatics/btr677
    pmc: null
    pubmed: '22180411'
    title: The Virtual Fly Brain Browser and Query Interface
    year: 2011
  synonyms:
  - FBbt
  - FBbt_root
  uri_format: http://purl.obolibrary.org/obo/FBbt_$1
fbcv:
  aberowl:
    description: A structured controlled vocabulary used for various aspects of annotation
      by FlyBase.
    download_owl: http://aber-owl.net/media/ontologies/FBCV/42/fbcv.owl
    homepage: http://purl.obolibrary.org/obo/fbcv
    name: FlyBase Controlled Vocabulary
    prefix: FBCV
  biocontext:
    prefix: FBcv
  bioportal:
    contact:
      email: cp390@cam.ac.uk
      name: Clare Pilgrim
    description: A structured controlled vocabulary used for various aspects of annotation
      by FlyBase. It includes the Drosophila Phenotype Ontology (DPO) which is also
      released separately. This ontology is maintained by FlyBase for various aspects
      of annotation not covered, or not yet covered, by other OBO ontologies. If and
      when community ontologies are available for the domains here covered FlyBase
      will use them., A miscellaneous ontology of terms used for curation in FlyBase,
      including the DPO.
    homepage: http://purl.obolibrary.org/obo/fbcv
    license: CC-BY-4.0
    name: FlyBase Controlled Vocabulary
    prefix: FB-CV
    version: '2025-10-17'
  download_obo: https://raw.githubusercontent.com/FlyBase/flybase-controlled-vocabulary/master/fbcv.obo
  example: 0000586
  fairsharing:
    abbreviation: FBcv
    contact:
      email: cp390@cam.ac.uk
      name: Clare Pilgrim
      orcid: 0000-0002-1373-1705
    description: A structured controlled vocabulary developed and used by FlyBase,
      including the Drosophila phenotype ontology. It is used in annotation and classification
      of data related to Drosophila, including phenotypes and expression.
    domains:
    - Expression data
    - phenotype
    homepage: https://github.com/FlyBase/flybase-controlled-vocabulary
    license: CC-BY-4.0
    name: FlyBase Controlled Vocabulary
    prefix: FAIRsharing.6tgyxf
    publications:
    - doi: 10.1186/2041-1480-4-30
      pubmed: '24138933'
      title: The Drosophila phenotype ontology
      year: 2013
    repository: https://github.com/FlyBase/flybase-controlled-vocabulary
    subjects:
    - Life Science
  mappings:
    aberowl: FBCV
    biocontext: FBcv
    bioportal: FB-CV
    fairsharing: FAIRsharing.6tgyxf
    obofoundry: fbcv
    ols: fbcv
    ontobee: FBcv
    prefixcommons: fbcv
    wikidata.entity: Q81661622
  obofoundry:
    appears_in:
    - ontoavida
    contact: cp390@cam.ac.uk
    contact.github: Clare72
    contact.label: Clare Pilgrim
    contact.orcid: 0000-0002-1373-1705
    deprecated: false
    description: A structured controlled vocabulary used for various aspects of annotation
      by FlyBase.
    domain: organisms
    download.json: http://purl.obolibrary.org/obo/fbcv.json
    download.obo: http://purl.obolibrary.org/obo/fbcv.obo
    download.owl: http://purl.obolibrary.org/obo/fbcv.owl
    homepage: http://purl.obolibrary.org/obo/fbcv
    license: CC BY 4.0
    license.url: http://creativecommons.org/licenses/by/4.0/
    name: FlyBase Controlled Vocabulary
    preferredPrefix: FBcv
    prefix: fbcv
    repository: https://github.com/FlyBase/flybase-controlled-vocabulary
  ols:
    description: A structured controlled vocabulary used for various aspects of annotation
      by FlyBase.
    download_owl: http://purl.obolibrary.org/obo/fbcv.owl
    homepage: http://purl.obolibrary.org/obo/fbcv
    name: FlyBase Controlled Vocabulary
    prefix: fbcv
    tracker: https://github.com/FlyBase/flybase-controlled-vocabulary/issues
    version: '2025-10-17'
    version.iri: http://purl.obolibrary.org/obo/fbcv/releases/2025-10-17/fbcv.owl
  ontobee:
    library: Library
    name: Drosophila Phenotype Ontology
    prefix: FBcv
  part_of_database: flybase
  pattern: ^\d{7}$
  prefix: fbcv
  prefixcommons:
    bioportal: '1017'
    description: A structured controlled vocabulary used for various aspects of annotation
      by FlyBase. This ontology is maintained by FlyBase for various aspects of annotation
      not covered, or not yet covered, by other OBO ontologies.  If and when community
      ontologies are available for the domains here covered FlyBase will use them.
    example: FBcv_0000013
    homepage: http://www.flybase.org/
    keywords:
    - obo
    - descriptor
    - fly
    name: FlyBase Controlled Vocabulary
    pattern: ^FBcv_\d{7}$
    prefix: fbcv
  publications:
  - doi: 10.1186/2041-1480-4-30
    pmc: PMC3816596
    pubmed: '24138933'
    title: The Drosophila phenotype ontology
    year: 2013
  - doi: 10.1186/2041-1480-4-30
    pmc: null
    pubmed: '24138933'
    title: The Drosophila phenotype ontology
    year: 2013
  - doi: 10.1186/2041-1480-4-30
    pmc: null
    pubmed: '24138933'
    title: The Drosophila phenotype ontology
    year: 2013
  synonyms:
  - FBcv
  uri_format: http://purl.obolibrary.org/obo/FBcv_$1
fbdv:
  aberowl:
    description: A structured controlled vocabulary of the development of Drosophila
      melanogaster.
    download_owl: http://aber-owl.net/media/ontologies/FBDV/44/fbdv.owl
    homepage: http://purl.obolibrary.org/obo/fbdv
    name: Drosophila development
    prefix: FBDV
  biocontext:
    prefix: FBdv
  bioportal:
    contact:
      email: mmc46@gen.cam.ac.uk
      name: Marta Costa
    description: A structured controlled vocabulary of the development of <i>Drosophila
      melanogaster</i>.
    homepage: http://sourceforge.net/p/fbbtdv/wiki/Home/
    name: Drosophila Development Ontology
    prefix: FB-DV
    version: '2025-10-16'
  example: '00000000'
  fairsharing:
    abbreviation: FBdv
    contact:
      email: cp390@cam.ac.uk
      name: Clare Pilgrim
      orcid: 0000-0002-1373-1705
    description: An ontology of the developmental stages of Drosophila melanogaster.
      It provides a controlled vocabulary for use in annotation and classification
      of data related to Drosophila, such as gene expression, phenotypes and images.
    domains:
    - life cycle
    - life cycle stage
    homepage: http://flybase.org/vocabularies
    license: CC-BY-4.0
    name: Drosophila developmental ontology
    prefix: FAIRsharing.p52pzj
    repository: https://github.com/FlyBase/drosophila-developmental-ontology
    subjects:
    - Life Science
    - Developmental Biology
  go:
    homepage: http://flybase.org/
    name: Drosophila development
    prefix: FBdv
    uri_format: http://flybase.org/cgi-bin/fbcvq.html?query=FBdv:$1
  mappings:
    aberowl: FBDV
    biocontext: FBdv
    bioportal: FB-DV
    fairsharing: FAIRsharing.p52pzj
    go: FBdv
    obofoundry: fbdv
    ols: fbdv
    ontobee: FBdv
    prefixcommons: fbdv
    wikidata.entity: Q81661623
  obofoundry:
    contact: cp390@cam.ac.uk
    contact.github: Clare72
    contact.label: Clare Pilgrim
    contact.orcid: 0000-0002-1373-1705
    deprecated: false
    description: A structured controlled vocabulary of the development of Drosophila
      melanogaster.
    domain: anatomy and development
    download.json: http://purl.obolibrary.org/obo/fbdv.json
    download.obo: http://purl.obolibrary.org/obo/fbdv.obo
    download.owl: http://purl.obolibrary.org/obo/fbdv.owl
    homepage: http://purl.obolibrary.org/obo/fbdv
    license: CC BY 4.0
    license.url: http://creativecommons.org/licenses/by/4.0/
    name: Drosophila development
    preferredPrefix: FBdv
    prefix: fbdv
    repository: https://github.com/FlyBase/drosophila-developmental-ontology
  ols:
    description: A structured controlled vocabulary of the development of Drosophila
      melanogaster.
    download_owl: http://purl.obolibrary.org/obo/fbdv.owl
    homepage: http://purl.obolibrary.org/obo/fbdv
    name: Drosophila development
    prefix: fbdv
    tracker: http://purl.obolibrary.org/obo/fbdv/tracker
    version: '2025-10-16'
    version.iri: http://purl.obolibrary.org/obo/fbdv/releases/2025-10-16/fbdv.owl
  ontobee:
    library: Library
    name: Drosophila development
    prefix: FBdv
  pattern: ^\d{8}$
  prefix: fbdv
  prefixcommons:
    alt_uri_formats:
    - http://purl.org/obo/owl/FBDV#$1
    bioportal: '1016'
    description: A structured controlled vocabulary of the development of Drosophila
      melanogaster.
    example: FBdv_00005291
    homepage: http://www.flybase.org/
    keywords:
    - obo
    - development
    - fly
    name: Drosophila development
    pattern: ^FBdv_\d{8}$
    prefix: fbdv
    synonyms:
    - fbdv.root
  synonyms:
  - FBdv
  uri_format: http://purl.obolibrary.org/obo/FBdv_$1
fbol:
  biocontext:
    prefix: FBOL
  comment: Website down, checked on 2021-10-07
  deprecated: true
  mappings:
    biocontext: FBOL
    miriam: fbol
    n2t: fbol
    ncbi: FBOL
  miriam:
    deprecated: false
    description: DNA barcoding is the use of short standardised segments of the genome
      for identification of species in all the Kingdoms of Life. The goal of the Fungal
      Barcoding site is to promote the DNA barcoding of fungi and other fungus-like
      organisms.
    homepage: http://www.fungalbarcoding.org/
    id: '00000410'
    name: Fungal Barcode
    namespaceEmbeddedInLui: false
    pattern: ^\d+$
    prefix: fbol
    sampleId: '2224'
    uri_format: http://www.fungalbarcoding.org/BioloMICS.aspx?Table=Fungal barcodes&Rec=$1&Fields=All&ExactMatch=T
  n2t:
    description: DNA barcoding is the use of short standardised segments of the genome
      for identification of species in all the Kingdoms of Life. The goal of the Fungal
      Barcoding site is to promote the DNA barcoding of fungi and other fungus-like
      organisms.
    example: '2224'
    homepage: http://www.fungalbarcoding.org/
    name: Fungal Barcode at Fungal Biodiversity Centre
    namespaceEmbeddedInLui: false
    pattern: ^\d+$
    prefix: fbol
    uri_format: http://www.fungalbarcoding.org/BioloMICS.aspx?Table=Fungal barcodes&Rec=$1&Fields=All&ExactMatch=T
  ncbi:
    example: '2224'
    homepage: http://www.fungalbarcoding.org/
    name: International Fungal Working Group Fungal Barcoding.
    prefix: FBOL
  prefix: fbol
fbql:
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  deprecated: true
  example: '00005254'
  name: FlyBase Qualifiers
  pattern: ^\d+$
  prefix: fbql
fbrf:
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: FlyBase internal citation identifiers
  example: 0187632
  homepage: https://flybase.org
  name: FlyBase Reference Report
  part_of_database: flybase
  pattern: ^\d{7}$
  prefix: fbrf
  uri_format: https://flybase.org/reports/FBrf$1
fbsp:
  aberowl:
    description: The taxonomy of the family <i>Drosophilidae</i> (largely after Baechli)
      and of other taxa referred to in FlyBase.
    download_obo: http://aber-owl.net/media/ontologies/FB-SP/7/fb-sp.obo
    homepage: http://www.flybase.org/
    name: Fly Taxonomy
    prefix: FB-SP
    version: unknown
  biocontext:
    prefix: FBSP
  bioportal:
    contact:
      email: mmc46@gen.cam.ac.uk
      name: Marta Costa
    description: The taxonomy of the family <i>Drosophilidae</i> (largely after Baechli)
      and of other taxa referred to in FlyBase.
    homepage: http://www.flybase.org/
    name: Fly Taxonomy
    prefix: FB-SP
  example: '00000000'
  mappings:
    aberowl: FB-SP
    biocontext: FBSP
    bioportal: FB-SP
    obofoundry: fbsp
    ols: fbsp
    wikidata.entity: Q114677887
  obofoundry:
    contact: cp390@cam.ac.uk
    contact.github: Clare72
    contact.label: Clare Pilgrim
    contact.orcid: 0000-0002-1373-1705
    deprecated: true
    description: The taxonomy of the family <i>Drosophilidae</i> (largely after Baechli)
      and of other taxa referred to in FlyBase.
    domain: organisms
    download.owl: http://purl.obolibrary.org/obo/fbsp.owl
    homepage: http://www.flybase.org/
    name: Fly taxonomy
    prefix: fbsp
  ols:
    description: The taxonomy of the family <i>Drosophilidae</i> (largely after Baechli)
      and of other taxa referred to in FlyBase.
    homepage: http://www.flybase.org/
    name: Fly taxonomy
    prefix: fbsp
    version: '2017-11-19'
    version.iri: http://purl.obolibrary.org/obo/fbsp/releases/2017-11-19/fbsp.owl
  part_of_database: flybase
  pattern: ^\d{8}$
  prefix: fbsp
fbtc:
  cellosaurus:
    category: Cell line databases/resources
    homepage: https://flybase.org/cgi-bin/cvreport.pl?id=FBbt%3A00005329
    name: Drosophila genome database; cell line entry
    prefix: FlyBase_Cell_line
    uri_format: https://flybase.org/reports/$1.htm
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: The cell line vocabulary inside FlyBase
  example: 0000190
  homepage: https://flybase.org
  mappings:
    cellosaurus: FlyBase_Cell_line
  name: Flybase Cell Line
  part_of_database: flybase
  pattern: ^\d{7}$
  prefix: fbtc
  synonyms:
  - FlyBase_Cell_line
  uri_format: https://flybase.org/reports/FBtc$1
fcb:
  homepage: https://w3id.org/faircookbook/
  mappings:
    miriam: fcb
  miriam:
    deprecated: false
    description: 'Created by researchers and data managers professionals, the FAIR
      Cookbook is an online resource for the Life Sciences with recipes that help
      you to make and keep data Findable, Accessible, Interoperable, and Reusable
      (FAIR).


      '
    homepage: https://w3id.org
    id: 00000891
    name: the FAIR Cookbook
    namespaceEmbeddedInLui: false
    pattern: ^FCB\d{3}$
    prefix: fcb
    sampleId: FCB005
    uri_format: https://w3id.org/faircookbook/$1
  name: FAIR Cookbook
  prefix: fcb
  repository: https://github.com/FAIRplus/the-fair-cookbook
  synonyms:
  - faircookbook
fcsfree:
  cellosaurus:
    category: Cell line databases/resources
    homepage: https://fcs-free.org/
    name: Fetal Calf Serum-Free Database
    prefix: FCS-free
    uri_format: https://fcs-free.org/fcs-database?$1
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  example: 240-17-488-3-4-12
  homepage: https://fcs-free.org
  mappings:
    cellosaurus: FCS-free
  name: Fetal Calf Serum-Free Database
  prefix: fcsfree
  uri_format: https://fcs-free.org/fcs-database?$1
fda.application:
  comment: The official FDA website doesn't appear to be able to resolve application
    IDs but these IDs do appear in some PDF documents, e.g., https://www.fda.gov/media/159183/download.
  contributor:
    email: b.gyori@northeastern.edu
    github: bgyori
    name: Benjamin M. Gyori
    orcid: 0000-0001-9439-5346
  description: This prefix is for FDA application identifiers. There are multiple
    types of FDA applications (https://www.fda.gov/drugs/how-drugs-are-developed-and-approved/types-applications),
    including New Drug Application (NDA). FDA.report provides access to all FDA databases,
    including applications, in a single portal, and can resolve FDA application identifiers.
  example: 070886
  github_request_issue: 1146
  homepage: https://fda.report/applications
  name: FDA Application
  pattern: ^\d{6}$
  prefix: fda.application
  reviewer:
    email: tiago.lubiana.alves@usp.br
    github: lubianat
    name: Tiago Lubiana
    orcid: 0000-0003-2473-2313
  uri_format: https://fda.report/applications/$1
fema:
  contact:
    email: staylor@vertosolutions.net
    github: null
    name: Sean Taylor
    orcid: 0000-0002-7806-4173
  contributor:
    email: m.naguthana@hotmail.com
    github: nagutm
    name: Mufaddal Naguthanawala
    orcid: 0009-0009-5240-7463
  description: FEMA provides identifiers for flavor ingredients deemed safe for food
    use. These entities include chemical compounds and natural substances used as
    flavoring agents, each reviewed by the FEMA Expert Panel for GRAS (Generally Recognized
    As Safe) status. The identifiers link to safety data and regulatory assessments,
    including evaluations by the U.S. FDA and, where applicable, the Joint FAO/WHO
    Expert Committee on Food Additives (JECFA).
  example: '4667'
  github_request_issue: 1247
  homepage: https://www.femaflavor.org
  name: Flavor and Extract Manufacturers Association
  pattern: ^\d+$
  prefix: fema
  reviewer:
    email: b.gyori@northeastern.edu
    github: bgyori
    name: Benjamin M. Gyori
    orcid: 0000-0001-9439-5346
ferroliganddb:
  contact:
    email: guqiong@mail.sysu.edu.cn
    github: null
    name: Qiong Gu
    orcid: null
  contributor:
    email: shah.tanay2@northeastern.edu
    github: tanayshah2
    name: Tanay Shah
    orcid: 0009-0001-1912-5132
  description: FerroLigandDB is a meticulously curated, high-quality database of ferroptosis
    regulators, including inducers and inhibitors.
  example: '486'
  github_request_issue: 1145
  homepage: https://ferr.gulab.org.cn/
  name: FerroLigandDB
  prefix: ferroliganddb
  publications:
  - doi: 10.1021/acs.jcim.4c00525
    pmc: null
    pubmed: '38885636'
    title: 'FerroLigandDB: A Ferroptosis Ligand Database of Structure-Activity Relations'
    year: 2024
  reviewer:
    email: b.gyori@northeastern.edu
    github: bgyori
    name: Benjamin M. Gyori
    orcid: 0000-0001-9439-5346
  uri_format: https://ferr.gulab.org.cn/browse/$1
fhir.implementation:
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: A set of guides on implementing various processes within hospitals
    or healthcare systems.
  example: immds
  homepage: https://hl7.org/fhir/us/
  name: FHIR United States Implementation Guides
  prefix: fhir.implementation
  uri_format: https://hl7.org/fhir/us/$1
fidbaudigital.subject:
  example: 004d64e9-a7ab-4a73-b117-0c6fc6c76d81
  mappings:
    tib: bdsubj
  prefix: fidbaudigital.subject
  tib:
    description: This subject heading system has beeen developed for use in FID BAUdigital
      and its future web services. It covers scientific fields of Civil Engineering,
      Architecture and Urban Studies with a special section on digitization. This
      subject classification has been mapped to several other classification systems.
      The latest version of the subject classification including these mappings is
      available at https://gitlab.com/fid-bau/terminologie/fid-baudigital-faecherklassifikation/-/raw/main/Subject_Headings_all_mappings.owl.
    homepage: https://gitlab.com/fid-bau/terminologie/fid-baudigital-faecherklassifikation
    keywords:
    - Digital Planning and Construction
    - FID BAUdigital
    - NFDI4ING
    - civil engineering
    - architecture
    name: FID BAUdigital Subject Headings
    prefix: bdsubj
    tracker: https://gitlab.com/fid-bau/terminologie/fid-baudigital-faecherklassifikation/-/issues
    uri_format: https://purl.org/fidbaudigital/subjects#$1
    version.iri: https://gitlab.com/fid-bau/terminologie/fid-baudigital-faecherklassifikation/-/raw/0.0.12/SubjectHeadings_all.owl
fideo:
  aberowl:
    description: Food-Drug interactions automatically extracted from scientific literature
    download_owl: http://aber-owl.net/media/ontologies/FIDEO/9/fideo.owl
    homepage: https://gitub.u-bordeaux.fr/erias/fideo
    name: Food Interactions with Drugs Evidence Ontology
    prefix: FIDEO
  bioportal:
    contact:
      email: georgeta.bordea@u-bordeaux.fr
      name: Georgeta Bordea
    description: The Food Interactions with Drugs Evidence Ontology (FIDEO) is an
      ontology used for annotation and retrieval of scientific articles about food-drug
      interactions.
    homepage: https://gitub.u-bordeaux.fr/erias/fideo
    name: Food Interactions with Drugs Evidence Ontology
    prefix: FIDEO
    publications:
    - http://www.informatik.uni-leipzig.de/~loebe/tmp/ICBO2020/paperL.pdf
    version: '2023-12-18'
  example: '00000021'
  example_extras:
  - '000001507'
  mappings:
    aberowl: FIDEO
    bioportal: FIDEO
    obofoundry: fideo
    ols: fideo
    ontobee: FIDEO
    wikidata.entity: Q111854958
  obofoundry:
    contact: georgeta.bordea@u-bordeaux.fr
    contact.github: getbordea
    contact.label: Georgeta Bordea
    contact.orcid: 0000-0001-9921-8234
    deprecated: false
    description: Food-Drug interactions automatically extracted from scientific literature
    domain: diet, metabolomics, and nutrition
    download.owl: http://purl.obolibrary.org/obo/fideo.owl
    homepage: https://gitub.u-bordeaux.fr/erias/fideo
    license: CC0 1.0
    license.url: https://creativecommons.org/publicdomain/zero/1.0/
    name: Food Interactions with Drugs Evidence Ontology
    preferredPrefix: FIDEO
    prefix: fideo
    repository: https://gitub.u-bordeaux.fr/erias/fideo
  ols:
    description: Food-Drug interactions automatically extracted from scientific literature
    download_owl: http://purl.obolibrary.org/obo/fideo.owl
    homepage: https://gitub.u-bordeaux.fr/erias/fideo
    name: Food Interactions with Drugs Evidence Ontology
    prefix: fideo
    version: '2023-12-18'
    version.iri: http://purl.obolibrary.org/obo/fideo/releases/2023-12-18/fideo.owl
  ontobee:
    library: Library
    name: Food Interactions with Drugs Evidence Ontology
    prefix: FIDEO
  pattern: ^\d+$
  prefix: fideo
  uri_format: http://purl.obolibrary.org/obo/FIDEO_$1
fiesta.iot:
  homepage: https://github.com/fiesta-iot/ontology
  lov:
    description: The  FIESTA-IoT ontology takes inspiration from the well-known Noy
      et al. methodology  for reusing and interconnecting existing ontologies. To
      build the ontology, we leverage a number of core concepts from various mainstream
      ontologies and taxonomies, such as Semantic Sensor Network (SSN), M3-lite (a
      lite version of M3 ontology), WGS84, IoT-lite, Time, and DUL ontology.
    homepage: http://purl.org/iot/ontology/fiesta-iot
    keywords:
    - IoT
    modified: '2017-02-09'
    name: FIESTA-IoT Ontology
    prefix: fiesta-iot
    uri_prefix: http://purl.org/iot/ontology/fiesta-iot#$1
  mappings:
    lov: fiesta-iot
    tib: fiestaiot
  no_own_terms: true
  prefix: fiesta.iot
  references:
  - https://zenodo.org/record/1193299
  repository: https://github.com/fiesta-iot/ontology
  tib:
    description: "Many testbeds owning devices or applications interacting with the\
      \ sensors, store their inherent observations and other related data in their\
      \ own proprietary format. In other words, making a testbed independent and isolated\
      \ from others that cannot directly interact with each other. Differences in\
      \ the data format lead to interoperability issues between the testbeds and much\
      \ work has to be done in order to ensure the compatibility. One has to understand\
      \ different data formats and create the mapping between them. As a result, a\
      \ testbed must understand other testbed's format and create the mapping both\
      \ while sending and receiving information. One method to accomplish interoperability\
      \ is through the usage of semantic-based technologies to annotate all the information\
      \ shared by the platforms. Nevertheless, some of the relevant existing ontologies\
      \ promise interoperability but: \n\n- do not address the problem to describe\
      \ the observation in an interoperable manner to ease further tasks, such as\
      \ reasoning, \n- many of them are domain-specific and cannot be applied across\
      \ domains, \n- they have missing concepts and do not suffice the needs of the\
      \ measurements provided by the sensors, and \n- many ontologies do not follow\
      \ best practices making it hard to correctly interpret and reuse concepts.\n\
      \n\nIn order to address the above-mentioned limitations, we provide FIESTA-IoT\
      \ ontology (a unified semantic model) that follows best practices. FIESTA-IoT\
      \ Ontology is a merge of concepts from various ontologies such as IoT-lite,\
      \ M3-lite Taxonomy, SSN, Time and DUL (see Figure 1). The FIESTA-IoT Ontology\
      \ is divided into 2 parts: resource description and observations produced. One\
      \ has to follow the Figure 2 and Figure 3, respectively, for understanding what\
      \ all concepts are associated with resource description and observation. Using\
      \ such information testbeds can annotate their data to FIESTA-IoT specific requirements\
      \ and the annotators developed can achieve FIESTA-IoT certification. For reference\
      \ we provide sample annotations as figure (see Figure 4 and Figure 5) for both\
      \ resource graph and observation graph.\n\nFor more details please see:\n\n\
      - R. Agarwal, D. Fernandez, T. Elsaleh, A. Gyrard, J. Lanza, L. Sanchez, N.\
      \ Georgantas, V. Issarny, \"Unified IoT Ontology to Enable Interoperability\
      \ and Federation of Testbeds\", 3rd IEEE WF-IoT, Reston, VA, USA, 12-14 December\
      \ 2016. (https://hal.inria.fr/hal-01386917/document)\n- FIESTA-IoT Consortium\
      \ (R. Agarwal editor), \"Deliverable D3.1.2 Semantic Models for Testbeds, Interoperability\
      \ and Mobility Support, and Best Practices\", project FIESTA-IoT deliverable,\
      \ 2016.\n- FIESTA-IoT Consortium (R. Agarwal editor), \"Deliverable D3.1.1 Semantic\
      \ Models for Testbeds, Interoperability and Mobility Support, and Best Practices\"\
      , project FIESTA-IoT deliverable, 2016.\n\nWe further acknowledge, testbed provider\
      \ such as SmartSantander, UniS, KETI, Inria, and other open call testbeds for\
      \ their valuable comments. Please report any errors to rachit.agarwal@inria.fr."
    download_owl: https://raw.githubusercontent.com/fiesta-iot/ontology/master/fiesta-iot.owl
    homepage: https://zenodo.org/record/1193299
    keywords:
    - NFDI4ING
    - engineering
    name: FIESTA-IoT Ontology
    prefix: fiestaiot
    tracker: https://github.com/fiesta-iot/ontology/issues
    uri_format: http://purl.org/iot/ontology/fiesta-iot#$1
findex.bau:
  example: B10000000000_3
  homepage: https://gitlab.com/fid-bau/terminologie
  mappings:
    tib: bau
  prefix: findex.bau
  repository: https://gitlab.com/fid-bau/terminologie
  tib:
    description: SKOS Model of FINDEX Bau by Fraunhofer-Informationszentrum Raum und
      Bau IRB
    download_owl: https://gitlab.com/fid-bau/terminologie/findex-bau/-/raw/0.0.6/TS/findex-bau-skos.owl
    keywords:
    - Digital Planning and Construction
    - FID BAUdigital
    - NFDI4ING
    - civil engineering
    name: FINDEX Bau as a SKOS Thesaurus - Facetted Indexing System for Civil Engineering
    prefix: bau
    tracker: https://gitlab.com/fid-bau/terminologie/findex-bau/issues
    uri_format: https://terminology.fraunhofer.de/voc/bau#$1
    version.iri: https://gitlab.com/fid-bau/terminologie/findex-bau/-/raw/0.0.6/findex-bau.owl
findex.raum:
  example: R00000000000_3
  mappings:
    tib: raum
  prefix: findex.raum
  tib:
    description: SKOS-Modellierung des Thesaurus FINDEX Raum des Fraunhofer-Informationszentrums
      Raum und Bau IRB
    download_owl: https://gitlab.com/fid-bau/terminologie/findex-raum/-/raw/0.0.7/TS/findex-raum-skos.owl
    homepage: https://terminology.fraunhofer.de/findex-thesauri
    keywords:
    - Digital Planning and Construction
    - FID BAUdigital
    - NFDI4ING
    - earth sciences
    - civil engineering
    name: FINDEX Raum
    prefix: raum
    tracker: https://gitlab.com/fid-bau/terminologie/findex-raum/-/issues
    uri_format: https://terminology.fraunhofer.de/voc/raum#$1
    version.iri: https://gitlab.com/fid-bau/terminologie/findex-raum/-/raw/0.0.7/findex-raum.owl
fishbase.species:
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: 'Global biodiversity database on finfishes. It offers a wide range
    of information on all species currently known in the world: taxonomy, biology,
    trophic ecology, life history, and uses, as well as historical data reaching back
    to 250 years.'
  example: '6472'
  homepage: http://fishbase.org
  integbio:
    description: FishBase is a relational database containing information about fish
      around the world to cater to different professionals such as research scientists,
      fisheries managers, zoologists and many more. Each entry contains scientific
      names, common names , pictures, links to other tables, links to internet sources,
      etc. Moreover, various genetic data are available for many species. All items
      are referenced, with full citation. Scientific names are verified against Eschmeyer's
      Catalog of Fishes. Users enter FishBase through common names which classified
      by country and language. Full academic course with exercises in Ichthyology
      is available in Fish-On-Line.
    homepage: http://www.fishbase.org/search.php?lang=English
    information_keywords:
    - Ontology/Terminology/Nomenclature
    - Image/Movie
    maintainer: FishBase Consortium
    name: FishBase
    prefix: nbdc00270
    status: Active
    target_keywords:
    - Organism
  mappings:
    integbio: nbdc00270
    re3data: r3d100010912
    wikidata: P938
  name: FishBase
  pattern: ^\d+$
  prefix: fishbase.species
  re3data:
    description: Fishbase is a global species database and encyclopedia of over 30,000
      species and subspecies of fishes that is searchable by common name, genus, species,
      geography, family, ecosystem, references literature, tools, etc. Links to other,
      related databases such as the Catalog of Fishes, GenBack, and LarvalBase. Associated
      with a partner journal, Acta Ichthyologica et Piscatoria. With mirror sites
      in English, German, French Spanish, Portuguese, French, Swedish, Chinese and
      Arabian language.
    doi: 10.17616/R3MW57
    homepage: https://www.fishbase.se/home.php
    name: Fishbase
    prefix: r3d100010912
  synonyms:
  - fishbase
  uri_format: https://www.fishbase.ca/summary/$1
  wikidata:
    description: identifier for a species in FishBase
    example:
    - '1234'
    - '19053'
    - '5918'
    name: FishBase species ID
    pattern: ^[1-9]\d{0,4}$
    prefix: P938
    uri_format: https://www.fishbase.org/summary/$1
fivestars:
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: An ontology written in OWL 2 DL to enable characterization of the five
    attributes of an online journal article - peer review, open access, enriched content,
    available datasets and machine-readable metadata.
  example: hasOpenAccessRating
  fairsharing:
    abbreviation: FiveStars
    contact:
      email: silvio.peroni@unibo.it
      name: Silvio Peroni
      orcid: 0000-0003-0530-4305
    description: The Five Stars of Online Research Articles Ontology (FiveStars) is
      an ontology written in OWL 2 DL to enable characterization of the five attributes
      of an online journal article - peer review, open access, enriched content, available
      datasets and machine-readable metadata.
    homepage: http://www.sparontologies.net/ontologies/fivestars
    license: CC-BY-4.0
    name: 'Five Stars of Online Research Articles Ontology '
    prefix: FAIRsharing.6dfe9b
    publications:
    - doi: 10.1045/january2012-shotton
      title: The Five Stars of Online Journal Articles - a Framework for Article Evaluation
      year: 2012
    repository: https://github.com/sparontologies/fivestars
    subjects:
    - Subject Agnostic
    twitter: sparontologies
  homepage: http://www.sparontologies.net/ontologies/fivestars
  mappings:
    fairsharing: FAIRsharing.6dfe9b
  name: Five Stars of Online Research Articles Ontology
  preferred_prefix: FiveStars
  prefix: fivestars
  publications:
  - doi: 10.1045/january2012-shotton
    pmc: null
    pubmed: null
    title: The Five Stars of Online Journal Articles - a Framework for Article Evaluation
    year: 2012
  repository: https://github.com/sparontologies/fivestars
fix:
  aberowl:
    description: An ontology of physico-chemical methods and properties.
    download_owl: http://aber-owl.net/media/ontologies/FIX/119/fix.owl
    name: Physico-chemical methods and properties
    prefix: FIX
  biocontext:
    prefix: FIX
  bioportal:
    contact:
      email: chebi-help@ebi.ac.uk
      name: Chebi Administrators
    description: 'FIX consists of two ontologies: methods and properties (but not
      objects, which are subject of the chemical ontology). The methods are applied
      to study the properties.'
    name: Physico-Chemical Methods and Properties
    prefix: FIX
    version: '1.2'
  contact:
    email: amalik@ebi.ac.uk
    github: amalik01
    name: Adnan Malik
    orcid: 0000-0001-8123-5351
  contact_group_email: chebi-help@ebi.ac.uk
  example: 0000390
  fairsharing:
    abbreviation: FIX
    description: 'FIX consists of two ontologies: methods and properties (but not
      objects, which are subject of the chemical ontology). The methods are applied
      to study the properties. While this ontology is available via BioPortal and
      the OBO Foundry, we cannot find a home page or a publication for the resource,
      and the resource itself is no longer maintained.'
    domains:
    - Experimental measurement
    homepage: http://purl.bioontology.org/ontology/FIX
    name: Physico-chemical methods and properties
    prefix: FAIRsharing.wwy1ns
    subjects:
    - Chemistry
  homepage: https://www.ebi.ac.uk/chebi/
  mappings:
    aberowl: FIX
    biocontext: FIX
    bioportal: FIX
    fairsharing: FAIRsharing.wwy1ns
    obofoundry: fix
    ols: fix
    ontobee: FIX
    prefixcommons: fix
    tib: fix
    wikidata.entity: Q114677850
  obofoundry:
    contact.label: chEBI
    deprecated: true
    description: An ontology of physico-chemical methods and properties.
    domain: chemistry and biochemistry
    download.obo: http://purl.obolibrary.org/obo/fix.obo
    download.owl: http://purl.obolibrary.org/obo/fix.owl
    homepage: http://www.ebi.ac.uk/chebi
    name: Physico-chemical methods and properties
    prefix: fix
  ols:
    description: An ontology of physico-chemical methods and properties.
    download_owl: http://purl.obolibrary.org/obo/fix.owl
    homepage: http://www.ebi.ac.uk/chebi
    name: Physico-chemical methods and properties
    prefix: fix
  ontobee:
    library: Library
    name: Physico-chemical methods and properties
    prefix: FIX
  owners:
  - name: European Bioinformatics Institute
    partnered: false
    ror: 02catss52
    wikidata: null
  part_of_database: chebi
  pattern: ^\d{7}$
  prefix: fix
  prefixcommons:
    bioportal: '1014'
    description: 'FIX consists of two ontologies: methods and properties (but not
      objects, which are subject of the chemical ontology). The methods are applied
      to study the properties.'
    example: FIX_0000000
    keywords:
    - obo
    - property
    - experiment
    name: Physico-chemical methods and properties
    pattern: ^FIX_\d{7}$
    prefix: fix
  tib:
    description: An ontology of physico-chemical methods and properties.
    download_owl: http://purl.obolibrary.org/obo/fix.owl
    keywords:
    - NFDI4CHEM
    - chemistry
    name: Physico-chemical methods and properties
    prefix: fix
    version.iri: http://purl.obolibrary.org/obo/fix/releases/2020-04-13/fix.owl
flopo:
  aberowl:
    description: Traits and phenotypes of flowering plants occurring in digitized
      Floras
    download_owl: http://aber-owl.net/media/ontologies/FLOPO/10/flopo.owl
    homepage: https://github.com/flora-phenotype-ontology/flopoontology
    name: Flora Phenotype Ontology
    prefix: FLOPO
  agroportal:
    contact:
      email: robert.hoehndorf@kaust.edu.sa
      name: Robert Hoehndorf
    description: The Flora Phenotype Ontology (FLOPO) is an ontology of phenotypes
      reported in Floras. The original version was developed at the pro-iBiosphere
      Hackathon in Leiden. This is the pre-classified version of the ontology. The
      Flora Phenotype Ontology is generated from the Flora Malesiana, Flora Gabon,
      Flora of Central Africa, and a collection of Kew's African Floras. Every class
      in the ontology has at least one taxon annotation. The (draft) taxon annotation
      are available at http://jagannath.pdn.cam.ac.uk/plant/flora/clean-rerun/
    example_uri: http://purl.obolibrary.org/obo/FLOPO_0000003
    homepage: https://github.com/flora-phenotype-ontology
    license: CC0-1.0
    name: Flora Phenotype Ontology
    prefix: FLOPO
    repository: https://github.com/flora-phenotype-ontology/flopoontology/
    version: '0.9'
  biocontext:
    prefix: FLOPO
  bioportal:
    contact:
      email: leechuck@leechuck.de
      name: Robert Hoehndorf
    description: The Flora Phenotype Ontology is an ontology of phenotypes reported
      in Floras. The original version was developed at the pro-iBiosphere Hackathon
      in Leiden. This is the pre-classified version of the ontology; the original
      OWL file is at https://github.com/flora-phenotype-ontology/flopoontology/blob/master/ontology/flopo.owl
      The Flora Phenotype Ontology is generated from the Flora Malesiana, Flora Gabon,
      Flora of Central Africa, and a collection of Kew's African Floras. Every class
      in the ontology has at least one taxon annotation. The (draft) taxon annotation
      are available at http://jagannath.pdn.cam.ac.uk/plant/flora/clean-rerun/
    homepage: http://wiki.pro-ibiosphere.eu/wiki/Traits_Task_Group
    name: Flora Phenotype Ontology
    prefix: FLOPO
    version: '0.9'
  example: '0005250'
  fairsharing:
    abbreviation: FLOPO
    contact:
      email: robert.hoehndorf@kaust.edu.sa
      name: Robert Hoehndorf
      orcid: 0000-0001-8149-5890
    description: 'The Flora Phenotype Ontology is a domain ontology for the description
      of plant characters. FLOPO contains more than 25000 phenotype and traits classes,
      the creation of FLOPO is data-driven: For each trait/phenotype class exists
      a taxon annotation in the underlying Floras.'
    domains:
    - phenotype
    - whole plant development stage
    homepage: https://github.com/flora-phenotype-ontology/flopoontology
    license: CC0-1.0
    name: Flora Phenotype Ontology
    prefix: FAIRsharing.ny9vnm
    publications:
    - doi: 10.3897/bdj.2.e1125
      pubmed: '25057255'
      title: Enriched biodiversity data as a resource and service
      year: 2014
    - doi: 10.1186/s13326-016-0107-8
      pubmed: '27842607'
      title: 'The flora phenotype ontology (FLOPO): tool for integrating morphological
        traits and phenotypes of vascular plants'
      year: 2016
    repository: https://github.com/flora-phenotype-ontology/flopoontology/issues
    subjects:
    - Horticulture
    - Botany
    - Biodiversity
    - Phenomics
    - Plant Anatomy
    - Plant Cell Biology
  mappings:
    aberowl: FLOPO
    agroportal: FLOPO
    biocontext: FLOPO
    bioportal: FLOPO
    fairsharing: FAIRsharing.ny9vnm
    obofoundry: flopo
    ols: flopo
    ontobee: FLOPO
    tib: flopo
    wikidata.entity: Q81661625
  obofoundry:
    appears_in:
    - gallont
    contact: robert.hoehndorf@kaust.edu.sa
    contact.github: leechuck
    contact.label: Robert Hoehndorf
    contact.orcid: 0000-0001-8149-5890
    deprecated: false
    description: Traits and phenotypes of flowering plants occurring in digitized
      Floras
    domain: phenotype
    download.owl: http://purl.obolibrary.org/obo/flopo.owl
    homepage: https://github.com/flora-phenotype-ontology/flopoontology
    license: CC0 1.0
    license.url: https://creativecommons.org/publicdomain/zero/1.0/
    name: Flora Phenotype Ontology
    preferredPrefix: FLOPO
    prefix: flopo
    publications:
    - id: https://www.ncbi.nlm.nih.gov/pubmed/27842607
      title: 'The flora phenotype ontology (FLOPO): tool for integrating morphological
        traits and phenotypes of vascular plants'
    repository: https://github.com/flora-phenotype-ontology/flopoontology
  ols:
    description: Traits and phenotypes of flowering plants occurring in digitized
      Floras
    download_owl: http://purl.obolibrary.org/obo/flopo.owl
    homepage: https://github.com/flora-phenotype-ontology/flopoontology
    name: Flora Phenotype Ontology
    prefix: flopo
    tracker: https://github.com/flora-phenotype-ontology/flopoontology/issues
  ontobee:
    library: Library
    name: Flora Phenotype Ontology
    prefix: FLOPO
  pattern: ^\d{7}$
  prefix: flopo
  publications:
  - doi: 10.1186/s13326-016-0107-8
    pmc: PMC5109718
    pubmed: '27842607'
    title: 'The flora phenotype ontology (FLOPO): tool for integrating morphological
      traits and phenotypes of vascular plants'
    year: 2016
  - doi: 10.3897/bdj.2.e1125
    pmc: PMC4092319
    pubmed: '25057255'
    title: Enriched biodiversity data as a resource and service
    year: 2014
  tib:
    contact: robert.hoehndorf@kaust.edu.sa
    description: The Flora Phenotype Ontology (FLOPO) is an ontology of phenotypes
      reported in Floras. The original version was developed at the pro-iBiosphere
      Hackathon in Leiden. This is the pre-classified version of the ontology. The
      Flora Phenotype Ontology is generated from the Flora Malesiana, Flora Gabon,
      Flora of Central Africa, and a collection of Kew's African Floras. Every class
      in the ontology has at least one taxon annotation. The (draft) taxon annotation
      are available at http://jagannath.pdn.cam.ac.uk/plant/flora/clean-rerun/ .
    download_owl: http://purl.obolibrary.org/obo/flopo.owl
    keywords:
    - DataPLANT
    - life sciences, biology
    name: Flora Phenotype Ontology
    prefix: flopo
    tracker: https://github.com/flora-phenotype-ontology/flopoontology/issues/
  uri_format: http://purl.obolibrary.org/obo/FLOPO_$1
flowrepository:
  fairsharing:
    abbreviation: FlowRepository
    contact:
      email: rbrinkman@bccrc.ca
      name: Ryan Brinkman
      orcid: 0000-0002-9765-2990
    description: FlowRepository is a database of flow cytometry experiments where
      you can query and download data collected and annotated according to the MIFlowCyt
      standard. Data are generally associated with peer reviewed manuscripts.
    homepage: http://www.flowrepository.org
    name: FlowRepository
    prefix: FAIRsharing.veg2d6
    publications:
    - doi: 10.1002/cyto.a.22106
      pubmed_id: 22887982
      title: 'FlowRepository: a resource of annotated flow cytometry datasets associated
        with peer-reviewed publications'
    - doi: 10.1002/0471142956.cy1018s61
      pubmed_id: 22752950
      title: Preparing a Minimum Information about a Flow Cytometry Experiment (MIFlowCyt)
        compliant manuscript using the International Society for Advancement of Cytometry
        (ISAC) FCS file repository (FlowRepository.org).
    subjects:
    - Life Science
    - Cell Biology
    - Biology
  integbio:
    description: FlowRepository is a database of flow cytometry experiments where
      you can query and download data collected and annotated according to the MIFlowCyt
      standard. Data are generally associated with peer reviewed manuscripts.
    fairsharing: FAIRsharing.veg2d6
    homepage: http://www.flowrepository.org
    information_keywords:
    - Method
    - Bibliography/Documents
    name: FlowRepository
    prefix: nbdc01698
    pubmeds:
    - '22887982'
    - '22752950'
    status: Active
  mappings:
    fairsharing: FAIRsharing.veg2d6
    integbio: nbdc01698
    miriam: flowrepository
    n2t: flowrepository
    re3data: r3d100011280
  miriam:
    deprecated: false
    description: FlowRepository is a database of flow cytometry experiments where
      you can query and download data collected and annotated according to the MIFlowCyt
      standard. It is primarily used as a data deposition place for experimental findings
      published in peer-reviewed journals in the flow cytometry field.
    homepage: http://flowrepository.org/
    id: '00000672'
    name: FlowRepository
    namespaceEmbeddedInLui: false
    pattern: ^FR\-FCM\-\w{4}$
    prefix: flowrepository
    sampleId: FR-FCM-ZYGW
    uri_format: http://flowrepository.org/id/$1
  n2t:
    description: FlowRepository is a database of flow cytometry experiments where
      you can query and download data collected and annotated according to the MIFlowCyt
      standard. It is primarily used as a data deposition place for experimental findings
      published in peer-reviewed journals in the flow cytometry field.
    example: FR-FCM-ZYGW
    homepage: https://flowrepository.org/
    name: FlowRepository
    namespaceEmbeddedInLui: false
    pattern: ^FR\-FCM\-\w{4}$
    prefix: flowrepository
    uri_format: https://flowrepository.org/id/$1
  prefix: flowrepository
  publications:
  - doi: 10.1002/cyto.a.22106
    pmc: null
    pubmed: '22887982'
    title: 'FlowRepository: a resource of annotated flow cytometry datasets associated
      with peer-reviewed publications'
    year: 2012
  - doi: 10.1002/0471142956.cy1018s61
    pmc: null
    pubmed: '22752950'
    title: Preparing a Minimum Information about a Flow Cytometry Experiment (MIFlowCyt)
      compliant manuscript using the International Society for Advancement of Cytometry
      (ISAC) FCS file repository (FlowRepository.org)
    year: 2012
  - doi: 10.1002/cyto.a.22106
    pmc: null
    pubmed: null
    title: 'FlowRepository: a resource of annotated flow cytometry datasets associated
      with peer-reviewed publications'
    year: null
  - doi: 10.1002/0471142956.cy1018s61
    pmc: null
    pubmed: null
    title: Preparing a Minimum Information about a Flow Cytometry Experiment (MIFlowCyt)
      compliant manuscript using the International Society for Advancement of Cytometry
      (ISAC) FCS file repository (FlowRepository.org).
    year: null
  re3data:
    description: FlowRepository is a web-based application accessible from a web browser
      that serves as an online database of flow cytometry experiments where users
      can query and download data collected and annotated according to the MIFlowCyt
      standard. It is primarily used as a data deposition place for experimental findings
      published in peer-reviewed journals in the flow cytometry field. FlowRepository
      is funded by the International Society for Advancement of Cytometry (ISAC) and
      powered by the Cytobank engine specifically extended for the purposes of this
      repository. FlowRepository has been developed by forking and extending Cytobank
      in 2011.
    doi: 10.17616/R3R90Q
    homepage: http://flowrepository.org/
    license: other
    name: FlowRepository
    prefix: r3d100011280
flu:
  aberowl:
    description: Starting in the fall of 2007, a collaborative group of influenza
      researchers have established an influenza ontology. The influenza ontology is
      an application ontology.  Consolidated influenza sequence and surveillance terms
      from resources such as the BioHealthBase (BHB), a Bioinformatics Resource Center
      (BRC) for Biodefense and Emerging and Re-emerging Infectious Diseases, the Centers
      for Excellence in Influenza Research and Surveillance (CEIRS)
    download_owl: http://aber-owl.net/media/ontologies/FLU/27/flu.owl
    homepage: http://purl.obolibrary.org/obo/flu/
    name: Influenza Ontology
    prefix: FLU
    version: 0.9.0
  biocontext:
    prefix: FLU
  bioportal:
    contact:
      email: burkesquires@gmail.com
      name: Burke Squires
    description: Starting in the fall of 2007, a collaborative group of influenza
      researchers have established an influenza ontology. The influenza ontology is
      an application ontology. Consolidated influenza sequence and surveillance terms
      from resources such as the BioHealthBase (BHB), a Bioinformatics Resource Center
      (BRC) for Biodefense and Emerging and Re-emerging Infectious Diseases, the Centers
      for Excellence in Influenza Research and Surveillance (CEIRS)
    homepage: http://purl.obolibrary.org/obo/flu/
    name: Influenza Ontology
    prefix: FLU
    version: 0.9.0
  contact:
    email: burkesquires@gmail.com
    github: null
    name: R. Burke Squires
    orcid: 0000-0001-9666-6285
  example: '0000404'
  mappings:
    aberowl: FLU
    biocontext: FLU
    bioportal: FLU
    obofoundry: flu
  obofoundry:
    contact: burkesquires@gmail.com
    contact.label: Burke Squires
    deprecated: true
    domain: health
    download.owl: http://purl.obolibrary.org/obo/flu.owl
    homepage: http://purl.obolibrary.org/obo/flu/
    name: Influenza Ontology
    prefix: flu
  pattern: ^\d{7}$
  prefix: flu
flybase:
  biocontext:
    prefix: FlyBase
    uri_format: http://flybase.org/reports/$1
  cellosaurus:
    category: Organism-specific databases
    homepage: https://flybase.org
    name: Drosophila genome database
    prefix: FlyBase
    uri_format: https://flybase.org/reports/$1.html
  contact:
    email: vjenkins@morgan.harvard.edu
    github: null
    name: Victoria K. Jenkins
    orcid: 0000-0002-1567-7626
  domain: gene
  edam:
    description: Identifier of an object from the FlyBase database.
    name: FlyBase
    obsolete: false
    prefix: '1089'
  fairsharing:
    abbreviation: FlyBase
    description: Genetic, genomic and molecular information pertaining to the model
      organism Drosophila melanogaster and related sequences. This database also contains
      information relating to human disease models in Drosophila, the use of transgenic
      constructs containing sequence from other organisms in Drosophila, and information
      on where to buy Drosophila strains and constructs.
    homepage: http://flybase.org/
    name: FlyBase
    prefix: FAIRsharing.wrvze3
    publications:
    - doi: null
      pubmed_id: 7925011
      title: FlyBase--the Drosophila genetic database.
    - doi: 10.1007/978-1-59745-583-1_3
      pubmed_id: 18641940
      title: 'FlyBase : a database for the Drosophila research community.'
    - doi: 10.1093/nar/25.1.63
      pubmed_id: 9045212
      title: 'FlyBase: a Drosophila database. The FlyBase consortium.'
    - doi: 10.1093/nar/gkm930
      pubmed_id: 18160408
      title: 'FlyBase: integration and improvements to query tools.'
    - doi: 10.1093/nar/gkl827
      pubmed_id: 17099233
      title: 'FlyBase: genomes by the dozen.'
    - doi: 10.1093/nar/gkt1092
      pubmed_id: 24234449
      title: FlyBase 102--advanced approaches to interrogating FlyBase.
    - doi: 10.1093/nar/30.1.106
      pubmed_id: 11752267
      title: The FlyBase database of the Drosophila genome projects and community
        literature.
    - doi: 10.1093/nar/26.1.85
      pubmed_id: 9399806
      title: 'FlyBase: a Drosophila database.'
    - doi: 10.1093/nar/22.17.3456
      pubmed_id: 7937045
      title: FlyBase--the Drosophila database
    - doi: 10.1093/nar/27.1.85
      pubmed_id: 9847148
      title: The FlyBase database of the Drosophila Genome Projects and community
        literature.
    - doi: 10.1093/nar/24.1.53
      pubmed_id: 8594600
      title: 'FlyBase: the Drosophila database.'
    - doi: 10.1093/nar/gkj068
      pubmed_id: 16381917
      title: 'FlyBase: anatomical data, images and queries.'
    - doi: 10.1093/nar/gki046
      pubmed_id: 15608223
      title: 'FlyBase: genes and gene models.'
    - doi: 10.1093/nar/gkg094
      pubmed_id: 12519974
      title: The FlyBase database of the Drosophila genome projects and community
        literature.
    - doi: 10.1093/nar/gkn788.
      pubmed_id: 18948289
      title: 'FlyBase: enhancing Drosophila Gene Ontology annotations.'
    - doi: 10.1093/nar/gkr1030
      pubmed_id: 22127867
      title: FlyBase 101--the basics of navigating FlyBase.
    - doi: 10.1093/database/bas024
      pubmed_id: 22554788
      title: Directly e-mailing authors of newly published papers encourages community
        curation.
    - doi: 10.1093/nar/gkv1046
      pubmed_id: 26467478
      title: 'FlyBase: establishing a Gene Group resource for Drosophila melanogaster.'
    - doi: 10.1534/g3.115.018929
      pubmed_id: 26109357
      title: 'Gene Model Annotations for Drosophila melanogaster: Impact of High-Throughput
        Data.'
    - doi: 10.1534/g3.115.018937
      pubmed_id: 26109356
      title: 'Gene Model Annotations for Drosophila melanogaster: The Rule-Benders.'
    - doi: 10.1007/978-1-4939-7737-6_16
      pubmed_id: 29761468
      title: Using FlyBase to Find Functionally Related Drosophila Genes.
    - doi: 10.1093/nar/gkw1016
      pubmed_id: 27799470
      title: 'FlyBase at 25: looking to the future.'
    - doi: 10.1093/nar/gky1003
      pubmed_id: 30364959
      title: 'FlyBase 2.0: the next generation.'
    - doi: 10.1002/cpbi.19
      pubmed_id: 27930807
      title: Exploring FlyBase Data Using QuickSearch.
    - doi: 10.1242/dmm.023317
      pubmed_id: 26935103
      title: FlyBase portals to human disease research using Drosophila models.
    - doi: 10.1093/nar/gku1099
      pubmed_id: 25398896
      title: 'FlyBase: introduction of the Drosophila melanogaster Release 6 reference
        genome assembly and large-scale migration of genome annotations.'
    - doi: 10.1093/nar/gkaa1026
      pubmed_id: null
      title: 'FlyBase: updates to the Drosophila melanogaster knowledge base'
    subjects:
    - Functional Genomics
    - Anatomy
    - Molecular biology
    - Genomics
    - Bioinformatics
    - Genetics
    - Life Science
    - Molecular Genetics
    - Comparative Genomics
    twitter: flybasedotorg
  go:
    homepage: http://flybase.org/
    name: FlyBase
    prefix: FB
    synonyms:
    - FLYBASE
  integbio:
    alt_name: A Database of Drosophila Genes & Genomes
    description: This database contains genetic information on Drosophila. It allows
      users to search using BLAST, GenomeBrowser or QuickSearch tool with taxonomical
      information and image-based data on the life-cycle stages of Drosophila. The
      information of Drosophila material resources are also provided.
    fairsharing: biodbcore-000037
    homepage: http://flybase.org/
    information_keywords:
    - Bioresource
    - Ontology/Terminology/Nomenclature
    - Sequence
    - Expression
    - Interaction/Pathway
    - Image/Movie
    - Bibliography/Documents
    - Taxonomy
    - Repository
    maintainer: Genetics Society of America
    name: FlyBase
    prefix: nbdc00064
    pubmeds:
    - '7925011'
    - '7937045'
    - '27799470'
    status: Active
    target_keywords:
    - Genome/Gene
    - cDNA/EST
    - Genetic variation
    - RNA
    - Protein
    - Organism
    - Health/Disease
  license: CC-BY-4.0
  logo: http://flybase.org/images/fly_logo.png
  mappings:
    biocontext: FlyBase
    cellosaurus: FlyBase
    edam: '1089'
    fairsharing: FAIRsharing.wrvze3
    go: FB
    integbio: nbdc00064
    miriam: fb
    n2t: fb
    ncbi: FLYBASE
    pathguide: '460'
    prefixcommons: flybase
    re3data: r3d100010591
    rrid: FlyBase
    uniprot: DB-0026
    wikidata: P3852
  miriam:
    deprecated: false
    description: FlyBase is the database of the Drosophila Genome Projects and of
      associated literature.
    homepage: https://bioentity.link/
    id: '00000030'
    name: FlyBase
    namespaceEmbeddedInLui: false
    pattern: ^FB\w{2}\d{7}$
    prefix: fb
    providers:
    - code: agr
      description: FlyBase through the Alliance of Genome Resources
      homepage: https://www.alliancegenome.org
      name: FlyBase through the Alliance of Genome Resources
      uri_format: https://www.alliancegenome.org/gene/FB:$1
    - code: ''
      description: The FlyBase Database
      homepage: http://flybase.org/
      name: The FlyBase Database
      uri_format: http://flybase.org/reports/$1.html
    sampleId: FBgn0011293
    uri_format: https://bioentity.link/#/lexicon/public/$1
  n2t:
    description: FlyBase is the database of the Drosophila Genome Projects and of
      associated literature.
    example: FBgn0011293
    homepage: https://www.alliancegenome.org
    name: FlyBase through the Alliance of Genome Resources
    namespaceEmbeddedInLui: false
    pattern: ^FB\w{2}\d{7}$
    prefix: fb
    uri_format: https://www.alliancegenome.org/gene/FB:$1
  name: FlyBase Gene
  ncbi:
    example: FBgn0000024
    homepage: http://www.flybase.org/
    name: Database of Genetic and molecular data of Drosophila.
    prefix: FLYBASE
  pathguide:
    abbreviation: FlyBase
    homepage: http://flybase.org/
    name: 'FlyBase: a database of Drosophila Genes & Genomes'
    prefix: '460'
  preferred_prefix: FlyBase
  prefix: flybase
  prefixcommons:
    description: FlyBase is an integrated resource for genetic, molecular, and descriptive
      data concerning the Drosophilidae, including interactive genomic maps, gene
      product descriptions, mutant allele phenotypes, genetic interactions, expression
      patterns, transgenic constructs and their insertions, anatomy and images, and
      genetic stock collections.
    example: FBgn0011293
    homepage: http://flybase.org/
    keywords:
    - genome
    - interaction
    - anatomy
    - DNA
    license: http://flybase.org/static_pages/docs/copyright.html
    name: Drosophila genome database
    pattern: ^FB\w{2}\d{7}$
    prefix: flybase
    synonyms:
    - fb
    uri_format: http://flybase.org/reports/$1.html
  publications:
  - doi: 10.1093/nar/gkaa1026
    pmc: PMC7779046
    pubmed: '33219682'
    title: 'FlyBase: updates to the Drosophila melanogaster knowledge base'
    year: 2021
  - doi: 10.1093/nar/gky1003
    pmc: PMC6323960
    pubmed: '30364959'
    title: 'FlyBase 2.0: the next generation'
    year: 2019
  - doi: 10.1007/978-1-4939-7737-6_16
    pmc: PMC5996772
    pubmed: '29761468'
    title: Using FlyBase to Find Functionally Related Drosophila Genes
    year: 2018
  - doi: 10.1002/cpbi.19
    pmc: PMC5152691
    pubmed: '27930807'
    title: Exploring FlyBase Data Using QuickSearch
    year: 2016
  - doi: 10.1093/nar/gkw1016
    pmc: PMC5210523
    pubmed: '27799470'
    title: 'FlyBase at 25: looking to the future'
    year: 2016
  - doi: 10.1242/dmm.023317
    pmc: PMC4826978
    pubmed: '26935103'
    title: FlyBase portals to human disease research using Drosophila models
    year: 2016
  - doi: 10.1093/nar/gkv1046
    pmc: PMC4702782
    pubmed: '26467478'
    title: 'FlyBase: establishing a Gene Group resource for Drosophila melanogaster'
    year: 2015
  - doi: 10.1534/g3.115.018929
    pmc: PMC4528329
    pubmed: '26109357'
    title: 'Gene Model Annotations for Drosophila melanogaster: Impact of High-Throughput
      Data'
    year: 2015
  - doi: 10.1534/g3.115.018937
    pmc: PMC4528330
    pubmed: '26109356'
    title: 'Gene Model Annotations for Drosophila melanogaster: The Rule-Benders'
    year: 2015
  - doi: 10.1093/nar/gku1099
    pmc: PMC4383921
    pubmed: '25398896'
    title: 'FlyBase: introduction of the Drosophila melanogaster Release 6 reference
      genome assembly and large-scale migration of genome annotations'
    year: 2014
  - doi: 10.1093/nar/gkt1092
    pmc: PMC3964969
    pubmed: '24234449'
    title: FlyBase 102--advanced approaches to interrogating FlyBase
    year: 2013
  - doi: 10.1093/database/bas024
    pmc: PMC3342516
    pubmed: '22554788'
    title: Directly e-mailing authors of newly published papers encourages community
      curation
    year: 2012
  - doi: 10.1093/nar/gkr1030
    pmc: PMC3245098
    pubmed: '22127867'
    title: FlyBase 101--the basics of navigating FlyBase
    year: 2011
  - doi: 10.1007/978-1-59745-583-1_3
    pmc: null
    pubmed: '18641940'
    title: 'FlyBase : a database for the Drosophila research community'
    year: 2008
  - doi: 10.1093/nar/gkn788
    pmc: PMC2686450
    pubmed: '18948289'
    title: 'FlyBase: enhancing Drosophila Gene Ontology annotations'
    year: 2008
  - doi: 10.1093/nar/gkm930
    pmc: PMC2238994
    pubmed: '18160408'
    title: 'FlyBase: integration and improvements to query tools'
    year: 2007
  - doi: 10.1093/nar/gkj068
    pmc: PMC1347431
    pubmed: '16381917'
    title: 'FlyBase: anatomical data, images and queries'
    year: 2006
  - doi: 10.1093/nar/gkl827
    pmc: PMC1669768
    pubmed: '17099233'
    title: 'FlyBase: genomes by the dozen'
    year: 2006
  - doi: 10.1093/nar/gki046
    pmc: PMC540000
    pubmed: '15608223'
    title: 'FlyBase: genes and gene models'
    year: 2005
  - doi: 10.1093/nar/gkg094
    pmc: PMC165541
    pubmed: '12519974'
    title: The FlyBase database of the Drosophila genome projects and community literature
    year: 2003
  - doi: 10.1093/nar/30.1.106
    pmc: PMC99082
    pubmed: '11752267'
    title: The FlyBase database of the Drosophila genome projects and community literature
    year: 2002
  - doi: 10.1093/nar/27.1.85
    pmc: PMC148103
    pubmed: '9847148'
    title: The FlyBase database of the Drosophila Genome Projects and community literature
    year: 1999
  - doi: 10.1093/nar/26.1.85
    pmc: PMC147222
    pubmed: '9399806'
    title: 'FlyBase: a Drosophila database'
    year: 1998
  - doi: 10.1093/nar/25.1.63
    pmc: PMC146418
    pubmed: '9045212'
    title: 'FlyBase: a Drosophila database. The FlyBase consortium'
    year: 1997
  - doi: 10.1093/nar/24.1.53
    pmc: PMC145580
    pubmed: '8594600'
    title: 'FlyBase: the Drosophila database'
    year: 1996
  - doi: 10.1093/nar/22.17.3456
    pmc: PMC308301
    pubmed: '7937045'
    title: FlyBase--the Drosophila database. The FlyBase Consortium
    year: 1994
  - doi: 10.1242/dev.120.7.2077
    pmc: null
    pubmed: '7925011'
    title: FlyBase--the Drosophila genetic database
    year: 1994
  re3data:
    description: FlyBase is a database of genetic, genomic and functional data for
      Drosophila species, with a focus on the model organism Drosophila melanogaster.FlyBase
      contains a complete annotation of the Drosophila melanogaster genome that is
      updated several times per year.It also includes a searchable bibliography of
      research on Drosophila genetics in the last century. The site also provides
      a large database of images illustrating the full genome, and several movies
      detailing embryogenesis.
    doi: 10.17616/R3903Q
    homepage: https://flybase.org/
    license: Copyrights
    name: FlyBase
    prefix: r3d100010591
    synonyms:
    - A Database of Drosophila Genes and Genomes
    xrefs:
      nif: 0000-00558
      omics: 01649
  rrid:
    abbreviation: FB
    homepage: http://flybase.org/
    keywords:
    - FASEB list
    - allele
    - bio.tools
    - blast
    - controlled term
    - drosophilidae
    - expression
    - gene
    - genetics
    - genome
    - genotype
    - image
    - image collection
    - life-cycle
    - movie
    - mutant
    - phenotype
    - rna-seq
    - sequence
    - stock
    - video resource
    name: FlyBase
    prefix: FlyBase
    pubmeds:
    - '24234449'
    - '22127867'
    - '18948289'
    - '18641940'
    - '18160408'
    - '17099233'
    - '16381917'
    - '15608223'
    - '12519974'
    - '11752267'
    - '11465064'
    - '9847148'
    - '9399806'
    - '9045212'
    - '8594600'
    - '8578603'
    - '7937045'
    - '7925011'
    scr: 006549
  synonyms:
  - FB
  - FlyBase
  uniprot:
    abbreviation: FlyBase
    category: Organism-specific databases
    homepage: https://flybase.org/
    name: Drosophila genome database
    prefix: DB-0026
    publications:
    - doi: 10.1093/nar/gky1003
      pubmed: '30364959'
    uri_format: https://flybase.org/reports/$1.html
  uri_format: https://flybase.org/reports/$1
  wikidata:
    description: Identifier for a gene in the FlyBase database of Drosophila genes
      and genomes
    example:
    - FBgn0000490
    - FBgn0000604
    - FBgn0260464
    homepage: http://flybase.org/
    miriam: fb
    name: FlyBase Gene ID
    pattern: ^FBgn\d{7}$
    prefix: P3852
    uri_format: http://flybase.org/reports/$1
flybrain.ndb:
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: A database of fly neurons and pathways with an associated 3D viewer.
  example: '10531'
  homepage: https://flybrain-ndb.virtualflybrain.org
  integbio:
    alt_name: FLYBRAIN Neuron Database
    description: "FLYBRAIN Neuron Database is a integrated database about a central\
      \ brain of Drosophila melanogaster. It's constructed with three databases and\
      \ a tool; \n1) Neuron Data provides projection patterns of the identified neurons\
      \ in diverse areas of the brain which were recorded in a unified format, with\
      \ text-based descriptions as well as images and movies.\n2) Strain/Antibody\
      \ Data contains information about the labeling patterns of various antibodies\
      \ and expression driver strains to visualize identified neurons.\n3) Brain Region\
      \ Data provides the nomenclature system of the neuropils.\n4) Brain Explorer\
      \ is a visualization tool with which users can interactively examine three-dimensional\
      \ reconstruction of the confocal serial section images with desired viewing\
      \ angles and cross sections. Furthermore, comprehensive collection and versatile\
      \ search function of the anatomical information reported in diverse publications\
      \ make it possible to analyze possible connectivity between different brain\
      \ regions."
    homepage: https://flybrain-ndb.virtualflybrain.org
    information_keywords:
    - Expression
    - Interaction/Pathway
    - Image/Movie
    maintainer: The University of Tokyo
    name: Flybrain NDB
    prefix: nbdc01446
    pubmeds:
    - '21280038'
    - '16802334'
    status: Active
    target_keywords:
    - Protein
    - Cell/Organelle
  mappings:
    integbio: nbdc01446
  name: FlyBrain Neuron Database
  pattern: ^\d+$
  prefix: flybrain.ndb
  uri_format: https://flybrain-ndb.virtualflybrain.org/fmi/xsl/browserecord.xsl@-lay=NDB&Accession+number.op=eq&Accession+number=$1&-find=-find.html
flymine.chromosome:
  mappings:
    prefixcommons: flymine
  name: FlyMine Chromosome Band
  prefix: flymine.chromosome
  prefixcommons:
    description: FlyMine is an integrated database of genomic, expression and protein
      data for Drosophila, Anopheles and C. elegans. Integrating data makes it possible
      to run sophisticated data mining queries that span domains of biological knowledge.
    example: '1047874'
    homepage: http://www.flymine.org/
    keywords:
    - genome
    - protein
    - gene expression
    name: 'FlyMine: An integrated database for Drosophila and Anopheles genomics'
    pattern: ^\d+$
    prefix: flymine
    uri_format: http://www.flymine.org/release-25.0/objectDetails.do?id=$1
  reviewer:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  uri_format: https://www.flymine.org/flymine/report/ChromosomeBand/$1
fma:
  aberowl:
    description: This is currently a slimmed down version of FMA
    download_owl: http://aber-owl.net/media/ontologies/FMA/139/fma.owl
    homepage: http://si.washington.edu/projects/fma
    name: Foundational Model of Anatomy Ontology (subset)
    prefix: FMA
  bartoc:
    abbreviation: FMA
    description: The Foundational Model of Anatomy Ontology (FMA) is an evolving computer-based
      knowledge source for biomedical informatics; it is concerned with the representation
      of classes or types and relationships necessary for the symbolic representation
      of the phenotypic structure of the human body in a form that is understandable
      to humans and is also navigable, parseable and interpretable by machine-based
      systems. Specifically, the FMA is a domain ontology that represents a coherent
      body of explicit declarative knowledge about human anatomy. Its ontological
      framework can be applied and extended to all other species.
    homepage: http://si.washington.edu/projects/fma/
    name: Foundational Model of Anatomy
    prefix: '571'
    wikidata_database: Q1406710
  biocontext:
    prefix: FMA
  biolink:
    is_identifiers: false
    is_obo: true
    prefix: FMA
    uri_format: http://purl.obolibrary.org/obo/FMA_$1
  bioportal:
    contact:
      email: mejino@uw.edu
      name: Onard Mejino
    description: 'FMA is a domain ontology that represents a coherent body of explicit
      declarative knowledge about human anatomy. For a description of how this OWL
      version is generated, see: "Pushing the Envelope: Challenges in a Frame-Based
      Representation of Human Anatomy" by N. F. Noy, M. A. Musen, J. L. Mejino Jr.,
      C. Rosse (https://www.sciencedirect.com/science/article/pii/S0169023X03001253).'
    homepage: http://si.washington.edu/projects/fma
    name: Foundational Model of Anatomy
    prefix: FMA
    publications:
    - http://sigpubs.si.washington.edu/view/subjects/FMA.html
    version: 5.0.0
  edam:
    description: An identifier of a concept from Foundational Model of Anatomy.
    name: FMA concept
    obsolete: false
    prefix: '1182'
  example: '63189'
  fairsharing:
    abbreviation: FMA
    description: The Foundational Model of Anatomy Ontology (FMA) is an evolving computer-based
      knowledge source for biomedical informatics; it is concerned with the representation
      of classes or types and relationships necessary for the symbolic representation
      of the phenotypic structure of the human body in a form that is understandable
      to humans and is also navigable, parseable and interpretable by machine-based
      systems. Specifically, the FMA is a domain ontology that represents a coherent
      body of explicit declarative knowledge about human anatomy. Its ontological
      framework can be applied and extended to all other species
    domains:
    - phenotype
    - neuroimaging measurement
    homepage: http://si.washington.edu/projects/fma
    license: CC-BY-3.0
    logo: https://api.fairsharing.org/rails/active_storage/blobs/redirect/eyJfcmFpbHMiOnsibWVzc2FnZSI6IkJBaHBBYTg9IiwiZXhwIjpudWxsLCJwdXIiOiJibG9iX2lkIn19--16f323877b0cea5b9b3df9ea964ed441ad10cff1/fma.png?disposition=inline
    name: Foundational Model of Anatomy
    prefix: FAIRsharing.x56jsy
    publications:
    - doi: 10.1016/j.jbi.2003.11.007
      pubmed: '14759820'
      title: 'A reference ontology for biomedical informatics: the Foundational Model
        of Anatomy'
      year: 2004
    - doi: 10.1016/j.artmed.2016.04.003
      pubmed: '27235801'
      title: 'From frames to OWL2: Converting the Foundational Model of Anatomy'
      year: 2016
    - doi: 10.1016/j.websem.2007.12.001
      title: Translating the Foundational Model of Anatomy into OWL
      year: 2008
    - doi: 10.1016/j.websem.2006.05.007
      title: 'The foundational model of anatomy in OWL: Experience and perspectives'
      year: 2006
    - pubmed: '16779026'
      title: 'Challenges in converting frame-based ontology into OWL: the Foundational
        Model of Anatomy case-study'
      year: 2005
    subjects:
    - Anatomy
    - Biomedical Science
    - Radiology
  go:
    homepage: http://sig.biostr.washington.edu/projects/fm/index.html
    name: Foundational Model of Anatomy
    prefix: FMA
  hl7:
    description: Digital Anatomist Foundational Model of Anatomy (FMA)http://depts.washington.edu/ventures/UW_Technology/Express_Licenses/FMA.php
    homepage: http://depts.washington.edu/ventures/UW_Technology/
    name: Foundational Model of Anatomy Ontology
    organization: Jose Leonardo V Mejino Jr. MD, Structural Informatics Group
    preferred_prefix: fma
    prefix: 2.16.840.1.113883.6.119
    status: Complete
  integbio:
    alt_name: Foundational Model Anatomy
    description: FMA is a computer-based knowledge source for biomedical informatics.
      This site is open source and available for general use. It contains a domain
      ontology that represents a coherent body of explicit declarative knowledge about
      human anatomy. Its ontological framework can be applied and extended to all
      other species.
    homepage: http://si.washington.edu/projects/fma
    information_keywords:
    - Ontology/Terminology/Nomenclature
    maintainer: University of Washington
    name: FMA
    prefix: nbdc00273
    pubmeds:
    - '14759820'
    - '14759821'
    status: Active
    target_keywords:
    - Organism
  mappings:
    aberowl: FMA
    bartoc: '571'
    biocontext: FMA
    biolink: FMA
    bioportal: FMA
    edam: '1182'
    fairsharing: FAIRsharing.x56jsy
    go: FMA
    hl7: 2.16.840.1.113883.6.119
    integbio: nbdc00273
    miriam: fma
    n2t: fma
    obofoundry: fma
    ols: fma
    ontobee: FMA
    prefixcommons: fma
    wikidata: P1402
    wikidata.entity: Q1406710
  miriam:
    deprecated: false
    description: The Foundational Model of Anatomy Ontology (FMA) is a biomedical
      informatics ontology. It is concerned with the representation of classes or
      types and relationships necessary for the symbolic representation of the phenotypic
      structure of the human body.  Specifically, the FMA is a domain ontology that
      represents a coherent body of explicit declarative knowledge about human anatomy.
    homepage: https://www.ebi.ac.uk/ols4/ontologies/fma/
    id: '00000067'
    name: FMA
    namespaceEmbeddedInLui: true
    pattern: ^FMA:\d+$
    prefix: fma
    sampleId: '67112'
    uri_format: https://www.ebi.ac.uk/ols4/ontologies/fma/terms?obo_id=FMA:$1
  n2t:
    description: The Foundational Model of Anatomy Ontology (FMA) is a biomedical
      informatics ontology. It is concerned with the representation of classes or
      types and relationships necessary for the symbolic representation of the phenotypic
      structure of the human body.  Specifically, the FMA is a domain ontology that
      represents a coherent body of explicit declarative knowledge about human anatomy.
    example: '67112'
    homepage: http://bioportal.bioontology.org/ontologies/FMA
    name: Foundational Model of Anatomy through BioPortal
    namespaceEmbeddedInLui: true
    pattern: ^FMA:\d+$
    prefix: fma
    uri_format: http://purl.bioontology.org/ontology/FMA_subset/FMA:$1
  name: Foundational Model of Anatomy
  obofoundry:
    contact: mejino@u.washington.edu
    contact.label: Onard Mejino
    deprecated: true
    description: This is currently a slimmed down version of FMA
    domain: anatomy and development
    download.owl: http://purl.obolibrary.org/obo/fma.owl
    homepage: http://si.washington.edu/projects/fma
    license: CC BY 3.0
    license.url: https://creativecommons.org/licenses/by/3.0/
    name: Foundational Model of Anatomy Ontology (subset)
    preferredPrefix: FMA
    prefix: fma
    publications:
    - id: https://www.ncbi.nlm.nih.gov/pubmed/18688289
      title: Translating the Foundational Model of Anatomy into OWL
    - id: https://www.ncbi.nlm.nih.gov/pubmed/18360535
      title: 'The foundational model of anatomy in OWL: Experience and perspectives'
    - id: https://www.ncbi.nlm.nih.gov/pubmed/16779026
      title: 'Challenges in converting frame-based ontology into OWL: the Foundational
        Model of Anatomy case-study'
    repository: https://bitbucket.org/uwsig/fma
  ols:
    description: This is currently a slimmed down version of FMA
    download_owl: http://purl.org/sig/ont/fma.owl
    homepage: http://si.washington.edu/projects/fma
    name: Foundational Model of Anatomy Ontology (subset)
    prefix: fma
    tracker: https://bitbucket.org/uwsig/fma/issues
    version: 5.0.0
    version.iri: http://purl.org/sig/ont/fma_5.0.0.owl
  ontobee:
    library: Library
    name: Foundational Model of Anatomy Ontology (subset)
    prefix: FMA
  pattern: ^\d+$
  prefix: fma
  prefixcommons:
    alt_uri_formats:
    - http://purl.org/obo/owlapi/fma#$1
    - http://sig.uw.edu/fma#$1
    - http://purl.org/obo/owl/FMA#$1
    bioportal: '1053'
    description: FMA is a domain ontology that represents a coherent body of explicit
      declarative knowledge about human anatomy.
    example: FMA:67112
    homepage: http://sig.biostr.washington.edu/projects/fm/
    keywords:
    - owl
    - anatomy
    - human
    license: http://www.ebi.ac.uk/Information/termsofuse.html
    name: The Foundational Model of Anatomy Ontology
    pattern: ^FMA:\d+$
    prefix: fma
    pubmed_ids:
    - '17271570'
    synonyms:
    - obo.fma
    - fmaid
  publications:
  - doi: 10.1016/j.artmed.2016.04.003
    pmc: PMC4915823
    pubmed: '27235801'
    title: 'From frames to OWL2: Converting the Foundational Model of Anatomy'
    year: 2016
  - doi: 10.1016/j.websem.2007.12.001
    pmc: PMC2500209
    pubmed: '18688289'
    title: Translating the Foundational Model of Anatomy into OWL
    year: 2008
  - doi: 10.1016/j.websem.2006.05.007
    pmc: PMC2270940
    pubmed: '18360535'
    title: 'The foundational model of anatomy in OWL: Experience and perspectives'
    year: 2006
  - doi: null
    pmc: PMC1560487
    pubmed: '16779026'
    title: 'Challenges in converting frame-based ontology into OWL: the Foundational
      Model of Anatomy case-study'
    year: 2005
  - doi: 10.1109/iembs.2004.1404513
    pmc: null
    pubmed: '17271570'
    title: 'The foundational model of anatomy: a template for the symbolic representation
      of multi-scale physiological functions'
    year: 2004
  - doi: 10.1016/j.jbi.2003.11.007
    pmc: null
    pubmed: '14759820'
    title: 'A reference ontology for biomedical informatics: the Foundational Model
      of Anatomy'
    year: 2003
  - doi: null
    pmc: null
    pubmed: '18688289'
    title: Translating the Foundational Model of Anatomy into OWL
    year: null
  - doi: null
    pmc: null
    pubmed: '18360535'
    title: 'The foundational model of anatomy in OWL: Experience and perspectives'
    year: null
  - doi: null
    pmc: null
    pubmed: '16779026'
    title: 'Challenges in converting frame-based ontology into OWL: the Foundational
      Model of Anatomy case-study'
    year: null
  - doi: 10.1016/j.jbi.2003.11.007
    pmc: null
    pubmed: '14759820'
    title: 'A reference ontology for biomedical informatics: the Foundational Model
      of Anatomy'
    year: 2004
  - doi: 10.1016/j.artmed.2016.04.003
    pmc: null
    pubmed: '27235801'
    title: 'From frames to OWL2: Converting the Foundational Model of Anatomy'
    year: 2016
  - doi: 10.1016/j.websem.2007.12.001
    pmc: null
    pubmed: null
    title: Translating the Foundational Model of Anatomy into OWL
    year: 2008
  - doi: 10.1016/j.websem.2006.05.007
    pmc: null
    pubmed: null
    title: 'The foundational model of anatomy in OWL: Experience and perspectives'
    year: 2006
  - doi: null
    pmc: null
    pubmed: '16779026'
    title: 'Challenges in converting frame-based ontology into OWL: the Foundational
      Model of Anatomy case-study'
    year: 2005
  - doi: null
    pmc: null
    pubmed: '17271570'
    title: null
    year: null
  - doi: null
    pmc: null
    pubmed: '18688289'
    title: Translating the Foundational Model of Anatomy into OWL
    year: null
  - doi: null
    pmc: null
    pubmed: '18360535'
    title: 'The foundational model of anatomy in OWL: Experience and perspectives'
    year: null
  - doi: null
    pmc: null
    pubmed: '16779026'
    title: 'Challenges in converting frame-based ontology into OWL: the Foundational
      Model of Anatomy case-study'
    year: null
  - doi: 10.1016/j.jbi.2003.11.007
    pmc: null
    pubmed: '14759820'
    title: 'A reference ontology for biomedical informatics: the Foundational Model
      of Anatomy'
    year: 2004
  - doi: 10.1016/j.artmed.2016.04.003
    pmc: null
    pubmed: '27235801'
    title: 'From frames to OWL2: Converting the Foundational Model of Anatomy'
    year: 2016
  - doi: 10.1016/j.websem.2007.12.001
    pmc: null
    pubmed: null
    title: Translating the Foundational Model of Anatomy into OWL
    year: 2008
  - doi: 10.1016/j.websem.2006.05.007
    pmc: null
    pubmed: null
    title: 'The foundational model of anatomy in OWL: Experience and perspectives'
    year: 2006
  - doi: null
    pmc: null
    pubmed: '16779026'
    title: 'Challenges in converting frame-based ontology into OWL: the Foundational
      Model of Anatomy case-study'
    year: 2005
  - doi: null
    pmc: null
    pubmed: '17271570'
    title: null
    year: null
  - doi: null
    pmc: null
    pubmed: '18688289'
    title: Translating the Foundational Model of Anatomy into OWL
    year: null
  - doi: null
    pmc: null
    pubmed: '18360535'
    title: 'The foundational model of anatomy in OWL: Experience and perspectives'
    year: null
  - doi: null
    pmc: null
    pubmed: '16779026'
    title: 'Challenges in converting frame-based ontology into OWL: the Foundational
      Model of Anatomy case-study'
    year: null
  - doi: 10.1016/j.jbi.2003.11.007
    pmc: null
    pubmed: '14759820'
    title: 'A reference ontology for biomedical informatics: the Foundational Model
      of Anatomy'
    year: 2004
  - doi: 10.1016/j.artmed.2016.04.003
    pmc: null
    pubmed: '27235801'
    title: 'From frames to OWL2: Converting the Foundational Model of Anatomy'
    year: 2016
  - doi: 10.1016/j.websem.2007.12.001
    pmc: null
    pubmed: null
    title: Translating the Foundational Model of Anatomy into OWL
    year: 2008
  - doi: 10.1016/j.websem.2006.05.007
    pmc: null
    pubmed: null
    title: 'The foundational model of anatomy in OWL: Experience and perspectives'
    year: 2006
  - doi: null
    pmc: null
    pubmed: '16779026'
    title: 'Challenges in converting frame-based ontology into OWL: the Foundational
      Model of Anatomy case-study'
    year: 2005
  - doi: null
    pmc: null
    pubmed: '17271570'
    title: null
    year: null
  - doi: null
    pmc: null
    pubmed: '18688289'
    title: Translating the Foundational Model of Anatomy into OWL
    year: null
  - doi: null
    pmc: null
    pubmed: '18360535'
    title: 'The foundational model of anatomy in OWL: Experience and perspectives'
    year: null
  - doi: null
    pmc: null
    pubmed: '16779026'
    title: 'Challenges in converting frame-based ontology into OWL: the Foundational
      Model of Anatomy case-study'
    year: null
  - doi: 10.1016/j.jbi.2003.11.007
    pmc: null
    pubmed: '14759820'
    title: 'A reference ontology for biomedical informatics: the Foundational Model
      of Anatomy'
    year: 2004
  - doi: 10.1016/j.artmed.2016.04.003
    pmc: null
    pubmed: '27235801'
    title: 'From frames to OWL2: Converting the Foundational Model of Anatomy'
    year: 2016
  - doi: 10.1016/j.websem.2007.12.001
    pmc: null
    pubmed: null
    title: Translating the Foundational Model of Anatomy into OWL
    year: 2008
  - doi: 10.1016/j.websem.2006.05.007
    pmc: null
    pubmed: null
    title: 'The foundational model of anatomy in OWL: Experience and perspectives'
    year: 2006
  - doi: null
    pmc: null
    pubmed: '16779026'
    title: 'Challenges in converting frame-based ontology into OWL: the Foundational
      Model of Anatomy case-study'
    year: 2005
  - doi: null
    pmc: null
    pubmed: '17271570'
    title: null
    year: null
  synonyms:
  - FMAID
  - FMA_RETIRED
  wikidata:
    database: Q1406710
    description: identifier for human anatomical terminology
    example:
    - '24476'
    - '311256'
    homepage: http://www.ontobee.org/ontology/fma
    miriam: FMA
    name: Foundational Model of Anatomy ID
    pattern: ^[1-9][0-9]{3,5}$
    prefix: P1402
    uri_format: https://purl.org/sig/ont/fma/fma$1
foaf:
  aberowl:
    description: This file is imported by vivo-core-public-1.5.owl. It contains terms
      relating to people, groups and organizations from the http://xmlns.com/foaf/0.1/
      namespace that are included in the vivo ontology.
    download_owl: http://aber-owl.net/media/ontologies/foaf/1/foaf.owl
    homepage: http://sourceforge.net/apps/mediawiki/vivo/index.php?title=Ontology
    name: FOAF (people, organizations, groups)
    prefix: foaf
    version: '1.5'
  biocontext:
    prefix: foaf
    uri_format: http://xmlns.com/foaf/0.1/$1
  biolink:
    is_identifiers: false
    is_obo: false
    prefix: foaf
    uri_format: http://xmlns.com/foaf/0.1/$1
  bioportal:
    contact:
      email: rafael.goncalves@stanford.edu
      name: Rafael Gonçalves
    description: Friend of a Friend Vocabulary
    name: Friend of a Friend Vocabulary
    prefix: FOAF
    version: '0.99'
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: 'FOAF is a project devoted to linking people and information using
    the Web. Regardless of whether information is in people''s heads, in physical
    or digital documents, or in the form of factual data, it can be linked. FOAF integrates
    three kinds of network: social networks of human collaboration, friendship and
    association; representational networks that describe a simplified view of a cartoon
    universe in factual terms, and information networks that use Web-based linking
    to share independently published descriptions of this inter-connected world.'
  example: familyName
  homepage: http://xmlns.com/foaf/spec/
  lov:
    description: FOAF is a project devoted to linking people and information using
      the Web. Regardless of whether information is in people's heads, in physical
      or digital documents, or in the form of factual data, it can be linked.
    homepage: http://www.foaf-project.org/
    keywords:
    - People
    modified: '2014-01-14'
    name: Friend of a Friend vocabulary
    prefix: foaf
    uri_prefix: http://xmlns.com/foaf/0.1/$1
  mappings:
    aberowl: foaf
    biocontext: foaf
    biolink: foaf
    bioportal: FOAF
    lov: foaf
    zazuko: foaf
  name: Friend of a Friend
  preferred_prefix: foaf
  prefix: foaf
  uri_format: http://xmlns.com/foaf/0.1/$1
  zazuko:
    prefix: foaf
    uri_format: http://xmlns.com/foaf/0.1/$1
fobi:
  aberowl:
    description: FOBI (Food-Biomarker Ontology) is an ontology to represent food intake
      data and associate it with metabolomic data
    download_owl: http://aber-owl.net/media/ontologies/FOBI/7/fobi.owl
    homepage: https://github.com/pcastellanoescuder/FoodBiomarkerOntology
    name: Food-Biomarker Ontology
    prefix: FOBI
  agroportal:
    contact:
      email: polcaes@gmail.com
      name: Pol Castellano Escuder
    description: FOBI (Food-Biomarker Ontology) is an ontology composed of two interconnected
      sub-ontologies. One is a ”Food Ontology” consisting of raw foods and multi-component
      foods while the second is a ”Biomarker Ontology” containing food intake biomarkers
      classified by their chemical classes. These two sub-ontologies are conceptually
      independent but interconnected by different properties. This allows data and
      information regarding foods and food biomarkers to be visualized in a bidirectional
      way, going from metabolomics to nutritional data or vice versa. Potential applications
      of this ontology include the annotation of foods and biomarkers using a well-defined
      and consistent nomenclature, the standardized reporting of metabolomics workflows
      (e.g. metabolite identification, experimental design), or the application of
      different enrichment analysis approaches to analyze nutrimetabolomic data.
    example_uri: http://purl.obolibrary.org/obo/FOBI_040001
    homepage: https://github.com/pcastellanoescuder/FoodBiomarkerOntology
    name: Food-Biomarker Ontology
    prefix: FOBI
    publications:
    - https://doi.org/10.1093/bioinformatics/btab626
    - https://doi.org/10.1093/databa/baaa033
    repository: https://github.com/pcastellanoescuder/FoodBiomarkerOntology
    version: 1.0.0
  bioportal:
    contact:
      email: polcaes@gmail.com
      name: Pol Castellano Escuder
    description: FOBI (Food-Biomarker Ontology) is an ontology to represent food intake
      data and associate it with metabolomic data.
    homepage: https://github.com/pcastellanoescuder/FoodBiomarkerOntology
    name: FOBI (Food-Biomarker Ontology)
    prefix: FOBI
  example: 030719
  example_extras:
  - '0142'
  - '07504'
  homepage: https://github.com/pcastellanoescuder/FoodBiomarkerOntology
  mappings:
    aberowl: FOBI
    agroportal: FOBI
    bioportal: FOBI
    obofoundry: fobi
    ols: fobi
    ontobee: FOBI
    wikidata.entity: Q113012660
  name: Food-Biomarker Ontology
  obofoundry:
    contact: polcaes@gmail.com
    contact.github: pcastellanoescuder
    contact.label: Pol Castellano Escuder
    contact.orcid: 0000-0001-6466-877X
    depends_on:
    - chebi
    - foodon
    deprecated: false
    description: FOBI (Food-Biomarker Ontology) is an ontology to represent food intake
      data and associate it with metabolomic data
    domain: diet, metabolomics, and nutrition
    download.owl: http://purl.obolibrary.org/obo/fobi.owl
    homepage: https://github.com/pcastellanoescuder/FoodBiomarkerOntology
    license: CC BY 3.0
    license.url: http://creativecommons.org/licenses/by/3.0/
    name: Food-Biomarker Ontology
    preferredPrefix: FOBI
    prefix: fobi
    publications:
    - id: https://www.ncbi.nlm.nih.gov/pubmed/32556148
      title: 'FOBI: an ontology to represent food intake data and associate it with
        metabolomic data'
    - id: https://www.ncbi.nlm.nih.gov/pubmed/34601570
      title: 'The fobitools framework: the first steps towards food enrichment analysis'
    repository: https://github.com/pcastellanoescuder/FoodBiomarkerOntology
  ols:
    description: FOBI (Food-Biomarker Ontology) is an ontology to represent food intake
      data and associate it with metabolomic data
    download_owl: http://purl.obolibrary.org/obo/fobi.owl
    homepage: https://github.com/pcastellanoescuder/FoodBiomarkerOntology
    name: Food-Biomarker Ontology
    prefix: fobi
    tracker: https://github.com/pcastellanoescuder/FoodBiomarkerOntology/issues
    version.iri: http://purl.obolibrary.org/obo/fobi/fobi.owl
  ontobee:
    library: Library
    name: Food-Biomarker Ontology
    prefix: FOBI
  pattern: ^\d{4,6}$
  prefix: fobi
  providers:
  - code: fobi.legacy
    description: An incorrect encoding of OBO purls
    example: null
    first_party: null
    homepage: http://purl.obolibrary.org/obo/fobi
    name: FOBI Hash
    publications: null
    status: null
    uri_format: http://purl.obolibrary.org/obo/fobi.owl#FOBI:$1
  publications:
  - doi: 10.1093/bioinformatics/btab626
    pmc: null
    pubmed: '34601570'
    title: 'The fobitools framework: the first steps towards food enrichment analysis'
    year: 2021
  - doi: 10.1093/databa/baaa033
    pmc: PMC7298227
    pubmed: '32556148'
    title: 'FOBI: an ontology to represent food intake data and associate it with
      metabolomic data'
    year: 2020
  - doi: null
    pmc: null
    pubmed: '32556148'
    title: 'FOBI: an ontology to represent food intake data and associate it with
      metabolomic data'
    year: null
  - doi: null
    pmc: null
    pubmed: '34601570'
    title: 'The fobitools framework: the first steps towards food enrichment analysis'
    year: null
  uri_format: http://purl.obolibrary.org/obo/FOBI_$1
foodb.compound:
  biocontext:
    prefix: FOODB.COMPOUND
  biolink:
    is_identifiers: false
    is_obo: false
    prefix: foodb.compound
    uri_format: http://foodb.ca/compounds/$1
  homepage: https://foodb.ca/
  mappings:
    biocontext: FOODB.COMPOUND
    biolink: foodb.compound
    miriam: foodb.compound
    n2t: foodb.compound
    re3data: r3d100012152
    wikidata: P8117
  miriam:
    deprecated: false
    description: FooDB is resource on food and its constituent compounds. It includes
      data on the compound’s nomenclature, its description, information on its structure,
      chemical class, its physico-chemical data, its food source(s), its color, its
      aroma, its taste, its physiological effect, presumptive health effects (from
      published studies), and concentrations in various foods. This collection references
      compounds.
    homepage: http://foodb.ca/foods
    id: '00000530'
    name: FooDB Compound
    namespaceEmbeddedInLui: false
    pattern: ^FDB\d+$
    prefix: foodb.compound
    sampleId: FDB002100
    uri_format: http://foodb.ca/compounds/$1
  n2t:
    description: FooDB is resource on food and its constituent compounds. It includes
      data on the compound&#x2019;s nomenclature, its description, information on
      its structure, chemical class, its physico-chemical data, its food source(s),
      its color, its aroma, its taste, its physiological effect, presumptive health
      effects (from published studies), and concentrations in various foods. This
      collection references compounds.
    example: FDB002100
    homepage: http://foodb.ca/foods
    name: FooDB database of food additives at University of Alberta
    namespaceEmbeddedInLui: false
    pattern: ^FDB\d+$
    prefix: foodb.compound
    uri_format: http://foodb.ca/compounds/$1
  name: FooDB compound
  prefix: foodb.compound
  re3data:
    description: FooDB is the world’s largest and most comprehensive resource on food
      constituents, chemistry and biology. It provides information on both macronutrients
      and micronutrients, including many of the constituents that give foods their
      flavor, color, taste, texture and aroma.
    doi: 10.17616/R3GH1P
    homepage: https://foodb.ca/
    license: CC
    name: FooDB
    prefix: r3d100012152
    synonyms:
    - Food Database
  synonyms:
  - foodb
  wikidata:
    description: ID of chemical compound in FooDB
    example:
    - FDB000082
    - FDB000316
    - FDB002100
    name: FooDB compound ID
    prefix: P8117
    uri_format: https://foodb.ca/compounds/$1
foodb.food:
  biolink:
    is_identifiers: false
    is_obo: false
    prefix: foodb.food
    uri_format: http://foodb.ca/foods/$1
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: Foods in FooDB
  example: FOOD00020
  homepage: https://foodb.ca/foods
  mappings:
    biolink: foodb.food
  name: FooDB Food
  pattern: ^FOOD\d+$
  prefix: foodb.food
  uri_format: https://foodb.ca/foods/$1
foodex2:
  agroportal:
    contact:
      email: data@food.gov.uk
      name: UK Food Standard Agency
    description: Food Type identifiers, supporting codes and vocabularies based on
      the EFSA FoodEx2 (https://www.efsa.europa.eu/en/data/data-standardisation) that
      are being tested in the development of the FSA's code and data standards repository.
      These codes may be used within FSA data.
    example_uri: http://data.food.gov.uk/codes/foodtype/id/A0TMC
    homepage: https://data.food.gov.uk/codes/_foodtype
    name: Food Classification and Description System (from FSA Food Type identifiers)
    prefix: FOODEX2
    version: '2'
  example: A0TMC
  mappings:
    agroportal: FOODEX2
  prefix: foodex2
  uri_format: http://data.food.gov.uk/codes/foodtype/id/$1
foodon:
  aberowl:
    description: A broadly scoped ontology representing entities which bear a “food
      role”. It encompasses materials in natural ecosystems and agriculture that are
      consumed by humans and domesticated animals. This includes any generic (unbranded)
      raw or processed food material found in processing plants, markets, stores or
      food distribution points. FoodOn also imports nutritional component and dietary
      pattern terms from other OBO Foundry ontologies to support interoperability
      in diet and nutrition research
    download_owl: http://aber-owl.net/media/ontologies/FOODON/90/foodon.owl
    homepage: https://foodon.org/
    name: Food Ontology
    prefix: FOODON
  agroportal:
    contact:
      email: damion_dooley@sfu.ca
      name: Damion Dooley
    description: FoodOn is a consortium-driven project to build a comprehensive and
      easily accessible global farm-to-fork ontology about food, that accurately and
      consistently describes foods commonly known in cultures from around the world.,
      that accurately and consistently describes foods commonly known in cultures
      from around the world. See https://foodon.org for more details.
    example_uri: http://purl.obolibrary.org/obo/FOODON_03412974
    homepage: https://foodon.org
    license: CC-BY-4.0
    name: FoodOn
    prefix: FOODON
    repository: https://github.com/FoodOntology/foodon
    version: '2025-08-01'
  biocontext:
    prefix: FOODON
  bioportal:
    contact:
      email: damion_dooley@sfu.ca
      name: Damion Dooley
    description: FoodOn is an ontology built to represent entities which bear a “food
      role” and is initially focused on categorizing and processing of food for humans.
      We aim to develop semantics for food safety, food security, the agricultural
      and animal husbandry practices linked to food production, culinary, nutritional
      and chemical ingredients and processes. FoodOn belongs to the OBOFoundry.org
      family of ontologies.
    homepage: http://foodon.org
    name: The FoodOn Food Ontology
    prefix: FOODON
    publications:
    - https://www.nature.com/articles/s41538-018-0032-6
    version: '2025-06-07'
  download_obo: http://purl.obolibrary.org/obo/foodon.obo
  fairsharing:
    abbreviation: FOODON
    contact:
      email: damion.dooley@bccdc.ca
      name: Damion Dooley
      orcid: 0000-0002-8844-9165
    description: The need to represent knowledge about food is central to many human
      activities including agriculture, medicine, food safety inspection, shopping
      patterns, and sustainable development. FoodOn is built to interoperate with
      the OBO Library and to represent entities which bear a food role. Initially
      the ontology will focus on the human-centric categorization and handling of
      food, but in the future it will also encompass materials in natural ecosystems
      and food webs. We aim to develop semantics for food safety, food security, the
      agricultural and animal husbandry practices linked to food production, culinary,
      nutritional and chemical ingredients and processes.
    domains:
    - Sustainability
    - food
    - disease
    homepage: https://foodon.org/
    license: CC-BY-3.0
    name: Food Ontology
    prefix: FAIRsharing.dzxae
    publications:
    - doi: 10.3389/fmicb.2017.01068
      pubmed: '28694792'
      title: 'Context Is Everything: Harmonization of Critical Food Microbiology Descriptors
        and Metadata for Improved Food Safety and Surveillance'
      year: 2017
    - doi: 10.1038/s41538-018-0032-6
      pubmed: '31304272'
      title: 'FoodOn: a harmonized food ontology to increase global food traceability,
        quality control and data integration'
      year: 2019
    repository: https://github.com/FoodOntology/foodon
    subjects:
    - Agriculture
    - Environmental Science
    - Botany
    - Medicine
  mappings:
    aberowl: FOODON
    agroportal: FOODON
    biocontext: FOODON
    bioportal: FOODON
    fairsharing: FAIRsharing.dzxae
    miriam: foodon
    n2t: foodon
    obofoundry: foodon
    ols: foodon
    ontobee: FOODON
    wikidata.entity: Q55118395
  miriam:
    deprecated: false
    description: FoodOn is a comprehensive and easily accessible global farm-to-fork
      ontology about food that accurately and consistently describes foods commonly
      known in cultures from around the world. It is a consortium-driven project built
      to interoperate with the The Open Biological and Biomedical Ontology Foundry
      library of ontologies.
    homepage: https://foodon.org
    id: '00000661'
    name: FoodOn Food Ontology
    namespaceEmbeddedInLui: true
    pattern: ^FOODON:[0-9]{8}$
    prefix: foodon
    sampleId: 03307879
    uri_format: https://www.ebi.ac.uk/ols4/ontologies/foodon/terms?obo_id=FOODON:$1
  n2t:
    description: FoodOn is a comprehensive and easily accessible global farm-to-fork
      ontology about food that accurately and consistently describes foods commonly
      known in cultures from around the world. It is a consortium-driven project built
      to interoperate with the The Open Biological and Biomedical Ontology Foundry
      library of ontologies.
    example: 03307879
    homepage: https://foodon.org
    name: FoodOn Food Ontology through OLS
    namespaceEmbeddedInLui: true
    pattern: ^FOODON:[0-9]{8}$
    prefix: foodon
    uri_format: https://www.ebi.ac.uk/ols/ontologies/foodon/terms?obo_id=FOODON:$1
  name: The Food Ontology
  obofoundry:
    appears_in:
    - agro
    - envo
    - fobi
    - maxo
    - one
    - ons
    contact: damion_dooley@sfu.ca
    contact.github: ddooley
    contact.label: Damion Dooley
    contact.orcid: 0000-0002-8844-9165
    depends_on:
    - bfo
    - chebi
    - envo
    - eo
    - ncbitaxon
    - obi
    - ro
    - uberon
    deprecated: false
    description: A broadly scoped ontology representing entities which bear a “food
      role”. It encompasses materials in natural ecosystems and agriculture that are
      consumed by humans and domesticated animals. This includes any generic (unbranded)
      raw or processed food material found in processing plants, markets, stores or
      food distribution points. FoodOn also imports nutritional component and dietary
      pattern terms from other OBO Foundry ontologies to support interoperability
      in diet and nutrition research
    domain: diet, metabolomics, and nutrition
    download.owl: http://purl.obolibrary.org/obo/foodon.owl
    homepage: https://foodon.org/
    license: CC BY 4.0
    license.url: http://creativecommons.org/licenses/by/4.0/
    name: Food Ontology
    preferredPrefix: FOODON
    prefix: foodon
    publications:
    - id: https://www.ncbi.nlm.nih.gov/pubmed/31304272
      title: 'FoodOn: a harmonized food ontology to increase global food traceability,
        quality control and data integration'
    repository: https://github.com/FoodOntology/foodon
  ols:
    description: A broadly scoped ontology representing entities which bear a “food
      role”. It encompasses materials in natural ecosystems and agriculture that are
      consumed by humans and domesticated animals. This includes any generic (unbranded)
      raw or processed food material found in processing plants, markets, stores or
      food distribution points. FoodOn also imports nutritional component and dietary
      pattern terms from other OBO Foundry ontologies to support interoperability
      in diet and nutrition research
    download_owl: http://purl.obolibrary.org/obo/foodon.owl
    homepage: https://foodon.org/
    name: Food Ontology
    prefix: foodon
    tracker: https://github.com/FoodOntology/foodon/issues/
    version: '2025-08-01'
    version.iri: http://purl.obolibrary.org/obo/foodon/releases/2025-08-01/foodon.owl
  ontobee:
    library: Library
    name: Food Ontology
    prefix: FOODON
  pattern: ^[0-9]{8}$
  prefix: foodon
  publications:
  - doi: 10.1038/s41538-018-0032-6
    pmc: PMC6550238
    pubmed: '31304272'
    title: 'FoodOn: a harmonized food ontology to increase global food traceability,
      quality control and data integration'
    year: 2018
  - doi: 10.3389/fmicb.2017.01068
    pmc: PMC5483436
    pubmed: '28694792'
    title: 'Context Is Everything: Harmonization of Critical Food Microbiology Descriptors
      and Metadata for Improved Food Safety and Surveillance'
    year: 2017
  - doi: null
    pmc: null
    pubmed: '31304272'
    title: 'FoodOn: a harmonized food ontology to increase global food traceability,
      quality control and data integration'
    year: null
  - doi: 10.3389/fmicb.2017.01068
    pmc: null
    pubmed: '28694792'
    title: 'Context Is Everything: Harmonization of Critical Food Microbiology Descriptors
      and Metadata for Improved Food Safety and Surveillance'
    year: 2017
  - doi: 10.1038/s41538-018-0032-6
    pmc: null
    pubmed: '31304272'
    title: 'FoodOn: a harmonized food ontology to increase global food traceability,
      quality control and data integration'
    year: 2019
  - doi: null
    pmc: null
    pubmed: '31304272'
    title: 'FoodOn: a harmonized food ontology to increase global food traceability,
      quality control and data integration'
    year: null
  - doi: 10.3389/fmicb.2017.01068
    pmc: null
    pubmed: '28694792'
    title: 'Context Is Everything: Harmonization of Critical Food Microbiology Descriptors
      and Metadata for Improved Food Safety and Surveillance'
    year: 2017
  - doi: 10.1038/s41538-018-0032-6
    pmc: null
    pubmed: '31304272'
    title: 'FoodOn: a harmonized food ontology to increase global food traceability,
      quality control and data integration'
    year: 2019
  uri_format: http://purl.obolibrary.org/obo/FOODON_$1
fossilworks.journal:
  contributor:
    email: meghan.balk@gmail.com
    github: megbalk
    name: Meghan Balk
    orcid: 0000-0003-2699-3066
  description: Identifier for a journal article in the fossilworks website
  example: '61467'
  github_request_issue: 468
  homepage: http://fossilworks.org
  mappings:
    wikidata: P7720
  name: Fossilworks Journal
  part_of_database: fossilworks
  pattern: ^\d+$
  prefix: fossilworks.journal
  reviewer:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  uri_format: http://fossilworks.org/?a=referenceInfo&reference_no=$1
  wikidata:
    description: identifier for a reference (scholarly articles) in the Fossilworks
      database
    example:
    - '55763'
    - '61467'
    - '65044'
    homepage: http://www.fossilworks.org
    name: Fossilworks reference ID
    pattern: ^\d+$
    prefix: P7720
    uri_format: https://web.archive.org/web/0/http://www.fossilworks.org/cgi-bin/bridge.pl?a=displayReference&reference_no=$1
fossilworks.taxon:
  contributor:
    email: meghan.balk@gmail.com
    github: megbalk
    name: Meghan Balk
    orcid: 0000-0003-2699-3066
  description: Identifier for an animal, plant, or microorganism from the fossilworks
    website
  example: '40565'
  github_request_issue: 469
  homepage: http://www.fossilworks.org
  mappings:
    wikidata: P842
  name: Fossilworks Taxon
  part_of_database: fossilworks
  pattern: ^[1-9]\d{0,5}$
  prefix: fossilworks.taxon
  reviewer:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  uri_format: http://www.fossilworks.org/cgi-bin/bridge.pl?a=taxonInfo&taxon_no=$1
  wikidata:
    description: identifier for an animal, plant, or microorganism in the Fossilworks
      database
    example:
    - '40565'
    - '49734'
    homepage: http://www.fossilworks.org
    name: Fossilworks taxon ID
    pattern: ^([1-9]\d{0,5})$
    prefix: P842
    uri_format: https://web.archive.org/web/0/http://www.fossilworks.org/cgi-bin/bridge.pl?a=taxonInfo&taxon_no=$1
fovt:
  aberowl:
    description: FuTRES Ontology of Vertebrate Traits is an application ontology used
      to convert vertebrate trait data in spreadsheet to triples. FOVT leverages the
      BioCollections Ontology (BCO) to link observations of individual specimens to
      their trait values. Traits are defined in the Ontology of Biological Attributes
      (OBA).
    download_owl: http://aber-owl.net/media/ontologies/FOVT/7/fovt.owl
    homepage: https://github.com/futres/fovt
    name: FuTRES Ontology of Vertebrate Traits
    prefix: FOVT
  bioportal:
    contact:
      email: rlwalls2008@gmail.com
      name: Ramona Walls
    description: FuTRES Ontology of Vertebrate Traits is an application ontology used
      to convert vertebrate trait data in spreadsheet to triples. FOVT leverages the
      BioCollections Ontology (BCO) to link observations of individual specimens to
      their trait values. Traits are defined in the Ontology of Biological Attributes
      (OBA).
    homepage: https://github.com/futres/fovt
    name: FuTRES Ontology of Vertebrate Traits
    prefix: FOVT
    version: '2023-05-31'
  ecoportal:
    contact:
      email: meghan.balk@gmail.com
      name: Meghan Balk
    description: FuTRES Ontology of Vertebrate Traits is an application ontology used
      to convert vertebrate trait data in spreadsheet to triples. FOVT leverages the
      BioCollections Ontology (BCO) to link observations of individual specimens to
      their trait values. Traits are defined in the Ontology of Biological Attributes
      (OBA). For more details on FOVT, see https://futres.org/.
    homepage: https://futres.org
    license: CC0-1.0
    name: FuTRES Ontology of Vertebrate Traits
    prefix: FOVT
    version: '2023-05-31'
  example: 0000009
  mappings:
    aberowl: FOVT
    bioportal: FOVT
    ecoportal: FOVT
    obofoundry: fovt
    ols: fovt
    ontobee: FOVT
    wikidata.entity: Q113012661
  obofoundry:
    contact: meghan.balk@gmail.com
    contact.github: megbalk
    contact.label: Meghan Balk
    contact.orcid: 0000-0003-2699-3066
    depends_on:
    - bco
    - bfo
    - bspo
    - iao
    - oba
    - pato
    - ro
    - uberon
    deprecated: false
    description: FuTRES Ontology of Vertebrate Traits is an application ontology used
      to convert vertebrate trait data in spreadsheet to triples. FOVT leverages the
      BioCollections Ontology (BCO) to link observations of individual specimens to
      their trait values. Traits are defined in the Ontology of Biological Attributes
      (OBA).
    domain: phenotype
    download.obo: http://purl.obolibrary.org/obo/fovt.obo
    download.owl: http://purl.obolibrary.org/obo/fovt.owl
    homepage: https://github.com/futres/fovt
    license: CC0 1.0
    license.url: https://creativecommons.org/publicdomain/zero/1.0/
    name: FuTRES Ontology of Vertebrate Traits
    preferredPrefix: FOVT
    prefix: fovt
    repository: https://github.com/futres/fovt
  ols:
    description: These are the terms that are improted for FOVT to describe vertebrate
      traits.
    download_owl: http://purl.obolibrary.org/obo/fovt.owl
    homepage: https://github.com/futres/fovt
    name: FuTRES Ontology of Vertebrate Traits
    prefix: fovt
    tracker: https://github.com/futres/fovt/issues
    version: '2023-05-31'
    version.iri: http://purl.obolibrary.org/obo/fovt/releases/2023-05-31/fovt.owl
  ontobee:
    library: Library
    name: FuTRES Ontology of Vertebrate Traits
    prefix: FOVT
  pattern: ^\d{7}$
  prefix: fovt
  uri_format: http://purl.obolibrary.org/obo/FOVT_$1
fplx:
  aberowl:
    name: FamPlex
    prefix: FPLX
  biocontext:
    prefix: FPLX
  bioportal:
    contact:
      email: benjamin_gyori@hms.harvard.edu
      name: Benjamin Gyori
    description: FamPlex is a collection of resources for grounding biological entities
      from text and describing their hierarchical relationships.
    homepage: https://github.com/sorgerlab/famplex
    name: FamPlex
    prefix: FPLX
    publications:
    - https://www.biorxiv.org/content/early/2018/03/26/225698
    version: '1.0'
  contact:
    email: benjamin_gyori@hms.harvard.edu
    github: bgyori
    name: Benjamin M. Gyori
    orcid: 0000-0001-9439-5346
  domain: protein family
  example: GPIb_IX_V
  homepage: https://sorgerlab.github.io/famplex/
  license: CC0-1.0
  mappings:
    aberowl: FPLX
    biocontext: FPLX
    bioportal: FPLX
    miriam: fplx
    n2t: fplx
  miriam:
    deprecated: false
    description: FamPlex is a collection of resources for grounding biological entities
      from text and describing their hierarchical relationships.
    homepage: https://sorgerlab.github.io/famplex
    id: '00000651'
    name: FamPlex
    namespaceEmbeddedInLui: false
    pattern: ^[a-zA-Z0-9][A-Za-z0-9_]+$
    prefix: fplx
    sampleId: RAS
    uri_format: https://sorgerlab.github.io/famplex/$1
  n2t:
    description: FamPlex is a collection of resources for grounding biological entities
      from text and describing their hierarchical relationships.
    example: RAS
    homepage: http://bioportal.bioontology.org/ontologies/FPLX/
    name: FPLX through BioPortal
    namespaceEmbeddedInLui: false
    pattern: ^[a-zA-Z0-9][A-Za-z0-9_]+$
    prefix: fplx
    uri_format: http://bioportal.bioontology.org/ontologies/FPLX/?p=classes&conceptid=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FFPLX%23_$1
  name: FamPlex
  prefix: fplx
  publications:
  - doi: 10.1186/s12859-018-2211-5
    pmc: PMC6022344
    pubmed: '29954318'
    title: 'FamPlex: a resource for entity recognition and relationship resolution
      of human protein families and complexes in biomedical text mining'
    year: 2018
  synonyms:
  - famplex
  uri_format: https://sorgerlab.github.io/famplex/$1
  wikidata:
    paper: Q55505864
fr:
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: An ontology that enables the description of reviews of scientific articles
    and other scholarly resources.
  example: ReviewVersion
  fairsharing:
    abbreviation: FR
    contact:
      email: silvio.peroni@unibo.it
      name: Silvio Peroni
      orcid: 0000-0003-0530-4305
    description: The FAIR* Reviews Ontology (FR) enables the description of reviews
      of scientific articles and other scholarly resources.
    homepage: http://www.sparontologies.net/ontologies/fr
    license: CC-BY-4.0
    name: 'FAIR* Reviews Ontology '
    prefix: FAIRsharing.e7e609
    repository: https://github.com/sparontologies/fr
    subjects:
    - Subject Agnostic
    twitter: sparontologies
  homepage: http://www.sparontologies.net/ontologies/fr
  mappings:
    fairsharing: FAIRsharing.e7e609
  name: FAIR* Reviews Ontology
  preferred_prefix: FR
  prefix: fr
  repository: https://github.com/sparontologies/fr
frapo:
  aberowl:
    name: Funding, Research Administration and Projects Ontology
    prefix: FRAPO
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: An ontology for describing the administrative information of research
    projects, e.g., grant applications, funding bodies, project partners, etc.
  example: Grant
  fairsharing:
    abbreviation: FRAPO
    contact:
      email: silvio.peroni@unibo.it
      name: Silvio Peroni
      orcid: 0000-0003-0530-4305
    description: The Funding, Research Administration and Projects Ontology (FRAPO)
      is an ontology for describing the administrative information of research projects,
      e.g., grant applications, funding bodies, project partners, etc.
    homepage: http://www.sparontologies.net/ontologies/frapo
    license: CC-BY-4.0
    name: 'Funding, Research Administration and Projects Ontology '
    prefix: FAIRsharing.0a2576
    repository: https://github.com/sparontologies/frapo
    subjects:
    - Subject Agnostic
    twitter: sparontologies
    user_defined_tags:
    - Funding bodies
    - grant application
    - research project
  homepage: http://www.sparontologies.net/ontologies/frapo
  lov:
    description: FRAPO, the Funding, Research Administration and Projects Ontology,
      is a CERIF-compliant ontology written in OWL 2 DL for describing research project
      administrative information.
    homepage: http://purl.org/cerif/frapo/
    keywords:
    - Academy
    modified: '2014-01-31'
    name: Funding, Research Administration and Projects Ontology
    prefix: frapo
    uri_prefix: http://purl.org/cerif/frapo/$1
  mappings:
    aberowl: FRAPO
    fairsharing: FAIRsharing.0a2576
    lov: frapo
  name: Funding, Research Administration and Projects Ontology
  preferred_prefix: FRAPO
  prefix: frapo
  repository: https://github.com/sparontologies/frapo
  uri_format: http://purl.org/cerif/frapo/$1
frbr:
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: The Essential FRBR in OWL2 DL Ontology (FRBR) is an expression in OWL
    2 DL of the basic concepts and relations described in the IFLA report on the Functional
    Requirements for Bibliographic Records (FRBR), also described in Ian Davis's RDF
    vocabulary. It is imported by FaBiO and BiRO.
  example: Expression
  fairsharing:
    abbreviation: FRBR
    contact:
      email: silvio.peroni@unibo.it
      name: Silvio Peroni
      orcid: 0000-0003-0530-4305
    description: The Essential FRBR in OWL2 DL Ontology (FRBR) is an expression in
      OWL 2 DL of the basic concepts and relations described in the IFLA report on
      the Functional Requirements for Bibliographic Records (FRBR), also described
      in Ian Davis's RDF vocabulary. It is imported by FaBiO and BiRO.
    homepage: http://www.sparontologies.net/ontologies/frbr
    license: CC-BY-4.0
    name: 'Essential FRBR in OWL2 DL Ontology '
    prefix: FAIRsharing.b34b43
    repository: https://github.com/sparontologies/frbr
    subjects:
    - Subject Agnostic
    twitter: sparontologies
  homepage: http://www.sparontologies.net/ontologies/frbr
  lov:
    description: An expression in RDF of the concepts and relations described in the
      IFLA report on the Functional Requirements for Bibliographic Records (FRBR)
    homepage: http://vocab.org/frbr/core.html
    keywords:
    - FRBR
    modified: '2009-05-16'
    name: Expression of Core FRBR Concepts in RDF
    prefix: frbr
    uri_prefix: http://purl.org/vocab/frbr/core#$1
  mappings:
    fairsharing: FAIRsharing.b34b43
    lov: frbr
    zazuko: frbr
  name: Functional Requirements for Bibliographic Records
  preferred_prefix: FRBR
  prefix: frbr
  repository: https://github.com/sparontologies/frbr
  uri_format: http://purl.org/vocab/frbr/core#$1
  zazuko:
    prefix: frbr
    uri_format: http://purl.org/vocab/frbr/core#$1
frbrer:
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: This is the element set of native RDF classes and properties described
    in the current text (Feb 2009) of the Functional Requirements for Bibliographic
    Records (FRBR) entity-relationship model. (from https://www.iflastandards.info/fr/frbr/frbrer.html)
  download_rdf: http://iflastandards.info/ns/fr/frbr/frbrer.jsonld
  example: '1001'
  homepage: https://www.iflastandards.info/fr/frbr/frbrer
  lov:
    description: This is the element set of native RDF classes and properties described
      in the current text (Feb 2009) of the Functional Requirements for Bibliographic
      Records (FRBR) entity-relationship model.
    homepage: http://iflastandards.info/ns/fr/frbr/frbrer/
    keywords:
    - FRBR
    modified: '2015-07-14'
    name: FRBRer model
    prefix: frbrer
    uri_prefix: http://iflastandards.info/ns/fr/frbr/frbrer/$1
  mappings:
    lov: frbrer
  name: Functional Requirements for Bibliographic Records Entity-Relationship Model
  prefix: frbrer
  uri_format: http://iflastandards.info/ns/fr/frbr/frbrer/$1
fsnp:
  biocontext:
    prefix: FSNP
  mappings:
    biocontext: FSNP
    miriam: fsnp
    n2t: fsnp
    prefixcommons: fsnp
  miriam:
    deprecated: true
    description: The Functional Single Nucleotide Polymorphism (F-SNP) database integrates
      information obtained from databases about the functional effects of SNPs. These
      effects are predicted and indicated at the splicing, transcriptional, translational
      and post-translational level. In particular, users can retrieve SNPs that disrupt
      genomic regions known to be functional, including splice sites and transcriptional
      regulatory regions. Users can also identify non-synonymous SNPs that may have
      deleterious effects on protein structure or function, interfere with protein
      translation or impede post-translational modification.
    homepage: http://compbio.cs.queensu.ca/F-SNP/
    id: 00000496
    name: F-SNP
    namespaceEmbeddedInLui: false
    pattern: ^rs\d+$
    prefix: fsnp
    sampleId: rs17852708
    uri_format: http://compbio.cs.queensu.ca/cgi-bin/compbio/search/main.cgi?search_mode=id&amp;id_type=snp_id&amp;id_val=$1
  n2t:
    description: The Functional Single Nucleotide Polymorphism (F-SNP) database integrates
      information obtained from databases about the functional effects of SNPs. These
      effects are predicted and indicated at the splicing, transcriptional, translational
      and post-translational level. In particular, users can retrieve SNPs that disrupt
      genomic regions known to be functional, including splice sites and transcriptional
      regulatory regions. Users can also identify non-synonymous SNPs that may have
      deleterious effects on protein structure or function, interfere with protein
      translation or impede post-translational modification.
    example: rs17852708
    homepage: http://compbio.cs.queensu.ca/F-SNP/
    name: F-SNP at Queen's University (Canada)
    namespaceEmbeddedInLui: false
    pattern: ^rs\d+$
    prefix: fsnp
    uri_format: http://compbio.cs.queensu.ca/cgi-bin/compbio/search/main.cgi?search_mode=id&amp;id_type=snp_id&amp;id_val=$1
  prefix: fsnp
  prefixcommons:
    description: F-SNP database provides integrated information about the functional
      effects of SNPs obtained from 16 bioinformatics tools and databases. The functional
      effects are predicted and indicated at the splicing, transcriptional, translational,
      and post-translational level. As such, the F-SNP database helps identify and
      focus on SNPs with potential pathological effect to human health.
    example: rs36095613
    homepage: http://compbio.cs.queensu.ca/F-SNP/
    keywords:
    - DNA
    - protein
    name: 'F-SNP: a collection of functional SNPs, specifically prioritized for disease
      association studies'
    pattern: ^rs\d+$
    prefix: fsnp
ftonto:
  comment: Don't confuse with MASON, which is referenced by FTOnto
  description: The FTOnto enables reseachers to sematically describe a physical fischertechnik
    factory simulation environment. This is archieved by aligning concepts from MASON
    and SOSA with own concepts. Furthermore the FTOnto can capture knowledge about
    semantic web services which are used to interact between the service-layer and
    the cyber-physical layer in a cyber-physical production system. This includes
    precondition which have to be met before a webservice can be performed, postconditions
    which check if the webservice execution was performed successfully and effects
    which describe the changed state of the domain after performing a service. [from
    homepage]
  example: ADXL345_Pi_1_AccSensor_1_Result_2019-02-26_14_53_54.97
  mappings:
    tib: ftonto
  name: Fischertechnik Ontology
  prefix: ftonto
  references:
  - https://ceur-ws.org/Vol-2454/paper_10.pdf
  repository: https://gitlab.rlp.net/iot-lab-uni-trier/ftonto
  tib:
    description: MAnufacturing's Semantics Ontology, Ontology of tools and concepts
      of industrial manufacturing
    download_owl: https://gitlab.rlp.net/iot-lab-uni-trier/ftonto/-/raw/master/mason.owl
    homepage: https://wi2.pages.gitlab.rlp.net/iot-lab/ftonto-web-doku/
    keywords:
    - NFDI4ING
    - CoyPu
    - engineering
    name: FTOnto
    prefix: ftonto
    uri_format: http://www.owl-ontologies.com/mason.owl#$1
  uri_format: http://iot.uni-trier.de/FTOnto#$1
ftt:
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: Types of named geographic features. Applicable also to many unnamed
    features but reflects the level of detail traditionally shown on maps, so some
    feature types specified in scientific studies may not be well represented here.
    Not highly specific.
  example: '273'
  homepage: https://apps.usgs.gov/thesaurus/thesaurus-full.php?thcode=3
  name: Feature Type Thesaurus
  pattern: ^\d+$
  prefix: ftt
  references:
  - https://obo-communitygroup.slack.com/archives/C023P0Z304T/p1638380238036200
  - https://github.com/EnvironmentOntology/envo/issues/1130
  uri_format: https://apps.usgs.gov/thesaurus/term-simple.php?thcode=3&code=$1
funcbase.fly:
  biocontext:
    prefix: FUNCBASE.FLY
  mappings:
    biocontext: FUNCBASE.FLY
    miriam: funcbase.fly
    n2t: funcbase.fly
  miriam:
    deprecated: false
    description: Computational gene function prediction can serve to focus experimental
      resources on high-priority experimental tasks. FuncBase is a web resource for
      viewing quantitative machine learning-based gene function annotations. Quantitative
      annotations of genes, including fungal and mammalian genes, with Gene Ontology
      terms are accompanied by a community feedback system. Evidence underlying function
      annotations is shown. FuncBase provides links to external resources, and may
      be accessed directly or via links from species-specific databases. This collection
      references Drosophila data.
    homepage: http://func.mshri.on.ca/fly
    id: '00000461'
    name: FuncBase Fly
    namespaceEmbeddedInLui: false
    pattern: ^\d+$
    prefix: funcbase.fly
    sampleId: '10194'
    uri_format: http://func.mshri.on.ca/fly/genes/list_functional_scores/$1
  n2t:
    description: Computational gene function prediction can serve to focus experimental
      resources on high-priority experimental tasks. FuncBase is a web resource for
      viewing quantitative machine learning-based gene function annotations. Quantitative
      annotations of genes, including fungal and mammalian genes, with Gene Ontology
      terms are accompanied by a community feedback system. Evidence underlying function
      annotations is shown. FuncBase provides links to external resources, and may
      be accessed directly or via links from species-specific databases. This collection
      references Drosophila data.
    example: '10194'
    homepage: http://func.mshri.on.ca/fly
    name: FuncBase Fly at Harvard Medical School
    namespaceEmbeddedInLui: false
    pattern: ^\d+$
    prefix: funcbase.fly
    uri_format: http://func.mshri.on.ca/fly/genes/list_functional_scores/$1
  prefix: funcbase.fly
funcbase.human:
  biocontext:
    prefix: FUNCBASE.HUMAN
  mappings:
    biocontext: FUNCBASE.HUMAN
    miriam: funcbase.human
    n2t: funcbase.human
  miriam:
    deprecated: false
    description: Computational gene function prediction can serve to focus experimental
      resources on high-priority experimental tasks. FuncBase is a web resource for
      viewing quantitative machine learning-based gene function annotations. Quantitative
      annotations of genes, including fungal and mammalian genes, with Gene Ontology
      terms are accompanied by a community feedback system. Evidence underlying function
      annotations is shown. FuncBase provides links to external resources, and may
      be accessed directly or via links from species-specific databases. This collection
      references human data.
    homepage: http://func.mshri.on.ca/human/
    id: '00000462'
    name: FuncBase Human
    namespaceEmbeddedInLui: false
    pattern: ^\d+$
    prefix: funcbase.human
    sampleId: '119514'
    uri_format: http://func.mshri.on.ca/human/genes/list_functional_scores/$1
  n2t:
    description: Computational gene function prediction can serve to focus experimental
      resources on high-priority experimental tasks. FuncBase is a web resource for
      viewing quantitative machine learning-based gene function annotations. Quantitative
      annotations of genes, including fungal and mammalian genes, with Gene Ontology
      terms are accompanied by a community feedback system. Evidence underlying function
      annotations is shown. FuncBase provides links to external resources, and may
      be accessed directly or via links from species-specific databases. This collection
      references human data.
    example: '119514'
    homepage: http://func.mshri.on.ca/human/
    name: FuncBase Human at Harvard Medical School
    namespaceEmbeddedInLui: false
    pattern: ^\d+$
    prefix: funcbase.human
    uri_format: http://func.mshri.on.ca/human/genes/list_functional_scores/$1
  prefix: funcbase.human
funcbase.mouse:
  biocontext:
    prefix: FUNCBASE.MOUSE
  mappings:
    biocontext: FUNCBASE.MOUSE
    miriam: funcbase.mouse
    n2t: funcbase.mouse
  miriam:
    deprecated: false
    description: Computational gene function prediction can serve to focus experimental
      resources on high-priority experimental tasks. FuncBase is a web resource for
      viewing quantitative machine learning-based gene function annotations. Quantitative
      annotations of genes, including fungal and mammalian genes, with Gene Ontology
      terms are accompanied by a community feedback system. Evidence underlying function
      annotations is shown. FuncBase provides links to external resources, and may
      be accessed directly or via links from species-specific databases. This collection
      references mouse.
    homepage: http://func.mshri.on.ca/mouse/
    id: '00000463'
    name: FuncBase Mouse
    namespaceEmbeddedInLui: false
    pattern: ^\d+$
    prefix: funcbase.mouse
    sampleId: '1351341'
    uri_format: http://func.mshri.on.ca/mouse/genes/list_functional_scores/$1
  n2t:
    description: Computational gene function prediction can serve to focus experimental
      resources on high-priority experimental tasks. FuncBase is a web resource for
      viewing quantitative machine learning-based gene function annotations. Quantitative
      annotations of genes, including fungal and mammalian genes, with Gene Ontology
      terms are accompanied by a community feedback system. Evidence underlying function
      annotations is shown. FuncBase provides links to external resources, and may
      be accessed directly or via links from species-specific databases. This collection
      references mouse.
    example: '1351341'
    homepage: http://func.mshri.on.ca/mouse/
    name: FuncBase Mouse at Harvard Medical School
    namespaceEmbeddedInLui: false
    pattern: ^\d+$
    prefix: funcbase.mouse
    uri_format: http://func.mshri.on.ca/mouse/genes/list_functional_scores/$1
  prefix: funcbase.mouse
funcbase.yeast:
  biocontext:
    prefix: FUNCBASE.YEAST
  mappings:
    biocontext: FUNCBASE.YEAST
    miriam: funcbase.yeast
    n2t: funcbase.yeast
  miriam:
    deprecated: false
    description: Computational gene function prediction can serve to focus experimental
      resources on high-priority experimental tasks. FuncBase is a web resource for
      viewing quantitative machine learning-based gene function annotations. Quantitative
      annotations of genes, including fungal and mammalian genes, with Gene Ontology
      terms are accompanied by a community feedback system. Evidence underlying function
      annotations is shown. FuncBase provides links to external resources, and may
      be accessed directly or via links from species-specific databases. This collection
      references yeast.
    homepage: http://func.mshri.on.ca/yeast
    id: '00000464'
    name: FuncBase Yeast
    namespaceEmbeddedInLui: false
    pattern: ^\d+$
    prefix: funcbase.yeast
    sampleId: '2701'
    uri_format: http://func.mshri.on.ca/yeast/genes/list_functional_scores/$1
  n2t:
    description: Computational gene function prediction can serve to focus experimental
      resources on high-priority experimental tasks. FuncBase is a web resource for
      viewing quantitative machine learning-based gene function annotations. Quantitative
      annotations of genes, including fungal and mammalian genes, with Gene Ontology
      terms are accompanied by a community feedback system. Evidence underlying function
      annotations is shown. FuncBase provides links to external resources, and may
      be accessed directly or via links from species-specific databases. This collection
      references yeast.
    example: '2701'
    homepage: http://func.mshri.on.ca/yeast
    name: FuncBase Yeast at Harvard Medical School
    namespaceEmbeddedInLui: false
    pattern: ^\d+$
    prefix: funcbase.yeast
    uri_format: http://func.mshri.on.ca/yeast/genes/list_functional_scores/$1
  prefix: funcbase.yeast
funderregistry:
  example_extras:
  - '501100001230'
  mappings:
    miriam: funderregistry
  miriam:
    deprecated: false
    description: The Funder Registry is an open registry of persistent identifiers
      for grant-giving organizations around the world.
    homepage: https://www.crossref.org/
    id: 00000847
    name: FunderRegistry
    namespaceEmbeddedInLui: false
    pattern: ^\d{9,9}$
    prefix: funderregistry
    sampleId: '100000001'
    uri_format: http://data.crossref.org/fundingdata/funder/10.13039/$1
  pattern: ^\d+$
  prefix: funderregistry
  providers:
  - code: crossref.api
    description: Access funder data through the Crossref API
    example: null
    first_party: null
    homepage: https://api.crossref.org
    name: Crossref API
    publications: null
    status: null
    uri_format: https://api.crossref.org/funders/$1
  - code: doi
    description: Access funder data through a DOI for crossref funders.
    example: null
    first_party: null
    homepage: https://doi.org
    name: DOI
    publications: null
    status: null
    uri_format: https://dx.doi.org/10.13039/$1
  synonyms:
  - FundRef
  - crossref.funder
funggrowth:
  contact:
    email: v.robert@wi.knaw.nl
    github: null
    name: Vincent Robert
    orcid: 0000-0002-9370-4677
  contributor:
    email: ji.kang@northeastern.edu
    github: kanghosaeyo
    name: Kangho Ji
    orcid: 0009-0009-3402-8013
  description: Identifiers represent experimental growth profiles documenting fungal
    species' ability to utilize specific carbon sources (plant biomass components,
    polysaccharides, and monosaccharides) in the FUNG-GROWTH database, which provides
    phenotypic data to support functional genome annotation and comparative analysis
    of carbohydrate metabolism across fungal species.
  example: '86'
  github_request_issue: 1720
  homepage: https://www.fung-growth.org
  keywords:
  - fungi
  - growth profiles
  - monosaccharides
  - plant biomass
  - polysaccharides
  name: Fungal Growth Database
  pattern: ^\d+$
  prefix: funggrowth
  publications:
  - doi: 10.1128/mra.00378-25
    pmc: PMC12424322
    pubmed: '40767478'
    title: 'The FUNG-GROWTH database: linking fungal phenotype to genome'
    year: 2025
  reviewer:
    email: b.gyori@northeastern.edu
    github: bgyori
    name: Benjamin M. Gyori
    orcid: 0000-0001-9439-5346
  uri_format: https://www.fung-growth.org/page/Display%20page%20FG/$1
fungidb:
  biocontext:
    prefix: FUNGIDB
  fairsharing:
    abbreviation: FungiDB
    contact:
      email: jason.stajich@ucr.edu
      name: Jason E. Stajich
      orcid: 0000-0002-7591-0020
    description: FungiDB is an integrated genomic and functional genomic database
      for the kingdom Fungi. The database integrates whole genome sequence and annotation
      and also includes experimental and environmental isolate sequence data. The
      database includes comparative genomics, analysis of gene expression, and supplemental
      bioinformatics analyses and a web interface for data-mining.
    homepage: http://fungidb.org
    name: Fungal and Oomycete genomics resource
    prefix: FAIRsharing.xf30yc
    publications:
    - doi: 10.1016/j.fgb.2016.04.002
      pubmed_id: 27259951
      title: Database whiplash, crowdsourcing, and FungiDB.
    - doi: 10.1093/nar/gkr918
      pubmed_id: 22064857
      title: 'FungiDB: an integrated functional genomics database for fungi.'
    - doi: 10.1128/EC.00083-14
      pubmed_id: 24813190
      title: Literature-based gene curation and proposed genetic nomenclature for
        cryptococcus.
    subjects:
    - Genomics
    twitter: fungidb
  mappings:
    biocontext: FUNGIDB
    fairsharing: FAIRsharing.xf30yc
    miriam: fungidb
    n2t: fungidb
    re3data: r3d100011906
  miriam:
    deprecated: false
    description: FungiDB is a genomic resource for fungal genomes. It contains contains
      genome sequence and annotation from several fungal classes, including the Ascomycota
      classes, Eurotiomycetes, Sordariomycetes, Saccharomycetes and the Basidiomycota
      orders, Pucciniomycetes and Tremellomycetes, and the basal 'Zygomycete' lineage
      Mucormycotina.
    homepage: https://fungidb.org/fungidb
    id: '00000365'
    name: FungiDB
    namespaceEmbeddedInLui: false
    pattern: ^[A-Za-z_0-9]+$
    prefix: fungidb
    sampleId: CNBG_0001
    uri_format: https://fungidb.org/fungidb/app/record/gene/$1
  n2t:
    description: FungiDB is a genomic resource for fungal genomes. It contains contains
      genome sequence and annotation from several fungal classes, including the Ascomycota
      classes, Eurotiomycetes, Sordariomycetes, Saccharomycetes and the Basidiomycota
      orders, Pucciniomycetes and Tremellomycetes, and the basal 'Zygomycete' lineage
      Mucormycotina.
    example: CNBG_0001
    homepage: https://fungidb.org/fungidb
    name: FungiDB at University of California
    namespaceEmbeddedInLui: false
    pattern: ^[A-Za-z_0-9]+$
    prefix: fungidb
    uri_format: https://fungidb.org/fungidb/app/record/gene/$1
  prefix: fungidb
  publications:
  - doi: 10.1016/j.fgb.2016.04.002
    pmc: null
    pubmed: '27259951'
    title: Database whiplash, crowdsourcing, and FungiDB
    year: 2016
  - doi: 10.1128/ec.00083-14
    pmc: PMC4135733
    pubmed: '24813190'
    title: Literature-based gene curation and proposed genetic nomenclature for cryptococcus
    year: 2014
  - doi: 10.1093/nar/gkr918
    pmc: PMC3245123
    pubmed: '22064857'
    title: 'FungiDB: an integrated functional genomics database for fungi'
    year: 2011
  - doi: 10.1016/j.fgb.2016.04.002
    pmc: null
    pubmed: null
    title: Database whiplash, crowdsourcing, and FungiDB.
    year: null
  - doi: 10.1093/nar/gkr918
    pmc: null
    pubmed: null
    title: 'FungiDB: an integrated functional genomics database for fungi.'
    year: null
  - doi: 10.1128/EC.00083-14
    pmc: null
    pubmed: null
    title: Literature-based gene curation and proposed genetic nomenclature for cryptococcus.
    year: null
  - doi: 10.1016/j.fgb.2016.04.002
    pmc: null
    pubmed: null
    title: Database whiplash, crowdsourcing, and FungiDB.
    year: null
  - doi: 10.1093/nar/gkr918
    pmc: null
    pubmed: null
    title: 'FungiDB: an integrated functional genomics database for fungi.'
    year: null
  - doi: 10.1128/EC.00083-14
    pmc: null
    pubmed: null
    title: Literature-based gene curation and proposed genetic nomenclature for cryptococcus.
    year: null
  re3data:
    description: FungiDB belongs to the EuPathDB family of databases and is an integrated
      genomic and functional genomic database for the kingdom Fungi. FungiDB was first
      released in early 2011 as a collaborative project between EuPathDB and the group
      of Jason Stajich (University of California, Riverside). At the end of 2015,
      FungiDB was integrated into the EuPathDB bioinformatic resource center. FungiDB
      integrates whole genome sequence and annotation and also includes experimental
      and environmental isolate sequence data. The database includes comparative genomics,
      analysis of gene expression, and supplemental bioinformatics analyses and a
      web interface for data-mining.
    doi: 10.17616/R35K9M
    homepage: https://fungidb.org/fungidb/app
    license: other
    name: FungiDB
    prefix: r3d100011906
    synonyms:
    - The Fungal and Oomycete Genomics Resource
    xrefs:
      omics: '03103'
fungorum:
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: identifier for a fungus taxon in Index Fungorum
  example: '154022'
  homepage: http://www.indexfungorum.org
  mappings:
    ncbi: Fungorum
    wikidata: P1391
  name: Index Fungorum
  ncbi:
    example: ID550186
    homepage: http://www.indexfungorum.org
    name: Index Fungorum
    prefix: Fungorum
  pattern: ^[1-9]\d{0,5}$
  prefix: fungorum
  uri_format: http://www.indexfungorum.org/names/NamesRecord.asp?RecordID=$1
  wikidata:
    database: Q1860469
    description: identifier for a fungus taxon in Index Fungorum
    example:
    - '154022'
    - '17030'
    - '90345'
    name: Index Fungorum taxon ID
    pattern: ^[1-9]\d{0,5}|$
    prefix: P1391
    uri_format: https://www.indexfungorum.org/names/NamesRecord.asp?RecordID=$1
fyeco:
  biolink:
    is_identifiers: false
    is_obo: false
    prefix: FYECO
    uri_format: https://www.pombase.org/term/$1
  comment: Rather than admitting FYECO to the OBO foundry, we secure the prefix here
    at bioregistry. The FYECO namespace shows up in a lot of ingests (basically anywhere
    you ingest PomBase gene-phenotype data). Future work includes mapping FYECO to
    other OBO ontologies, but this is way ahead in the future.
  contact:
    email: vw253@cam.ac.uk
    github: ValWood
    name: Valerie Wood
    orcid: 0000-0001-6330-7526
  contributor:
    email: vw253@cam.ac.uk
    github: ValWood
    name: Valerie Wood
    orcid: 0000-0001-6330-7526
  description: PomBase manages gene and phenotype data related to Fission Yeast. FYECO
    contains experimental conditions relevant to fission yeast biology. The FYECO
    namespace shows up in data ingests from PomBase.
  example: '0000003'
  github_request_issue: 268
  homepage: https://github.com/pombase/fypo
  mappings:
    biolink: FYECO
  name: Fission Yeast Experimental Conditions Ontology
  pattern: ^\d{7}$
  preferred_prefix: FYECO
  prefix: fyeco
  repository: https://github.com/pombase/fypo
  reviewer:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
fyler:
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: A hierarchical classification of congenital heart disease
  example: '4447'
  homepage: https://www.elsevier.com/books/nadas-pediatric-cardiology/9781416023906
  name: Fyler
  pattern: ^\d+$
  prefix: fyler
  references:
  - https://github.com/obophenotype/human-phenotype-ontology/issues/2568
  - https://github.com/obophenotype/human-phenotype-ontology/issues/2511
fypo:
  aberowl:
    description: FYPO is a formal ontology of phenotypes observed in fission yeast.
    download_owl: http://aber-owl.net/media/ontologies/FYPO/483/fypo.owl
    homepage: https://github.com/pombase/fypo
    name: Fission Yeast Phenotype Ontology
    prefix: FYPO
  biocontext:
    prefix: FYPO
  biolink:
    is_identifiers: false
    is_obo: true
    prefix: FYPO
    uri_format: http://purl.obolibrary.org/obo/FYPO_$1
  bioportal:
    contact:
      email: vw253@cam.ac.uk
      name: Valerie Wood
    description: Fission Yeast Phenotype Ontology, A formal ontology of phenotypes
      observed in fission yeast.
    homepage: https://github.com/pombase/fypo
    license: CC-BY-4.0
    name: Fission Yeast Phenotype Ontology
    prefix: FYPO
    version: '2025-09-27'
  download_json: http://purl.obolibrary.org/obo/fypo.json
  download_obo: http://purl.obolibrary.org/obo/fypo.obo
  example: '0001707'
  fairsharing:
    abbreviation: FYPO
    contact:
      email: vw253@cam.ac.uk
      name: Valerie Wood
      orcid: 0000-0001-6330-7526
    description: FYPO is being developed to support the comprehensive and detailed
      representation of phenotypes in PomBase, the online fission yeast resource (www.pombase.org).
      Its scope is similar to that of the Ascomycete Phenotype Ontology (APO), but
      FYPO includes more detailed pre-composed terms as well as computable definitions.
    domains:
    - GO-term enrichment data
    - phenotype
    homepage: http://sourceforge.net/apps/trac/pombase/wiki/FissionYeastPhenotypeOntology
    license: CC-BY-4.0
    name: Fission Yeast Phenotype Ontology
    prefix: FAIRsharing.4vr0ys
    publications:
    - doi: 10.1093/bioinformatics/btt266
      pubmed: '23658422'
      title: 'FYPO: the fission yeast phenotype ontology'
      year: 2013
    repository: https://github.com/pombase/fypo
    subjects:
    - Life Science
    - Phylogenetics
    - Genetics
  go:
    homepage: http://www.pombase.org/
    name: Fission Yeast Phenotype Ontology
    prefix: FYPO
  mappings:
    aberowl: FYPO
    biocontext: FYPO
    biolink: FYPO
    bioportal: FYPO
    fairsharing: FAIRsharing.4vr0ys
    go: FYPO
    obofoundry: fypo
    ols: fypo
    ontobee: FYPO
    wikidata.entity: Q55118393
  name: Fission Yeast Phenotype Ontology
  obofoundry:
    contact: vw253@cam.ac.uk
    contact.github: ValWood
    contact.label: Val Wood
    contact.orcid: 0000-0001-6330-7526
    deprecated: false
    description: FYPO is a formal ontology of phenotypes observed in fission yeast.
    domain: phenotype
    download.obo: http://purl.obolibrary.org/obo/fypo.obo
    download.owl: http://purl.obolibrary.org/obo/fypo.owl
    homepage: https://github.com/pombase/fypo
    license: CC BY 4.0
    license.url: http://creativecommons.org/licenses/by/4.0/
    logo: https://github.com/pombase/website/blob/master/src/assets/FYPO_logo_tiny.png
    name: Fission Yeast Phenotype Ontology
    preferredPrefix: FYPO
    prefix: fypo
    publications:
    - id: https://www.ncbi.nlm.nih.gov/pubmed/23658422
      title: 'FYPO: The Fission Yeast Phenotype Ontology.'
    repository: https://github.com/pombase/fypo
  ols:
    description: A formal ontology of phenotypes observed in fission yeast.
    download_owl: http://purl.obolibrary.org/obo/fypo.owl
    homepage: https://github.com/pombase/fypo
    name: Fission Yeast Phenotype Ontology (FYPO)
    prefix: fypo
    tracker: https://github.com/pombase/fypo/issues
    version: '2025-09-27'
    version.iri: http://purl.obolibrary.org/obo/fypo/releases/2025-09-27/fypo.owl
  ontobee:
    library: Library
    name: Fission Yeast Phenotype Ontology
    prefix: FYPO
  pattern: ^\d{7}$
  prefix: fypo
  publications:
  - doi: 10.1093/bioinformatics/btt266
    pmc: PMC3694669
    pubmed: '23658422'
    title: 'FYPO: the fission yeast phenotype ontology'
    year: 2013
  - doi: null
    pmc: null
    pubmed: '23658422'
    title: 'FYPO: The Fission Yeast Phenotype Ontology'
    year: null
  - doi: 10.1093/bioinformatics/btt266
    pmc: null
    pubmed: '23658422'
    title: 'FYPO: the fission yeast phenotype ontology'
    year: 2013
  uri_format: http://purl.obolibrary.org/obo/FYPO_$1
ga4ghdos:
  biocontext:
    prefix: GA4GHDOS
  mappings:
    biocontext: GA4GHDOS
    miriam: ga4ghdos
    n2t: ga4ghdos
  miriam:
    deprecated: false
    description: Assists in resolving data across cloud resources.
    homepage: http://github.com/ga4gh/data-object-service-schemas
    id: '00000671'
    name: Data Object Service
    namespaceEmbeddedInLui: false
    pattern: ^[a-zA-Z0-9\-:#/\.]+$
    prefix: ga4ghdos
    sampleId: dg.4503/01b048d0-e128-4cb0-94e9-b2d2cab7563d
    uri_format: https://dataguids.org/ga4gh/dos/v1/dataobjects/$1
  n2t:
    description: Assists in resolving data across cloud resources.
    example: dg.4503/01b048d0-e128-4cb0-94e9-b2d2cab7563d
    homepage: http://github.com/ga4gh/data-object-service-schemas
    name: Data Object Service
    namespaceEmbeddedInLui: false
    pattern: ^[a-zA-Z0-9\-:#/\.]+$
    prefix: ga4ghdos
    uri_format: https://dataguids.org/ga4gh/dos/v1/dataobjects/$1
  prefix: ga4ghdos
gabi:
  biocontext:
    prefix: GABI
  contact:
    email: birgit.kersten@thuenen.de
    github: null
    name: Birgit Kersten
    orcid: 0000-0001-9900-9133
  mappings:
    biocontext: GABI
    miriam: gabi
    n2t: gabi
    ncbi: GABI
    prefixcommons: gabi
  miriam:
    deprecated: true
    description: GabiPD (Genome Analysis of Plant Biological Systems Primary Database)
      constitutes a repository for a wide array of heterogeneous data from high-throughput
      experiments in several plant species. These data (i.e. genomics, transcriptomics,
      proteomics and metabolomics), originating from different model or crop species,
      can be accessed through a central gene 'Green Card'.
    homepage: http://www.gabipd.org/
    id: '00000164'
    name: GABI
    namespaceEmbeddedInLui: false
    pattern: ^\w+$
    prefix: gabi
    sampleId: '2679240'
    uri_format: http://www.gabipd.org/database/cgi-bin/GreenCards.pl.cgi?BioObjectId=$1&Mode=ShowBioObject
  n2t:
    description: GabiPD (Genome Analysis of Plant Biological Systems Primary Database)
      constitutes a repository for a wide array of heterogeneous data from high-throughput
      experiments in several plant species. These data (i.e. genomics, transcriptomics,
      proteomics and metabolomics), originating from different model or crop species,
      can be accessed through a central gene 'Green Card'.
    example: '2679240'
    homepage: http://www.gabipd.org/
    name: GABI at Max Planck
    namespaceEmbeddedInLui: false
    pattern: ^\w+$
    prefix: gabi
    uri_format: http://www.gabipd.org/database/cgi-bin/GreenCards.pl.cgi?BioObjectId=$1&Mode=ShowBioObject
  ncbi:
    example: HA05J18
    homepage: http://www.gabipd.org/information/about.shtml
    name: Network of Different Plant Genomic Research Projects
    prefix: GABI
  prefix: gabi
  prefixcommons:
    description: GabiPD (Genome Analysis of Plant Biological Systems Primary Database)
      constitutes a repository for a wide array of heterogeneous data from high-throughput
      experiments in several plant species. These data (i.e. genomics, transcriptomics,
      proteomics and metabolomics), originating from different model or crop species,
      can be accessed through a central gene 'Green Card'.
    example: '2679240'
    homepage: http://www.gabi.de/
    keywords:
    - gene
    - genome
    - plant
    name: Network of Different Plant Genomic Research Projects
    pattern: ^\w+$
    prefix: gabi
    pubmed_ids:
    - '18812395'
    uri_format: http://gabi.rzpd.de/database/cgi-bin/GreenCards.pl.cgi?BioObjectId=$1&Mode=ShowBioObject
  publications:
  - doi: 10.1093/nar/gkn611
    pmc: PMC2686513
    pubmed: '18812395'
    title: 'GabiPD: the GABI primary database--a plant integrative ''omics'' database'
    year: 2008
  - doi: null
    pmc: null
    pubmed: '18812395'
    title: null
    year: null
  - doi: null
    pmc: null
    pubmed: '18812395'
    title: null
    year: null
gaidet:
  contact:
    email: serhii.nazarovets@gmail.com
    github: panbibliotekar
    name: Serhii Nazarovets
    orcid: 0000-0002-5067-4498
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: The Generative Artificial Intelligence Delegation Taxonomy (GAIDeT)
    assigns identifiers to contributor roles as an extension to the Contributor Roles
    Taxonomy (CRediT) to support promoting transparency and accountability in academic
    publishing when AI contribtors are involved in research. It is operationalized
    in the [GAIDeT Declaration Generator](https://panbibliotekar.github.io/gaidet-declaration/),
    an interactive tool for researchers to disclose the delegation of tasks to generative
    AI (GAI) tools in accordance with the GAIDeT taxonomy.
  download_owl: https://w3id.org/gaidet/gaidet.owl
  example: '0000001'
  fairsharing:
    abbreviation: GAIDeT
    contact:
      email: serhii.nazarovets@gmail.com
      name: 'Serhii Nazarovets '
      orcid: 0000-0002-5067-4498
    description: 'GAIDeT (Generative AI Delegation Taxonomy) is a taxonomy and ontology
      for transparently disclosing which research and writing tasks were delegated
      to generative AI tools. GAIDeT provides a structured framework for documenting
      GAI’s role in scholarly research. It classifies research activities into key
      domains – conceptualization, literature review, methodology, data analysis,
      writing, supervision, and ethical review – ensuring transparency and human accountability.

      '
    homepage: https://doi.org/10.1080/08989621.2025.2544331
    name: Generative AI Delegation Taxonomy
    prefix: FAIRsharing.23b8a3
    publications:
    - doi: 10.1080/08989621.2025.2544331
      title: 'GAIDeT (Generative AI Delegation Taxonomy): A taxonomy for humans to
        delegate tasks to generative artificial intelligence in scientific research
        and publishing'
      year: 2025
    - doi: 10.59350/psjb9-z1x39
      title: 'GAIDeT: a practical taxonomy for declaring AI use in research and publishing'
      year: 2025
    repository: https://github.com/panbibliotekar/gaidet-declaration
    subjects:
    - Artificial Intelligence
  homepage: https://github.com/panbibliotekar/gaidet-declaration
  keywords:
  - attribution
  - contributor roles
  - delegation
  mappings:
    fairsharing: FAIRsharing.23b8a3
  name: Generative Artificial Intelligence Delegation Taxonomy
  pattern: ^\d{7}$
  prefix: gaidet
  publications:
  - doi: 10.1080/08989621.2025.2544331
    pmc: null
    pubmed: null
    title: A taxonomy for humans to delegate tasks to generative artificial intelligence
      in scientific research and publishing
    year: 2025
  rdf_uri_format: https://w3id.org/gaidet/$1
  repository: https://github.com/panbibliotekar/gaidet-declaration
  uri_format: https://w3id.org/gaidet/$1
gainesville.core:
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: Describes typical Computational Chemistry experiments, including Molecular
    Publications, Molecular Systems, Molecular Calculations
  download_owl: http://ontologies.makolab.com/gc06/gc.owl
  example: Aromatic
  homepage: http://ontologies.makolab.com/gc06/gc.html
  license: CC-BY-3.0
  mappings:
    tib: gc
  name: Gainesville Core Ontology
  prefix: gainesville.core
  references:
  - http://ontologies.makolab.com/gc/
  tib:
    description: "This ontology aims at complete description of typical Computational\
      \ Chemistry experiment.\n\n    Gainesville Core describes:\n    - Molecular\
      \ Publications\n    - Molecular Systems\n    - Molecular Calculations\n    Â\
      \ \n    Molecular Systems contains Molecules\n    The Molecules may have Residues\
      \ (for biopolymers and polymers)\n    Molecular Calculations contain Initial\
      \ Data and Results\n    The Initial Data may have Methods, Basis Sets, Functionals,\
      \ etc.\n    The Results may have Energies, Wave Functions and Spectra, etc."
    download_owl: https://raw.githubusercontent.com/NFDI4Chem/GC-Ontology-Mirror/refs/heads/main/gc07_without_imports.owl
    homepage: https://web.archive.org/web/20230828122046/http://chemicalsemantics.com/
    keywords:
    - NFDI4CHEM
    - chemistry
    name: 'GNVC: Gainesville Core Ontology - standard for publishing results of computational
      chemistry.'
    prefix: gc
    uri_format: http://purl.org/gc/$1
  uri_format: http://purl.org/gc/$1
galen:
  aberowl:
    description: A translation of the full Galen ontology (from the OpenGALEN project)
      into the OWL description logic.
    download_owl: http://aber-owl.net/media/ontologies/GALEN/1/galen.owl
    homepage: http://www.co-ode.org/galen/
    name: Galen Ontology
    prefix: GALEN
    version: '1.1'
  bioportal:
    contact:
      email: j@deltaflow.com
      name: Julian Seidenberg
    description: A translation of the full Galen ontology (from the OpenGALEN project)
      into the OWL description logic.
    homepage: http://www.co-ode.org/galen/
    name: Galen Ontology
    prefix: GALEN
    version: '1.1'
  comment: I really tried, but could not figure out what GALEN stands for
  deprecated: true
  example: MagnitudeValueType
  homepage: https://www.opengalen.org
  mappings:
    aberowl: GALEN
    bioportal: GALEN
  name: GALEN
  prefix: galen
  uri_format: http://www.co-ode.org/ontologies/galen#$1
gallont:
  aberowl:
    description: Ontology of plant gall phenotypes. Plant galls are novel plant structures,
      generated by plants in response to biotic stressors. This ontology is used to
      annotate gall phenotypes (e.g., their colors, textures, sizes, locations on
      the plant) in a semantic way, in order to facilitate discoveries about the genetic
      and physiologic mechanisms responsible for such phenotypes. The ontology can
      also be used as a controlled vocabulary for natural language descriptions of
      plant galls.
    download_owl: http://aber-owl.net/media/ontologies/GALLONT/5/gallont.owl
    homepage: https://adeans.github.io/gallont/
    name: Plant Gall Ontology
    prefix: GALLONT
  agroportal:
    contact:
      email: adeans@psu.edu
      name: Andy Deans
    description: Ontology of plant gall phenotypes. Plant galls are novel plant structures,
      generated by plants in response to biotic stressors. This ontology is used to
      annotate gall phenotypes (e.g., their colors, textures, sizes, locations on
      the plant) in a semantic way, in order to facilitate discoveries about the genetic
      and physiologic mechanisms responsible for such phenotypes. The ontology can
      also be used as a controlled vocabulary for natural language descriptions of
      plant galls., None
    example_uri: http://purl.obolibrary.org/obo/GALLONT_0000008
    homepage: https://adeans.github.io/gallont/
    license: CC0-1.0
    name: Plant Gall Ontology
    prefix: GALLONT
    publications:
    - https://doi.org/10.3897/arphapreprints.e128953
    repository: https://github.com/adeans/gallont
    version: '2024-04-19'
  bioportal:
    contact:
      email: adeans@psu.edu
      name: Andy Deans
    description: Ontology of plant gall phenotypes. Plant galls are novel plant structures,
      generated by plants in response to biotic stressors. This ontology is used to
      annotate gall phenotypes (e.g., their colors, textures, sizes, locations on
      the plant) in a semantic way, in order to facilitate discoveries about the genetic
      and physiologic mechanisms responsible for such phenotypes. The ontology can
      also be used as a controlled vocabulary for natural language descriptions of
      plant galls.
    homepage: https://adeans.github.io/gallont/
    name: Plant Gall Ontology
    prefix: GALLONT
    version: '2024-04-19'
  download_json: https://github.com/adeans/gallont/raw/refs/heads/main/gallont.json
  example: '0000001'
  mappings:
    aberowl: GALLONT
    agroportal: GALLONT
    bioportal: GALLONT
    obofoundry: gallont
    ols: gallont
    ontobee: GALLONT
  obofoundry:
    contact: adeans@psu.edu
    contact.github: adeans
    contact.label: Andy Deans
    contact.orcid: 0000-0002-2119-4663
    depends_on:
    - caro
    - flopo
    - ncbitaxon
    - obi
    - pato
    - po
    - poro
    - ro
    deprecated: false
    description: Ontology of plant gall phenotypes. Plant galls are novel plant structures,
      generated by plants in response to biotic stressors. This ontology is used to
      annotate gall phenotypes (e.g., their colors, textures, sizes, locations on
      the plant) in a semantic way, in order to facilitate discoveries about the genetic
      and physiologic mechanisms responsible for such phenotypes. The ontology can
      also be used as a controlled vocabulary for natural language descriptions of
      plant galls.
    domain: phenotype
    download.json: http://purl.obolibrary.org/obo/gallont.json
    download.obo: http://purl.obolibrary.org/obo/gallont.obo
    download.owl: http://purl.obolibrary.org/obo/gallont.owl
    homepage: https://adeans.github.io/gallont/
    license: CC0 1.0
    license.url: https://creativecommons.org/publicdomain/zero/1.0/
    name: Plant Gall Ontology
    preferredPrefix: GALLONT
    prefix: gallont
    repository: https://github.com/adeans/gallont
  ols:
    description: Ontology of plant gall phenotypes. Plant galls are novel plant structures,
      generated by plants in response to biotic stressors. This ontology is used to
      annotate gall phenotypes (e.g., their colors, textures, sizes, locations on
      the plant) in a semantic way, in order to facilitate discoveries about the genetic
      and physiologic mechanisms responsible for such phenotypes. The ontology can
      also be used as a controlled vocabulary for natural language descriptions of
      plant galls.
    download_owl: http://purl.obolibrary.org/obo/gallont.owl
    homepage: https://adeans.github.io/gallont/
    name: Plant Gall Ontology
    prefix: gallont
    tracker: https://github.com/adeans/gallont/issues
    version: '2024-04-19'
    version.iri: http://purl.obolibrary.org/obo/gallont/releases/2024-04-19/gallont.owl
  ontobee:
    library: Library
    name: Plant Gall Ontology
    prefix: GALLONT
  pattern: ^\d{7}$
  prefix: gallont
gard:
  contact:
    email: eric.sid@nih.gov
    github: ericsid
    name: Eric Sid
    orcid: 0000-0001-7697-3026
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: Database of rare diseases and related terms, including symptoms, healthcare
    resources, and organizations supporting research of the disease.
  domain: disease
  example: '6038'
  homepage: https://rarediseases.info.nih.gov/diseases
  keywords:
  - condition
  - disease
  - symptom
  logo: https://rarediseases.info.nih.gov/assets/GARD_Logo_Mobile.svg
  mappings:
    wikidata: P4317
  name: Genetic and Rare Diseases Information Center
  pattern: ^\d+$
  prefix: gard
  publications:
  - doi: 10.1080/02763869.2022.2131143
    pmc: null
    pubmed: '36394913'
    title: Genetic and Rare Diseases Information Center (GARD)
    year: 2022
  - doi: 10.3233/trd-170011
    pmc: PMC5685198
    pubmed: '29152459'
    title: Marking 15 years of the Genetic and Rare Diseases Information Center
    year: 2017
  synonyms:
  - GARD
  - Genetic and Rare Diseases Information Center
  uri_format: https://rarediseases.info.nih.gov/diseases/$1/index
  wikidata:
    description: identifier for a rare disease in the United States National Institutes
      of Health's Genetic and Rare Diseases (GARD) Information Center database
    example:
    - '1062'
    - '10716'
    - '12136'
    homepage: https://rarediseases.info.nih.gov/diseases/
    name: GARD rare disease ID
    pattern: ^[1-9]\d*$
    prefix: P4317
    uri_format: https://rarediseases.info.nih.gov/diseases/$1/index
gateway:
  mappings:
    miriam: gateway
  miriam:
    deprecated: false
    description: The Health Data Research Innovation Gateway (the 'Gateway') provides
      a common entry point to discover and enquire about access to UK health datasets
      for research and innovation. It provides detailed information about the datasets,
      which are held by members of the UK Health Data Research Alliance, such as a
      description, size of the population, and the legal basis for access.
    homepage: https://www.hdruk.ac.uk
    id: 00000796
    name: gateway
    namespaceEmbeddedInLui: false
    pattern: ^[a-fA-F0-9]{8}-[a-fA-F0-9]{4}-[a-fA-F0-9]{4}-[a-fA-F0-9]{4}-[a-fA-F0-9]{12}$
    prefix: gateway
    sampleId: fd8d0743-344a-4758-bb97-f8ad84a37357
    uri_format: https://web.www.healthdatagateway.org/dataset/$1
  name: Health Data Research Innovation Gateway
  prefix: gateway
gaz:
  aberowl:
    description: Gazetteer
    download_obo: http://aber-owl.net/media/ontologies/GAZ/14/gaz.obo
    homepage: http://gensc.org/gc_wiki/index.php/GAZ_Project
    name: Gazetteer
    prefix: GAZ
    version: '$Revision: 1.512 $'
  biocontext:
    prefix: GAZ
  bioportal:
    contact:
      email: lschriml@som.umaryland.edu
      name: Lynne Schriml
    description: GAZ is a large, ontologically-oriented resource listing place names
      which can be treated as instances of environments.
    homepage: http://environmentontology.github.io/gaz/
    name: Gazetteer
    prefix: GAZ
    version: '$Revision: 1.512 $'
  download_obo: http://purl.obolibrary.org/obo/gaz.obo
  example: '00620027'
  fairsharing:
    abbreviation: GAZ
    description: A controlled vocabulary following ontological rules that describes
      named geographical locations. GAZ represents a first step towards an open source
      gazetteer, constructed on ontological principles, that describes places and
      place names and the relations between them.
    domains:
    - Geographic location
    homepage: http://environmentontology.github.io/gaz/
    license: CC0-1.0
    name: Gazetteer
    prefix: FAIRsharing.wkdjpb
    subjects:
    - Environmental Science
  mappings:
    aberowl: GAZ
    biocontext: GAZ
    bioportal: GAZ
    fairsharing: FAIRsharing.wkdjpb
    obofoundry: gaz
    ols: gaz
    ontobee: GAZ
    wikidata: P6778
    wikidata.entity: Q81661634
  obofoundry:
    appears_in:
    - scdo
    contact: lschriml@som.umaryland.edu
    contact.github: lschriml
    contact.label: Lynn Schriml
    contact.orcid: 0000-0001-8910-9851
    deprecated: false
    description: A gazetteer constructed on ontological principles. The countries
      are actively maintained.
    domain: environment
    download.obo: http://purl.obolibrary.org/obo/gaz.obo
    download.owl: http://purl.obolibrary.org/obo/gaz.owl
    homepage: http://environmentontology.github.io/gaz/
    license: CC0 1.0
    license.url: https://creativecommons.org/publicdomain/zero/1.0/
    name: Gazetteer
    preferredPrefix: GAZ
    prefix: gaz
    repository: https://github.com/EnvironmentOntology/gaz
  ols:
    description: A gazetteer constructed on ontological principles. The countries
      are actively maintained.
    download_owl: http://purl.obolibrary.org/obo/gaz.owl
    homepage: http://environmentontology.github.io/gaz/
    name: Gazetteer
    prefix: gaz
    tracker: https://github.com/EnvironmentOntology/gaz/issues
  ontobee:
    library: Library
    name: Gazetteer
    prefix: GAZ
  pattern: ^\d{8}$
  prefix: gaz
  wikidata:
    description: identifier from the Open Bio Ontologies Gazetteer (GAZ) (without
      prefix)
    example:
    - '00000005'
    - '00001460'
    - 00008990
    homepage: http://obofoundry.org/ontology/gaz
    name: OBO Gazetteer ID
    pattern: ^\d{8}$
    prefix: P6778
    uri_format: http://purl.obolibrary.org/obo/GAZ_$1
    uri_format_rdf: http://purl.obolibrary.org/obo/GAZ_$1
gbif:
  contact:
    email: timrobertson100@gmail.com
    github: timrobertson100
    name: Tim Robertson
    orcid: 0000-0001-6215-3617
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: "Database of living organisms, taxonomic. \n The GBIF—the Global Biodiversity\
    \ Information Facility—is international network and data infrastructure funded\
    \ by the world's governments and aimed at providing anyone, anywhere, open access\
    \ to data about all types of life on Earth."
  example: '4238'
  fairsharing:
    abbreviation: GBIF.org
    description: "GBIF—the Global Biodiversity Information Facility—is an international\
      \ network and data infrastructure funded by the world's governments and aimed\
      \ at providing anyone, anywhere, open access to data about all types of life\
      \ on Earth.\n\nStrictly speaking, GBIF is not a data repository. Rather, GBIF\
      \ indexes thousands of datasets through a distributed infrastructure involving\
      \ more than 100 formal participants that supports hundreds of data-publishing\
      \ institutions worldwide. GBIF.org makes the FAIR and open data discoverable\
      \ and citable, assigning each download a DOI and storing it for an extended\
      \ period of time. More than three peer-reviewed research articles make use of\
      \ data from the GBIF network every day, in studies spanning the impacts of climate\
      \ change, the spread of pests and diseases, priority areas for conservation\
      \ and food security. \n\nTo share data with GBIF, follow this quick guide: http://www.gbif.org/publishing-data/quick-guide.\
      \ To deposit or host data, we suggest using one of the trusted data hosting\
      \ centres (DHC) listed in FAIRsharing.org that uses GBIF's IPT (Integrated Publishing\
      \ Toolkit) software. The DHC provides data publishers with a hosted IPT account\
      \ enabling them to manage and publish datasets through GBIF.org."
    homepage: https://www.gbif.org
    license: CC0-1.0
    name: GBIF.org
    prefix: FAIRsharing.zv11j3
    publications:
    - doi: 10.1371/journal.pone.0102623
      pubmed_id: 25099149
      title: 'The GBIF integrated publishing toolkit: facilitating the efficient publishing
        of biodiversity data on the internet.'
    repository: https://github.com/gbif/
    subjects:
    - Metagenomics
    - Bioinformatics
    - Taxonomy
    - Marine Biology
    - Biodiversity
    - Natural Science
    - Natural History
    twitter: GBIF
  homepage: https://www.gbif.org/species
  integbio:
    alt_name: Global Biodiversity Information Facility free and open access to biodiversity
      data
    description: "GBIF (Global Biodiversity Information Facility) is a database of\
      \ information on Biodiversity and its global effect.\nA network of countries\
      \ across the globe has access to, and participates in supplying, information\
      \ to the database. \nThere are 38 countries that support the facility financially\
      \ and are therefore members of the voting governing board.\nThe database contains\
      \ 396,026,747 indexed records and 10,004 sets of data provided by 464 publishers.\n\
      It is imperative that the users of any data obtained by means of the GBIF Portal\
      \ will always give credit to the original data publishers. \nA keyword search\
      \ option is provided whereby the facility can be searched for information on\
      \ a specific group of organisms of a specific country or as displayed in a specific\
      \ set of data."
    fairsharing: biodbcore-000635
    homepage: http://www.gbif.org/
    information_keywords:
    - Ontology/Terminology/Nomenclature
    - Repository
    maintainer: GBIF Secretariat
    name: GBIF
    prefix: nbdc00069
    status: Active
    target_keywords:
    - Organism
  mappings:
    fairsharing: FAIRsharing.zv11j3
    integbio: nbdc00069
    re3data: r3d100000039
    wikidata: P846
  name: Global Biodiversity Information Facility
  pattern: ^\d+$
  prefix: gbif
  publications:
  - doi: 10.1371/journal.pone.0102623
    pmc: PMC4123864
    pubmed: '25099149'
    title: 'The GBIF integrated publishing toolkit: facilitating the efficient publishing
      of biodiversity data on the internet'
    year: 2014
  re3data:
    description: 'GBIF is an international organisation that is working to make the
      world''s biodiversity data accessible everywhere in the world. GBIF and its
      many partners work to mobilize the data, and to improve search mechanisms, data
      and metadata standards, web services, and the other components of an Internet-based
      information infrastructure for biodiversity.

      GBIF makes available data that are shared by hundreds of data publishers from
      around the world. These data are shared according to the GBIF Data Use Agreement,
      which includes the provision that users of any data accessed through or retrieved
      via the GBIF Portal will always give credit to the original data publishers.'
    doi: 10.17616/R3J014
    homepage: https://www.gbif.org/
    name: Global Biodiversity Information Facility
    prefix: r3d100000039
    synonyms:
    - Data index of the Global Biodiversity Information Facility
    - GBIF.org
  twitter: GBIF
  uri_format: https://www.gbif.org/species/$1
  wikidata:
    description: taxon identifier in GBIF
    example:
    - '1948418'
    - '3239598'
    - '4656467'
    - '5963040'
    name: GBIF taxon ID
    pattern: ^([1-9]\d{0,8}|)$
    prefix: P846
    uri_format: https://www.gbif.org/species/$1
gcst:
  mappings:
    miriam: gcst
    n2t: gcst
  miriam:
    deprecated: false
    description: The GWAS Catalog provides a consistent, searchable, visualisable
      and freely available database of published SNP-trait associations, which can
      be easily integrated with other resources, and is accessed by scientists, clinicians
      and other users worldwide.
    homepage: https://www.ebi.ac.uk
    id: '00000715'
    name: GWAS Catalog
    namespaceEmbeddedInLui: false
    pattern: ^GCST\d{6}\d*$
    prefix: gcst
    sampleId: GCST000035
    uri_format: https://www.ebi.ac.uk/gwas/studies/$1
  n2t:
    description: The GWAS Catalog provides a consistent, searchable, visualisable
      and freely available database of published SNP-trait associations, which can
      be easily integrated with other resources, and is accessed by scientists, clinicians
      and other users worldwide.
    example: GCST000035
    homepage: https://www.ebi.ac.uk/gwas/studies
    name: GWAS Catalog
    namespaceEmbeddedInLui: false
    pattern: ^GCST\d{6}$
    prefix: gcst
    uri_format: https://www.ebi.ac.uk/gwas/studies/$1
  owners:
  - name: European Bioinformatics Institute
    partnered: false
    ror: 02catss52
    wikidata: null
  prefix: gcst
gdc:
  biocontext:
    prefix: GDC
  mappings:
    biocontext: GDC
    miriam: gdc
    n2t: gdc
  miriam:
    deprecated: false
    description: The GDC Data Portal is a robust data-driven platform that allows
      cancer researchers and bioinformaticians to search and download cancer data
      for analysis.
    homepage: https://gdc.cancer.gov
    id: '00000604'
    name: Genomic Data Commons Data Portal
    namespaceEmbeddedInLui: false
    pattern: ^[a-z0-9]{8}-[a-z0-9]{4}-[a-z0-9]{4}-[a-z0-9]{4}-[a-z0-9]{12}$
    prefix: gdc
    sampleId: ae8c77fe-e6c8-44d5-8265-4a38c637bbef
    uri_format: https://portal.gdc.cancer.gov/cases/$1
  n2t:
    description: The GDC Data Portal is a robust data-driven platform that allows
      cancer researchers and bioinformaticians to search and download cancer data
      for analysis.
    example: ae8c77fe-e6c8-44d5-8265-4a38c637bbef
    homepage: https://gdc.cancer.gov
    name: Genomic Data Commons
    namespaceEmbeddedInLui: false
    pattern: ^[a-z0-9]{8}-[a-z0-9]{4}-[a-z0-9]{4}-[a-z0-9]{4}-[a-z0-9]{12}$
    prefix: gdc
    uri_format: https://portal.gdc.cancer.gov/cases/$1
  prefix: gdc
gdo:
  contact:
    email: mclarkson@uky.edu
    github: null
    name: Melissa D Clarkson
    orcid: 0000-0001-9979-176X
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: The Graphic Descriptor Ontology (GDO) is intended for use in describing
    graphics that represent the form of objects. It uses the language of visual communication,
    illustration, and technical drawing. The GDO is rooted in the Basic Formal Ontology
    (BFO) and uses several classes from the Information Entity Ontology of the Common
    Core Ontologies as a mid-level ontology. [from https://gdo.endlessforms.info/about]
  download_owl: https://github.com/endlessforms-info/GDO-GDOA/raw/refs/heads/main/gdoa.owl
  example: '0000016'
  homepage: https://gdo.endlessforms.info
  name: Graphic Descriptor Ontology
  prefix: gdo
  repository: https://github.com/endlessforms-info/GDO-GDOA
  uri_format: https://gdo.endlessforms.info/view/classes?uuid=GDO_$1
gdsc:
  cellosaurus:
    category: Chemistry resources
    homepage: https://www.cancerrxgene.org
    name: Genomics of Drug Sensitivity in Cancer Project
    prefix: GDSC
    uri_format: https://www.cancerrxgene.org/translation/CellLine/$1
  mappings:
    cellosaurus: GDSC
    miriam: gdsc
    n2t: gdsc
  miriam:
    deprecated: false
    description: The Genomics of Drug Sensitivity in Cancer (GDSC) database is designed
      to facilitate an increased understanding of the molecular features that influence
      drug response in cancer cells and which will enable the design of improved cancer
      therapies.
    homepage: https://www.cancerrxgene.org
    id: 00000678
    name: Genomics of Drug Sensitivity in Cancer
    namespaceEmbeddedInLui: false
    pattern: ^[0-9]+$
    prefix: gdsc
    sampleId: '1242'
    uri_format: https://www.cancerrxgene.org/translation/Drug/$1
  n2t:
    description: The Genomics of Drug Sensitivity in Cancer (GDSC) database is designed
      to facilitate an increased understanding of the molecular features that influence
      drug response in cancer cells and which will enable the design of improved cancer
      therapies.
    example: '1242'
    homepage: https://www.cancerrxgene.org
    name: Genomics of Drug Sensitivity in Cancer
    namespaceEmbeddedInLui: false
    pattern: ^[0-9]+$
    prefix: gdsc
    uri_format: https://www.cancerrxgene.org/translation/Drug/$1
  prefix: gdsc
gear:
  contact:
    email: jorvis@gmail.com
    github: jorvis
    name: Joshua Orvis
    orcid: 0000-0002-5705-5710
  contributor:
    email: jorvis@gmail.com
    github: jorvis
    name: Joshua Orvis
    orcid: 0000-0002-5705-5710
  description: The gEAR portal is a website for visualization and analysis of multi-omic
    data both in public and private domains.
  example: d.a59037e8
  example_extras:
  - p.bfd178f5
  github_request_issue: 728
  homepage: https://umgear.org
  license: AGPL-3.0-only
  name: Gene Expression Analysis Resource
  pattern: ^[dp]\.[a-z0-9]{8}$
  prefix: gear
  repository: https://github.com/IGS/gEAR
  reviewer:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  uri_format: https://umgear.org/p?id=$1
gecko:
  aberowl:
    description: An ontology to represent genomics cohort attributes
    download_owl: http://aber-owl.net/media/ontologies/GECKO/10/gecko.owl
    homepage: https://github.com/IHCC-cohorts/GECKO
    name: Genomics Cohorts Knowledge Ontology
    prefix: GECKO
  bioportal:
    contact:
      email: rbca.jackson@gmail.com
      name: Rebecca Jackson
    description: An ontology to represent genomics cohort attributes.
    homepage: https://github.com/IHCC-cohorts/GECKO
    name: Genomics Cohorts Knowledge Ontology
    prefix: GECKO
  example: '0000044'
  fairsharing:
    abbreviation: GECKO
    contact:
      email: mcourtot@gmail.com
      name: Mélanie Courtot
      orcid: 0000-0002-9551-6370
    description: GECKO is an ontology to represent genomics cohort attributes. The
      GECKO is maintained by the CINECA project, and standardises attributes commonly
      used for genomics cohort description as well as individual-level data items.
    domains:
    - Experimental measurement
    - Biospecimen
    homepage: https://github.com/IHCC-cohorts/GECKO
    license: CC-BY-4.0
    name: Genomics Cohorts Knowledge Ontology
    prefix: FAIRsharing.3da56b
    subjects:
    - Life Science
    - Statistics
    - Genomics
  mappings:
    aberowl: GECKO
    bioportal: GECKO
    fairsharing: FAIRsharing.3da56b
    obofoundry: gecko
    ols: gecko
    ontobee: GECKO
    wikidata.entity: Q113012662
  obofoundry:
    contact: rbca.jackson@gmail.com
    contact.github: beckyjackson
    contact.label: Rebecca Jackson
    contact.orcid: 0000-0003-4871-5569
    deprecated: false
    description: An ontology to represent genomics cohort attributes
    domain: organisms
    download.owl: http://purl.obolibrary.org/obo/gecko.owl
    homepage: https://github.com/IHCC-cohorts/GECKO
    license: CC BY 4.0
    license.url: https://creativecommons.org/licenses/by/4.0/
    name: Genomics Cohorts Knowledge Ontology
    preferredPrefix: GECKO
    prefix: gecko
    repository: https://github.com/IHCC-cohorts/GECKO
  ols:
    description: An ontology to represent genomics cohort attributes.
    download_owl: http://purl.obolibrary.org/obo/gecko.owl
    homepage: https://github.com/IHCC-cohorts/GECKO
    name: Genomics Cohorts Knowledge Ontology
    prefix: gecko
    tracker: https://github.com/IHCC-cohorts/GECKO/issues
    version: '2021-01-18'
    version.iri: http://purl.obolibrary.org/obo/gecko/releases/2021-01-18/gecko.owl
  ontobee:
    library: Library
    name: Genomics Cohorts Knowledge Ontology
    prefix: GECKO
  pattern: ^\d{7}$
  prefix: gecko
  uri_format: http://purl.obolibrary.org/obo/GECKO_$1
gemet.concept:
  agroportal:
    contact:
      email: helpdesk@eionet.europa.eu
      name: Eionet Helpdesk
    description: The basic idea for the development of GEMET was to use the best of
      the presently available excellent multilingual thesauri, in order to save time,
      energy and funds. GEMET was conceived as a “general” thesaurus, aimed to define
      a common general language, a core of general terminology for the environment.
      Specific thesauri and descriptor systems (e.g. on Nature Conservation, on Wastes,
      on Energy, etc.) have been excluded from the first step of development of the
      thesaurus and have been taken into account only for their structure and upper
      level terminology.
    example_uri: http://www.eionet.europa.eu/gemet/concept/5580
    homepage: http://www.eionet.europa.eu/gemet/en/about/
    license: http://creativecommons.org/licenses/by/2.5/dk
    name: GEneral Multilingual Environmental Thesaurus
    prefix: GEMET
    publications:
    - http://www.eionet.europa.eu/gemet/en/about/#chapter-VII
    version: 4.2.3
  bartoc:
    abbreviation: GEMET
    description: 'The basic idea for the development of GEMET was to use the best
      of the presently available excellent multilingual thesauri, in order to save
      time, energy and funds. GEMET was conceived as a ''general'' thesaurus, aimed
      to define a common general language, a core of general terminology for the environment.
      Specific thesauri and descriptor systems (e.g. on Nature Conservation, on Wastes,
      on Energy, etc.) have been excluded from the first step of development of the
      thesaurus and have been taken into account only for their structure and upper
      level terminology. The merging has been performed both on conceptual and formal
      basis. Coinciding concepts in the different thesauri have been identified and
      scored. Like in other multilingual thesauri, e. g. Infoterra EnVoc, a neutral
      alphanumerical notation allows the identification of a concept independently
      on the user''s language.


      The links with the original thesauri are ensured by the respective identifiers
      or code notations. Following the identification of the coinciding concepts,
      a selection was made by the experts of the National Focal Points of the organisations
      involved. The resulting 6.562 terms have been arranged in a classification scheme
      made of 3 super-groups, 30 groups plus 5 accessory, instrumental groups. Each
      descriptor has been arranged in a hierarchical structure headed by a Top Term.
      The level of poly-hierarchy, i.e. the allocation of a descriptor to more than
      one group, has been kept to a minimum. Further, to allow a thematic retrieval
      of terms thematically related but scattered in different groups, a set of 40
      themes have been agreed upon with the EEA and each descriptor has been assigned
      to as many themes as necessary. Thus, the user can access the thesaurus through
      the group- hierarchical list, through the thematic list or through the alphabetical
      list. As a complement to the hierarchical ''vertical'' relations, an exhaustive
      series of strong ''horizontal'' relations between terms (RT, Related Terms)
      have been introduced. A progressive Line Number has been assigned to each descriptor
      of the systematic list, in order to help the user of the lists to identify the
      descriptor in the different lists. The Line Number is merely a neutral identifier
      for the present version. The GEMET size, formerly figured at about 200000 descriptors,
      rose to more than 5.000 in the course of merging, due to the limited overlapping
      between the different thesauri, to constraints of the selection work carried
      out by the parental organisations and to a few new additions, mainly from CDS
      indexing work. The present version 2001* of GEMET is the result of a close collaboration
      between CNR and UBA under contract and supervision of the ETC/CDS. It presents
      5.298 descriptors, including 109 Top Terms, and 1.264 synonyms in English. The
      5.524 terms belonging to the parental thesauri and not included in GEMET, constitute
      an accessory alphabetical list of free terms. GEMET has been developed as an
      indexing, retrieval and control tool for the European Topic Centre on Catalogue
      of Data Sources (ETC/CDS) and the European Environment Agency (EEA), Copenhagen.'
    homepage: http://www.eionet.europa.eu/gemet/
    license: CC-BY-3.0
    name: General Multilingual Environmental Thesaurus
    prefix: '16'
    wikidata_database: Q1485161
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: The European Environment Information and Observation Network (Eionet)
    is a partnership network of the European Environment Agency (EEA) and its 38 member
    and cooperating countries. The EEA is responsible for developing Eionet and coordinating
    its activities together with National Focal Points (NFPs) in the countries. This
    terminology supports those efforts.
  example: '627'
  fairsharing:
    abbreviation: GEMET
    description: The GEneral Multilingual Environmental Thesaurus (GEMET) was created
      as a “general” environmental thesaurus, aimed to define a common general language
      with a core of general terminology for the environment. It is the reference
      vocabulary of the European Environment Agency (EEA) and its Network (Eionet).
    homepage: https://www.eionet.europa.eu/gemet/en/themes/
    name: GEneral Multilingual Environmental Thesaurus
    prefix: FAIRsharing.9091d9
    subjects:
    - Environmental Science
    - Biodiversity
    - Ecology
  homepage: https://www.eionet.europa.eu/gemet/en/themes/
  license: CC-BY-4.0
  mappings:
    agroportal: GEMET
    bartoc: '16'
    fairsharing: FAIRsharing.9091d9
    tib: gemet
    wikidata.entity: Q1485161
  name: General Multilingual Environmental Thesaurus Concept
  part_of_database: gemet
  pattern: ^\d+$
  prefix: gemet.concept
  providers:
  - code: gemet.multilingual
    description: An alternate URI that doesn't have the language encoded in it
    example: null
    first_party: null
    homepage: https://www.eionet.europa.eu/gemet
    name: GEMET Multilingual
    publications: null
    status: null
    uri_format: http://www.eionet.europa.eu/gemet/concept/$1
  rdf_uri_format: ' http://www.eionet.europa.eu/gemet/concept/$1'
  tib:
    description: GEMET, the GEneral Multilingual Environmental Thesaurus, has been
      developed since 1995 as a tool for indexing, retrieval, and control for the
      European Environment Agency. It was created to utilize the best available multilingual
      thesauri, saving time and resources. GEMET serves as a "general" thesaurus,
      aiming to establish a common core of environmental terminology.
    homepage: https://www.eionet.europa.eu/gemet/en/themes/
    keywords:
    - ESS
    - earth sciences
    name: GEMET - General Multilingual Environmental Thesaurus
    prefix: gemet
    uri_format: http://www.eionet.europa.eu/gemet/concept/$1
  uri_format: https://www.eionet.europa.eu/gemet/en/concept/$1
gemet.group:
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: Groups listed in GEMET
  example: '893'
  homepage: https://www.eionet.europa.eu/gemet/en/groups/
  license: CC-BY-4.0
  name: General Multilingual Environmental Thesaurus Group
  part_of_database: gemet
  pattern: ^\d+$
  prefix: gemet.group
  rdf_uri_format: http://www.eionet.europa.eu/gemet/group/$1
  uri_format: https://www.eionet.europa.eu/gemet/en/group/$1
gemet.relation:
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: Relations in GEMET
  example: '6237'
  homepage: https://www.eionet.europa.eu/gemet/en
  license: CC-BY-4.0
  name: General Multilingual Environmental Thesaurus Relation
  part_of_database: gemet
  pattern: ^\d+$
  prefix: gemet.relation
  uri_format: https://www.eionet.europa.eu/gemet/en/relations/$1
gemet.theme:
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: Themes listed in GEMET
  example: '4'
  homepage: https://www.eionet.europa.eu/gemet/en/themes
  license: CC-BY-4.0
  name: General Multilingual Environmental Thesaurus Theme
  part_of_database: gemet
  pattern: ^\d+$
  prefix: gemet.theme
  rdf_uri_format: http://www.eionet.europa.eu/gemet/theme/$1
  uri_format: https://www.eionet.europa.eu/gemet/en/theme/$1
genatlas:
  biocontext:
    prefix: GENATLAS
  fairsharing:
    abbreviation: GenAtlas
    description: GenAtlas is a database containing information on human genes, markers
      and phenotypes.
    homepage: http://www.genatlas.org/
    name: GenAtlas
    prefix: FAIRsharing.pmg2vd
    publications:
    - doi: 10.1016/s0764-4469(99)80021-3
      pubmed_id: 9835018
      title: Genatlas database, genes and development defects
    - doi: 10.1006/mgme.1999.2867
      pubmed_id: 10444337
      title: 'Human genes involved in chromatin remodeling in transcription initiation,
        and associated diseases: An overview using the GENAtlas database'
    subjects:
    - Life Science
  integbio:
    description: "Genatlas is a collection of information on gene mapping and the\
      \ diseases they are genetically related to. \nThe data is obtained by scanning\
      \ available literature on a regular basis.\nThis database contains information\
      \ on 22,723 genes, 5,065 phenotypes and 113,755 citations.\nNew information\
      \ is available immediately after the site is updated and this is done daily.\n\
      Several search options are available. \nA search for all genes involved with\
      \ one disease, called a phenotype search, reveals information pertaining to\
      \ chromosomal diseases.\nA full search of the gene Database, on the basis of\
      \ DNA characteristics, RNA characteristics, protein characteristics, expression,\
      \ and/or pathology gives information about all diseases related to one gene.\n\
      A search of the Citation Database leads to a list of all citations about a particular\
      \ gene or disease."
    fairsharing: biodbcore-000377
    homepage: http://genatlas.medecine.univ-paris5.fr/
    information_keywords:
    - Phenotype
    - Sequence
    - Expression
    - Bibliography/Documents
    maintainer: Universite Rene Descartes
    name: GENATLAS
    prefix: nbdc00275
    status: Active
    target_keywords:
    - Genome/Gene
    - RNA
    - Protein
    - Health/Disease
  mappings:
    biocontext: GENATLAS
    fairsharing: FAIRsharing.pmg2vd
    integbio: nbdc00275
    miriam: genatlas
    n2t: genatlas
    prefixcommons: genatlas
    uniprot: DB-0027
  miriam:
    deprecated: false
    description: GenAtlas is a database containing information on human genes, markers
      and phenotypes.
    homepage: http://genatlas.medecine.univ-paris5.fr/
    id: 00000208
    name: Genatlas
    namespaceEmbeddedInLui: false
    pattern: ^\w+$
    prefix: genatlas
    sampleId: HBB
    uri_format: http://genatlas.medecine.univ-paris5.fr/fiche.php?symbol=$1
  n2t:
    description: GenAtlas is a database containing information on human genes, markers
      and phenotypes.
    example: HBB
    homepage: http://genatlas.medecine.univ-paris5.fr/
    name: Genatlas at Paris Descartes University
    namespaceEmbeddedInLui: false
    pattern: ^\w+$
    prefix: genatlas
    uri_format: http://genatlas.medecine.univ-paris5.fr/fiche.php?symbol=$1
  prefix: genatlas
  prefixcommons:
    description: GenAtlas is a database containing information on human genes, markers
      and phenotypes.
    example: HBB
    homepage: http://www.genatlas.org/
    keywords:
    - disorder
    - gene
    - human
    name: 'GenAtlas: human gene database'
    pattern: ^\w+$
    prefix: genatlas
    pubmed_ids:
    - '9835018'
    uri_format: http://genatlas.medecine.univ-paris5.fr/fiche.php?symbol=$1
  publications:
  - doi: 10.1006/mgme.1999.2867
    pmc: null
    pubmed: '10444337'
    title: 'Human genes involved in chromatin remodeling in transcription initiation,
      and associated diseases: An overview using the GENATLAS database'
    year: 1999
  - doi: 10.1016/s0764-4469(99)80021-3
    pmc: null
    pubmed: '9835018'
    title: Genatlas database, genes and development defects
    year: 1998
  uniprot:
    abbreviation: GenAtlas
    category: Organism-specific databases
    homepage: http://genatlas.medecine.univ-paris5.fr/
    name: GenAtlas
    prefix: DB-0027
    publications:
    - doi: 10.1016/s0764-4469(99)80021-3
      pubmed: '9835018'
    uri_format: http://genatlas.medecine.univ-paris5.fr/fiche.php?symbol=$1
genbank:
  biocontext:
    prefix: GenBank
    uri_format: http://www.ncbi.nlm.nih.gov/nuccore/$1
  cheminf:
    description: []
    name: GenBank Nucleotide Identifier
    obsolete: false
    prefix: '000304'
  contact:
    email: nawrocke@ncbi.nlm.nih.gov
    github: nawrockie
    name: Eric P. Nawrocki
    orcid: 0000-0002-2497-3427
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: GenBank ® is the NIH genetic sequence database, an annotated collection
    of all publicly available DNA sequences (Nucleic Acids Research, 2013 Jan;41(D1):D36-42).
  edam:
    description: Accession number of an entry from the GenBank sequence database.
    name: GenBank
    obsolete: false
    prefix: '2292'
  example: U49845
  fairsharing:
    abbreviation: GenBank
    description: 'GenBank ® is the NIH genetic sequence database of annotated collections
      of all publicly available DNA sequences. GenBank is part of an International
      Nucleotide Sequence Database Collaboration, which comprises the DNA DataBank
      of Japan (DDBJ), the European Nucleotide Archive (ENA), and GenBank at NCBI.
      The GenBank database is designed to provide and encourage access within the
      scientific community to the most up-to-date and comprehensive DNA sequence information,
      and release available versioned collections every two months from the ftp site.
      As part of the International Nucleotide Sequence Database Collaboration (INSDC),
      a long-standing foundational initiative (operating between DDBJ, EMBL-EBI and
      NCBI), the INSDC covers the spectrum of data raw reads, through alignments and
      assemblies to functional annotation, enriched with contextual information relating
      to samples and experimental configurations. GenBank data submission types include:  mRNA
      sequences, Prokaryotic genes, Eukaryotic genes, rRNA and/or ITS, viral sequences,
      transposon or insertion sequences, microsatellite sequences, pseudogenes, cloning
      vectors, phylogenetic or population sets, and non-coding RNAs.

      '
    homepage: https://www.ncbi.nlm.nih.gov/genbank/
    license: https://www.insdc.org/policy
    name: GenBank Nucleotide Sequence Database
    prefix: FAIRsharing.9kahy4
    publications:
    - doi: 10.1093/nar/gkr1202
      pubmed_id: 22144687
      title: GenBank.
    - doi: 10.1093/nar/gkq1079
      pubmed_id: 21071399
      title: GenBank.
    - doi: 10.1093/nar/gkm929
      pubmed_id: 18073190
      title: GenBank.
    - doi: 10.1093/nar/gkn723
      pubmed_id: 18940867
      title: GenBank.
    - doi: 10.1093/nar/gks1195
      pubmed_id: 23193287
      title: GenBank.
    - doi: 10.1093/nar/gkt1030
      pubmed_id: 24217914
      title: GenBank.
    - doi: 10.1093/nar/gkx1094
      pubmed_id: 29140468
      title: GenBank
    - doi: 10.1093/nar/gkz956
      pubmed_id: 31665464
      title: GenBank.
    - doi: 10.1093/nar/gky989
      pubmed_id: 30365038
      title: GenBank.
    - doi: 10.1093/nar/gkw1070
      pubmed_id: 27899564
      title: GenBank.
    - doi: 10.1093/nar/gkv1276
      pubmed_id: 26590407
      title: GenBank.
    - doi: 10.1093/nar/gku1216
      pubmed_id: 25414350
      title: GenBank.
    - doi: 10.1186/s12859-020-3537-3
      pubmed_id: null
      title: 'VADR: validation and annotation of virus sequence submissions to GenBank'
    - doi: 10.1093/nar/gks1195
      pubmed_id: 23193287
      title: GenBank
    subjects:
    - Functional Genomics
    - Metagenomics
    - Genomics
    - Bioinformatics
    - Data Management
    - Virology
    - Transcriptomics
    - Epidemiology
  go:
    description: The NIH genetic sequence database, an annotated collection of all
      publicly available DNA sequences.
    homepage: http://www.ncbi.nlm.nih.gov/Genbank/
    name: GenBank
    prefix: GenBank
    synonyms:
    - GB
  homepage: https://www.ncbi.nlm.nih.gov/genbank/
  integbio:
    description: This is a public database of DNA sequences with annotations. It is
      a part of the International Nucleotide Sequence Database Collaboration, and
      cooperates with the DNA DataBank of Japan (DDBJ) as well as the European Molecular
      Biology Laboratory (EMBL).
    fairsharing: biodbcore-000001
    homepage: http://www.ncbi.nlm.nih.gov/genbank/
    information_keywords:
    - Sequence
    - Repository
    maintainer: NCBI (National Center for Biotechnology Information)
    name: GenBank
    prefix: nbdc00276
    pubmeds:
    - '22144687'
    - '21071399'
    status: Active
    target_keywords:
    - Genome/Gene
    - cDNA/EST
    - Genetic variation
    - DNA
    - RNA
  mappings:
    biocontext: GenBank
    cheminf: '000304'
    edam: '2292'
    fairsharing: FAIRsharing.9kahy4
    go: GenBank
    integbio: nbdc00276
    prefixcommons: genbank
    re3data: r3d100010528
    uniprot: DB-0028
  name: GenBank
  prefix: genbank
  prefixcommons:
    description: GenBank is the NIH genetic sequence database, an annotated collection
      of all publicly available DNA sequences.
    example: AP008229
    homepage: http://www.ncbi.nlm.nih.gov/genbank/
    keywords:
    - DNA
    license: http://www.nlm.nih.gov/copyright.html
    name: GenBank
    pattern: ^\w+$
    prefix: genbank
    synonyms:
    - genbank_nucl_gi
    - genbank_protein_gi
    - gb
    - GenPept
    uri_format: http://www.ncbi.nlm.nih.gov/entrez/viewer.fcgi?val=$1
  publications:
  - doi: 10.1093/nar/gkae1114
    pmc: null
    pubmed: '39558184'
    title: GenBank 2025 update
    year: 2024
  - doi: 10.1093/nar/gkz956
    pmc: PMC7145611
    pubmed: '31665464'
    title: GenBank
    year: 2020
  - doi: 10.1186/s12859-020-3537-3
    pmc: PMC7245624
    pubmed: '32448124'
    title: 'VADR: validation and annotation of virus sequence submissions to GenBank'
    year: 2020
  - doi: 10.1093/nar/gky989
    pmc: PMC6323954
    pubmed: '30365038'
    title: GenBank
    year: 2019
  - doi: 10.1093/nar/gkx1094
    pmc: PMC5753231
    pubmed: '29140468'
    title: GenBank
    year: 2018
  - doi: 10.1093/nar/gkw1070
    pmc: PMC5210553
    pubmed: '27899564'
    title: GenBank
    year: 2016
  - doi: 10.1093/nar/gkv1276
    pmc: PMC4702903
    pubmed: '26590407'
    title: GenBank
    year: 2015
  - doi: 10.1093/nar/gku1216
    pmc: PMC4383990
    pubmed: '25414350'
    title: GenBank
    year: 2014
  - doi: 10.1093/nar/gkt1030
    pmc: PMC3965104
    pubmed: '24217914'
    title: GenBank
    year: 2013
  - doi: 10.1093/nar/gks1195
    pmc: PMC3531190
    pubmed: '23193287'
    title: GenBank
    year: 2012
  - doi: 10.1093/nar/gkr1202
    pmc: PMC3245039
    pubmed: '22144687'
    title: GenBank
    year: 2011
  - doi: 10.1093/nar/gkq1079
    pmc: PMC3013681
    pubmed: '21071399'
    title: GenBank
    year: 2010
  - doi: 10.1093/nar/gkn723
    pmc: PMC2686462
    pubmed: '18940867'
    title: GenBank
    year: 2008
  - doi: 10.1093/nar/gkm929
    pmc: PMC2238942
    pubmed: '18073190'
    title: GenBank
    year: 2007
  - doi: 10.1093/nar/gkl1031
    pmc: PMC1781113
    pubmed: '17170002'
    title: Database resources of the National Center for Biotechnology Information
    year: 2006
  - doi: 10.1093/nar/gkr1202
    pmc: null
    pubmed: null
    title: GenBank.
    year: null
  - doi: 10.1093/nar/gkq1079
    pmc: null
    pubmed: null
    title: GenBank.
    year: null
  - doi: 10.1093/nar/gkm929
    pmc: null
    pubmed: null
    title: GenBank.
    year: null
  - doi: 10.1093/nar/gkn723
    pmc: null
    pubmed: null
    title: GenBank.
    year: null
  - doi: 10.1093/nar/gks1195
    pmc: null
    pubmed: null
    title: GenBank.
    year: null
  - doi: 10.1093/nar/gkt1030
    pmc: null
    pubmed: null
    title: GenBank.
    year: null
  - doi: 10.1093/nar/gkx1094
    pmc: null
    pubmed: null
    title: GenBank
    year: null
  - doi: 10.1093/nar/gkz956
    pmc: null
    pubmed: null
    title: GenBank.
    year: null
  - doi: 10.1093/nar/gky989
    pmc: null
    pubmed: null
    title: GenBank.
    year: null
  - doi: 10.1093/nar/gkw1070
    pmc: null
    pubmed: null
    title: GenBank.
    year: null
  - doi: 10.1093/nar/gkv1276
    pmc: null
    pubmed: null
    title: GenBank.
    year: null
  - doi: 10.1093/nar/gku1216
    pmc: null
    pubmed: null
    title: GenBank.
    year: null
  - doi: 10.1186/s12859-020-3537-3
    pmc: null
    pubmed: null
    title: 'VADR: validation and annotation of virus sequence submissions to GenBank'
    year: null
  - doi: 10.1093/nar/gks1195
    pmc: null
    pubmed: null
    title: GenBank
    year: null
  - doi: 10.1093/nar/gkz956
    pmc: null
    pubmed: '31665464'
    title: null
    year: null
  - doi: 10.1093/nar/gkr1202
    pmc: null
    pubmed: null
    title: GenBank.
    year: null
  - doi: 10.1093/nar/gkq1079
    pmc: null
    pubmed: null
    title: GenBank.
    year: null
  - doi: 10.1093/nar/gkm929
    pmc: null
    pubmed: null
    title: GenBank.
    year: null
  - doi: 10.1093/nar/gkn723
    pmc: null
    pubmed: null
    title: GenBank.
    year: null
  - doi: 10.1093/nar/gks1195
    pmc: null
    pubmed: null
    title: GenBank.
    year: null
  - doi: 10.1093/nar/gkt1030
    pmc: null
    pubmed: null
    title: GenBank.
    year: null
  - doi: 10.1093/nar/gkx1094
    pmc: null
    pubmed: null
    title: GenBank
    year: null
  - doi: 10.1093/nar/gkz956
    pmc: null
    pubmed: null
    title: GenBank.
    year: null
  - doi: 10.1093/nar/gky989
    pmc: null
    pubmed: null
    title: GenBank.
    year: null
  - doi: 10.1093/nar/gkw1070
    pmc: null
    pubmed: null
    title: GenBank.
    year: null
  - doi: 10.1093/nar/gkv1276
    pmc: null
    pubmed: null
    title: GenBank.
    year: null
  - doi: 10.1093/nar/gku1216
    pmc: null
    pubmed: null
    title: GenBank.
    year: null
  - doi: 10.1186/s12859-020-3537-3
    pmc: null
    pubmed: null
    title: 'VADR: validation and annotation of virus sequence submissions to GenBank'
    year: null
  - doi: 10.1093/nar/gks1195
    pmc: null
    pubmed: null
    title: GenBank
    year: null
  - doi: 10.1093/nar/gkz956
    pmc: null
    pubmed: '31665464'
    title: null
    year: null
  re3data:
    description: GenBank® is a comprehensive database that contains publicly available
      nucleotide sequences for almost 260 000 formally described species. These sequences
      are obtained primarily through submissions from individual laboratories and
      batch submissions from large-scale sequencing projects, including whole-genome
      shotgun (WGS) and environmental sampling projects. Most submissions are made
      using the web-based BankIt or standalone Sequin programs, and GenBank staff
      assigns accession numbers upon data receipt. Daily data exchange with the European
      Nucleotide Archive (ENA) and the DNA Data Bank of Japan (DDBJ) ensures worldwide
      coverage. GenBank is accessible through the NCBI Entrez retrieval system, which
      integrates data from the major DNA and protein sequence databases along with
      taxonomy, genome, mapping, protein structure and domain information, and the
      biomedical journal literature via PubMed. BLAST provides sequence similarity
      searches of GenBank and other sequence databases. Complete bimonthly releases
      and daily updates of the GenBank database are available by FTP.
    doi: 10.17616/R3D31X
    homepage: https://www.ncbi.nlm.nih.gov/genbank/
    name: GenBank
    prefix: r3d100010528
    xrefs:
      nif: 0000-02873
      omics: '01650'
  uniprot:
    abbreviation: GenBank
    category: Sequence databases
    homepage: https://www.ncbi.nlm.nih.gov/
    name: GenBank nucleotide sequence database
    prefix: DB-0028
    publications:
    - doi: 10.1093/nar/gkz956
      pubmed: '31665464'
    uri_format: https://www.ncbi.nlm.nih.gov/nuccore/$1
  uri_format: https://www.ncbi.nlm.nih.gov/nucleotide/$1
genbase:
  comment: 'CTH: this is a provider of the INSDC resources, not a new prefix.'
  contact:
    email: zhaoxuetong@big.ac.cn
    github: null
    name: Xuetong Zhao
    orcid: 0000-0002-3019-8615
  contributor:
    email: shah.tanay2@northeastern.edu
    github: tanayshah2
    name: Tanay Shah
    orcid: 0009-0001-1912-5132
  example: C_AA001108.1
  github_request_issue: 1140
  mappings:
    re3data: r3d100014353
  name: GenBase
  prefix: genbase
  re3data:
    description: GenBase is a genetic sequence database that accepts user submissions
      (mRNA, genomic DNAs, ncRNA, or small genomes such as organelles, viruses, plasmids,
      phages from any organism) and integrates data from INSDC.
    doi: 10.17616/R31NJNKH
    homepage: https://ngdc.cncb.ac.cn/genbase/?lang=en
    name: GenBase
    prefix: r3d100014353
  reviewer:
    email: b.gyori@northeastern.edu
    github: bgyori
    name: Benjamin M. Gyori
    orcid: 0000-0001-9439-5346
  uri_format: https://ngdc.cncb.ac.cn/genbase/search/gb/$1
gendis:
  comment: This resource doesn't exist on the web anymore
  deprecated: true
  mappings:
    prefixcommons: gendis
  prefix: gendis
  prefixcommons:
    description: Genomic Distribution of structural Superfamilies identifies and classifies
      evolutionary related proteins at the superfamily level in whole genome databases.
    example: '46946'
    homepage: http://caps.ncbs.res.in/gendis/home.html
    keywords:
    - genome
    - classification
    name: Genomic Distribution of structural Superfamilies
    pattern: ^\d+$
    prefix: gendis
    uri_format: http://caps.ncbs.res.in/cgi-bin/mini/databases/gendis/sf.cgi?code=$1
  reviewer:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
genecards.gene:
  biocontext:
    prefix: GENECARDS
  fairsharing:
    abbreviation: GeneCards
    contact:
      email: marilyn.safran@weizmann.ac.il
      name: Marilyn Safran
      orcid: 0000-0001-5424-1393
    description: GeneCards is a searchable, integrated, database of human genes that
      provides concise genomic, transcriptomic, genetic, proteomic, functional and
      disease related information on all known and predicted human genes.
    homepage: https://www.genecards.org/
    license: https://www.lifemapsc.com/genecards-suite-terms-of-use
    name: Human Gene Database
    prefix: FAIRsharing.g7jbvn
    publications:
    - doi: 10.1093/database/baw030
      pubmed_id: null
      title: Genic Insights From Integrated Human Proteomics in GeneCards
    - doi: 10.1002/cpbi.5
      pubmed_id: null
      title: 'The GeneCards Suite: From Gene Data Mining to Disease Genome Sequence
        Analysis'
    - doi: 10.1093/database/bav006
      pubmed_id: null
      title: 'PathCards: multi-source consolidation of human biological pathways'
    - doi: 10.1093/database/baq020
      pubmed_id: 20689021
      title: 'GeneCards Version 3: the human gene integrator.'
    - doi: 10.1093/bioinformatics/18.11.1542
      pubmed_id: 12424129
      title: 'GeneCards 2002: towards a complete, object-oriented, human gene compendium.'
    - doi: 10.1016/S0168-9525(97)01103-7
      pubmed_id: 9097728
      title: 'GeneCards: integrating information about genes, proteins and diseases.'
    - doi: 10.1089/omi.2015.0168
      pubmed_id: null
      title: 'GeneAnalytics:  An integrative gene set analysis tool'
    - doi: 10.1186/s12864-016-2722-2
      pubmed_id: null
      title: 'VarElect: the phenotype-based variation prioritizer of the GeneCards
        suite'
    subjects:
    - Genetics
    - Life Science
    - Transcriptomics
  integbio:
    description: 'geneCards Version 3 is a database of human genes that provides brief
      but comprehensive genomic related data, on all known human genes.

      The information consists of data on transcriptomes, proteomes, functions and
      disease involvement of human genes.

      This content was obtained from a large number of relevant sources.

      Approved gene symbols and standard nomenclature is used.

      The site provides information on a total of 122,413 genes, which include 21660
      protein-coding genes, 79,344 RNA genes, 16,763 pseudogenes, 767 genetic loci,
      146 gene clusters and 3,733 genes that cannot be placed in any of these categories.

      A simple keyword search option and an advanced search option are available.'
    fairsharing: biodbcore-000593
    homepage: https://www.genecards.org/
    information_keywords:
    - Expression
    maintainer: Weizmann Institute of Science
    name: GeneCards
    prefix: nbdc00242
    pubmeds:
    - '9097728'
    - '9789091'
    - '12424129'
    - '20689021'
    status: Inactive
    target_keywords:
    - Genome/Gene
    - cDNA/EST
    - Genetic variation
    - RNA
    - Protein
    - Health/Disease
  mappings:
    biocontext: GENECARDS
    fairsharing: FAIRsharing.g7jbvn
    integbio: nbdc00242
    miriam: genecards
    n2t: genecards
    prefixcommons: genecards
    re3data: r3d100012015
    uniprot: DB-0030
  miriam:
    deprecated: false
    description: The GeneCards human gene database stores gene related transcriptomic,
      genetic, proteomic, functional and disease information. It uses standard nomenclature
      and approved gene symbols. GeneCards presents a complete summary for each human
      gene.
    homepage: http://www.genecards.org/
    id: '00000323'
    name: GeneCards
    namespaceEmbeddedInLui: false
    pattern: ^[A-Za-z-0-9_]+(\@)?$
    prefix: genecards
    sampleId: ABL1
    uri_format: https://www.genecards.org/cgi-bin/carddisp.pl?gene=$1
  n2t:
    description: The GeneCards human gene database stores gene related transcriptomic,
      genetic, proteomic, functional and disease information. It uses standard nomenclature
      and approved gene symbols. GeneCards presents a complete summary for each human
      gene.
    example: ABL1
    homepage: http://www.genecards.org/
    name: GeneCards at Weizmann Institute
    namespaceEmbeddedInLui: false
    pattern: ^[A-Za-z-0-9_]+(\@)?$
    prefix: genecards
    uri_format: https://www.genecards.org/cgi-bin/carddisp.pl?gene=$1
  name: GeneCards Gene
  part_of_database: genecards
  prefix: genecards.gene
  prefixcommons:
    description: GeneCards is a searchable, integrated, database of human genes that
      provides concise genomic, transcriptomic, genetic, proteomic, functional and
      disease related information on all known and predicted human genes.
    example: ABL1
    homepage: http://bioinfo.weizmann.ac.il/genecards/
    keywords:
    - genome
    name: 'GeneCards: human genes, protein and diseases'
    pattern: ^\w+$
    prefix: genecards
    pubmed_ids:
    - '20689021'
    synonyms:
    - genecard
    uri_format: http://www.genecards.org/cgi-bin/carddisp.pl?gene=$1
  publications:
  - doi: 10.1089/omi.2015.0168
    pmc: PMC4799705
    pubmed: '26983021'
    title: 'GeneAnalytics: An Integrative Gene Set Analysis Tool for Next Generation
      Sequencing, RNAseq and Microarray Data'
    year: 2016
  - doi: 10.1093/database/baw030
    pmc: PMC4820835
    pubmed: '27048349'
    title: Genic insights from integrated human proteomics in GeneCards
    year: 2016
  - doi: 10.1002/cpbi.5
    pmc: null
    pubmed: '27322403'
    title: 'The GeneCards Suite: From Gene Data Mining to Disease Genome Sequence
      Analyses'
    year: 2016
  - doi: 10.1186/s12864-016-2722-2
    pmc: PMC4928145
    pubmed: '27357693'
    title: 'VarElect: the phenotype-based variation prioritizer of the GeneCards Suite'
    year: 2016
  - doi: 10.1093/database/bav006
    pmc: PMC4343183
    pubmed: '25725062'
    title: 'PathCards: multi-source consolidation of human biological pathways'
    year: 2015
  - doi: 10.1093/database/baq020
    pmc: PMC2938269
    pubmed: '20689021'
    title: 'GeneCards Version 3: the human gene integrator'
    year: 2010
  - doi: 10.1093/bioinformatics/18.11.1542
    pmc: null
    pubmed: '12424129'
    title: 'GeneCards 2002: towards a complete, object-oriented, human gene compendium'
    year: 2002
  - doi: 10.1016/s0168-9525(97)01103-7
    pmc: null
    pubmed: '9097728'
    title: 'GeneCards: integrating information about genes, proteins and diseases'
    year: 1997
  - doi: 10.1093/database/baw030
    pmc: null
    pubmed: null
    title: Genic Insights From Integrated Human Proteomics in GeneCards
    year: null
  - doi: 10.1002/cpbi.5
    pmc: null
    pubmed: null
    title: 'The GeneCards Suite: From Gene Data Mining to Disease Genome Sequence
      Analysis'
    year: null
  - doi: 10.1093/database/bav006
    pmc: null
    pubmed: null
    title: 'PathCards: multi-source consolidation of human biological pathways'
    year: null
  - doi: 10.1093/database/baq020
    pmc: null
    pubmed: null
    title: 'GeneCards Version 3: the human gene integrator.'
    year: null
  - doi: 10.1093/bioinformatics/18.11.1542
    pmc: null
    pubmed: null
    title: 'GeneCards 2002: towards a complete, object-oriented, human gene compendium.'
    year: null
  - doi: 10.1016/S0168-9525(97)01103-7
    pmc: null
    pubmed: null
    title: 'GeneCards: integrating information about genes, proteins and diseases.'
    year: null
  - doi: 10.1089/omi.2015.0168
    pmc: null
    pubmed: null
    title: 'GeneAnalytics:  An integrative gene set analysis tool'
    year: null
  - doi: 10.1186/s12864-016-2722-2
    pmc: null
    pubmed: null
    title: 'VarElect: the phenotype-based variation prioritizer of the GeneCards suite'
    year: null
  - doi: null
    pmc: null
    pubmed: '20689021'
    title: null
    year: null
  - doi: 10.1002/cpbi.5
    pmc: null
    pubmed: '27322403'
    title: null
    year: null
  re3data:
    description: GeneCards is a searchable, integrative database that provides comprehensive,
      user-friendly information on all annotated and predicted human genes. It automatically
      integrates gene-centric data from ~125 web sources, including genomic, transcriptomic,
      proteomic, genetic, clinical and functional information.
    doi: 10.17616/R3D643
    homepage: https://www.genecards.org/
    name: GeneCards
    prefix: r3d100012015
    synonyms:
    - The Human Gene Database
    xrefs:
      nif: 0000-02879
      omics: '01652'
  synonyms:
  - genecards
  uniprot:
    abbreviation: GeneCards
    category: Organism-specific databases
    homepage: https://www.genecards.org/
    name: GeneCards
    prefix: DB-0030
    publications:
    - doi: 10.1002/cpbi.5
      pubmed: '27322403'
    uri_format: https://www.genecards.org/cgi-bin/carddisp.pl?gene=$1
genecards.geneannot:
  mappings:
    prefixcommons: geneannot
  part_of_database: genecards
  prefix: genecards.geneannot
  prefixcommons:
    description: GeneAnnot provides a revised and improved annotation of Affymetrix
      probe-sets from HG-U95, HG-U133 and HG-U133 Plus2.0. Probe-sets are related
      to GeneCards genes, by direct sequence comparison of probes to GenBank, RefSeq
      and Ensembl mRNA sequences, while assigning sensitivity and specificity scores
      to each probe-set to gene match.
    example: GSTA1
    homepage: http://genecards.weizmann.ac.il/geneannot/
    keywords:
    - gene expression
    name: 'GeneAnnot: Microarray Gene Annotation'
    pattern: ^[A-Z]+/\d+$
    prefix: geneannot
genecards.geneloc:
  mappings:
    prefixcommons: geneloc
  part_of_database: genecards
  prefix: genecards.geneloc
  prefixcommons:
    description: GeneLoc presents an integrated map for each human chromosome, based
      on data integrated by the GeneLoc algorithm. GeneLoc includes further links
      to GeneCards, NCBI's Human Genome Sequencing, UniGene, and mapping resources
    example: '17503'
    homepage: http://genecards.weizmann.ac.il/geneloc/
    keywords:
    - genome
    name: Gene Location
    pattern: ^\d+$
    prefix: geneloc
    uri_format: http://genecards.weizmann.ac.il/geneloc-bin/marker_cards.pl?id=$1
  reviewer:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
genecards.genenote:
  mappings:
    prefixcommons: genenote
  part_of_database: genecards
  prefix: genecards.genenote
  prefixcommons:
    description: GeneNote is a database of human genes and their expression profiles
      in healthy tissues. It is based on Weizmann Institute of Science DNA array experiments,
      which were performed on the Affymetrix HG-U95 set A-E.
    example: GC06M052656
    homepage: http://genecards.weizmann.ac.il/genenote/
    keywords:
    - gene expression
    name: Gene Normal Tissue Expression
    pattern: ^GC\d+$
    prefix: genenote
    uri_format: http://bioinfo2.weizmann.ac.il/cgi-bin/genenote/GN_results.pl?keyword_type=2_gc_id&keyword=$1&data_type=norm2&results=yes
genedb:
  biocontext:
    prefix: GENEDB
  deprecated: true
  edam:
    description: Identifier of a gene from the GeneDB database.
    name: Gene ID (GeneDB)
    obsolete: false
    prefix: '1035'
  fairsharing:
    abbreviation: GeneDB
    description: GeneDB is a genome database for prokaryotic and eukaryotic organisms
      and provides a portal through which data generated by the "Pathogen Genomics"
      group at the Wellcome Trust Sanger Institute and other collaborating sequencing
      centres can be accessed.
    homepage: http://www.genedb.org/
    license: http://www.sanger.ac.uk/legal
    name: GeneDB
    prefix: FAIRsharing.j7esqq
    publications:
    - doi: 10.1093/nar/gkh007
      pubmed_id: 14681429
      title: 'GeneDB: a resource for prokaryotic and eukaryotic organisms.'
    subjects:
    - Life Science
  go:
    homepage: http://www.genedb.org/gene/
    name: GeneDB
    prefix: GeneDB
    uri_format: http://www.genedb.org/gene/$1
  integbio:
    description: geneDB is a database of genomic and proteomic data of several species
      generally regarded as pests or parasites. The database contains information
      pages for dozens of species across six large classes including viruses, protozoa,
      helminths, bacteria, and vectors. Users can search by sequence feature or ID
      or browse the database.
    fairsharing: biodbcore-000044
    homepage: http://www.genedb.org
    information_keywords:
    - Sequence
    maintainer: Wellcome Sanger Institute
    name: GeneDB
    prefix: nbdc00469
    pubmeds:
    - '22116062'
    target_keywords:
    - Genome/Gene
    - Protein
  logo: https://www.genedb.org/errors/genedb_logo.png
  mappings:
    biocontext: GENEDB
    edam: '1035'
    fairsharing: FAIRsharing.j7esqq
    go: GeneDB
    integbio: nbdc00469
    miriam: genedb
    n2t: genedb
    ncbi: GeneDB
    prefixcommons: genedb
    re3data: r3d100010626
    wikidata: P3382
  miriam:
    deprecated: true
    description: GeneDB is a genome database for prokaryotic and eukaryotic organisms
      and provides a portal through which data generated by the "Pathogen Genomics"
      group at the Wellcome Trust Sanger Institute and other collaborating sequencing
      centres can be accessed.
    homepage: https://www.genedb.org/
    id: '00000106'
    name: GeneDB
    namespaceEmbeddedInLui: false
    pattern: ^[\w\d\.-]*$
    prefix: genedb
    sampleId: LinJ.20.0070
    uri_format: https://www.genedb.org/gene/$1
  n2t:
    description: GeneDB is a genome database for prokaryotic and eukaryotic organisms
      and provides a portal through which data generated by the "Pathogen Genomics"
      group at the Wellcome Trust Sanger Institute and other collaborating sequencing
      centres can be accessed.
    example: LinJ.20.0070
    homepage: https://www.genedb.org/
    name: GeneDB at Sanger Institute
    namespaceEmbeddedInLui: false
    pattern: ^[\w\d\.-]*$
    prefix: genedb
    uri_format: https://www.genedb.org/gene/$1
  name: GeneDB
  ncbi:
    example: SPCC285.16c
    homepage: http://www.genedb.org/
    name: Curated gene database for Leishmania major and Trypanosoma brucei
    prefix: GeneDB
  prefix: genedb
  prefixcommons:
    description: GeneDB is a genome database for prokaryotic and eukaryotic organisms
      and provides a portal through which data generated by the "Pathogen Genomics"
      group at the Wellcome Trust Sanger Institute and other collaborating sequencing
      centres can be accessed.
    example: Cj1536c
    homepage: http://www.genedb.org/
    keywords:
    - genome
    - sequence
    license: http://www.sanger.ac.uk/legal
    name: GeneDB
    pattern: ^[\w\d\.-]*$
    prefix: genedb
    pubmed_ids:
    - '14681429'
    uri_format: http://www.genedb.org/gene/$1
  publications:
  - doi: 10.1093/nar/gkh007
    pmc: PMC308742
    pubmed: '14681429'
    title: 'GeneDB: a resource for prokaryotic and eukaryotic organisms'
    year: 2004
  re3data:
    description: <<<!!!<<<  GeneDB will be taken offline 1st of August 2021, as none
      of the genomes are curated at Sanger anymore. All genomes on GeneDB can now
      be found on PlasmoDB, FungiDB, TriTrypDB and Wormbase Parasite.   >>>!!!<<<
    doi: 10.17616/R31C8X
    homepage: https://www.genedb.org/
    license: other
    name: GeneDB
    prefix: r3d100010626
    xrefs:
      nif: 0000-02880
  wikidata:
    description: gene identifier in GeneDB
    example:
    - '244180'
    - PBANKA_1200800
    - PF3D7_0531100
    homepage: http://www.genedb.org/
    name: GeneDB ID
    prefix: P3382
    uri_format: https://web.archive.org/web/*/https://www.genedb.org/gene/$1
genefarm:
  biocontext:
    prefix: GENEFARM
  contact:
    email: sebastien.aubourg@inrae.fr
    github: null
    name: sébastien Aubourg
    orcid: 0000-0002-0695-4767
  fairsharing:
    abbreviation: GeneFarm
    description: GeneFarm is a database whose purpose is to store traceable annotations
      for Arabidopsis nuclear genes and gene products.
    homepage: http://urgi.versailles.inra.fr/Genefarm/index.htpl
    license: http://opendatacommons.org/licenses/pddl/1.0
    name: Structural and functional annotation of Arabidopsis thaliana gene and protein
      families
    prefix: FAIRsharing.2mayq0
    publications:
    - doi: 10.1093/nar/gki115
      pubmed_id: 15608279
      title: GeneFarm, structural and functional annotation of Arabidopsis gene and
        protein families by a network of experts.
    subjects:
    - Life Science
  mappings:
    biocontext: GENEFARM
    fairsharing: FAIRsharing.2mayq0
    miriam: genefarm
    n2t: genefarm
    prefixcommons: genefarm
  miriam:
    deprecated: true
    description: GeneFarm is a database whose purpose is to store traceable annotations
      for Arabidopsis nuclear genes and gene products.
    homepage: http://urgi.versailles.inra.fr/Genefarm/
    id: '00000211'
    name: GeneFarm
    namespaceEmbeddedInLui: false
    pattern: ^\d+$
    prefix: genefarm
    sampleId: '4892'
    uri_format: https://urgi.versailles.inra.fr/Genefarm/Gene/display_gene.htpl?GENE_ID=$1
  n2t:
    description: GeneFarm is a database whose purpose is to store traceable annotations
      for Arabidopsis nuclear genes and gene products.
    example: '4892'
    homepage: http://urgi.versailles.inra.fr/Genefarm/
    name: GeneFarm at Unit&#xE9; de Recherche en G&#xE9;nomique V&#xE9;g&#xE9;tale
    namespaceEmbeddedInLui: false
    pattern: ^\d+$
    prefix: genefarm
    uri_format: https://urgi.versailles.inra.fr/Genefarm/Gene/display_gene.htpl?GENE_ID=$1
  prefix: genefarm
  prefixcommons:
    description: GeneFarm is a database whose purpose is to store traceable annotations
      for Arabidopsis nuclear genes and gene products.
    example: '4892'
    homepage: http://urgi.versailles.inra.fr/Genefarm/index.htpl
    keywords:
    - expression
    - genome
    - nucleotide
    - sequence
    name: Structural and functional annotation of Arabidopsis thaliana gene and protein
      families.
    pattern: ^\d+$
    prefix: genefarm
    pubmed_ids:
    - '15608279'
    uri_format: http://urgi.versailles.inra.fr/Genefarm/Gene/display_gene.htpl?GENE_ID=$1
  publications:
  - doi: 10.1093/nar/gki115
    pmc: PMC540069
    pubmed: '15608279'
    title: GeneFarm, structural and functional annotation of Arabidopsis gene and
      protein families by a network of experts
    year: 2005
  - doi: 10.1093/nar/gki115
    pmc: null
    pubmed: null
    title: GeneFarm, structural and functional annotation of Arabidopsis gene and
      protein families by a network of experts.
    year: null
  - doi: null
    pmc: null
    pubmed: '15608279'
    title: null
    year: null
  - doi: 10.1093/nar/gki115
    pmc: null
    pubmed: null
    title: GeneFarm, structural and functional annotation of Arabidopsis gene and
      protein families by a network of experts.
    year: null
  - doi: null
    pmc: null
    pubmed: '15608279'
    title: null
    year: null
genepio:
  aberowl:
    description: The Genomic Epidemiology Ontology (GenEpiO) covers vocabulary necessary
      to identify, document and research foodborne pathogens and associated outbreaks.
    download_owl: http://aber-owl.net/media/ontologies/GENEPIO/25/genepio.owl
    homepage: http://genepio.org/
    name: Genomic Epidemiology Ontology
    prefix: GENEPIO
  biocontext:
    prefix: GENEPIO
  bioportal:
    contact:
      email: damion_dooley@sfu.ca
      name: Damion Dooley
    description: The Genomic Epidemiology Application Ontology describes the genomics,
      laboratory, clinical and epidemiological contextual information required to
      support data sharing and integration for foodborne infectious disease surveillance
      and outbreak investigations.
    homepage: https://genepio.org/
    name: Genomic Epidemiology Application Ontology
    prefix: GENEPIO
  example: 0001885
  fairsharing:
    abbreviation: GenEpiO
    description: The Genomic Epidemiology Ontology (GenEpiO) covers vocabulary necessary
      to identify, document and research food-borne pathogens, infectious disease
      surveillance and outbreak investigations. This includes descriptions of the
      genomics, laboratory, clinical and epidemiological contextual information required
      to support data sharing and integration for food-borne infectious disease surveillance
      and outbreak investigations.
    domains:
    - food
    - genome
    - pathogen
    homepage: https://genepio.org/
    license: CC-BY-3.0
    name: Genomic Epidemiology Ontology
    prefix: FAIRsharing.y1mmbv
    repository: https://github.com/GenEpiO/genepio
    subjects:
    - Epidemiology
    - Genomics
  mappings:
    aberowl: GENEPIO
    biocontext: GENEPIO
    bioportal: GENEPIO
    fairsharing: FAIRsharing.y1mmbv
    obofoundry: genepio
    ols: genepio
    ontobee: GENEPIO
    wikidata.entity: Q55118402
  obofoundry:
    contact: damion_dooley@sfu.ca
    contact.github: ddooley
    contact.label: Damion Dooley
    contact.orcid: 0000-0002-8844-9165
    depends_on:
    - chebi
    - ncbitaxon
    - po
    - ro
    - uberon
    deprecated: false
    description: The Genomic Epidemiology Ontology (GenEpiO) covers vocabulary necessary
      to identify, document and research foodborne pathogens and associated outbreaks.
    domain: health
    download.owl: http://purl.obolibrary.org/obo/genepio.owl
    homepage: http://genepio.org/
    license: CC BY 3.0
    license.url: http://creativecommons.org/licenses/by/3.0/
    name: Genomic Epidemiology Ontology
    preferredPrefix: GENEPIO
    prefix: genepio
    repository: https://github.com/GenEpiO/genepio
  ols:
    description: The Genomic Epidemiology Ontology (GenEpiO) covers vocabulary necessary
      to identify, document and research foodborne pathogens and associated outbreaks.
    download_owl: http://purl.obolibrary.org/obo/genepio.owl
    homepage: http://genepio.org/
    name: Genomic Epidemiology Ontology
    prefix: genepio
    tracker: https://github.com/GenEpiO/genepio/issues/
    version: '2024-12-18'
    version.iri: http://purl.obolibrary.org/obo/genepio/releases/2024-12-18/genepio.owl
  ontobee:
    library: Library
    name: Genomic Epidemiology Ontology
    prefix: GENEPIO
  pattern: ^\d{7}$
  prefix: genepio
  uri_format: http://purl.obolibrary.org/obo/GENEPIO_$1
genetree:
  biocontext:
    prefix: GENETREE
  contact:
    email: flicek@ebi.ac.uk
    github: null
    name: Paul Flicek
    orcid: 0000-0002-3897-7955
  mappings:
    biocontext: GENETREE
    miriam: genetree
    n2t: genetree
    prefixcommons: genetree
    uniprot: DB-0162
  miriam:
    deprecated: false
    description: Genetree displays the maximum likelihood phylogenetic (protein) trees
      representing the evolutionary history of the genes. These are constructed using
      the canonical protein for every gene in Ensembl.
    homepage: http://www.ensembl.org/
    id: '00000214'
    name: GeneTree
    namespaceEmbeddedInLui: false
    pattern: ^ENSGT\d+$
    prefix: genetree
    sampleId: ENSGT00550000074763
    uri_format: http://www.ensembl.org/Multi/GeneTree/Image?db=core;gt=$1
  n2t:
    description: Genetree displays the maximum likelihood phylogenetic (protein) trees
      representing the evolutionary history of the genes. These are constructed using
      the canonical protein for every gene in Ensembl.
    example: ENSGT00550000074763
    homepage: http://www.ensembl.org/
    name: GeneTree at Ensembl
    namespaceEmbeddedInLui: false
    pattern: ^ENSGT\d+$
    prefix: genetree
    uri_format: http://www.ensembl.org/Multi/GeneTree/Image?db=core;gt=$1
  prefix: genetree
  prefixcommons:
    description: Genetree displays the maximum likelihood phylogenetic (protein) trees
      representing the evolutionary history of the genes. These are constructed using
      the canonical protein for every gene in Ensembl.
    example: ENSGT00550000074763
    keywords:
    - classification
    - gene
    - protein
    name: Ensembl GeneTree
    pattern: ^ENSGT\d+$
    prefix: genetree
    pubmed_ids:
    - '16381931'
    uri_format: http://www.ensembl.org/Multi/GeneTree/Image?db=core;gt=$1
  publications:
  - doi: 10.1093/database/bav096
    pmc: PMC4761110
    pubmed: '26896847'
    title: Ensembl comparative genomics resources
    year: 2016
  - doi: 10.1093/nar/gkj133
    pmc: PMC1347495
    pubmed: '16381931'
    title: Ensembl 2006
    year: 2006
  - doi: null
    pmc: null
    pubmed: '16381931'
    title: null
    year: null
  - doi: 10.1093/database/bav096
    pmc: null
    pubmed: '26896847'
    title: null
    year: null
  - doi: null
    pmc: null
    pubmed: '16381931'
    title: null
    year: null
  - doi: 10.1093/database/bav096
    pmc: null
    pubmed: '26896847'
    title: null
    year: null
  uniprot:
    abbreviation: GeneTree
    category: Phylogenomic databases
    homepage: https://ensemblgenomes.org
    name: Ensembl GeneTree
    prefix: DB-0162
    publications:
    - doi: 10.1093/database/bav096
      pubmed: '26896847'
    uri_format: https://www.ensemblgenomes.org/id-genetree/$1
genewiki:
  biocontext:
    prefix: GENEWIKI
  contact:
    email: asu@scripps.edu
    github: andrewsu
    name: Andrew I Su
    orcid: 0000-0002-9859-4104
  fairsharing:
    abbreviation: Gene Wiki
    description: 'The goal of the Gene Wiki is to apply community intelligence to
      the annotation of gene and protein function. The Gene Wiki is an informal collection
      of pages on human genes and proteins, and this effort to develop these pages
      is tightly coordinated with the Molecular and Cellular Biology Wikiproject.
      Our specific aims are summarized as follows: To provide a well written and informative
      Wikipedia article for every notable human gene; To invite participation by interested
      lay editors, students, professionals, and academics from around the world; To
      integrate Gene Wiki articles with existing Wikipedia content through the use
      of internal wiki links increasing the value of both.'
    homepage: http://en.wikipedia.org/wiki/Portal:Gene_Wiki
    license: CC BY-SA 3.0
    name: Gene Wiki
    prefix: FAIRsharing.t3snf
    publications:
    - doi: 10.1093/nar/gkr925
      pubmed_id: 22075991
      title: 'The Gene Wiki in 2011: community intelligence applied to human gene
        annotation.'
    - doi: 10.1093/nar/gkp760
      pubmed_id: 19755503
      title: 'The Gene Wiki: community intelligence applied to human gene annotation.'
    - doi: 10.1093/database/baw015
      pubmed_id: 26989148
      title: Wikidata as a semantic framework for the Gene Wiki initiative.
    subjects:
    - Genetics
    - Life Science
    twitter: GeneWikiPulse
  integbio:
    description: geneWiki is a database of gene and protein function. The database
      contains articles for all human genes featuring links to and from Wikipedia.
      Users can search, browse, and participate in editing of articles.
    fairsharing: biodbcore-000133
    homepage: https://en.wikipedia.org/wiki/Wikipedia:WikiProject_Genetics/Gene_Wiki
    information_keywords:
    - Bibliography/Documents
    maintainer: Wikimedia Foundation Inc.
    name: Gene Wiki
    prefix: nbdc00834
    pubmeds:
    - '18613750'
    - '19755503'
    - '22075991'
    - '22165947'
    status: Active
    target_keywords:
    - Genome/Gene
    - Protein
  mappings:
    biocontext: GENEWIKI
    fairsharing: FAIRsharing.t3snf
    integbio: nbdc00834
    miriam: genewiki
    n2t: genewiki
  miriam:
    deprecated: false
    description: The Gene Wiki is project which seeks to provide detailed information
      on human genes. Initial 'stub' articles are created in an automated manner,
      with further information added by the community. Gene Wiki can be accessed in
      wikipedia using Gene identifiers from NCBI.
    homepage: http://en.wikipedia.org/wiki/Gene_Wiki
    id: 00000487
    name: Gene Wiki
    namespaceEmbeddedInLui: false
    pattern: ^\d+$
    prefix: genewiki
    sampleId: '1017'
    uri_format: http://plugins.biogps.org/cgi-bin/wp.cgi?id=$1
  n2t:
    description: The Gene Wiki is project which seeks to provide detailed information
      on human genes. Initial 'stub' articles are created in an automated manner,
      with further information added by the community. Gene Wiki can be accessed in
      wikipedia using Gene identifiers from NCBI.
    example: '1017'
    homepage: http://en.wikipedia.org/wiki/Gene_Wiki
    name: Gene Wiki through BioGPS
    namespaceEmbeddedInLui: false
    pattern: ^\d+$
    prefix: genewiki
    uri_format: http://plugins.biogps.org/cgi-bin/wp.cgi?id=$1
  prefix: genewiki
  provides: ncbigene
  publications:
  - doi: 10.1093/database/baw015
    pmc: PMC4795929
    pubmed: '26989148'
    title: Wikidata as a semantic framework for the Gene Wiki initiative
    year: 2016
  - doi: 10.1093/nar/gkr925
    pmc: PMC3245148
    pubmed: '22075991'
    title: 'The Gene Wiki in 2011: community intelligence applied to human gene annotation'
    year: 2011
  - doi: 10.1093/nar/gkp760
    pmc: PMC2808918
    pubmed: '19755503'
    title: 'The Gene Wiki: community intelligence applied to human gene annotation'
    year: 2009
  - doi: 10.1371/journal.pbio.0060175
    pmc: PMC2443188
    pubmed: '18613750'
    title: A gene wiki for community annotation of gene function
    year: 2008
  - doi: 10.1093/nar/gkr925
    pmc: null
    pubmed: null
    title: 'The Gene Wiki in 2011: community intelligence applied to human gene annotation.'
    year: null
  - doi: 10.1093/nar/gkp760
    pmc: null
    pubmed: null
    title: 'The Gene Wiki: community intelligence applied to human gene annotation.'
    year: null
  - doi: 10.1093/database/baw015
    pmc: null
    pubmed: null
    title: Wikidata as a semantic framework for the Gene Wiki initiative.
    year: null
geno:
  aberowl:
    description: An integrated ontology for representing the genetic variations described
      in genotypes, and their causal relationships to phenotype and diseases.
    download_owl: http://aber-owl.net/media/ontologies/GENO/29/geno.owl
    homepage: https://github.com/monarch-initiative/GENO-ontology/
    name: Genotype Ontology
    prefix: GENO
  biocontext:
    prefix: GENO
  bioportal:
    contact:
      email: mhb120@gmail.com
      name: Matthew Brush
    description: An integrated ontology for representing the genetic variations described
      in genotypes, and their causal relationships to phenotype and diseases.
    homepage: https://github.com/monarch-initiative/GENO-ontology/
    name: Genotype Ontology
    prefix: GENO
    version: '2023-10-08'
  download_json: http://purl.obolibrary.org/obo/geno.json
  download_obo: https://raw.githubusercontent.com/monarch-initiative/GENO-ontology/develop/geno-full.obo
  example: '0000632'
  fairsharing:
    abbreviation: GENO
    description: An integrated ontology for representing the genetic variations described
      in genotypes, and their causal relationships to phenotype and diseases.
    domains:
    - disease phenotype
    - genotype
    homepage: https://github.com/monarch-initiative/GENO-ontology/
    license: CC-BY-4.0
    name: Genotype Ontology
    prefix: FAIRsharing.kpbna7
    subjects:
    - Genomics
  mappings:
    aberowl: GENO
    biocontext: GENO
    bioportal: GENO
    fairsharing: FAIRsharing.kpbna7
    obofoundry: geno
    ols: geno
    ontobee: GENO
    wikidata.entity: Q81661639
  obofoundry:
    contact: mhb120@gmail.com
    contact.github: mbrush
    contact.label: Matthew Brush
    contact.orcid: 0000-0002-1048-5019
    deprecated: false
    description: An integrated ontology for representing the genetic variations described
      in genotypes, and their causal relationships to phenotype and diseases.
    domain: biological systems
    download.owl: http://purl.obolibrary.org/obo/geno.owl
    homepage: https://github.com/monarch-initiative/GENO-ontology/
    license: CC BY 4.0
    license.url: https://creativecommons.org/licenses/by/4.0/
    name: Genotype Ontology
    preferredPrefix: GENO
    prefix: geno
    repository: https://github.com/monarch-initiative/GENO-ontology
  ols:
    description: "GENO is an OWL model of genotypes, their more fundamental sequence\
      \ components, and links to related biological and experimental entities.  At\
      \ present many parts of the model are exploratory and set to undergo refactoring.\
      \  In addition, many classes and properties have GENO URIs but are place holders\
      \ for classes that will be imported from an external ontology (e.g. SO, ChEBI,\
      \ OBI, etc).  Furthermore, ongoing work will implement a model of genotype-to-phenotype\
      \ associations. This will support description of asserted and inferred relationships\
      \ between a genotypes, phenotypes, and environments, and the evidence/provenance\
      \ behind these associations. \n\nDocumentation is under development as well,\
      \ and for now a slidedeck is available at http://www.slideshare.net/mhb120/brush-icbo-2013"
    download_owl: http://purl.obolibrary.org/obo/geno.owl
    homepage: https://github.com/monarch-initiative/GENO-ontology/
    name: GENO ontology
    prefix: geno
    tracker: https://github.com/monarch-initiative/GENO-ontology/issues
    version: '2025-07-25'
    version.iri: http://purl.obolibrary.org/obo/geno/releases/2025-07-25/geno.owl
  ontobee:
    library: Library
    name: Genotype Ontology
    prefix: GENO
  pattern: ^\d{7}$
  prefix: geno
  uri_format: http://purl.obolibrary.org/obo/GENO_$1
genpept:
  biocontext:
    prefix: GENPEPT
  mappings:
    biocontext: GENPEPT
    miriam: genpept
    n2t: genpept
  miriam:
    deprecated: false
    description: The GenPept database is a collection of sequences based on translations
      from annotated coding regions in GenBank.
    homepage: https://www.ncbi.nlm.nih.gov/protein
    id: '00000345'
    name: GenPept
    namespaceEmbeddedInLui: false
    pattern: ^\w{3}\d{5}(\.\d+)?$
    prefix: genpept
    sampleId: CAA71118.1
    uri_format: https://www.ncbi.nlm.nih.gov/protein/$1?report=genpept
  n2t:
    description: The GenPept database is a collection of sequences based on translations
      from annotated coding regions in GenBank.
    example: CAA71118.1
    homepage: https://www.ncbi.nlm.nih.gov/protein
    name: GenPept at NCBI
    namespaceEmbeddedInLui: false
    pattern: ^\w{3}\d{5}(\.\d+)?$
    prefix: genpept
    uri_format: https://www.ncbi.nlm.nih.gov/protein/$1?report=genpept
  prefix: genpept
genprop:
  biocontext:
    prefix: GENPROP
  mappings:
    biocontext: GENPROP
    miriam: genprop
    n2t: genprop
    prefixcommons: jcvi.genprop
  miriam:
    deprecated: false
    description: Genome properties is an annotation system whereby functional attributes
      can be assigned to a genome, based on the presence of a defined set of protein
      signatures within that genome.
    homepage: https://www.ebi.ac.uk/interpro/genomeproperties/
    id: '00000443'
    name: Genome Properties
    namespaceEmbeddedInLui: false
    pattern: ^GenProp\d+$
    prefix: genprop
    sampleId: GenProp0699
    uri_format: https://www.ebi.ac.uk/interpro/genomeproperties/#$1
  n2t:
    description: Genome properties is an annotation system whereby functional attributes
      can be assigned to a genome, based on the presence of a defined set of protein
      signatures within that genome.
    example: GenProp0699
    homepage: https://www.ebi.ac.uk/interpro/genomeproperties/
    name: Genome Properties
    namespaceEmbeddedInLui: false
    pattern: ^GenProp\d+$
    prefix: genprop
    uri_format: https://www.ebi.ac.uk/interpro/genomeproperties/#$1
  owners:
  - name: European Bioinformatics Institute
    partnered: false
    ror: 02catss52
    wikidata: null
  prefix: genprop
  prefixcommons:
    description: The Genome Properties system consists of a suite of "Properties"
      which are carefully defined attributes of prokaryotic organisms whose status
      can be described by numerical values or controlled vocabulary terms for individual
      completely sequenced genomes.
    example: GenProp0151
    homepage: http://cmr.jcvi.org/tigr-scripts/CMR/shared/GenomePropertiesHomePage.cgi
    keywords:
    - classification
    - genome
    name: Genome Properties database at the J. Craig Venter Institute
    pattern: ^GenProp\d+$
    prefix: jcvi.genprop
    synonyms:
    - genprop
    uri_format: http://cmr.jcvi.org/tigr-scripts/CMR/shared/GenomePropDefinition.cgi?prop_acc=$1
geo:
  banana_peel: _
  cellosaurus:
    category: Gene expression databases
    homepage: https://www.ncbi.nlm.nih.gov/geo/
    name: Gene Expression Omnibus
    prefix: GEO
    uri_format: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=$1
  contact:
    email: barrett@ncbi.nlm.nih.gov
    github: null
    name: Tanya Barrett
    orcid: 0000-0002-9448-8064
  edam:
    description: Accession number of an entry from the GEO database.
    name: GEO accession number
    obsolete: false
    prefix: '1147'
  fairsharing:
    abbreviation: GEO
    description: The Gene Expression Omnibus (GEO) is a public repository that archives
      and freely distributes microarray, next-generation sequencing, and other forms
      of high-throughput functional genomic data submitted by the scientific community.
      Accepts next generation sequence data that examine quantitative gene expression,
      gene regulation, epigenomics or other aspects of functional genomics using methods
      such as RNA-seq, miRNA-seq, ChIP-seq, RIP-seq, HiC-seq, methyl-seq, etc. GEO
      will process all components of your study, including the samples, project description,
      processed data files, and will submit the raw data files to the Sequence Read
      Archive (SRA) on the researchers behalf. In addition to data storage, a collection
      of web-based interfaces and applications are available to help users query and
      download the studies and gene expression patterns stored in GEO.
    homepage: https://www.ncbi.nlm.nih.gov/geo/
    license: http://opendatacommons.org/licenses/pddl/1.0
    name: Gene Expression Omnibus
    prefix: FAIRsharing.5hc8vt
    publications:
    - doi: 10.1093/nar/30.1.207
      pubmed_id: 11752295
      title: 'Gene Expression Omnibus: NCBI gene expression and hybridization array
        data repository.'
    - doi: 10.1093/nar/gks1193
      pubmed_id: 23193258
      title: 'NCBI GEO: archive for functional genomics data sets--update.'
    - doi: 10.5281/zenodo.5706412
      pubmed_id: null
      title: 'MINSEQE: Minimum Information about a high-throughput Nucleotide SeQuencing
        Experiment - a proposal for standards in functional genomic data reporting'
    - doi: 10.1038/35001676
      pubmed_id: null
      title: One-stop shop for microarray data
    - doi: 10.1038/nbt1206-1471
      pubmed_id: 17160034
      title: NCBI GEO standards and services for microarray data
    - doi: 10.1093/nar/gks1193
      pubmed_id: null
      title: 'NCBI GEO: archive for functional genomics data sets—update'
    subjects:
    - Epigenomics
    - Genomics
    - Life Science
    - Transcriptomics
    - Phenomics
    - Comparative Genomics
    - Omics
  go:
    homepage: http://www.ncbi.nlm.nih.gov/geo/
    name: NCBI Gene Expression Omnibus
    prefix: GEO
    uri_format: http://www.ncbi.nlm.nih.gov/sites/GDSbrowser?acc=$1
  integbio:
    alt_name: Gene Expression Omnibus
    description: This is a public data repository of functional genomics data obtained
      through microarrays and sequencing. Records are carefully examined by experts
      and standardized to comply with Minimum Information About a Microarray Experiment
      (MIAME) standards. The data can be searched by sample name, analysis platform,
      organism, assay details, and keywords. Raw data can also be downloaded from
      the database.
    fairsharing: biodbcore-000441
    homepage: http://www.ncbi.nlm.nih.gov/geo/
    information_keywords:
    - Sequence
    - Expression
    - Image/Movie
    - Repository
    maintainer: NCBI (National Center for Biotechnology Information)
    name: GEO
    prefix: nbdc00080
    pubmeds:
    - '21097893'
    - '18940857'
    - '17160034'
    - '17099226'
    - '16939800'
    - '16888359'
    - '15608262'
    - '11752295'
    status: Active
    target_keywords:
    - cDNA/EST
  logo: https://www.ncbi.nlm.nih.gov/geo/img/geo_main.gif
  mappings:
    cellosaurus: GEO
    edam: '1147'
    fairsharing: FAIRsharing.5hc8vt
    go: GEO
    integbio: nbdc00080
    miriam: geo
    n2t: geo
    prefixcommons: geo
    re3data: r3d100010283
  miriam:
    deprecated: false
    description: The Gene Expression Omnibus (GEO) is a gene expression repository
      providing a curated, online resource for gene expression data browsing, query
      and retrieval.
    homepage: https://www.ncbi.nlm.nih.gov/geo/
    id: '00000054'
    name: GEO
    namespaceEmbeddedInLui: false
    pattern: ^G(PL|SM|SE|DS)\d+$
    prefix: geo
    sampleId: GDS1234
    uri_format: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=$1
  n2t:
    description: The Gene Expression Omnibus (GEO) is a gene expression repository
      providing a curated, online resource for gene expression data browsing, query
      and retrieval.
    example: GDS1234
    homepage: https://www.ncbi.nlm.nih.gov/geo/
    name: Gene Expression Omnibus at NCBI
    namespaceEmbeddedInLui: false
    pattern: ^G(PL|SM|SE|DS)\d+$
    prefix: geo
    uri_format: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=$1
  prefix: geo
  prefixcommons:
    description: The Gene Expression Omnibus (GEO) is a gene expression repository
      providing a curated, online resource for gene expression data browsing, query
      and retrieval.
    example: GDS1234
    homepage: http://www.ncbi.nlm.nih.gov/geo/
    keywords:
    - gene expression
    - genome
    license: http://www.nlm.nih.gov/copyright.html
    name: Gene Expression Omnibus
    pattern: ^GDS\d+$
    prefix: geo
    pubmed_ids:
    - '11752295'
    uri_format: http://www.ncbi.nlm.nih.gov/sites/GDSbrowser?acc=$1
  publications:
  - doi: 10.5281/zenodo.5706412
    pmc: null
    pubmed: null
    title: 'MINSEQE: Minimum Information about a high-throughput Nucleotide SeQuencing
      Experiment - a proposal for standards in functional genomic data reporting'
    year: 2012
  - doi: 10.1093/nar/gks1193
    pmc: PMC3531084
    pubmed: '23193258'
    title: 'NCBI GEO: archive for functional genomics data sets--update'
    year: 2012
  - doi: 10.1038/nbt1206-1471
    pmc: PMC2270403
    pubmed: '17160034'
    title: NCBI GEO standards and services for microarray data
    year: 2006
  - doi: 10.1093/nar/30.1.207
    pmc: PMC99122
    pubmed: '11752295'
    title: 'Gene Expression Omnibus: NCBI gene expression and hybridization array
      data repository'
    year: 2002
  - doi: 10.1038/35001676
    pmc: null
    pubmed: '10693778'
    title: One-stop shop for microarray data
    year: 2000
  - doi: 10.1093/nar/30.1.207
    pmc: null
    pubmed: null
    title: 'Gene Expression Omnibus: NCBI gene expression and hybridization array
      data repository.'
    year: null
  - doi: 10.1093/nar/gks1193
    pmc: null
    pubmed: null
    title: 'NCBI GEO: archive for functional genomics data sets--update.'
    year: null
  - doi: 10.5281/zenodo.5706412
    pmc: null
    pubmed: null
    title: 'MINSEQE: Minimum Information about a high-throughput Nucleotide SeQuencing
      Experiment - a proposal for standards in functional genomic data reporting'
    year: null
  - doi: 10.1038/35001676
    pmc: null
    pubmed: null
    title: One-stop shop for microarray data
    year: null
  - doi: 10.1038/nbt1206-1471
    pmc: null
    pubmed: null
    title: NCBI GEO standards and services for microarray data
    year: null
  - doi: 10.1093/nar/gks1193
    pmc: null
    pubmed: null
    title: 'NCBI GEO: archive for functional genomics data sets—update'
    year: null
  - doi: null
    pmc: null
    pubmed: '11752295'
    title: null
    year: null
  re3data:
    description: 'Gene Expression Omnibus: a public functional genomics data repository
      supporting MIAME-compliant data submissions. Array- and sequence-based data
      are accepted. Tools are provided to help users query and download experiments
      and curated gene expression profiles.'
    doi: 10.17616/R33P44
    homepage: https://www.ncbi.nlm.nih.gov/geo/
    name: Gene Expression Omnibus
    prefix: r3d100010283
    synonyms:
    - GEO
    xrefs:
      nif: 0000-00142
      omics: '01030'
geogeo:
  aberowl:
    description: An ontology of geographical entities
    download_owl: http://aber-owl.net/media/ontologies/GEO/6/geo.owl
    homepage: https://github.com/ufbmi/geographical-entity-ontology/wiki
    name: Geographical Entity Ontology
    prefix: GEO
  banana: GEO
  banana_peel: _
  biocontext:
    prefix: GEO
  bioportal:
    contact:
      email: hoganwr@gmail.com
      name: William Hogan
    description: An ontology of geographical entities implemented in Web Ontology
      Language 2 (OWL2) and based on Basic Formal Ontology (BFO).
    homepage: https://github.com/ufbmi/geographical-entity-ontology/
    name: Geographical Entity Ontology
    prefix: GEO
    version: production version 2018-02-23
  example: '000000021'
  fairsharing:
    abbreviation: GEO
    description: The Geographical Entity Ontology (GEO) is an ontology of geographical
      entities (such as sovereign states and their administrative subdivisions) as
      well as various geographical regions (including but not limited to the specific
      ones over which the governments have jurisdiction).
    domains:
    - Geographic location
    homepage: https://github.com/mcwdsi/geographical-entity-ontology
    license: CC-BY-4.0
    name: Geographical Entity Ontology
    prefix: FAIRsharing.27rndz
    subjects:
    - Physical Geography
    - Human Geography
  mappings:
    aberowl: GEO
    biocontext: GEO
    bioportal: GEO
    fairsharing: FAIRsharing.27rndz
    miriam: geogeo
    obofoundry: geo
    ols: geo
    ontobee: GEO
    wikidata.entity: Q81661641
  miriam:
    deprecated: false
    description: An ontology and inventory of geopolitical entities such as nations
      and their components (states, provinces, districts, counties) and the actual
      physical territories over which they have jurisdiction.  We thus distinguish
      and assign different identifiers to the US in "The US declared war on Germany"
      vs. the US in "The plane entered US airspace".
    homepage: https://github.com/ufbmi
    id: 00000824
    name: Geographical Entity Ontology
    namespaceEmbeddedInLui: false
    pattern: ^GEO_[0-9]{9}$
    prefix: geogeo
    sampleId: GEO_000000021
    uri_format: http://purl.obolibrary.org/obo/$1
  namespace_in_lui: true
  obofoundry:
    contact: hoganwr@gmail.com
    contact.github: hoganwr
    contact.label: Bill Hogan
    contact.orcid: 0000-0002-9881-1017
    deprecated: false
    description: An ontology of geographical entities
    domain: environment
    download.owl: http://purl.obolibrary.org/obo/geo.owl
    homepage: https://github.com/ufbmi/geographical-entity-ontology/wiki
    license: CC BY 4.0
    license.url: https://creativecommons.org/licenses/by/4.0/
    name: Geographical Entity Ontology
    preferredPrefix: GEO
    prefix: geo
    repository: https://github.com/ufbmi/geographical-entity-ontology
  ols:
    description: An ontology of geographical entities
    download_owl: http://purl.obolibrary.org/obo/geo.owl
    homepage: https://github.com/ufbmi/geographical-entity-ontology/wiki
    name: Geographical Entity Ontology
    prefix: geo
    tracker: https://github.com/ufbmi/geographical-entity-ontology/issues
    version: '2016-03-26'
  ontobee:
    library: Library
    name: Geographical Entity Ontology
    prefix: GEO
  pattern: ^\d{9}$
  preferred_prefix: GEOGEO
  prefix: geogeo
  repository: https://github.com/ufbmi/geographical-entity-ontology
  uri_format: http://purl.obolibrary.org/obo/GEO_$1
geonames:
  contact:
    email: marc@geonames.org
    github: null
    name: Marc Wick
    orcid: null
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: The GeoNames geographical database covers all countries and contains
    over eleven million placenames that are available for download free of charge.
  domain: geography
  example: '3532759'
  fairsharing:
    abbreviation: GeoNames Ontology
    description: The GeoNames Ontology makes it possible to add geospatial semantic
      information to the Word Wide Web. It maps to the DB schema that is used by GeoNames
      data export.
    domains:
    - Geographic location
    homepage: http://www.geonames.org/ontology/documentation.html
    license: CC-BY-4.0
    name: GeoNames Ontology
    prefix: FAIRsharing.6dba71
    subjects:
    - Geography
    - Geoinformatics
  homepage: https://www.geonames.org
  license: CC-BY-4.0
  logo: https://www.geonames.org/img/globe.gif
  mappings:
    fairsharing: FAIRsharing.6dba71
    re3data: r3d100010245
  name: GeoNames
  part_of_database: geonames
  pattern: ^\d+$
  prefix: geonames
  re3data:
    description: The GeoNames geographical database covers all countries and contains
      over eight million placenames that are available for download free of charge.
    doi: 10.17616/R3MS4T
    homepage: https://www.geonames.org/
    license: CC
    name: GeoNames
    prefix: r3d100010245
  synonyms:
  - Geomames
  - Geonamaes
  uri_format: https://www.geonames.org/$1
geonames.feature:
  contact:
    email: marc@geonames.org
    github: null
    name: Marc Wick
    orcid: null
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: All geographical features in GeoNames are categorized into one out
    of nine feature classes and further subcategorized into one out of 645 feature
    codes.
  domain: geography
  example: ADM1
  homepage: https://www.geonames.org/export/codes.html
  keywords:
  - geography
  license: CC-BY-4.0
  logo: https://www.geonames.org/img/globe.gif
  name: GeoNames Feature Code
  part_of_database: geonames
  prefix: geonames.feature
  uri_format: https://www.geonames.org/recent-changes/featurecode/$1/
geonames.ontology:
  description: An ontology used to enable annotating geospatial semantic information
    to entities in GeoNames
  download_rdf: https://www.geonames.org/ontology/ontology_v3.3.rdf
  example: parentFeature
  homepage: https://www.geonames.org/ontology/documentation.html
  mappings:
    zazuko: gn
  name: GeoNames Ontology
  part_of_database: geonames
  prefix: geonames.ontology
  zazuko:
    prefix: gn
    uri_format: http://www.geonames.org/ontology#$1
geosparql:
  aberowl:
    description: The OGC GeoSPARQL standard supports representing and querying geospatial
      data on the Semantic Web. GeoSPARQL defines a vocabulary for representing geospatial
      data in RDF, and it defines an extension to the SPARQL query language for processing
      geospatial data. In addition, GeoSPARQL is designed to accommodate systems based
      on qualitative spatial reasoning and systems based on quantitative spatial computations.
    download_owl: http://aber-owl.net/media/ontologies/GEOSPARQL/1/geosparql.owl
    name: GeoSPARQL
    prefix: GEOSPARQL
    version: OGC GeoSPARQL 1.0
  bioportal:
    contact:
      email: kdurante@stanford.edu
      name: Kim Durante
    description: The OGC GeoSPARQL standard supports representing and querying geospatial
      data on the Semantic Web. GeoSPARQL defines a vocabulary for representing geospatial
      data in RDF, and it defines an extension to the SPARQL query language for processing
      geospatial data. In addition, GeoSPARQL is designed to accommodate systems based
      on qualitative spatial reasoning and systems based on quantitative spatial computations.
    name: GeoSPARQL
    prefix: GEOSPARQL
    version: OGC GeoSPARQL 1.0
  example: hasDefaultGeometry
  mappings:
    aberowl: GEOSPARQL
    bioportal: GEOSPARQL
    tib: geo
    zazuko: geo
  prefix: geosparql
  tib:
    description: An RDF/OWL vocabulary for representing spatial information
    download_rdf: https://opengeospatial.github.io/ogc-geosparql/geosparql11/geo.ttl
    homepage: https://opengeospatial.github.io/ogc-geosparql/geosparql11/index.html
    keywords:
    - FAIR Data Spaces
    - NFDI4ING
    - ESS
    - earth sciences
    name: GeoSPARQL Ontology
    prefix: geo
    uri_format: http://www.opengis.net/ont/geosparql#$1
    version.iri: http://www.opengis.net/ont/geosparql/1.1
  zazuko:
    prefix: geo
    uri_format: http://www.opengis.net/ont/geosparql#$1
geosparql.function:
  description: Functions for GeoSPARQL
  example: sfEquals
  homepage: https://opengeospatial.github.io/ogc-geosparql/geosparql10/servicedescription_all_functions.html
  mappings:
    zazuko: geof
  name: GeoSPARQL Function
  prefix: geosparql.function
  zazuko:
    prefix: geof
    uri_format: http://www.opengis.net/def/function/geosparql/$1
geosparql.rule:
  description: Rules for GeoSPARQL
  example: rcc
  homepage: https://opengeospatial.github.io/ogc-geosparql/geosparql11/rules.html
  mappings:
    zazuko: geor
  name: GeoSPARQL Rule
  prefix: geosparql.rule
  zazuko:
    prefix: geor
    uri_format: http://www.opengis.net/def/rule/geosparql/$1
gesah:
  example: applies_to
  mappings:
    tib: gesah
  prefix: gesah
  tib:
    contact: sammlung.haupt@tib.eu
    description: The GESAH Graphic Arts Ontology is designed for the inventory, classification
      and structured description of works on paper.
    download_rdf: https://raw.githubusercontent.com/tibonto/gesah/main/gesah.ttl
    homepage: https://sah.tib.eu/
    keywords:
    - NFDI4CULTURE
    - architecture
    - history
    name: GESAH Graphic Arts Ontology
    prefix: gesah
    tracker: https://github.com/tibonto/gesah/issues
    uri_format: http://ontology.tib.eu/gesah/$1
    version.iri: http://ontology.tib.eu/gesah/1.0/2024-11-25/
gesis.kategorienschemawahlstudien:
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: The Category Scheme Election Studies provides the ability to categorize
    election studies at the question and/or variable level.
  example: '01'
  homepage: https://vocabularies.cessda.eu/vocabulary/KategorienschemaWahlstudien
  license: CC-BY-4.0
  name: Category Scheme Election Studies
  owners:
  - name: GESIS - Leibniz-Institute for the Social Sciences
    partnered: false
    ror: 018afyw53
    wikidata: null
  part_of_database: gesis
  prefix: gesis.kategorienschemawahlstudien
  uri_format: https://vocabularies.cessda.eu/vocabulary/KategorienschemaWahlstudien?lang=en#code_$1
  version: 1.0.1
gesis.rexconcepts:
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: This CV, developed within the framework of the DP-R|EX joint project,
    involving the partner institutions DeZIM, Qualiservice and GESIS, maps the central
    concepts and theoretical approaches in research on racism and right-wing extremism.
    The compilation is based on a systematic evaluation of the relevant national and
    international empirical research literature. The CV equally takes into account
    the different thematic (racism, right-wing extremism, discrimination) as well
    as methodological (qualitative research, standardised surveys, data from social
    media and messaging services) research strands.
  example: '33'
  homepage: https://vocabularies.cessda.eu/vocabulary/rexconcepts
  license: CC-BY-4.0
  name: Central concepts of R|EX research
  owners:
  - name: GESIS - Leibniz-Institute for the Social Sciences
    partnered: false
    ror: 018afyw53
    wikidata: null
  part_of_database: gesis
  prefix: gesis.rexconcepts
  uri_format: https://vocabularies.cessda.eu/vocabulary/rexconcepts?lang=en#code_$1
  version: 1.9.0
gesis.rexdatatype:
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: This CV, developed as part of the DP-R|EX joint project, involving
    the partner institutions DeZIM, Qualiservice and GESIS, maps the data types relevant
    to the research field. The CV includes data types that can result from a variety
    of different collection methods. These include, for example, standardised or unstandardised
    surveys, individual or repeated observations, as well as process-produced or user-generated
    types of data generation. The data types can be subject-, event-, space- or time-related
    and refer to the individual or aggregate level.
  example: 01a
  homepage: https://vocabularies.cessda.eu/vocabulary/rexdatatype
  license: CC-BY-4.0
  name: Data types in R|EX research
  owners:
  - name: GESIS - Leibniz-Institute for the Social Sciences
    partnered: false
    ror: 018afyw53
    wikidata: null
  part_of_database: gesis
  prefix: gesis.rexdatatype
  uri_format: https://vocabularies.cessda.eu/vocabulary/rexdatatype?lang=en#code_$1
  version: 1.4.1
gesis.rexgroups:
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: This CV, developed within the framework of the DP-R|EX joint project,  involving
    the partner institutions DeZIM, Qualiservice and GESIS, maps the dimensions of
    discrimination and racialised characteristics relevant to the research area. The
    compilation is based on a systematic evaluation of the relevant national and international
    empirical research literature. These include self-attributed characteristics as
    well as anticipated attributions by others. The characteristics do not necessarily
    correspond to the studied units in the data set, but can also be the subject of
    studied concepts or theories in the surveys, such as on specific prejudices and
    attitudes.
  example: v1
  homepage: https://vocabularies.cessda.eu/vocabulary/rexgroups
  license: CC-BY-4.0
  name: Diversification criteria of R|EX research
  owners:
  - name: GESIS - Leibniz-Institute for the Social Sciences
    partnered: false
    ror: 018afyw53
    wikidata: null
  part_of_database: gesis
  prefix: gesis.rexgroups
  uri_format: https://vocabularies.cessda.eu/vocabulary/rexgroups?lang=en#code_$1
  version: 1.10.0
gesis.variables-relations:
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: As the variable is one of the most relevant entities to enhance data
    reuse in the Social Sciences, we provide a framework design to better semantics
    the variables' relations descriptions. These explicit relations between variables
    enable comparability and facilitate harmonization across waves. We provide a brief
    textual identification of the relation type, supported by a controlled vocabulary
    (CV) and an extended description of the relationship. These relations within variables
    include but are not limited to different versions, derived formats in new waves,
    new labels and name wording, and alternative response schema through questionnaires
    and surveys. For instance, a given variable label is changed from one wave to
    another, even though its concept remains the same. Their values also are subject
    to change, such as new cardinalities settings, their categorization, or response
    scheme and scale measurement. They change based on different conditions, e.g.,
    values are updated by any constraints or modified to comply with the study evolution
    requirements or a new sociological approach. In the Social Sciences, Economics,
    and Behaviour Sciences, which investigate, for instance, the social structure
    of the population, political attitudes of voters and candidates, opinions on family,
    work, religion, politics and society or competencies of adults, those topics are
    highly subject to change to fit the empirical reality in a constantly changing
    world. Thus, we propose widening relations descriptions for Social Sciences variables
    within datasets beginning from the BasedOnObjectType DDI as a first approach.
  example: '01'
  homepage: https://vocabularies.cessda.eu/vocabulary/Variables-Relations
  license: CC-BY-4.0
  name: Variables relations for Social Sciences research data
  owners:
  - name: GESIS - Leibniz-Institute for the Social Sciences
    partnered: false
    ror: 018afyw53
    wikidata: null
  part_of_database: gesis
  prefix: gesis.variables-relations
  uri_format: https://vocabularies.cessda.eu/vocabulary/Variables-Relations?lang=en#code_$1
  version: 1.0.0
gesiskg:
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: Predicates that are used to construct the GESIS Knowledge Graph, a
    bibliometrics KG.
  example: linkContext
  github_request_issue: 1632
  homepage: https://data.gesis.org/gesiskg
  keywords:
  - data schema
  - nfdi
  name: GESIS Knowledge Graph Schema
  prefix: gesiskg
  uri_format: https://data.gesis.org/gesiskg/schema/$1
getty.att:
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: The AAT includes generic terms, and associated dates, relationships,
    and other rich information about concepts related to or required to catalog, discover,
    and retrieve information about art, architecture, and other visual cultural heritage,
    including related disciplines such as archaeology and conservation. Visual works
    include not only visual cultural works classified as "art" according to Western
    aesthetics, but also utilitarian and ceremonial works. Terminology may be used
    for work types, roles, materials, styles, cultures, techniques, subject, etc.,
    so long as terms are within the defined scope of AAT. [from https://www.getty.edu/research/tools/vocabularies/aat/aat_faq.html]
  download_rdf: https://vocab.getty.edu/aat.ttl
  example: '300011154'
  homepage: http://vocab.getty.edu/ontology
  license: ODC-By-1.0
  name: Art and Architecture Thesaurus
  prefix: getty.att
  providers:
  - code: legacy
    description: null
    example: null
    first_party: null
    homepage: null
    name: null
    publications: null
    status: null
    uri_format: http://vocab.getty.edu/resource/aat/$1
  references:
  - https://www.getty.edu/research/tools/vocabularies/lod/aat_semantic_representation.pdf
  - https://www.getty.edu/research/tools/vocabularies/lod/index.html
  uri_format: http://vocab.getty.edu/aat/$1
getty.cona:
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: CONA compiles titles, attributions, depicted subjects, and other metadata
    about works of art, architecture, and cultural heritage, both extant and historical,
    physical and conceptual. Metadata is gathered and linked from museum collections,
    special collections, archives, libraries, scholarly research, and other sources.
    CONA is linked to the AAT, TGN, ULAN, and the IA (Iconography Authority). Through
    rich metadata and links, CONA may provide a powerful conduit for research and
    discovery for digital art history. [from homepage]
  example: '700054086'
  homepage: https://www.getty.edu/research/tools/vocabularies/cona/
  license: ODC-By-1.0
  name: Cultural Objects Names Authority
  prefix: getty.cona
  uri_format: http://vocab.getty.edu/page/cona/$1
getty.gvp:
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: The GVP Ontology defines classes, properties and values (skos:Concepts)
    used in GVP LOD. As of version 3.0, it is complete regarding AAT, TGN and ULAN,
    and will be extended in time with more elements needed for other GVP vocabularies
    (CONA).
  download_rdf: http://vocab.getty.edu/ontology.ttl
  example: prefLabelGVP
  homepage: http://vocab.getty.edu/ontology
  name: Getty Vocabulary Program ontology
  prefix: getty.gvp
  providers:
  - code: legacy
    description: null
    example: null
    first_party: null
    homepage: null
    name: null
    publications: null
    status: null
    uri_format: http://vocab.getty.edu/resource/ontology#$1
  references:
  - https://www.getty.edu/research/tools/vocabularies/lod/aat_semantic_representation.pdf
  - https://www.getty.edu/research/tools/vocabularies/lod/index.html
  uri_format: http://vocab.getty.edu/ontology#$1
getty.ia:
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: The Getty Iconography Authority ™ (IA), Cultural Objects Name Authority
    ® (CONA), the Union List of Artist Names ® (ULAN), the Art & Architecture Thesaurus
    ® (AAT), the Getty Thesaurus of Geographic Names ® (TGN) are structured resources
    that can be used to improve access to information about art, architecture, and
    other material culture. The Vocabularies are not simply 'value vocabularies,'
    but knowledge bases. Through rich metadata and links, the Getty Vocabularies provide
    powerful conduits for knowledge creation, complex research, and discovery for
    digital art history and related disciplines. [from https://www.getty.edu/research/tools/vocabularies/cona/about.html#purpose_ia]
  example: '901001034'
  homepage: https://www.getty.edu/cona/CONAIconographyHierarchy.aspx?iconid=901000000
  name: Getty Iconography Authority
  prefix: getty.ia
  uri_format: http://vocab.getty.edu/page/ia/$1
getty.tgn:
  bartoc:
    abbreviation: TGN
    description: 'TGN is a structured vocabulary currently containing around 1,106,000
      names and other information about places. Names for a place may include names
      in the vernacular language, English, other languages, historical names, names
      and in natural order and inverted order. Among these names, one is flagged as
      the preferred name. TGN is a thesaurus, compliant with ISO and NISO standards
      for thesaurus construction; it contains hierarchical, equivalence, and associative
      relationships. Note that TGN is not a GIS (Geographic Information System). While
      many records in TGN include coordinates, these coordinates are approximate and
      are intended for reference only. The focus of each TGN record is a place. There
      are around 912,000 places in the TGN. In the database, each place record (also
      called a subject) is identified by a unique numeric ID. Linked to the record
      for the place are names, the place''s parent or position in the hierarchy, other
      relationships, geographic coordinates, notes, sources for the data, and place
      types, which are terms describing the role of the place (e.g., inhabited place
      and state capital). The temporal coverage of the TGN ranges from prehistory
      to the present and the scope is global. The TGN is a hierarchical database;
      its trees branch from a root called Top of the TGN hierarchies (Subject_ID:
      1000000). Currently there are two TGN facets, World and Extraterrestrial Places.
      Under the facet World, places are arranged in hierarchies generally representing
      the current political and physical world, although some historical nations and
      empires are also included. There may be multiple broader contexts, making the
      TGN polyhierarchical. The primary users of the Getty vocabularies include museums,
      art libraries, archives, visual resource collection catalogers, bibliographic
      projects concerned with art, researchers in art and art history, and the information
      specialists who are dealing with the needs of these users. In addition, a significant
      number of users of the Getty vocabularies are students or members of the general
      public.'
    homepage: http://www.getty.edu/research/tools/vocabularies/tgn/
    license: http://www.opendatacommons.org/licenses/by/1.0
    name: Getty Thesaurus of Geographic Names
    prefix: '109'
    wikidata_database: Q1520117
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  example: '1023371'
  fairsharing:
    abbreviation: TGN
    description: The Thesaurus of Geographic Names (TGN) is a terminology that focuses
      on places relevant to art, architecture, and related disciplines, recording
      names, relationships, place types, dates, notes, and coordinates for current
      and historical cities, nations, empires, archaeological sites, lost settlements,
      and physical features. The TGN is one of 5 Getty Vocabularies intended to provide
      terminology and other information about the objects, artists, concepts, and
      places important to various disciplines that specialize in art, architecture,
      and other material culture.
    domains:
    - Geographic location
    homepage: http://www.getty.edu/research/tools/vocabularies/tgn/index.html
    license: http://opendatacommons.org/licenses/by/1.0
    name: Thesaurus of Geographic Names
    prefix: FAIRsharing.1413b5
    subjects:
    - Architecture
    - Culture
    - Geography
    - History
    - Ancient Cultures
    - Fine Arts
    - Art History
    - Human Geography
  homepage: https://www.getty.edu/research/tools/vocabularies/tgn/
  license: ODC-By-1.0
  mappings:
    bartoc: '109'
    fairsharing: FAIRsharing.1413b5
    wikidata.entity: Q1520117
  name: Getty Thesaurus of Geographic Names
  pattern: ^\d+$
  prefix: getty.tgn
  providers:
  - code: getty.tgn.page
    description: null
    example: null
    first_party: null
    homepage: null
    name: null
    publications: null
    status: null
    uri_format: http://vocab.getty.edu/page/tgn/$1
  references:
  - https://obo-communitygroup.slack.com/archives/C023P0Z304T/p1638380238036200
  synonyms:
  - tgn
  uri_format: http://vocab.getty.edu/tgn/$1
getty.ulan:
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: The Getty Thesaurus of Geographic Names (TGN) is a structured vocabulary,
    including names, descriptions, and other metadata for extant and historical cities,
    empires, archaeological sites, and physical features important to research of
    art and architecture. TGN may be linked to GIS (Geographical Information System),
    maps, and other geographic resources. [from https://collectionstrust.org.uk/resource/thesaurus-of-geographic-names-tgn-getty/]
  example: '500202846'
  homepage: http://vocab.getty.edu/ulan/
  license: ODC-By-1.0
  name: Union List of Artist Names
  prefix: getty.ulan
  uri_format: http://vocab.getty.edu/ulan/$1
gexo:
  aberowl:
    description: An application ontology for the domain of gene expression. The ontology
      integrates fragments of GO and MI with data from GOA, IntAct, UniProt, NCBI,
      and orthology relations using ontological properties from RO and ISO.
    download_owl: http://aber-owl.net/media/ontologies/GEXO/2/gexo.owl
    homepage: http://www.semantic-systems-biology.org/apo
    name: Gene Expression Ontology
    prefix: GEXO
    version: '2015'
  bioportal:
    contact:
      email: vladimir.n.mironov@gmail.com
      name: Vladimir Mironov
    description: An application ontology for the domain of gene expression. The ontology
      integrates fragments of GO and MI with data from GOA, IntAct, UniProt, NCBI,
      and orthology relations using ontological properties from RO and ISO.
    homepage: http://www.semantic-systems-biology.org/apo
    name: Gene Expression Ontology
    prefix: GEXO
    publications:
    - http://bmcbioinformatics.biomedcentral.com/articles/10.1186/s12859-014-0386-y
    version: '2015'
  contact:
    email: kuiper@bio.ntnu.no
    github: makuintnu
    name: Martin Kuiper
    orcid: 0000-0002-1171-9876
  download_obo: https://www.bio.ntnu.no/ontology/GeXO/gexo.obo
  download_owl: https://www.bio.ntnu.no/ontology/GeXO/gexo.owl
  fairsharing:
    abbreviation: GeXO
    contact:
      email: kuiper@bio.ntnu.no
      name: Martin Kuiper
      orcid: 0000-0002-1171-9876
    description: An application ontology for the domain of gene expression. The ontology
      integrates fragments of GO and MI with data from GOA, IntAct, UniProt, NCBI,
      and orthology relations using ontological properties from RO and ISO.
    domains:
    - Expression data
    - gene expression
    homepage: https://www.biogateway.eu/tools/#GeXKB
    name: Gene Expression Ontology
    prefix: FAIRsharing.3e0sn4
    publications:
    - doi: 10.1186/s12859-014-0386-y
      pubmed: '25490885'
      title: Finding gene regulatory network candidates using the gene expression
        knowledge base
      year: 2014
    subjects:
    - Life Science
  mappings:
    aberowl: GEXO
    bioportal: GEXO
    fairsharing: FAIRsharing.3e0sn4
    ols: gexo
  no_own_terms: true
  ols:
    contact: vladimir.n.mironov@gmail.com
    description: Gene Expression Ontology
    download_rdf: http://www.bio.ntnu.no/ontology/GeXO/gexo.rdf
    homepage: http://www.semantic-systems-biology.org/apo
    name: Gene Expression Ontology
    prefix: gexo
    uri_format: http://purl.obolibrary.org/obo/GeXO_$1
  prefix: gexo
  publications:
  - doi: 10.1186/s12859-014-0386-y
    pmc: PMC4279962
    pubmed: '25490885'
    title: Finding gene regulatory network candidates using the gene expression knowledge
      base
    year: 2014
  - doi: 10.1186/s12859-014-0386-y
    pmc: null
    pubmed: '25490885'
    title: Finding gene regulatory network candidates using the gene expression knowledge
      base
    year: 2014
gfbio.ets:
  example: BiodiversityExploratories
  mappings:
    tib: ets
  name: Ecological Trait-data Standard
  prefix: gfbio.ets
  tib:
    description: The Ecological Trait-data Standard defines terms for the use in datasets
      containing quantitative and qualitative functional traits.
    download_owl: https://terminologies.gfbio.org/terms/ets/pages/ets.owl
    homepage: https://terminologies.gfbio.org/terms/ets/pages/index.html
    keywords:
    - FAIR Data Spaces
    - ESS
    - life sciences, biology
    - earth sciences
    name: Ecological Trait-data Standard (ETS)
    prefix: ets
    uri_format: http://terminologies.gfbio.org/terms/ETS/$1
    version.iri: http://terminologies.gfbio.org/terms/ets/2019-03-15/ets.owl
gfo:
  aberowl:
    description: The General Formal Ontology (GFO) is a top-level ontology integrating
      objects and processes.
    download_owl: http://aber-owl.net/media/ontologies/GFO/1/gfo.owl
    homepage: http://www.onto-med.de/ontologies/gfo/
    name: General Formal Ontology
    prefix: GFO
    version: 'Version 1.0 ($Revision: 1.13 $)'
  bioportal:
    contact:
      email: heinrich.herre@imise.uni-leipzig.de
      name: Heinrich Herre
    description: The General Formal Ontology (GFO) is a top-level ontology integrating
      objects and processes.
    homepage: http://www.onto-med.de/ontologies/gfo/
    name: General Formal Ontology
    prefix: GFO
    version: 'Version 1.0 ($Revision: 1.13 $)'
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: The General Formal Ontology is a top-level ontology for conceptual
    modeling, which is being constantly further developed by Onto-Med. It includes
    elaborations of categories like objects, processes, time and space, properties,
    relations, roles, functions, facts, and situations. Moreover, we are working on
    an integration with the notion of levels of reality in order to more appropriately
    capture entities in the material, mental, and social areas.
  download_owl: http://www.onto-med.de/ontologies/gfo.owl
  example: projects_to
  fairsharing:
    abbreviation: GFO
    description: The General Formal Ontology is a top-level ontology for conceptual
      modeling, which is being constantly further developed by Onto-Med. It includes
      elaborations of categories like objects, processes, time and space, properties,
      relations, roles, functions, facts, and situations. Moreover, we are working
      on an integration with the notion of levels of reality in order to more appropriately
      capture entities in the material, mental, and social areas.
    homepage: https://www.onto-med.de/ontologies/gfo/
    name: General Formal Ontology
    prefix: FAIRsharing.175hsz
    subjects:
    - Life Science
    - Biomedical Science
  homepage: https://www.onto-med.de/ontologies/gfo
  mappings:
    aberowl: GFO
    bioportal: GFO
    fairsharing: FAIRsharing.175hsz
    tib: gfo
  name: General Formal Ontology
  prefix: gfo
  providers:
  - code: alt1
    description: Alternate identifier using gfo-basic.owl instead of gfo.owl
    example: null
    first_party: null
    homepage: http://www.onto-med.de/ontologies
    name: Alternate 1
    publications: null
    status: null
    uri_format: http://www.onto-med.de/ontologies/gfo-basic.owl#$1
  tib:
    description: It comprises a set of selected major and rather stable GFO categories,
      with the intention to serve as a comprehensible starting point which 1. should
      be useful for immediate modeling purposes, 2. covers GFO's areas and exhibits
      outstanding GFO features 3. omits categories of more theoretical character or
      those which are easily definable
    homepage: https://github.com/Onto-Med/GFO
    keywords:
    - Foundational Ontologies
    - engineering
    name: General Formal Ontology (GFO)
    prefix: gfo
    tracker: https://github.com/Onto-Med/GFO/issues
    uri_format: https://w3id.org/gfo/base/$1
    version.iri: https://w3id.org/gfo/release/2024-11-18
  uri_format: http://www.onto-med.de/ontologies/gfo.owl#$1
ghr:
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: MedlinePlus Genetics contains detailed information about the effects
    of genetic variation on human health, covering more than 1,300 genetic conditions
    and 1,400 genes, all of the human chromosomes, and mitochondrial DNA (mtDNA).
  example: saddan
  homepage: https://medlineplus.gov/genetics/condition
  name: Genetics Home Reference
  prefix: ghr
  uri_format: https://medlineplus.gov/genetics/condition/$1
giardiadb:
  biocontext:
    prefix: GIARDIADB
  contact:
    email: oharb@upenn.edu
    github: ramobrah
    name: Omar S. Harb
    orcid: 0000-0003-4446-6200
  fairsharing:
    abbreviation: GiardiaDB
    description: A detailed study of Giardia lamblia's genome will provide insights
      into an early evolutionary stage of eukaryotic chromosome organization as well
      as other aspects of the prokaryotic / eukaryotic divergence.
    homepage: http://giardiadb.org
    license: http://opendatacommons.org/licenses/pddl/1.0
    name: GiardiaDB
    prefix: FAIRsharing.e7skwg
    publications:
    - doi: 10.1093/nar/gkn631
      pubmed_id: 18824479
      title: 'GiardiaDB and TrichDB: integrated genomic resources for the eukaryotic
        protist pathogens Giardia lamblia and Trichomonas vaginalis.'
    subjects:
    - Genomics
    twitter: EuPathDB
  integbio:
    description: A detailed study of Giardia lamblia's genome will provide insights
      into an early evolutionary stage of eukaryotic chromosome organization as well
      as other aspects of the prokaryotic / eukaryotic divergence.
    fairsharing: FAIRsharing.e7skwg
    homepage: http://giardiadb.org
    information_keywords:
    - Sequence
    - Expression
    - Ontology/Terminology/Nomenclature
    name: GiardiaDB
    prefix: nbdc01782
    pubmeds:
    - '18824479'
    status: Active
    target_keywords:
    - Cell/Organelle
    - Genome/Gene
    - cDNA/EST
    - Organism
  mappings:
    biocontext: GIARDIADB
    fairsharing: FAIRsharing.e7skwg
    integbio: nbdc01782
    miriam: giardiadb
    n2t: giardiadb
    prefixcommons: giardiadb
    re3data: r3d100012458
  miriam:
    deprecated: false
    description: GiardiaDB is one of the databases that can be accessed through the
      EuPathDB (http://EuPathDB.org; formerly ApiDB) portal, covering eukaryotic pathogens
      of the genera Cryptosporidium, Giardia, Leishmania, Neospora, Plasmodium, Toxoplasma,
      Trichomonas and Trypanosoma. While each of these groups is supported by a taxon-specific
      database built upon the same infrastructure, the EuPathDB portal offers an entry
      point to all these resources, and the opportunity to leverage orthology for
      searches across genera.
    homepage: https://giardiadb.org/giardiadb/
    id: '00000151'
    name: GiardiaDB
    namespaceEmbeddedInLui: false
    pattern: ^\w+$
    prefix: giardiadb
    sampleId: GL50803_102438
    uri_format: https://giardiadb.org/giardiadb/app/record/gene/$1
  n2t:
    description: GiardiaDB is one of the databases that can be accessed through the
      EuPathDB (http://EuPathDB.org; formerly ApiDB) portal, covering eukaryotic pathogens
      of the genera Cryptosporidium, Giardia, Leishmania, Neospora, Plasmodium, Toxoplasma,
      Trichomonas and Trypanosoma. While each of these groups is supported by a taxon-specific
      database built upon the same infrastructure, the EuPathDB portal offers an entry
      point to all these resources, and the opportunity to leverage orthology for
      searches across genera.
    example: GL50803_102438
    homepage: https://giardiadb.org/giardiadb/
    name: GiardiaDB at EuPathDB
    namespaceEmbeddedInLui: false
    pattern: ^\w+$
    prefix: giardiadb
    uri_format: https://giardiadb.org/giardiadb/app/record/gene/$1
  prefix: giardiadb
  prefixcommons:
    description: A detailed study of Giardia lamblia's genome will provide insights
      into an early evolutionary stage of eukaryotic chromosome organization as well
      as other aspects of the prokaryotic / eukaryotic divergence.
    example: GL50803_102438
    homepage: http://giardiadb.org
    keywords:
    - eukaryotic
    - genome
    name: GiardiaDB
    pattern: ^GL\d+_\d+$
    prefix: giardiadb
    pubmed_ids:
    - '18824479'
    uri_format: http://giardiadb.org/giardiadb/showRecord.do?name=GeneRecordClasses.GeneRecordClass&primary_key=$1
  publications:
  - doi: 10.1093/nar/gkn631
    pmc: PMC2686445
    pubmed: '18824479'
    title: 'GiardiaDB and TrichDB: integrated genomic resources for the eukaryotic
      protist pathogens Giardia lamblia and Trichomonas vaginalis'
    year: 2008
  - doi: 10.1093/nar/gkn631
    pmc: null
    pubmed: null
    title: 'GiardiaDB and TrichDB: integrated genomic resources for the eukaryotic
      protist pathogens Giardia lamblia and Trichomonas vaginalis.'
    year: null
  - doi: null
    pmc: null
    pubmed: '18824479'
    title: null
    year: null
  re3data:
    description: 'Giardia lamblia is a significant, environmentally transmitted, human
      pathogen and an amitochondriate protist. It is a major contributor to the enormous
      worldwide burden of human diarrheal diseases, yet the basic biology of this
      parasite is not well understood. No virulence factor has been identified. The
      Giardia lamblia genome contains only 12 million base pairs distributed onto
      five chromosomes. Its analysis promises to provide insights about the origins
      of nuclear genome organization, the metabolic pathways used by parasitic protists,
      and the cellular biology of host interaction and avoidance of host immune systems.

      Since the divergence of Giardia lamblia lies close to the transition between
      eukaryotes and prokaryotes in universal ribosomal RNA phylogenies, it is a valuable,
      if not unique, model for gaining basic insights into genetic innovations that
      led to formation of eukaryotic cells. In evolutionary terms, the divergence
      of this organism is at least twice as ancient as the common ancestor for yeast
      and man. A detailed study of its genome will provide insights into an early
      evolutionary stage of eukaryotic chromosome organization as well as other aspects
      of the prokaryotic / eukaryotic divergence.'
    doi: 10.17616/R3XF5J
    homepage: https://giardiadb.org/giardiadb/app
    name: GiardiaDB
    prefix: r3d100012458
    xrefs:
      nif: 0000-02908
      omics: '03161'
gist:
  example: Account
  mappings:
    tib: gist
  prefix: gist
  tib:
    description: gist is a minimalist upper ontology created by Semantic Arts.
    homepage: https://www.semanticarts.com/gist/
    keywords:
    - NFDI4ING
    - Foundational Ontologies
    - engineering
    license: https://creativecommons.org/licenses/by/4.0/
    name: gist
    prefix: gist
    tracker: https://github.com/semanticarts/gist/issues
    uri_format: https://w3id.org/semanticarts/ns/ontology/gist/$1
    version.iri: https://w3id.org/semanticarts/ontology/gistCore14.0.0
github:
  example: biopragmatics/bioregistry
  example_extras:
  - biopragmatics
  - cthoyt
  fairsharing:
    abbreviation: GitHub
    description: GitHub Inc. is a Git-based software repository that provides version
      control. It offers all of the distributed version control and source code management
      (SCM) functionality of Git as well as adding its own features. It provides access
      control and several collaboration features such as bug tracking, feature requests,
      task management, and wikis for each project. It provides a number of different
      access levels, from free through to paid services.
    homepage: https://github.com/
    license: https://help.github.com/articles/github-terms-of-service
    name: GitHub
    prefix: FAIRsharing.c55d5e
    publications: []
    repository: https://services.github.com/
    subjects:
    - Knowledge and Information Systems
    - Subject Agnostic
    - Software Engineering
  mappings:
    fairsharing: FAIRsharing.c55d5e
    miriam: github
    re3data: r3d100010375
    wikidata: P2037
  miriam:
    deprecated: false
    description: GitHub is an online host of Git source code repositories.
    homepage: https://github.com/
    id: 00000853
    name: github
    namespaceEmbeddedInLui: false
    pattern: ^[a-zA-Z0-9-_]+/[a-zA-Z0-9-_]+$
    prefix: github
    sampleId: identifiers-org/registry
    uri_format: https://github.com/$1
  part_of_database: github
  pattern: ^[a-zA-Z0-9-_]+(/[a-zA-Z0-9-_]+)?$
  prefix: github
  re3data:
    description: GitHub is the best place to share code with friends, co-workers,
      classmates, and complete strangers. Over three million people use GitHub to
      build amazing things together. With the collaborative features of GitHub.com,
      our desktop and mobile apps, and GitHub Enterprise, it has never been easier
      for individuals and teams to write better code, faster. Originally founded by
      Tom Preston-Werner, Chris Wanstrath, and PJ Hyett to simplify sharing code,
      GitHub has grown into the largest code host in the world.
    doi: 10.17616/R3559G
    homepage: https://github.com
    license: Copyrights
    name: GitHub
    prefix: r3d100010375
  wikidata:
    database: Q364
    description: username of this project, person or organization on GitHub
    example:
    - google
    - michaelni
    homepage: https://github.com/
    name: GitHub username
    pattern: ^[0-9A-Za-z]([0-9A-Za-z\-]{0,37}[0-9A-Za-z])?$
    prefix: P2037
    short_name:
    - GitHub
    uri_format: https://github.com/$1
github.issue:
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: An issue in any public repository on GitHub.
  example: biopragmatics/bioregistry/424
  homepage: https://github.com/
  keywords:
  - knowledge and information systems
  - project management
  - software engineering
  - version control
  name: GitHub Issue
  part_of_database: github
  prefix: github.issue
  uri_format: https://bioregistry.io/resolve/github/issue/$1
github.pull:
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: A pull request in any public repository on GitHub.
  example: biopragmatics/bioregistry/416
  homepage: https://github.com/
  keywords:
  - knowledge and information systems
  - project management
  - software engineering
  - version control
  name: GitHub Pull Request
  part_of_database: github
  prefix: github.pull
  uri_format: https://bioregistry.io/resolve/github/pull/$1
gitlab:
  fairsharing:
    abbreviation: GitLab
    description: GitLab is a Git-based source code repository with wiki and issue
      tracker functionality. It provides a number of different access levels, from
      free through to a number of paid services.
    homepage: https://about.gitlab.com/
    name: GitLab
    prefix: FAIRsharing.530e61
    publications: []
    subjects:
    - Knowledge and Information Systems
    - Subject Agnostic
    - Software Engineering
    twitter: gitlab
  mappings:
    fairsharing: FAIRsharing.530e61
    miriam: gitlab
  miriam:
    deprecated: false
    description: GitLab is The DevOps platform that empowers organizations to maximize
      the overall return on software development by delivering software faster and
      efficiently, while strengthening security and compliance. With GitLab, every
      team in your organization can collaboratively plan, build, secure, and deploy
      software to drive business outcomes faster with complete transparency, consistency
      and traceability.
    homepage: https://gitlab.com/
    id: 00000901
    name: GitLab
    namespaceEmbeddedInLui: false
    pattern: ^[0-9A-Za-z_][0-9A-Za-z-_()\. ]*/[0-9A-Za-z_][0-9A-Za-z-_\. ]*$
    prefix: gitlab
    sampleId: morpheus.lab/morpheus
    uri_format: https://gitlab.com/$1
  pattern: ^.*/.*$
  prefix: gitlab
glida.gpcr:
  biocontext:
    prefix: GLIDA.GPCR
  mappings:
    biocontext: GLIDA.GPCR
    miriam: glida.gpcr
    n2t: glida.gpcr
  miriam:
    deprecated: true
    description: The GPCR-LIgand DAtabase (GLIDA) is a GPCR-related chemical genomic
      database that is primarily focused on the correlation of information between
      GPCRs and their ligands. It provides correlation data between GPCRs and their
      ligands, along with chemical information on the ligands. This collection references
      G-protein coupled receptors.
    homepage: http://pharminfo.pharm.kyoto-u.ac.jp/services/glida/
    id: 00000493
    name: GLIDA GPCR
    namespaceEmbeddedInLui: false
    pattern: ^[A-Z-_0-9]+$
    prefix: glida.gpcr
    sampleId: ACM1_HUMAN
    uri_format: http://pharminfo.pharm.kyoto-u.ac.jp/services/glida/gpcr_information.php?id=$1
  n2t:
    description: The GPCR-LIgand DAtabase (GLIDA) is a GPCR-related chemical genomic
      database that is primarily focused on the correlation of information between
      GPCRs and their ligands. It provides correlation data between GPCRs and their
      ligands, along with chemical information on the ligands. This collection references
      G-protein coupled receptors.
    example: ACM1_HUMAN
    homepage: http://pharminfo.pharm.kyoto-u.ac.jp/services/glida/
    name: GLIDA GPCR at Kyoto University
    namespaceEmbeddedInLui: false
    pattern: ^[A-Z-_0-9]+$
    prefix: glida.gpcr
    uri_format: http://pharminfo.pharm.kyoto-u.ac.jp/services/glida/gpcr_information.php?id=$1
  prefix: glida.gpcr
glida.ligand:
  biocontext:
    prefix: GLIDA.LIGAND
  mappings:
    biocontext: GLIDA.LIGAND
    miriam: glida.ligand
    n2t: glida.ligand
  miriam:
    deprecated: true
    description: The GPCR-LIgand DAtabase (GLIDA) is a GPCR-related chemical genomic
      database that is primarily focused on the correlation of information between
      GPCRs and their ligands. It provides correlation data between GPCRs and their
      ligands, along with chemical information on the ligands. This collection references
      ligands.
    homepage: http://pharminfo.pharm.kyoto-u.ac.jp/services/glida/
    id: 00000494
    name: GLIDA Ligand
    namespaceEmbeddedInLui: false
    pattern: ^L\d+$
    prefix: glida.ligand
    sampleId: L000001
    uri_format: http://pharminfo.pharm.kyoto-u.ac.jp/services/glida/ligand_information.php?id=$1
  n2t:
    description: The GPCR-LIgand DAtabase (GLIDA) is a GPCR-related chemical genomic
      database that is primarily focused on the correlation of information between
      GPCRs and their ligands. It provides correlation data between GPCRs and their
      ligands, along with chemical information on the ligands. This collection references
      ligands.
    example: L000001
    homepage: http://pharminfo.pharm.kyoto-u.ac.jp/services/glida/
    name: GLIDA Ligand at Kyoto University
    namespaceEmbeddedInLui: false
    pattern: ^L\d+$
    prefix: glida.ligand
    uri_format: http://pharminfo.pharm.kyoto-u.ac.jp/services/glida/ligand_information.php?id=$1
  prefix: glida.ligand
glottolog:
  appears_in:
  - gsso
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: Comprehensive reference information for the world's languages, especially
    the lesser known languages. [from homepage]
  example: nort3314
  github_request_issue: 1310
  homepage: https://glottolog.org
  license: CC-BY-4.0
  name: Glottolog
  prefix: glottolog
  uri_format: https://glottolog.org/resource/languoid/id/$1
glycoepitope:
  biocontext:
    prefix: GLYCOEPITOPE
  integbio:
    description: Glyco epitopes are carbohydrate antigens involved in various physiological
      functions such as cell to cell recognition, fertilization, and blood hormone
      regulation. This database provides information on the glyco epitopes and antibodies
      that have been used to analyze their expression. The glycol epitopes are linked
      to their antibodies, as well as to the original manuscripts on the internet.
    homepage: http://www.glycoepitope.jp/
    information_keywords:
    - Interaction/Pathway
    maintainer: Ritsumeikan University
    name: GlycoEpitope
    prefix: nbdc00087
    status: Active
    target_keywords:
    - Protein
    - Carbohydrate
    - Lipid
  mappings:
    biocontext: GLYCOEPITOPE
    integbio: nbdc00087
    miriam: glycoepitope
    n2t: glycoepitope
  miriam:
    deprecated: false
    description: GlycoEpitope is a database containing useful information about carbohydrate
      antigens (glyco-epitopes) and the antibodies (polyclonal or monoclonal) that
      can be used to analyze their expression. This collection references Glycoepitopes.
    homepage: https://www.glycoepitope.jp/epitopes/
    id: 00000478
    name: GlycoEpitope
    namespaceEmbeddedInLui: false
    pattern: ^EP\d{4}$
    prefix: glycoepitope
    sampleId: EP0311
    uri_format: https://www.glycoepitope.jp/epitopes/$1
  n2t:
    description: GlycoEpitope is a database containing useful information about carbohydrate
      antigens (glyco-epitopes) and the antibodies (polyclonal or monoclonal) that
      can be used to analyze their expression. This collection references Glycoepitopes.
    example: EP0311
    homepage: https://www.glycoepitope.jp/epitopes/
    name: GlycoEpitope at Ritsumeikan University
    namespaceEmbeddedInLui: false
    pattern: ^EP\d{4}$
    prefix: glycoepitope
    uri_format: https://www.glycoepitope.jp/epitopes/$1
  prefix: glycoepitope
glycomapsdb:
  mappings:
    prefixcommons: glycomapsdb
  prefix: glycomapsdb
  prefixcommons:
    description: A database of GlycoMaps containing 2585 conformational maps.
    example: '6819'
    homepage: http://www.glycosciences.de/modeling/glycomapsdb/
    keywords:
    - small molecule
    name: GlycoMapsDB
    pattern: ^\d+$
    prefix: glycomapsdb
    synonyms:
    - glycomaps
    uri_format: http://www.glycosciences.de/modeling/glycomapsdb/showdetails.php?mapid=$1
  reviewer:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
glycomedb:
  biocontext:
    prefix: GLYCOMEDB
  contact:
    email: rr@uga.edu
    github: ReneRanzinger
    name: René Ranzinger
    orcid: 0000-0003-3147-448X
  edam:
    description: Identifier of an entry from the GlycomeDB database.
    name: GlycomeDB
    obsolete: false
    prefix: '2664'
  fairsharing:
    abbreviation: GlycomeDB
    description: GlycomeDB is the result of a systematic data integration effort,
      and provides an overview of all carbohydrate structures available in public
      databases, as well as cross-links.
    homepage: http://www.glycome-db.org/showMenu.action?major=database
    name: GlycomeDB
    prefix: FAIRsharing.k5k0yh
    publications:
    - doi: 10.1093/glycob/cwp137
      pubmed_id: 19759275
      title: 'Glycome-DB.org: a portal for querying across the digital world of carbohydrate
        sequences.'
    - doi: 10.1093/nar/gkq1014
      pubmed_id: 21045056
      title: GlycomeDB--a unified database for carbohydrate structures.
    - doi: 10.1186/1471-2105-9-384
      pubmed_id: 18803830
      title: GlycomeDB - integration of open-access carbohydrate structure databases.
    subjects:
    - Life Science
  has_canonical: glytoucan
  integbio:
    alt_name: The carbohydrate structures metadatabase
    description: GlycomeDB is a database of carbohydrate structural information. The
      database contains structural information collected from other sites and studies
      which can be searched, accessed, and compared using several tools. Users can
      search by ID, structure, similarity, or species. Data is available for download.
      GlycomeDB is now closed, please use GlyTouCan (http://glytoucan.org/).
    fairsharing: biodbcore-000353
    homepage: http://www.glycome-db.org/
    information_keywords:
    - Sequence
    - Chemical structure
    maintainer: German Cancer Research Center
    name: GlycomeDB
    prefix: nbdc00899
    pubmeds:
    - '25753706'
    - '21045056'
    - '19759275'
    - '18803830'
    status: Active
    target_keywords:
    - Carbohydrate
  mappings:
    biocontext: GLYCOMEDB
    edam: '2664'
    fairsharing: FAIRsharing.k5k0yh
    integbio: nbdc00899
    miriam: glycomedb
    n2t: glycomedb
    prefixcommons: glycomedb
    re3data: r3d100011527
  miriam:
    deprecated: false
    description: GlycomeDB is the result of a systematic data integration effort,
      and provides an overview of all carbohydrate structures available in public
      databases, as well as cross-links.
    homepage: https://glytoucan.org/
    id: '00000114'
    name: GlycomeDB
    namespaceEmbeddedInLui: false
    pattern: ^\w+$
    prefix: glycomedb
    sampleId: G77500AY
    uri_format: https://glytoucan.org/Structures/Glycans/$1
  n2t:
    description: GlycomeDB is the result of a systematic data integration effort,
      and provides an overview of all carbohydrate structures available in public
      databases, as well as cross-links.
    example: G77500AY
    homepage: https://glytoucan.org/
    name: GlycomeDB carbohydrate structure database
    namespaceEmbeddedInLui: false
    pattern: ^\w+$
    prefix: glycomedb
    uri_format: https://glytoucan.org/Structures/Glycans/$1
  prefix: glycomedb
  prefixcommons:
    description: GlycomeDB is the result of a systematic data integration effort,
      and provides an overview of all carbohydrate structures available in public
      databases, as well as cross-links.
    example: '1'
    homepage: http://www.glycome-db.org/showMenu.action?major=database
    keywords:
    - molecules
    - small molecules
    - structure
    name: GlycomeDB Carbohydrate Structure Database
    pattern: ^\d+$
    prefix: glycomedb
    pubmed_ids:
    - '19759275'
    uri_format: http://www.glycome-db.org/database/showStructure.action?glycomeId=$1
  publications:
  - doi: 10.1093/nar/gkq1014
    pmc: PMC3013643
    pubmed: '21045056'
    title: GlycomeDB--a unified database for carbohydrate structures
    year: 2010
  - doi: 10.1093/glycob/cwp137
    pmc: null
    pubmed: '19759275'
    title: 'Glycome-DB.org: a portal for querying across the digital world of carbohydrate
      sequences'
    year: 2009
  - doi: 10.1186/1471-2105-9-384
    pmc: PMC2567997
    pubmed: '18803830'
    title: GlycomeDB - integration of open-access carbohydrate structure databases
    year: 2008
  re3data:
    description: '<<<!!!<< With the implementation of GlyTouCan (https://glytoucan.org/)
      https://www.re3data.org/repository/r3d100012388 the mission of GlycomeDB comes
      to an end. >>>!!!>>>

      With the new database, GlycomeDB, it is possible to get an overview of all carbohydrate
      structures in the different databases and to crosslink common structures in
      the different databases. Scientists are now able to search for a particular
      structure in the meta database and get information about the occurrence of this
      structure in the five carbohydrate structure databases.'
    doi: 10.17616/R34M07
    homepage: http://www.glycome-db.org/
    name: GlycomeDB
    prefix: r3d100011527
    synonyms:
    - A carbohydrate structure metadatabase
glyconavi:
  example: GN_G03681DA
  example_extras:
  - GN_GlyTouCan_G03681DA
  fairsharing:
    abbreviation: GlycoNAVI
    contact:
      email: issaku@noguchi.or.jp
      name: Issaku Yamada
      orcid: 0000-0001-9504-189X
    description: GlycoNAVI is a repository of data relevant to carbohydrate research.
      It contains a free suite of carbohydrate research tools organized by domain,
      including glycans, proteins, lipids, genes, diseases and samples.
    homepage: https://glyconavi.org/
    license: CC-BY-4.0
    name: GlycoNAVI
    prefix: FAIRsharing.wvp1t7
    publications: []
    repository: https://glyconavi.github.io/doc/
    subjects:
    - Organic Chemistry
    - Chemistry
    - Life Science
    - Glycomics
  integbio:
    description: GlycoNAVI is a web site for carbohydrate research. It consist of
      the 'GlycoNAVI DataBase' for molecular information of carbohydrates, and chemical
      reactions of carbohydrate synthesis, the 'Route Searching System for Glycan
      Synthesis', and 'GlycoNAVI Tools' for editing two-dimensional molecular structure
      of carbohydrates.
    fairsharing: biodbcore-000002
    homepage: https://glyconavi.org
    information_keywords:
    - 3D structure
    - Chemical structure
    maintainer: The Noguchi Institute
    name: GlycoNAVI
    prefix: nbdc01174
    status: Active
    target_keywords:
    - Carbohydrate
  mappings:
    fairsharing: FAIRsharing.wvp1t7
    integbio: nbdc01174
    miriam: glyconavi
  miriam:
    deprecated: false
    description: GlycoNAVI is a website for carbohydrate research. It consists of
      the "GlycoNAVI Database" that provides information such as existence ratios
      and names of glycans, 3D structures of glycans and complex glycoconjugates,
      and the "GlycoNAVI tools" such as editing of 2D structures of glycans, glycan
      structure viewers, and conversion tools.
    homepage: https://www.noguchi.or.jp/
    id: 00000830
    name: GlycoNAVI
    namespaceEmbeddedInLui: false
    pattern: ^GN_[A-Za-z]*[_]*[A-Za-z0-9-:_]+$
    prefix: glyconavi
    sampleId: GN_GlyTouCan_G03681DA
    uri_format: https://glyconavi.org/hub/?id=$1
  pattern: ^GN_[A-Za-z0-9_:]+$
  prefix: glyconavi
glycopost:
  fairsharing:
    abbreviation: GlycoPOST
    description: GlycoPOST is a mass spectrometry data repository for glycomics. Users
      can release their "raw/processed" data via this site with a unique identifier
      number for the paper publication. Submission conditions are in accordance with
      the Minimum Information Required for a Glycomics Experiment (MIRAGE) guidelines.
    homepage: https://glycopost.glycosmos.org
    license: CC-BY-4.0
    name: GlycoPOST
    prefix: FAIRsharing.2y1KMt
    publications: []
    subjects:
    - Life Science
    - Glycomics
  mappings:
    fairsharing: FAIRsharing.2y1KMt
    miriam: glycopost
  miriam:
    deprecated: false
    description: GlycoPOST is a mass spectrometry data repository for glycomics and
      glycoproteomics. Users can release their "raw/processed" data via this site
      with a unique identifier number for the paper publication. Submission conditions
      are in accordance with the Minimum Information Required for a Glycomics Experiment
      (MIRAGE) guidelines.
    homepage: https://glycopost.glycosmos.org
    id: '00000721'
    name: GlycoPOST
    namespaceEmbeddedInLui: false
    pattern: ^GPST[0-9]{6}$
    prefix: glycopost
    sampleId: GPST000024
    uri_format: https://glycopost.glycosmos.org/entry/$1
  prefix: glycopost
glycosciencesdb:
  contact:
    email: thomas@luetteke-online.de
    github: glycosciences
    name: Thomas Lütteke
    orcid: 0000-0002-7140-9933
  contributor:
    email: cjmungall@lbl.gov
    github: cmungall
    name: Chris Mungall
    orcid: 0000-0002-6601-2165
  description: A database to support glycobiology and glycomics research. Its main
    focus is on 3D structures, including 3D structure models as well as references
    to PDB entries that feature carbohydrates.
  example: '1'
  github_request_issue: 537
  homepage: http://www.glycosciences.de/database/
  name: Glycosciences.DB
  pattern: ^\d+$
  prefix: glycosciencesdb
  publications:
  - doi: 10.1093/nar/gky994
    pmc: PMC6323918
    pubmed: '30357361'
    title: 'Glycosciences.DB: an annotated data collection linking glycomics and proteomics
      data (2018 update)'
    year: 2019
  reviewer:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  synonyms:
  - glycosciences.db
  uri_format: http://www.glycosciences.de/database/start.php?action=explore_linucsid&linucsid=$1
glytoucan:
  biocontext:
    prefix: GLYTOUCAN
  contact:
    email: rr@uga.edu
    github: ReneRanzinger
    name: René Ranzinger
    orcid: 0000-0003-3147-448X
  fairsharing:
    abbreviation: GlyTouCan
    description: The international glycan structure repository for glycans published
      in the literature. Any glycan structure, ranging in resolution from monosaccharide
      composition to fully defined structures can be registered and have an accession
      number assigned as long as there are no inconsistencies in the structure.
    homepage: https://glytoucan.org
    license: CC-BY-4.0
    name: GlyTouCan
    prefix: FAIRsharing.5Pze7l
    publications:
    - doi: 10.1093/glycob/cwx066
      pubmed_id: 28922742
      title: 'GlyTouCan: an accessible glycan structure repository.'
    - doi: 10.1093/nar/gkv1041
      pubmed_id: 26476458
      title: GlyTouCan 1.0--The international glycan structure repository.
    subjects:
    - Structural Biology
    - Glycomics
    twitter: glytoucan
  integbio:
    description: 'GlyGen is an integrated database for carbohydrate and glycoconjugate
      related data. It retrieves information from multiple international data sources
      and integrates and harmonizes this data including glycomics, genomics, proteomics
      (and glycoproteomics), cell biology, developmental biology and biochemistry.
      Users are able to seach data in three categories;

      1) Glyvcan: Search for glycan structures based on their chemical and structural
      properties.

      2) Protein: Search for proteins based on their sequences, accessions, and annotations.

      3) Glycoprotein: Search for glycoproteins based on the protein or glycan structures
      involved.'
    homepage: https://www.glygen.org
    information_keywords:
    - Sequence
    - Chemical structure
    - Expression
    - Interaction/Pathway
    - Portal
    maintainer: University of Georgia||George Washington University
    name: GlyGen
    prefix: nbdc02434
    status: Active
    target_keywords:
    - Protein
    - Carbohydrate
    - Health/Disease
  mappings:
    biocontext: GLYTOUCAN
    fairsharing: FAIRsharing.5Pze7l
    integbio: nbdc02434
    miriam: glytoucan
    n2t: glytoucan
    re3data: r3d100012388
    togoid: Glytoucan
    uniprot: DB-0254
  miriam:
    deprecated: false
    description: GlyTouCan is the single worldwide registry of glycan (carbohydrate
      sugar chain) data.
    homepage: https://glytoucan.org
    id: 00000608
    name: GlyTouCan
    namespaceEmbeddedInLui: false
    pattern: ^G[0-9]{5}[A-Z]{2}$
    prefix: glytoucan
    sampleId: G00054MO
    uri_format: https://glytoucan.org/Structures/Glycans/$1
  n2t:
    description: GlyTouCan is the single worldwide registry of glycan (carbohydrate
      sugar chain) data.
    example: G00054MO
    homepage: https://glytoucan.org
    name: The Glycan Repository
    namespaceEmbeddedInLui: false
    pattern: ^G[0-9]{5}[A-Z]{2}$
    prefix: glytoucan
    uri_format: https://glytoucan.org/Structures/Glycans/$1
  prefix: glytoucan
  providers:
  - code: glygen
    description: 'GlyGen is a data integration and dissemination project for carbohydrate
      and glycoconjugate related data. '
    example: null
    first_party: null
    homepage: https://www.glygen.org/
    name: GlyGen
    publications: null
    status: null
    uri_format: https://glygen.org/glycan/$1
  publications:
  - doi: 10.1093/glycob/cwx066
    pmc: PMC5881658
    pubmed: '28922742'
    title: 'GlyTouCan: an accessible glycan structure repository'
    year: 2017
  - doi: 10.1093/nar/gkv1041
    pmc: PMC4702779
    pubmed: '26476458'
    title: GlyTouCan 1.0--The international glycan structure repository
    year: 2015
  - doi: 10.1093/glycob/cwx066
    pmc: null
    pubmed: null
    title: 'GlyTouCan: an accessible glycan structure repository.'
    year: null
  - doi: 10.1093/nar/gkv1041
    pmc: null
    pubmed: null
    title: GlyTouCan 1.0--The international glycan structure repository.
    year: null
  - doi: 10.1093/glycob/cwz080
    pmc: null
    pubmed: '31616925'
    title: null
    year: null
  - doi: 10.1093/glycob/cwx066
    pmc: null
    pubmed: null
    title: 'GlyTouCan: an accessible glycan structure repository.'
    year: null
  - doi: 10.1093/nar/gkv1041
    pmc: null
    pubmed: null
    title: GlyTouCan 1.0--The international glycan structure repository.
    year: null
  - doi: 10.1093/glycob/cwz080
    pmc: null
    pubmed: '31616925'
    title: null
    year: null
  re3data:
    description: GlyTouCan is the international glycan structure repository. This
      repository is a freely available, uncurated registry for glycan structures that
      assigns globally unique accession numbers to any glycan independent of the level
      of information provided by the experimental method used to identify the structure(s).
      Any glycan structure, ranging in resolution from monosaccharide composition
      to fully defined structures can be registered as long as there are no inconsistencies
      in the structure.
    doi: 10.17616/R3119V
    homepage: https://glytoucan.org/
    license: CC0
    name: GlyTouCan
    prefix: r3d100012388
    synonyms:
    - International Glycan Repository
  synonyms:
  - glygen
  togoid:
    catalog: nbdc01535
    description: GlyTouCan is an international repository of glycan structures. This
      database contains uncurated glycan structures ranging in resolution from monosaccharide
      composition to fully defined structures, as long as there are no inconsistencies
      in the structure. The database allows users to search by text, graphic input
      or motif, and browse using motif-list or glycan-list.
    examples:
    - G88006IV
    - G53085MI
    - G17896UT
    - G50341PG
    - G19379ID
    - G08110WX
    - G70101JE
    - G45504EY
    - G81263BG
    - G02815KT
    keywords:
    - Glycan
    name: GlyTouCan
    pattern: ^(?G[0-9]{5}[A-Z]{2})$
    prefix: Glytoucan
    uri_format: http://identifiers.org/glytoucan/$1
  uniprot:
    abbreviation: GlyGen
    category: PTM databases
    homepage: https://glygen.org
    name: GlyGen
    prefix: DB-0254
    publications:
    - doi: 10.1093/glycob/cwz080
      pubmed: '31616925'
    uri_format: https://glygen.org/protein/$1#glycosylation
gmd:
  biocontext:
    prefix: GMD
  contact:
    email: kopka@mpimp-golm.mpg.de
    github: null
    name: Joachim Kopka
    orcid: 0000-0001-9675-4883
  fairsharing:
    abbreviation: GMD
    description: The Golm Metabolome Database (GMD) provides gas chromatography (GC)
      mass spectrometry (MS) reference spectra, reference metabolite profiles and
      tools for one of the most widespread routine technologies applied to the large
      scale screening and discovery of novel metabolic biomarkers.
    homepage: http://gmd.mpimp-golm.mpg.de/
    name: Golm Metabolome Database
    prefix: FAIRsharing.jykmkw
    publications:
    - doi: doi:10.1007/s11306-010-0198-7
      pubmed_id: 20526350
      title: Decision tree supported substructure prediction of metabolites from GC-MS
        profiles
    subjects:
    - Life Science
    - Metabolomics
  mappings:
    biocontext: GMD
    fairsharing: FAIRsharing.jykmkw
    miriam: gmd
    n2t: gmd
    re3data: r3d100011046
  miriam:
    deprecated: false
    description: Golm Metabolome Database (GMD) provides public access to custom mass
      spectral libraries, metabolite profiling experiments as well as additional information
      and tools. This collection references metabolite information, relating the biologically
      active substance to metabolic pathways or signalling phenomena.
    homepage: http://gmd.mpimp-golm.mpg.de/
    id: '00000274'
    name: Golm Metabolome Database
    namespaceEmbeddedInLui: false
    pattern: ^([0-9a-fA-F]){8}(-([0-9a-fA-F]){4}){3}-([0-9a-fA-F]){12}$
    prefix: gmd
    sampleId: 68513255-fc44-4041-bc4b-4fd2fae7541d
    uri_format: http://gmd.mpimp-golm.mpg.de/Metabolites/$1.aspx
  n2t:
    description: Golm Metabolome Database (GMD) provides public access to custom mass
      spectral libraries, metabolite profiling experiments as well as additional information
      and tools. This collection references metabolite information, relating the biologically
      active substance to metabolic pathways or signalling phenomena.
    example: 68513255-fc44-4041-bc4b-4fd2fae7541d
    homepage: http://gmd.mpimp-golm.mpg.de/
    name: Golm Metabolome Database at Max Planck Institute of Molecular Plant Physiology
    namespaceEmbeddedInLui: false
    pattern: ^([0-9a-fA-F]){8}(-([0-9a-fA-F]){4}){3}-([0-9a-fA-F]){12}$
    prefix: gmd
    uri_format: http://gmd.mpimp-golm.mpg.de/Metabolites/$1.aspx
  prefix: gmd
  publications:
  - doi: 10.1007/s11306-010-0198-7
    pmc: PMC2874469
    pubmed: '20526350'
    title: Decision tree supported substructure prediction of metabolites from GC-MS
      profiles
    year: 2010
  re3data:
    description: The Golm Metabolome Database (GMD) facilitates the search for and
      dissemination of reference mass spectra from biologically active metabolites
      quantified using gas chromatography (GC) coupled to mass spectrometry (MS)
    doi: 10.17616/R3MC9K
    homepage: http://gmd.mpimp-golm.mpg.de/
    license: Copyrights
    name: Golm Metabolome Database
    prefix: r3d100011046
    synonyms:
    - GMD
    xrefs:
      nif: 0000-21180
gmd.analyte:
  biocontext:
    prefix: GMD.ANALYTE
  mappings:
    biocontext: GMD.ANALYTE
    miriam: gmd.analyte
    n2t: gmd.analyte
  miriam:
    deprecated: false
    description: Golm Metabolome Database (GMD) provides public access to custom mass
      spectral libraries, metabolite profiling experiments as well as additional information
      and tools. For GC-MS profiling analyses, polar metabolite extracts are chemically
      converted, i.e. derivatised into less polar and volatile compounds, so called
      analytes.  This collection references analytes.
    homepage: http://gmd.mpimp-golm.mpg.de/
    id: '00000426'
    name: Golm Metabolome Database Analyte
    namespaceEmbeddedInLui: false
    pattern: ^([0-9a-fA-F]){8}(-([0-9a-fA-F]){4}){3}-([0-9a-fA-F]){12}$
    prefix: gmd.analyte
    sampleId: 4f0fa9b6-514f-4ff4-98cc-0009bc08eb80
    uri_format: http://gmd.mpimp-golm.mpg.de/Analytes/$1
  n2t:
    description: Golm Metabolome Database (GMD) provides public access to custom mass
      spectral libraries, metabolite profiling experiments as well as additional information
      and tools. For GC-MS profiling analyses, polar metabolite extracts are chemically
      converted, i.e. derivatised into less polar and volatile compounds, so called
      analytes.  This collection references analytes.
    example: 4f0fa9b6-514f-4ff4-98cc-0009bc08eb80
    homepage: http://gmd.mpimp-golm.mpg.de/
    name: Golm Metabolome Database (Analyte) at Max Planck Institute of Molecular
      Plant Physiology
    namespaceEmbeddedInLui: false
    pattern: ^([0-9a-fA-F]){8}(-([0-9a-fA-F]){4}){3}-([0-9a-fA-F]){12}$
    prefix: gmd.analyte
    uri_format: http://gmd.mpimp-golm.mpg.de/Analytes/$1
  part_of_database: gmd
  prefix: gmd.analyte
gmd.gcms:
  biocontext:
    prefix: GMD.GCMS
  mappings:
    biocontext: GMD.GCMS
    miriam: gmd.gcms
    n2t: gmd.gcms
  miriam:
    deprecated: false
    description: Golm Metabolome Database (GMD) provides public access to custom mass
      spectral libraries, metabolite profiling experiments as well as additional information
      and tools. Analytes are subjected to a gas chromatograph coupled to a mass spectrometer,
      which records the mass spectrum and the retention time linked to an analyte.
      This collection references GC-MS spectra.
    homepage: http://gmd.mpimp-golm.mpg.de/
    id: '00000424'
    name: Golm Metabolome Database GC-MS spectra
    namespaceEmbeddedInLui: false
    pattern: ^([0-9a-fA-F]){8}(-([0-9a-fA-F]){4}){3}-([0-9a-fA-F]){12}$
    prefix: gmd.gcms
    sampleId: 53d583d8-40c6-40e1-9296-23f821cd77a5
    uri_format: http://gmd.mpimp-golm.mpg.de/Spectrums/$1
  n2t:
    description: Golm Metabolome Database (GMD) provides public access to custom mass
      spectral libraries, metabolite profiling experiments as well as additional information
      and tools. Analytes are subjected to a gas chromatograph coupled to a mass spectrometer,
      which records the mass spectrum and the retention time linked to an analyte.
      This collection references GC-MS spectra.
    example: 53d583d8-40c6-40e1-9296-23f821cd77a5
    homepage: http://gmd.mpimp-golm.mpg.de/
    name: Golm Metabolome Database (GC-MS Spectra) at Max Planck Institute of Molecular
      Plant Physiology
    namespaceEmbeddedInLui: false
    pattern: ^([0-9a-fA-F]){8}(-([0-9a-fA-F]){4}){3}-([0-9a-fA-F]){12}$
    prefix: gmd.gcms
    uri_format: http://gmd.mpimp-golm.mpg.de/Spectrums/$1
  part_of_database: gmd
  prefix: gmd.gcms
gmd.profile:
  biocontext:
    prefix: GMD.PROFILE
  mappings:
    biocontext: GMD.PROFILE
    miriam: gmd.profile
    n2t: gmd.profile
  miriam:
    deprecated: false
    description: Golm Metabolome Database (GMD) provides public access to custom mass
      spectral libraries, metabolite profiling experiments as well as additional information
      and tools. GMD's metabolite profiles provide relative metabolite concentrations
      normalised according to fresh weight (or comparable quantitative data, such
      as volume, cell count, etc.) and internal standards (e.g. ribotol) of biological
      reference conditions and tissues.
    homepage: http://gmd.mpimp-golm.mpg.de/
    id: '00000423'
    name: Golm Metabolome Database Profile
    namespaceEmbeddedInLui: false
    pattern: ^([0-9a-fA-F]){8}(-([0-9a-fA-F]){4}){3}-([0-9a-fA-F]){12}$
    prefix: gmd.profile
    sampleId: 10b38aaf-b977-4950-85b8-f4775f66658d
    uri_format: http://gmd.mpimp-golm.mpg.de/profile/default.aspx?XemlId=$1
  n2t:
    description: Golm Metabolome Database (GMD) provides public access to custom mass
      spectral libraries, metabolite profiling experiments as well as additional information
      and tools. GMD's metabolite profiles provide relative metabolite concentrations
      normalised according to fresh weight (or comparable quantitative data, such
      as volume, cell count, etc.) and internal standards (e.g. ribotol) of biological
      reference conditions and tissues.
    example: 10b38aaf-b977-4950-85b8-f4775f66658d
    homepage: http://gmd.mpimp-golm.mpg.de/
    name: Golm Metabolome Database (Profile) at Max Planck Institute of Molecular
      Plant Physiology
    namespaceEmbeddedInLui: false
    pattern: ^([0-9a-fA-F]){8}(-([0-9a-fA-F]){4}){3}-([0-9a-fA-F]){12}$
    prefix: gmd.profile
    uri_format: http://gmd.mpimp-golm.mpg.de/profile/default.aspx?XemlId=$1
  part_of_database: gmd
  prefix: gmd.profile
gmd.ref:
  biocontext:
    prefix: GMD.REF
  mappings:
    biocontext: GMD.REF
    miriam: gmd.ref
    n2t: gmd.ref
  miriam:
    deprecated: false
    description: Golm Metabolome Database (GMD) provides public access to custom mass
      spectral libraries, metabolite profiling experiments as well as additional information
      and tools. Since metabolites often cannot be obtained in their respective native
      biological state, for example organic acids may be only acquirable as salts,
      the concept of reference substance was introduced. This collection references
      reference substances.
    homepage: http://gmd.mpimp-golm.mpg.de/
    id: '00000425'
    name: Golm Metabolome Database Reference Substance
    namespaceEmbeddedInLui: false
    pattern: ^([0-9a-fA-F]){8}(-([0-9a-fA-F]){4}){3}-([0-9a-fA-F]){12}$
    prefix: gmd.ref
    sampleId: 8cf84adb-b4db-4807-ac98-0004247c35df
    uri_format: http://gmd.mpimp-golm.mpg.de/ReferenceSubstances/$1
  n2t:
    description: Golm Metabolome Database (GMD) provides public access to custom mass
      spectral libraries, metabolite profiling experiments as well as additional information
      and tools. Since metabolites often cannot be obtained in their respective native
      biological state, for example organic acids may be only acquirable as salts,
      the concept of reference substance was introduced. This collection references
      reference substances.
    example: 8cf84adb-b4db-4807-ac98-0004247c35df
    homepage: http://gmd.mpimp-golm.mpg.de/
    name: Golm Metabolome Database (Reference Substance) at Max Planck Institute of
      Molecular Plant Physiology
    namespaceEmbeddedInLui: false
    pattern: ^([0-9a-fA-F]){8}(-([0-9a-fA-F]){4}){3}-([0-9a-fA-F]){12}$
    prefix: gmd.ref
    uri_format: http://gmd.mpimp-golm.mpg.de/ReferenceSubstances/$1
  part_of_database: gmd
  prefix: gmd.ref
gmelin:
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: The Gmelin database is a large database of organometallic and inorganic
    compounds updated quarterly. It is based on the German publication Gmelins Handbuch
    der anorganischen Chemie which was originally published by Leopold Gmelin in 1817;
    the last print edition, the 8th, appeared in the 1990s.
  edam:
    description: Gmelin registry number of a chemical compound.
    name: Chemical registry number (Gmelin)
    obsolete: false
    prefix: '1004'
  example: '1466'
  example_extras:
  - '606'
  - '80'
  homepage: https://link.springer.com/bookseries/562
  mappings:
    edam: '1004'
    wikidata: P1578
  name: Gmelin's Handbook of Inorganic Chemistry
  pattern: ^[1-9][0-9]{1,6}$
  prefix: gmelin
  proprietary: true
  references:
  - https://en.wikipedia.org/wiki/Gmelin_database
  wikidata:
    description: identifier for inorganic chemical compounds, in the Gmelin database
    example:
    - '1466'
    - '349'
    - '917'
    name: Gmelin number
    pattern: ^[1-9][0-9]{3,6}$
    prefix: P1578
gnd:
  bartoc:
    abbreviation: GND
    description: 'GND is a standard file for people, bodies, conferences, geographics,
      subject - matter and work titles, mainly for the cataloging of literature in
      libraries, but increasingly also for archives, museums, projects and web applications
      Is co-operated by the Deutsche Nationalbibliothek, all German-speaking library
      associations, the Zeitungsdatenatenbank (ZDB) and numerous other institutions.
      The GND is either co-organized or by direct agreement with the Deutsche Nationalbibliothek.


      The OGND provides access to the GND (common standard file), in which the previous
      standard file names (PND), slogan standard file (SWD) and common corporate file
      (GKD) as well as the single unit title file of the Deutsches Musikarchiv were
      merged into a common standard file (GND). The OGND is updated online from the
      GND of the cataloging database of the Südwestdeutschen Bibliotheksverbundes
      (SWB). The objective of the GND project, which has been running for several
      years, has been a standard file, which includes all types of entities, as a
      common, clear reference system for libraries'' bibliographic data, as well as
      data for other standard data users such as archives, museums, projects and scientific
      and cultural institutions.'
    homepage: http://www.dnb.de/gnd
    license: CC0-1.0
    name: Integrated Authority File
    pattern: ^[0-9X]+(-[0-9X])?$
    prefix: '430'
    wikidata_database: Q36578
  fairsharing:
    abbreviation: GND
    description: The Integrated Authority File (GND) is a service facilitating the
      collaborative use and administration of authority data. These authority data
      represent and describe entities, i.e. persons, corporate bodies, conferences
      and events, geographic entities, topics and works relating to cultural and academic
      collections. Libraries in particular use the GND to catalogue publications.
      However, archives, museums, cultural and academic institutions, and researchers
      involved in research projects are also increasingly working with the GND. Authority
      data make cataloguing easier, offer definitive search entries and forge links
      between different information resources. Every entity in the GND features a
      unique and stable identifier (GND ID). This makes it possible to link the authority
      data with both each other and external data sets and web resources. This results
      in a cross-organisational, machine-readable data network.
    homepage: https://www.dnb.de/EN/Professionell/Standardisierung/GND/gnd_node.html
    license: CC0-1.0
    name: Integrated Authority File
    prefix: FAIRsharing.8337e2
    subjects:
    - Knowledge and Information Systems
    - Culture
    - Social Science
    twitter: gndnet
  mappings:
    bartoc: '430'
    fairsharing: FAIRsharing.8337e2
    miriam: gnd
    wikidata: P227
    wikidata.entity: Q54506313
  miriam:
    deprecated: false
    description: The Gemeinsame Normdatei (Integrated Authority File) or GND is an
      international authority file for person names, subject headings and corporate
      bodies. It is used mainly for documentation in libraries and increasingly also
      by archives and museums. The GND is managed by the German National Library in
      cooperation with various regional library networks in German-speaking Europe
      and other partners.
    homepage: https://lobid.org/
    id: '00001002'
    name: Gemeinsame Normdatei
    namespaceEmbeddedInLui: false
    pattern: ^[0-9X\-]+$
    prefix: gnd
    sampleId: '117145750'
    uri_format: https://lobid.org/gnd/$1
  prefix: gnd
  wikidata:
    database: Q54506313
    description: identifier from an international authority file of names, subjects,
      and organizations
    example:
    - '118540238'
    - '118604740'
    - '118627813'
    - 1231643-X
    - 4010921-5
    - 4079154-3
    - 4131406-2
    - 4426550-5
    - 7505698-7
    homepage: https://portal.dnb.de
    name: GND ID
    pattern: ^1[0123]?\d{7}[0-9X]|[47]\d{6}-\d|[1-9]\d{0,7}-[0-9X]|3\d{7}[0-9X]$
    prefix: P227
    short_name:
    - GND
    uri_format: https://d-nb.info/gnd/$1
    uri_format_rdf: https://d-nb.info/gnd/$1
gndo:
  example: AdministrativeUnit
  lov:
    description: GND stands for "Gemeinsame Normdatei" (Integrated Authority File)
      and offers a broad range of elements to describe authorities. The GND originates
      from the German library community and aims to solve the name ambiguity problem
      in the library world.
    homepage: http://d-nb.info/standards/elementset/gnd#
    keywords:
    - Catalogs
    modified: '2019-02-12'
    name: GND-Ontologie
    prefix: gndo
    uri_prefix: http://d-nb.info/standards/elementset/gnd#$1
  mappings:
    lov: gndo
    tib: gndo
  prefix: gndo
  tib:
    description: GND stands for Gemeinsame Normdatei (Integrated Authority File) and
      offers a broad range of elements to describe authorities. The GND originates
      from the German library community and aims to solve the name ambiguity problem
      in the library world.
    download_rdf: https://d-nb.info/standards/elementset/gnd.rdf
    homepage: https://d-nb.info/standards/elementset/gnd
    keywords:
    - ESS
    - computer science
    name: GND Ontology
    prefix: gndo
    uri_format: https://d-nb.info/standards/elementset/gnd#$1
    version.iri: https://d-nb.info/standards/elementset/gnd_20240806
gno:
  aberowl:
    description: GlyTouCan provides stable accessions for glycans described at varyious
      degrees of characterization, including compositions (no linkage) and topologies
      (no carbon bond positions or anomeric configurations). GNOme organizes these
      stable accessions for interative browsing, for text-based searching, and for
      automated reasoning with well-defined characterization levels.
    download_owl: http://aber-owl.net/media/ontologies/GNO/30/gno.owl
    homepage: https://gnome.glyomics.org/
    name: Glycan Naming and Subsumption Ontology (GNOme)
    prefix: GNO
  bioportal:
    contact:
      email: nje5@georgetown.edu
      name: Nathan Edwards
    description: An ontology for glycans based on GlyTouCan, but organized by subsumption.
    homepage: https://github.com/glygen-glycan-data/GNOme
    license: CC-BY-4.0
    name: Glycan Naming Ontology
    prefix: GNO
    version: V2.5.0
  example: '10004892'
  example_extras:
  - G99373GG
  mappings:
    aberowl: GNO
    bioportal: GNO
    obofoundry: gno
    ols: gno
    ontobee: GNO
    wikidata.entity: Q113012663
  name: Glycan Naming and Subsumption Ontology
  obofoundry:
    contact: nje5@georgetown.edu
    contact.github: edwardsnj
    contact.label: Nathan Edwards
    contact.orcid: 0000-0001-5168-3196
    deprecated: false
    description: GlyTouCan provides stable accessions for glycans described at varyious
      degrees of characterization, including compositions (no linkage) and topologies
      (no carbon bond positions or anomeric configurations). GNOme organizes these
      stable accessions for interative browsing, for text-based searching, and for
      automated reasoning with well-defined characterization levels.
    domain: chemistry and biochemistry
    download.json: http://purl.obolibrary.org/obo/gno.json
    download.obo: http://purl.obolibrary.org/obo/gno.obo
    download.owl: http://purl.obolibrary.org/obo/gno.owl
    homepage: https://gnome.glyomics.org/
    license: CC BY 4.0
    license.url: https://creativecommons.org/licenses/by/4.0/
    name: Glycan Naming and Subsumption Ontology (GNOme)
    preferredPrefix: GNO
    prefix: gno
    publications:
    - id: https://doi.org/10.5281/zenodo.6678278
      title: GNOme - Glycan Naming and Subsumption Ontology
    repository: https://github.com/glygen-glycan-data/GNOme
  ols:
    description: An ontology for glycans based on GlyTouCan, but organized by subsumption.
    download_owl: http://purl.obolibrary.org/obo/gno.owl
    homepage: https://gnome.glyomics.org/
    name: Glycan Naming Ontology
    prefix: gno
    tracker: https://github.com/glygen-glycan-data/GNOme/issues
    version: '2025-10-10'
    version.iri: http://purl.obolibrary.org/obo/gno/2025-10-10/gno.owl
  ontobee:
    library: Library
    name: Glycan Naming and Subsumption Ontology (GNOme)
    prefix: GNO
  pattern: ^(\d{8}|(\w+\d+\w+))$
  prefix: gno
  providers:
  - code: gno.structure
    description: GNOme structure browser
    example: null
    first_party: null
    homepage: https://gnome.glyomics.org/StructureBrowser.html
    name: GNOme Structure Viewer
    publications: null
    status: null
    uri_format: https://gnome.glyomics.org/StructureBrowser.html?focus=$1
  - code: gno.composition
    description: GNOme composition browser
    example: null
    first_party: null
    homepage: https://gnome.glyomics.org/CompositionBrowser.html
    name: GNOme Composition Browser
    publications: null
    status: null
    uri_format: https://gnome.glyomics.org/CompositionBrowser.html?focus=$1
  publications:
  - doi: 10.5281/zenodo.6678278
    pmc: null
    pubmed: null
    title: GNOme - Glycan Naming and Subsumption Ontology
    year: 2021
  - doi: 10.5281/zenodo.6678278
    pmc: null
    pubmed: null
    title: GNOme - Glycan Naming and Subsumption Ontology
    year: null
  synonyms:
  - gnome
  uri_format: http://purl.obolibrary.org/obo/GNO_$1
gnomad:
  contact:
    email: hrehm@mgh.harvard.edu
    github: heidirehm
    name: Heidi L. Rehm
    orcid: 0000-0002-6025-0015
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: The Genome Aggregation Database (gnomAD) is a resource developed by
    an international coalition of investigators, with the goal of aggregating and
    harmonizing both exome and genome sequencing data from a wide variety of large-scale
    sequencing projects, and making summary data available for the wider scientific
    community (from https://gnomad.broadinstitute.org).
  example: 1-55516888-G-GA
  example_extras:
  - M-8602-T-C
  - DUP_2_5708
  github_request_issue: 695
  homepage: https://gnomad.broadinstitute.org
  integbio:
    alt_name: Genome Aggregation Database
    description: "GnomAD is a resource for exome and genome sequencing data from a\
      \ wide variety of large-scale sequencing projects. It contains following datasets;\
      \ \nThe v2 data set (GRCh37/hg19) provided on this website spans 125,748 exome\
      \ sequences and 15,708 whole-genome sequences from unrelated individuals sequenced\
      \ as part of various disease-specific and population genetic studies. The v3.1\
      \ data set (GRCh38) spans 76,156 genomes, selected as in v2. Mitochondrial DNA\
      \ (mtDNA) variants for gnomAD are also available."
    homepage: https://gnomad.broadinstitute.org/
    information_keywords:
    - Sequence
    maintainer: Genome Aggregation Database Consortium
    name: gnomAD
    prefix: nbdc02561
    pubmeds:
    - '32461654'
    status: Active
    target_keywords:
    - Genome/Gene
    - Genetic variation
    - Health/Disease
  license: CC0-1.0
  mappings:
    integbio: nbdc02561
  name: Genome Aggregation Database
  prefix: gnomad
  publications:
  - doi: 10.1038/s41586-020-2287-8
    pmc: PMC7334194
    pubmed: '32461652'
    title: A structural variation reference for medical and population genetics
    year: 2020
  - doi: 10.1038/s41586-020-2308-7
    pmc: PMC7334197
    pubmed: '32461654'
    title: The mutational constraint spectrum quantified from variation in 141,456
      humans
    year: 2020
  uri_format: https://gnomad.broadinstitute.org/variant/$1
gnpis:
  biocontext:
    prefix: GNPIS
  contact:
    email: hadi.quesneville@versailles.inra.fr
    github: null
    name: Hadi Quesneville
    orcid: 0000-0003-3001-4908
  contact_group_email: urgi-contact@versailles.inra.fr
  fairsharing:
    abbreviation: GnpIS
    contact:
      email: urgi-contact@versailles.inra.fr
      name: URGI Contact
      orcid: 0000-0003-3001-4908
    description: GnpIS is a multispecies integrative information system dedicated
      to plant and fungi pests. It bridges genetic and genomic data, allowing researchers
      access to both genetic information (e.g. genetic maps, quantitative trait loci,
      association genetics, markers, polymorphisms, germplasms, phenotypes and genotypes)
      and genomic data (e.g. genomic sequences, physical maps, genome annotation and
      expression data) for species of agronomical interest. GnpIS is used by both
      large international projects and plant science departments at the French National
      Institute for Agricultural Research. It is regularly improved and released several
      times per year. GnpIS is accessible through a web portal and allows to browse
      different types of data either independently through dedicated interfaces or
      simultaneously using a quick search ('google like search') or advanced search
      (Biomart, Galaxy, Intermine) tools.
    homepage: https://urgi.versailles.inra.fr/gnpis
    name: Genetic and Genomic Information System
    prefix: FAIRsharing.dw22y3
    publications:
    - doi: 10.1093/database/bat058
      pubmed_id: 23959375
      title: 'GnpIS: an information system to integrate genetic and genomic data from
        plants and fungi'
    subjects:
    - Life Science
  mappings:
    biocontext: GNPIS
    fairsharing: FAIRsharing.dw22y3
    miriam: gnpis
    n2t: gnpis
    re3data: r3d100012647
  miriam:
    deprecated: false
    description: GnpIS is an integrative information system focused on plants and
      fungal pests. It provides both genetic (e.g. genetic maps, quantitative trait
      loci, markers, single nucleotide polymorphisms, germplasms and genotypes) and
      genomic data (e.g. genomic sequences, physical maps, genome annotation and expression
      data) for species of agronomical interest.
    homepage: https://urgi.versailles.inra.fr/gnpis/
    id: '00000627'
    name: GnpIS
    namespaceEmbeddedInLui: false
    pattern: ^[A-Za-z0-9]+$
    prefix: gnpis
    sampleId: AY109603
    uri_format: https://urgi.versailles.inra.fr/gnpis/#result/term=$1
  n2t:
    description: GnpIS is an integrative information system focused on plants and
      fungal pests. It provides both genetic (e.g. genetic maps, quantitative trait
      loci, markers, single nucleotide polymorphisms, germplasms and genotypes) and
      genomic data (e.g. genomic sequences, physical maps, genome annotation and expression
      data) for species of agronomical interest.
    example: AY109603
    homepage: https://urgi.versailles.inra.fr/gnpis/
    name: GnpIS
    namespaceEmbeddedInLui: false
    pattern: ^[A-Za-z0-9]+$
    prefix: gnpis
    uri_format: https://urgi.versailles.inra.fr/gnpis/#result/term=$1
  prefix: gnpis
  publications:
  - doi: 10.1093/database/bat058
    pmc: PMC3746681
    pubmed: '23959375'
    title: 'GnpIS: an information system to integrate genetic and genomic data from
      plants and fungi'
    year: 2013
  re3data:
    description: GnpIS is a multispecies integrative information system dedicated
      to plant and fungi pests. It bridges genetic and genomic data, allowing researchers
      access to both genetic information (e.g. genetic maps, quantitative trait loci,
      association genetics, markers, polymorphisms, germplasms, phenotypes and genotypes)
      and genomic data (e.g. genomic sequences, physical maps, genome annotation and
      expression data) for species of agronomical interest. GnpIS is used by both
      large international projects and plant science departments at the French National
      Research Institute for Agriculture, Food and Environment. It is regularly improved
      and released several times per year. GnpIS is accessible through a web portal
      and allows to browse different types of data either independently through dedicated
      interfaces or simultaneously using a quick search ('google like search') or
      advanced search (Biomart, Galaxy, Intermine) tools.
    doi: 10.17616/R3RF6C
    homepage: https://urgi.versailles.inrae.fr/gnpis
    name: GnpIS
    prefix: r3d100012647
    synonyms:
    - Genetic and Genomic Information System
gnps.task:
  contact:
    email: mingxun.wang@cs.ucr.edu
    github: mwang87
    name: Mingxun Wang
    orcid: 0000-0001-7647-6097
  contributor:
    email: cjmungall@lbl.gov
    github: cmungall
    name: Chris Mungall
    orcid: 0000-0002-6601-2165
  description: GNPS is a web-based mass spectrometry ecosystem that aims to be an
    open-access knowledge base for community-wide organization and sharing of raw,
    processed, or annotated fragmentation mass spectrometry data (MS/MS)
  example: 4b848c342a4f4abc871bdf8a09a60807
  github_request_issue: 833
  homepage: https://gnps.ucsd.edu/
  name: Global Natural Products Social Molecular Networking Task
  pattern: ^[a-f0-9]+$
  prefix: gnps.task
  reviewer:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  uri_format: https://gnps.ucsd.edu/ProteoSAFe/status.jsp?task=$1
go:
  aberowl:
    description: An ontology for describing the function of genes and gene products
    download_owl: http://aber-owl.net/media/ontologies/GO/1796/go.owl
    homepage: http://geneontology.org/
    name: Gene Ontology
    prefix: GO
  agroportal:
    contact:
      email: go@geneontology.org
      name: Gene Ontology
    description: The Gene Ontology (GO) provides a framework and set of concepts for
      describing the functions of gene products from all organisms.
    example_uri: http://purl.obolibrary.org/obo/GO_0015219
    homepage: http://www.geneontology.org/
    license: CC-BY-4.0
    name: Gene Ontology
    prefix: GO
    publications:
    - http://geneontology.org/page/publications
    repository: https://sourceforge.net/projects/geneontology/
    version: '2025-10-10'
  bartoc:
    abbreviation: GO
    description: The Gene Ontology project is a major bioinformatics initiative with
      the aim of standardizing the representation of gene and gene product attributes
      across species and databases. The project provides a controlled vocabulary of
      terms for describing gene product characteristics and gene product annotation
      data from GO Consortium members, as well as tools to access and process this
      data.
    homepage: http://www.geneontology.org/
    name: Gene Ontology
    prefix: '572'
    wikidata_database: Q135085
  biocontext:
    prefix: GO
  bioportal:
    description: Provides structured controlled vocabularies for the annotation of
      gene products with respect to their molecular function, cellular component,
      and biological role. The Gene Ontology consists of three Vocabularies.
    homepage: http://www.geneontology.org
    name: Gene Ontology
    prefix: GO
    version: '2025-10-10'
  contributor_extras:
  - email: jmcl@ebi.ac.uk
    github: jamesamcl
    name: James Alastair McLaughlin
    orcid: 0000-0002-8361-2795
  edam:
    description: An identifier of a concept from The Gene Ontology.
    name: GO concept
    obsolete: false
    prefix: '1176'
  example: '0032571'
  fairsharing:
    abbreviation: GO
    contact:
      email: suzia@stanford.edu
      name: Suzi Aleksander
      orcid: 0000-0001-6787-2901
    description: The Gene Ontology (GO) is a structured vocabulary for use by the
      research community for the annotation of genes, gene products and sequences.
      The GO defines concepts/classes used to describe gene function and relationships
      between these concepts.
    domains:
    - Expression data
    - GO-term enrichment data
    - Annotation
    - Sequence annotation
    - Gene functional annotation
    - molecular_function
    - cellular_component
    - biological_process
    - protein
    - transcript
    - gene
    - Knowledge representation
    - Biocuration
    homepage: http://www.geneontology.org
    license: CC-BY-4.0
    logo: https://api.fairsharing.org/rails/active_storage/blobs/redirect/eyJfcmFpbHMiOnsibWVzc2FnZSI6IkJBaHBBY0k9IiwiZXhwIjpudWxsLCJwdXIiOiJibG9iX2lkIn19--17999ec75f811e894e6a645034077964b591019b/gologo.png?disposition=inline
    name: Gene Ontology
    prefix: FAIRsharing.6xq0ee
    publications:
    - doi: 10.1093/nar/gky1055
      pubmed: '30395331'
      title: 'The Gene Ontology Resource: 20 years and still GOing strong'
      year: 2018
    - doi: 10.1093/nar/gkr1028
      pubmed: '22102568'
      title: 'The Gene Ontology: enhancements for 2011'
      year: 2011
    - doi: 10.1093/nar/gkp1018
      pubmed: '19920128'
      title: 'The Gene Ontology in 2010: extensions and refinements'
      year: 2009
    - doi: 10.1093/nar/gku1179
      pubmed: '25428369'
      title: 'Gene Ontology Consortium: going forward'
      year: 2014
    - doi: 10.1093/nar/gks1050
      pubmed: '23161678'
      title: Gene Ontology annotations and resources
      year: 2012
    - doi: 10.1038/75556
      pubmed: '10802651'
      title: 'Gene ontology: tool for the unification of biology. The Gene Ontology
        Consortium'
      year: 2000
    - doi: 10.1093/nar/gkh036
      pubmed: '14681407'
      title: The Gene Ontology (GO) database and informatics resource
      year: 2003
    - doi: 10.1186/1471-2164-14-513
      pubmed: '23895341'
      title: 'Dovetailing biology and chemistry: integrating the Gene Ontology with
        the ChEBI chemical ontology'
      year: 2013
    - doi: 10.1093/nar/gkaa1113
      title: 'The Gene Ontology resource: enriching a GOld mine'
      year: 2020
    subjects:
    - Life Science
    twitter: news4go
  go:
    homepage: http://amigo.geneontology.org/
    name: Gene Ontology Database
    prefix: GO
  hl7:
    description: 'Gene Ontology: tool for the unification of biology. The Gene Ontology
      Consortium (2000) Nature Genet. 25: 25-29, http://www.geneontology.org/#cite_go.ftp://ftp.geneontology.org/pub/go/ontology-archive/'
    homepage: http://www.geneontology.org/
    name: Gene Ontology
    organization: The Gene Ontology Consortium
    preferred_prefix: go
    prefix: 2.16.840.1.113883.6.128
    status: Complete
  integbio:
    alt_name: Gene Ontology
    description: GO is a database which provides a controlled vocabulary of terms
      for describing gene product characteristics and gene product annotation data.
      It contains data of terms, definitions and ontology structure. The most recent
      version of the ontology and the annotation files contributed by members of the
      GO Consortium are available for download. The GO provides the AmiGO browser
      and search engine which are web browser-based access to the GO database.
    homepage: http://www.geneontology.org/
    information_keywords:
    - Ontology/Terminology/Nomenclature
    maintainer: GO (Gene Ontology) Consortium
    name: GO
    prefix: nbdc00074
    pubmeds:
    - '22102568'
    - '19578431'
    status: Active
    target_keywords:
    - Genome/Gene
    - RNA
    - Protein
  mappings:
    aberowl: GO
    agroportal: GO
    bartoc: '572'
    biocontext: GO
    bioportal: GO
    edam: '1176'
    fairsharing: FAIRsharing.6xq0ee
    go: GO
    hl7: 2.16.840.1.113883.6.128
    integbio: nbdc00074
    miriam: go
    n2t: go
    ncbi: GO
    obofoundry: go
    ols: go
    ontobee: GO
    pathguide: '272'
    prefixcommons: go
    re3data: r3d100014165
    tib: go
    togoid: Go
    uniprot: DB-0037
    wikidata: P686
    wikidata.entity: Q135085
  mastodon: go@genomic.social
  miriam:
    deprecated: false
    description: The Gene Ontology project provides a controlled vocabulary to describe
      gene and gene product attributes in any organism.
    homepage: http://amigo.geneontology.org/
    id: '00000022'
    name: Gene Ontology
    namespaceEmbeddedInLui: true
    pattern: ^GO:\d{7}$
    prefix: go
    providers:
    - code: quickgo
      description: QuickGO (Gene Ontology browser)
      homepage: https://www.ebi.ac.uk/QuickGO/
      name: QuickGO (Gene Ontology browser)
      uri_format: https://www.ebi.ac.uk/QuickGO/GTerm?id=GO:$1
    - code: ''
      description: GO Browser
      homepage: http://www.informatics.jax.org/searches/GO_form.shtml
      name: GO Browser
      uri_format: http://www.informatics.jax.org/searches/GO.cgi?id=GO:$1
    - code: ''
      description: GO through PANTHER
      homepage: http://www.pantherdb.org/
      name: GO through PANTHER
      uri_format: http://www.pantherdb.org/panther/category.do?categoryAcc=GO:$1
    sampleId: 0006915
    uri_format: http://amigo.geneontology.org/amigo/term/GO:$1
  n2t:
    description: The Gene Ontology project provides a controlled vocabulary to describe
      gene and gene product attributes in any organism.
    example: 0006915
    homepage: http://amigo.geneontology.org/
    name: AmiGO 2
    namespaceEmbeddedInLui: true
    pattern: ^GO:\d{7}$
    prefix: go
    uri_format: http://amigo.geneontology.org/amigo/term/GO:$1
  ncbi:
    example: '123'
    homepage: http://amigo.geneontology.org/
    name: Gene Ontology Database identifier
    prefix: GO
  obofoundry:
    appears_in:
    - agro
    - chiro
    - cl
    - ecocore
    - ecto
    - envo
    - maxo
    - pcl
    - pco
    - planp
    - uberon
    - xpo
    - zp
    contact: suzia@stanford.edu
    contact.github: suzialeksander
    contact.label: Suzi Aleksander
    contact.orcid: 0000-0001-6787-2901
    depends_on:
    - cl
    - ncbitaxon
    - ro
    - uberon
    deprecated: false
    description: An ontology for describing the function of genes and gene products
    domain: biological systems
    download.json: http://purl.obolibrary.org/obo/go.json
    download.obo: http://purl.obolibrary.org/obo/go.obo
    download.owl: http://purl.obolibrary.org/obo/go.owl
    homepage: http://geneontology.org/
    license: CC BY 4.0
    license.url: https://creativecommons.org/licenses/by/4.0/
    logo: https://obofoundry.org/images/go_logo.png
    name: Gene Ontology
    preferredPrefix: GO
    prefix: go
    publications:
    - id: https://www.ncbi.nlm.nih.gov/pubmed/10802651
      title: 'Gene ontology: tool for the unification of biology. The Gene Ontology
        Consortium'
    - id: https://www.ncbi.nlm.nih.gov/pubmed/33290552
      title: 'The Gene Ontology resource: enriching a GOld mine'
    repository: https://github.com/geneontology/go-ontology
    twitter: news4go
  ols:
    description: The Gene Ontology (GO) provides a framework and set of concepts for
      describing the functions of gene products from all organisms.
    download_owl: http://purl.obolibrary.org/obo/go/extensions/go-plus.owl
    homepage: http://geneontology.org/
    name: Gene Ontology
    prefix: go
    tracker: https://github.com/geneontology/go-ontology/issues/
    version: '2025-10-10'
    version.iri: http://purl.obolibrary.org/obo/go/releases/2025-10-10/extensions/go-plus.owl
  ontobee:
    library: Foundry
    name: Gene Ontology
    prefix: GO
  pathguide:
    abbreviation: GO
    homepage: 'http://www.geneontology.org '
    name: Gene Ontology Consortium
    prefix: '272'
  pattern: ^\d{7}$
  prefix: go
  prefixcommons:
    alt_uri_formats:
    - http://purl.org/obo/owl/GO#$1
    bioportal: '1070'
    description: 'The Gene Ontology project provides an ontology of defined terms
      representing gene product properties. The ontology covers three domains: cellular
      component, molecular function, and biological process.'
    example: 0006915
    homepage: http://www.geneontology.org/
    keywords:
    - obo
    - gene
    - ontology
    name: The Gene Ontology
    pattern: ^\d{7}$
    prefix: go
    pubmed_ids:
    - '14681407'
    - '10802651'
    synonyms:
    - gene_ontology
    - obo.go
    uri_format: http://amigo.geneontology.org/cgi-bin/amigo/term-details.cgi?term=GO:$1
  providers:
  - code: jax
    description: The JAX endpoint for exploring GO
    example: null
    first_party: null
    homepage: http://www.informatics.jax.org
    name: Jackson Laboratories
    publications: null
    status: null
    uri_format: http://www.informatics.jax.org/vocab/gene_ontology/GO:$1
  - code: nextprot
    description: The neXtProt endpoint for exploring GO
    example: null
    first_party: null
    homepage: https://www.nextprot.org/
    name: neXtProt GO Browser
    publications: null
    status: null
    uri_format: https://www.nextprot.org/term/GO:$1
  - code: miriam_obo_legacy
    description: An old URI style for MIRIAM + GO
    example: null
    first_party: null
    homepage: https://identifiers.org/
    name: MIRIAM OBO Legacy
    publications: null
    status: null
    uri_format: http://identifiers.org/obo.go/GO:$1
  - code: go_site
    description: A non-PURL link through the GO site
    example: null
    first_party: null
    homepage: http://www.geneontology.org
    name: GO Site Link
    publications: null
    status: null
    uri_format: http://www.geneontology.org/GO:$1
  - code: quickgo.legacy
    description: QuickGO (Gene Ontology browser)
    example: null
    first_party: null
    homepage: https://www.ebi.ac.uk/QuickGO/
    name: QuickGO (Legacy URL)
    publications: null
    status: null
    uri_format: https://www.ebi.ac.uk/QuickGO/GTerm?id=GO:$1
  - code: quickgo
    description: Gene Ontology browser from the EBI
    example: null
    first_party: null
    homepage: https://www.ebi.ac.uk/QuickGO/
    name: QuickGO
    publications: null
    status: null
    uri_format: https://www.ebi.ac.uk/QuickGO/term/GO:$1
  - code: pantherdb
    description: GO Browser in PantherDB
    example: null
    first_party: null
    homepage: http://www.pantherdb.org/panther
    name: PatherDB
    publications: null
    status: null
    uri_format: http://www.pantherdb.org/panther/category.do?categoryAcc=GO:$1
  - code: purlorg
    description: null
    example: null
    first_party: null
    homepage: null
    name: PURL.org Legacy
    publications: null
    status: null
    uri_format: http://purl.org/obo/owl/GO#GO_$1
  publications:
  - doi: 10.1093/nar/gkaa1113
    pmc: PMC7779012
    pubmed: '33290552'
    title: 'The Gene Ontology resource: enriching a GOld mine'
    year: 2021
  - doi: 10.1093/nar/gky1055
    pmc: PMC6323945
    pubmed: '30395331'
    title: 'The Gene Ontology Resource: 20 years and still GOing strong'
    year: 2019
  - doi: 10.1093/nar/gku1179
    pmc: PMC4383973
    pubmed: '25428369'
    title: 'Gene Ontology Consortium: going forward'
    year: 2014
  - doi: 10.1186/1471-2164-14-513
    pmc: PMC3733925
    pubmed: '23895341'
    title: 'Dovetailing biology and chemistry: integrating the Gene Ontology with
      the ChEBI chemical ontology'
    year: 2013
  - doi: 10.1093/nar/gks1050
    pmc: PMC3531070
    pubmed: '23161678'
    title: Gene Ontology annotations and resources
    year: 2012
  - doi: 10.1093/nar/gkr1028
    pmc: PMC3245151
    pubmed: '22102568'
    title: 'The Gene Ontology: enhancements for 2011'
    year: 2011
  - doi: 10.1093/nar/gkp1018
    pmc: PMC2808930
    pubmed: '19920128'
    title: 'The Gene Ontology in 2010: extensions and refinements'
    year: 2009
  - doi: 10.1093/nar/gkh036
    pmc: PMC308770
    pubmed: '14681407'
    title: The Gene Ontology (GO) database and informatics resource
    year: 2004
  - doi: 10.1038/75556
    pmc: PMC3037419
    pubmed: '10802651'
    title: 'Gene ontology: tool for the unification of biology. The Gene Ontology
      Consortium'
    year: 2000
  - doi: null
    pmc: null
    pubmed: '10802651'
    title: 'Gene ontology: tool for the unification of biology. The Gene Ontology
      Consortium'
    year: null
  - doi: null
    pmc: null
    pubmed: '33290552'
    title: 'The Gene Ontology resource: enriching a GOld mine'
    year: null
  - doi: 10.1093/nar/gky1055
    pmc: null
    pubmed: '30395331'
    title: 'The Gene Ontology Resource: 20 years and still GOing strong'
    year: 2018
  - doi: 10.1093/nar/gkr1028
    pmc: null
    pubmed: '22102568'
    title: 'The Gene Ontology: enhancements for 2011'
    year: 2011
  - doi: 10.1093/nar/gkp1018
    pmc: null
    pubmed: '19920128'
    title: 'The Gene Ontology in 2010: extensions and refinements'
    year: 2009
  - doi: 10.1093/nar/gku1179
    pmc: null
    pubmed: '25428369'
    title: 'Gene Ontology Consortium: going forward'
    year: 2014
  - doi: 10.1093/nar/gks1050
    pmc: null
    pubmed: '23161678'
    title: Gene Ontology annotations and resources
    year: 2012
  - doi: 10.1038/75556
    pmc: null
    pubmed: '10802651'
    title: 'Gene ontology: tool for the unification of biology. The Gene Ontology
      Consortium'
    year: 2000
  - doi: 10.1093/nar/gkh036
    pmc: null
    pubmed: '14681407'
    title: The Gene Ontology (GO) database and informatics resource
    year: 2003
  - doi: 10.1186/1471-2164-14-513
    pmc: null
    pubmed: '23895341'
    title: 'Dovetailing biology and chemistry: integrating the Gene Ontology with
      the ChEBI chemical ontology'
    year: 2013
  - doi: 10.1093/nar/gkaa1113
    pmc: null
    pubmed: null
    title: 'The Gene Ontology resource: enriching a GOld mine'
    year: 2020
  - doi: null
    pmc: null
    pubmed: '14681407'
    title: null
    year: null
  - doi: null
    pmc: null
    pubmed: '10802651'
    title: null
    year: null
  - doi: 10.1093/genetics/iyad031
    pmc: null
    pubmed: '36866529'
    title: null
    year: null
  - doi: null
    pmc: null
    pubmed: '10802651'
    title: 'Gene ontology: tool for the unification of biology. The Gene Ontology
      Consortium'
    year: null
  - doi: null
    pmc: null
    pubmed: '33290552'
    title: 'The Gene Ontology resource: enriching a GOld mine'
    year: null
  - doi: 10.1093/nar/gky1055
    pmc: null
    pubmed: '30395331'
    title: 'The Gene Ontology Resource: 20 years and still GOing strong'
    year: 2018
  - doi: 10.1093/nar/gkr1028
    pmc: null
    pubmed: '22102568'
    title: 'The Gene Ontology: enhancements for 2011'
    year: 2011
  - doi: 10.1093/nar/gkp1018
    pmc: null
    pubmed: '19920128'
    title: 'The Gene Ontology in 2010: extensions and refinements'
    year: 2009
  - doi: 10.1093/nar/gku1179
    pmc: null
    pubmed: '25428369'
    title: 'Gene Ontology Consortium: going forward'
    year: 2014
  - doi: 10.1093/nar/gks1050
    pmc: null
    pubmed: '23161678'
    title: Gene Ontology annotations and resources
    year: 2012
  - doi: 10.1038/75556
    pmc: null
    pubmed: '10802651'
    title: 'Gene ontology: tool for the unification of biology. The Gene Ontology
      Consortium'
    year: 2000
  - doi: 10.1093/nar/gkh036
    pmc: null
    pubmed: '14681407'
    title: The Gene Ontology (GO) database and informatics resource
    year: 2003
  - doi: 10.1186/1471-2164-14-513
    pmc: null
    pubmed: '23895341'
    title: 'Dovetailing biology and chemistry: integrating the Gene Ontology with
      the ChEBI chemical ontology'
    year: 2013
  - doi: 10.1093/nar/gkaa1113
    pmc: null
    pubmed: null
    title: 'The Gene Ontology resource: enriching a GOld mine'
    year: 2020
  - doi: null
    pmc: null
    pubmed: '14681407'
    title: null
    year: null
  - doi: null
    pmc: null
    pubmed: '10802651'
    title: null
    year: null
  - doi: 10.1093/genetics/iyad031
    pmc: null
    pubmed: '36866529'
    title: null
    year: null
  - doi: null
    pmc: null
    pubmed: '10802651'
    title: 'Gene ontology: tool for the unification of biology. The Gene Ontology
      Consortium'
    year: null
  - doi: null
    pmc: null
    pubmed: '33290552'
    title: 'The Gene Ontology resource: enriching a GOld mine'
    year: null
  - doi: 10.1093/nar/gky1055
    pmc: null
    pubmed: '30395331'
    title: 'The Gene Ontology Resource: 20 years and still GOing strong'
    year: 2018
  - doi: 10.1093/nar/gkr1028
    pmc: null
    pubmed: '22102568'
    title: 'The Gene Ontology: enhancements for 2011'
    year: 2011
  - doi: 10.1093/nar/gkp1018
    pmc: null
    pubmed: '19920128'
    title: 'The Gene Ontology in 2010: extensions and refinements'
    year: 2009
  - doi: 10.1093/nar/gku1179
    pmc: null
    pubmed: '25428369'
    title: 'Gene Ontology Consortium: going forward'
    year: 2014
  - doi: 10.1093/nar/gks1050
    pmc: null
    pubmed: '23161678'
    title: Gene Ontology annotations and resources
    year: 2012
  - doi: 10.1038/75556
    pmc: null
    pubmed: '10802651'
    title: 'Gene ontology: tool for the unification of biology. The Gene Ontology
      Consortium'
    year: 2000
  - doi: 10.1093/nar/gkh036
    pmc: null
    pubmed: '14681407'
    title: The Gene Ontology (GO) database and informatics resource
    year: 2003
  - doi: 10.1186/1471-2164-14-513
    pmc: null
    pubmed: '23895341'
    title: 'Dovetailing biology and chemistry: integrating the Gene Ontology with
      the ChEBI chemical ontology'
    year: 2013
  - doi: 10.1093/nar/gkaa1113
    pmc: null
    pubmed: null
    title: 'The Gene Ontology resource: enriching a GOld mine'
    year: 2020
  - doi: null
    pmc: null
    pubmed: '14681407'
    title: null
    year: null
  - doi: null
    pmc: null
    pubmed: '10802651'
    title: null
    year: null
  - doi: 10.1093/genetics/iyad031
    pmc: null
    pubmed: '36866529'
    title: null
    year: null
  re3data:
    description: 'The mission of the GO Consortium is to develop a comprehensive,
      computational model of biological systems, ranging from the molecular to the
      organism level, across the multiplicity of species in the tree of life.

      The Gene Ontology (GO) knowledgebase is the world’s largest source of information
      on the functions of genes. This knowledge is both human-readable and machine-readable,
      and is a foundation for computational analysis of large-scale molecular biology
      and genetics experiments in biomedical research.'
    doi: 10.17616/R31NJNF9
    homepage: http://geneontology.org
    name: Gene Ontology
    prefix: r3d100014165
    synonyms:
    - GO
  synonyms:
  - gobp
  - gobpid
  - gocc
  - goccid
  - gomf
  - gomfid
  tib:
    contact: go@geneontology.org
    description: The Gene Ontology (GO) provides a framework and set of concepts for
      describing the functions of gene products from all organisms.
    download_owl: http://purl.obolibrary.org/obo/go.owl
    homepage: http://geneontology.org/
    keywords:
    - DataPLANT
    - life sciences, biology
    - medicine
    name: Gene Ontology
    prefix: go
    tracker: https://github.com/geneontology/go-ontology/issues/
    version.iri: http://purl.obolibrary.org/obo/go/releases/2025-10-10/go.owl
  togoid:
    catalog: nbdc00074
    description: GO is a database which provides a controlled vocabulary of terms
      for describing gene product characteristics and gene product annotation data.
      It contains data of terms, definitions and ontology structure. The most recent
      version of the ontology and the annotation files contributed by members of the
      GO Consortium are available for download. The GO provides the AmiGO browser
      and search engine which are web browser-based access to the GO database.
    examples:
    - GO:0005643
    - GO:0097110
    - GO:0097225
    - GO:0052855
    - GO:2000012
    - GO:0042921
    - GO:0019774
    - GO:0085018
    - GO:0009508
    - GO:0046470
    keywords:
    - Function
    name: Gene ontology
    pattern: ^GO[:_](?\d{7})$
    prefix: Go
    uri_format: http://purl.obolibrary.org/obo/GO_$1
  uniprot:
    abbreviation: GO
    category: Ontologies
    homepage: https://geneontology.org/
    name: Gene Ontology
    prefix: DB-0037
    publications:
    - doi: 10.1093/genetics/iyad031
      pubmed: '36866529'
    uri_format: https://www.ebi.ac.uk/QuickGO/term/$1
  uri_format: http://purl.obolibrary.org/obo/GO_$1
  wikidata:
    description: identifier in the Gene Ontology
    example:
    - GO:0005773
    - GO:0046872
    homepage: http://amigo.geneontology.org/
    miriam: GO
    name: Gene Ontology ID
    pattern: ^GO:\d{7}$
    prefix: P686
    uri_format: https://amigo.geneontology.org/amigo/term/$1
go.gpi:
  biolink:
    is_identifiers: false
    is_obo: false
    prefix: gpi
    uri_format: https://github.com/geneontology/go-annotation/blob/master/specs/gpad-gpi-2-0.md#$1
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  contributor_extras:
  - email: smoxon@lbl.gov
    github: sierra-moxon
    name: Sierra Moxon
    orcid: 0000-0002-8719-7760
  description: This describes the metadata schema for the Gene Product Information
    (GPI) files in the Gene Ontology, i.e., the local unique identifiers in this identifier
    space refer to the columns in GPI files.
  example: db-object-id
  homepage: http://geneontology.org/docs/gene-product-information-gpi-format/#db-object-id
  mappings:
    biolink: gpi
  name: Gene Product Information Schema
  part_of_database: go
  prefix: go.gpi
  uri_format: http://geneontology.org/docs/gene-product-information-gpi-format/#$1
go.issue:
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: An issue on the Gene Ontology GitHub issue tracker
  example: '23000'
  github_request_issue: 1553
  homepage: https://github.com/geneontology/go-ontology/issues
  name: Gene Ontology Issue Tracker
  pattern: ^\d+$
  prefix: go.issue
  uri_format: https://github.com/geneontology/go-ontology/issues/$1
go.model:
  description: GO-Causal Activity Models (GO-CAMs) use a defined “grammar” for linking
    multiple GO annotations into larger models of biological function (such as “pathways”)
    in a semantically structured manner. GO-CAMs are created by expert biocurators
    from the GO Consortium, using the Noctua Curation Platform.
  example: 5fce9b7300001250
  go:
    homepage: https://geneontology.org/go-cam
    name: Gene Ontology Causal Activity Model (GO-CAM)
    prefix: gomodel
    uri_format: https://model.geneontology.org/$1
  mappings:
    go: gomodel
  name: Gene Ontology Causal Activity Model
  part_of_database: go
  prefix: go.model
  providers:
  - code: legacy
    description: This was the old URI for the GO CAM editor
    example: null
    first_party: null
    homepage: https://model.geneontology.org
    name: Legacy
    publications: null
    status: null
    uri_format: http://noctua.geneontology.org/editor/graph/gomodel:$1
  uri_format: https://model.geneontology.org/$1
go.ref:
  banana: GO_REF
  biocontext:
    prefix: GO_REF
    uri_format: http://www.geneontology.org/cgi-bin/references.cgi#GO_REF:$1
  go:
    homepage: http://geneontology.org/gorefs
    name: Gene Ontology Database references
    prefix: GO_REF
  mappings:
    biocontext: GO_REF
    go: GO_REF
    miriam: go_ref
    n2t: go.ref
  miriam:
    deprecated: false
    description: The GO reference collection is a set of abstracts that can be cited
      in the GO ontologies (e.g. as dbxrefs for term definitions) and annotation files
      (in the Reference column). It provides two types of reference; It can be used
      to provide details of why specific Evidence codes (see http://identifiers.org/eco/)
      are assigned, or to present abstract-style descriptions of "GO content" meetings
      at which substantial changes in the ontologies are discussed and made.
    homepage: http://www.geneontology.org
    id: '00000450'
    name: Gene Ontology Reference
    namespaceEmbeddedInLui: true
    pattern: ^GO_REF:\d{7}$
    prefix: go_ref
    sampleId: '0000041'
    uri_format: https://geneontology.org/GO_REF/$1
  n2t:
    description: The GO reference collection is a set of abstracts that can be cited
      in the GO ontologies (e.g. as dbxrefs for term definitions) and annotation files
      (in the Reference column). It provides two types of reference; It can be used
      to provide details of why specific Evidence codes (see http://identifiers.org/eco/)
      are assigned, or to present abstract-style descriptions of "GO content" meetings
      at which substantial changes in the ontologies are discussed and made.
    example: GO_REF:0000041
    homepage: http://www.geneontology.org/cgi-bin/references.cgi
    name: Gene Ontology Reference at The Gene Ontology Consortium
    namespaceEmbeddedInLui: false
    pattern: ^GO_REF:\d{7}$
    prefix: go.ref
    uri_format: http://www.geneontology.org/cgi-bin/references.cgi#$1
  part_of_database: go
  pattern: ^\d{7}$
  prefix: go.ref
  providers:
  - code: legacy
    description: The README file on GO's github repository has been replaced with
      a structured YAML file, so this URl is no longer available.
    example: null
    first_party: null
    homepage: https://github.com/geneontology/go-site/blob/master/metadata/gorefs.yaml
    name: Legacy
    publications: null
    status: null
    uri_format: https://github.com/geneontology/go-site/blob/master/metadata/gorefs/README.md#goref$1
  uri_format: https://geneontology.org/GO_REF/$1
go.resource:
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: A database-specific registry supporting curation in the Gene Ontology
  example: CHEBI
  homepage: https://raw.githubusercontent.com/geneontology/go-site/master/metadata/db-xrefs.yaml
  name: Gene Ontology Registry
  part_of_database: go
  prefix: go.resource
  uri_format: https://bioregistry.io/metaregistry/go/$1
go.rule:
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: GO Rules are a way of documenting the set of filters and reports that
    should apply to GAF annotation data. Some rules are expressed as SPARQL on a triplestore,
    some are code in the GAF parsing software, ontobio.
  example: '0000004'
  homepage: https://github.com/geneontology/go-site/tree/master/metadata/rules
  name: Gene Ontology Rules
  part_of_database: go
  pattern: ^\d{7}$
  preferred_prefix: GORULE
  prefix: go.rule
  uri_format: https://github.com/geneontology/go-site/blob/master/metadata/rules/gorule-$1.md
goa:
  biocontext:
    prefix: GOA
  contact:
    email: r.huntley@ucl.ac.uk
    github: rachhuntley
    name: Rachael P. Huntley
    orcid: 0000-0001-6718-3559
  fairsharing:
    abbreviation: GOA
    description: The GO Annotation Database (GOA) provides Gene Ontology (GO) annotations
      to proteins in the UniProt Knowledgebase (UniProtKB), RNA molecules from RNACentral
      and protein complexes from the Complex Portal. GOA files contain a mixture of
      manual annotation supplied by members of the Gene Onotology Consortium and computationally
      assigned GO terms describing gene products. Annotation type is clearly indicated
      by associated evidence codes and there are links to the source data.
    homepage: http://www.ebi.ac.uk/GOA
    license: http://opendatacommons.org/licenses/pddl/1.0
    name: Gene Ontology Annotation Database
    prefix: FAIRsharing.7zffgc
    publications:
    - doi: 10.1093/nar/gkn803
      pubmed_id: 18957448
      title: The GOA database in 2009--an integrated Gene Ontology Annotation resource.
    - doi: 10.1093/nar/gku1113
      pubmed_id: 25378336
      title: 'The GOA database: gene Ontology annotation updates for 2015.'
    subjects:
    - Life Science
    - Biology
  integbio:
    alt_name: Gene Ontology Annotation Database
    description: GOA is a database of gene function and interaction information. The
      database contains manual and automated annotations of gene ontology. Users can
      download current and previous versions of the database including gene annotations,
      gene interactions, and ontology mapping files.
    fairsharing: biodbcore-000313
    homepage: https://www.ebi.ac.uk/GOA
    information_keywords:
    - Ontology/Terminology/Nomenclature
    maintainer: EMBL-EBI (European Bioinformatics Institute)
    name: GOA
    prefix: nbdc00468
    pubmeds:
    - '18957448'
    - '22123736'
    - '19744993'
    status: Active
    target_keywords:
    - RNA
    - Protein
  mappings:
    biocontext: GOA
    fairsharing: FAIRsharing.7zffgc
    integbio: nbdc00468
    miriam: goa
    n2t: goa
    ncbi: GOA
    prefixcommons: goa
  miriam:
    deprecated: false
    description: The GOA (Gene Ontology Annotation) project provides high-quality
      Gene Ontology (GO) annotations to proteins in the UniProt Knowledgebase (UniProtKB)
      and International Protein Index (IPI). This involves electronic annotation and
      the integration of high-quality manual GO annotation from all GO Consortium
      model organism groups and specialist groups.
    homepage: https://www.ebi.ac.uk/GOA/
    id: 00000196
    name: GOA
    namespaceEmbeddedInLui: false
    pattern: ^(([A-N,R-Z][0-9][A-Z][A-Z, 0-9][A-Z, 0-9][0-9])|([O,P,Q][0-9][A-Z, 0-9][A-Z,
      0-9][A-Z, 0-9][0-9]))|(URS[0-9A-F]{10}(_[0-9]+){0,1})|(EBI-[0-9]+)$
    prefix: goa
    sampleId: P12345
    uri_format: https://www.ebi.ac.uk/QuickGO/GProtein?ac=$1
  n2t:
    description: The GOA (Gene Ontology Annotation) project provides high-quality
      Gene Ontology (GO) annotations to proteins in the UniProt Knowledgebase (UniProtKB)
      and International Protein Index (IPI). This involves electronic annotation and
      the integration of high-quality manual GO annotation from all GO Consortium
      model organism groups and specialist groups.
    example: P12345
    homepage: https://www.ebi.ac.uk/GOA/
    name: GOA through QuickGO
    namespaceEmbeddedInLui: false
    pattern: ^(([A-N,R-Z][0-9][A-Z][A-Z, 0-9][A-Z, 0-9][0-9])|([O,P,Q][0-9][A-Z, 0-9][A-Z,
      0-9][A-Z, 0-9][0-9]))|(URS[0-9A-F]{10}(_[0-9]+){0,1})|(EBI-[0-9]+)$
    prefix: goa
    uri_format: https://www.ebi.ac.uk/QuickGO/GProtein?ac=$1
  name: Gene Ontology Annotation Database
  ncbi:
    example: P01100
    homepage: http://www.ebi.ac.uk/GOA/
    name: Gene Ontology Annotation Database Identifier
    prefix: GOA
  part_of_database: go
  prefix: goa
  prefixcommons:
    description: The GOA (Gene Ontology Annotation) project provides high-quality
      Gene Ontology (GO) annotations to proteins in the UniProt Knowledgebase (UniProtKB)
      and International Protein Index (IPI). This involves electronic annotation and
      the integration of high-quality manual GO annotation from all GO Consortium
      model organism groups and specialist groups.
    example: go:0006915
    homepage: http://www.ebi.ac.uk/GOA
    keywords:
    - gene
    - ontology
    - protein
    name: Gene Ontology Annotation
    pattern: ^([A-N,R-Z][0-9][A-Z][A-Z, 0-9][A-Z, 0-9][0-9])|([O,P,Q][0-9][A-Z, 0-9][A-Z,
      0-9][A-Z, 0-9][0-9])$
    prefix: goa
    pubmed_ids:
    - '18957448'
    synonyms:
    - goa-projects
    uri_format: http://www.ebi.ac.uk/QuickGO/GTerm?id=$1
  provides: uniprot
  publications:
  - doi: 10.1093/nar/gku1113
    pmc: PMC4383930
    pubmed: '25378336'
    title: 'The GOA database: gene Ontology annotation updates for 2015'
    year: 2014
  - doi: 10.1093/nar/gkn803
    pmc: PMC2686469
    pubmed: '18957448'
    title: The GOA database in 2009--an integrated Gene Ontology Annotation resource
    year: 2008
  - doi: 10.1093/nar/gkn803
    pmc: null
    pubmed: null
    title: The GOA database in 2009--an integrated Gene Ontology Annotation resource.
    year: null
  - doi: 10.1093/nar/gku1113
    pmc: null
    pubmed: null
    title: 'The GOA database: gene Ontology annotation updates for 2015.'
    year: null
  - doi: null
    pmc: null
    pubmed: '18957448'
    title: null
    year: null
goche:
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: Represent chemical entities having particular CHEBI roles
  download_owl: https://raw.githubusercontent.com/geneontology/go-ontology/master/src/ontology/imports/chebi_roles.owl
  example: '25512'
  homepage: https://github.com/geneontology/go-ontology
  name: GO Chemicals
  part_of_database: go
  pattern: ^\d+$
  preferred_prefix: GOCHE
  prefix: goche
  rdf_uri_format: http://purl.obolibrary.org/obo/GOCHE_$1
  references:
  - https://obo-communitygroup.slack.com/archives/C023P0Z304T/p1638472847049400
  - https://github.com/geneontology/go-ontology/issues/19535
  repository: https://github.com/geneontology/go-ontology
  synonyms:
  - go.chebi
  - go.chemical
  - go.chemicals
  uri_format: https://biopragmatics.github.io/providers/goche/$1
goeco:
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: A GO annotation is a statement about the function of a particular gene.
    Each annotation includes an evidence code to indicate how the annotation to a
    particular term is supported.
  example: IPI
  homepage: http://geneontology.org/docs/guide-go-evidence-codes/
  name: GO Evidence Code
  part_of_database: go
  prefix: goeco
gold:
  contact:
    email: tbreddy@lbl.gov
    github: TBKReddy
    name: TBK Reddy
    orcid: 0000-0002-0871-5567
  fairsharing:
    abbreviation: JGI-GOLD
    description: 'Genomes Online Database, is a World Wide Web resource for comprehensive
      access to information regarding genome and metagenome sequencing projects, and
      their associated metadata, around the world. Information in GOLD is organized
      into levels to include Study, Organism or Biosample, Sequencing Project (SP),
      and Analysis Project (AP). All four levels, along with their complex list of
      metadata fields and controlled vocabulary (CV) terms, are connected to each
      other in a lucid framework to enhance scientific discovery. GOLD is a curated
      resource serving the research community and your input is critical to ensure
      high quality, accurate metadata in GOLD. '
    homepage: https://gold.jgi.doe.gov/
    name: Joint Genome Institute, Genomes OnLine Database
    prefix: FAIRsharing.5q1p14
    publications:
    - doi: '11125068'
      pubmed_id: 11125068
      title: 'Genomes OnLine Database (GOLD): a monitor of genome projects world-wide.'
    - doi: 10.1093/nar/gkm884
      pubmed_id: 17981842
      title: 'The Genomes On Line Database (GOLD) in 2007: status of genomic and metagenomic
        projects and their associated metadata.'
    - doi: 10.1093/bioinformatics/15.9.773
      pubmed_id: 10498782
      title: 'Genomes OnLine Database (GOLD 1.0): a monitor of complete and ongoing
        genome projects world-wide.'
    - doi: 10.1093/nar/gkp848
      pubmed_id: 19914934
      title: 'The Genomes On Line Database (GOLD) in 2009: status of genomic and metagenomic
        projects and their associated metadata.'
    - doi: 10.1093/nar/gky977
      pubmed_id: 30357420
      title: 'Genomes OnLine database (GOLD) v.7: updates and new features.'
    - doi: 10.1093/nar/gkaa983
      pubmed_id: null
      title: 'Genomes OnLine Database (GOLD) v.8: overview and updates'
    subjects:
    - Metagenomics
    - Genomics
    - Phylogenetics
    - Metabolomics
    - Ontology and Terminology
  integbio:
    alt_name: Genomes Online Database
    description: GOLD is a data management system that catalogs genome and metagenome
      sequencing projects with associated metadata from around the world. GOLD (v.6)
      provides information for 28,744 Studies, 272,234 Organisms, 21,910 Biosamples,
      134,884 Sequencing Projects and 111,625 Analysis Projects. Advanced Search feature
      allow users to explore GOLD's different project levels above.
    fairsharing: biodbcore-000117
    homepage: https://gold.jgi.doe.gov/index
    information_keywords:
    - Bibliography/Documents
    - Portal
    - Repository
    maintainer: DOE Joint Genome Institute
    name: GOLD
    prefix: nbdc00483
    pubmeds:
    - '27794040'
    status: Active
    target_keywords:
    - Genome/Gene
  mappings:
    fairsharing: FAIRsharing.5q1p14
    integbio: nbdc00483
    miriam: gold
    ols: gold
    prefixcommons: gold
    re3data: r3d100010808
  miriam:
    deprecated: false
    description: 'The Genomes OnLine Database (GOLD) catalogues genome and metagenome
      sequencing projects from around the world, along with their associated metadata.
      Information in GOLD is organized into four levels: Study, Biosample/Organism,
      Sequencing Project and Analysis Project.'
    homepage: https://gold.jgi.doe.gov/
    id: '00000733'
    name: Genomes OnLine Database (GOLD)
    namespaceEmbeddedInLui: false
    pattern: ^[A-Z][a-z][0-9]+$
    prefix: gold
    sampleId: Gs0000008
    uri_format: https://gold.jgi.doe.gov/resolver?id=$1
  name: Genomes Online Database
  ols:
    download_owl: https://raw.githubusercontent.com/cmungall/gold-ontology/refs/heads/main/gold.owl
    prefix: gold
  prefix: gold
  prefixcommons:
    description: 'GOLD: Genomes Online Database, is a World Wide Web resource for
      comprehensive access to information regarding complete and ongoing genome projects,
      as well as metagenomes and metadata, around the world.'
    example: Gc01070
    homepage: http://www.genomesonline.org/
    keywords:
    - genome
    name: Genomes Online Database
    pattern: ^G[a-z]\d+$
    prefix: gold
    uri_format: http://genomesonline.org/cgi-bin/GOLD/bin/GOLDCards.cgi?goldstamp=$1
  publications:
  - doi: 10.1093/nar/gkae1000
    pmc: null
    pubmed: '39498478'
    title: 'Genomes OnLine Database (GOLD) v.10: new features and updates'
    year: 2024
  - doi: 10.1093/nar/gkaa983
    pmc: PMC7778979
    pubmed: '33152092'
    title: 'Genomes OnLine Database (GOLD) v.8: overview and updates'
    year: 2021
  - doi: 10.1093/nar/gky977
    pmc: PMC6323969
    pubmed: '30357420'
    title: 'Genomes OnLine database (GOLD) v.7: updates and new features'
    year: 2019
  - doi: 10.1093/nar/gkp848
    pmc: PMC2808860
    pubmed: '19914934'
    title: 'The Genomes On Line Database (GOLD) in 2009: status of genomic and metagenomic
      projects and their associated metadata'
    year: 2009
  - doi: 10.1093/nar/gkm884
    pmc: PMC2238992
    pubmed: '17981842'
    title: 'The Genomes On Line Database (GOLD) in 2007: status of genomic and metagenomic
      projects and their associated metadata'
    year: 2007
  - doi: 10.1093/nar/29.1.126
    pmc: PMC29859
    pubmed: '11125068'
    title: 'Genomes OnLine Database (GOLD): a monitor of genome projects world-wide'
    year: 2001
  - doi: 10.1093/bioinformatics/15.9.773
    pmc: null
    pubmed: '10498782'
    title: 'Genomes OnLine Database (GOLD 1.0): a monitor of complete and ongoing
      genome projects world-wide'
    year: 1999
  re3data:
    description: GOLD is currently the largest repository for genome project information
      world-wide. The accurate and efficient genome project tracking is a vital criterion
      for launching new genome sequencing projects, and for avoiding significant overlap
      between various sequencing efforts and centers.
    doi: 10.17616/R39310
    homepage: https://gold.jgi.doe.gov/index
    license: Copyrights
    name: Genomes OnLine Database
    prefix: r3d100010808
    synonyms:
    - GOLD
    xrefs:
      nif: 0000-02918
      omics: 06148
gold.genome:
  biocontext:
    prefix: GOLD.GENOME
  deprecated: true
  mappings:
    biocontext: GOLD.GENOME
    miriam: gold.genome
    n2t: gold.genome
  miriam:
    deprecated: false
    description: '- DEPRECATION NOTE -

      Please, keep in mind that this namespace has been superseeded by ‘gold’ prefix
      at https://registry.identifiers.org/registry/gold, and this namespace is kept
      here for support to already existing citations, new ones would need to use the
      pointed ‘gold’ namespace.


      The GOLD (Genomes OnLine Database)is a resource for centralised monitoring of
      genome and metagenome projects worldwide. It stores information on complete
      and ongoing projects, along with their associated metadata. This collection
      references the sequencing status of individual genomes.'
    homepage: http://www.genomesonline.org/cgi-bin/GOLD/index.cgi
    id: '00000401'
    name: GOLD genome
    namespaceEmbeddedInLui: false
    pattern: ^(Gi|Gc)\d+$
    prefix: gold.genome
    sampleId: Gi07796
    uri_format: http://www.genomesonline.org/cgi-bin/GOLD/GOLDCards.cgi?goldstamp=$1
  n2t:
    description: The GOLD (Genomes OnLine Database)is a resource for centralized monitoring
      of genome and metagenome projects worldwide. It stores information on complete
      and ongoing projects, along with their associated metadata. This collection
      references the sequencing status of individual genomes.
    example: Gi07796
    homepage: http://www.genomesonline.org/cgi-bin/GOLD/index.cgi
    name: GOLD genome at Department of Energy Joint Genome Institute
    namespaceEmbeddedInLui: false
    pattern: ^[Gi|Gc]\d+$
    prefix: gold.genome
    uri_format: http://www.genomesonline.org/cgi-bin/GOLD/GOLDCards.cgi?goldstamp=$1
  prefix: gold.genome
  provides: gold
gold.meta:
  biocontext:
    prefix: GOLD.META
  has_canonical: gold
  mappings:
    biocontext: GOLD.META
    miriam: gold.meta
    n2t: gold.meta
  miriam:
    deprecated: false
    description: "- DEPRECATION NOTE -\nPlease, keep in mind that this namespace has\
      \ been superseeded by ‘gold’ prefix at https://registry.identifiers.org/registry/gold,\
      \ and this namespace is kept here for support to already existing citations,\
      \ new ones would need to use the pointed ‘gold’ namespace. \n\nThe GOLD (Genomes\
      \ OnLine Database)is a resource for centralized monitoring of genome and metagenome\
      \ projects worldwide. It stores information on complete and ongoing projects,\
      \ along with their associated metadata. This collection references metadata\
      \ associated with samples."
    homepage: http://www.genomesonline.org/cgi-bin/GOLD/index.cgi
    id: '00000402'
    name: GOLD metadata
    namespaceEmbeddedInLui: false
    pattern: ^Gm\d+$
    prefix: gold.meta
    sampleId: Gm00047
    uri_format: http://genomesonline.org/cgi-bin/GOLD/bin/GOLDCards.cgi?goldstamp=$1
  n2t:
    description: The GOLD (Genomes OnLine Database)is a resource for centralized monitoring
      of genome and metagenome projects worldwide. It stores information on complete
      and ongoing projects, along with their associated metadata. This collection
      references metadata associated with samples.
    example: Gm00047
    homepage: http://www.genomesonline.org/cgi-bin/GOLD/index.cgi
    name: GOLD metadata at Department of Energy Joint Genome Institute
    namespaceEmbeddedInLui: false
    pattern: ^Gm\d+$
    prefix: gold.meta
    uri_format: http://genomesonline.org/cgi-bin/GOLD/bin/GOLDCards.cgi?goldstamp=$1
  prefix: gold.meta
goldbook:
  bartoc:
    description: 'The Compendium is popularly referred to as the ''Gold Book'', in
      recognition of the contribution of the late Victor Gold, who initiated work
      on the first edition. It is one of the series of IUPAC ''Colour Books'' on chemical
      nomenclature, terminology, symbols and units (see the list of source documents),
      and collects together terminology definitions from IUPAC recommendations already
      published in Pure and Applied Chemistry and in the other Colour Books.


      Terminology definitions published by IUPAC are drafted by international committees
      of experts in the appropriate chemistry sub-disciplines, and ratified by IUPAC''s
      Interdivisional Committee on Terminology, Nomenclature and Symbols (ICTNS).
      In this edition of the Compendium these IUPAC-approved definitions are supplemented
      with some definitions from ISO and from the International Vocabulary of Basic
      and General Terms in Metrology; both these sources are recognised by IUPAC as
      authoritative. The result is a collection of nearly 7000 terms, with authoritative
      definitions, spanning the whole range of chemistry.


      Some minor editorial changes were made to the originally published definitions,
      to harmonise the presentation and to clarify their applicability, if this is
      limited to a particular sub-discipline. Verbal definitions of terms from Quantities,
      Units and Symbols in Physical Chemistry (the IUPAC Green Book, in which definitions
      are generally given as mathematical expressions) were developed specially for
      this Compendium by the Physical Chemistry Division of IUPAC. Definitions of
      a few physicochemical terms not mentioned in the Green Book were added at the
      same time (referred to here as Physical Chemistry Division, unpublished).


      The first reference given at the end of each definition is to the page of Pure
      Appl. Chem. or other source where the original definition appears; other references
      given designate other places where compatible definitions of the same term or
      additional information may be found, in other IUPAC documents. The complete
      reference citations are given in the appended list of source documents. Highlighted
      terms within individual definitions link to other entries where additional information
      is available.'
    homepage: http://goldbook.iupac.org/
    name: IUPAC Compendium of Chemical Terminology
    prefix: '1884'
    wikidata_database: Q902163
  contact:
    email: schalk@unf.edu
    github: stuchalk
    name: Stuart Chalk
    orcid: 0000-0002-0703-7776
  contact_group_email: goldbook@iupac.org
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: 'The Compendium is popularly referred to as the "Gold Book", in recognition
    of the contribution of the late Victor Gold, who initiated work on the first edition.
    It is one of the series of IUPAC "Colour Books" on chemical nomenclature, terminology,
    symbols and units (see the list of source documents), and collects together terminology
    definitions from IUPAC recommendations already published in Pure and Applied Chemistry
    and in the other Colour Books.


    Terminology definitions published by IUPAC are drafted by international committees
    of experts in the appropriate chemistry sub-disciplines, and ratified by IUPAC''s
    Interdivisional Committee on Terminology, Nomenclature and Symbols (ICTNS). In
    this edition of the Compendium these IUPAC-approved definitions are supplemented
    with some definitions from ISO and from the International Vocabulary of Basic
    and General Terms in Metrology; both these sources are recognised by IUPAC as
    authoritative. The result is a collection of nearly 7000 terms, with authoritative
    definitions, spanning the whole range of chemistry.


    The API can be accessed [here](https://goldbook.iupac.org/pages/api)'
  example: G02681
  example_extras:
  - 08306
  - '11214'
  - A00494
  - AT07327
  - B00737
  - BT07002
  - C00778
  - CT07136
  homepage: https://goldbook.iupac.org
  license: CC BY 4.0-SA
  mappings:
    bartoc: '1884'
    wikidata: P4732
    wikidata.entity: Q902163
  name: IUPAC Gold Book Compendium of Chemical Terminology
  pattern: ^(\wT?)?\d{5}$
  prefix: goldbook
  providers:
  - code: goldbook.html
    description: This appears in REX
    example: null
    first_party: null
    homepage: http://goldbook.iupac.org
    name: GoldBook direct
    publications: null
    status: null
    uri_format: http://goldbook.iupac.org/$1.html
  references:
  - https://goldbook.iupac.org/pages/api
  - https://github.com/biopragmatics/bioregistry/pull/1689
  uri_format: https://goldbook.iupac.org/terms/view/$1
  wikidata:
    description: identifier of definition in ''Compendium of Chemical Terminology''
      (''IUPAC GoldBook'')
    example:
    - A00204
    - A00212
    homepage: http://goldbook.iupac.org/
    name: IUPAC Gold Book ID
    pattern: ^[A-Z]{1,2}\d{5}$
    prefix: P4732
    uri_format: https://goldbook.iupac.org/terms/view/$1
    uri_format_rdf: http://dx.doi.org/10.1351/goldbook.$1
google.book:
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: Search the world's most comprehensive index of full-text books.
  example: qafeQTWIWmcC
  github_request_issue: 511
  homepage: https://books.google.com
  mappings:
    wikidata: P675
  name: Google Books
  prefix: google.book
  providers:
  - code: alt1
    description: Alternate URL 1
    example: null
    first_party: null
    homepage: https://books.google.com
    name: Alternate URL 1
    publications: null
    status: null
    uri_format: https://books.google.com/books/?id=$1
  uri_format: https://books.google.com/books?id=$1
  wikidata:
    description: identifier for a book edition in Google Books
    example:
    - 2Zc3AAAAYAAJ
    - 7r14FzJdSuAC
    homepage: https://books.google.com/books
    name: Google Books ID
    prefix: P675
    uri_format: https://books.google.com/books?id=$1
google.patent:
  biocontext:
    prefix: GOOGLE.PATENT
  cellosaurus:
    category: Reference resources
    homepage: https://patents.google.com
    name: Google Patents
    prefix: Patent
    uri_format: https://patents.google.com/patent/$1
  contributor_extras:
  - email: benjamin_gyori@hms.harvard.edu
    github: bgyori
    name: Benjamin M. Gyori
    orcid: 0000-0001-9439-5346
  example_extras:
  - USRE38117E1
  mappings:
    biocontext: GOOGLE.PATENT
    cellosaurus: Patent
    miriam: google.patent
    n2t: google.patent
  miriam:
    deprecated: false
    description: Google Patents covers the entire collection of granted patents and
      published patent applications from the USPTO, EPO, and WIPO. US patent documents
      date back to 1790, EPO and WIPO to 1978. Google Patents can be searched using
      patent number, inventor, classification, and filing date.
    homepage: https://www.google.com/patents/
    id: '00000537'
    name: Google Patents
    namespaceEmbeddedInLui: false
    pattern: ^[A-Z]{2}\d+([A-Z])?$
    prefix: google.patent
    sampleId: US4145692
    uri_format: https://www.google.com/patents/$1
  n2t:
    description: Google Patents covers the entire collection of granted patents and
      published patent applications from the USPTO, EPO, and WIPO. US patent documents
      date back to 1790, EPO and WIPO to 1978. Google Patents can be searched using
      patent number, inventor, classification, and filing date.
    example: US4145692
    homepage: https://www.google.com/patents/
    name: Google Patents at Google
    namespaceEmbeddedInLui: false
    pattern: ^[A-Z]{2}\d+([A-Z])?$
    prefix: google.patent
    uri_format: https://www.google.com/patents/$1
  pattern: ^[A-Z]{2,4}\d+([A-Z])?([0-9])?$
  prefix: google.patent
  synonyms:
  - Patent
  - patent
google.scholar:
  biolink:
    is_identifiers: false
    is_obo: false
    prefix: GSID
    uri_format: https://scholar.google.com/citations?user=$1
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: 'Google Scholar provides a simple way to broadly search for scholarly
    literature. You can search across many disciplines and sources: articles, theses,
    books, abstracts and court opinions, from academic publishers, professional societies,
    online repositories, universities and other web sites.'
  example: PjrpzUIAAAAJ
  homepage: https://scholar.google.com/
  mappings:
    biolink: GSID
    wikidata: P1960
  name: Google Scholar Researcher
  prefix: google.scholar
  wikidata:
    description: identifier of a person, in the Google Scholar academic search service
    example:
    - CUO0vDcAAAAJ
    - QPdLuj8AAAAJ
    homepage: https://scholar.google.com/
    name: Google Scholar author ID
    pattern: ^[-_0-9A-Za-z]{12}$
    prefix: P1960
    uri_format: https://scholar.google.com/citations?user=$1
gorel:
  biolink:
    is_identifiers: false
    is_obo: true
    prefix: GOREL
    uri_format: http://purl.obolibrary.org/obo/GOREL_$1
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  contributor_extras:
  - email: null
    github: ArslaanZahid
    name: Arslaan Zahid
    orcid: 0009-0006-4842-7427
  description: Documentation of GO that provides a description of some of the commonly
    used relationships and conventions in GO.
  download_owl: ftp://ftp.geneontology.org/pub/go/ontology/extensions/gorel.owl
  example: '0002005'
  go:
    description: Additional relations pending addition into RO
    name: GO Extensions to OBO Relation Ontology Ontology
    prefix: GOREL
  homepage: http://geneontology.org/docs/ontology-relations/
  mappings:
    biolink: GOREL
    go: GOREL
  name: GO Relations
  pattern: ^\d{7}$
  prefix: gorel
  providers:
  - code: obo.legacy
    description: Legacy OBO PURLs
    example: null
    first_party: null
    homepage: http://purl.obolibrary.org/obo/gorel.owl
    name: Legacy OBO
    publications: null
    status:
      contributor: 0009-0006-4842-7427
      date: '2024-04-14'
      notes: The URL is not working and no alternate link found on homepage
      value: degraded
    uri_format: http://purl.obolibrary.org/obo/GOREL_$1
  uri_format: http://purl.obolibrary.org/obo/GOREL_$1
gpcrdb:
  biocontext:
    prefix: GPCRDB
  fairsharing:
    abbreviation: GPCRdb
    contact:
      email: david.gloriam@sund.ku.dk
      name: David Gloriam
      orcid: 0000-0002-4299-7561
    description: The GPCRDB is a molecular-class information system that collects,
      combines, validates and stores large amounts of heterogenous data on G protein-coupled
      receptors (GPCRs). The GPCRDB contains data on sequences, ligand binding constants
      and mutations. In addition, many different types of computationally derived
      data are stored such as multiple sequence alignments and homology models.
    homepage: http://gpcrdb.org/
    license: Apache 2.0 License
    name: Information system for G protein-coupled receptors
    prefix: FAIRsharing.e4n3an
    publications:
    - doi: 10.1093/nar/gkaa1080
      pubmed_id: 33270898
      title: 'GPCRdb in 2021: integrating GPCR sequence, structure and function.'
    - doi: 10.1093/nar/gkq1009
      pubmed_id: 21045054
      title: 'GPCRDB: information system for G protein-coupled receptors.'
    - doi: 10.1093/nar/26.1.275
      pubmed_id: 9399852
      title: 'GPCRDB: an information system for G protein-coupled receptors.'
    - doi: 10.1093/nar/gkg103
      pubmed_id: 12520006
      title: GPCRDB information system for G protein-coupled receptors.
    - doi: 10.1093/nar/gkt1255
      pubmed_id: 24304901
      title: 'GPCRDB: an information system for G protein-coupled receptors.'
    - doi: 10.1093/nar/gkv1178
      pubmed_id: 26582914
      title: 'GPCRdb: an information system for G protein-coupled receptors.'
    - doi: 10.1111/bph.13509
      pubmed_id: 27155948
      title: 'GPCRdb: the G protein-coupled receptor database - an introduction.'
    - doi: 10.1093/nar/gkx1109
      pubmed_id: 29155946
      title: 'GPCRdb in 2018: adding GPCR structure models and ligands.'
    subjects:
    - Molecular biology
    - Life Science
    twitter: gpcrdb
  integbio:
    description: GPCRdb is a database of G-coupled protein receptor information. The
      database contains gene and protein sequence information as well as protein structure,
      binding site, and conservation data. Users can search by protein ID or keyword,
      browse by family, structure, model, or oligomers, or utilize several GPCR-specific
      tools.
    fairsharing: biodbcore-000292
    homepage: http://gpcrdb.org
    information_keywords:
    - Sequence
    - 3D structure
    maintainer: CMBI (Centre for Molecular and Biomolecular Informatics)
    name: GPCRdb
    prefix: nbdc00484
    pubmeds:
    - '21045054'
    status: Active
    target_keywords:
    - Protein
  mappings:
    biocontext: GPCRDB
    fairsharing: FAIRsharing.e4n3an
    integbio: nbdc00484
    miriam: gpcrdb
    n2t: gpcrdb
    prefixcommons: gpcrdb
    uniprot: DB-0038
  miriam:
    deprecated: false
    description: The G protein-coupled receptor database (GPCRDB) collects, large
      amounts of heterogeneous data on GPCRs. It contains experimental data on sequences,
      ligand-binding constants, mutations and oligomers, and derived data such as
      multiple sequence alignments and homology models.
    homepage: http://www.gpcrdb.org/
    id: '00000212'
    name: GPCRDB
    namespaceEmbeddedInLui: false
    pattern: ^\w+$
    prefix: gpcrdb
    sampleId: RL3R1_HUMAN
    uri_format: http://www.gpcrdb.org/protein/$1/
  n2t:
    description: The G protein-coupled receptor database (GPCRDB) collects, large
      amounts of heterogeneous data on GPCRs. It contains experimental data on sequences,
      ligand-binding constants, mutations and oligomers, and derived data such as
      multiple sequence alignments and homology models.
    example: RL3R1_HUMAN
    homepage: http://www.gpcrdb.org/
    name: GPCRDB at Radboud University
    namespaceEmbeddedInLui: false
    pattern: ^\w+$
    prefix: gpcrdb
    uri_format: http://www.gpcrdb.org/protein/$1/
  name: G protein-coupled receptor database
  prefix: gpcrdb
  prefixcommons:
    description: The GPCRDB is a molecular-class information system that collects,
      combines, validates and stores large amounts of heterogenous data on G protein-coupled
      receptors (GPCRs). The GPCRDB contains data on sequences, ligand binding constants
      and mutations. In addition, many different types of computationally derived
      data are stored such as multiple sequence alignments and homology models.
    example: RL3R1_HUMAN
    homepage: http://www.gpcr.org/7tm/
    keywords:
    - small molecule
    - protein
    name: Information system for G protein-coupled receptors (GPCRs)
    pattern: ^\w+$
    prefix: gpcrdb
    pubmed_ids:
    - '21045054'
    uri_format: http://www.gpcr.org/7tm/proteins/$1
  publications:
  - doi: 10.1093/nar/gkae1065
    pmc: null
    pubmed: '39558158'
    title: 'GPCRdb in 2025: adding odorant receptors, data mapper, structure similarity
      search and models of physiological ligand complexes'
    year: 2024
  - doi: 10.1093/nar/gkaa1080
    pmc: PMC7778909
    pubmed: '33270898'
    title: 'GPCRdb in 2021: integrating GPCR sequence, structure and function'
    year: 2021
  - doi: 10.1093/nar/gkx1109
    pmc: PMC5753179
    pubmed: '29155946'
    title: 'GPCRdb in 2018: adding GPCR structure models and ligands'
    year: 2018
  - doi: 10.1111/bph.13509
    pmc: PMC4919580
    pubmed: '27155948'
    title: 'GPCRdb: the G protein-coupled receptor database - an introduction'
    year: 2016
  - doi: 10.1093/nar/gkv1178
    pmc: PMC4702843
    pubmed: '26582914'
    title: 'GPCRdb: an information system for G protein-coupled receptors'
    year: 2015
  - doi: 10.1093/nar/gkt1255
    pmc: PMC3965068
    pubmed: '24304901'
    title: 'GPCRDB: an information system for G protein-coupled receptors'
    year: 2013
  - doi: 10.1093/nar/gkq1009
    pmc: PMC3013641
    pubmed: '21045054'
    title: 'GPCRDB: information system for G protein-coupled receptors'
    year: 2010
  - doi: 10.1093/nar/gkg103
    pmc: PMC165550
    pubmed: '12520006'
    title: GPCRDB information system for G protein-coupled receptors
    year: 2003
  - doi: 10.1093/nar/29.1.346
    pmc: PMC29816
    pubmed: '11125133'
    title: 'Collecting and harvesting biological data: the GPCRDB and NucleaRDB information
      systems'
    year: 2001
  - doi: 10.1093/nar/26.1.275
    pmc: PMC147194
    pubmed: '9399852'
    title: 'GPCRDB: an information system for G protein-coupled receptors'
    year: 1998
  - doi: 10.1093/nar/gkaa1080
    pmc: null
    pubmed: null
    title: 'GPCRdb in 2021: integrating GPCR sequence, structure and function.'
    year: null
  - doi: 10.1093/nar/gkq1009
    pmc: null
    pubmed: null
    title: 'GPCRDB: information system for G protein-coupled receptors.'
    year: null
  - doi: 10.1093/nar/26.1.275
    pmc: null
    pubmed: null
    title: 'GPCRDB: an information system for G protein-coupled receptors.'
    year: null
  - doi: 10.1093/nar/gkg103
    pmc: null
    pubmed: null
    title: GPCRDB information system for G protein-coupled receptors.
    year: null
  - doi: 10.1093/nar/gkt1255
    pmc: null
    pubmed: null
    title: 'GPCRDB: an information system for G protein-coupled receptors.'
    year: null
  - doi: 10.1093/nar/gkv1178
    pmc: null
    pubmed: null
    title: 'GPCRdb: an information system for G protein-coupled receptors.'
    year: null
  - doi: 10.1111/bph.13509
    pmc: null
    pubmed: null
    title: 'GPCRdb: the G protein-coupled receptor database - an introduction.'
    year: null
  - doi: 10.1093/nar/gkx1109
    pmc: null
    pubmed: null
    title: 'GPCRdb in 2018: adding GPCR structure models and ligands.'
    year: null
  - doi: null
    pmc: null
    pubmed: '21045054'
    title: null
    year: null
  - doi: 10.1093/nar/gkae1065
    pmc: null
    pubmed: '39558158'
    title: null
    year: null
  uniprot:
    abbreviation: GPCRDB
    category: Protein family/group databases
    homepage: https://gpcrdb.org
    name: Information system for G protein-coupled receptors (GPCRs)
    prefix: DB-0038
    publications:
    - doi: 10.1093/nar/gkae1065
      pubmed: '39558158'
    uri_format: https://gpcrdb.org/protein/$1/
  uri_format: https://gpcrdb.org/protein/$1
gpcrnava:
  mappings:
    prefixcommons: gnd
  prefix: gpcrnava
  prefixcommons:
    description: The GPCR NaVa database describes sequence variants within the family
      of human G Protein-Coupled Receptors (GPCRs). GPCRs regulate many physiological
      functions and are the targets for most of today's medicines. The acronym NaVa
      stands for Natural Variant, which means any (non-artificial) variant that occurs
      in humans.
    example: '1150'
    homepage: http://nava.liacs.nl/
    keywords:
    - protein
    - pathway
    name: GPCR Natural Variants database
    pattern: ^\d+$
    prefix: gnd
    uri_format: http://nava.liacs.nl/cgi-bin/nava.py?id=$1
gpmdb:
  biocontext:
    prefix: GPMDB
  contact:
    email: rbeavis@thegpm.org
    github: RonBeavis
    name: Ronald C. Beavis (Ron Beavis)
    orcid: 0000-0001-5782-1000
  fairsharing:
    abbreviation: gpmDB
    description: 'The Global Proteome Machine Database (gpmDB holds the minimum amount
      of information necessary for common bioinformatics-related tasks (such as sequence
      assignment validation) rather than being a complete record of a proteomics experiment.
      It was also created to aid in the process of validating peptide MS/MS spectra
      as well as protein coverage patterns. Most of the data is held in a set of XML
      files: the database serves as an index to those files, allowing for rapid lookups
      and reduced database storage requirements.'
    homepage: https://www.thegpm.org/GPMDB/index.html
    name: The Global Proteome Machine Database
    prefix: FAIRsharing.fhcmwq
    publications:
    - doi: 10.1021/pr049882h
      pubmed_id: 15595733
      title: Open source system for analyzing, validating, and storing protein identification
        data.
    subjects:
    - Bioinformatics
    - Proteomics
    twitter: GPMDB
  mappings:
    biocontext: GPMDB
    fairsharing: FAIRsharing.fhcmwq
    miriam: gpmdb
    n2t: gpmdb
  miriam:
    deprecated: false
    description: The Global Proteome Machine Database was constructed to utilize the
      information obtained by GPM servers to aid in the difficult process of validating
      peptide MS/MS spectra as well as protein coverage patterns.
    homepage: http://gpmdb.thegpm.org/
    id: 00000649
    name: GPMDB
    namespaceEmbeddedInLui: false
    pattern: ^GPM\d+$
    prefix: gpmdb
    providers:
    - code: omicsdi
      description: GPMDB through OmicsDI
      homepage: https://www.omicsdi.org/
      name: GPMDB through OmicsDI
      uri_format: https://www.omicsdi.org/dataset/gpmdb/$1
    sampleId: GPM32310002988
    uri_format: http://gpmdb.thegpm.org/~/dblist_gpmnum/gpmnum=$1
  n2t:
    description: The Global Proteome Machine Database was constructed to utilize the
      information obtained by GPM servers to aid in the difficult process of validating
      peptide MS/MS spectra as well as protein coverage patterns.
    example: GPM32310002988
    homepage: http://gpmdb.thegpm.org/
    name: GPMDB
    namespaceEmbeddedInLui: false
    pattern: ^GPM\d+$
    prefix: gpmdb
    uri_format: http://gpmdb.thegpm.org/~/dblist_gpmnum/gpmnum=$1
  name: Global Proteome Machine Database
  prefix: gpmdb
  publications:
  - doi: 10.1021/pr049882h
    pmc: null
    pubmed: '15595733'
    title: Open source system for analyzing, validating, and storing protein identification
      data
    year: 2004
  - doi: 10.1021/pr049882h
    pmc: null
    pubmed: null
    title: Open source system for analyzing, validating, and storing protein identification
      data.
    year: null
gpml:
  aberowl:
    description: 'GPML is the file format used to store pathway content at WikiPathways.
      GPML is short for Graphical Pathway Markup Language, and it is a custom XML
      format compatible with pathway visualization and analysis tools such as Cytoscape
      and PathVisio. Get it as RDFa in HTML: http://vocabularies.wikipathways.org/gpml
      Or get it translated to RDF/XML from either of these URLs: http://getschema.org/rdfaliteextractor?url=http%3A%2F%2Fvocabularies.wikipathways.org%2Fgpml&out=rdf
      or http://rdf-translator.appspot.com/convert/rdfa/xml/http%3A%2F%2Fvocabularies.wikipathways.org%2Fgpml'
    download_owl: http://aber-owl.net/media/ontologies/GPML/331/gpml.owl
    name: Graphical Pathway Markup Language
    prefix: GPML
    version: 2013a
  bioportal:
    contact:
      email: wikipathways-devel@googlegroups.com
      name: WikiPathways Team
    description: GPML is the file format used to store pathway content at WikiPathways.
      GPML is short for Graphical Pathway Markup Language, and it is a custom XML
      format compatible with pathway visualization and analysis tools such as Cytoscape
      and PathVisio.
    homepage: https://vocabularies.wikipathways.org/gpml
    name: Graphical Pathway Markup Language
    prefix: GPML
    version: 2013a
  contact:
    email: egon.willighagen@gmail.com
    github: egonw
    name: Egon Willighagen
    orcid: 0000-0001-7542-0286
  contributor:
    email: javier.millanacosta@maastrichtuniversity.nl
    github: jmillanacosta
    name: Javier Millán Acosta
    orcid: 0000-0001-5608-781X
  contributor_extras:
  - email: b.gyori@northeastern.edu
    github: bgyori
    name: Benjamin M. Gyori
    orcid: 0000-0001-9439-5346
  description: The WikiPatwhays Graphical Pathway Markup Language (GPML) vocabulary.
  download_owl: https://github.com/wikipathways/WpVocabularies/raw/refs/heads/master/docs/gpml.owl
  example: DataNode
  github_request_issue: 1754
  homepage: https://vocabularies.wikipathways.org/gpml
  license: CC0-1.0
  mappings:
    aberowl: GPML
    bioportal: GPML
  mastodon: wikipathways@fosstodon.org
  name: WikiPathways GPML Vocabulary
  part_of_database: wikipathways
  pattern: ^[A-Za-z]+$
  prefix: gpml
  publications:
  - doi: 10.1093/nar/gkad960
    pmc: PMC10767877
    pubmed: '37941138'
    title: 'WikiPathways 2024: next generation pathway database'
    year: 2025
  repository: https://github.com/wikipathways/WpVocabularies
  reviewer:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  synonyms:
  - wikipathways.gpml
  uri_format: http://vocabularies.wikipathways.org/gpml#$1
gr:
  aberowl:
    download_owl: http://aber-owl.net/media/ontologies/gr/1/gr.owl
    name: gr_ontology
    prefix: gr
    version: juhiygh
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: A vocabulary for e-commerce
  example: category
  homepage: http://purl.org/goodrelations
  lov:
    description: The GoodRelations ontology provides the vocabulary for annotating
      e-commerce offerings (1) to sell, lease, repair, dispose, or maintain commodity
      products and (2) to provide commodity services.
    homepage: http://www.heppnetz.de/ontologies/goodrelations/v1.html
    keywords:
    - eBusiness
    modified: '2011-10-01'
    name: The GoodRelations Ontology for Semantic Web-based E-Commerce
    prefix: gr
    uri_prefix: http://purl.org/goodrelations/v1#$1
  mappings:
    aberowl: gr
    lov: gr
    zazuko: gr
  name: GoodRelations
  prefix: gr
  uri_format: http://purl.org/goodrelations/v1#$1
  zazuko:
    prefix: gr
    uri_format: http://purl.org/goodrelations/v1#$1
graingenes.reference:
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: A database for Triticeae and Avena references.
  example: WGS-95-1333
  homepage: http://wheat.pw.usda.gov
  name: GrainGenes reference
  prefix: graingenes.reference
  uri_format: https://wheat.pw.usda.gov/cgi-bin/GG3/report.cgi?class=reference&name=$1
graingenes.symbol:
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: A database for Triticeae and Avena gene symbols.
  example: 1-FEH+w3
  homepage: http://wheat.pw.usda.gov
  name: GrainGenes symbol
  prefix: graingenes.symbol
  uri_format: http://wheat.pw.usda.gov/report?class=gene;name=$1
gramene.gene:
  biocontext:
    prefix: GRAMENE.GENE
  go:
    homepage: http://www.gramene.org/
    name: Gramene
    prefix: GR_GENE
    synonyms:
    - GR_gene
    uri_format: http://www.gramene.org/db/genes/search_gene?acc=$1
  mappings:
    biocontext: GRAMENE.GENE
    go: GR_GENE
    miriam: gramene.gene
    n2t: gramene.gene
  miriam:
    deprecated: false
    description: Gramene is a comparative genome mapping database for grasses and
      crop plants. It combines a semi-automatically generated database of cereal genomic
      and expressed sequence tag sequences, genetic maps, map relations, quantitative
      trait loci (QTL), and publications, with a curated database of mutants (genes
      and alleles), molecular markers, and proteins. This datatype refers to genes
      in Gramene.
    homepage: http://www.gramene.org/
    id: 00000182
    name: Gramene genes
    namespaceEmbeddedInLui: false
    pattern: ^GR\:\d+$
    prefix: gramene.gene
    sampleId: GR:0080039
    uri_format: http://www.gramene.org/db/genes/search_gene?acc=$1
  n2t:
    description: Gramene is a comparative genome mapping database for grasses and
      crop plants. It combines a semi-automatically generated database of cereal genomic
      and expressed sequence tag sequences, genetic maps, map relations, quantitative
      trait loci (QTL), and publications, with a curated database of mutants (genes
      and alleles), molecular markers, and proteins. This datatype refers to genes
      in Gramene.
    example: GR:0080039
    homepage: http://www.gramene.org/
    name: Gramene Genes at Cold Spring Harbor
    namespaceEmbeddedInLui: false
    pattern: ^GR\:\d+$
    prefix: gramene.gene
    uri_format: http://www.gramene.org/db/genes/search_gene?acc=$1
  name: Gramene Gene
  prefix: gramene.gene
  synonyms:
  - GR_GENE
gramene.growthstage:
  banana: GRO
  biocontext:
    prefix: GRAMENE.GROWTHSTAGE
  bioportal:
    contact:
      email: jaiswalp@oregonstate.edu
      name: Pankaj Jaiswal
    description: A structured controlled vocabulary for the anatomy of Gramineae.
      Please note that this ontology has now been superseded by the <a http://bioportal.bioontology.org/ontologies/1587>
      Plant Ontology</a>.
    homepage: https://planteome.org/
    name: Cereal Plant Gross Anatomy Ontology
    prefix: GRO-CPGA
    publications:
    - https://planteome.org/pub
    version: unknown
  mappings:
    biocontext: GRAMENE.GROWTHSTAGE
    bioportal: GRO-CPGA
    miriam: gro
    n2t: gramene.growthstage
    obofoundry: gro
    prefixcommons: gramene.po
    wikidata.entity: Q114677888
  miriam:
    deprecated: false
    description: Gramene is a comparative genome mapping database for grasses and
      crop plants. It combines a semi-automatically generated database of cereal genomic
      and expressed sequence tag sequences, genetic maps, map relations, quantitative
      trait loci (QTL), and publications, with a curated database of mutants (genes
      and alleles), molecular markers, and proteins. This collection refers to growth
      stage ontology information in Gramene.
    homepage: http://www.gramene.org/
    id: 00000508
    name: Gramene Growth Stage Ontology
    namespaceEmbeddedInLui: true
    pattern: ^GRO:\d+$
    prefix: gro
    sampleId: '0007133'
    uri_format: http://www.gramene.org/db/ontology/search?id=GRO:$1
  n2t:
    description: Gramene is a comparative genome mapping database for grasses and
      crop plants. It combines a semi-automatically generated database of cereal genomic
      and expressed sequence tag sequences, genetic maps, map relations, quantitative
      trait loci (QTL), and publications, with a curated database of mutants (genes
      and alleles), molecular markers, and proteins. This collection refers to growth
      stage ontology information in Gramene.
    example: '0007133'
    homepage: http://www.gramene.org/
    name: Gramene Growth Stage Ontology at Cold Spring Harbor
    namespaceEmbeddedInLui: true
    pattern: ^GRO\:\d+$
    prefix: gramene.growthstage
    uri_format: http://www.gramene.org/db/ontology/search?id=GRO:$1
  name: Gramene Growth Stage Ontology
  obofoundry:
    contact: po-discuss@plantontology.org
    contact.label: Plant Ontology Administrators
    deprecated: true
    domain: anatomy and development
    homepage: http://www.gramene.org/plant_ontology/
    name: Cereal Plant Gross Anatomy
    prefix: gro
  pattern: ^\d{7}$
  prefix: gramene.growthstage
  prefixcommons:
    description: A controlled vocabulary to describe phenotypic traits in plants.
      Each trait is a distinguishable feature, characteristic, quality or phenotypic
      feature of a developing or mature plant, or a plant part.
    example: GRO:0007143
    homepage: http://www.gramene.org/plant_ontology/
    keywords:
    - obo
    - ontology
    - anatomy
    name: Plant Ontology
    pattern: ^GRO:\d+$
    prefix: gramene.po
  synonyms:
  - cpga
  - gro-cpga
  uri_format: http://www.gramene.org/db/ontology/search?id=GRO:$1
gramene.protein:
  biocontext:
    prefix: GRAMENE.PROTEIN
  go:
    homepage: http://www.gramene.org/
    name: Gramene
    prefix: GR_PROTEIN
    synonyms:
    - GR_protein
    uri_format: http://www.gramene.org/db/protein/protein_search?acc=$1
  mappings:
    biocontext: GRAMENE.PROTEIN
    go: GR_PROTEIN
    miriam: gramene.protein
    n2t: gramene.protein
  miriam:
    deprecated: false
    description: Gramene is a comparative genome mapping database for grasses and
      crop plants. It combines a semi-automatically generated database of cereal genomic
      and expressed sequence tag sequences, genetic maps, map relations, quantitative
      trait loci (QTL), and publications, with a curated database of mutants (genes
      and alleles), molecular markers, and proteins. This datatype refers to proteins
      in Gramene.
    homepage: http://www.gramene.org/
    id: 00000181
    name: Gramene protein
    namespaceEmbeddedInLui: false
    pattern: ^\d+$
    prefix: gramene.protein
    sampleId: '78073'
    uri_format: http://www.gramene.org/db/protein/protein_search?protein_id=$1
  n2t:
    description: Gramene is a comparative genome mapping database for grasses and
      crop plants. It combines a semi-automatically generated database of cereal genomic
      and expressed sequence tag sequences, genetic maps, map relations, quantitative
      trait loci (QTL), and publications, with a curated database of mutants (genes
      and alleles), molecular markers, and proteins. This datatype refers to proteins
      in Gramene.
    example: '78073'
    homepage: http://www.gramene.org/
    name: Gramene Protein at Cold Spring Harbor
    namespaceEmbeddedInLui: false
    pattern: ^\d+$
    prefix: gramene.protein
    uri_format: http://www.gramene.org/db/protein/protein_search?protein_id=$1
  name: Gramene protein
  prefix: gramene.protein
  synonyms:
  - GR_PROTEIN
gramene.qtl:
  biocontext:
    prefix: GRAMENE.QTL
  go:
    homepage: http://www.gramene.org/
    name: Gramene
    prefix: GR_QTL
    uri_format: http://www.gramene.org/db/qtl/qtl_display?qtl_accession_id=$1
  mappings:
    biocontext: GRAMENE.QTL
    go: GR_QTL
    miriam: gramene.qtl
    n2t: gramene.qtl
  miriam:
    deprecated: false
    description: Gramene is a comparative genome mapping database for grasses and
      crop plants. It combines a semi-automatically generated database of cereal genomic
      and expressed sequence tag sequences, genetic maps, map relations, quantitative
      trait loci (QTL), and publications, with a curated database of mutants (genes
      and alleles), molecular markers, and proteins. This datatype refers to quantitative
      trait loci identified in Gramene.
    homepage: http://www.gramene.org/
    id: 00000184
    name: Gramene QTL
    namespaceEmbeddedInLui: false
    pattern: ^\w+$
    prefix: gramene.qtl
    sampleId: CQG5
    uri_format: http://www.gramene.org/db/qtl/qtl_display?qtl_accession_id=$1
  n2t:
    description: Gramene is a comparative genome mapping database for grasses and
      crop plants. It combines a semi-automatically generated database of cereal genomic
      and expressed sequence tag sequences, genetic maps, map relations, quantitative
      trait loci (QTL), and publications, with a curated database of mutants (genes
      and alleles), molecular markers, and proteins. This datatype refers to quantitative
      trait loci identified in Gramene.
    example: CQG5
    homepage: http://www.gramene.org/
    name: Gramene Quantitative Trait Loci at Cold Spring Harbor
    namespaceEmbeddedInLui: false
    pattern: ^\w+$
    prefix: gramene.qtl
    uri_format: http://www.gramene.org/db/qtl/qtl_display?qtl_accession_id=$1
  name: Gramene QTL
  prefix: gramene.qtl
  synonyms:
  - GR_QTL
gramene.reference:
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: Literature references in Gramene
  example: '6200'
  homepage: http://www.gramene.org
  name: Gramene Reference
  pattern: ^\d+$
  prefix: gramene.reference
  synonyms:
  - gramene.ref
  uri_format: http://www.gramene.org/db/literature/pub_search?ref_id=$1
gramene.taxonomy:
  banana: GR_tax
  banana_peel: ':'
  biocontext:
    prefix: GRAMENE.TAXONOMY
  example: 013681
  mappings:
    biocontext: GRAMENE.TAXONOMY
    miriam: gramene.taxonomy
    n2t: gramene.taxonomy
  miriam:
    deprecated: false
    description: Gramene is a comparative genome mapping database for grasses and
      crop plants. It combines a semi-automatically generated database of cereal genomic
      and expressed sequence tag sequences, genetic maps, map relations, quantitative
      trait loci (QTL), and publications, with a curated database of mutants (genes
      and alleles), molecular markers, and proteins. This datatype refers to taxonomic
      information in Gramene.
    homepage: http://www.gramene.org/
    id: 00000183
    name: Gramene Taxonomy
    namespaceEmbeddedInLui: false
    pattern: ^GR\_tax\:\d+$
    prefix: gramene.taxonomy
    sampleId: GR_tax:013681
    uri_format: http://www.gramene.org/db/ontology/search?id=$1
  n2t:
    description: Gramene is a comparative genome mapping database for grasses and
      crop plants. It combines a semi-automatically generated database of cereal genomic
      and expressed sequence tag sequences, genetic maps, map relations, quantitative
      trait loci (QTL), and publications, with a curated database of mutants (genes
      and alleles), molecular markers, and proteins. This datatype refers to taxonomic
      information in Gramene.
    example: GR_tax:013681
    homepage: http://www.gramene.org/
    name: Gramene Taxonomy at Cold Spring Harbor
    namespaceEmbeddedInLui: false
    pattern: ^GR\_tax\:\d+$
    prefix: gramene.taxonomy
    uri_format: http://www.gramene.org/db/ontology/search?id=$1
  pattern: ^\d+$
  prefix: gramene.taxonomy
  uri_format: https://archive.gramene.org/db/ontology/search?id=GR_tax:$1
grassbase:
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: GrassBase provides an interactive guide to nomenclature for the whole
    grass family. It provides lists of over 60,000 names for any given genus, geographical
    region or genus within a geographical region, helps find the accepted name, synonyms
    and distribution for any given name, and gives a desription for each species.
  example: imp10873
  github_request_issue: 218
  homepage: https://www.kew.org/data/grasses-syn/index.htm
  mappings:
    wikidata: P1832
  name: GrassBase
  pattern: ^(imp|gen)\d{5}$
  prefix: grassbase
  uri_format: https://www.kew.org/data/grasses-db/www/$1
  wikidata:
    description: identifier in GrassBase - The Online World Grass Flora
    example:
    - gen00495
    - imp10873
    homepage: http://www.kew.org/data/grasses-syn/index.htm
    name: GrassBase ID
    pattern: ^(imp|gen){1}\d{5}$
    prefix: P1832
    uri_format: http://www.kew.org/data/grasses-db/www/$1
grddl:
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: GRDDL is a mechanism for Gleaning Resource Descriptions from Dialects
    of Languages. It is a technique for obtaining RDF data from XML documents and
    in particular XHTML pages. Authors may explicitly associate documents with transformation
    algorithms, typically represented in XSLT, using a link element in the head of
    the document. Alternatively, the information needed to obtain the transformation
    may be held in an associated metadata profile document or namespace document.
    Clients reading the document can follow links across the Web using techniques
    described in the GRDDL specification to discover the appropriate transformations.
    This document uses a number of examples from the GRDDL Use Cases document to illustrate,
    in detail, the techniques GRDDL provides for associating documents with appropriate
    instructions for extracting any embedded data. (from homepage)
  example: transformation
  homepage: https://www.w3.org/TR/grddl-primer/
  lov:
    description: Gleaning Resource Descriptions from Dialects of Languages Vocabulary
    homepage: http://www.w3.org/2003/g/data-view
    keywords:
    - Vocabularies
    modified: '2007-10-31'
    name: Gleaning Resource Descriptions from Dialects of Languages Vocabulary
    prefix: grddl
    uri_prefix: http://www.w3.org/2003/g/data-view#$1
  mappings:
    lov: grddl
    zazuko: grddl
  name: Gleaning Resource Descriptions from Dialects of Languages
  prefix: grddl
  rdf_uri_format: http://www.w3.org/2003/g/data-view#$1
  uri_format: http://www.w3.org/2003/g/data-view#$1
  zazuko:
    prefix: grddl
    uri_format: http://www.w3.org/2003/g/data-view#$1
greengenes:
  biocontext:
    prefix: GREENGENES
  fairsharing:
    abbreviation: Greengenes
    contact:
      email: GLAndersen@lbl.gov
      name: Gary L Andersen
      orcid: 0000-0002-1618-9827
    description: A 16S rRNA gene database which provides chimera screening, standard
      alignment, and taxonomic classification using multiple published taxonomies.
      Please note that this is a downloadable resource only, without an interactive
      web interface.
    homepage: http://greengenes.lbl.gov
    name: Greengenes
    prefix: FAIRsharing.bpxgb6
    publications:
    - doi: 10.1128/AEM.03006-05
      pubmed_id: 16820507
      title: Greengenes, a chimera-checked 16S rRNA gene database and workbench compatible
        with ARB.
    subjects:
    - Genetics
    - Life Science
  integbio:
    description: A 16S rRNA gene database which provides chimera screening, standard
      alignment, and taxonomic classification using multiple published taxonomies.
      Please note that this is a downloadable resource only, without an interactive
      web interface.
    fairsharing: FAIRsharing.bpxgb6
    homepage: http://greengenes.lbl.gov
    information_keywords:
    - Sequence
    - Taxonomy
    maintainer: LBNL (Lawrence Berkeley National Laboratory)
    name: Greengenes
    prefix: nbdc01824
    pubmeds:
    - '16820507'
    status: Active
    target_keywords:
    - Genome/Gene
    - RNA
  mappings:
    biocontext: GREENGENES
    fairsharing: FAIRsharing.bpxgb6
    integbio: nbdc01824
    miriam: greengenes
    n2t: greengenes
    ncbi: Greengenes
    prefixcommons: greengenes
    re3data: r3d100010549
  miriam:
    deprecated: true
    description: A 16S rRNA gene database which provides chimera screening, standard
      alignment, and taxonomic classification using multiple published taxonomies.
    homepage: http://greengenes.lbl.gov/
    id: '00000165'
    name: GreenGenes
    namespaceEmbeddedInLui: false
    pattern: ^\d+$
    prefix: greengenes
    sampleId: '100000'
    uri_format: http://greengenes.lbl.gov/cgi-bin/show_one_record_v2.pl?prokMSA_id=$1
  n2t:
    description: A 16S rRNA gene database which provides chimera screening, standard
      alignment, and taxonomic classification using multiple published taxonomies.
    example: '100000'
    homepage: http://greengenes.lbl.gov/
    name: GreenGenes at Lawrence Berkeley
    namespaceEmbeddedInLui: false
    pattern: ^\d+$
    prefix: greengenes
    uri_format: http://greengenes.lbl.gov/cgi-bin/show_one_record_v2.pl?prokMSA_id=$1
  ncbi:
    example: '269185'
    homepage: http://greengenes.lbl.gov/
    name: 16S rRNA gene database
    prefix: Greengenes
  prefix: greengenes
  prefixcommons:
    description: A 16S rRNA gene database which provides chimera screening, standard
      alignment, and taxonomic classification using multiple published taxonomies.
    example: '100000'
    homepage: http://greengenes.lbl.gov
    keywords:
    - RNA
    name: Greengenes:16S rRNA gene database
    pattern: ^\d+$
    prefix: greengenes
    pubmed_ids:
    - '16820507'
    uri_format: http://greengenes.lbl.gov/cgi-bin/show_one_record_v2.pl?prokMSA_id=$1
  publications:
  - doi: 10.1128/aem.03006-05
    pmc: PMC1489311
    pubmed: '16820507'
    title: Greengenes, a chimera-checked 16S rRNA gene database and workbench compatible
      with ARB
    year: 2006
  re3data:
    description: <<<!!!<<< This repository is no longer available. >>>!!!>>>
    doi: 10.17616/R36C8G
    homepage: https://greengenes.secondgenome.com/
    license: CC
    name: Greengenes
    prefix: r3d100010549
    synonyms:
    - The Greengenes Database
    xrefs:
      nif: 0000-02927
grid:
  biocontext:
    prefix: GRID
  fairsharing:
    abbreviation: GRID
    description: Global Research Identifier Database (GRID) stores information on
      research-related organisations worldwide. GRID record contains a unique GRID
      ID, relevant metadata, and relationships between associated institutions.
    homepage: https://grid.ac/
    license: CC0-1.0
    name: Global Research Identifier Database
    prefix: FAIRsharing.0pUMYW
    publications: []
    subjects:
    - Data Management
    twitter: grid_ac
  mappings:
    biocontext: GRID
    fairsharing: FAIRsharing.0pUMYW
    miriam: grid
    n2t: grid
  miriam:
    deprecated: false
    description: International coverage of the world's leading research organisations,
      indexing 92% of funding allocated globally.
    homepage: https://www.grid.ac/
    id: 00000593
    name: GRID
    namespaceEmbeddedInLui: false
    pattern: ^grid\.[0-9]+\.[a-f0-9]{1,2}$
    prefix: grid
    sampleId: grid.225360.0
    uri_format: https://www.grid.ac/institutes/$1
  n2t:
    description: International coverage of the world's leading research organisations,
      indexing 92% of funding allocated globally.
    example: grid.225360.0
    homepage: https://www.grid.ac/
    name: GRID at Digital Science & Research Ltd.
    namespaceEmbeddedInLui: false
    pattern: ^grid\.[0-9]+\.[a-f0-9]{1,2}$
    prefix: grid
    uri_format: https://www.grid.ac/institutes/$1
  name: Global Research Identifier Database
  prefix: grid
grin.publication:
  fairsharing:
    abbreviation: GRIN
    description: GRIN provides National Genetic Resources Program (NGRP) personnel
      and germplasm users continuous access to databases for the maintenance of passport,
      characterization, evaluation, inventory, and distribution data important for
      the effective management and utilization of national germplasm collections.
    homepage: https://www.ars-grin.gov/
    name: Germplasm Resources Information Network
    prefix: FAIRsharing.3axym7
    publications: []
    subjects:
    - Life Science
  mappings:
    fairsharing: FAIRsharing.3axym7
    prefixcommons: grin
  part_of_database: grin
  prefix: grin.publication
  prefixcommons:
    description: GRIN provides National Genetic Resources Program (NGRP) personnel
      and germplasm users continuous access to databases for the maintenance of passport,
      characterization, evaluation, inventory, and distribution data important for
      the effective management and utilization of national germplasm collections.
    example: '159787'
    homepage: http://www.ars-grin.gov/
    name: Germplasm Resources Information Network
    pattern: ^\d+$
    prefix: grin
    uri_format: http://www.ars.usda.gov/research/publications/publications.htm?seq_no_115=$1
  reviewer:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  synonyms:
  - grin
grin.taxonomy:
  biocontext:
    prefix: GRIN.TAXONOMY
  go:
    homepage: https://www.ars-grin.gov/
    name: Germplasm Resources Information Network
    prefix: GRIN
    synonyms:
    - grin
    uri_format: https://npgsweb.ars-grin.gov/gringlobal/accessiondetail.aspx?id=$1
  mappings:
    biocontext: GRIN.TAXONOMY
    go: GRIN
    miriam: grin.taxonomy
    n2t: grin.taxonomy
    ncbi: GRIN
    wikidata: P1421
    wikidata.entity: Q19576476
  miriam:
    deprecated: false
    description: GRIN (Germplasm Resources Information Network) Taxonomy for Plants
      provides information on scientific and common names, classification, distribution,
      references, and economic impact.
    homepage: https://npgsweb.ars-grin.gov/gringlobal/taxon/abouttaxonomy
    id: '00000166'
    name: GRIN Plant Taxonomy
    namespaceEmbeddedInLui: false
    pattern: ^\d+$
    prefix: grin.taxonomy
    sampleId: '19333'
    uri_format: https://npgsweb.ars-grin.gov/gringlobal/taxon/taxonomydetail?id=$1
  n2t:
    description: GRIN (Germplasm Resources Information Network) Taxonomy for Plants
      provides information on scientific and common names, classification, distribution,
      references, and economic impact.
    example: '19333'
    homepage: http://www.ars-grin.gov/cgi-bin/npgs/html/index.pl?language=en
    name: GRIN at Maryland
    namespaceEmbeddedInLui: false
    pattern: ^\d+$
    prefix: grin.taxonomy
    uri_format: http://www.ars-grin.gov/cgi-bin/npgs/html/taxon.pl?$1
  ncbi:
    example: '1005973'
    homepage: http://www.ars-grin.gov/
    name: Germplasm Resources Information Network
    prefix: GRIN
  part_of_database: grin
  prefix: grin.taxonomy
  wikidata:
    database: Q19576476
    description: URL for a taxon in the GRIN website
    example:
    - https://npgsweb.ars-grin.gov/gringlobal/taxonomydetail.aspx?id=42207
    - https://npgsweb.ars-grin.gov/gringlobal/taxonomyfamily.aspx?id=897
    - https://npgsweb.ars-grin.gov/gringlobal/taxonomygenus.aspx?id=10404
    name: GRIN URL
    prefix: P1421
gro:
  aberowl:
    description: The Gene Regulation Ontology (GRO) is a conceptual model for the
      domain of gene regulation. It covers processes that are linked to the regulation
      of gene expression as well as physical entities that are involved in these processes
      (such as genes and transcription factors) in terms of ontology classes and semantic
      relations between classes.
    download_owl: http://aber-owl.net/media/ontologies/GRO/5/gro.owl
    homepage: http://www.ebi.ac.uk/Rebholz-srv/GRO/GRO.html
    name: Gene Regulation Ontology
    prefix: GRO
    version: '0.5'
  biocontext:
    prefix: BOOTSTREP
  bioportal:
    contact:
      email: vlee@ebi.ac.uk
      name: Vivian Lee
    description: The Gene Regulation Ontology (GRO) is a conceptual model for the
      domain of gene regulation. It covers processes that are linked to the regulation
      of gene expression as well as physical entities that are involved in these processes
      (such as genes and transcription factors) in terms of ontology classes and semantic
      relations between classes.
    homepage: http://www.ebi.ac.uk/Rebholz-srv/GRO/GRO.html
    name: Gene Regulation Ontology
    prefix: GRO
    version: '0.5'
  deprecated: true
  example: Lipid
  mappings:
    aberowl: GRO
    biocontext: BOOTSTREP
    bioportal: GRO
    obofoundry: bootstrep
  obofoundry:
    contact: vlee@ebi.ac.uk
    contact.label: Vivian Lee
    deprecated: true
    domain: chemistry and biochemistry
    homepage: http://www.ebi.ac.uk/Rebholz-srv/GRO/GRO.html
    name: Gene Regulation Ontology
    prefix: bootstrep
  prefix: gro
  synonyms:
  - bootstrep
  uri_format: http://www.bootstrep.eu/ontology/GRO#$1
grsdb:
  biocontext:
    prefix: GRSDB
  mappings:
    biocontext: GRSDB
    miriam: grsdb
    n2t: grsdb
    prefixcommons: grsdb
  miriam:
    deprecated: true
    description: GRSDB is a database of G-quadruplexes and contains information on
      composition and distribution of putative Quadruplex-forming G-Rich Sequences
      (QGRS) mapped in the eukaryotic pre-mRNA sequences, including those that are
      alternatively processed (alternatively spliced or alternatively polyadenylated).
      The data stored in the GRSDB is based on computational analysis of NCBI Entrez
      Gene entries and their corresponding annotated genomic nucleotide sequences
      of RefSeq/GenBank.
    homepage: http://bioinformatics.ramapo.edu/GRSDB2/
    id: 00000495
    name: GRSDB
    namespaceEmbeddedInLui: false
    pattern: ^\d+$
    prefix: grsdb
    sampleId: '10142'
    uri_format: http://bioinformatics.ramapo.edu/GRSDB2/geneview.php?geneID=$1
  n2t:
    description: GRSDB is a database of G-quadruplexes and contains information on
      composition and distribution of putative Quadruplex-forming G-Rich Sequences
      (QGRS) mapped in the eukaryotic pre-mRNA sequences, including those that are
      alternatively processed (alternatively spliced or alternatively polyadenylated).
      The data stored in the GRSDB is based on computational analysis of NCBI Entrez
      Gene entries and their corresponding annotated genomic nucleotide sequences
      of RefSeq/GenBank.
    example: '10142'
    homepage: http://bioinformatics.ramapo.edu/GRSDB2/
    name: GRSDB v2 at  Ramapo College of New Jersey
    namespaceEmbeddedInLui: false
    pattern: ^\d+$
    prefix: grsdb
    uri_format: http://bioinformatics.ramapo.edu/GRSDB2/geneview.php?geneID=$1
  name: G-Rich Sequences Database
  prefix: grsdb
  prefixcommons:
    description: GRSDB2 is a second generation database of G-quadruplexes. Like its
      first version, GRSDB, it contains information on composition and distribution
      of putative Quadruplex-forming G-Rich Sequences (QGRS) mapped in the eukaryotic
      pre-mRNA sequences, including that are alternatively processed (alternatively
      spliced or alternatively polyadenylated).
    example: '3191'
    homepage: http://bioinformatics.ramapo.edu/GRSDB2/
    keywords:
    - DNA
    - RNA
    name: GRSDB
    pattern: ^\d+$
    prefix: grsdb
    uri_format: http://bioinformatics.ramapo.edu/GRSDB2/geneview.php?geneID=$1
gs1:
  description: The initial focus of the GS1 Web Vocabulary is consumer-facing properties
    for clothing, shoes, food beverage/tobacco and properties common to all products.
    [from homepage]
  download_rdf: https://ref.gs1.org/voc/data/gs1Voc.ttl
  example: AllergenTypeCode-3-AMINOPHENOL
  homepage: https://ref.gs1.org/voc/
  mappings:
    zazuko: gs1
  name: GS1 Web Vocabulary
  prefix: gs1
  repository: https://github.com/gs1/WebVoc
  zazuko:
    prefix: gs1
    uri_format: https://gs1.org/voc/$1
gsfa:
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: The "Codex General Standard for Food Additives" (GSFA, Codex STAN 192-1995)
    sets forth the conditions under which permitted food additives may be used in
    all foods, whether or not they have previously been standardized by Codex. The
    Preamble of the GSFA contains additional information for interpreting the data.
    Users are encouraged to consult the Preamble when using this database.
  example: '174'
  homepage: http://www.fao.org/gsfaonline
  name: General Standard for Food Additives Online Database
  pattern: ^\d+$
  prefix: gsfa
  synonyms:
  - FAO/WHO_standards
  uri_format: http://www.fao.org/gsfaonline/additives/details.html?id=$1
gsso:
  aberowl:
    description: The Gender, Sex, and Sexual Orientation (GSSO) ontology has terms
      for annotating interdisciplinary information concerning gender, sex, and sexual
      orientation for primary usage in the biomedical and adjacent sciences.
    download_owl: http://aber-owl.net/media/ontologies/GSSO/73/gsso.owl
    homepage: https://gsso.research.cchmc.org/
    name: Gender, Sex, and Sexual Orientation (GSSO) ontology
    prefix: GSSO
  bartoc:
    abbreviation: lgbtDB
    description: The Gender, Sex, and Sexual Orientation (GSSO) ontology is an interdisciplinary
      ontology connecting terms from biology, medicine, psychology, sociology, and
      gender studies, aiming to bridge gaps between linguistic variations inside and
      outside of the health care environment. A large focus of the ontology is its
      consideration of LGBTQIA+ terminology.
    homepage: https://bioportal.bioontology.org/ontologies/GSSO
    license: Apache 2.0 License
    name: Gender, Sex, and Sexual Orientation Ontology
    prefix: '20833'
  bioportal:
    contact:
      email: Clair.Kronk@mountsinai.org
      name: Clair Kronk
    description: The Gender, Sex, and Sexual Orientation (GSSO) ontology is an interdisciplinary
      ontology connecting terms from biology, medicine, psychology, sociology, and
      gender studies, aiming to bridge gaps between linguistic variations inside and
      outside of the health care environment. A large focus of the ontology is its
      consideration of LGBTQIA+ terminology.
    homepage: https://gsso.research.cchmc.org/
    name: Gender, Sex, and Sexual Orientation Ontology
    prefix: GSSO
    publications:
    - https://doi.org/10.1093/jamia/ocaa061
    version: 2.0.6
  mappings:
    aberowl: GSSO
    bartoc: '20833'
    bioportal: GSSO
    miriam: gsso
    obofoundry: gsso
    ols: gsso
    ontobee: GSSO
    wikidata.entity: Q97063846
  miriam:
    deprecated: false
    description: The Gender, Sex, and Sexual Orientation (GSSO) ontology is an interdisciplinary
      ontology connecting terms from biology, medicine, psychology, sociology, and
      gender studies, aiming to bridge gaps between linguistic variations inside and
      outside of the health care environment. A large focus of the ontology is its
      consideration of LGBTQIA+ terminology.
    homepage: https://bioportal.bioontology.org/
    id: '00000712'
    name: Gender, Sex, and Sexual Orientation (GSSO) Ontology
    namespaceEmbeddedInLui: true
    pattern: ^GSSO:\d{6}$
    prefix: gsso
    sampleId: 002368
    uri_format: http://purl.obolibrary.org/obo/GSSO_$1
  name: Gender, Sex, and Sexual Orientation Ontology
  obofoundry:
    appears_in:
    - ontoavida
    - scdo
    contact: kronkcj@mail.uc.edu
    contact.github: Superraptor
    contact.label: Clair Kronk
    contact.orcid: 0000-0001-8397-8810
    deprecated: false
    description: The Gender, Sex, and Sexual Orientation (GSSO) ontology has terms
      for annotating interdisciplinary information concerning gender, sex, and sexual
      orientation for primary usage in the biomedical and adjacent sciences.
    domain: organisms
    download.json: http://purl.obolibrary.org/obo/gsso.json
    download.obo: http://purl.obolibrary.org/obo/gsso.obo
    download.owl: http://purl.obolibrary.org/obo/gsso.owl
    homepage: https://gsso.research.cchmc.org/
    license: Apache 2.0 License
    license.url: http://www.apache.org/licenses/LICENSE-2.0
    name: Gender, Sex, and Sexual Orientation (GSSO) ontology
    preferredPrefix: GSSO
    prefix: gsso
    repository: https://github.com/Superraptor/GSSO
  ols:
    description: GSSO is the Gender, Sex, and Sex Orientation ontology, including
      terms related to gender identity and expression, sexual and romantic identity
      and orientation, and sexual and reproductive behavior.
    download_owl: http://purl.obolibrary.org/obo/gsso.owl
    homepage: https://gsso.research.cchmc.org/
    name: GSSO - the Gender, Sex, and Sexual Orientation ontology
    prefix: gsso
    tracker: https://github.com/Superraptor/GSSO/issues
    version: 2.0.5
    version.iri: http://purl.obolibrary.org/obo/gsso/releases/2.0.5/gsso.owl
  ontobee:
    library: Library
    name: Gender, Sex, and Sexual Orientation (GSSO) ontology
    prefix: GSSO
  pattern: ^\d{6}$
  prefix: gsso
  uri_format: http://purl.obolibrary.org/obo/GSSO_$1
gtdb:
  contact:
    email: donovan.parks@gmail.com
    github: donovan-h-parks
    name: Donovan Parks
    orcid: 0000-0001-6662-9010
  contributor:
    email: aireland@lbl.gov
    github: ialarmedalien
    name: AJ Ireland
    orcid: 0000-0003-1982-9065
  description: The Genome Taxonomy Database (GTDB) is an initiative to establish a
    standardized microbial taxonomy based on genome phylogeny.
  domain: taxonomy
  example: g__Prochlorococcus_A
  github_request_issue: 1242
  homepage: https://gtdb.ecogenomic.org
  keywords:
  - taxonomy
  license: CC-BY-SA-4.0
  logo: https://encrypted-tbn0.gstatic.com/images?q=tbn:ANd9GcQqQRuB8VW0FaaLLXHx8O6oKfFEZzY5jtgtRg&s
  mappings:
    pathguide: '190'
  name: Genome Taxonomy Database
  pathguide:
    abbreviation: GTDB
    homepage: http://web.mit.edu/glycomics/gt/gtdb.shtml
    name: Glycosylation Pathways Database
    prefix: '190'
  pattern: ^[cdfgops]__\w+\S+$
  prefix: gtdb
  publications:
  - doi: 10.1038/s41564-021-00918-8
    pmc: null
    pubmed: '34155373'
    title: A standardized archaeal taxonomy for the Genome Taxonomy Database
    year: 2021
  - doi: 10.1093/nar/gkab776
    pmc: PMC8728215
    pubmed: '34520557'
    title: 'GTDB: an ongoing census of bacterial and archaeal diversity through a
      phylogenetically consistent, rank normalized and complete genome-based taxonomy'
    year: 2021
  - doi: 10.1038/s41587-020-0501-8
    pmc: null
    pubmed: '32341564'
    title: A complete domain-to-species taxonomy for Bacteria and Archaea
    year: 2020
  - doi: 10.1038/nbt.4229
    pmc: null
    pubmed: '30148503'
    title: A standardized bacterial taxonomy based on genome phylogeny substantially
      revises the tree of life
    year: 2018
  reviewer:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  uri_format: https://gtdb.ecogenomic.org/tree?r=$1
gtex:
  biocontext:
    prefix: GTEX
  biolink:
    is_identifiers: false
    is_obo: false
    prefix: GTEx
    uri_format: https://www.gtexportal.org/home/gene/$1
  mappings:
    biocontext: GTEX
    biolink: GTEx
    miriam: gtex
    n2t: gtex
  miriam:
    deprecated: false
    description: The Genotype-Tissue Expression (GTEx) project aims to provide to
      the scientific community a resource with which to study human gene expression
      and regulation and its relationship to genetic variation.
    homepage: https://www.gtexportal.org
    id: '00000663'
    name: GTEx
    namespaceEmbeddedInLui: false
    pattern: ^\w.+$
    prefix: gtex
    sampleId: BRIP1
    uri_format: https://www.gtexportal.org/home/gene/$1
  n2t:
    description: 'The Genotype-Tissue Expression (GTEx) project aims to provide to
      the scientific community a resource with which to study human gene expression
      and regulation and its relationship to genetic variation. '
    example: BRIP1
    homepage: https://www.gtexportal.org
    name: The GTEx Project
    namespaceEmbeddedInLui: false
    pattern: ^\w.+$
    prefix: gtex
    uri_format: https://www.gtexportal.org/home/gene/$1
  name: Genotype-Tissue Expression
  prefix: gtex
gtn:
  contact:
    email: saskia.hiltemann@rz.uni-freiburg.de
    github: shiltemann
    name: Saskia Hiltemann
    orcid: 0000-0003-3803-468X
  contributor:
    email: d.djamalova@fz-juelich.de
    github: ddjamalova
    name: Dilfuza Djamalova
    orcid: 0009-0004-7782-2894
  contributor_extras:
  - email: jacobo.miranda@embl.de
    github: mirandaembl
    name: Jacobo Miranda
    orcid: 0009-0005-0673-021X
  description: Identifiers in the GTN correspond to training materials in various
    formats (markdown, slides, video). The users can apply learned concepts directly
    within the framework via galaxy workflows.
  example: T00148
  github_request_issue: 1778
  homepage: https://training.galaxyproject.org/training-material/
  keywords:
  - galaxy
  - learning materials
  - learning resources
  - training materials
  license: CC-BY-4.0
  name: Galaxy Training Network
  pattern: ^[A-Z]\d+$
  prefix: gtn
  publications:
  - doi: 10.1371/journal.pcbi.1010752
    pmc: PMC9829167
    pubmed: '36622853'
    title: 'Galaxy Training: A powerful framework for teaching!'
    year: 2023
  - doi: 10.1371/journal.pcbi.1007854
    pmc: PMC7241697
    pubmed: '32437350'
    title: Ten simple rules for making training materials FAIR
    year: 2020
  - doi: 10.1016/j.cels.2018.05.012
    pmc: PMC6296361
    pubmed: '29953864'
    title: Community-Driven Data Analysis Training for Biology
    year: 2018
  repository: https://github.com/galaxyproject/training-material
  reviewer:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  uri_format: https://gxy.io/GTN:$1
gtr.condition:
  appears_in:
  - mondo
  comment: Identifiers appearing in MONDO don't match any of the resources apparent
    endpoints
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: The Genetic Testing Registry (GTR®) provides a central location for
    voluntary submission of genetic test information by providers. The scope includes
    the test's purpose, methodology, validity, evidence of the test's usefulness,
    and laboratory contacts and credentials. The overarching goal of the GTR is to
    advance the public health and research into the genetic basis of health and disease
  example: AN0097748
  homepage: https://www.ncbi.nlm.nih.gov/gtr/
  name: Genetic Testing Registry
  prefix: gtr.condition
  synonyms:
  - gtr
  - medgen.gtr
  uri_format: https://www.ncbi.nlm.nih.gov/gtr/conditions/$1
gtr.lab:
  mappings:
    miriam: gtrl
  miriam:
    deprecated: false
    description: The Genetic Testing Registry provides a central location for voluntary
      submission of genetic test information by providers. The scope includes the
      test's purpose, methodology, validity, evidence of the test's usefulness, and
      laboratory contacts and credentials. The overarching goal of the GTR is to advance
      the public health and research into the genetic basis of health and disease.
    homepage: https://www.ncbi.nlm.nih.gov/
    id: '00001115'
    name: Genetic Testing Registry Labs
    namespaceEmbeddedInLui: false
    pattern: \d+
    prefix: gtrl
    sampleId: '000320401'
    uri_format: https://www.ncbi.nlm.nih.gov/gtr/labs/$1
  prefix: gtr.lab
gtr.test:
  mappings:
    miriam: gtr
  miriam:
    deprecated: false
    description: The Genetic Testing Registry provides a central location for voluntary
      submission of genetic test information by providers. The scope includes the
      test's purpose, methodology, validity, evidence of the test's usefulness, and
      laboratory contacts and credentials. The overarching goal of the GTR is to advance
      the public health and research into the genetic basis of health and disease.
    homepage: https://www.ncbi.nlm.nih.gov/
    id: '00001117'
    name: Genetic Testing Registry Tests
    namespaceEmbeddedInLui: false
    pattern: \d+
    prefix: gtr
    sampleId: '000260236'
    uri_format: https://www.ncbi.nlm.nih.gov/gtr/tests/$1
  prefix: gtr.test
gudmap:
  biocontext:
    prefix: GUDMAP
  contact:
    email: simon.harding@ed.ac.uk
    github: simondharding
    name: Simon Douglas Harding
    orcid: 0000-0002-9262-8318
  fairsharing:
    abbreviation: GUDMAP
    description: The GenitoUrinary Development Molecular Anatomy Project (GUDMAP)
      provides data and tools to facilitate research on the GenitoUrinary (GU) tract
      for the scientific and medical community. In addition to current GUDMAP data,
      this resource incorporates data generated by previous phases of GUDMAP and by
      the (Re)Building a Kidney (RBK) consortium.
    homepage: https://gudmap.org
    name: GenitoUrinary Development Molecular Anatomy Project
    prefix: FAIRsharing.910c39
    publications:
    - doi: 10.1242/dev.063594
      pubmed_id: 21652655
      title: The GUDMAP database--an online resource for genitourinary research.
    - doi: 10.1681/ASN.2007101078
      pubmed_id: 18287559
      title: 'GUDMAP: the genitourinary developmental molecular anatomy project.'
    subjects:
    - Molecular biology
    - Genomics
    - Developmental Biology
    - Cell Biology
    twitter: GUDMAP
  mappings:
    biocontext: GUDMAP
    fairsharing: FAIRsharing.910c39
    miriam: gudmap
    n2t: gudmap
    re3data: r3d100012193
  miriam:
    deprecated: false
    description: The GenitoUrinary Development Molecular Anatomy Project (GUDMAP)
      is a consortium of laboratories working to provide the scientific and medical
      community with tools to facilitate research on the GenitoUrinary (GU) tract.
    homepage: http://www.gudmap.org/
    id: '00000643'
    name: GUDMAP
    namespaceEmbeddedInLui: false
    pattern: ^[-0-9a-zA-Z]+(@[-0-9a-zA-Z]+)?$
    prefix: gudmap
    sampleId: Q-2958
    uri_format: https://gudmap.org/id/$1
  n2t:
    description: The GenitoUrinary Development Molecular Anatomy Project (GUDMAP)
      is a consortium of laboratories working to provide the scientific and medical
      community with tools to facilitate research on the GenitoUrinary (GU) tract.
    example: Q-2958
    homepage: http://www.gudmap.org/
    name: GUDMAP
    namespaceEmbeddedInLui: false
    pattern: ^[-0-9a-zA-Z]+(@[-0-9a-zA-Z]+)?$
    prefix: gudmap
    uri_format: https://gudmap.org/id/$1
  name: Genitourinary Development Molecular Anatomy Project
  prefix: gudmap
  publications:
  - doi: 10.1242/dev.063594
    pmc: PMC3188593
    pubmed: '21652655'
    title: The GUDMAP database--an online resource for genitourinary research
    year: 2011
  - doi: 10.1681/asn.2007101078
    pmc: null
    pubmed: '18287559'
    title: 'GUDMAP: the genitourinary developmental molecular anatomy project'
    year: 2008
  re3data:
    description: 'The GenitoUrinary Development Molecular Anatomy Project (GUDMAP)
      is a consortium of laboratories working to provide the scientific and medical
      community with tools to facilitate research. The key components are: (1) a molecular
      atlas of gene expression for the developing organs of the GenitoUrinary (GU)
      tract; (2) a high resolution molecular anatomy that highlights development of
      the GU system; (3) mouse strains to facilitate developmental and functional
      studies within the GU system; (4) tutorials describing GU organogenesis; and
      (5) rapid access to primary data via the GUDMAP database.'
    doi: 10.17616/R3M36P
    homepage: https://www.gudmap.org/index.html
    name: GUDMAP
    prefix: r3d100012193
    synonyms:
    - GenitoUrinary Development Molecular Anatomy Project
    xrefs:
      nif: 0000-33426
gufo:
  contact:
    email: null
    github: jpalmeida
    name: João Paulo A. Almeida
    orcid: null
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: An _gentle_ implementation of the Unified Foundational Ontology (UFO),
    which is an upper level ontology like BFO that is concerned with e.g. expressing
    temporal relationships between events.
  domain: classification
  download_rdf: https://github.com/nemo-ufes/gufo/raw/refs/heads/master/gufo.ttl
  example: Person
  github_request_issue: 1704
  homepage: https://nemo-ufes.github.io/gufo
  keywords:
  - ontology
  - upper level
  license: CC-BY-4.0
  lov:
    description: "The objective of gUFO is to provide a lightweight implementation\
      \ of the Unified Foundational Ontology (UFO) [1-5] suitable for Semantic Web\
      \ OWL 2 DL applications. \n\nIntended users are those implementing UFO-based\
      \ lightweight ontologies that reuse gUFO by specializing and instantiating its\
      \ elements.\n\nThere are three implications of the use of the term lightweight.\
      \ First of all, we have employed little expressive means in an effort to retain\
      \ computational properties for the resulting OWL ontology. Second, we have selected\
      \ a subset of UFO-A [1, 2] and UFO-B [3] to include here. In particular, there\
      \ is minimalistic support for UFO-B (only that which is necessary to establish\
      \ the participation of objects in events and to capture historical dependence\
      \ between events). Third, a lightweight ontology, differently from a reference\
      \ ontology, is designed with the purpose of providing an implementation artifact\
      \ to structure a knowledge base (or knowledge graph). This has driven a number\
      \ of pragmatic implementation choices which are discussed in comments annotated\
      \ to the various elements of this implementation. \n\nThe 'g' in gUFO stands\
      \ for gentle. At the same time, \"gufo\" is the Italian word for \"owl\".\n\n\
      \nFor the source repository, see: <https://github.com/nemo-ufes/gufo>"
    homepage: https://github.com/nemo-ufes/gufo
    keywords:
    - Events
    - General & Upper
    modified: '2019-11-11'
    name: 'gUFO: A Lightweight Implementation of the Unified Foundational Ontology
      (UFO)'
    prefix: gufo
    uri_prefix: http://purl.org/nemo/gufo#$1
  mappings:
    lov: gufo
  name: Unified Foundational Ontology
  prefix: gufo
  publications:
  - doi: 10.1007/978-3-030-33223-5_4
    pmc: null
    pubmed: null
    title: Relations in ontology-driven conceptual modeling
    year: 2019
  - doi: 10.1007/978-3-030-00847-5_12
    pmc: null
    pubmed: null
    title: 'Endurant Types in Ontology-Driven Conceptual Modeling: Towards OntoUML
      2.0'
    year: 2018
  - doi: 10.3233/ao-150157
    pmc: null
    pubmed: null
    title: 'Towards ontological foundations for conceptual modeling: The unified foundational
      ontology (UFO) story'
    year: 2015
  - doi: 10.1007/978-3-642-41924-9_27
    pmc: null
    pubmed: null
    title: Towards Ontological Foundations for the Conceptual Modeling of Events
    year: 2013
  rdf_uri_format: http://purl.org/nemo/gufo#$1
  repository: https://github.com/nemo-ufes/gufo
  uri_format: http://purl.org/nemo/gufo#$1
gwascentral.marker:
  biocontext:
    prefix: GWASCENTRAL.MARKER
  contact:
    email: tb143@leicester.ac.uk
    github: null
    name: Tim Beck
    orcid: 0000-0002-0292-7972
  homepage: https://www.gwascentral.org/markers
  logo: https://help.gwascentral.org/wp-content/uploads/2017/04/logo.png
  mappings:
    biocontext: GWASCENTRAL.MARKER
    miriam: gwascentral.marker
    n2t: gwascentral.marker
  miriam:
    deprecated: false
    description: GWAS Central (previously the Human Genome Variation database of Genotype-to-Phenotype
      information) is a database of summary level findings from genetic association
      studies, both large and small. It gathers datasets from public domain projects,
      and accepts direct data submission. It is based upon Marker information encompassing
      SNP and variant information from public databases, to which allele and genotype
      frequency data, and genetic association findings are additionally added. A Study
      (most generic level) contains one or more Experiments, one or more Sample Panels
      of test subjects, and one or more Phenotypes. This collection references a GWAS
      Central Marker.
    homepage: https://www.gwascentral.org/markers/
    id: '00000542'
    name: GWAS Central Marker
    namespaceEmbeddedInLui: false
    pattern: ^HGVM\d+$
    prefix: gwascentral.marker
    sampleId: HGVM15354
    uri_format: https://www.gwascentral.org/marker/$1
  n2t:
    description: GWAS Central (previously the Human Genome Variation database of Genotype-to-Phenotype
      information) is a database of summary level findings from genetic association
      studies, both large and small. It gathers datasets from public domain projects,
      and accepts direct data submission. It is based upon Marker information encompassing
      SNP and variant information from public databases, to which allele and genotype
      frequency data, and genetic association findings are additionally added. A Study
      (most generic level) contains one or more Experiments, one or more Sample Panels
      of test subjects, and one or more Phenotypes. This collection references a GWAS
      Central Marker.
    example: HGVM15354
    homepage: https://www.gwascentral.org/markers/
    name: GWAS Central Marker at University of Leicester
    namespaceEmbeddedInLui: false
    pattern: ^HGVM\d+$
    prefix: gwascentral.marker
    uri_format: https://www.gwascentral.org/marker/$1
  prefix: gwascentral.marker
  publications:
  - doi: 10.1093/nar/gkac1017
    pmc: PMC9825503
    pubmed: '36350644'
    title: 'GWAS Central: an expanding resource for finding and visualising genotype
      and phenotype data from genome-wide association studies'
    year: 2023
  - doi: 10.1038/ejhg.2013.274
    pmc: PMC4060122
    pubmed: '24301061'
    title: 'GWAS Central: a comprehensive resource for the comparison and interrogation
      of genome-wide association studies'
    year: 2014
gwascentral.phenotype:
  biocontext:
    prefix: GWASCENTRAL.PHENOTYPE
  contact:
    email: tb143@leicester.ac.uk
    github: null
    name: Tim Beck
    orcid: 0000-0002-0292-7972
  domain: disease
  homepage: https://www.gwascentral.org/phenotypes
  keywords:
  - condition
  - disease
  - phenotype
  - symptom
  logo: https://help.gwascentral.org/wp-content/uploads/2017/04/logo.png
  mappings:
    biocontext: GWASCENTRAL.PHENOTYPE
    miriam: gwascentral.phenotype
    n2t: gwascentral.phenotype
  miriam:
    deprecated: false
    description: GWAS Central (previously the Human Genome Variation database of Genotype-to-Phenotype
      information) is a database of summary level findings from genetic association
      studies, both large and small. It gathers datasets from public domain projects,
      and accepts direct data submission. It is based upon Marker information encompassing
      SNP and variant information from public databases, to which allele and genotype
      frequency data, and genetic association findings are additionally added. A Study
      (most generic level) contains one or more Experiments, one or more Sample Panels
      of test subjects, and one or more Phenotypes. This collection references a GWAS
      Central Phenotype.
    homepage: https://www.gwascentral.org/phenotypes
    id: '00000543'
    name: GWAS Central Phenotype
    namespaceEmbeddedInLui: false
    pattern: ^HGVPM\d+$
    prefix: gwascentral.phenotype
    sampleId: HGVPM623
    uri_format: https://www.gwascentral.org/phenotype/$1
  n2t:
    description: GWAS Central (previously the Human Genome Variation database of Genotype-to-Phenotype
      information) is a database of summary level findings from genetic association
      studies, both large and small. It gathers datasets from public domain projects,
      and accepts direct data submission. It is based upon Marker information encompassing
      SNP and variant information from public databases, to which allele and genotype
      frequency data, and genetic association findings are additionally added. A Study
      (most generic level) contains one or more Experiments, one or more Sample Panels
      of test subjects, and one or more Phenotypes. This collection references a GWAS
      Central Phenotype.
    example: HGVPM623
    homepage: https://www.gwascentral.org/phenotypes
    name: GWAS Central Phenotype at University of Leicester
    namespaceEmbeddedInLui: false
    pattern: ^HGVP\d+$
    prefix: gwascentral.phenotype
    uri_format: https://www.gwascentral.org/phenotype/$1
  pattern: ^HGVPM\d+$
  prefix: gwascentral.phenotype
  publications:
  - doi: 10.1093/nar/gkac1017
    pmc: PMC9825503
    pubmed: '36350644'
    title: 'GWAS Central: an expanding resource for finding and visualising genotype
      and phenotype data from genome-wide association studies'
    year: 2023
  - doi: 10.1038/ejhg.2013.274
    pmc: PMC4060122
    pubmed: '24301061'
    title: 'GWAS Central: a comprehensive resource for the comparison and interrogation
      of genome-wide association studies'
    year: 2014
gwascentral.study:
  biocontext:
    prefix: GWASCENTRAL.STUDY
  contact:
    email: tb143@leicester.ac.uk
    github: null
    name: Tim Beck
    orcid: 0000-0002-0292-7972
  domain: study
  homepage: https://www.gwascentral.org/studies
  logo: https://help.gwascentral.org/wp-content/uploads/2017/04/logo.png
  mappings:
    biocontext: GWASCENTRAL.STUDY
    miriam: gwascentral.study
    n2t: gwascentral.study
    prefixcommons: hgvbase
  miriam:
    deprecated: false
    description: GWAS Central (previously the Human Genome Variation database of Genotype-to-Phenotype
      information) is a database of summary level findings from genetic association
      studies, both large and small. It gathers datasets from public domain projects,
      and accepts direct data submission. It is based upon Marker information encompassing
      SNP and variant information from public databases, to which allele and genotype
      frequency data, and genetic association findings are additionally added. A Study
      (most generic level) contains one or more Experiments, one or more Sample Panels
      of test subjects, and one or more Phenotypes. This collection references a GWAS
      Central Study.
    homepage: https://www.gwascentral.org/studies
    id: '00000540'
    name: GWAS Central Study
    namespaceEmbeddedInLui: false
    pattern: ^HGVST\d+$
    prefix: gwascentral.study
    sampleId: HGVST1828
    uri_format: https://www.gwascentral.org/study/$1
  n2t:
    description: GWAS Central (previously the Human Genome Variation database of Genotype-to-Phenotype
      information) is a database of summary level findings from genetic association
      studies, both large and small. It gathers datasets from public domain projects,
      and accepts direct data submission. It is based upon Marker information encompassing
      SNP and variant information from public databases, to which allele and genotype
      frequency data, and genetic association findings are additionally added. A Study
      (most generic level) contains one or more Experiments, one or more Sample Panels
      of test subjects, and one or more Phenotypes. This collection references a GWAS
      Central Study.
    example: HGVST1828
    homepage: https://www.gwascentral.org/studies
    name: GWAS Central Study at University of Leicester
    namespaceEmbeddedInLui: false
    pattern: ^HGVST\d+$
    prefix: gwascentral.study
    uri_format: https://www.gwascentral.org/study/$1
  prefix: gwascentral.study
  prefixcommons:
    description: HGVbase was set up in an effort to improve analysis of common human
      genetic polymorphism by maintaining a high-quality database of all publicly
      available genomic variation data (primarily SNPs). Currently maintained by an
      academic European consortium it contains close to 2 million non-redundant entries.
      Data is harvested from three main areas, (i) collaboration with other variation
      databases, (ii) extraction from scientific literature and (iii) submissions
      from various research groups.
    example: HGVST315
    homepage: http://hgvbase.cgb.ki.se
    keywords:
    - gene
    - genome
    name: 'Human Genome Variation Database: Genotype-to-Phenotype'
    pattern: ^HGVST\d+$
    prefix: hgvbase
    uri_format: http://www.hgvbaseg2p.org/study/$1
  publications:
  - doi: 10.1093/nar/gkac1017
    pmc: PMC9825503
    pubmed: '36350644'
    title: 'GWAS Central: an expanding resource for finding and visualising genotype
      and phenotype data from genome-wide association studies'
    year: 2023
  - doi: 10.1038/ejhg.2013.274
    pmc: PMC4060122
    pubmed: '24301061'
    title: 'GWAS Central: a comprehensive resource for the comparison and interrogation
      of genome-wide association studies'
    year: 2014
gxa.expt:
  biocontext:
    prefix: GXA.EXPT
  mappings:
    biocontext: GXA.EXPT
    miriam: gxa.expt
    n2t: gxa.expt
  miriam:
    deprecated: false
    description: The Gene Expression Atlas (GXA) is a semantically enriched database
      of meta-analysis based summary statistics over a curated subset of ArrayExpress
      Archive, servicing queries for condition-specific gene expression patterns as
      well as broader exploratory searches for biologically interesting genes/samples.
      This collection references experiments.
    homepage: https://www.ebi.ac.uk/gxa/
    id: 00000379
    name: GXA Expt
    namespaceEmbeddedInLui: false
    pattern: ^[AEP]-\w{4}-\d+$
    prefix: gxa.expt
    providers:
    - code: omicsdi
      description: GXA Expt through OmicsDI
      homepage: https://www.omicsdi.org/
      name: GXA Expt through OmicsDI
      uri_format: https://www.omicsdi.org/dataset/atlas-experiments/$1
    sampleId: E-MTAB-2037
    uri_format: https://www.ebi.ac.uk/gxa/experiments/$1
  n2t:
    description: The Gene Expression Atlas (GXA) is a semantically enriched database
      of meta-analysis based summary statistics over a curated subset of ArrayExpress
      Archive, servicing queries for condition-specific gene expression patterns as
      well as broader exploratory searches for biologically interesting genes/samples.
      This collection references experiments.
    example: E-MTAB-2037
    homepage: https://www.ebi.ac.uk/gxa/
    name: GXA Expt at EBI
    namespaceEmbeddedInLui: false
    pattern: ^[AEP]-\w{4}-\d+$
    prefix: gxa.expt
    uri_format: https://www.ebi.ac.uk/gxa/experiments/$1
  owners:
  - name: European Bioinformatics Institute
    partnered: false
    ror: 02catss52
    wikidata: null
  prefix: gxa.expt
gxa.gene:
  biocontext:
    prefix: GXA.GENE
  mappings:
    biocontext: GXA.GENE
    miriam: gxa.gene
    n2t: gxa.gene
  miriam:
    deprecated: false
    description: The Gene Expression Atlas (GXA) is a semantically enriched database
      of meta-analysis based summary statistics over a curated subset of ArrayExpress
      Archive, servicing queries for condition-specific gene expression patterns as
      well as broader exploratory searches for biologically interesting genes/samples.
      This collection references genes.
    homepage: https://www.ebi.ac.uk/gxa/
    id: 00000378
    name: GXA Gene
    namespaceEmbeddedInLui: false
    pattern: ^\w+$
    prefix: gxa.gene
    sampleId: AT4G01080
    uri_format: https://www.ebi.ac.uk/gxa/genes/$1
  n2t:
    description: The Gene Expression Atlas (GXA) is a semantically enriched database
      of meta-analysis based summary statistics over a curated subset of ArrayExpress
      Archive, servicing queries for condition-specific gene expression patterns as
      well as broader exploratory searches for biologically interesting genes/samples.
      This collection references genes.
    example: AT4G01080
    homepage: https://www.ebi.ac.uk/gxa/
    name: GXA Gene at EBI
    namespaceEmbeddedInLui: false
    pattern: ^\w+$
    prefix: gxa.gene
    uri_format: https://www.ebi.ac.uk/gxa/genes/$1
  owners:
  - name: European Bioinformatics Institute
    partnered: false
    ror: 02catss52
    wikidata: null
  prefix: gxa.gene
habronattus:
  biocontext:
    prefix: HABRONATTUS
  mappings:
    biocontext: HABRONATTUS
    obofoundry: habronattus
    wikidata.entity: Q114677889
  obofoundry:
    contact: peteremidford@yahoo.com
    contact.label: Peter Midford
    contact.orcid: 0000-0001-6512-3296
    deprecated: true
    domain: organisms
    homepage: http://www.mesquiteproject.org/ontology/Habronattus/index.html
    name: Habronattus courtship
    prefix: habronattus
  prefix: habronattus
hagr.genage:
  contact:
    email: jp@senescence.info
    github: null
    name: Joao Pedro de Magalhaes
    orcid: 0000-0002-6363-2465
  mappings:
    prefixcommons: genage
  name: The Ageing Gene Database
  prefix: hagr.genage
  prefixcommons:
    description: GenAge is a database of human and model organism genes related to
      longevity and aging, maintained by the Human Ageing Genomics Resources (HAGR)
      group.
    example: '0001'
    homepage: http://genomics.senescence.info/genes/
    keywords:
    - aging
    - longevity
    - genes
    license: http://genomics.senescence.info/legal.html
    name: 'GenAge: The Ageing Gene Database'
    pattern: ^\d+$
    prefix: genage
    pubmed_ids:
    - '23193293'
    uri_format: http://genomics.senescence.info/genes/details.php?id=$1
  publications:
  - doi: 10.1093/nar/gks1155
    pmc: PMC3531213
    pubmed: '23193293'
    title: 'Human Ageing Genomic Resources: integrated databases and tools for the
      biology and genetics of ageing'
    year: 2012
  - doi: null
    pmc: null
    pubmed: '23193293'
    title: null
    year: null
  reviewer:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
hagr.gendr:
  contact:
    email: jp@senescence.info
    github: null
    name: Joao Pedro de Magalhaes
    orcid: 0000-0002-6363-2465
  mappings:
    prefixcommons: gendr
  name: The Dietary Restriction Gene Database
  prefix: hagr.gendr
  prefixcommons:
    description: 'GenDR is a database of genes associated with dietary restriction
      (DR). GenDR includes two datasets: 1) genes inferred from experiments in model
      organisms in which genetic manipulations cancel out or disrupt the life-extending
      effects of DR; 2) genes robustly altered due to DR, derived from a meta-analysis
      of microarray DR studies in mammals'
    example: '2'
    homepage: http://genomics.senescence.info/diet/
    keywords:
    - dietary restriction
    - aging
    - longevity
    - genes
    license: http://genomics.senescence.info/legal.html
    name: 'GenDR: The Dietary Restriction Gene Database'
    pattern: ^\d+$
    prefix: gendr
    pubmed_ids:
    - '22912585'
    uri_format: http://genomics.senescence.info/diet/details.php?id=$1
  publications:
  - doi: 10.1371/journal.pgen.1002834
    pmc: PMC3415404
    pubmed: '22912585'
    title: Dissecting the gene network of dietary restriction to identify evolutionarily
      conserved pathways and new functional genes
    year: 2012
  reviewer:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
hamap:
  biocontext:
    prefix: HAMAP
  edam:
    description: Name of a protein family from the HAMAP database.
    name: HAMAP
    obsolete: false
    prefix: '2766'
  fairsharing:
    abbreviation: HAMAP
    contact:
      email: alan.bridge@isb-sib.ch
      name: Alan Bridge
      orcid: 0000-0003-2148-9135
    description: 'HAMAP is a system, based on manual protein annotation, that identifies
      and semi-automatically annotates proteins that are part of well-conserved families
      or subfamilies: the HAMAP families. HAMAP is based on manually created family
      rules and is applied to bacterial, archaeal and plastid-encoded proteins.'
    homepage: https://hamap.expasy.org/
    license: http://opendatacommons.org/licenses/pddl/1.0
    name: HAMAP database of microbial protein families
    prefix: FAIRsharing.63m4ss
    publications:
    - doi: 10.1093/nar/gks1157
      pubmed_id: 23193261
      title: HAMAP in 2013, new developments in the protein family classification
        and annotation system.
    - doi: 10.1093/nar/gku1002
      pubmed_id: 25348399
      title: 'HAMAP in 2015: updates to the protein family classification and annotation
        system.'
    subjects:
    - Life Science
  go:
    homepage: http://hamap.expasy.org/
    name: High-quality Automated and Manual Annotation of microbial Proteomes
    prefix: HAMAP
    uri_format: http://hamap.expasy.org/unirule/$1
  mappings:
    biocontext: HAMAP
    edam: '2766'
    fairsharing: FAIRsharing.63m4ss
    go: HAMAP
    miriam: hamap
    n2t: hamap
    prefixcommons: hamap
    uniprot: DB-0041
  miriam:
    deprecated: false
    description: HAMAP is a system that identifies and semi-automatically annotates
      proteins that are part of well-conserved and orthologous microbial families
      or subfamilies. These are used to build rules which are used to propagate annotations
      to member bacterial, archaeal and plastid-encoded protein entries.
    homepage: https://hamap.expasy.org/
    id: 00000292
    name: HAMAP
    namespaceEmbeddedInLui: false
    pattern: ^MF_\d+$
    prefix: hamap
    sampleId: MF_01400
    uri_format: https://hamap.expasy.org/unirule/$1
  n2t:
    description: HAMAP is a system that identifies and semi-automatically annotates
      proteins that are part of well-conserved and orthologous microbial families
      or subfamilies. These are used to build rules which are used to propagate annotations
      to member bacterial, archaeal and plastid-encoded protein entries.
    example: MF_01400
    homepage: https://hamap.expasy.org/
    name: HAPMAP at Swiss Institute of Bioinformatics
    namespaceEmbeddedInLui: false
    pattern: ^MF_\d+$
    prefix: hamap
    uri_format: https://hamap.expasy.org/unirule/$1
  prefix: hamap
  prefixcommons:
    description: 'HAMAP is a system, based on manual protein annotation, that identifies
      and semi-automatically annotates proteins that are part of well-conserved families
      or subfamilies: the HAMAP families. HAMAP is based on manually created family
      rules and is applied to bacterial, archaeal and plastid-encoded proteins.'
    example: MF_00323
    homepage: http://us.expasy.org/sprot/hamap/
    keywords:
    - protein
    name: HAMAP database of microbial protein families
    pattern: ^MF_\d+$
    prefix: hamap
    uri_format: http://us.expasy.org/unirule/$1
  publications:
  - doi: 10.1093/nar/gku1002
    pmc: PMC4383873
    pubmed: '25348399'
    title: 'HAMAP in 2015: updates to the protein family classification and annotation
      system'
    year: 2014
  - doi: 10.1093/nar/gks1157
    pmc: PMC3531088
    pubmed: '23193261'
    title: HAMAP in 2013, new developments in the protein family classification and
      annotation system
    year: 2012
  uniprot:
    abbreviation: HAMAP
    category: Family and domain databases
    homepage: https://hamap.expasy.org/
    name: HAMAP database of protein families
    prefix: DB-0041
    publications:
    - doi: 10.1093/nar/gku1002
      pubmed: '25348399'
    uri_format: https://hamap.expasy.org/signature/$1
hancestro:
  aberowl:
    description: The Human Ancestry Ontology (HANCESTRO) provides a systematic description
      of the ancestry concepts used in the NHGRI-EBI Catalog of published genome-wide
      association studies.
    download_owl: http://aber-owl.net/media/ontologies/HANCESTRO/21/hancestro.owl
    homepage: https://ebispot.github.io/hancestro/
    name: Human Ancestry Ontology
    prefix: HANCESTRO
  biolink:
    is_identifiers: false
    is_obo: false
    prefix: HANCESTRO
    uri_format: http://www.ebi.ac.uk/ancestro/ancestro_$1
  bioportal:
    contact:
      email: dwelter.ontologist@gmail.com
      name: Danielle Welter
    description: The Human Ancestry Ontology (HANCESTRO) provides a systematic description
      of the ancestry concepts used in the NHGRI-EBI Catalog of published genome-wide
      association studies. Please note that as of v2.0 (released July 2018), HANCESTRO
      (formerly ANCESTRO) has undergone some major changes including a revised namespace.,
      Human ancestry ontology for the NHGRI GWAS Catalog
    homepage: https://github.com/EBISPOT/hancestro
    license: CC-BY-4.0
    name: Human Ancestry Ontology
    prefix: HANCESTRO
    publications:
    - https://genomebiology.biomedcentral.com/articles/10.1186/s13059-018-1396-2
    version: '2025-10-14'
  example: 0290
  fairsharing:
    abbreviation: HANCESTRO
    description: The Human Ancestry Ontology (HANCESTRO) provides a systematic description
      of the ancestry concepts used in the NHGRI-EBI Catalog of published genome-wide
      association studies.
    domains:
    - genome-wide association study
    homepage: https://github.com/EBISPOT/hancestro
    license: CC-BY-4.0
    name: Human Ancestry Ontology
    prefix: FAIRsharing.rja8qp
    publications:
    - doi: 10.1186/s13059-018-1396-2
      pubmed: '29448949'
      title: A standardized framework for representation of ancestry data in genomics
        studies, with application to the NHGRI-EBI GWAS Catalog
      year: 2018
    repository: https://github.com/EBISPOT/ancestro/issues
    subjects:
    - Population Genetics
    - Human Genetics
    - Demographics
  mappings:
    aberowl: HANCESTRO
    biolink: HANCESTRO
    bioportal: HANCESTRO
    fairsharing: FAIRsharing.rja8qp
    obofoundry: hancestro
    ols: hancestro
    ontobee: HANCESTRO
    wikidata.entity: Q81661647
  obofoundry:
    contact: dwelter.ontologist@gmail.com
    contact.github: daniwelter
    contact.label: Danielle Welter
    contact.orcid: 0000-0003-1058-2668
    deprecated: false
    description: The Human Ancestry Ontology (HANCESTRO) provides a systematic description
      of the ancestry concepts used in the NHGRI-EBI Catalog of published genome-wide
      association studies.
    domain: organisms
    download.owl: http://purl.obolibrary.org/obo/hancestro.owl
    homepage: https://ebispot.github.io/hancestro/
    license: CC BY 4.0
    license.url: https://creativecommons.org/licenses/by/4.0/
    name: Human Ancestry Ontology
    preferredPrefix: HANCESTRO
    prefix: hancestro
    publications:
    - id: https://www.ncbi.nlm.nih.gov/pubmed/29448949
      title: A standardized framework for representation of ancestry data in genomics
        studies, with application to the NHGRI-EBI GWAS Catalog
    repository: https://github.com/EBISPOT/hancestro
  ols:
    description: Human ancestry ontology for the NHGRI GWAS Catalog
    download_owl: http://purl.obolibrary.org/obo/hancestro.owl
    homepage: https://ebispot.github.io/hancestro/
    name: Human Ancestry Ontology
    prefix: hancestro
    tracker: https://github.com/EBISPOT/hancestro/issues
    version: '2025-10-14'
    version.iri: http://purl.obolibrary.org/obo/hancestro/releases/2025-10-14/hancestro.owl
  ontobee:
    library: Library
    name: Human Ancestry Ontology
    prefix: HANCESTRO
  owners:
  - name: European Bioinformatics Institute
    partnered: false
    ror: 02catss52
    wikidata: null
  pattern: ^\d{4}$
  prefix: hancestro
  providers:
  - code: legacy
    description: Legacy URI
    example: null
    first_party: null
    homepage: http://www.ebi.ac.uk/ancestro
    name: Legacy
    publications: null
    status: null
    uri_format: http://www.ebi.ac.uk/ancestro/ancestro_$1
  publications:
  - doi: 10.1186/s13059-018-1396-2
    pmc: PMC5815218
    pubmed: '29448949'
    title: A standardized framework for representation of ancestry data in genomics
      studies, with application to the NHGRI-EBI GWAS Catalog
    year: 2018
  repository: https://github.com/EBISPOT/ancestro
  uri_format: http://purl.obolibrary.org/obo/HANCESTRO_$1
hao:
  aberowl:
    description: A structured controlled vocabulary of the anatomy of the Hymenoptera
      (bees, wasps, and ants)
    download_owl: http://aber-owl.net/media/ontologies/HAO/28/hao.owl
    homepage: http://hymao.org
    name: Hymenoptera Anatomy Ontology
    prefix: HAO
  biocontext:
    prefix: HAO
  bioportal:
    contact:
      email: diapriid@gmail.com
      name: HAO developers
    description: A structured controlled vocabulary of the anatomy of the Hymenoptera
      (bees, wasps, sawflies and ants)
    homepage: http://hymao.org
    name: Hymenoptera Anatomy Ontology
    prefix: HAO
    version: '2023-06-01'
  example: 0000187
  fairsharing:
    abbreviation: HAO
    contact:
      email: andy_deans@ncsu.edu
      name: Andrew R Deans
      orcid: 0000-0002-2119-4663
    description: The Hymenoptera Anatomy Ontology is a structured controlled vocabulary
      of the anatomy of the Hymenoptera (bees, wasps, and ants)
    homepage: http://portal.hymao.org/projects/32/public/ontology/
    name: Hymenoptera Anatomy Ontology
    prefix: FAIRsharing.kj3m5n
    publications:
    - doi: 10.1371/journal.pone.0015991
      pubmed: '21209921'
      title: A gross anatomy ontology for hymenoptera
      year: 2011
    subjects:
    - Life Science
    - Anatomy
  mappings:
    aberowl: HAO
    biocontext: HAO
    bioportal: HAO
    fairsharing: FAIRsharing.kj3m5n
    obofoundry: hao
    ols: hao
    ontobee: HAO
    wikidata.entity: Q81661648
  obofoundry:
    contact: diapriid@gmail.com
    contact.github: mjy
    contact.label: Matt Yoder
    contact.orcid: 0000-0002-5640-5491
    deprecated: false
    description: A structured controlled vocabulary of the anatomy of the Hymenoptera
      (bees, wasps, and ants)
    domain: anatomy and development
    download.obo: http://purl.obolibrary.org/obo/hao.obo
    download.owl: http://purl.obolibrary.org/obo/hao.owl
    homepage: http://hymao.org
    license: CC0 1.0
    license.url: https://creativecommons.org/publicdomain/zero/1.0/
    name: Hymenoptera Anatomy Ontology
    preferredPrefix: HAO
    prefix: hao
    publications:
    - id: https://www.ncbi.nlm.nih.gov/pubmed/21209921
      title: A gross anatomy ontology for hymenoptera
    repository: https://github.com/hymao/hao
  ols:
    description: A structured controlled vocabulary of the anatomy of the Hymenoptera
      (bees, wasps, and ants)
    download_owl: http://purl.obolibrary.org/obo/hao.owl
    homepage: http://hymao.org
    name: Hymenoptera Anatomy Ontology
    prefix: hao
    tracker: https://github.com/hymao/hao/issues
    version: '2023-06-01'
    version.iri: http://purl.obolibrary.org/obo/hao/2023-06-01/hao.owl
  ontobee:
    library: Library
    name: Hymenoptera Anatomy Ontology
    prefix: HAO
  pattern: ^\d{7}$
  prefix: hao
  publications:
  - doi: 10.1371/journal.pone.0015991
    pmc: PMC3012123
    pubmed: '21209921'
    title: A gross anatomy ontology for hymenoptera
    year: 2010
  - doi: null
    pmc: null
    pubmed: '21209921'
    title: A gross anatomy ontology for hymenoptera
    year: null
  - doi: 10.1371/journal.pone.0015991
    pmc: null
    pubmed: '21209921'
    title: A gross anatomy ontology for hymenoptera
    year: 2011
  uri_format: http://purl.obolibrary.org/obo/HAO_$1
hao.ref:
  contact:
    email: diapriid@gmail.com
    github: mjy
    name: Matt Yoder
    orcid: 0000-0002-5640-5491
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: Literature references in the Hymenoptera Anatomy Ontology Portal
  example: '98127'
  github_request_issue: 1322
  homepage: http://hymao.org
  name: Hymenoptera Anatomy Reference
  pattern: ^\d+$
  prefix: hao.ref
  uri_format: http://api.hymao.org/api/ref/$1
hathitrust:
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: Hathitrust is a partnership of academic and research institutions,
    offering a collection of millions of titles digitized from libraries around the
    world.
  example: 008893080
  github_request_issue: 510
  homepage: https://www.hathitrust.org
  name: Hathi Trust Digital Library
  pattern: ^\d+$
  prefix: hathitrust
  uri_format: https://catalog.hathitrust.org/Record/$1
hba:
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: A controlled vocabulary to support the study of transcription in the
    human brain
  download_obo: https://raw.githubusercontent.com/obophenotype/uberon/master/source-ontologies/allen-hba.obo
  example: '4005'
  example_extras:
  - '265504410'
  homepage: https://human.brain-map.org
  mappings:
    ols: hba
  name: Human Brain Atlas
  ols:
    description: An application ontology built by combining ontologised versions of
      the Allen Institute Human Brain Atlas (HBA) Structure Graph mapped to Uberon.
    download_owl: https://purl.brain-bican.org/ontology/hbao/hbao.owl
    homepage: https://purl.brain-bican.org/ontology/hbao
    name: Human Brain Atlas Ontology
    prefix: hba
    uri_format: https://purl.brain-bican.org/ontology/hbao/HBA_$1
    version: '2025-02-10'
    version.iri: https://purl.brain-bican.org/ontology/hbao/releases/2025-02-10/hbao.owl
  pattern: ^\d+$
  preferred_prefix: HBA
  prefix: hba
  providers:
  - code: biopragmatics
    description: A static site generated for the HBA resource
    example: null
    first_party: null
    homepage: https://biopragmatics.github.io/providers
    name: Biopragmatics Browser
    publications: null
    status: null
    uri_format: https://biopragmatics.github.io/providers/hba/$1
  repository: https://github.com/brain-bican/human_brain_atlas_ontology
  uri_format: https://purl.brain-bican.org/ontology/hbao/HBA_$1
hbvar:
  mappings:
    prefixcommons: hbvar
  prefix: hbvar
  prefixcommons:
    description: This is a relational database of information about hemoglobin variants
      and mutations that cause thalassemia.
    example: '2526'
    homepage: http://globin.cse.psu.edu/globin/hbvar
    keywords:
    - protein
    name: A Database of Human Hemoglobin Variants and Thalassemias
    pattern: ^\d+$
    prefix: hbvar
    uri_format: http://globin.bx.psu.edu/cgi-bin/hbvar/query_vars3?mode=output&display_format=page&i=$1
  reviewer:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
hc.din:
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: A Drug Identification Number (DIN) is a computer-generated eight digit
    number assigned by Health Canada to a drug product prior to being marketed in
    Canada. It uniquely identifies all drug products sold in a dosage form in Canada
    and is located on the label of prescription and over-the-counter drug products
    that have been evaluated and authorized for sale in Canada.
  example: 02069237
  hl7:
    description: 'A Drug Identification Number (DIN) is a computer-generated eight
      digit number assigned by Health Canada to a drug product prior to being marketed
      in Canada. It uniquely identifies all drug products sold in a dosage form in
      Canada and is located on the label of prescription and over-the-counter drug
      products that have been evaluated and authorized for sale in Canada.A DIN uniquely
      identifies the following product characteristics:manufacturer;product name;active
      ingredient(s);strength(s) of active ingredient(s);pharmaceutical form; androute
      of administration.Note: The number has a leading zeroMore information can be
      found here: https://www.canada.ca/en/health-canada/services/drugs-health-products/drug-products/applications-submissions/guidance-documents/regulatory-requirements-drug-identification-numbers/document.html'
    homepage: http://www.hc-sc.gc.ca/index-eng.php
    name: Health Canada Drug Id Number
    organization: Health Canada,Health Canada
    preferred_prefix: hc-DIN
    prefix: 2.16.840.1.113883.5.1105
    status: Complete
  homepage: https://www.canada.ca/en/health-canada/services/drugs-health-products/drug-products/fact-sheets/drug-identification-number.html
  mappings:
    hl7: 2.16.840.1.113883.5.1105
  name: Health Canada Drug Identification Number
  pattern: ^\d{8}$
  prefix: hc.din
  references:
  - http://www.hc-sc.gc.ca/dhp-mps/prodpharma/databasdon/index-eng.php
hc.npn:
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: The Licensed Natural Health Products Database contains information
    about natural health products that have been issued a product licence by Health
    Canada.
  example: '18125'
  hl7:
    description: 'Natural Product Number (NPN) is an eight digit numerical code assigned
      to each natural health product approved to be marketed under the Natural Health
      Products Regulations. A Homeopathic Medicine Number (DIN-HM) is an eight digit
      numerical code assigned to each homeopathic medicine approved to be marketed
      under the Natural Health Products Regulations. More information can be found
      here: https://www.canada.ca/en/health-canada/services/drugs-health-products/natural-non-prescription/applications-submissions/product-licensing/licensed-natural-health-products-database.html'
    homepage: http://www.hc-sc.gc.ca/index-eng.php
    name: Health Canada Natural Product Number
    organization: Health Canada,Health Canada
    preferred_prefix: hc-NPN
    prefix: 2.16.840.1.113883.5.1107
    status: Complete
  homepage: http://webprod.hc-sc.gc.ca/nhpid-bdipsn/search-rechercheReq.do?lang=eng
  mappings:
    hl7: 2.16.840.1.113883.5.1107
  name: Health Canada Natural Product Number
  pattern: ^\d+$
  prefix: hc.npn
  references:
  - https://www.canada.ca/en/health-canada/services/drugs-health-products/natural-non-prescription/applications-submissions/product-licensing/licensed-natural-health-products-database.html
  uri_format: http://webprod.hc-sc.gc.ca/nhpid-bdipsn/ingredReq.do?id=$1
hc.trial:
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: Health Canada, through its Clinical Trials Database, is providing to
    the public a listing of specific information relating to phase I, II and III clinical
    trials in patients. The database is managed by Health Canada and provides a source
    of information about Canadian clinical trials involving human pharmaceutical and
    biological drugs. [from website]
  example: '239287'
  homepage: https://health-products.canada.ca/ctdb-bdec
  name: Health Canada Clinical Trials Database
  pattern: ^\d+$
  prefix: hc.trial
  uri_format: https://health-products.canada.ca/ctdb-bdec/brand/?submissionNo=$1
hcao:
  homepage: https://www.humancellatlas.org
  mappings:
    ols: hcao
  no_own_terms: true
  ols:
    description: Application ontology for human cell types, anatomy and development
      stages for the Human Cell Atlas.
    download_owl: https://raw.githubusercontent.com/ebi-ait/ontology/master/hcao.owl
    name: Human Cell Atlas Ontology
    prefix: hcao
    uri_format: http://ontology.data.humancellatlas.org/ontologies/HCA_$1
    version.iri: http://ontology.data.humancellatlas.org/ontologies/hcao/releases/2023-05-16/hcao.owl
  prefix: hcao
hco:
  mappings:
    miriam: hco
  miriam:
    deprecated: false
    description: The Human Chromosome Ontology (HCO) provides simple and stable URIs
      for human reference genome versions to semantically identify human chromosomes.
    homepage: https://dbcls.rois.ac.jp/
    id: '00001040'
    name: Human Chromosome Ontology
    namespaceEmbeddedInLui: false
    pattern: ^.+$
    prefix: hco
    sampleId: MT
    uri_format: http://biohackathon.org/resource/hco#$1
  prefix: hco
hcpcs:
  aberowl:
    description: Healthcare Common Procedure Coding System
    homepage: http://cms.hhs.gov
    name: Healthcare Common Procedure Coding System
    prefix: HCPCS
    version: 2016AB
  biolink:
    is_identifiers: false
    is_obo: false
    prefix: HCPCS
    uri_format: http://purl.bioontology.org/ontology/HCPCS/$1
  bioportal:
    contact:
      email: Cynthia.Hake@cms.hhs.gov
      name: Cynthia Hake
    description: Healthcare Common Procedure Coding System
    homepage: http://www.cms.gov/Medicare/Coding/MedHCPCSGenInfo/index.html
    name: Healthcare Common Procedure Coding System
    prefix: HCPCS
    publications:
    - http://cms.hhs.gov
    version: HCPCS2024
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: HCPCS is a collection of standardized codes that represent medical
    procedures, supplies, products and services. The codes are used to facilitate
    the processing of health insurance claims by Medicare and other insurers.
  example: G8944
  fairsharing:
    abbreviation: HCPCS
    description: Each year, in the United States, health care insurers process over
      5 billion claims for payment. For Medicare and other health insurance programs
      to ensure that these claims are processed in an orderly and consistent manner,
      standardized coding systems are essential. The HCPCS is divided into two principal
      subsystems, referred to as level I and level II of the HCPCS. Level I of the
      HCPCS is comprised of CPT (Current Procedural Terminology), a numeric coding
      system maintained by the American Medical Association (AMA). Level II of the
      HCPCS is a standardized coding system that is used primarily to identify products,
      supplies, and services not included in the CPT codes, such as ambulance services
      and durable medical equipment, prosthetics, orthotics, and supplies (DMEPOS)
      when used outside a physician's office.
    homepage: https://www.cms.gov/medicare/coding/medhcpcsgeninfo/index.html
    name: Healthcare Common Procedure Coding System
    prefix: FAIRsharing.x81wz8
    subjects:
    - Biomedical Science
    - Business Administration
  homepage: https://www.cms.gov/Medicare/Coding/MedHCPCSGenInfo
  mappings:
    aberowl: HCPCS
    biolink: HCPCS
    bioportal: HCPCS
    fairsharing: FAIRsharing.x81wz8
  name: Healthcare Common Procedure Coding System
  prefix: hcpcs
  uri_format: http://purl.bioontology.org/ontology/HCPCS/$1
hcvdb:
  biocontext:
    prefix: HCVDB
  mappings:
    biocontext: HCVDB
    miriam: hcvdb
    n2t: hcvdb
    prefixcommons: hcv
  miriam:
    deprecated: false
    description: the European Hepatitis C Virus Database (euHCVdb, euhcvdb.lyon.inserm.fr),
      a collection of computer-annotated sequences based on reference genomes.mainly
      dedicated to HCV protein sequences, 3D structures and functional analyses.
    homepage: https://euhcvdb.lyon.inserm.fr/euHCVdb
    id: '00000207'
    name: HCVDB
    namespaceEmbeddedInLui: false
    pattern: ^M\d{5}$
    prefix: hcvdb
    sampleId: M58335
    uri_format: https://euhcvdb.lyon.inserm.fr/euHCVdb/do/displayHCVEntry?primaryAC=$1
  n2t:
    description: the European Hepatitis C Virus Database (euHCVdb, http://euhcvdb.ibcp.fr),
      a collection of computer-annotated sequences based on reference genomes.mainly
      dedicated to HCV protein sequences, 3D structures and functional analyses.
    example: M58335
    homepage: http://euhcvdb.ibcp.fr/euHCVdb/
    name: HCVDB at CNRS
    namespaceEmbeddedInLui: false
    pattern: ^M\d{5}$
    prefix: hcvdb
    uri_format: https://euhcvdb.ibcp.fr/euHCVdb/do/displayHCVEntry?primaryAC=$1
  name: Hepatitis C Virus Database Project
  prefix: hcvdb
  prefixcommons:
    description: The HCV database group strives to present HCV-associated, hand-annotated
      genetic data in a userfriendly way, by providing access to the central database
      via web-accessible search interfaces and supplying a number of analysis tools.
    example: '71867'
    homepage: http://hcv.lanl.gov/
    keywords:
    - gene
    name: Hepatitis C Virus (HCV) Database Project
    pattern: ^\d+$
    prefix: hcv
    synonyms:
    - hcv_database
    uri_format: http://hcv.lanl.gov/components/sequence/HCV/asearch/query_one.comp?se_id=$1
hdl:
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: Welcome to the web site of the Handle.Net Registry (HNR), run by Corporation
    for National Research Initiatives (CNRI). CNRI is a Multi-Primary Administrator
    (MPA) of the Global Handle Registry (GHR), authorized by the DONA Foundation to
    allot prefixes to users of the Handle System. The DONA Foundation is a non-profit
    organization based in Geneva that has taken over responsibility for the evolution
    of CNRI's Digital Object (DO) Architecture including outreach around the world.
    One of the Foundation's responsibilities is to administer and maintain the overall
    operation of the GHR, a task that was previously performed by CNRI. (from website)
  example: 2381/12775
  example_extras:
  - 391/00-0000-0000-0009-3C7E-F
  fairsharing:
    abbreviation: hdl
    description: The Handle System is the Corporation for National Research Initiatives's
      proprietary registry assigning persistent identifiers, or handles, to information
      resources, and for resolving "those handles into the information necessary to
      locate, access, and otherwise make use of the resources". As with handles used
      elsewhere in computing, Handle System handles are opaque, and encode no information
      about the underlying resource, being bound only to metadata regarding the resource.
      Consequently, the handles are not rendered invalid by changes to the metadata.
    domains:
    - centrally registered identifier
    homepage: http://handle.net
    name: Handle
    prefix: FAIRsharing.0b7e54
    subjects:
    - Subject Agnostic
  homepage: https://www.handle.net/
  mappings:
    fairsharing: FAIRsharing.0b7e54
  name: Handle
  pattern: ^\d+/.+$
  prefix: hdl
  synonyms:
  - handle
  uri_format: http://hdl.handle.net/$1
hdr:
  biocontext:
    prefix: HDR
  mappings:
    biocontext: HDR
    miriam: hdr
    n2t: hdr
    pathguide: '307'
    prefixcommons: hdr
  miriam:
    deprecated: true
    description: The Homeodomain Resource is a curated collection of sequence, structure,
      interaction, genomic and functional information on the homeodomain family. It
      contains sets of curated homeodomain sequences from fully sequenced genomes,
      including experimentally derived homeodomain structures, homeodomain protein-protein
      interactions, homeodomain DNA-binding sites and homeodomain proteins implicated
      in human genetic disorders.
    homepage: http://research.nhgri.nih.gov/apps/homeodomain/web/
    id: 00000497
    name: Homeodomain Research
    namespaceEmbeddedInLui: false
    pattern: ^\d+$
    prefix: hdr
    sampleId: '63'
    uri_format: http://research.nhgri.nih.gov/apps/homeodomain/web/index.cgi?mode=view&amp;view=proteins&amp;id=$1
  n2t:
    description: The Homeodomain Resource is a curated collection of sequence, structure,
      interaction, genomic and functional information on the homeodomain family. It
      contains sets of curated homeodomain sequences from fully sequenced genomes,
      including experimentally derived homeodomain structures, homeodomain protein-protein
      interactions, homeodomain DNA-binding sites and homeodomain proteins implicated
      in human genetic disorders.
    example: '63'
    homepage: http://research.nhgri.nih.gov/apps/homeodomain/web/
    name: Homeodomain Research at National Human Genome Research Institute (NIH)
    namespaceEmbeddedInLui: false
    pattern: ^\d+$
    prefix: hdr
    uri_format: http://research.nhgri.nih.gov/apps/homeodomain/web/index.cgi?mode=view&amp;view=proteins&amp;id=$1
  pathguide:
    abbreviation: HDR
    homepage: http://research.nhgri.nih.gov/homeodomain/
    name: Homeodomain Resource Database
    prefix: '307'
  prefix: hdr
  prefixcommons:
    description: The Homeodomain Resource is a curated collection of sequence, structure,
      interaction, genomic, and functional information on the homeodomain family.
      A description of each of the major sections of the database can be found below,
      and users can navigate through the site using the links found in the menu that
      appears on the left-hand side of every page within the site.
    example: '5978'
    homepage: http://research.nhgri.nih.gov/homeodomain/
    keywords:
    - genome
    name: Homeodomain Resource Database
    pattern: ^\d+$
    prefix: hdr
    synonyms:
    - homeodb
    uri_format: http://research.nhgri.nih.gov/homeodomain/?mode=view&view=proteins&id=$1
hemonc:
  comment: It is unclear if identifiers can be resolved on the website but a spreadsheet
    of the terminology is available via the NCI at https://evs.nci.nih.gov/ftp1/HemOnc/HemOnc_Terminology.xls
  contributor:
    email: b.gyori@northeastern.edu
    github: bgyori
    name: Benjamin M. Gyori
    orcid: 0000-0001-9439-5346
  description: HemOnc.org is the largest freely available medical wiki of interventions,
    regimens, and general information relevant to the fields of hematology and oncology.
  example: '15543'
  github_request_issue: 1149
  homepage: https://hemonc.org/
  name: HemOnc Terminology
  pattern: ^\d+$
  prefix: hemonc
  publications:
  - doi: 10.1016/j.jbi.2019.103239
    pmc: PMC6697579
    pubmed: '31238109'
    title: 'HemOnc: A new standard vocabulary for chemotherapy regimen representation
      in the OMOP common data model'
    year: 2019
  reviewer:
    email: null
    github: callahantiff
    name: Tiffany J. Callahan
    orcid: 0000-0002-8169-9049
hepro:
  contact:
    email: paul.fabry@usherbrooke.ca
    github: pfabry
    name: Paul Fabry
    orcid: 0000-0002-3336-2476
  contributor:
    email: paul.fabry@usherbrooke.ca
    github: pfabry
    name: Paul Fabry
    orcid: 0000-0002-3336-2476
  description: HEPRO is an ontology of informational entities and processes related
    to health procedures and health activities.
  download_owl: https://github.com/OpenLHS/HEPRO/raw/main/HEPRO.owl
  example: '0000001'
  github_request_issue: 810
  homepage: https://openlhs.github.io/HEPRO/
  license: CC-BY-4.0
  name: Health Procedure Ontology
  owners:
  - name: Université de Sherbrooke
    partnered: false
    ror: 00kybxq39
    wikidata: null
  pattern: ^\d{7}$
  preferred_prefix: HEPRO
  prefix: hepro
  repository: https://github.com/OpenLHS/HEPRO
  reviewer:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  uri_format: http://purl.obolibrary.org/obo/HEPRO_$1
hesa:
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: An identifier for institutions in the United Kingdom, used in GRID
    and ROR.
  example: '0154'
  homepage: https://www.hesa.ac.uk
  keywords:
  - bibliometrics
  - institution
  name: UK Higher Education Statistics Agency
  pattern: ^\d+$
  prefix: hesa
hgmd:
  biocontext:
    prefix: HGMD
    uri_format: http://www.hgmd.cf.ac.uk/ac/gene.php?gene=$1
  edam:
    description: Identifier of a HGMD database entry.
    name: HGMD
    obsolete: false
    prefix: '3265'
  integbio:
    alt_name: The Human Gene Mutation Database
    description: HGMD is a integrated database of germ-line mutations which are underlying
      or associated with human inherited disease in nuclear genes. This database contains
      all germ-line disease-causing mutations and disease-associated/functional polymorphisms
      reported in the literature. Furthermore, it includes the data about single base-pair
      substitutions in coding (e.g. missense and nonsense), regulatory and splicing-relevant
      regions of human nuclear genes, micro-deletions and micro-insertions, indels,
      repeat expansions, as well as gross gene lesions (deletions, insertions and
      duplications) and complex gene rearrangements. These data are provided in a
      readily accessible format to all interested parties, whether they are from an
      academic, clinical or commercial background.
    homepage: https://www.hgmd.cf.ac.uk
    information_keywords:
    - Sequence
    maintainer: Institute of Medical Genetics in Cardiff
    name: HGMD
    prefix: nbdc00097
    status: Active
    target_keywords:
    - Genome/Gene
    - cDNA/EST
    - Health/Disease
  mappings:
    biocontext: HGMD
    edam: '3265'
    integbio: nbdc00097
    miriam: hgmd
    n2t: hgmd
  miriam:
    deprecated: false
    description: The Human Gene Mutation Database (HGMD) collates data on germ-line
      mutations in nuclear genes associated with human inherited disease. It includes
      information on single base-pair substitutions in coding, regulatory and splicing-relevant
      regions; micro-deletions and micro-insertions; indels; triplet repeat expansions
      as well as gross deletions; insertions; duplications; and complex rearrangements.
      Each mutation entry is unique, and includes cDNA reference sequences for most
      genes, splice junction sequences, disease-associated and functional polymorphisms,
      as well as links to data present in publicly available online locus-specific
      mutation databases.
    homepage: http://www.hgmd.cf.ac.uk/ac/index.php
    id: 00000392
    name: HGMD
    namespaceEmbeddedInLui: false
    pattern: ^[A-Z_0-9]+$
    prefix: hgmd
    sampleId: CALM1
    uri_format: http://www.hgmd.cf.ac.uk/ac/gene.php?gene=$1
  n2t:
    description: The Human Gene Mutation Database (HGMD) collates data on germ-line
      mutations in nuclear genes associated with human inherited disease. It includes
      information on single base-pair substitutions in coding, regulatory and splicing-relevant
      regions; micro-deletions and micro-insertions; indels; triplet repeat expansions
      as well as gross deletions; insertions; duplications; and complex rearrangements.
      Each mutation entry is unique, and includes cDNA reference sequences for most
      genes, splice junction sequences, disease-associated and functional polymorphisms,
      as well as links to data present in publicly available online locus-specific
      mutation databases.
    example: CALM1
    homepage: http://www.hgmd.cf.ac.uk/ac/index.php
    name: HGMD at Cardiff University
    namespaceEmbeddedInLui: false
    pattern: ^[A-Z_0-9]+$
    prefix: hgmd
    uri_format: http://www.hgmd.cf.ac.uk/ac/gene.php?gene=$1
  name: Human Gene Mutation Database
  prefix: hgmd
hgnc:
  aberowl:
    description: Human Genome Organisation (HUGO) Gene Nomenclature Committee at the
      European Bioinformatics Institute approves a gene name and symbol (short-form
      abbreviation) for each known human gene. All approved symbols are stored in
      the HGNC database.
    download_owl: http://aber-owl.net/media/ontologies/HGNC/7/hgnc.owl
    homepage: http://www.genenames.org/
    name: HUGO Gene Nomenclature
    prefix: HGNC
    version: dev
  bartoc:
    abbreviation: HGNC
    description: The HGNC is responsible for approving unique symbols and names for
      human loci, including protein coding genes, ncRNA genes and pseudogenes, to
      allow unambiguous scientific communication.
    homepage: https://www.genenames.org/
    license: CC0-1.0
    name: HUGO Gene Nomenclature Committee
    prefix: '20688'
  biocontext:
    prefix: HGNC
    uri_format: http://www.genenames.org/cgi-bin/gene_symbol_report?hgnc_id=$1
  bioportal:
    contact:
      email: hgnc@genenames.org
      name: Elspeth Bruford
    description: Human Genome Organisation (HUGO) Gene Nomenclature Committee at the
      European Bioinformatics Institute approves a gene name and symbol (short-form
      abbreviation) for each known human gene. All approved symbols are stored in
      the HGNC database.
    homepage: http://www.genenames.org/
    name: HUGO Gene Nomenclature
    prefix: HGNC
    publications:
    - http://www.genenames.org/
    version: dev
  cellosaurus:
    category: Organism-specific databases
    homepage: https://www.genenames.org
    name: Human Gene Nomenclature Committee Database
    prefix: HGNC
    uri_format: https://www.genenames.org/data/gene-symbol-report/#!/hgnc_id/$1
  contact:
    email: elspeth@genenames.org
    github: null
    name: Elspeth Bruford
    orcid: 0000-0002-8380-5247
  contact_extras:
  - email: null
    github: sartweedie
    name: Susan Tweedie
    orcid: 0000-0003-1818-8243
  contact_group_email: hgnc@genenames.org
  domain: gene
  edam:
    description: Identifier for a gene approved by the HUGO Gene Nomenclature Committee.
    name: Gene ID (HGNC)
    obsolete: false
    prefix: '2298'
  example: '16793'
  fairsharing:
    abbreviation: HGNC
    description: The HGNC approves both a short-form abbreviation known as a gene
      symbol, and also a longer and more descriptive name. Each symbol is unique and
      the committee ensures that each gene is only given one approved gene symbol.
      This allows for clear and unambiguous reference to genes in scientific communications,
      and facilitates electronic data retrieval from databases and publications.
    domains:
    - Gene name
    - protein
    - pseudogene
    - ncRNA
    homepage: https://www.genenames.org/
    name: HGNC Gene Symbols, Gene Names and IDs
    prefix: FAIRsharing.amcv1e
    publications:
    - doi: 10.1159/000131404
      pubmed: '295268'
      title: International system for human gene nomenclature (1979) ISGN (1979)
      year: 1979
    - doi: 10.1093/nar/gky930
      pubmed: '30304474'
      title: 'Genenames.org: the HGNC and VGNC resources in 2019'
      year: 2018
    subjects:
    - Life Science
  go:
    homepage: http://www.genenames.org/
    name: HUGO Gene Nomenclature Committee
    prefix: HGNC
    uri_format: https://www.genenames.org/data/gene-symbol-report/#!/hgnc_id/HGNC:$1
  hl7:
    description: HUGO Gene Nomenclature Committee (HGNC) is committee jointly funded
      by the US National Human Genome Research Institute and the Wellcome Trust (UK).  It
      operates under the auspices of HUGO, with key policy advice from an International
      Advisory Committee, and is responsible for approving gene names and symbols.  All
      approved symbols are stored in the HGNC database.  Each symbol is unique and
      each gene is only given one approved gene symbol.  More than 28,000 human gene
      symbols and names have been approved so far.  The vast majority of these is
      for protein-coding genes, but also includes symbols for peudogenes, non-coding
      RNAs, phenotypes and genomic features.  HGNC gene symbols can be used with the
      HL7 coded data type.  For example, in the HL7 messages specified according to
      the HL7 V2 Clinical Genomics Fully LOINC-Qualified Genetic Variation Model Implementation
      Guide, HGNC gene symbols can be used to as the observation values for gene identifiers.  For
      example, OBX|1|CWE|48018-6^Gene identifier^||BRCA1^HGNC|Versioning Information:The
      version of the HGNC database is reported using the last updated date and timestamp.  The
      last updated date and timestamp is posted on the main HGNC Search screen in
      the format like "Monday March 30 23:00:56 2009".HGNC is updated daily.HGNC is
      a free database for the public.
    homepage: http://www.genenames.org/
    name: HUGO Gene Nomenclature
    organization: HUGO Gene Nomenclature Committee,HUGO Gene Nomenclature Committee
    preferred_prefix: hgnc
    prefix: 2.16.840.1.113883.6.281
    status: Complete
  homepage: http://www.genenames.org
  license: CC0-1.0
  logo: https://www.genenames.org/img/hgnc/logo/hgnc-logo-dark-bckgrnd-large.svg
  mappings:
    aberowl: HGNC
    bartoc: '20688'
    biocontext: HGNC
    bioportal: HGNC
    cellosaurus: HGNC
    edam: '2298'
    fairsharing: FAIRsharing.amcv1e
    go: HGNC
    hl7: 2.16.840.1.113883.6.281
    miriam: hgnc
    n2t: hgnc
    ncbi: HGNC
    ols: hgnc
    prefixcommons: hgnc
    togoid: Hgnc
    uniprot: DB-0042
    wikidata: P354
  miriam:
    deprecated: false
    description: The HGNC (HUGO Gene Nomenclature Committee) provides an approved
      gene name and symbol (short-form abbreviation) for each known human gene.  All
      approved symbols are stored in the HGNC database, and each symbol is unique.
      HGNC identifiers refer to records in the HGNC symbol database.
    homepage: https://www.genenames.org
    id: 00000080
    name: HGNC
    namespaceEmbeddedInLui: false
    pattern: ^((HGNC|hgnc):)?\d{1,5}$
    prefix: hgnc
    sampleId: '2674'
    uri_format: https://www.genenames.org/data/gene-symbol-report/#!/hgnc_id/$1
  n2t:
    description: The HGNC (HUGO Gene Nomenclature Committee) provides an approved
      gene name and symbol (short-form abbreviation) for each known human gene.  All
      approved symbols are stored in the HGNC database, and each symbol is unique.
      HGNC identifiers refer to records in the HGNC symbol database.
    example: '2674'
    homepage: https://www.genenames.org
    name: HUGO Genome Nomenclature Committee
    namespaceEmbeddedInLui: false
    pattern: ^((HGNC|hgnc):)?\d{1,5}$
    prefix: hgnc
    uri_format: https://www.genenames.org/data/gene-symbol-report/#!/hgnc_id/$1
  name: HUGO Gene Nomenclature Committee
  ncbi:
    example: HGNC:2041
    homepage: http://www.genenames.org/cgi-bin/search
    name: Human Gene Nomenclature Database
    prefix: HGNC
  ols:
    contact: hgnc@genenames.org
    description: The HGNC (HUGO Gene Nomenclature Committee) provides an approved
      gene name and symbol (short-form abbreviation) for each known human gene.  All
      approved symbols are stored in the HGNC database, and each symbol is unique.
      HGNC identifiers refer to records in the HGNC symbol database.
    homepage: http://www.genenames.org
    name: HUGO Gene Nomenclature Committee
    prefix: hgnc
    uri_format: https://www.genenames.org/data/gene-symbol-report/#!/hgnc_id/$1
    version.iri: https://w3id.org/biopragmatics/resources/hgnc/2025-10-07/hgnc.ofn
  pattern: ^\d{1,5}$
  prefix: hgnc
  prefixcommons:
    bioportal: '1528'
    description: The HGNC gives unique and meaningful names to every human gene. For
      each known human gene we approve a gene name and symbol (short-form abbreviation).  All
      approved symbols are stored in the HGNC database.
    example: '7'
    homepage: http://www.genenames.org/
    keywords:
    - classification
    - gene
    name: HUGO Gene Nomenclature Committee
    pattern: ^\d+$
    prefix: hgnc
    synonyms:
    - hugo
    uri_format: http://www.genenames.org/data/hgnc_data.php?hgnc_id=$1
  providers:
  - code: indra
    description: A large scale database of biomedical statements.
    example: null
    first_party: null
    homepage: https://db.indra.bio
    name: INDRA Database
    publications:
    - doi: 10.15252/msb.202211325
      pmc: PMC10167483
      pubmed: '36938926'
      title: Automated assembly of molecular mechanisms at scale from text mining
        and curated databases
      year: 2023
    - doi: 10.15252/msb.20177651
      pmc: PMC5731347
      pubmed: '29175850'
      title: From word models to executable models of signaling networks using automated
        assembly
      year: 2017
    status: null
    uri_format: https://db.indra.bio/statements/from_agents?&format=html&agent0=$1@HGNC
  - code: gencc
    description: The GenCC DB provides information pertaining to the validity of gene-disease
      relationships, with a current focus on Mendelian diseases. Curated gene-disease
      relationships are submitted by GenCC member organizations. The GenCC comprises
      organizations that currently provide online resources (e.g. ClinGen, DECIPHER,
      Genomics England PanelApp, OMIM, Orphanet, PanelApp Australia, TGMI’s G2P),
      as well as diagnostic laboratories that have committed to sharing their internal
      curated gene-level knowledge (e.g. Ambry, Illumina, Invitae, Myriad Women’s
      Health, Mass General Brigham Laboratory for Molecular Medicine).
    example: null
    first_party: null
    homepage: https://thegencc.org
    name: The Gene Curation Coalition
    publications: null
    status: null
    uri_format: https://search.thegencc.org/genes/HGNC:$1
  publications:
  - doi: 10.1093/nar/gkaa980
    pmc: PMC7779007
    pubmed: '33152070'
    title: 'Genenames.org: the HGNC and VGNC resources in 2021'
    year: 2021
  - doi: 10.1093/nar/gky930
    pmc: PMC6324057
    pubmed: '30304474'
    title: 'Genenames.org: the HGNC and VGNC resources in 2019'
    year: 2019
  - doi: 10.1159/000131404
    pmc: null
    pubmed: '295268'
    title: International system for human gene nomenclature (1979) ISGN (1979)
    year: 1979
  - doi: 10.1159/000131404
    pmc: null
    pubmed: '295268'
    title: International system for human gene nomenclature (1979) ISGN (1979)
    year: 1979
  - doi: 10.1093/nar/gky930
    pmc: null
    pubmed: '30304474'
    title: 'Genenames.org: the HGNC and VGNC resources in 2019'
    year: 2018
  - doi: 10.1093/nar/gkaa980
    pmc: null
    pubmed: '33152070'
    title: null
    year: null
  - doi: 10.15252/msb.202211325
    pmc: PMC10167483
    pubmed: '36938926'
    title: Automated assembly of molecular mechanisms at scale from text mining and
      curated databases
    year: 2023
  - doi: 10.15252/msb.20177651
    pmc: PMC5731347
    pubmed: '29175850'
    title: From word models to executable models of signaling networks using automated
      assembly
    year: 2017
  - doi: 10.1159/000131404
    pmc: null
    pubmed: '295268'
    title: International system for human gene nomenclature (1979) ISGN (1979)
    year: 1979
  - doi: 10.1093/nar/gky930
    pmc: null
    pubmed: '30304474'
    title: 'Genenames.org: the HGNC and VGNC resources in 2019'
    year: 2018
  - doi: 10.1093/nar/gkaa980
    pmc: null
    pubmed: '33152070'
    title: null
    year: null
  - doi: 10.15252/msb.202211325
    pmc: PMC10167483
    pubmed: '36938926'
    title: Automated assembly of molecular mechanisms at scale from text mining and
      curated databases
    year: 2023
  - doi: 10.15252/msb.20177651
    pmc: PMC5731347
    pubmed: '29175850'
    title: From word models to executable models of signaling networks using automated
      assembly
    year: 2017
  togoid:
    catalog: nbdc01774
    examples:
    - '26199'
    - '38937'
    - '14027'
    - '21498'
    - '18185'
    - '1314'
    - '25960'
    - '2206'
    - '22224'
    - '19741'
    keywords:
    - Gene
    name: HGNC
    pattern: ^(?:(?:HGNC|hgnc):)?(?\d{1,5})$
    prefix: Hgnc
    uri_format: http://identifiers.org/hgnc/$1
  uniprot:
    abbreviation: HGNC
    category: Organism-specific databases
    homepage: https://www.genenames.org/
    name: Human Gene Nomenclature Database
    prefix: DB-0042
    publications:
    - doi: 10.1093/nar/gkaa980
      pubmed: '33152070'
    uri_format: https://www.genenames.org/data/gene-symbol-report/#!/hgnc_id/$1
  wikidata:
    description: a unique ID provided by the HGNC for each gene with an approved symbol.
      HGNC IDs remain stable even if a name or symbol changes
    example:
    - '108'
    - '9957'
    homepage: http://www.genenames.org/
    miriam: hgnc
    name: HGNC ID
    pattern: ^[1-9]\d{0,4}$
    prefix: P354
    uri_format: https://www.genenames.org/data/gene-symbol-report/#!/hgnc_id/HGNC:$1
hgnc.genefamily:
  biocontext:
    prefix: HGNC.GENEFAMILY
  contact:
    email: elspeth@genenames.org
    github: null
    name: Elspeth Bruford
    orcid: 0000-0002-8380-5247
  domain: gene family
  example: '2029'
  has_canonical: hgnc.genegroup
  homepage: http://www.genenames.org
  keywords:
  - gene
  - gene family
  - gene group
  license: CC0-1.0
  logo: https://www.genenames.org/img/hgnc/logo/hgnc-logo-dark-bckgrnd-large.svg
  mappings:
    biocontext: HGNC.GENEFAMILY
    miriam: hgnc.genefamily
    n2t: hgnc.genefamily
  miriam:
    deprecated: false
    description: The HGNC (HUGO Gene Nomenclature Committee) provides an approved
      gene name and symbol (short-form abbreviation) for each known human gene. All
      approved symbols are stored in the HGNC database, and each symbol is unique.
      In addition, HGNC also provides a unique numerical ID to identify gene families,
      providing a display of curated hierarchical relationships between families.
    homepage: https://www.genenames.org/
    id: '00000573'
    name: HGNC gene family
    namespaceEmbeddedInLui: false
    pattern: ^\d+$
    prefix: hgnc.genefamily
    sampleId: '141'
    uri_format: https://www.genenames.org/cgi-bin/genefamilies/set/$1
  n2t:
    description: The HGNC (HUGO Gene Nomenclature Committee) provides an approved
      gene name and symbol (short-form abbreviation) for each known human gene. All
      approved symbols are stored in the HGNC database, and each symbol is unique.
      In addition, HGNC also provides a unique numerical ID to identify gene families,
      providing a display of curated hierarchical relationships between families.
    example: '141'
    homepage: https://www.genenames.org/
    name: HGNC gene family at HUGO Genome Nomenclature Committee
    namespaceEmbeddedInLui: false
    pattern: ^\d+$
    prefix: hgnc.genefamily
    uri_format: https://www.genenames.org/cgi-bin/genefamilies/set/$1
  part_of_database: hgnc
  prefix: hgnc.genefamily
  synonyms:
  - GFAM
  - HGNC_GROUP
  - hgnc.family
hgnc.genegroup:
  contact:
    email: elspeth@genenames.org
    github: null
    name: Elspeth Bruford
    orcid: 0000-0002-8380-5247
  domain: gene family
  keywords:
  - gene
  - gene family
  - gene group
  license: CC0-1.0
  logo: https://www.genenames.org/img/hgnc/logo/hgnc-logo-dark-bckgrnd-large.svg
  mappings:
    miriam: hgnc.genegroup
    ols: hgnc.genegroup
  miriam:
    deprecated: false
    description: The HGNC (HUGO Gene Nomenclature Committee) provides an approved
      gene name and symbol (short-form abbreviation) for each known human gene. All
      approved symbols are stored in the HGNC database, and each symbol is unique.
      In addition, HGNC also provides a unique numerical ID to identify gene families,
      providing a display of curated hierarchical relationships between families.
    homepage: https://www.genenames.org
    id: 00000709
    name: HGNC Gene Group
    namespaceEmbeddedInLui: false
    pattern: ^\d+$
    prefix: hgnc.genegroup
    sampleId: '141'
    uri_format: https://www.genenames.org/data/genegroup/#!/group/$1
  ols:
    contact: elspeth@genenames.org
    description: The HGNC (HUGO Gene Nomenclature Committee) provides an approved
      gene name and symbol (short-form abbreviation) for each known human gene. All
      approved symbols are stored in the HGNC database, and each symbol is unique.
      In addition, HGNC also provides a unique numerical ID to identify gene families,
      providing a display of curated hierarchical relationships between families.
      Licensed under CC0-1.0.
    download_owl: https://w3id.org/biopragmatics/resources/hgnc.genegroup/hgnc.genegroup.owl
    homepage: https://www.genenames.org
    name: HGNC Gene Group
    prefix: hgnc.genegroup
    uri_format: https://www.genenames.org/data/genegroup/#!/group/$1
    version.iri: https://w3id.org/biopragmatics/resources/hgnc.genegroup/2025-10-07/hgnc.genegroup.ofn
  part_of_database: hgnc
  prefix: hgnc.genegroup
hgnc.symbol:
  biocontext:
    prefix: HGNC.SYMBOL
  license: CC0-1.0
  logo: https://www.genenames.org/img/hgnc/logo/hgnc-logo-dark-bckgrnd-large.svg
  mappings:
    biocontext: HGNC.SYMBOL
    miriam: hgnc.symbol
    n2t: hgnc.symbol
    togoid: HgncSymbol
    wikidata: P353
  miriam:
    deprecated: false
    description: The HGNC (HUGO Gene Nomenclature Committee) provides an approved
      gene name and symbol (short-form abbreviation) for each known human gene. All
      approved symbols are stored in the HGNC database, and each symbol is unique.
      This collection refers to records using the HGNC symbol.
    homepage: https://www.genenames.org/
    id: '00000362'
    name: HGNC Symbol
    namespaceEmbeddedInLui: false
    pattern: ^[A-Za-z-0-9_]+(\@)?$
    prefix: hgnc.symbol
    sampleId: DAPK1
    uri_format: https://www.genenames.org/data/gene-symbol-report/#!/symbol/$1
  n2t:
    description: The HGNC (HUGO Gene Nomenclature Committee) provides an approved
      gene name and symbol (short-form abbreviation) for each known human gene. All
      approved symbols are stored in the HGNC database, and each symbol is unique.
      This collection refers to records using the HGNC symbol.
    example: DAPK1
    homepage: https://www.genenames.org/
    name: HGNC Symbol at HUGO Genome Nomenclature Committee
    namespaceEmbeddedInLui: false
    pattern: ^[A-Za-z-0-9_]+(\@)?$
    prefix: hgnc.symbol
    uri_format: https://www.genenames.org/cgi-bin/gene_symbol_report?match=$1
  part_of_database: hgnc
  prefix: hgnc.symbol
  providers:
  - code: cbgda
    description: A database of key host genes involved in the pathogenesis of different
      diseases identified through genome-wide CRISPR screens
    example: null
    first_party: null
    homepage: http://cbgda.zhounan.org/main
    name: CRISPR Based Gene-Disease Associations
    publications:
    - doi: 10.1093/database/baae077
      pmc: PMC11363955
      pubmed: '39213392'
      title: 'CBGDA: a manually curated resource for gene-disease associations based
        on genome-wide CRISPR'
      year: 2024
    status: null
    uri_format: http://cbgda.zhounan.org/geneinfo?gene=$1
  - code: resolute
    description: RESOLUTE is a knowledge base on human SLCs (Solute carrier transporters).
    example: null
    first_party: null
    homepage: https://re-solute.eu
    name: RESOLUTE
    publications:
    - doi: 10.1038/s44320-025-00108-2
      pmc: PMC12130315
      pubmed: '40355757'
      title: Data- and knowledge-derived functional landscape of human solute carriers
      year: 2025
    status: null
    uri_format: https://re-solute.eu/knowledgebase/gene/$1
  - code: g2p
    description: A resource for linking genetic screening outputs to protein sequences
      and structures
    example: null
    first_party: null
    homepage: https://g2p.broadinstitute.org/
    name: Genomics 2 Proteins Portal
    publications:
    - doi: 10.1038/s41592-024-02409-0
      pmc: PMC11466821
      pubmed: '39294369'
      title: 'Genomics 2 Proteins portal: a resource and discovery tool for linking
        genetic screening outputs to protein sequences and structures'
      year: 2024
    status: null
    uri_format: https://g2p.broadinstitute.org/gene/$1
  - code: depmap
    description: DepMap summary of the given gene
    example: null
    first_party: null
    homepage: https://depmap.org
    name: DepMap Gene Summary
    publications: null
    status: null
    uri_format: https://depmap.org/portal/gene/$1
  - code: pathwaycommons
    description: Interactions between a given gene and other molecular entities
    example: null
    first_party: null
    homepage: https://www.pathwaycommons.org/
    name: Pathway Commons Gene Interations
    publications: null
    status: null
    uri_format: https://apps.pathwaycommons.org/interactions?source=$1
  - code: oncomx
    description: Mutation profiles for a gene
    example: null
    first_party: null
    homepage: https://oncomx.org
    name: OncoMX
    publications: null
    status: null
    uri_format: https://oncomx.org/searchview/?gene=$1
  - code: hubmap.biomarker
    description: The Biomarkers subsection of HuBMAP allows you to look up specific
      information about a gene.
    example: null
    first_party: null
    homepage: https://portal.hubmapconsortium.org/biomarkers
    name: Human BioMolecular Atlas Program Biomarkers
    publications: null
    status: null
    uri_format: https://portal.hubmapconsortium.org/genes/$1
  togoid:
    catalog: nbdc01774
    examples:
    - MBNL2
    - RGS20
    - LINC02011
    - IGHV1-14
    - SH3RF2
    - SPATA13
    - HNRNPCP10
    - LINC00334
    - TMEM241
    - RN7SL753P
    keywords:
    - Gene
    name: HGNC gene symbol
    pattern: ^(?[A-Z0-9_(orf)\-]+\@?)$
    prefix: HgncSymbol
    uri_format: http://identifiers.org/hgnc.symbol/$1
  wikidata:
    description: the official gene symbol approved by the HGNC, which is typically
      a short form of the gene name
    example:
    - ACHE
    - RELN
    homepage: http://www.genenames.org/
    miriam: hgnc.symbol
    name: HGNC gene symbol
    pattern: ^[A-Z][0-9A-Za-z]{0,13}@?(-[0-9A-Z][0-9A-Za-z]{0,6})*$
    prefix: P353
    uri_format: https://www.genenames.org/tools/search/#!/all?query=$1
hgvs:
  contact:
    email: reecehart@gmail.com
    github: reece
    name: Reece Hart
    orcid: 0000-0003-3463-0775
  contributor:
    email: miseming@sfu.ca
    github: miseminger
    name: Madeline Iseminger
    orcid: 0000-0002-0548-891X
  description: The HGVS Nomenclature is an internationally-recognized standard for
    the description of DNA, RNA and protein sequence variants. It is used to convey
    variants in clinical reports and to share variants in publications and databases.
    The HGVS Nomenclature is administered by the [HGVS Variant Nomenclature Committee
    (HVNC)](https://hgvs-nomenclature.org/stable/hvnc/) under the auspices of the
    [Human Genome Organization (HUGO)](https://hugo-int.org/).
  domain: variant
  example: NP_003997.1:p.Trp24Cys
  example_extras:
  - NG_012337.3(NM_003002.4):c.274G>T
  - NG_012337.3(NM_003002.4):r.(274g>u)
  - NC_000011.10:g.112088970del
  - NC_000011.10(NM_001276503.2):c.169+998del
  - GRCh38(chr11):g.112088970del
  github_request_issue: 1032
  hl7:
    description: HGVS nomenclatures are the guidelines for mutation nomenclature made
      by the Human Genome Variation Society. HGVS nomenclature can be used with the
      HL7 coded data type (code data type that accepts expression data, or a coded
      expression data type).  This coded data type should be able to distinguish expressions
      in HGVS nomenclature from coded concepts.  For example, in the HL7 messages
      specified according to the HL7 V2 Clinical Genomics Fully LOINC-Qualified Genetic
      Variation Model, HGVS nomenclature can be used to as the observation values
      for DNA sequence variations.  For example, OBX|1|CWE|48004-6^DNA Sequence Variation^LN||c.1129C>T^^HGVS|Versioning
      information:The HGVS nomenclature for the description of sequence variants was
      last modified Feb 20, 2008.The HGVS nomenclature for the description of protein
      sequence variants was last modified May 12, 2007.  The HGVS nomenclature for
      the description of DNA sequence variants was last modified June 15, 2007The
      HGVS nomenclature for the description of RNA sequence variants was last modified
      May 12, 2007HGVS nomenclatures can be used freely by the public.
    homepage: http://www.hgvs.org/
    organization: HUGO Gene Nomenclature Committee,HUGO Gene Nomenclature Committee
    preferred_prefix: hgvs
    prefix: 2.16.840.1.113883.6.282
    status: Complete
  homepage: https://hgvs-nomenclature.org/stable/background/simple/
  mappings:
    hl7: 2.16.840.1.113883.6.282
    wikidata: P3331
  name: Human Genome Variation Society Nomenclature
  prefix: hgvs
  providers:
  - code: mutalyzer
    description: ' The Mutalyzer tool suite is designed to be of help when working
      with HGVS sequence variant nomenclature descriptions.'
    example: null
    first_party: null
    homepage: https://mutalyzer.nl
    name: LUMC Mutalyzer 3
    publications: null
    status: null
    uri_format: https://mutalyzer.nl/api/description_to_model/$1
  publications:
  - doi: 10.1002/humu.22981
    pmc: null
    pubmed: '26931183'
    title: 'HGVS Recommendations for the Description of Sequence Variants: 2016 Update'
    year: 2016
  - doi: 10.1093/bioinformatics/btu630
    pmc: PMC4287946
    pubmed: '25273102'
    title: A Python package for parsing, validating, mapping and formatting sequence
      variants using HGVS nomenclature
    year: 2014
  references:
  - https://github.com/biopragmatics/bioregistry/issues/460
  repository: https://github.com/HGVSnomenclature/hgvs-nomenclature
  reviewer:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  wikidata:
    description: Sequence Variant Nomenclature from the Human Genome Variation Society
      (HGVS)
    homepage: https://civic.genome.wustl.edu/#/home
    name: HGVS nomenclature
    prefix: P3331
    uri_format: http://reg.clinicalgenome.org/allele?hgvs=$1
hinv.locus:
  biocontext:
    prefix: HINV.LOCUS
  mappings:
    biocontext: HINV.LOCUS
    miriam: hinv.locus
    n2t: hinv.locus
  miriam:
    deprecated: true
    description: H-Invitational Database (H-InvDB) is an integrated database of human
      genes and transcripts. It provides curated annotations of human genes and transcripts
      including gene structures, alternative splicing isoforms, non-coding functional
      RNAs, protein functions, functional domains, sub-cellular localizations, metabolic
      pathways, protein 3D structure, genetic polymorphisms (SNPs, indels and microsatellite
      repeats), relation with diseases, gene expression profiling, molecular evolutionary
      features, protein-protein interactions (PPIs) and gene families/groups. This
      datatype provides access to the 'Locus' view.
    homepage: http://h-invitational.jp/hinv/ahg-db/index.jsp
    id: '00000167'
    name: H-InvDb Locus
    namespaceEmbeddedInLui: false
    pattern: ^HIX\d{7}(\.\d+)?$
    prefix: hinv.locus
    sampleId: HIX0004394
    uri_format: http://h-invitational.jp/hinv/spsoup/locus_view?hix_id=$1
  n2t:
    description: H-Invitational Database (H-InvDB) is an integrated database of human
      genes and transcripts. It provides curated annotations of human genes and transcripts
      including gene structures, alternative splicing isoforms, non-coding functional
      RNAs, protein functions, functional domains, sub-cellular localizations, metabolic
      pathways, protein 3D structure, genetic polymorphisms (SNPs, indels and microsatellite
      repeats), relation with diseases, gene expression profiling, molecular evolutionary
      features, protein-protein interactions (PPIs) and gene families/groups. This
      datatype provides access to the 'Locus' view.
    example: HIX0004394
    homepage: http://h-invitational.jp/hinv/ahg-db/index.jsp
    name: H-Invitational Locus View at BIRC
    namespaceEmbeddedInLui: false
    pattern: ^HIX\d{7}(\.\d+)?$
    prefix: hinv.locus
    uri_format: http://h-invitational.jp/hinv/spsoup/locus_view?hix_id=$1
  prefix: hinv.locus
hinv.protein:
  biocontext:
    prefix: HINV.PROTEIN
  mappings:
    biocontext: HINV.PROTEIN
    miriam: hinv.protein
    n2t: hinv.protein
  miriam:
    deprecated: true
    description: H-Invitational Database (H-InvDB) is an integrated database of human
      genes and transcripts. It provides curated annotations of human genes and transcripts
      including gene structures, alternative splicing isoforms, non-coding functional
      RNAs, protein functions, functional domains, sub-cellular localizations, metabolic
      pathways, protein 3D structure, genetic polymorphisms (SNPs, indels and microsatellite
      repeats), relation with diseases, gene expression profiling, molecular evolutionary
      features, protein-protein interactions (PPIs) and gene families/groups. This
      datatype provides access to the 'Protein' view.
    homepage: http://h-invitational.jp/hinv/ahg-db/index.jsp
    id: 00000169
    name: H-InvDb Protein
    namespaceEmbeddedInLui: false
    pattern: ^HIP\d{9}(\.\d+)?$
    prefix: hinv.protein
    sampleId: HIP000030660
    uri_format: http://h-invitational.jp/hinv/protein/protein_view.cgi?hip_id=$1
  n2t:
    description: H-Invitational Database (H-InvDB) is an integrated database of human
      genes and transcripts. It provides curated annotations of human genes and transcripts
      including gene structures, alternative splicing isoforms, non-coding functional
      RNAs, protein functions, functional domains, sub-cellular localizations, metabolic
      pathways, protein 3D structure, genetic polymorphisms (SNPs, indels and microsatellite
      repeats), relation with diseases, gene expression profiling, molecular evolutionary
      features, protein-protein interactions (PPIs) and gene families/groups. This
      datatype provides access to the 'Protein' view.
    example: HIP000030660
    homepage: http://h-invitational.jp/hinv/ahg-db/index.jsp
    name: H-Invitational Protein View at BIRC
    namespaceEmbeddedInLui: false
    pattern: ^HIP\d{9}(\.\d+)?$
    prefix: hinv.protein
    uri_format: http://h-invitational.jp/hinv/protein/protein_view.cgi?hip_id=$1
  prefix: hinv.protein
hinv.transcript:
  biocontext:
    prefix: HINV.TRANSCRIPT
  mappings:
    biocontext: HINV.TRANSCRIPT
    miriam: hinv.transcript
    n2t: hinv.transcript
  miriam:
    deprecated: true
    description: H-Invitational Database (H-InvDB) is an integrated database of human
      genes and transcripts. It provides curated annotations of human genes and transcripts
      including gene structures, alternative splicing isoforms, non-coding functional
      RNAs, protein functions, functional domains, sub-cellular localizations, metabolic
      pathways, protein 3D structure, genetic polymorphisms (SNPs, indels and microsatellite
      repeats), relation with diseases, gene expression profiling, molecular evolutionary
      features, protein-protein interactions (PPIs) and gene families/groups. This
      datatype provides access to the 'Transcript' view.
    homepage: http://h-invitational.jp/hinv/ahg-db/index.jsp
    id: 00000168
    name: H-InvDb Transcript
    namespaceEmbeddedInLui: false
    pattern: ^HIT\d{9}(\.\d+)?$
    prefix: hinv.transcript
    sampleId: HIT000195363
    uri_format: http://h-invitational.jp/hinv/spsoup/transcript_view?hit_id=$1
  n2t:
    description: H-Invitational Database (H-InvDB) is an integrated database of human
      genes and transcripts. It provides curated annotations of human genes and transcripts
      including gene structures, alternative splicing isoforms, non-coding functional
      RNAs, protein functions, functional domains, sub-cellular localizations, metabolic
      pathways, protein 3D structure, genetic polymorphisms (SNPs, indels and microsatellite
      repeats), relation with diseases, gene expression profiling, molecular evolutionary
      features, protein-protein interactions (PPIs) and gene families/groups. This
      datatype provides access to the 'Transcript' view.
    example: HIT000195363
    homepage: http://h-invitational.jp/hinv/ahg-db/index.jsp
    name: H-Invitational Transcript View at BIRC
    namespaceEmbeddedInLui: false
    pattern: ^HIT\d{9}(\.\d+)?$
    prefix: hinv.transcript
    uri_format: http://h-invitational.jp/hinv/spsoup/transcript_view?hit_id=$1
  prefix: hinv.transcript
hipsci:
  cellosaurus:
    category: Cell line databases/resources
    homepage: https://www.hipsci.org
    name: Human Induced Pluripotent Stem Cells Initiative
    prefix: HipSci
    uri_format: https://www.hipsci.org/lines/#/lines/$1
  contributor_extras:
  - email: mjj@ebi.ac.uk
    github: mattjeffryes
    name: Matt Jeffryes
    orcid: 0000-0001-9868-6271
  example: HPSI0114i-bezi_1
  mappings:
    cellosaurus: HipSci
  prefix: hipsci
  uri_format: https://www.hipsci.org/#/lines/$1
hivreagentprogram:
  cellosaurus:
    category: Cell line collections (Providers)
    homepage: https://www.hivreagentprogram.org/
    name: NIH HIV Reagent Program
    prefix: HIVReagentProgram
    uri_format: https://www.hivreagentprogram.org/Catalog/HRPCellLines/$1.aspx
  example: ARP-1513
  mappings:
    cellosaurus: HIVReagentProgram
  prefix: hivreagentprogram
hl7.v2codesystem:
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: A registry of code systems (each are small vocabularies themselves)
    used by HL7 international, related to FHIR.
  example: 0778
  homepage: https://terminology.hl7.org/codesystems-v2.html
  name: HL7 V2 Code System
  pattern: ^\d+$
  prefix: hl7.v2codesystem
  uri_format: http://terminology.hl7.org/CodeSystem/v2-$1
hl7.v3codesystem:
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: A registry of code systems (each are small vocabularies themselves)
    used by HL7 international, related to FHIR.
  example: AcknowledgementCondition
  homepage: https://terminology.hl7.org/codesystems-v2.html
  name: HL7 V3 Code System
  pattern: ^\w+$
  prefix: hl7.v3codesystem
  uri_format: https://terminology.hl7.org/CodeSystem-v3-$1
hmdb:
  biocontext:
    prefix: HMDB
    uri_format: http://www.hmdb.ca/metabolites/$1
  cheminf:
    description: Database identifier used by Human Metabolome Database.
    name: HMDB
    obsolete: false
    prefix: 000408
  contact:
    email: david.wishart@ualberta.ca
    github: DavidWishartLab
    name: David S. Wishart
    orcid: 0000-0002-3207-2434
  edam:
    description: Identifier of a small molecule metabolite from the Human Metabolome
      Database (HMDB).
    name: Compound ID (HMDB)
    obsolete: false
    prefix: '2622'
  fairsharing:
    abbreviation: HMDB
    description: "The Human Metabolome Database (HMDB) is a freely available electronic\
      \ database containing detailed information about small molecule metabolites\
      \ found in the human body. It is intended to be used for applications in metabolomics,\
      \ clinical chemistry, biomarker discovery and general education. The database\
      \ is designed to contain or link three kinds of data: 1) chemical data, 2) clinical\
      \ data, and 3) molecular biology/biochemistry data. The database contains 220,945\
      \ metabolite entries including both water-soluble and lipid soluble metabolites.\
      \ Additionally, 8,610 protein sequences (enzymes and transporters) are linked\
      \ to these metabolite entries. Each MetaboCard entry contains 130 data fields\
      \ with 2/3 of the information being devoted to chemical/clinical data and the\
      \ other 1/3 devoted to enzymatic or biochemical data. Many data fields are hyperlinked\
      \ to other databases (KEGG, PubChem, MetaCyc, ChEBI, PDB, UniProt, and GenBank)\
      \ and a variety of structure and pathway viewing applets. The HMDB database\
      \ supports extensive text, sequence, chemical structure, MS and NMR spectral\
      \ query searches. Four additional databases, DrugBank, T3DB, SMPDB and FooDB\
      \ are also part of the HMDB suite of databases. \n"
    homepage: https://hmdb.ca/
    name: The Human Metabolome Database
    prefix: FAIRsharing.sye5js
    publications:
    - doi: 10.1093/nar/gks1065
      pubmed_id: 23161693
      title: HMDB 3.0--The Human Metabolome Database in 2013
    - doi: 10.1093/nar/gkl923
      pubmed_id: 17202168
      title: 'HMDB: the Human Metabolome Database.'
    - doi: 10.1093/nar/gkn810
      pubmed_id: 17202168
      title: 'HMDB: a knowledgebase for the human metabolome'
    - doi: 10.1093/nar/gkx1089
      pubmed_id: 29140435
      title: 'HMDB 4.0: the human metabolome database for 2018'
    - doi: 10.1093/nar/gkab1062
      pubmed_id: 34986597
      title: 'HMDB 5.0: the Human Metabolome Database for 2022'
    subjects:
    - Molecular biology
    - Biochemistry
    - Bioinformatics
    - Proteomics
    - Life Science
    - Metabolomics
    - Phenomics
    - Omics
    twitter: WishartLab
  integbio:
    alt_name: Human Metabolome Database
    description: HUMDB is a database of human metabolites. The database contains information
      on thousands of metabolites produced by and found in the human body as a result
      of metabolic processes. genes and proteins related to the metabolites are also
      affiliated with records, where appropriate. Data on metabolites and the associated
      genes and proteins are available for download.
    fairsharing: biodbcore-000552
    homepage: http://www.hmdb.ca/
    information_keywords:
    - Sequence
    - Interaction/Pathway
    - Classification
    maintainer: University of Alberta
    name: HMDB
    prefix: nbdc00909
    pubmeds:
    - '18953024'
    status: Active
    target_keywords:
    - RNA
    - Protein
    - Health/Disease
    - Metabolite
  logo: https://www.hmdb.ca/assets/hmdb_logo-f7bd764aa882bbbb2cfb8930f5f784e60576755c3de62a23a6d99c845cbff7e3.png
  mappings:
    biocontext: HMDB
    cheminf: 000408
    edam: '2622'
    fairsharing: FAIRsharing.sye5js
    integbio: nbdc00909
    miriam: hmdb
    n2t: hmdb
    pathguide: '244'
    prefixcommons: hmdb
    re3data: r3d100011285
    togoid: Hmdb
    wikidata: P2057
  miriam:
    deprecated: false
    description: The Human Metabolome Database (HMDB) is a database containing detailed
      information about small molecule metabolites found in the human body.It contains
      or links 1) chemical 2) clinical and 3) molecular biology/biochemistry data.
    homepage: http://www.hmdb.ca/
    id: '00000051'
    name: HMDB
    namespaceEmbeddedInLui: false
    pattern: ^HMDB\d+$
    prefix: hmdb
    sampleId: HMDB00001
    uri_format: http://www.hmdb.ca/metabolites/$1
  n2t:
    description: The Human Metabolome Database (HMDB) is a database containing detailed
      information about small molecule metabolites found in the human body.It contains
      or links 1) chemical 2) clinical and 3) molecular biology/biochemistry data.
    example: HMDB00001
    homepage: http://www.hmdb.ca/
    name: The Human Metabolome Database
    namespaceEmbeddedInLui: false
    pattern: ^HMDB\d+$
    prefix: hmdb
    uri_format: http://www.hmdb.ca/metabolites/$1
  name: Human Metabolome Database
  pathguide:
    abbreviation: HMDB
    homepage: http://www.hmdb.ca/
    name: Human Metabolome Database
    prefix: '244'
  prefix: hmdb
  prefixcommons:
    description: The Human Metabolome Database (HMDB) is a database containing detailed
      information about small molecule metabolites found in the human body.It contains
      or links 1) chemical 2) clinical and 3) molecular biology/biochemistry data.
    example: HMDB00001
    homepage: http://www.hmdb.ca
    keywords:
    - chemical
    - human
    - metabolite
    license: http://www.hmdb.ca/about#cite
    name: The Human Metabolome Database
    pattern: ^HMDB\d{5}$
    prefix: hmdb
    pubmed_ids:
    - '17202168'
    uri_format: http://www.hmdb.ca/metabolites/$1
  publications:
  - doi: 10.1093/nar/gkab1062
    pmc: PMC8728138
    pubmed: '34986597'
    title: 'HMDB 5.0: the Human Metabolome Database for 2022'
    year: 2022
  - doi: 10.1093/nar/gkx1089
    pmc: PMC5753273
    pubmed: '29140435'
    title: 'HMDB 4.0: the human metabolome database for 2018'
    year: 2018
  - doi: 10.1093/nar/gks1065
    pmc: PMC3531200
    pubmed: '23161693'
    title: HMDB 3.0--The Human Metabolome Database in 2013
    year: 2012
  - doi: 10.1093/nar/gkl923
    pmc: PMC1899095
    pubmed: '17202168'
    title: 'HMDB: the Human Metabolome Database'
    year: 2007
  - doi: 10.1093/nar/gks1065
    pmc: null
    pubmed: null
    title: HMDB 3.0--The Human Metabolome Database in 2013
    year: null
  - doi: 10.1093/nar/gkl923
    pmc: null
    pubmed: null
    title: 'HMDB: the Human Metabolome Database.'
    year: null
  - doi: 10.1093/nar/gkn810
    pmc: null
    pubmed: null
    title: 'HMDB: a knowledgebase for the human metabolome'
    year: null
  - doi: 10.1093/nar/gkx1089
    pmc: null
    pubmed: null
    title: 'HMDB 4.0: the human metabolome database for 2018'
    year: null
  - doi: 10.1093/nar/gkab1062
    pmc: null
    pubmed: null
    title: 'HMDB 5.0: the Human Metabolome Database for 2022'
    year: null
  - doi: null
    pmc: null
    pubmed: '17202168'
    title: null
    year: null
  re3data:
    description: The Human Metabolome Database (HMDB) is a freely available electronic
      database containing detailed information about small molecule metabolites found
      in the human body. It is intended to be used for applications in metabolomics,
      clinical chemistry, biomarker discovery and general education.
    doi: 10.17616/R33K90
    homepage: https://hmdb.ca/
    name: Human Metabolome Database
    prefix: r3d100011285
    synonyms:
    - HMDB
  synonyms:
  - HMDB
  togoid:
    catalog: nbdc00909
    description: HUMDB is a database of human metabolites. The database contains information
      on thousands of metabolites produced by and found in the human body as a result
      of metabolic processes. genes and proteins related to the metabolites are also
      affiliated with records, where appropriate. Data on metabolites and the associated
      genes and proteins are available for download.
    examples:
    - HMDB0029433
    - HMDB0015609
    - HMDB0000042
    - HMDB0002360
    - HMDB0003345
    - HMDB0003550
    - HMDB0036769
    - HMDB0000935
    - HMDB0002755
    - HMDB0004369
    keywords:
    - Compound
    name: HMDB
    pattern: ^(?:hmdb:)?(?HMDB\d+)$
    prefix: Hmdb
    uri_format: http://identifiers.org/hmdb/$1
  wikidata:
    description: ID in Human Metabolome Database
    example:
    - HMDB0002111
    - HMDB0034235
    name: Human Metabolome Database ID
    pattern: ^HMDB\d+$
    prefix: P2057
    uri_format: https://www.hmdb.ca/metabolites/$1
hms.lincs.antibody:
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: Database contains all publicly available HMS LINCS datasets and information
    for each dataset about experimental reagents (small molecule perturbagens, cells,
    antibodies, and proteins) and experimental and data analysis protocols.
  domain: antibody
  example: '80001'
  homepage: https://lincs.hms.harvard.edu/db/antibodies/
  name: HMS Library of Integrated Network-based Cellular Signatures Antibodies
  pattern: ^8\d{4}$
  prefix: hms.lincs.antibody
  uri_format: https://lincs.hms.harvard.edu/db/antibodies/$1
hms.lincs.cell:
  comment: this is NOT the same as lincs.cell. On https://lincs.hms.harvard.edu/db/cells/?search=MCF-10A&extra_form_shown=&dataset_types=,
    you can see there's a mapping to the other resource.
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: Database contains all publicly available HMS LINCS datasets and information
    for each dataset about experimental reagents (small molecule perturbagens, cells,
    antibodies, and proteins) and experimental and data analysis protocols.
  example: '50583'
  homepage: https://lincs.hms.harvard.edu/db/cell/
  name: HMS LINCS Cell
  pattern: ^5\d{4}$
  prefix: hms.lincs.cell
  references:
  - https://github.com/identifiers-org/identifiers-org.github.io/issues/223
  uri_format: https://lincs.hms.harvard.edu/db/cells/$1
hms.lincs.compound:
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: Database contains all publicly available HMS LINCS datasets and information
    for each dataset about experimental reagents (small molecule perturbagens, cells,
    antibodies, and proteins) and experimental and data analysis protocols.
  example: 10001-101
  example_extras:
  - 11996-999
  homepage: https://lincs.hms.harvard.edu/db/sm/
  name: HMS LINCS Compound
  pattern: ^1\d{4}-\d{3}$
  prefix: hms.lincs.compound
  synonyms:
  - HMS-LINCS
  - hmsl_id
  uri_format: https://lincs.hms.harvard.edu/db/sm/$1
hms.lincs.dataset:
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: Database contains all publicly available HMS LINCS datasets and information
    for each dataset about experimental reagents (small molecule perturbagens, cells,
    antibodies, and proteins) and experimental and data analysis protocols.
  example: '20003'
  homepage: https://lincs.hms.harvard.edu/db/datasets/
  name: HMS Library of Integrated Network-based Cellular Signatures Datasets
  pattern: ^2\d{4}$
  prefix: hms.lincs.dataset
  uri_format: https://lincs.hms.harvard.edu/db/datasets/$1
hoelzel:
  contact:
    email: info@hoelzel.de
    github: null
    name: Carsten Linder
    orcid: 0009-0009-3816-8777
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: Hölzel is a life science reagent vendor based in Cologne, Germany.
    As a distributor, they offer products suitable for many kinds of research areas
    such as oncology, neuroscience, immunology, and more. Their portfolio consists
    of antibodies, recombinant proteins, inhibitors, ELISA-kits as well as other assays,
    arrays and kits. Their inhibitor portfolio can be easily accessed via the CAS-register
    catalog.
  example: 40592-R001-100
  homepage: https://www.hoelzel-biotech.com
  keywords:
  - antibodies
  - assays
  - biologics
  - elisa-kits
  - inhibitors
  - life sciences
  - proteins
  - vendor
  logo: https://www.hoelzel-biotech.com/skin/frontend/ultimo/custom/images/logo.png
  name: Hölzel Diagnostika
  prefix: hoelzel
  synonyms:
  - hölzel
  uri_format: https://www.hoelzel-biotech.com/de/catalogsearch/result/?q=$1
hog:
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: Documentation of HOGS (Homologous Organs Groups). Contains links to
    HOGs download, HOGs onthology, HOGs creation, composition, etc.
  download_obo: ftp://ftp.bgee.org/general/ontologies/HOG.obo
  example: '0000255'
  homepage: https://bgee.org/bgee/bgee?page=documentation#sectionHomologyRelationships
  name: Homologous Organ Groups
  pattern: ^\d{7}$
  prefix: hog
  uri_format: https://biopragmatics.github.io/providers/hog/$1
hogenom:
  biocontext:
    prefix: HOGENOM
  contact:
    email: perriere@biomserv.univ-lyon1.fr
    github: null
    name: Guy Perrière
    orcid: 0000-0002-6850-6265
  example: HOMO_3.PE998
  example_extras:
  - ATTCE_SCAFFOLD00004.PE150
  - AEDAE_SUPERCONT1_288.PE16
  fairsharing:
    abbreviation: HOGENOM
    description: HOGENOM is a phylogenomic database providing families of homologous
      genes and associated phylogenetic trees (and sequence alignments) for a wide
      set sequenced organisms.
    homepage: http://hogenom.univ-lyon1.fr/
    name: HOGENOM
    prefix: FAIRsharing.qe8tz8
    publications:
    - doi: 10.1186/1471-2105-10-S6-S3
      pubmed_id: 19534752
      title: Databases of homologous gene families for comparative genomics.
    subjects:
    - Phylogeny
    - Phylogenetics
    - Life Science
  integbio:
    description: HOGENOM is a phylogenomic database providing families of homologous
      genes and associated phylogenetic trees (and sequence alignments) for a wide
      set sequenced organisms.
    fairsharing: FAIRsharing.qe8tz8
    homepage: http://hogenom.univ-lyon1.fr/
    information_keywords:
    - Classification
    - Sequence
    - Taxonomy
    maintainer: PBIL
    name: HOGENOM
    prefix: nbdc01858
    pubmeds:
    - '19534752'
    status: Active
    target_keywords:
    - Genome/Gene
    - Protein
  mappings:
    biocontext: HOGENOM
    fairsharing: FAIRsharing.qe8tz8
    integbio: nbdc01858
    miriam: hogenom
    n2t: hogenom
    prefixcommons: hogenom
    uniprot: DB-0044
  miriam:
    deprecated: false
    description: HOGENOM is a database of homologous genes from fully sequenced organisms
      (bacteria, archeae and eukarya). This collection references phylogenetic trees
      which can be retrieved using either UniProt accession numbers, or HOGENOM tree
      family identifier.
    homepage: http://hogenom.univ-lyon1.fr/
    id: '00000213'
    name: HOGENOM
    namespaceEmbeddedInLui: false
    pattern: ^\w+$
    prefix: hogenom
    sampleId: HOMO_3.PE998
    uri_format: http://hogenom.univ-lyon1.fr/query_sequence?Go=Submit+Query&seq=$1
  n2t:
    description: HOGENOM is a database of homologous genes from fully sequenced organisms
      (bacteria, archeae and eukarya). This collection references phylogenetic trees
      which can be retrieved using either UniProt accession numbers, or HOGENOM tree
      family identifier.
    example: HBG284870
    homepage: http://pbil.univ-lyon1.fr/databases/hogenom/
    name: HOGENOM at CNRS
    namespaceEmbeddedInLui: false
    pattern: ^\w+$
    prefix: hogenom
    uri_format: http://pbil.univ-lyon1.fr/cgi-bin/view-tree.pl?db=HOGENOM5&query=$1
  name: Database of Complete Genome Homologous Genes Families
  pattern: ^[A-Z][A-Z0-9_]+\.PE\d+$
  prefix: hogenom
  prefixcommons:
    description: HOGENOM is a database of homologous genes from fully sequenced organisms
      (bacteria, archeae and eukarya). This collection references phylogenetic trees
      which can be retrieved using either UniProt accession numbers, or HOGENOM tree
      family identifier.
    example: HBG284870
    homepage: http://pbil.univ-lyon1.fr/databases/hogenom.php
    keywords:
    - classification
    - sequence
    name: The HOGENOM Database of Homologous Genes from Fully Sequenced Organisms
    pattern: ^\w+$
    prefix: hogenom
    pubmed_ids:
    - '19534752'
    uri_format: http://pbil.univ-lyon1.fr/cgi-bin/view-tree.pl?db=HOGENOM5&query=$1
  publications:
  - doi: 10.1186/1471-2105-10-s6-s3
    pmc: PMC2697650
    pubmed: '19534752'
    title: Databases of homologous gene families for comparative genomics
    year: 2009
  - doi: 10.1101/gr.10.3.379
    pmc: PMC311423
    pubmed: '10720578'
    title: 'HOBACGEN: database system for comparative genomics in bacteria'
    year: 2000
  - doi: 10.1186/1471-2105-10-S6-S3
    pmc: null
    pubmed: null
    title: Databases of homologous gene families for comparative genomics.
    year: null
  - doi: null
    pmc: null
    pubmed: '19534752'
    title: null
    year: null
  - doi: 10.1186/1471-2105-10-s6-s3
    pmc: null
    pubmed: '19534752'
    title: null
    year: null
  uniprot:
    abbreviation: HOGENOM
    category: Phylogenomic databases
    homepage: http://hogenom.univ-lyon1.fr/
    name: The HOGENOM Database of Homologous Genes from Fully Sequenced Organisms
    prefix: DB-0044
    publications:
    - doi: 10.1186/1471-2105-10-s6-s3
      pubmed: '19534752'
    uri_format: http://hogenom.univ-lyon1.fr/query_sequence?seq=$1
hoip:
  aberowl:
    description: Homeostasis imbalance process ontology (HoIP) is an ontology that
      systematizes a wide variety of terms involving homeostasis imbalance courses
      and processes. HoIP focuses on the course of COVID-19 infectious processes and
      cellular senescence.
    download_owl: http://aber-owl.net/media/ontologies/HOIP/65/hoip.owl
    homepage: https://github.com/yuki-yamagata/hoip
    name: Homeostasis imbalance process ontology
    prefix: HOIP
    version: 2024/04/03
  bioportal:
    contact:
      email: yuki.yamagata@riken.jp
      name: Yuki Yamagata
    description: Homeostasis imbalance process ontology (HoIP) is an ontology that
      systematizes a wide variety of terms involving homeostasis imbalance courses
      and processes. HoIP focuses on the course of COVID-19 infectious processes and
      cellular senescence.
    homepage: https://github.com/yuki-yamagata/hoip
    name: Homeostasis imbalance process ontology
    prefix: HOIP
    publications:
    - https://doi.org/10.1101/2023.03.09.531883
    version: 2024/04/03
  comment: The ontology file was deleted in https://github.com/yuki-yamagata/hoip/commit/73fcfa114d71a76a984a9ce1166e50d7ebafe158,
    making it impossible to link to the ontology afterwards.
  contact:
    email: yuki.yamagata@riken.jp
    github: yuki-yamagata
    name: Yuki Yamagata
    orcid: 0000-0002-9673-1283
  contributor:
    email: j.harry.caufield@gmail.com
    github: caufieldjh
    name: Harry Caufield
    orcid: 0000-0001-5705-7831
  description: An ontology of processes triggered by homeostatic imbalance, with a
    focus on COVID-19 infectious processes.
  download_owl: https://github.com/yuki-yamagata/hoip/blob/c70ae6d4868ca951d075cec409e863fa4abe19b2/hoip_0308.owl
  example: 0040379
  github_request_issue: 668
  homepage: https://knowledge.brc.riken.jp/bioresource/ontology/HOIP
  license: CC-BY-4.0
  mappings:
    aberowl: HOIP
    bioportal: HOIP
  name: Homeostasis imbalance process ontology
  pattern: ^\d{7}$
  prefix: hoip
  repository: https://github.com/yuki-yamagata/hoip
  reviewer:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  uri_format: http://purl.bioontology.org/ontology/HOIP/HOIP_$1
holofood.animal:
  contact:
    email: tgilbert@sund.ku.dk
    github: null
    name: Tom Gilbert
    orcid: 0000-0002-5805-7195
  contributor:
    email: palayoor.n@northeastern.edu
    github: nalikapalayoor
    name: Nalika Palayoor
    orcid: 0009-0008-8406-631X
  description: The HoloFood Data Portal centralizes access to datasets from the HoloFood
    project, which explores host microbiota interactions in salmon and chicken production.
    It links phenotypic data with microbiome samples and derived genomic resources
    and therefore simplifies data integration, supporting researchers in multiomics
    and microbiome studies. The identifiers in the animal semantic space correspond
    to animals that samples in the database are obtained from.
  example: SAMEA112904733
  github_request_issue: 1400
  homepage: https://www.holofooddata.org
  name: HoloFood animal
  pattern: ^SAMEA\d{9}$
  prefix: holofood.animal
  publications:
  - doi: 10.1093/database/baae112
    pmc: PMC11724189
    pubmed: '39797569'
    title: 'HoloFood Data Portal: holo-omic datasets for analysing host-microbiota
      interactions in animal production'
    year: 2025
  reviewer:
    email: b.gyori@northeastern.edu
    github: bgyori
    name: Benjamin M. Gyori
    orcid: 0000-0001-9439-5346
  uri_format: https://www.holofooddata.org/animal/$1
holofood.sample:
  contact:
    email: tgilbert@sund.ku.dk
    github: null
    name: Tom Gilbert
    orcid: 0000-0002-5805-7195
  contributor:
    email: palayoor.n@northeastern.edu
    github: nalikapalayoor
    name: Nalika Palayoor
    orcid: 0009-0008-8406-631X
  description: The HoloFood Data Portal centralizes access to datasets from the HoloFood
    project, which explores host microbiota interactions in salmon and chicken production.
    It links phenotypic data with microbiome samples and derived genomic resources
    and therefore simplifies data integration, supporting researchers in multiomics
    and microbiome studies. The identifiers in the samples semantic space represent
    samples derived from animals in HoloFood trials.
  example: SAMEA10104908
  github_request_issue: 1400
  homepage: https://www.holofooddata.org
  name: HoloFood sample
  pattern: ^SAMEA\d{8}$
  prefix: holofood.sample
  publications:
  - doi: 10.1093/database/baae112
    pmc: PMC11724189
    pubmed: '39797569'
    title: 'HoloFood Data Portal: holo-omic datasets for analysing host-microbiota
      interactions in animal production'
    year: 2025
  reviewer:
    email: b.gyori@northeastern.edu
    github: bgyori
    name: Benjamin M. Gyori
    orcid: 0000-0001-9439-5346
  uri_format: https://www.holofooddata.org/sample/$1
hom:
  aberowl:
    description: This ontology represents concepts related to homology, as well as
      other concepts used to describe similarity and non-homology.
    download_owl: http://aber-owl.net/media/ontologies/HOM/7/hom.owl
    homepage: http://bioinfo.unil.ch
    name: Homology Ontology
    prefix: HOM
  biocontext:
    prefix: HOM
  bioportal:
    contact:
      email: bgee@sib.swiss
      name: Bgee team
    description: This ontology represents concepts related to homology, as well as
      other concepts used to describe similarity and non-homology.
    homepage: https://bgee.org
    name: Ontology of Homology and Related Concepts in Biology
    prefix: HOM
    publications:
    - http://dx.doi.org/10.1016/j.tig.2009.12.012
    version: releases/2015-01-07
  example: 0000049
  fairsharing:
    abbreviation: HOM
    contact:
      email: julien.roux@unil.ch
      name: Julien Roux
      orcid: 0000-0002-4192-5099
    description: This ontology represents concepts related to homology, as well as
      other concepts used to describe similarity and non-homology.
    domains:
    - molecular entity
    - homologous
    - life cycle stage
    homepage: http://bioportal.bioontology.org/ontologies/HOM/?p=summary
    name: HOMology
    prefix: FAIRsharing.efv7gw
    publications:
    - doi: 10.1016/j.tig.2009.12.012
      pubmed: '20116127'
      title: An ontology to clarify homology-related concepts
      year: 2010
    subjects:
    - Life Science
    - Anatomy
  mappings:
    aberowl: HOM
    biocontext: HOM
    bioportal: HOM
    fairsharing: FAIRsharing.efv7gw
    obofoundry: hom
    ols: hom
    ontobee: HOM
    wikidata.entity: Q81661651
  obofoundry:
    contact: bgee@sib.swiss
    contact.github: fbastian
    contact.label: Frederic Bastian
    contact.orcid: 0000-0002-9415-5104
    deprecated: false
    description: This ontology represents concepts related to homology, as well as
      other concepts used to describe similarity and non-homology.
    domain: anatomy and development
    download.owl: http://purl.obolibrary.org/obo/hom.owl
    homepage: https://github.com/BgeeDB/homology-ontology
    license: CC0 1.0
    license.url: https://creativecommons.org/publicdomain/zero/1.0/
    name: Homology Ontology
    preferredPrefix: HOM
    prefix: hom
    publications:
    - id: https://doi.org/10.1016/j.tig.2009.12.012
      title: An ontology to clarify homology-related concepts
    repository: https://github.com/BgeeDB/homology-ontology
  ols:
    description: This ontology represents concepts related to homology, as well as
      other concepts used to describe similarity and non-homology.
    download_owl: http://purl.obolibrary.org/obo/hom.owl
    homepage: https://github.com/BgeeDB/homology-ontology
    name: Homology Ontology
    prefix: hom
    tracker: https://github.com/BgeeDB/homology-ontology/issues
  ontobee:
    library: Library
    name: Homology Ontology
    prefix: HOM
  pattern: ^\d{7}$
  prefix: hom
  publications:
  - doi: 10.1016/j.tig.2009.12.012
    pmc: null
    pubmed: '20116127'
    title: An ontology to clarify homology-related concepts
    year: 2010
  uri_format: http://purl.obolibrary.org/obo/HOM_$1
homd.seq:
  biocontext:
    prefix: HOMD.SEQ
  contact:
    email: tchen@forsyth.org
    github: tsute
    name: Tsute Chen
    orcid: 0000-0001-6689-317X
  example: SEQF1003.1
  mappings:
    biocontext: HOMD.SEQ
    miriam: homd.seq
    n2t: homd.seq
    prefixcommons: homd.seq
  miriam:
    deprecated: false
    description: The Human Oral Microbiome Database (HOMD) provides a site-specific
      comprehensive database for the more than 600 prokaryote species that are present
      in the human oral cavity. It contains genomic information based on a curated
      16S rRNA gene-based provisional naming scheme, and taxonomic information. This
      datatype contains genomic sequence information.
    homepage: https://www.homd.org/
    id: '00000170'
    name: HOMD Sequence Metainformation
    namespaceEmbeddedInLui: false
    pattern: ^SEQF\d+$
    prefix: homd.seq
    sampleId: SEQF1003.1
    uri_format: https://v31.homd.org/genome/genome_description?gid=$1
  n2t:
    description: The Human Oral Microbiome Database (HOMD) provides a site-specific
      comprehensive database for the more than 600 prokaryote species that are present
      in the human oral cavity. It contains genomic information based on a curated
      16S rRNA gene-based provisional naming scheme, and taxonomic information. This
      datatype contains genomic sequence information.
    example: SEQF1003
    homepage: http://www.homd.org/index.php
    name: HOMD sequence metainformation at The Forsyth Institute
    namespaceEmbeddedInLui: false
    pattern: ^SEQF\d+$
    prefix: homd.seq
    uri_format: http://www.homd.org/modules.php?op=modload&name=GenomeList&file=index&link=detailinfo&seqid=$1
  pattern: ^SEQF\d+(?:\.\d+)?$
  prefix: homd.seq
  prefixcommons:
    description: The Human Oral Microbiome Database (HOMD) provides a site-specific
      comprehensive database for the more than 600 prokaryote species that are present
      in the human oral cavity. It contains genomic information based on a curated
      16S rRNA gene-based provisional naming scheme, and taxonomic information. This
      datatype contains genomic sequence information.
    example: SEQF1003
    keywords:
    - genome
    - microbial
    name: HOMD Sequence Metainformation
    pattern: ^SEQF\d+$
    prefix: homd.seq
    pubmed_ids:
    - '20624719'
    uri_format: http://www.homd.org/modules.php?op=modload&name=GenomeList&file=index&link=detailinfo&seqid=$1
  publications:
  - doi: 10.1093/database/baq013
    pmc: PMC2911848
    pubmed: '20624719'
    title: 'The Human Oral Microbiome Database: a web accessible resource for investigating
      oral microbe taxonomic and genomic information'
    year: 2010
  uri_format: https://v31.homd.org/genome/genome_description?gid=$1
homd.taxon:
  biocontext:
    prefix: HOMD.TAXON
  contact:
    email: tchen@forsyth.org
    github: tsute
    name: Tsute Chen
    orcid: 0000-0001-6689-317X
  mappings:
    biocontext: HOMD.TAXON
    miriam: homd.taxon
    n2t: homd.taxon
    ncbi: HOMD
    prefixcommons: homd.taxon
  miriam:
    deprecated: false
    description: The Human Oral Microbiome Database (HOMD) provides a site-specific
      comprehensive database for the more than 600 prokaryote species that are present
      in the human oral cavity. It contains genomic information based on a curated
      16S rRNA gene-based provisional naming scheme, and taxonomic information. This
      datatype contains taxonomic information.
    homepage: http://www.homd.org/
    id: '00000171'
    name: HOMD Taxonomy
    namespaceEmbeddedInLui: false
    pattern: ^\d+$
    prefix: homd.taxon
    sampleId: '811'
    uri_format: https://www.homd.org/taxa/tax_description?otid=$1
  n2t:
    description: The Human Oral Microbiome Database (HOMD) provides a site-specific
      comprehensive database for the more than 600 prokaryote species that are present
      in the human oral cavity. It contains genomic information based on a curated
      16S rRNA gene-based provisional naming scheme, and taxonomic information. This
      datatype contains taxonomic information.
    example: '811'
    homepage: http://www.homd.org/index.php
    name: HOMD taxon information at The Forsyth Institute
    namespaceEmbeddedInLui: false
    pattern: ^\d+$
    prefix: homd.taxon
    uri_format: http://www.homd.org/modules.php?op=modload&name=HOMD&file=index&oraltaxonid=$1&view=dynamic
  ncbi:
    example: tax_078
    homepage: http://www.homd.org/
    name: Human Oral Microbiome Database
    prefix: HOMD
  prefix: homd.taxon
  prefixcommons:
    description: The Human Oral Microbiome Database (HOMD) provides a site-specific
      comprehensive database for the more than 600 prokaryote species that are present
      in the human oral cavity. It contains genomic information based on a curated
      16S rRNA gene-based provisional naming scheme, and taxonomic information. This
      datatype contains taxonomic information.
    example: '811'
    keywords:
    - microbial
    - taxonomy
    name: HOMD Taxonomy
    pattern: ^\d+$
    prefix: homd.taxon
    pubmed_ids:
    - '20624719'
    uri_format: http://www.homd.org/modules.php?op=modload&name=HOMD&file=index&oraltaxonid=$1&view=dynamic
  publications:
  - doi: 10.1093/database/baq013
    pmc: PMC2911848
    pubmed: '20624719'
    title: 'The Human Oral Microbiome Database: a web accessible resource for investigating
      oral microbe taxonomic and genomic information'
    year: 2010
  - doi: null
    pmc: null
    pubmed: '20624719'
    title: null
    year: null
  - doi: null
    pmc: null
    pubmed: '20624719'
    title: null
    year: null
  uri_format: http://www.homd.org/modules.php?op=modload&name=HOMD&view=dynamic&oraltaxonid=$1
homologene:
  biocontext:
    prefix: HOMOLOGENE
    uri_format: http://www.ncbi.nlm.nih.gov/homologene/$1
  contact:
    email: sayers@ncbi.nlm.nih.gov
    github: null
    name: Eric W. Sayers
    orcid: 0000-0001-8394-3802
  fairsharing:
    abbreviation: HomoloGene
    description: HomoloGene is an automated system for the detection of homologs among
      the annotated genes of several completely sequenced eukaryotic genomes. HomoloGene
      takes protein sequences from differing species and compares them to one another
      (using blastp) and matches are placed into groups, using a tree built from sequence
      similarity to guide the process, where closer related organisms are matched
      up first, and then further organisms are added as the tree is traversed toward
      the root. The protein alignments are mapped back to their corresponding DNA
      sequences, where distance metrics can be calculated (e.g. molecular distance,
      Ka/Ks ratio). Sequences are matched using synteny when applicable. Remaining
      sequences are matched up by using an algorithm for maximizing the score globally,
      rather than locally, in a bipartite matching. Cutoffs on bits per position and
      Ks values are set to prevent unlikely "orthologs" from being grouped together.
      These cutoffs are calculated based on the respective score distribution for
      the given groups of organisms. Paralogs are identified by finding sequences
      that are closer within species than other species.
    homepage: https://www.ncbi.nlm.nih.gov/homologene
    license: http://opendatacommons.org/licenses/pddl/1.0
    name: NCBI HomoloGene Database
    prefix: FAIRsharing.mzc066
    publications:
    - doi: 10.1093/nar/gkq1172
      pubmed_id: 21097890
      title: Database resources of the National Center for Biotechnology Information.
    subjects:
    - Life Science
  integbio:
    description: In Homologenes, users can find automatically constructed homologous
      gene sets from the full-length genome sequences of a wide range of eukaryotic
      species, as well as mRNA and protein sequences.
    fairsharing: biodbcore-000443
    homepage: http://www.ncbi.nlm.nih.gov/homologene
    information_keywords:
    - Sequence
    - Taxonomy
    maintainer: NCBI (National Center for Biotechnology Information)
    name: HomoloGene
    prefix: nbdc00101
    status: Active
    target_keywords:
    - Genome/Gene
    - Protein
  mappings:
    biocontext: HOMOLOGENE
    fairsharing: FAIRsharing.mzc066
    integbio: nbdc00101
    miriam: homologene
    n2t: homologene
    prefixcommons: homologene
    togoid: Homologene
    wikidata: P593
  miriam:
    deprecated: false
    description: HomoloGene is a system for automated detection of homologs among
      the annotated genes of several completely sequenced eukaryotic genomes.
    homepage: https://www.ncbi.nlm.nih.gov/homologene/
    id: '00000275'
    name: HomoloGene
    namespaceEmbeddedInLui: false
    pattern: ^\d+$
    prefix: homologene
    providers:
    - code: ''
      description: Bio2RDF
      homepage: http://bio2rdf.org
      name: Bio2RDF
      uri_format: http://bio2rdf.org/describe/?url=http://bio2rdf.org/homologene:$1
    sampleId: '1000'
    uri_format: https://www.ncbi.nlm.nih.gov/homologene/$1
  n2t:
    description: HomoloGene is a system for automated detection of homologs among
      the annotated genes of several completely sequenced eukaryotic genomes.
    example: '1000'
    homepage: https://www.ncbi.nlm.nih.gov/homologene/
    name: Homologene at NCBI
    namespaceEmbeddedInLui: false
    pattern: ^\d+$
    prefix: homologene
    uri_format: https://www.ncbi.nlm.nih.gov/homologene/$1
  name: HomoloGene
  prefix: homologene
  prefixcommons:
    description: HomoloGene is a system for automated detection of homologs among
      the annotated genes of several completely sequenced eukaryotic genomes.
    example: '1000'
    homepage: http://wwww.ncbi.nlm.nih.gov/homologene
    keywords:
    - gene
    - genome
    name: NCBI Homologene
    pattern: ^\d+$
    prefix: homologene
    pubmed_ids:
    - '21097890'
    uri_format: http://www.ncbi.nlm.nih.gov/homologene/$1
  publications:
  - doi: 10.1093/nar/gkq1172
    pmc: PMC3013733
    pubmed: '21097890'
    title: Database resources of the National Center for Biotechnology Information
    year: 2010
  togoid:
    catalog: nbdc00101
    description: In Homologenes, users can find automatically constructed homologous
      gene sets from the full-length genome sequences of a wide range of eukaryotic
      species, as well as mRNA and protein sequences.
    examples:
    - '117'
    - '17'
    - '6'
    - '142'
    - '55'
    - '132'
    - '61'
    - '109'
    - '137'
    - '134'
    keywords:
    - Ortholog
    name: HomoloGene
    pattern: ^(?\d+)$
    prefix: Homologene
    uri_format: http://identifiers.org/homologene/$1
  wikidata:
    description: identifier in the HomoloGene database
    example:
    - '193'
    - '68068'
    - '732'
    homepage: http://www.ncbi.nlm.nih.gov/homologene
    name: HomoloGene ID
    pattern: ^[1-9]\d{0,5}$
    prefix: P593
    uri_format: https://www.ncbi.nlm.nih.gov/homologene?term=$1
homosaurus:
  appears_in:
  - gsso
  contact:
    email: adolphok@vcu.edu
    github: null
    name: Keahi Kaʻiwalani Adolpho
    orcid: 0000-0003-1769-112X
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: An international LGBTQ+ linked data vocabulary
  example: queerNewspapers
  github_request_issue: 1310
  homepage: http://homosaurus.org
  license: CC BY NC-ND 4.0
  name: Homosaurus
  prefix: homosaurus
  providers:
  - code: homosaurus.v3
    description: Homosaurus API v3
    example: null
    first_party: null
    homepage: https://homosaurus.org
    name: Homosaurus API v3
    publications: null
    status: null
    uri_format: http://homosaurus.org/v3/$1
  - code: homosaurus.v2
    description: Homosaurus API v2
    example: null
    first_party: null
    homepage: https://homosaurus.org
    name: Homosaurus API v2
    publications: null
    status: null
    uri_format: http://homosaurus.org/v2/$1
  repository: https://github.com/DigitalTransgenderArchive/homosaurus_site
  uri_format: http://homosaurus.org/terms/$1
horizon_discovery:
  cellosaurus:
    category: Cell line collections (Providers)
    homepage: https://horizondiscovery.com/
    name: Horizon Discovery cell line collection
    prefix: Horizon_Discovery
    uri_format: https://horizondiscovery.com/en/search?searchterm=$1
  example: HD+118-001
  mappings:
    cellosaurus: Horizon_Discovery
  prefix: horizon_discovery
hoso:
  contact:
    email: paul.fabry@usherbrooke.ca
    github: pfabry
    name: Paul Fabry
    orcid: 0000-0002-3336-2476
  contributor:
    email: paul.fabry@usherbrooke.ca
    github: pfabry
    name: Paul Fabry
    orcid: 0000-0002-3336-2476
  description: HOSO is an ontology of informational entities and processes related
    to healthcare organizations and services.
  example: '0000001'
  github_request_issue: 813
  homepage: https://openlhs.github.io/HOSO/
  license: CC-BY-4.0
  name: Healthcare Organizations and Services Ontology
  pattern: ^\d{7}$
  prefix: hoso
  repository: https://github.com/OpenLHS/HOSO
  reviewer:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
hovergen:
  biocontext:
    prefix: HOVERGEN
  fairsharing:
    abbreviation: HOVERGEN
    contact:
      email: duret@biomserv.univ-lyon1.fr
      name: Laurent Duret
      orcid: 0000-0003-2836-3463
    description: HOVERGEN is a database of homologous vertebrate genes that allows
      one to select sets of homologous genes among vertebrate species, and to visualize
      multiple alignments and phylogenetic trees.
    homepage: http://pbil.univ-lyon1.fr/databases/hovergen.html
    name: Homologous Vertebrate Genes Database
    prefix: FAIRsharing.dg1f0e
    publications:
    - doi: 10.1093/bioinformatics/bti325
      pubmed_id: 15713731
      title: 'Tree pattern matching in phylogenetic trees: automatic search for orthologs
        or paralogs in homologous gene sequence databases.'
    subjects:
    - Life Science
  homepage: https://pbil.univ-lyon1.fr/databases/hovergen.php
  integbio:
    alt_name: Homologous Vertebrate Genes Database
    description: HOVERGEN is a database of homologous vertebrate genes using the ACNUC
      sequence database. It contains all of vertebrate protein sequences from the
      UniProt Knowledgebase and all the corresponding nucleotide sequences in EMBL,
      and those information were structured in the ACNUC database.
    fairsharing: biodbcore-000501
    homepage: http://pbil.univ-lyon1.fr/databases/hovergen.php
    information_keywords:
    - Sequence
    - Taxonomy
    maintainer: Pole Bioinformatique Lyonnais
    name: HOVERGEN
    prefix: nbdc00284
    pubmeds:
    - '8036164'
    - '15713731'
    target_keywords:
    - Genome/Gene
    - Protein
  mappings:
    biocontext: HOVERGEN
    fairsharing: FAIRsharing.dg1f0e
    integbio: nbdc00284
    miriam: hovergen
    n2t: hovergen
    prefixcommons: hovergen
  miriam:
    deprecated: true
    description: HOVERGEN is a database of homologous vertebrate genes that allows
      one to select sets of homologous genes among vertebrate species, and to visualize
      multiple alignments and phylogenetic trees.
    homepage: http://pbil.univ-lyon1.fr/databases/hovergen.php
    id: '00000074'
    name: HOVERGEN
    namespaceEmbeddedInLui: false
    pattern: ^HBG\d+$
    prefix: hovergen
    sampleId: HBG004341
    uri_format: http://pbil.univ-lyon1.fr/cgi-bin/view-tree.pl?query=$1&db=HOVERGEN
  n2t:
    description: HOVERGEN is a database of homologous vertebrate genes that allows
      one to select sets of homologous genes among vertebrate species, and to visualize
      multiple alignments and phylogenetic trees.
    example: HBG004341
    homepage: http://pbil.univ-lyon1.fr/databases/hovergen.php
    name: Hovergen
    namespaceEmbeddedInLui: false
    pattern: ^HBG\d+$
    prefix: hovergen
    uri_format: http://pbil.univ-lyon1.fr/cgi-bin/view-tree.pl?query=$1&db=HOVERGEN
  name: Homologous Vertebrate Genes Database
  prefix: hovergen
  prefixcommons:
    description: HOVERGEN is a database of homologous vertebrate genes that allows
      one to select sets of homologous genes among vertebrate species, and to visualize
      multiple alignments and phylogenetic trees.
    example: HBG004341
    homepage: http://pbil.univ-lyon1.fr/databases/hovergen.html
    keywords:
    - gene
    - DNA
    - protein
    license: http://pbil.univ-lyon1.fr/databases/hovergen.php
    name: 'HOVERGEN: Homologous Vertebrate Genes Database'
    pattern: ^HBG\d+$
    prefix: hovergen
    pubmed_ids:
    - '15713731'
    uri_format: http://pbil.univ-lyon1.fr/cgi-bin/view-tree.pl?query=$1&db=HOVERGEN
  publications:
  - doi: 10.1093/bioinformatics/bti325
    pmc: null
    pubmed: '15713731'
    title: 'Tree pattern matching in phylogenetic trees: automatic search for orthologs
      or paralogs in homologous gene sequence databases'
    year: 2005
  - doi: 10.1093/bioinformatics/bti325
    pmc: null
    pubmed: null
    title: 'Tree pattern matching in phylogenetic trees: automatic search for orthologs
      or paralogs in homologous gene sequence databases.'
    year: null
  - doi: null
    pmc: null
    pubmed: '15713731'
    title: null
    year: null
  - doi: 10.1093/bioinformatics/bti325
    pmc: null
    pubmed: null
    title: 'Tree pattern matching in phylogenetic trees: automatic search for orthologs
      or paralogs in homologous gene sequence databases.'
    year: null
  - doi: null
    pmc: null
    pubmed: '15713731'
    title: null
    year: null
hp:
  aberowl:
    description: The Hypertension Ontology, developed using the Protege tool, serves
      as a comprehensive knowledge framework for representing and organizing information
      related to hypertensive disorders. This ontology is designed to capture various
      aspects of hypertension, including its types, causes, and associated risks,
      with the aim of providing valuable insights for healthcare professionals, researchers,
      and policymakers. Leveraging the power of Protege, the ontology employs the
      OWL (Web Ontology Language) format to define classes, properties, and relationships,
      ensuring semantic clarity and interoperability. The taxonomy within the ontology
      encompasses a wide range of hypertensive conditions, allowing for detailed classification
      and representation. The ontology facilitates queries and exploration of hypertensive
      data through the use of the DL Query module in Protege, offering a practical
      tool for evaluating its usefulness. To enhance accessibility, the ontology is
      made available for download, enabling seamless integration into existing healthcare
      information systems. Its development involved a rigorous review of scientific
      literature and consideration of established methodologies, ensuring its alignment
      with best practices in ontology engineering. This Hypertension Ontology aims
      to contribute to the advancement of hypertension research, clinical practice,
      and healthcare decision-making.
    download_owl: http://aber-owl.net/media/ontologies/HPO/1/hpo.owl
    name: Hypertension-Ontology
    prefix: HPO
  bartoc:
    abbreviation: HP
    description: The Human Phenotype Ontology (HPO) aims to provide a standardized
      vocabulary of phenotypic abnormalities encountered in human disease. Each term
      in the HPO describes a phenotypic abnormality, such as atrial septal defect.
      The HPO is currently being developed using the medical literature, Orphanet,
      DECIPHER, and OMIM. HPO currently contains approximately 11,000 terms and over
      115,000 annotations to hereditary diseases. The HPO also provides a large set
      of HPO annotations to approximately 4000 common diseases. (...) The HPO can
      be used for clinical diagnostics in human genetics (Phenomizer), bioinformatics
      research on the relationships between human phenotypic abnormalities and cellular
      and biochemical networks, for mapping between human and model organism phenotypes,
      and for providing a standardized vocabulary for clinical databases, among many
      other things. There exists an HPO web browser. The HPO project encourages input
      from the medical and genetics community with regards to the ontology itself
      and to clinical annotations.
    homepage: https://hpo.jax.org/
    name: Human Phenotype Ontology
    prefix: '1937'
    wikidata_database: Q17027854
  biocontext:
    prefix: HPO
    uri_format: http://human-phenotype-ontology.org/$1
  bioportal:
    contact:
      email: fariyaprity7@gmail.com
      name: Fariya Sultana Prity
    description: The Hypertension Ontology, developed using the Protege tool, serves
      as a comprehensive knowledge framework for representing and organizing information
      related to hypertensive disorders. This ontology is designed to capture various
      aspects of hypertension, including its types, causes, and associated risks,
      with the aim of providing valuable insights for healthcare professionals, researchers,
      and policymakers. Leveraging the power of Protege, the ontology employs the
      OWL (Web Ontology Language) format to define classes, properties, and relationships,
      ensuring semantic clarity and interoperability. The taxonomy within the ontology
      encompasses a wide range of hypertensive conditions, allowing for detailed classification
      and representation. The ontology facilitates queries and exploration of hypertensive
      data through the use of the DL Query module in Protege, offering a practical
      tool for evaluating its usefulness. To enhance accessibility, the ontology is
      made available for download, enabling seamless integration into existing healthcare
      information systems. Its development involved a rigorous review of scientific
      literature and consideration of established methodologies, ensuring its alignment
      with best practices in ontology engineering. This Hypertension Ontology aims
      to contribute to the advancement of hypertension research, clinical practice,
      and healthcare decision-making.
    name: Hypertension-Ontology
    prefix: HPO
  download_json: http://purl.obolibrary.org/obo/hp.json
  download_obo: http://purl.obolibrary.org/obo/hp.obo
  example: '0011140'
  fairsharing:
    abbreviation: HP
    description: The Human Phenotype Ontology has been developed to provide a structured
      and controlled vocabulary for the phenotypic features encountered in human hereditary
      and other disease. The goal is to provide resource for the computational analysis
      of the human phenome, with a focus on monogenic diseases listed in the Online
      Mendelian Inheritance in Man (OMIM) and Orphanet databases, for which annotations
      are also provided.
    domains:
    - disease phenotype
    - disorder
    homepage: https://hpo.jax.org/
    license: hpo
    name: Human Phenotype Ontology
    prefix: FAIRsharing.kbtt7f
    publications:
    - doi: 10.1093/nar/gkt1026
      pubmed: '24217912'
      title: 'The Human Phenotype Ontology project: linking molecular biology and
        disease through phenotype data'
      year: 2013
    - doi: 10.1093/nar/gkw1039
      pubmed: '27899602'
      title: The Human Phenotype Ontology in 2017
      year: 2016
    - doi: 10.1111/j.1399-0004.2010.01436.x
      pubmed: '20412080'
      title: The human phenotype ontology
      year: 2010
    - doi: 10.1093/nar/gky1105
      pubmed: '30476213'
      title: Expansion of the Human Phenotype Ontology (HPO) knowledge base and resources
      year: 2018
    - doi: 10.1016/j.ajhg.2008.09.017
      pubmed: '18950739'
      title: 'The Human Phenotype Ontology: a tool for annotating and analyzing human
        hereditary disease'
      year: 2008
    - doi: 10.1093/nar/gkad1005
      pubmed: '37953324'
      title: 'The Human Phenotype Ontology in 2024: phenotypes around the world'
      year: 2024
    subjects:
    - Phenomics
    - Omics
    - Preclinical Studies
    - Biomedical Science
    - Genetics
    - Pathology
    twitter: hp_ontology
  hl7:
    description: The Human Phenotype Ontology (HPO) aims to provide a standardized
      vocabulary of phenotypic abnormalities encountered in human disease. Each term
      in the HPO describes a phenotypic abnormality, such as atrial septal defect.
    homepage: https://lhncbc.nlm.nih.gov/
    name: Human Phenotype Ontology
    organization: Lister Hill National Center for Biomedical Communications
    preferred_prefix: hpo
    prefix: 2.16.840.1.113883.6.339
    status: Complete
  integbio:
    alt_name: Human Phenotype Ontology
    description: The Human Phenotype Ontology (HPO) provides a standardized vocabulary
      of phenotype specialized in human disease. The medical literatures, Orphanet,
      DECIPHER, and OMIM are used for developing the HPO.
    fairsharing: FAIRsharing.kbtt7f
    homepage: https://hpo.jax.org
    information_keywords:
    - Phenotype
    - Ontology/Terminology/Nomenclature
    maintainer: The Jackson Laboratory
    name: HPO
    prefix: nbdc02559
    pubmeds:
    - '33264411'
    status: Active
    target_keywords:
    - Health/Disease
    - Genome/Gene
  mappings:
    aberowl: HPO
    bartoc: '1937'
    biocontext: HPO
    bioportal: HPO
    fairsharing: FAIRsharing.kbtt7f
    hl7: 2.16.840.1.113883.6.339
    integbio: nbdc02559
    miriam: hp
    n2t: hp
    obofoundry: hp
    ols: hp
    ontobee: HP
    tib: hp
    wikidata: P3841
    wikidata.entity: Q17027854
  mastodon: hpo@masto.ai
  miriam:
    deprecated: false
    description: The Human Phenotype Ontology (HPO) aims to provide a standardized
      vocabulary of phenotypic abnormalities encountered in human disease. Each term
      in the HPO describes a phenotypic abnormality, such as atrial septal defect.
      The HPO is currently being developed using the medical literature, Orphanet,
      DECIPHER, and OMIM.
    homepage: https://hpo.jax.org/
    id: '00000571'
    name: Human Phenotype Ontology
    namespaceEmbeddedInLui: true
    pattern: ^HP:\d{7}$
    prefix: hp
    sampleId: 0000118
    uri_format: https://hpo.jax.org/app/browse/term/HP:$1
  n2t:
    description: The Human Phenotype Ontology (HPO) aims to provide a standardized
      vocabulary of phenotypic abnormalities encountered in human disease. Each term
      in the HPO describes a phenotypic abnormality, such as atrial septal defect.
      The HPO is currently being developed using the medical literature, Orphanet,
      DECIPHER, and OMIM.
    example: 0000118
    homepage: http://human-phenotype-ontology.github.io/
    name: Human Phenotype Ontology at Institute for Medical Genetics and Human Genetics
    namespaceEmbeddedInLui: true
    pattern: ^HP:\d{7}$
    prefix: hp
    uri_format: http://compbio.charite.de/hpoweb/showterm?id=HP:$1
  name: Human Phenotype Ontology
  obofoundry:
    appears_in:
    - chiro
    - maxo
    - scdo
    contact: dr.sebastian.koehler@gmail.com
    contact.github: drseb
    contact.label: Sebastian Koehler
    contact.orcid: 0000-0002-5316-1399
    deprecated: false
    description: The Human Phenotype Ontology (HPO) is a structured and controlled
      vocabulary for the phenotypic features encountered in human hereditary and other
      disease.
    domain: phenotype
    download.json: http://purl.obolibrary.org/obo/hp.json
    download.obo: http://purl.obolibrary.org/obo/hp.obo
    download.owl: http://purl.obolibrary.org/obo/hp.owl
    homepage: http://www.human-phenotype-ontology.org/
    license: hpo
    license.url: https://hpo.jax.org/app/license
    logo: https://raw.githubusercontent.com/obophenotype/human-phenotype-ontology/master/logo/HPO-logo-black_small.png
    name: Human Phenotype Ontology (HPO)
    preferredPrefix: HP
    prefix: hp
    publications:
    - id: https://www.ncbi.nlm.nih.gov/pubmed/18950739
      title: 'The Human Phenotype Ontology: a tool for annotating and analyzing human
        hereditary disease.'
    - id: https://www.ncbi.nlm.nih.gov/pubmed/26119816
      title: 'The Human Phenotype Ontology: Semantic Unification of Common and Rare
        Disease.'
    - id: https://www.ncbi.nlm.nih.gov/pubmed/24217912
      title: 'The Human Phenotype Ontology project: linking molecular biology and
        disease through phenotype data.'
    - id: https://www.ncbi.nlm.nih.gov/pubmed/30476213
      title: Expansion of the Human Phenotype Ontology (HPO) knowledge base and resources.
    repository: https://github.com/obophenotype/human-phenotype-ontology
    twitter: hp_ontology
  ols:
    description: The Human Phenotype Ontology (HPO) provides a standardized vocabulary
      of phenotypic abnormalities and clinical features encountered in human disease.
    download_owl: http://purl.obolibrary.org/obo/hp/hp-international.owl
    homepage: http://www.human-phenotype-ontology.org/
    name: Human Phenotype Ontology
    prefix: hp
    tracker: https://github.com/obophenotype/human-phenotype-ontology/issues/
    version: '2025-11-24'
    version.iri: http://purl.obolibrary.org/obo/hp/releases/2025-11-24/hp-international.owl
  ontobee:
    library: Library
    name: Human Phenotype Ontology (HPO)
    prefix: HP
  pattern: ^\d{7}$
  prefix: hp
  publications:
  - doi: 10.1186/s13059-025-03616-4
    pmc: PMC12131445
    pubmed: '40462185'
    title: A resource for whole-body gene expression map of human tissues based on
      integration of single cell and bulk transcriptomics
    year: 2025
  - doi: 10.1093/nar/gky1105
    pmc: PMC6324074
    pubmed: '30476213'
    title: Expansion of the Human Phenotype Ontology (HPO) knowledge base and resources
    year: 2019
  - doi: 10.1093/nar/gkw1039
    pmc: PMC5210535
    pubmed: '27899602'
    title: The Human Phenotype Ontology in 2017
    year: 2016
  - doi: 10.1016/j.ajhg.2015.05.020
    pmc: PMC4572507
    pubmed: '26119816'
    title: 'The Human Phenotype Ontology: Semantic Unification of Common and Rare
      Disease'
    year: 2015
  - doi: 10.1093/nar/gkt1026
    pmc: PMC3965098
    pubmed: '24217912'
    title: 'The Human Phenotype Ontology project: linking molecular biology and disease
      through phenotype data'
    year: 2013
  - doi: 10.1111/j.1399-0004.2010.01436.x
    pmc: null
    pubmed: '20412080'
    title: The human phenotype ontology
    year: 2010
  - doi: 10.1016/j.ajhg.2008.09.017
    pmc: PMC2668030
    pubmed: '18950739'
    title: 'The Human Phenotype Ontology: a tool for annotating and analyzing human
      hereditary disease'
    year: 2008
  - doi: null
    pmc: null
    pubmed: '18950739'
    title: 'The Human Phenotype Ontology: a tool for annotating and analyzing human
      hereditary disease'
    year: null
  - doi: null
    pmc: null
    pubmed: '26119816'
    title: 'The Human Phenotype Ontology: Semantic Unification of Common and Rare
      Disease'
    year: null
  - doi: null
    pmc: null
    pubmed: '24217912'
    title: 'The Human Phenotype Ontology project: linking molecular biology and disease
      through phenotype data'
    year: null
  - doi: null
    pmc: null
    pubmed: '30476213'
    title: Expansion of the Human Phenotype Ontology (HPO) knowledge base and resources
    year: null
  - doi: 10.1093/nar/gkt1026
    pmc: null
    pubmed: '24217912'
    title: 'The Human Phenotype Ontology project: linking molecular biology and disease
      through phenotype data'
    year: 2013
  - doi: 10.1093/nar/gkw1039
    pmc: null
    pubmed: '27899602'
    title: The Human Phenotype Ontology in 2017
    year: 2016
  - doi: 10.1111/j.1399-0004.2010.01436.x
    pmc: null
    pubmed: '20412080'
    title: The human phenotype ontology
    year: 2010
  - doi: 10.1093/nar/gky1105
    pmc: null
    pubmed: '30476213'
    title: Expansion of the Human Phenotype Ontology (HPO) knowledge base and resources
    year: 2018
  - doi: 10.1016/j.ajhg.2008.09.017
    pmc: null
    pubmed: '18950739'
    title: 'The Human Phenotype Ontology: a tool for annotating and analyzing human
      hereditary disease'
    year: 2008
  - doi: 10.1093/nar/gkad1005
    pmc: null
    pubmed: '37953324'
    title: 'The Human Phenotype Ontology in 2024: phenotypes around the world'
    year: 2024
  synonyms:
  - hpo
  tib:
    description: The Human Phenotype Ontology (HPO) provides a standardized vocabulary
      of phenotypic abnormalities and clinical features encountered in human disease.
    download_owl: http://purl.obolibrary.org/obo/hp.owl
    homepage: https://hpo.jax.org/app/
    keywords:
    - FAIR Data Spaces
    - life sciences, biology
    - medicine
    name: Human Phenotype Ontology
    prefix: hp
    tracker: https://github.com/obophenotype/human-phenotype-ontology/issues/
    version.iri: http://purl.obolibrary.org/obo/hp/releases/2025-10-22/hp.owl
  uri_format: http://purl.obolibrary.org/obo/HP_$1
  wikidata:
    description: identifier of a concept in the widely used vocabulary of phenotypic
      abnormalities encountered in human disease
    example:
    - HP:0001094
    - HP:0002013
    - HP:0003581
    homepage: http://human-phenotype-ontology.github.io/about.html
    name: Human Phenotype Ontology ID
    pattern: ^HP:[0-9]{7}$
    prefix: P3841
    uri_format: https://hpo.jax.org/app/browse/term/$1
hpa:
  biocontext:
    prefix: HPA
  fairsharing:
    abbreviation: HPA
    contact:
      email: mathias.uhlen@scilifelab.se
      name: Mathias Uhlen
      orcid: 0000-0002-4858-8056
    description: 'The Human Protein Atlas (HPA) portal is a publicly available database
      with millions of high-resolution images showing the spatial distribution of
      proteins in a number of different wild-type tissues, cancer types and human
      cell lines. The goal of the HPA is to map all the human proteins in cells, tissues
      and organs using an integration of various omics technologies, including antibody-based
      imaging, mass spectrometry-based proteomics, transcriptomics and systems biology.
      The HPA is composed of six parts: the Tissue Atlas, the Single Cell Type Atlas,
      the Pathology Atlas, the Blood Atlas, the Brain Atlas, and the Cell Atlas.'
    homepage: https://www.proteinatlas.org/
    license: CC BY-SA 3.0
    name: The Human Protein Atlas
    prefix: FAIRsharing.j0t0pe
    publications:
    - doi: 10.1074/mcp.R800013-MCP200
      pubmed_id: 18669619
      title: A genecentric Human Protein Atlas for expression profiles based on antibodies.
    - doi: 10.1002/path.2440
      pubmed_id: 18853439
      title: The Human Protein Atlas--a tool for pathology.
    - doi: 10.15252/msb.20155865
      pubmed_id: 27044256
      title: Transcriptomics resources of human tissues and organs.
    - doi: 10.1126/science.1260419
      pubmed_id: 25613900
      title: Tissue-based map of the human proteome.
    - doi: 10.1126/science.aan2507
      pubmed_id: 28818916
      title: A pathology atlas of the human cancer transcriptome
    - doi: 10.1038/nbt1210-1248
      pubmed_id: 21139605
      title: Towards a knowledge-based Human Protein Atlas.
    - doi: 10.1074/mcp.M500279-MCP200
      pubmed_id: 16127175
      title: A human protein atlas for normal and cancer tissues based on antibody
        proteomics.
    - doi: eaal3321
      pubmed_id: 28495876
      title: A subcellular map of the human proteome.
    subjects:
    - Proteomics
    - Transcriptomics
    - Biomedical Science
    - Systems Biology
    twitter: ProteinAtlas
  go:
    homepage: http://www.proteinatlas.org/
    name: Human Protein Atlas tissue profile information
    prefix: HPA
    uri_format: http://www.proteinatlas.org/tissue_profile.php?antibody_id=$1
  mappings:
    biocontext: HPA
    fairsharing: FAIRsharing.j0t0pe
    go: HPA
    miriam: hpa
    n2t: hpa
    prefixcommons: hpa
    re3data: r3d100010931
    uniprot: DB-0046
  miriam:
    deprecated: false
    description: The Human Protein Atlas (HPA) is a publicly available database with
      high-resolution images showing the spatial distribution of proteins in different
      normal and cancer human cell lines. Primary access to this collection is through
      Ensembl Gene identifiers.
    homepage: http://www.proteinatlas.org/
    id: '00000336'
    name: HPA
    namespaceEmbeddedInLui: false
    pattern: ^ENSG\d{11}$
    prefix: hpa
    sampleId: ENSG00000026508
    uri_format: http://www.proteinatlas.org/$1
  n2t:
    description: The Human Protein Atlas (HPA) is a publicly available database with
      high-resolution images showing the spatial distribution of proteins in different
      normal and cancer human cell lines. Primary access to this collection is through
      Ensembl Gene identifiers.
    example: ENSG00000026508
    homepage: http://www.proteinatlas.org/
    name: Human Protein Atlas at AlbaNova University
    namespaceEmbeddedInLui: false
    pattern: ^ENSG\d{11}$
    prefix: hpa
    uri_format: http://www.proteinatlas.org/$1
  prefix: hpa
  prefixcommons:
    description: The Human Protein Atlas (HPA) portal is a publicly available database
      with millions of high-resolution images showing the spatial distribution of
      proteins in 48 different normal tissues and 20 different cancer types as well
      as 47 different human cell lines.
    example: ENSG00000026508
    homepage: http://www.proteinatlas.org/
    keywords:
    - protein
    - structure
    name: Human Protein Atlas
    pattern: ^ENSG\d{11}$
    prefix: hpa
    pubmed_ids:
    - '18669619'
    uri_format: http://www.proteinatlas.org/gene_info.php?ensembl_gene_id=$1
  publications:
  - doi: 10.1126/science.aan2507
    pmc: null
    pubmed: '28818916'
    title: A pathology atlas of the human cancer transcriptome
    year: 2017
  - doi: 10.1126/science.aal3321
    pmc: null
    pubmed: '28495876'
    title: A subcellular map of the human proteome
    year: 2017
  - doi: 10.15252/msb.20155865
    pmc: PMC4848759
    pubmed: '27044256'
    title: Transcriptomics resources of human tissues and organs
    year: 2016
  - doi: 10.1126/science.1260419
    pmc: null
    pubmed: '25613900'
    title: Proteomics. Tissue-based map of the human proteome
    year: 2015
  - doi: 10.1038/nbt1210-1248
    pmc: null
    pubmed: '21139605'
    title: Towards a knowledge-based Human Protein Atlas
    year: 2010
  - doi: 10.1074/mcp.r800013-mcp200
    pmc: null
    pubmed: '18669619'
    title: A genecentric Human Protein Atlas for expression profiles based on antibodies
    year: 2008
  - doi: 10.1002/path.2440
    pmc: null
    pubmed: '18853439'
    title: The Human Protein Atlas--a tool for pathology
    year: 2008
  - doi: 10.1074/mcp.m500279-mcp200
    pmc: null
    pubmed: '16127175'
    title: A human protein atlas for normal and cancer tissues based on antibody proteomics
    year: 2005
  - doi: 10.1074/mcp.R800013-MCP200
    pmc: null
    pubmed: null
    title: A genecentric Human Protein Atlas for expression profiles based on antibodies.
    year: null
  - doi: 10.1002/path.2440
    pmc: null
    pubmed: null
    title: The Human Protein Atlas--a tool for pathology.
    year: null
  - doi: 10.15252/msb.20155865
    pmc: null
    pubmed: null
    title: Transcriptomics resources of human tissues and organs.
    year: null
  - doi: 10.1126/science.1260419
    pmc: null
    pubmed: null
    title: Tissue-based map of the human proteome.
    year: null
  - doi: 10.1126/science.aan2507
    pmc: null
    pubmed: null
    title: A pathology atlas of the human cancer transcriptome
    year: null
  - doi: 10.1038/nbt1210-1248
    pmc: null
    pubmed: null
    title: Towards a knowledge-based Human Protein Atlas.
    year: null
  - doi: 10.1074/mcp.M500279-MCP200
    pmc: null
    pubmed: null
    title: A human protein atlas for normal and cancer tissues based on antibody proteomics.
    year: null
  - doi: eaal3321
    pmc: null
    pubmed: null
    title: A subcellular map of the human proteome.
    year: null
  - doi: null
    pmc: null
    pubmed: '18669619'
    title: null
    year: null
  - doi: 10.1126/science.1260419
    pmc: null
    pubmed: '25613900'
    title: null
    year: null
  re3data:
    description: The Swedish Human Protein Atlas project has been set up to allow
      for a systematic exploration of the human proteome using Antibody-Based Proteomics.
      This is accomplished by combining high-throughput generation of affinity-purified
      antibodies with protein profiling in a multitude of tissues and cells assembled
      in tissue microarrays. Confocal microscopy analysis using human cell lines is
      performed for more detailed protein localization. The program hosts the Human
      Protein Atlas portal with expression profiles of human proteins in tissues and
      cells.  The main objective of the resource centre is to produce specific antibodies
      to human target proteins using a high-throughput production method involving
      the cloning and protein expression of Protein Epitope Signature Tags (PrESTs).
      After purification, the antibodies are used to study expression profiles in
      cells and tissues and for functional analysis of the corresponding proteins
      in a wide range of platforms.
    doi: 10.17616/R35S55
    homepage: https://www.proteinatlas.org/
    name: The Human Protein Atlas
    prefix: r3d100010931
    synonyms:
    - HPA
    xrefs:
      nif: 0000-00204
  uniprot:
    abbreviation: HPA
    category: Organism-specific databases
    homepage: https://www.proteinatlas.org/
    name: Human Protein Atlas
    prefix: DB-0046
    publications:
    - doi: 10.1126/science.1260419
      pubmed: '25613900'
    uri_format: https://www.proteinatlas.org/$1
hpath:
  comment: 'This ontology used to be available in OLS3, but is no longer available
    in OLS4.


    The URI format string in this resource takes the form of an OBO PURL, but it is
    not itself registered with the OBO Foundry, and terms therefore redirect into
    http://ontologies.berkeleybop.org. This happens because the data is curated natively
    in the OBO Flat File Format from which CURIEs are automatically assumed to expand
    to OBO PURLs'
  contact:
    email: carlo.ravagli@novartis.com
    github: carloravagli
    name: Carlo Ravagli
    orcid: 0000-0001-8372-8387
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: 'An ontology of histopathological morphologies used by pathologists
    to classify/categorise animal lesions observed histologically during regulatory
    toxicology studies. The ontology was developed using real data from over 6000
    regulatory toxicology studies donated by 13 companies spanning nine species.


    The original structure of the histopathology ontology was designed ab initio when
    the [INHAND](http://www.goreni.org/) manuscripts were not available. However,
    the ontology has been repetitively reviewed and updated to align with the subsequently
    published INHAND manuscripts. During this process cross references to INHAND lesion
    identifiers were added to the ontology. [from GitHub]'
  download_obo: https://raw.githubusercontent.com/Novartis/hpath/master/src/hpath.obo
  example: '2000191'
  homepage: https://github.com/Novartis/hpath
  name: Histopathology Ontology
  pattern: ^\d+$
  prefix: hpath
  references:
  - https://github.com/biopragmatics/bioregistry/issues/927
  repository: https://github.com/Novartis/hpath
  synonyms:
  - MC
  uri_format: http://purl.obolibrary.org/obo/MC_$1
hpm.peptide:
  biocontext:
    prefix: HPM.PEPTIDE
  mappings:
    biocontext: HPM.PEPTIDE
    miriam: hpm.peptide
    n2t: hpm.peptide
  miriam:
    deprecated: false
    description: The Human Proteome Map (HPM) portal integrates the peptide sequencing
      result from the draft map of the human proteome project. The project was based
      on LC-MS/MS by utilizing of high resolution and high accuracy Fourier transform
      mass spectrometry. The HPM contains direct evidence of translation of a number
      of protein products derived from human genes, based on peptide identifications
      of multiple organs/tissues and cell types from individuals with clinically defined
      healthy tissues. The HPM portal provides data on individual proteins, as well
      as on individual peptide spectra. This collection references individual peptides
      through spectra.
    homepage: http://www.humanproteomemap.org/index.php
    id: '00000527'
    name: Human Proteome Map Peptide
    namespaceEmbeddedInLui: false
    pattern: ^\d+$
    prefix: hpm.peptide
    sampleId: '9606117'
    uri_format: http://www.humanproteomemap.org/spectrum.php?pep_id=$1
  n2t:
    description: The Human Proteome Map (HPM) portal integrates the peptide sequencing
      result from the draft map of the human proteome project. The project was based
      on LC-MS/MS by utilizing of high resolution and high accuracy Fourier transform
      mass spectrometry. The HPM contains direct evidence of translation of a number
      of protein products derived from human genes, based on peptide identifications
      of multiple organs/tissues and cell types from individuals with clinically defined
      healthy tissues. The HPM portal provides data on individual proteins, as well
      as on individual peptide spectra. This collection references individual peptides
      through spectra.
    example: '9606117'
    homepage: http://www.humanproteomemap.org/index.php
    name: Human Proteome Map Peptide at Institute of Bioinformatics (Bangalore)
    namespaceEmbeddedInLui: false
    pattern: ^\d+$
    prefix: hpm.peptide
    uri_format: http://www.humanproteomemap.org/spectrum.php?pep_id=$1
  prefix: hpm.peptide
hpm.protein:
  biocontext:
    prefix: HPM.PROTEIN
  mappings:
    biocontext: HPM.PROTEIN
    miriam: hpm.protein
    n2t: hpm.protein
    ncbi: HPM
  miriam:
    deprecated: true
    description: The Human Proteome Map (HPM) portal integrates the peptide sequencing
      result from the draft map of the human proteome project. The project was based
      on LC-MS/MS by utilizing of high resolution and high accuracy Fourier transform
      mass spectrometry. The HPM contains direct evidence of translation of a number
      of protein products derived from human genes, based on peptide identifications
      of multiple organs/tissues and cell types from individuals with clinically defined
      healthy tissues. The HPM portal provides data on individual proteins, as well
      as on individual peptide spectra. This collection references proteins.
    homepage: http://www.humanproteomemap.org/index.php
    id: '00000526'
    name: Human Proteome Map Protein
    namespaceEmbeddedInLui: false
    pattern: ^\d+$
    prefix: hpm.protein
    sampleId: '1968'
    uri_format: http://www.humanproteomemap.org/protein.php?hpm_id=$1
  n2t:
    description: The Human Proteome Map (HPM) portal integrates the peptide sequencing
      result from the draft map of the human proteome project. The project was based
      on LC-MS/MS by utilizing of high resolution and high accuracy Fourier transform
      mass spectrometry. The HPM contains direct evidence of translation of a number
      of protein products derived from human genes, based on peptide identifications
      of multiple organs/tissues and cell types from individuals with clinically defined
      healthy tissues. The HPM portal provides data on individual proteins, as well
      as on individual peptide spectra. This collection references proteins.
    example: '1968'
    homepage: http://www.humanproteomemap.org/index.php
    name: Human Proteome Map Protein at Institute of Bioinformatics (Bangalore)
    namespaceEmbeddedInLui: false
    pattern: ^\d+$
    prefix: hpm.protein
    uri_format: http://www.humanproteomemap.org/protein.php?hpm_id=$1
  ncbi:
    example: '8106'
    homepage: http://www.humanproteomemap.org/
    name: Human Proteome Map
    prefix: HPM
  prefix: hpm.protein
hprd:
  biocontext:
    prefix: HPRD
    uri_format: http://www.hprd.org/protein/$1
  fairsharing:
    abbreviation: HPRD
    contact:
      email: pandey@jhmi.edu
      name: Akhilesh Pandey
      orcid: 0000-0001-9943-6127
    description: The Human Protein Reference Database represents a centralized platform
      to visually depict and integrate information pertaining to domain architecture,
      post-translational modifications, interaction networks and disease association
      for each protein in the human proteome.
    homepage: http://www.hprd.org/
    name: Human Protein Reference Database
    prefix: FAIRsharing.y2qws7
    publications:
    - doi: 10.1093/nar/gkn892
      pubmed_id: 18988627
      title: Human Protein Reference Database--2009 update.
    subjects: []
  integbio:
    alt_name: Human Protein Reference Database
    description: "HPRD (Human Protein Reference Database) version 9 is a manually\
      \ curated, fully GO compliant protein database.\nThe repository contains 30,047\
      \ protein entries, 41,327 protein-protein interactions and 93,710 posttranslational\
      \ modifications. There are 112,158 occurrences of protein expression, 22,490\
      \ of subcellular positioning and 470 domains are identified. \nAll the information\
      \ in HPRD, including features of proteins such as post-translational modifications,\
      \ tissue expression, subcellular localization and protein-protein interactions,\
      \ may be downloaded as XML and FLAT files. Permission is, however, necessary\
      \ before this may be done.\nThe database can be browsed by selecting a protein,\
      \ domain, motif, PTM or localization class of interest from a list that is provided.\
      \ \nA Blast search option is available by entering a nucleotide or protein sequence."
    fairsharing: biodbcore-000395
    homepage: http://www.hprd.org
    information_keywords:
    - Sequence
    maintainer: Institute of Bioinformatics
    name: HPRD
    prefix: nbdc00103
    pubmeds:
    - '18988627'
    status: Inactive
    target_keywords:
    - cDNA/EST
    - Protein
    - Health/Disease
  mappings:
    biocontext: HPRD
    fairsharing: FAIRsharing.y2qws7
    integbio: nbdc00103
    miriam: hprd
    n2t: hprd
    pathguide: '14'
    prefixcommons: hprd
    re3data: r3d100010978
  miriam:
    deprecated: true
    description: The Human Protein Reference Database (HPRD) represents a centralized
      platform to visually depict and integrate information pertaining to domain architecture,
      post-translational modifications, interaction networks and disease association
      for each protein in the human proteome.
    homepage: http://www.hprd.org/
    id: '00000377'
    name: HPRD
    namespaceEmbeddedInLui: false
    pattern: ^\d+$
    prefix: hprd
    sampleId: '00001'
    uri_format: http://www.hprd.org/protein/$1
  n2t:
    description: The Human Protein Reference Database (HPRD) represents a centralized
      platform to visually depict and integrate information pertaining to domain architecture,
      post-translational modifications, interaction networks and disease association
      for each protein in the human proteome.
    example: '00001'
    homepage: http://www.hprd.org/
    name: Human Protein Reference Database
    namespaceEmbeddedInLui: false
    pattern: ^\d+$
    prefix: hprd
    uri_format: http://www.hprd.org/protein/$1
  name: Human Protein Reference Database
  pathguide:
    abbreviation: HPRD
    homepage: http://www.hprd.org/
    keywords:
    - PSI-MI
    name: Human Protein Reference Database
    prefix: '14'
  prefix: hprd
  prefixcommons:
    description: The Human Protein Reference Database represents a centralized platform
      to visually depict and integrate information pertaining to domain architecture,
      post-translational modifications, interaction networks and disease association
      for each protein in the human proteome.
    example: '00001'
    homepage: http://www.hprd.org/
    keywords:
    - protein
    - structure
    name: Human Protein Reference Database
    pattern: ^\d+$
    prefix: hprd
    pubmed_ids:
    - '18988627'
  publications:
  - doi: 10.1093/nar/gkn892
    pmc: PMC2686490
    pubmed: '18988627'
    title: Human Protein Reference Database--2009 update
    year: 2008
  - doi: 10.1093/nar/gkn892
    pmc: null
    pubmed: null
    title: Human Protein Reference Database--2009 update.
    year: null
  - doi: null
    pmc: null
    pubmed: '18988627'
    title: null
    year: null
  re3data:
    description: 'Human Protein Reference Database (HPRD) has been established by
      a team of biologists, bioinformaticists and software engineers. This is a joint
      project between the PandeyLab at Johns Hopkins University, and Institute of
      Bioinformatics, Bangalore.  HPRD is a definitive repository of human proteins.
      This database should serve as a ready reckoner for researchers in their quest
      for drug discovery, identification of disease markers and promote biomedical
      research in general.

      Human Proteinpedia (www.humanproteinpedia.org) is its associated data portal.'
    doi: 10.17616/R3MK9N
    homepage: http://www.hprd.org
    name: Human Protein Reference Database
    prefix: r3d100010978
    synonyms:
    - HPRD
    xrefs:
      nif: 0000-00137
      omics: 02439
hpscreg:
  cellosaurus:
    category: Cell line databases/resources
    homepage: https://hpscreg.eu
    name: Human Pluripotent Stem Cell Registry
    prefix: hPSCreg
    uri_format: https://hpscreg.eu/cell-line/$1
  fairsharing:
    abbreviation: hPSCreg
    contact:
      email: stefanie.seltmann@ibmt.fraunhofer.de
      name: Stefanie Seltmann
      orcid: 0000-0002-8411-3226
    description: The human pluripotent stem cell registry (hPSCreg) is a public registry
      and data portal for human embryonic and induced pluripotent stem cell lines
      (hESC and hiPSC). The Registry provides comprehensive and standardized biological
      and legal information as well as tools to search and compare information from
      multiple hPSC sources and hence addresses a translational research need. To
      facilitate unambiguous identification over different resources, hPSCreg automatically
      creates a unique standardized name for each cell line registered. In addition
      to biological information, hPSCreg stores extensive data about ethical standards
      regarding cell sourcing and conditions for application and privacy protection.
      hPSCreg is the first global registry that holds both, manually validated scientific
      and ethical information on hPSC lines, and provides access by means of a user-friendly,
      mobile-ready web application.
    homepage: https://hpscreg.eu/
    name: Human Pluripotent Stem Cell Registry
    prefix: FAIRsharing.7C0aVE
    publications:
    - doi: S2213-6711(20)30235-6
      pubmed_id: 32679065
      title: A Manually Curated Database on Clinical Studies Involving Cell Products
        Derived from Human Pluripotent Stem Cells.
    - doi: S1873-5061(20)30188-4
      pubmed_id: 32707486
      title: 'Access to stem cell data and registration of pluripotent cell lines:
        The Human Pluripotent Stem Cell Registry (hPSCreg).'
    - doi: S1873-5061(19)30169-2
      pubmed_id: 31450190
      title: 'A pathway for attesting ethical provenance of cell lines: Lessons from
        the European human pluripotent stem cell registry (hPSC(reg)).'
    - doi: S2213-6711(17)30531-3
      pubmed_id: 29320760
      title: A Standard Nomenclature for Referencing and Authentication of Pluripotent
        Stem Cells.
    - doi: 10.1093/nar/gkv963
      pubmed_id: 26400179
      title: hPSCreg--the human pluripotent stem cell registry.
    subjects:
    - Life Science
    - Biomedical Science
  mappings:
    cellosaurus: hPSCreg
    fairsharing: FAIRsharing.7C0aVE
    miriam: hpscreg
    n2t: hpscreg
    re3data: r3d100012863
  miriam:
    deprecated: false
    description: hPSCreg is a freely accessible global registry for human pluripotent
      stem cell lines (hPSC-lines).
    homepage: https://hpscreg.eu/
    id: '00000674'
    name: Human Pluripotent Stem Cell Registry
    namespaceEmbeddedInLui: false
    pattern: ^[A-Z]{2,6}(e|i)[A-Za-z0-9]{3}-[A-Z]{1,2}(-[A-Za-z0-9]{1,2})?$
    prefix: hpscreg
    sampleId: BCRTi001-A
    uri_format: https://hpscreg.eu/cell-line/$1
  n2t:
    description: hPSCreg is a freely accessible global registry for human pluripotent
      stem cell lines (hPSC-lines).
    example: BCRTi001-A
    homepage: https://hpscreg.eu/
    name: Human Pluripotent Stem Cell Registry
    namespaceEmbeddedInLui: false
    pattern: ^[A-Z]{2,6}(e|i)[A-Za-z0-9]{3}-[A-Z]{1,2}(-[A-Za-z0-9]{1,2})?$
    prefix: hpscreg
    uri_format: https://hpscreg.eu/cell-line/$1
  prefix: hpscreg
  publications:
  - doi: 10.1016/j.stemcr.2020.06.014
    pmc: PMC7419703
    pubmed: '32679065'
    title: A Manually Curated Database on Clinical Studies Involving Cell Products
      Derived from Human Pluripotent Stem Cells
    year: 2020
  - doi: 10.1016/j.scr.2020.101887
    pmc: null
    pubmed: '32707486'
    title: 'Access to stem cell data and registration of pluripotent cell lines: The
      Human Pluripotent Stem Cell Registry (hPSCreg)'
    year: 2020
  - doi: 10.1016/j.scr.2019.101539
    pmc: null
    pubmed: '31450190'
    title: 'A pathway for attesting ethical provenance of cell lines: Lessons from
      the European human pluripotent stem cell registry (hPSC'
    year: 2019
  - doi: 10.1016/j.stemcr.2017.12.002
    pmc: PMC5768986
    pubmed: '29320760'
    title: A Standard Nomenclature for Referencing and Authentication of Pluripotent
      Stem Cells
    year: 2018
  - doi: 10.1093/nar/gkv963
    pmc: PMC4702942
    pubmed: '26400179'
    title: hPSCreg--the human pluripotent stem cell registry
    year: 2015
  re3data:
    description: The human pluripotent stem cell registry (hPSCreg) is a public registry
      and data portal for human embryonic and induced pluripotent stem cell lines
      (hESC and hiPSC). The Registry provides comprehensive and standardized biological
      and legal information as well as tools to search and compare information from
      multiple hPSC sources and hence addresses a translational research need. To
      facilitate unambiguous identification over different resources, hPSCreg automatically
      creates a unique standardized name (identifier) for each cell line registered.
      In addition to biological information, hPSCreg stores extensive data about ethical
      standards regarding cell sourcing and conditions for application and privacy
      protection. hPSCreg is the first global registry that holds both, manually validated
      scientific and ethical information on hPSC lines, and provides access by means
      of a user-friendly, mobile-ready web application.
    doi: 10.17616/R36B9H
    homepage: https://hpscreg.eu/
    name: hPSCreg
    prefix: r3d100012863
    synonyms:
    - human Pluripotent Stem Cell registry
hsapdv:
  aberowl:
    description: Life cycle stages for Human
    download_owl: http://aber-owl.net/media/ontologies/HSAPDV/14/hsapdv.owl
    homepage: https://github.com/obophenotype/developmental-stage-ontologies/wiki/HsapDv
    name: Human Developmental Stages
    prefix: HSAPDV
  biocontext:
    prefix: HSAPDV
  biolink:
    is_identifiers: false
    is_obo: true
    prefix: HsapDv
    uri_format: http://purl.obolibrary.org/obo/HsapDv_$1
  bioportal:
    contact:
      email: cjmungall@lbl.gov
      name: Chris Mungall
    description: Life cycle stages for Human. HsapDv was developed by the Bgee group
      with assistance from the core Uberon developers and the Human developmental
      anatomy ontology (EHDAA2) developers. Currently it includes both embryonic (Carnegie)
      stages and adult stages.
    homepage: https://github.com/obophenotype/developmental-stage-ontologies/wiki/HsapDv
    name: Human Developmental Stages Ontology
    prefix: HSAPDV
    version: '2025-01-23'
  example: 0000194
  fairsharing:
    abbreviation: HSAPDV
    description: Life cycle stages for Human. HsapDv was developed by the Bgee group
      with assistance from the core Uberon developers and the Human developmental
      anatomy ontology (EHDAA2) developers. Currently it includes both embryonic (Carnegie)
      stages and adult stages.
    domains:
    - life cycle stage
    homepage: https://obofoundry.org/ontology/hsapdv.html
    license: CC-BY-3.0
    name: Human Developmental Stages Ontology
    prefix: FAIRsharing.c6vhm3
    repository: https://github.com/obophenotype/developmental-stage-ontologies/wiki/HsapDv
    subjects:
    - Anatomy
    - Developmental Biology
  mappings:
    aberowl: HSAPDV
    biocontext: HSAPDV
    biolink: HsapDv
    bioportal: HSAPDV
    fairsharing: FAIRsharing.c6vhm3
    obofoundry: hsapdv
    ols: hsapdv
    ontobee: HsapDv
    wikidata.entity: Q81661653
  obofoundry:
    appears_in:
    - scdo
    contact: frederic.bastian@unil.ch
    contact.github: fbastian
    contact.label: Frédéric Bastian
    contact.orcid: 0000-0002-9415-5104
    deprecated: false
    description: Life cycle stages for Human
    domain: anatomy and development
    download.obo: http://purl.obolibrary.org/obo/hsapdv.obo
    download.owl: http://purl.obolibrary.org/obo/hsapdv.owl
    homepage: https://github.com/obophenotype/developmental-stage-ontologies/wiki/HsapDv
    license: CC BY 3.0
    license.url: http://creativecommons.org/licenses/by/3.0/
    name: Human Developmental Stages
    preferredPrefix: HsapDv
    prefix: hsapdv
    repository: https://github.com/obophenotype/developmental-stage-ontologies
  ols:
    description: Life cycle stages for Human
    download_owl: http://purl.obolibrary.org/obo/hsapdv.owl
    homepage: https://github.com/obophenotype/developmental-stage-ontologies/wiki/HsapDv
    name: Human Developmental Stages
    prefix: hsapdv
    tracker: https://github.com/obophenotype/developmental-stage-ontologies/issues
    version: '2025-01-23'
    version.iri: http://purl.obolibrary.org/obo/life-stages/releases/2025-01-23/components/hsapdv.owl
  ontobee:
    library: Library
    name: Human Developmental Stages
    prefix: HsapDv
  pattern: ^\d{7}$
  prefix: hsapdv
  synonyms:
  - HsapDv
  uri_format: http://purl.obolibrary.org/obo/HsapDv_$1
hsdb:
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: The Hazardous Substances Data Bank (HSDB) is a toxicology database
    that focuses on the toxicology of potentially hazardous chemicals. It provides
    information on human exposure, industrial hygiene, emergency handling procedures,
    environmental fate, regulatory requirements, nanomaterials, and related areas.
  example: '5621'
  homepage: https://pubchem.ncbi.nlm.nih.gov/source/hsdb
  integbio:
    alt_name: Hazardous Substances Data Bank
    description: HSDB is a database of hazardous substances. The database contains
      information on toxic compounds gathered from primary, peer-reviewed literature.
      Users can search by compound, CAS, or symptom. Fact sheets and other support
      are also available.
    homepage: http://toxnet.nlm.nih.gov/cgi-bin/sis/htmlgen?HSDB
    information_keywords:
    - Bibliography/Documents
    - Chemical structure
    maintainer: NLM (National Library of Medicine)
    name: HSDB
    prefix: nbdc00930
    pubmeds:
    - '14728459'
    - '8545846'
    status: Inactive
    target_keywords:
    - Chemical compound
  mappings:
    integbio: nbdc00930
    wikidata: P2062
  name: Hazardous Substances Data Bank
  pattern: ^\d+$
  prefix: hsdb
  uri_format: https://pubchem.ncbi.nlm.nih.gov/source/hsdb/$1
  wikidata:
    description: ID in Hazardous Substances Data Bank
    example:
    - '1112'
    - '8055'
    name: HSDB ID
    pattern: ^\d+$
    prefix: P2062
    uri_format: https://pubchem.ncbi.nlm.nih.gov/source/hsdb/$1
hso:
  aberowl:
    description: The health Surveillance Ontology (HSO) focuses on "surveillance system
      level data", that is, data outputs from surveillance activities, such as number
      of samples collected, cases observed, etc. It aims to support One-Health surveillance,
      covering animal health, public health and food safety surveillance.
    download_owl: http://aber-owl.net/media/ontologies/HSO/11/hso.owl
    homepage: https://w3id.org/hso
    name: Health Surveillance Ontology
    prefix: HSO
  bioportal:
    contact:
      email: fernanda.dorea@sva.se
      name: Fernanda Dórea
    description: This is an ontology to support (one) health surveillance, focused
      on "surveillance system level data", that is, data outputs from surveillance
      activities, such as number of samples collected, cases observed, etc., An ontology
      to support semantic interoperability among domains involved in health surveillance
      (animal health, public health and food safety). More details at http://datadrivensurveillance.org.
    homepage: https://w3id.org/hso
    name: Health Surveillance Ontology
    prefix: HSO
    version: 3.1.1
  example: '0000062'
  mappings:
    aberowl: HSO
    bioportal: HSO
    obofoundry: hso
    ols: hso
    ontobee: HSO
    wikidata.entity: Q113012664
  obofoundry:
    contact: fernanda.dorea@sva.se
    contact.github: nandadorea
    contact.label: Fernanda Dorea
    contact.orcid: 0000-0001-8638-8525
    depends_on:
    - bfo
    - ncbitaxon
    - obi
    - ro
    - uberon
    deprecated: false
    description: The health Surveillance Ontology (HSO) focuses on "surveillance system
      level data", that is, data outputs from surveillance activities, such as number
      of samples collected, cases observed, etc. It aims to support One-Health surveillance,
      covering animal health, public health and food safety surveillance.
    domain: health
    download.owl: http://purl.obolibrary.org/obo/hso.owl
    homepage: https://w3id.org/hso
    license: CC BY 3.0
    license.url: http://creativecommons.org/licenses/by/3.0/
    name: Health Surveillance Ontology
    preferredPrefix: HSO
    prefix: hso
    repository: https://github.com/SVA-SE/HSO
  ols:
    description: The health Surveillance Ontology (HSO) focuses on "surveillance system
      level data", that is, data outputs from surveillance activities, such as number
      of samples collected, cases observed, etc. It aims to support One-Health surveillance,
      covering animal health, public health and food safety surveillance.
    download_owl: http://purl.obolibrary.org/obo/hso.owl
    homepage: https://w3id.org/hso
    name: Health Surveillance Ontology
    prefix: hso
    tracker: https://github.com/SVA-SE/HSO/issues/
    version: '2021-12-13'
    version.iri: http://purl.obolibrary.org/obo/hso/2021-12-13/hso.owl
  ontobee:
    library: Library
    name: Health Surveillance Ontology
    prefix: HSO
  pattern: ^\d{7}$
  prefix: hso
  providers:
  - code: hso.legacy
    description: An incorrect encoding of OBO purls
    example: null
    first_party: null
    homepage: http://purl.obolibrary.org/obo/hso
    name: HSO Hash
    publications: null
    status: null
    uri_format: http://purl.obolibrary.org/obo/hso.owl#HSO_$1
  uri_format: http://purl.obolibrary.org/obo/HSO_$1
hssp:
  biocontext:
    prefix: HSSP
  contact:
    email: chris@sanderlab.org
    github: sanderlab
    name: Chris Sander
    orcid: 0000-0001-6059-6270
  mappings:
    biocontext: HSSP
    miriam: hssp
    n2t: hssp
    ncbi: HSSP
    prefixcommons: hssp
  miriam:
    deprecated: false
    description: HSSP (homology-derived structures of proteins) is a derived database
      merging structural (2-D and 3-D) and sequence information (1-D). For each protein
      of known 3D structure from the Protein Data Bank, the database has a file with
      all sequence homologues, properly aligned to the PDB protein.
    homepage: http://swift.cmbi.kun.nl/swift/hssp/
    id: '00000215'
    name: HSSP
    namespaceEmbeddedInLui: false
    pattern: ^\w{4}$
    prefix: hssp
    providers:
    - code: ''
      description: HSSP at CMBI
      homepage: ftp://ftp.cmbi.ru.nl/pub/molbio/data/hssp/
      name: HSSP at CMBI
      uri_format: ftp://ftp.cmbi.ru.nl/pub/molbio/data/hssp/$1.hssp.bz2
    sampleId: 102l
    uri_format: ftp://ftp.embl-heidelberg.de/pub/databases/protein_extras/hssp/$1.hssp.bz2
  n2t:
    description: HSSP (homology-derived structures of proteins) is a derived database
      merging structural (2-D and 3-D) and sequence information (1-D). For each protein
      of known 3D structure from the Protein Data Bank, the database has a file with
      all sequence homologues, properly aligned to the PDB protein.
    example: 102l
    homepage: ftp://ftp.cmbi.ru.nl/pub/molbio/data/hssp/
    name: HSSP at CMBI
    namespaceEmbeddedInLui: false
    pattern: ^\w{4}$
    prefix: hssp
    uri_format: ftp://ftp.cmbi.ru.nl/pub/molbio/data/hssp/$1.hssp.bz2
  ncbi:
    example: 12GS
    name: Database of homology-derived secondary structure of proteins
    prefix: HSSP
  prefix: hssp
  prefixcommons:
    description: HSSP (homology-derived structures of proteins) is a derived database
      merging structural (2-D and 3-D) and sequence information (1-D). For each protein
      of known 3D structure from the Protein Data Bank, the database has a file with
      all sequence homologues, properly aligned to the PDB protein.
    example: 102l
    homepage: http://www.cmbi.kun.nl/gv/hssp/
    keywords:
    - clustering
    - protein
    - sequence
    name: Homology-derived secondary structure of proteins database
    pattern: ^\w{4}$
    prefix: hssp
    pubmed_ids:
    - '7937066'
    - '8594579'
  publications:
  - doi: 10.1093/nar/24.1.201
    pmc: PMC145595
    pubmed: '8594579'
    title: The HSSP database of protein structure-sequence alignments
    year: 1996
  - doi: null
    pmc: PMC308328
    pubmed: '7937066'
    title: The HSSP database of protein structure-sequence alignments
    year: 1994
htn:
  aberowl:
    description: An ontology for representing clinical data about hypertension, intended
      to support classification of patients according to various diagnostic guidelines
    download_owl: http://aber-owl.net/media/ontologies/HTN/1/htn.owl
    homepage: https://github.com/aellenhicks/htn_owl
    name: Hypertension Ontology
    prefix: HTN
  bioportal:
    contact:
      email: aellenhicks@gmail.com
      name: Amanda Hicks
    description: The Hypertension Ontology is a realism-based reference ontology for
      semantically managing clinical data about hypertension. Definitions of hypertension
      and elevated blood pressure are highly sensitive to context. Thresholds may
      vary according to population, guidelines, or clinical context. Variations in
      the clinical interpretation of blood pressure pose challenges to using blood
      pressure data for cohort identification, semantic data integration across data
      sets, and semantically enriching clinical data for clinical decision support
      applications. The Hypertension Ontology provides a framework for connecting
      clinical data to context-sensitive definitions of elevated blood pressure and
      hypertension.
    homepage: https://github.com/aellenhicks/htn_owl
    name: Hypertension Ontology
    prefix: HTN
  example: '00000014'
  mappings:
    aberowl: HTN
    bioportal: HTN
    obofoundry: htn
    ols: htn
    ontobee: HTN
    wikidata.entity: Q81661655
  obofoundry:
    contact: aellenhicks@gmail.com
    contact.github: aellenhicks
    contact.label: Amanda Hicks
    contact.orcid: 0000-0002-1795-5570
    deprecated: false
    description: An ontology for representing clinical data about hypertension, intended
      to support classification of patients according to various diagnostic guidelines
    domain: health
    download.owl: http://purl.obolibrary.org/obo/htn.owl
    homepage: https://github.com/aellenhicks/htn_owl
    license: CC BY 4.0
    license.url: http://creativecommons.org/licenses/by/4.0/
    name: Hypertension Ontology
    preferredPrefix: HTN
    prefix: htn
    repository: https://github.com/aellenhicks/htn_owl
  ols:
    description: An ontology for representing clinical data about hypertension, intended
      to support classification of patients according to various diagnostic guidelines
    download_owl: http://purl.obolibrary.org/obo/htn.owl
    homepage: https://github.com/aellenhicks/htn_owl
    name: Hypertension Ontology For Clinical Data
    prefix: htn
    tracker: https://github.com/aellenhicks/htn_owl/issues
  ontobee:
    library: Library
    name: Hypertension Ontology
    prefix: HTN
  pattern: ^\d{8}$
  prefix: htn
  uri_format: http://purl.obolibrary.org/obo/HTN_$1
hubmap.collection:
  contact:
    email: katy@indiana.edu
    github: katyb
    name: Katy Börner
    orcid: 0000-0002-3321-6137
  contributor:
    email: palayoor.n@northeastern.edu
    github: nalikapalayoor
    name: Nalika Palayoor
    orcid: 0009-0008-8406-631X
  description: The collections section of HuBMAP groups related datasets, samples,
    and metadata into organized categories. Each collection has a unique identifier
    that links it to its constituent datasets.
  example: 3ae4ddfc175d768af5526a010bfe95aa
  github_request_issue: 1548
  homepage: https://portal.hubmapconsortium.org/collections
  name: Human BioMolecular Atlas Program Collection
  pattern: ^[a-f0-9]{32}$
  prefix: hubmap.collection
  publications:
  - doi: 10.1038/s41592-024-02563-5
    pmc: PMC11978508
    pubmed: '40082611'
    title: 'Human BioMolecular Atlas Program (HuBMAP): 3D Human Reference Atlas construction
      and usage'
    year: 2025
  reviewer:
    email: b.gyori@northeastern.edu
    github: bgyori
    name: Benjamin M. Gyori
    orcid: 0000-0001-9439-5346
  uri_format: https://portal.hubmapconsortium.org/browse/collection/$1
hubmap.dataset:
  contact:
    email: katy@indiana.edu
    github: katyb
    name: Katy Börner
    orcid: 0000-0002-3321-6137
  contributor:
    email: palayoor.n@northeastern.edu
    github: nalikapalayoor
    name: Nalika Palayoor
    orcid: 0009-0008-8406-631X
  description: The HuBMAP dataset collection provides high resolution molecular data
    from human tissues, with unique identifiers that enable tracking, citation, and
    integration of datasets across diverse assay types and donor samples for biomedical
    research.
  example: 4bbe3b53a985e999eb66fee3297ec3f8
  github_request_issue: 1548
  homepage: https://portal.hubmapconsortium.org/search/datasets
  name: Human BioMolecular Atlas Program Dataset
  pattern: ^[a-f0-9]{32}$
  prefix: hubmap.dataset
  publications:
  - doi: 10.1038/s41592-024-02563-5
    pmc: PMC11978508
    pubmed: '40082611'
    title: 'Human BioMolecular Atlas Program (HuBMAP): 3D Human Reference Atlas construction
      and usage'
    year: 2025
  reviewer:
    email: b.gyori@northeastern.edu
    github: bgyori
    name: Benjamin M. Gyori
    orcid: 0000-0001-9439-5346
  uri_format: https://portal.hubmapconsortium.org/browse/dataset/$1
hubmap.donor:
  contact:
    email: katy@indiana.edu
    github: katyb
    name: Katy Börner
    orcid: 0000-0002-3321-6137
  contributor:
    email: palayoor.n@northeastern.edu
    github: nalikapalayoor
    name: Nalika Palayoor
    orcid: 0009-0008-8406-631X
  description: The HuBMAP donors dataset contains demographic and clinical metadata
    for individuals who donated tissue samples. Each donor has a unique identifier
    used to link them to their associated tissue samples and derived experimental
    data.
  example: a3bc9e6193c47998758ac9d9bf9ddbb6
  github_request_issue: 1548
  homepage: https://portal.hubmapconsortium.org/search/donors
  name: Human BioMolecular Atlas Program Donor
  pattern: ^[a-f0-9]{32}$
  prefix: hubmap.donor
  publications:
  - doi: 10.1038/s41592-024-02563-5
    pmc: PMC11978508
    pubmed: '40082611'
    title: 'Human BioMolecular Atlas Program (HuBMAP): 3D Human Reference Atlas construction
      and usage'
    year: 2025
  reviewer:
    email: b.gyori@northeastern.edu
    github: bgyori
    name: Benjamin M. Gyori
    orcid: 0000-0001-9439-5346
  uri_format: https://portal.hubmapconsortium.org/browse/donor/$1
hubmap.sample:
  contact:
    email: katy@indiana.edu
    github: katyb
    name: Katy Börner
    orcid: 0000-0002-3321-6137
  contributor:
    email: palayoor.n@northeastern.edu
    github: nalikapalayoor
    name: Nalika Palayoor
    orcid: 0009-0008-8406-631X
  description: The samples subsection of HuBMAP provides metadata about individual
    tissue samples collected from donors, and are the downstream experimental datasets
    for scRNA sequencing. Each sample has a unique identifier that links it to donor
    information, anatomical source, and related datasets.
  example: a3bc9e6193c47998758ac9d9bf9ddbb6
  github_request_issue: 1548
  homepage: https://portal.hubmapconsortium.org/search/samples
  name: Human BioMolecular Atlas Program Sample
  pattern: ^[a-f0-9]{32}$
  prefix: hubmap.sample
  publications:
  - doi: 10.1038/s41592-024-02563-5
    pmc: PMC11978508
    pubmed: '40082611'
    title: 'Human BioMolecular Atlas Program (HuBMAP): 3D Human Reference Atlas construction
      and usage'
    year: 2025
  reviewer:
    email: b.gyori@northeastern.edu
    github: bgyori
    name: Benjamin M. Gyori
    orcid: 0000-0001-9439-5346
  uri_format: https://portal.hubmapconsortium.org/browse/sample/$1
huge:
  biocontext:
    prefix: HUGE
  contact:
    email: ohara@kazusa.or.jp
    github: null
    name: Osamu Ohara
    orcid: 0000-0002-3328-9571
  fairsharing:
    abbreviation: HUGE
    description: HUGE is a database for human large proteins newly identified in the
      Kazusa cDNA project, the aim of which is to predict the primary structure of
      proteins from the sequences of human large cDNAs (>4 kb).
    homepage: http://www.kazusa.or.jp/huge/
    name: Human Unidentified Gene-Encoded large proteins database
    prefix: FAIRsharing.zx2ztd
    publications:
    - doi: 10.1093/nar/gkh035
      pubmed_id: 14681467
      title: 'HUGE: a database for human KIAA proteins, a 2004 update integrating
        HUGEppi and ROUGE.'
    subjects:
    - Computational Biology
    - Life Science
  integbio:
    alt_name: A Database of Human Unidentified Gene-Encoded Large Proteins Analyzed
      by Kazusa Human cDNA Project
    description: The HUGE database is published by the Kazusa DNA Research Institute
      based on the results of its Kazusa Human cDNA Project to sequence and analyze
      long (>4 kb) human cDNAs and establish methods to predict the primary structure
      of proteins with various biological activities. Information on the predicted
      primary structure of newly identified human proteins that may be involved in
      cellular structure/motility, gene expression and nucleic acid metabolism, cell
      signaling/communication, etc. is available.
    fairsharing: biodbcore-000407
    homepage: http://www.kazusa.or.jp/huge/
    information_keywords:
    - Sequence
    maintainer: Kazusa DNA Research Institute
    name: HUGE
    prefix: nbdc00104
    pubmeds:
    - '9847221'
    - '10592264'
    - '11752282'
    - '14681467'
    status: Active
    target_keywords:
    - Genome/Gene
    - cDNA/EST
    - Protein
  mappings:
    biocontext: HUGE
    fairsharing: FAIRsharing.zx2ztd
    integbio: nbdc00104
    miriam: huge
    n2t: huge
    prefixcommons: huge
    uniprot: DB-0049
  miriam:
    deprecated: false
    description: The Human Unidentified Gene-Encoded (HUGE) protein database contains  results
      from sequence analysis of human novel large (>4 kb) cDNAs identified in the
      Kazusa cDNA sequencing project.
    homepage: http://www.kazusa.or.jp/huge/
    id: '00000263'
    name: HUGE
    namespaceEmbeddedInLui: false
    pattern: ^KIAA\d{4}$
    prefix: huge
    sampleId: KIAA0001
    uri_format: http://www.kazusa.or.jp/huge/gfpage/$1/
  n2t:
    description: The Human Unidentified Gene-Encoded (HUGE) protein database contains  results
      from sequence analysis of human novel large (>4 kb) cDNAs identified in the
      Kazusa cDNA sequencing project.
    example: KIAA0001
    homepage: http://www.kazusa.or.jp/huge/
    name: HUGE at Kazusa DNA Research Institute
    namespaceEmbeddedInLui: false
    pattern: ^KIAA\d{4}$
    prefix: huge
    uri_format: http://www.kazusa.or.jp/huge/gfpage/$1/
  name: Human Unidentified Gene-Encoded
  prefix: huge
  prefixcommons:
    description: HUGE is a database for human large proteins newly identified in the
      Kazusa cDNA project, the aim of which is to predict the primary structure of
      proteins from the sequences of human large cDNAs (>4 kb).
    example: KIAA0001
    homepage: http://www.kazusa.or.jp/huge/
    keywords:
    - protein
    - DNA
    - structure
    name: Human Unidentified Gene-Encoded large proteins database
    pattern: ^KIAA\d{4}$
    prefix: huge
    pubmed_ids:
    - '14681467'
    uri_format: http://www.kazusa.or.jp/huge/cgi/view_direct.cgi?id=$1
  publications:
  - doi: 10.1093/nar/gkh035
    pmc: PMC308769
    pubmed: '14681467'
    title: 'HUGE: a database for human KIAA proteins, a 2004 update integrating HUGEppi
      and ROUGE'
    year: 2004
  - doi: 10.1093/nar/gkh035
    pmc: null
    pubmed: null
    title: 'HUGE: a database for human KIAA proteins, a 2004 update integrating HUGEppi
      and ROUGE.'
    year: null
  - doi: null
    pmc: null
    pubmed: '14681467'
    title: null
    year: null
  - doi: 10.1093/nar/gkh035
    pmc: null
    pubmed: '14681467'
    title: null
    year: null
  uniprot:
    abbreviation: HUGE
    category: Organism-specific databases
    homepage: http://www.kazusa.or.jp/huge/
    name: Human Unidentified Gene-Encoded large proteins database
    prefix: DB-0049
    publications:
    - doi: 10.1093/nar/gkh035
      pubmed: '14681467'
    uri_format: http://www.kazusa.or.jp/huge/gfpage/$1
  uri_format: https://www.kazusa.or.jp/huge/gfpage/$1
humap:
  contact:
    email: ksdrew@uic.edu
    github: ksdrew
    name: Kevin Drew
    orcid: 0000-0002-1260-4413
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: The hu.MAP integrates several large scale protein interaction datasets
    to obtain a comprehensive view of protein complexes.
  example: huMAP3_04143.1
  github_request_issue: 1249
  homepage: https://humap3.proteincomplexes.org
  license: CC0-1.0
  name: Human Protein Complex Map
  prefix: humap
  publications:
  - doi: 10.15252/msb.202010016
    pmc: PMC8111494
    pubmed: '33973408'
    title: 'hu.MAP 2.0: integration of over 15,000 proteomic experiments builds a
      global compendium of human multiprotein assemblies'
    year: 2021
  - doi: 10.15252/msb.20167490
    pmc: PMC5488662
    pubmed: '28596423'
    title: Integration of over 9,000 mass spectrometry experiments builds a global
      map of human protein complexes
    year: 2017
  synonyms:
  - humap3
  uri_format: https://humap3.proteincomplexes.org/displayComplexes?complex_key=$1
hydra:
  example: TemplatedLink
  lov:
    description: A lightweight vocabulary for hypermedia-driven Web APIs
    homepage: http://www.w3.org/ns/hydra/spec/latest/core/
    keywords:
    - RDF
    modified: '2015-01-11'
    name: The Hydra Core Vocabulary
    prefix: hydra
    uri_prefix: http://www.w3.org/ns/hydra/core#$1
  mappings:
    lov: hydra
    re3data: r3d100011525
    zazuko: hydra
  prefix: hydra
  re3data:
    description: '<<<!!!<<<We are moving content from our Hydra repository (hydra.hull.ac.uk)
      to new repositories.>>>!!!>>>  Hydra is a repository for digital materials at
      the University of Hull. It can hold and manage any type of digital material,
      and is being developed in response to the growth in the amount of digital material
      that is generated through the research, education and administrative activities
      within the University. Hydra contains different collections of datasets from
      University of Hull research projects as: ARCdoc, domesday dataset, History of
      Marine animal Populations (HMAP) and others.'
    doi: 10.17616/R38D25
    homepage: https://hydra.hull.ac.uk/
    name: Hydra
    prefix: r3d100011525
    synonyms:
    - Hull's digital repository
  zazuko:
    prefix: hydra
    uri_format: http://www.w3.org/ns/hydra/core#$1
iana.mediatype:
  contact:
    email: alexey.melnikov@isode.com
    github: null
    name: Alexey Melnikov
    orcid: null
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: The official list of MIME types, now renamed to media types
  domain: semantic web
  example: application/cdmi-queue
  example_extras:
  - application
  - application/3gpp-ims+xml
  - audio
  - audio/1d-interleaved-parityfec
  - font
  - font/woff
  - haptics
  - haptics/hmpg
  - image
  - image/heif-sequence
  - message
  - message/disposition-notification
  - model
  - model/3mf
  - multipart
  - multipart/parallel
  - text
  - text/directory
  - video
  - video/vnd.blockfact.factv
  homepage: https://www.iana.org/assignments/media-types/media-types.xhtml
  keywords:
  - data classification
  logo: https://www.iana.org/_img/2022/iana-logo-header.svg
  name: Media Types
  pattern: ^(application|audio|font|haptics|image|message|model|multipart|text|video)(/.*)?$
  prefix: iana.mediatype
  uri_format: https://www.iana.org/assignments/media-types/$1
iao:
  aberowl:
    description: An ontology of information entities.
    download_owl: http://aber-owl.net/media/ontologies/IAO/11/iao.owl
    homepage: https://github.com/information-artifact-ontology/IAO/
    name: Information Artifact Ontology
    prefix: IAO
  biocontext:
    prefix: IAO
  bioportal:
    contact:
      email: alanruttenberg@gmail.com
      name: Alan Ruttenberg
    description: 'The Information Artifact Ontology (IAO) is an ontology of information
      entities, originally driven by work by the OBI consortium.<p> <p><b>To import</b><p>
      Latest released version: <a href="http://purl.obolibrary.org/obo/iao.owl">http://purl.obolibrary.org/obo/iao.owl</a><p>
      <b>Other versions</b><p> Developer (live) version: <a href="http://purl.obolibrary.org/obo/iao/dev/iao.owl">http://purl.obolibrary.org/obo/iao/dev/iao.owl</a><p>
      Ontology metadata properties and classes only: <a href="http://purl.obolibrary.org/obo/iao/dev/ontology-metadata.owl">http://purl.obolibrary.org/obo/iao/dev/iao.owl</a><p>
      <b>Dated versions</b> <ul> <li><a href="http://purl.obolibrary.org/obo/iao/2009-11-06/iao.owl">http://purl.obolibrary.org/obo/iao/2009-11-06/iao.owl</a>
      <li><a href="http://purl.obolibrary.org/obo/iao/2010-09-14/iao.owl">http://purl.obolibrary.org/obo/iao/2010-09-14/iao.owl</a>
      <li><a href="http://purl.obolibrary.org/obo/iao/2010-10-26/iao.owl">http://purl.obolibrary.org/obo/iao/2010-10-26/iao.owl</a>
      <li><a href="http://purl.obolibrary.org/obo/iao/2011-05-09/iao.owl">http://purl.obolibrary.org/obo/iao/2011-05-09/iao.owl</a>
      <li><a href="http://purl.obolibrary.org/obo/iao/2015-02-23/iao.owl">http://purl.obolibrary.org/obo/iao/2015-02-23/iao.owl</a>
      </ul><p> <p>Please note: The ontology metrics displayed by BioPortal do not
      distinguish IAO-developed terms from terms imported from other ontologies. <p><b>Tracker</b>:
      <a href="http://purl.obolibrary.org/obo/iao/tracker">http://purl.obolibrary.org/obo/iao/tracker</a><br>
      <b>Discussion group</b>: <a href="http://groups.google.com/group/information-ontology">http://groups.google.com/group/information-ontology</a>'
    homepage: http://purl.obolibrary.org/obo/iao
    name: Information Artifact Ontology
    prefix: IAO
    publications:
    - http://purl.obolibrary.org/obo/iao/reports
    version: '2022-11-07'
  download_obo: http://purl.obolibrary.org/obo/iao.obo
  fairsharing:
    abbreviation: IAO
    contact:
      email: alanruttenberg@gmail.com
      name: Alan Ruttenberg
      orcid: 0000-0002-1604-3078
    description: The Information Artifact Ontology (IAO) is an ontology of information
      entities, originally driven by work by the OBI digital entity and realizable
      information entity branch.
    domains:
    - Drug report
    - Experimental measurement
    - Data identity and mapping
    - reagent
    - assay
    - study design
    homepage: https://github.com/information-artifact-ontology/IAO/
    license: CC-BY-3.0
    name: Information Artifact Ontology
    prefix: FAIRsharing.gq1xtx
    publications:
    - doi: 10.3233/978-1-61499-101-4-68
      pubmed: '22874154'
      title: An information artifact ontology perspective on data collections and
        associated representational artifacts
      year: 2012
    repository: https://github.com/information-artifact-ontology/IAO/wiki/Meeting_notes
    subjects:
    - Knowledge and Information Systems
    - Data Management
    - Biomedical Science
    - Subject Agnostic
  go:
    description: Ontology of information entities, including ontology metadata relations.
    name: Information Artifact Ontology
    prefix: IAO
  mappings:
    aberowl: IAO
    biocontext: IAO
    bioportal: IAO
    fairsharing: FAIRsharing.gq1xtx
    go: IAO
    miriam: iao
    n2t: iao
    obofoundry: iao
    ols: iao
    ontobee: IAO
    tib: iao
    wikidata.entity: Q55118415
  miriam:
    deprecated: false
    description: An ontology of information entities, originally driven by work by
      the Ontology of Biomedical Investigation (OBI) digital entity and realizable
      information entity branch.
    homepage: http://www.ontobee.org/ontology/IAO
    id: '00000603'
    name: Information Artifact Ontology
    namespaceEmbeddedInLui: false
    pattern: ^\d{7}$
    prefix: iao
    sampleId: '0000030'
    uri_format: http://purl.obolibrary.org/obo/IAO_$1
  n2t:
    description: An ontology of information entities, originally driven by work by
      the Ontology of Biomedical Investigation (OBI) digital entity and realizable
      information entity branch.
    example: '0000030'
    homepage: http://www.ontobee.org/ontology/IAO
    name: IAO through Ontobee
    namespaceEmbeddedInLui: false
    pattern: ^\d{7}$
    prefix: iao
    uri_format: http://purl.obolibrary.org/obo/IAO_$1
  obofoundry:
    appears_in:
    - agro
    - clyh
    - duo
    - ecocore
    - ecto
    - fovt
    - labo
    - maxo
    - mcro
    - pco
    - psdo
    - xpo
    contact: zhengj2007@gmail.com
    contact.github: zhengj2007
    contact.label: Jie Zheng
    contact.orcid: 0000-0002-2999-0103
    deprecated: false
    description: An ontology of information entities.
    domain: information
    download.owl: http://purl.obolibrary.org/obo/iao.owl
    homepage: https://github.com/information-artifact-ontology/IAO/
    license: CC BY 4.0
    license.url: http://creativecommons.org/licenses/by/4.0/
    logo: https://avatars0.githubusercontent.com/u/13591168?v=3&s=200
    name: Information Artifact Ontology
    preferredPrefix: IAO
    prefix: iao
    repository: https://github.com/information-artifact-ontology/IAO
  ols:
    description: The Information Artifact Ontology (IAO) is an ontology of information
      entities, originally driven by work by the OBI digital entity and realizable
      information entity branch.
    download_owl: http://purl.obolibrary.org/obo/iao.owl
    homepage: https://github.com/information-artifact-ontology/IAO/
    name: Information Artifact Ontology (IAO)
    prefix: iao
    tracker: https://github.com/information-artifact-ontology/IAO/issues
    version: '2022-11-07'
    version.iri: http://purl.obolibrary.org/obo/iao/2022-11-07/iao.owl
  ontobee:
    library: Library
    name: Information Artifact Ontology
    prefix: IAO
  prefix: iao
  providers:
  - code: legacy
    description: A URI from the semanticweb.og
    example: null
    first_party: null
    homepage: http://www.semanticweb.org
    name: Legacy URI
    publications: null
    status: null
    uri_format: http://www.semanticweb.org/ontologies/2011/9/Ontology1317751904226.owl#IAO_$1
  publications:
  - doi: 10.3233/978-1-61499-101-4-68
    pmc: null
    pubmed: '22874154'
    title: An information artifact ontology perspective on data collections and associated
      representational artifacts
    year: 2012
  tib:
    description: The Information Artifact Ontology (IAO) is an ontology of information
      entities, originally driven by work by the OBI digital entity and realizable
      information entity branch.
    download_owl: http://purl.obolibrary.org/obo/iao.owl
    homepage: https://github.com/information-artifact-ontology/IAO/
    keywords:
    - NFDI4ING
    - NFDI4CHEM
    - FAIR Data Spaces
    name: Information Artifact Ontology (IAO)
    prefix: iao
    tracker: https://github.com/information-artifact-ontology/IAO/issues
    version.iri: http://purl.obolibrary.org/obo/iao/2022-11-07/iao.owl
  uri_format: http://purl.obolibrary.org/obo/IAO_$1
iao.issue:
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: An issue on the Information Artifact Ontology GitHub issue tracker
  example: '206'
  github_request_issue: 1553
  homepage: https://github.com/information-artifact-ontology/IAO/issues
  name: Information Artifact Ontology Issue Tracker
  pattern: ^\d+$
  prefix: iao.issue
  uri_format: https://github.com/information-artifact-ontology/IAO/issues/$1
ical:
  description: A vocabulary for calendar events and related objects
  example: Vevent
  homepage: https://www.w3.org/2002/12/cal/
  mappings:
    zazuko: ical
  name: iCalendar in RDF
  prefix: ical
  zazuko:
    prefix: ical
    uri_format: http://www.w3.org/2002/12/cal/icaltzd#$1
icd10:
  aberowl:
    description: International Statistical Classification of Diseases and Related
      Health Problems (ICD-10). 10th rev. Geneva
    name: International Classification of Diseases, Version 10
    prefix: ICD10
    version: 2016AB
  bartoc:
    abbreviation: ICD
    description: The International Classification of Diseases (ICD) is the standard
      diagnostic tool for epidemiology, health management and clinical purposes. This
      includes the analysis of the general health situation of population groups.
      It is used to monitor the incidence and prevalence of diseases and other health
      problems. It is used to classify diseases and other health problems recorded
      on many types of health and vital records including death certificates and health
      records. In addition to enabling the storage and retrieval of diagnostic information
      for clinical, epidemiological and quality purposes, these records also provide
      the basis for the compilation of national mortality and morbidity statistics
      by WHO Member States. It is used for reimbursement and resource allocation decision-making
      by countries. ICD-10 was endorsed by the Forty-third World Health Assembly in
      May 1990 and came into use in WHO Member States as from 1994. The 11th revision
      of the classification has already started and will continue until 2015.
    homepage: https://www.who.int/standards/classifications/classification-of-diseases
    name: International Statistical Classification of Diseases
    prefix: '447'
    wikidata_database: Q50018
  biocontext:
    prefix: ICD
  biolink:
    is_identifiers: false
    is_obo: false
    prefix: ICD10
    uri_format: https://icd.who.int/browse10/2016/en#/$1
  bioportal:
    contact:
      email: info@who.int
      name: World Health Organization
    description: International Statistical Classification of Diseases and Related
      Health Problems (ICD-10). 10th rev. Geneva
    name: International Classification of Diseases, Version 10
    prefix: ICD10
    version: ICD10_1998
  contributor_extras:
  - email: null
    github: joeflack4
    name: Joe Flack
    orcid: 0000-0002-2906-7319
  - email: nicolas.matentzoglu@gmail.com
    github: matentzn
    name: Nicolas Matentzoglu
    orcid: 0000-0002-7356-1779
  - email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: 'The 10th revision of the International Classification of Diseases
    (ICD) issued by the World Health Organization (WHO). ICD is formally named ''The
    International Statistical Classification of Diseases and Related Health Problems''.
    It contains codes for diseases, signs and symptoms, abnormal findings, complaints,
    social circumstances, and external causes of injury or diseases.


    Note that the WHO version of ICD-10 is distinct from the ICD-10-CM (Clinical Modification)
    issued by the U.S. National Center for Health Statistics for use in the United
    States.'
  domain: disease
  edam:
    description: An identifier of a disease from the International Classification
      of Diseases (ICD) database.
    name: ICD
    obsolete: false
    prefix: '2611'
  example_decoys:
  - G00X
  - C34.90
  - C4A.8
  - C91.Z
  - C91.Z0
  example_extras:
  - V20
  - G00
  - A01.1
  - XVIII
  - R25-R29
  - R25
  - R25.3
  fairsharing:
    abbreviation: ICD-10
    description: The ICD is the international standard diagnostic classification for
      all general epidemiological, many health management purposes and clinical use.
      ICD-10 is the 10th revision of the International Statistical Classification
      of Diseases and Related Health Problems (ICD), a medical classification list
      by the World Health Organization (WHO). It contains codes for diseases, signs
      and symptoms, abnormal findings, complaints, social circumstances, and external
      causes of injury or diseases.
    domains:
    - disease
    - diagnosis
    homepage: http://www.who.int/classifications/icd/en/
    license: http://www.who.int/about/licensing/copyright_form/en
    name: International Classification of Diseases Version 10
    prefix: FAIRsharing.nj16g
    subjects:
    - Biomedical Science
    - Epidemiology
    - Health Science
    - Global Health
  hl7:
    description: International Classification of Diseases revision 10 (ICD 10)Note
      this does NOT have the CM changes, and is specifically for international use.This
      node is the ontological branch in the HL7 OID tree.  The actual ICD10 code systems
      (the various national and international versions) are defined below this node.
    homepage: https://who.int
    name: ICD10
    organization: World Health Organization
    preferred_prefix: icd10
    prefix: 2.16.840.1.113883.6.3
    status: Complete
  homepage: https://icd.who.int/browse10
  license: https://cdn.who.int/media/docs/default-source/publishing-policies/copyright/who-faq-licensing-icd-10.pdf
  logo: https://upload.wikimedia.org/wikipedia/commons/a/a4/Icd10codeslogo.png
  mappings:
    aberowl: ICD10
    bartoc: '447'
    biocontext: ICD
    biolink: ICD10
    bioportal: ICD10
    edam: '2611'
    fairsharing: FAIRsharing.nj16g
    hl7: 2.16.840.1.113883.6.3
    miriam: icd
    n2t: icd
    prefixcommons: icd
    wikidata: P494
    wikidata.entity: Q50018
  miriam:
    deprecated: false
    description: The International Classification of Diseases is the international
      standard diagnostic classification for all general epidemiological and many
      health management purposes.
    homepage: http://www.who.int/classifications/icd/en/
    id: 00000009
    name: ICD
    namespaceEmbeddedInLui: false
    pattern: ^[A-Z]\d+(\.[-\d+])?$
    prefix: icd
    sampleId: C34
    uri_format: https://icd.who.int/browse10/2019/en#/$1
  n2t:
    description: The International Classification of Diseases is the international
      standard diagnostic classification for all general epidemiological and many
      health management purposes.
    example: C34
    homepage: http://www.who.int/classifications/icd/en/
    name: International Statistical Classification of Diseases and Related Health
      Problems
    namespaceEmbeddedInLui: false
    pattern: ^[A-Z]\d+(\.[-\d+])?$
    prefix: icd
    uri_format: http://apps.who.int/classifications/icd10/browse/2010/en#/$1
  name: International Classification of Diseases, 10th Revision
  pattern: ^(([XVI]+)|([A-Z][0-9]+((-[A-Z][0-9]+)|(\.[0-9]))?))$
  prefix: icd10
  prefixcommons:
    description: The International Classification of Diseases is the international
      standard diagnostic classification for all general epidemiological and many
      health management purposes.
    example: C34
    homepage: http://www.who.int/classifications/icd/en/
    keywords:
    - disease
    - taxonomy
    - classification
    license: http://www.who.int/about/copyright/en/index.html
    name: International Classification of Diseases
    pattern: ^[A-Z]\d+(\.[-\d+])?$
    prefix: icd
    uri_format: http://apps.who.int/classifications/icd10/browse/2010/en#/$1
  providers:
  - code: icdcodelookup
    description: This site is dedicated exclusively to helping you look up ICD-10
      codes, quickly access the codes you use most, and become more comfortable with
      the new code set in general.
    example: null
    first_party: null
    homepage: https://icdcodelookup.com/icd-10/codes
    name: ICD Code Lookup
    publications: null
    status:
      contributor: 0000-0003-4423-4370
      date: '2025-10-25'
      notes: null
      value: hijacked
    uri_format: https://icdcodelookup.com/icd-10/codes/$1
  - code: icd10_2015
    description: The 2015 revision of ICD-10
    example: null
    first_party: null
    homepage: https://icd.who.int/browse10/2015/en#
    name: ICD-10 Version 2015
    publications: null
    status: null
    uri_format: https://icd.who.int/browse10/2015/en#/$1
  - code: icd10_2010
    description: The 2010 revision of ICD-10
    example: null
    first_party: null
    homepage: https://icd.who.int/browse10/2010/en#
    name: ICD-10 Version 2010
    publications: null
    status: null
    uri_format: https://icd.who.int/browse10/2010/en#/$1
  - code: icd10_2008
    description: The 2008 revision of ICD-10
    example: null
    first_party: null
    homepage: https://icd.who.int/browse10/2008/en#
    name: ICD-10 Version 2008
    publications: null
    status: null
    uri_format: https://icd.who.int/browse10/2008/en#/$1
  - code: icd10_2014
    description: The 2014 revision of ICD-10
    example: null
    first_party: null
    homepage: https://icd.who.int/browse10/2014/en#
    name: ICD-10 Version 2014
    publications: null
    status: null
    uri_format: https://icd.who.int/browse10/2014/en#/$1
  - code: icd10_2016
    description: The 2016 revision of ICD-10
    example: null
    first_party: null
    homepage: https://icd.who.int/browse10/2016/en#
    name: ICD-10 Version 2016
    publications: null
    status: null
    uri_format: https://icd.who.int/browse10/2016/en#/$1
  references:
  - https://www.who.int/about/policies/publishing/copyright
  synonyms:
  - ICD
  - ICD-10
  - ICD10
  - ICD10WHO
  uri_format: https://icd.who.int/browse10/2019/en#/$1
  wikidata:
    database: Q45127
    description: identifier in the ICD Terminology of Diseases - Version 10
    example:
    - J10
    - J11
    - R19.6
    name: ICD-10 ID
    pattern: ^[A-Z]\d{2}(\.\d{1,2})?$
    prefix: P494
    uri_format: https://icd.who.int/browse10/2019/en#/$1
icd10cm:
  aberowl:
    description: International Classification of Diseases, 10th Edition, Clinical
      Modification, 2011_01
    homepage: http://www.cms.hhs.gov/
    name: International Classification of Diseases, Version 10 - Clinical Modification
    prefix: ICD10CM
    version: 2016AB
  bioportal:
    contact:
      email: pbrooks@hcfa.gov
      name: Patricia Brooks
    description: International Classification of Diseases, 10th Edition, Clinical
      Modification
    homepage: https://www.cdc.gov/nchs/icd/icd-10-cm.htm
    name: International Classification of Diseases, Version 10 - Clinical Modification
    prefix: ICD10CM
    publications:
    - http://www.cms.hhs.gov/
    version: CD10CM_2025
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: ICD-10-CM is the official system of assigning codes to diagnoses and
    procedures associated with hospital utilization in the United States issued by
    the National Center for Health Statistics (NCHS) and Centers for Medicare & Medicaid
    Services (CMS).
  example: F45.21
  example_decoys:
  - C000
  - c00
  - C00-D499
  - C00-99
  - C34.90000
  example_extras:
  - C00-D49
  - U49
  - C34
  - C34.90
  - C4A.8
  - C91.Z
  - C91.Z0
  - T37.0X1A
  fairsharing:
    abbreviation: ICD-10-CM
    description: The International Classification of Diseases, Tenth Revision, Clinical
      Modification (ICD-10-CM) is a morbidity classification for classifying diagnoses
      and reason for visits in all American health care settings. The ICD-10-CM is
      based on the ICD-10, the statistical classification of disease published by
      the World Health Organization (WHO) which replaces ICD-9. ICD-10-CM replaced
      ICD-9-CM Volumes 1 and 2 from October 2015 onwards.
    domains:
    - Electronic Health Record
    - disease
    - diagnosis
    - morbidity
    homepage: https://www.cdc.gov/nchs/icd/icd-10-cm/
    name: International Classification of Diseases, Tenth Revision, Clinical Modification
    prefix: FAIRsharing.hpvbxb
    subjects:
    - Biomedical Science
    - Health Science
    - Medicine
  hl7:
    description: The International Classification of Diseases, 10th Revision, Clinical
      Modification (ICD-10-CM), describes the classification of morbidity and mortality
      information for statistical purposes and for the indexing of healthcare records
      by diseases. The ICD-10-CM codes can be used as the value of the Act.cd attribute.
    homepage: http://www.cdc.gov/nchs/about/otheract/icd9/icd10cm.htm
    name: International Classification of Diseases, 10th Revision, Clinical Modification
      (ICD-10-CM)
    organization: National Center for Health Statistics/Centers for Disease Control
      and Prevention
    preferred_prefix: icd10CM
    prefix: 2.16.840.1.113883.6.90
    status: Complete
  homepage: https://www.icd10data.com/ICD10CM
  license: CC BY-ND 3.0 IGO
  mappings:
    aberowl: ICD10CM
    bioportal: ICD10CM
    fairsharing: FAIRsharing.hpvbxb
    hl7: 2.16.840.1.113883.6.90
    wikidata: P4229
  name: International Classification of Diseases, 10th Revision, Clinical Modification
  pattern: ^([A-Z][0-9][0-9AB]((-[A-Z][0-9][0-9AB])|(\.[0-9A-KXZ]([0-9A-EXYZ]([0-9A-HX][0-59A-HJKMNP-S]?)?)?)?))$
  prefix: icd10cm
  providers:
  - code: bioportal.purl
    description: PURL from BioPortal
    example: null
    first_party: null
    homepage: http://purl.bioontology.org/ontology/ICD10CM
    name: BioPortal PURL
    publications: null
    status: null
    uri_format: http://purl.bioontology.org/ontology/ICD10CM/$1
  - code: icd.codes
    description: ICD Codes provider
    example: null
    first_party: null
    homepage: https://icd.codes
    name: ICD Codes provider
    publications: null
    status:
      contributor: 0000-0001-9439-5346
      date: '2025-07-28'
      notes: null
      value: gone
    uri_format: https://icd.codes/icd10cm/$1
  references:
  - https://www.who.int/about/policies/publishing/copyright
  synonyms:
  - ICD10CM
  uri_format: https://www.icd10data.com/search?s=$1
  wikidata:
    database: Q5969475
    description: identifier in the ICD-10-CM (International Classification of Diseases,
      10th Revision, Clinical Modification)
    example:
    - A00-Z99
    - G47.52
    - G71.2
    name: ICD-10-CM
    pattern: ^[A-Z]\d{2}(-[A-Z]\d{2}|[.][A-Z\d]+|)$
    prefix: P4229
icd10pcs:
  aberowl:
    description: ICD-10-PCS, 2009
    homepage: http://www.cms.hhs.gov
    name: International Classification of Diseases, Version 10 - Procedure Coding
      System
    prefix: ICD10PCS
    version: 2016AB
  bioportal:
    contact:
      email: patricia.brooks2@cms.hhs.gov
      name: Pat Brooks
    description: ICD-10-PCS is a medical classification coding system for procedural
      codes.
    homepage: https://www.cms.gov/Medicare/Coding/ICD10/index.html
    name: International Classification of Diseases, Version 10 - Procedure Coding
      System
    prefix: ICD10PCS
    publications:
    - http://www.cms.hhs.gov
    version: ICD10PCS_2025
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: 'ICD-10-PCS is being developed as the successor to Volume 3 of the
    International Classification of Diseases, Ninth Revision, Clinical Modification
    (ICD-9-CM). For more information about ICD-9-CM, see the ICD-9-CM source synopsis.


    ICD-10-PCS will be the official system of assigning codes to procedures associated
    with hospital utilization in the United States. ICD-10-PCS codes will support
    data collection, payment and electronic health records.'
  example: 01N50ZZ
  fairsharing:
    abbreviation: ICD-10-PCS
    description: The ICD-10 Procedure Coding System (ICD-10-PCS) is an international
      system of medical classification used for procedural coding. The ICD-10-PCS
      is a procedure classification published by the United States for classifying
      procedures performed in hospital inpatient health care settings. The ICD-10-PCS
      replaces the procedural coding portion (Volume 3) of ICD-9-CM.
    domains:
    - Electronic Health Record
    - disease
    - diagnosis
    - Classification
    - Hospital
    - morbidity
    homepage: https://www.cms.gov/Medicare/Coding/ICD10/2020-ICD-10-PCS
    name: International Classification of Diseases Version 10 - Procedure Coding System
    prefix: FAIRsharing.85k1jm
    subjects:
    - Biomedical Science
    - Epidemiology
    - Health Science
  hl7:
    description: The International Classification of Diseases, 10th Revision, Procedure
      Coding System (ICD-10-PCS), describes the classification of inpatient procedures
      for statistical purposes and for the indexing of healthcare records by procedures.
      The ICD-10-PCS codes can be used as the value of the Act.cd attribute
    homepage: http://cms.hhs.gov/paymentsystems/icd9/icd10.asp
    name: International Classification of Diseases, 10th Revision, Procedure Coding
      System (ICD-10-PCS)
    organization: Centers for Medicare and Medicaid Services
    preferred_prefix: icd10PCS
    prefix: 2.16.840.1.113883.6.4
    status: Complete
  homepage: https://www.nlm.nih.gov/research/umls/sourcereleasedocs/current/ICD10PCS
  mappings:
    aberowl: ICD10PCS
    bioportal: ICD10PCS
    fairsharing: FAIRsharing.85k1jm
    hl7: 2.16.840.1.113883.6.4
    wikidata: P1690
  name: International Classification of Diseases, 10th Revision, Procedure Coding
    System
  prefix: icd10pcs
  uri_format: https://www.findacode.com/code.php?set=ICD10PCS&c=$1
  wikidata:
    description: identifier in the ICD-10-PCS (Procedure Coding System, International
      Classification of Diseases, 10th revision)
    example:
    - 01N50ZZ
    - 0SRD0JZ
    name: ICD-10-PCS
    prefix: P1690
    uri_format: https://www.findacode.com/code.php?set=ICD10PCS&c=$1
icd11:
  biolink:
    is_identifiers: false
    is_obo: false
    prefix: icd11.foundation
    uri_format: http://id.who.int/icd/entity/$1
  comment: Clinical codes from an ICD-11 linearization (a structured subset of the
    ICD-11 Foundation tailored for specific use cases, such as morbidity or mortality
    coding), such as RA00.0, have their own namespace (icd11.code).
  contact:
    email: icd@who.int
    github: null
    name: ICD Helpdesk
    orcid: null
  contact_group_email: icd@who.int
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  contributor_extras:
  - email: nicolas.matentzoglu@gmail.com
    github: matentzn
    name: Nicolas Matentzoglu
    orcid: 0000-0002-7356-1779
  description: The ICD-11 Foundation is the comprehensive base layer of the International
    Classification of Diseases, encompassing all diagnostic concepts, definitions,
    and semantic relationships, designed for flexibility and adaptability across various
    use cases, including research, ontology development, and detailed health data
    analysis.
  domain: disease
  example: '402558626'
  fairsharing:
    abbreviation: ICD 11
    description: The International Classification of Diseases (ICD) was created to
      allow the recording, reporting and grouping of conditions and factors that influence
      health. It contains categories for diseases, health related conditions, and
      external causes of illness or death. The purpose of the ICD is to allow the
      systematic recording, analysis, interpretation and comparison of mortality and
      morbidity data collected in different countries or areas and at different times.
      The ICD is used to translate diagnoses of diseases and other health problems
      into an alphanumeric code, which allows storage, retrieval, and analysis of
      the data. The ICD has become the international standard diagnostic classification
      for all general epidemiological and many health management purposes. ICD-11
      was released in 2018 to allow Member States to prepare for implementation, including
      translating ICD into their national languages. Member States started reporting
      using ICD-11 on 1 January 2022.
    domains:
    - Electronic Health Record
    - disease
    - diagnosis
    - morbidity
    homepage: https://icd.who.int/en
    license: http://www.who.int/about/licensing/copyright_form/en
    name: International Classification of Diseases Version 11
    prefix: FAIRsharing.97805c
    subjects:
    - Biomedical Science
    - Epidemiology
    - Health Science
    - Global Health
  hl7:
    description: International Classification of Diseases 11th RevisionThe global
      standard for diagnostic health information
    homepage: https://who.int
    name: ICD-11
    organization: World Health Organization
    preferred_prefix: icd11
    prefix: 2.16.840.1.113883.6.347
    status: Complete
  homepage: https://icd.who.int/
  integbio:
    alt_name: International Classification of Diseases 11th Revision
    description: This is a website for ICD (International Statistical Classification
      of Diseases and Related Health Problems) -11, which is an organized collection
      of global standard terms for health data and clinical documentation. The ICD-11
      has been developed by the World Health Organization (WHO). There is a link to
      ICD-10 (previous version) in this site.
    fairsharing: bsg-s001436/
    homepage: https://icd.who.int/en
    information_keywords:
    - Ontology/Terminology/Nomenclature
    maintainer: World Health Organization
    name: ICD-11
    prefix: nbdc02556
    status: Active
    target_keywords:
    - Health/Disease
  license: CC-BY-ND-3.0-IGO
  logo: https://upload.wikimedia.org/wikipedia/commons/2/23/ICD-11_Logo.jpg
  mappings:
    biolink: icd11.foundation
    fairsharing: FAIRsharing.97805c
    hl7: 2.16.840.1.113883.6.347
    integbio: nbdc02556
    wikidata: P7807
  name: International Classification of Diseases, 11th Revision (Foundation Component)
  prefix: icd11
  providers:
  - code: api
    description: This goes to an API endpoint. For more information, see https://icd.who.int/icdapi
    example: null
    first_party: null
    homepage: https://icd.who.int
    name: ICD 11 API Endpoint
    publications: null
    status: null
    uri_format: http://id.who.int/icd/entity/$1
  - code: foundation
    description: This goes to the Foundation interface to ICD11
    example: null
    first_party: null
    homepage: https://icd.who.int/browse/2024-01/foundation
    name: ICD 11 Foundation
    publications: null
    status: null
    uri_format: https://icd.who.int/browse/2024-01/foundation/en#$1
  - code: mms
    description: This goes to the Mortality and Morbidity Statistics interface to
      ICD11
    example: null
    first_party: null
    homepage: https://icd.who.int/browse/2024-01/mms
    name: ICD 11 Mortality and Morbidity Statistics
    publications: null
    status: null
    uri_format: https://icd.who.int/browse/2024-01/mms/en#$1
  publications:
  - doi: 10.1016/s0140-6736(19)31205-x
    pmc: null
    pubmed: '31180012'
    title: ICD-11
    year: 2019
  rdf_uri_format: http://id.who.int/icd/entity/$1
  references:
  - https://icd.who.int/docs/icd-api/license/
  synonyms:
  - ICD-11
  - ICD11
  - icd11.foundation
  uri_format: https://icd.who.int/browse11/l-m/en#/http://id.who.int/icd/entity/$1
  wikidata:
    database: Q55695727
    description: identifier in ICD terminology of diseases - Version 11 (foundation
      ID) (not Mortality and Morbidity Statistics ID)
    example:
    - '402558626'
    - '698285441'
    - '784669405'
    name: ICD-11 ID (Foundation)
    pattern: ^[1-9]\d*$
    prefix: P7807
    uri_format: https://icd.who.int/browse/2025-01/mms/en#$1
icd11.code:
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: An ICD-11 code is a standardized alphanumeric identifier used to classify
    and document diseases, conditions, and health-related issues for global healthcare
    and statistical purposes.
  example: NA06.8D
  example_extras:
  - CA71.2
  - FB82.00
  - XM34M9
  github_request_issue: 1349
  homepage: https://icd.who.int/en
  license: http://www.who.int/about/licensing/copyright_form/en
  name: ICD 11 Codes
  pattern: ^[0-9A-Z]+(\.[0-9A-Z]+)?$
  prefix: icd11.code
  references:
  - https://github.com/biopragmatics/bioregistry/issues/1344
icd9:
  bartoc:
    abbreviation: ICD
    description: The International Classification of Diseases (ICD) is the standard
      diagnostic tool for epidemiology, health management and clinical purposes. This
      includes the analysis of the general health situation of population groups.
      It is used to monitor the incidence and prevalence of diseases and other health
      problems. It is used to classify diseases and other health problems recorded
      on many types of health and vital records including death certificates and health
      records. In addition to enabling the storage and retrieval of diagnostic information
      for clinical, epidemiological and quality purposes, these records also provide
      the basis for the compilation of national mortality and morbidity statistics
      by WHO Member States. It is used for reimbursement and resource allocation decision-making
      by countries. ICD-10 was endorsed by the Forty-third World Health Assembly in
      May 1990 and came into use in WHO Member States as from 1994. The 11th revision
      of the classification has already started and will continue until 2015.
    homepage: https://www.who.int/standards/classifications/classification-of-diseases
    name: International Statistical Classification of Diseases
    prefix: '447'
    wikidata_database: Q50018
  biolink:
    is_identifiers: false
    is_obo: false
    prefix: ICD9
    uri_format: http://translator.ncats.nih.gov/ICD9_$1
  comment: Note that ICD9 codes representing mid-hierarchy relations, such as those
    in the form of XXX-YYY are not possible to resolve, but are useful and appear
    in many places that make xrefs to ICD9
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: The International Classification of Diseases (ICD) is designed to promote
    international comparability in the collection, processing, classification, and
    presentation of mortality statistics.
  example: '277.9'
  example_extras:
  - '401'
  - 401-405
  - '995.81'
  - E950
  - V15.01
  hl7:
    description: International Classification of Diseases, Version 9 (ICD9)
    homepage: https://who.int
    name: International Classification of Diseases, Version 9
    organization: World Health Organization
    preferred_prefix: icd9
    prefix: 2.16.840.1.113883.6.42
    status: Complete
  homepage: https://www.cdc.gov/nchs/icd/icd9.htm
  license: CC BY-ND 3.0 IGO
  mappings:
    bartoc: '447'
    biolink: ICD9
    hl7: 2.16.840.1.113883.6.42
    wikidata: P493
    wikidata.entity: Q50018
  name: International Classification of Diseases, 9th Revision
  pattern: ^((\d\d\d|V\d\d|E[8-9]\d\d)(\.\d{1,2})?)|(\d{1,3}-\d{1,3})$
  prefix: icd9
  references:
  - https://www.who.int/about/policies/publishing/copyright
  synonyms:
  - ICD9
  - ICD9_2005
  - MTHICD9_2006
  uri_format: http://www.icd9data.com/getICD9Code.ashx?icd9=$1
  wikidata:
    database: Q50018
    description: identifier in the ICD catalogue codes for diseases – Version 9
    example:
    - '487'
    - '995.81'
    - E950
    - V15.01
    name: ICD-9 ID
    pattern: ^(\d\d\d|V\d\d|E[8-9]\d\d)(\.\d{1,2})?$
    prefix: P493
    uri_format: http://www.icd9data.com/getICD9Code.ashx?icd9=$1
icd9cm:
  aberowl:
    description: The ICD is the international standard diagnostic classification for
      all general epidemiological, many health management purposes and clinical use.
    homepage: http://www.cms.hhs.gov/
    name: International Classification of Diseases, Version 9 - Clinical Modification
    prefix: ICD9CM
    version: 2016AB
  bioportal:
    contact:
      email: pbrooks@hcfa.gov
      name: Patricia Brooks
    description: The ICD is the international standard diagnostic classification for
      all general epidemiological, many health management purposes and clinical use.
    homepage: http://www.cms.hhs.gov/
    name: International Classification of Diseases, Version 9 - Clinical Modification
    prefix: ICD9CM
    version: ICD9CM_2014
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: ICD-9-CM is the official system of assigning codes to diagnoses and
    procedures associated with hospital utilization in the United States.
  example: '784'
  fairsharing:
    abbreviation: ICD-9-CM
    description: The ICD is the international standard diagnostic classification for
      all general epidemiological, many health management purposes and clinical use.
      The International Classification of Diseases, Ninth Revision, Clinical Modification
      (ICD-9-CM) is an adaption created by the U.S. National Center for Health Statistics
      (NCHS) and used in assigning diagnostic and procedure codes associated with
      inpatient, outpatient, and physician office utilization in the United States.
      The ICD-9-CM is based on the ICD-9 but provides for additional morbidity detail.
    domains:
    - disease
    - diagnosis
    - morbidity
    homepage: https://archive.cdc.gov/#/details?url=https://www.cdc.gov/nchs/icd/icd9cm.htm
    name: International Classification of Diseases, Ninth Revision, Clinical Modification
    prefix: FAIRsharing.10zsxb
    subjects:
    - Preclinical Studies
    - Biomedical Science
    - Epidemiology
    - Health Science
    - Medicine
  hl7:
    description: The International Classification of Diseases, 9th Revision, Clinical
      Modification (ICD-9-CM), Volumes I, II (diagnoses) and III (procedures) describes
      the classification of morbidity and mortality information for statistical purposes
      and for the indexing of healthcare records by diseases and procedures. The ICD-9-CM
      codes can be used as the value of the Act.cd attribute.Note that this has been
      retired in favor of an explicit split between the diagnosis codes and the procedures
      codes as per the Vocablary TC decision on Wednesday Q4, January 21, 2004.  Replaced
      by 2.16.840.1.113883.6.103 and 2.16.840.1.113883.6.104 as voted by committee.  -T.
      Klein
    homepage: http://www.cdc.gov/nchs/icd9.htm.
    name: National Center for Health Statistics
    organization: National Center for Health Statistics
    preferred_prefix: icd9cm
    prefix: 2.16.840.1.113883.6.2
    status: Retired
  homepage: https://www.cdc.gov/nchs/icd/icd9cm.htm
  license: CC BY-ND 3.0 IGO
  mappings:
    aberowl: ICD9CM
    bioportal: ICD9CM
    fairsharing: FAIRsharing.10zsxb
    hl7: 2.16.840.1.113883.6.2
    wikidata: P1692
    wikidata.entity: Q5737131
  name: International Classification of Diseases, 9th Revision, Clinical Modification
  pattern: ^([\dA-Z]\d{2}(\.\d{1,3}|))|(\d{2}(\.\d{1,2}|))$
  prefix: icd9cm
  references:
  - https://www.who.int/about/policies/publishing/copyright
  synonyms:
  - IC9CM
  - ICD9CM
  - ICD9CM_2005
  - ICD9CM_2006
  - ICDCM_2005
  uri_format: http://icd9cm.chrisendres.com/index.php?action=search&srchtext=$1
  wikidata:
    database: Q5737131
    description: identifier in the ICD adaption assigning diagnostic and procedure
      codes
    example:
    - '135'
    - '42'
    - '503'
    name: ICD-9-CM
    pattern: ^([\dA-Z]\d{2}(\.\d{1,3}|))|(\d{2}(\.\d{1,2}|))$
    prefix: P1692
    uri_format: http://icd9cm.chrisendres.com/index.php?action=search&srchtext=$1
icdc:
  fairsharing:
    abbreviation: ICDC
    contact:
      email: annika.jahnke-bornemann@uni-hamburg.de
      name: Annika Jahnke-Bornemann
      orcid: 0000-0001-7815-151X
    description: The Integrated Climate Data Center (ICDC) allows easy access to climate
      relevant data from in-situ measurements and satellite remote sensing. These
      data are important to determine the status and the changes in the climate system.
      Some relevant re-analysis data are included, which are modeled on the basis
      of observational data.
    homepage: https://icdc.cen.uni-hamburg.de/en/icdc.html
    name: Integrated Climate Data Center
    prefix: FAIRsharing.d95034
    publications: []
    subjects:
    - Social Science
    - Meteorology
    - Earth Science
    - Atmospheric Science
    - Remote Sensing
    - Oceanography
    twitter: ICDC_Hamburg
  mappings:
    fairsharing: FAIRsharing.d95034
    miriam: icdc
    re3data: r3d100010405
  miriam:
    deprecated: false
    description: The Integrated Canine Data Commons is one of several repositories
      within the NCI Cancer Research Data Commons (CRDC), a cloud-based data science
      infrastructure that provides secure access to a large, comprehensive, and expanding
      collection of cancer research data. The ICDC was established to further research
      on human cancers by enabling comparative analysis with canine cancer.
    homepage: https://caninecommons.cancer.gov/#/
    id: 00000812
    name: Integrated Canine Data Commons
    namespaceEmbeddedInLui: false
    pattern: ^\d{6}$
    prefix: icdc
    sampleId: 000009
    uri_format: https://caninecommons.cancer.gov/#/study/$1
  prefix: icdc
  re3data:
    description: The CliSAP-Integrated Climate Data Center (ICDC) allows easy access
      to climate relevant data from satellite remote sensing and in situ and other
      measurements in Earth System Sciences. These data are important to determine
      the status and the changes in the climate system. Additionally some relevant
      re-analysis data are included, which are modeled on the basis of observational
      data. ICDC cooperates with the "Zentrum für Nachhaltiges Forschungsdatenmanagement
      "https://www.fdr.uni-hamburg.de/ to publish observational data with a doi.
    doi: 10.17616/R39S3N
    homepage: https://www.cen.uni-hamburg.de/en/icdc/data.html
    name: Integrated Climate Data Center
    prefix: r3d100010405
    synonyms:
    - ICDC
icdo:
  bartoc:
    abbreviation: ICD-O
    description: 'Used principally in tumour or cancer registries for coding the site
      (topography) and the histology (morphology) of neoplasms, usually obtained from
      a pathology report.


      A multi-axial classification of the site, morphology, behaviour, and grading
      of neoplasms. The topography axis uses the ICD-10 classification of malignant
      neoplasms (except those categories which relate to secondary neoplasms and to
      specified morphological types of tumours) for all types of tumours, thereby
      providing greater site detail for non-malignant tumours than is provided in
      ICD-10. In contrast to ICD-10, the ICD-O includes topography for sites of haematopoietic
      and reticuloendothelial tumours. The morphology axis provides five-digit codes
      ranging from M-8000/0 to M-9989/3. The first four digits indicate the specific
      histological term. The fifth digit after the slash (/) is the behaviour code,
      which indicates whether a tumour is malignant, benign, in situ, or uncertain
      (whether benign or malignant). A separate one-digit code is also provided for
      histologic grading (differentiation).'
    homepage: http://www.who.int/classifications/icd/adaptations/oncology/
    name: International Classification of Diseases for Oncology
    prefix: '445'
    wikidata_database: Q1430635
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: The International Classification of Diseases for Oncology (ICD-O) is
    a domain-specific extension of the International Statistical Classification of
    Diseases and Related Health Problems for tumor diseases
  example: 9861/3
  hl7:
    description: This branch node heads up the different versions of the International
      Classification of Diseases for Oncology, which must be identified as different
      coding systems under HL7 terminology rules.
    homepage: http://www.who.int/en/
    name: 'International Classification of Diseases for Oncology:  ICD-O'
    organization: World Health Organization (WHO)
    preferred_prefix: icd-o
    prefix: 2.16.840.1.113883.6.43
    status: Complete
  homepage: https://www.who.int/classifications/icd/adaptations/oncology/en/
  license: CC BY-ND 3.0 IGO
  mappings:
    bartoc: '445'
    hl7: 2.16.840.1.113883.6.43
    prefixcommons: icdo
    wikidata: P563
    wikidata.entity: Q1430635
  name: International Classification of Diseases for Oncology
  pattern: ^[8-9]\d{3}(/[0-3])?$
  prefix: icdo
  prefixcommons:
    bioportal: '1670'
    description: Ontology of Oncology as based on CDC SEER's ICDO-3 Code classification
    example: M-8272/O
    name: International Classification of Diseases for Oncology
    pattern: ^[A-Z0-9]+\/[0-9]+$
    prefix: icdo
    synonyms:
    - icdo3
    - icd-o
  references:
  - https://www.who.int/about/policies/publishing/copyright
  synonyms:
  - ICD-O
  - ICDO
  uri_format: http://codes.iarc.fr/search.php?cx=009987501641899931167%3A2_7lsevqpdm&cof=FORID%3A9&ie=UTF-8&ie=ISO-8859-1&oe=ISO-8859-1&sa=&q=$1
  wikidata:
    description: International Classification of Diseases for Oncology
    example:
    - 8561/0
    - M9860/3
    name: ICD-O
    pattern: ^[8-9]\d{3}(/[0-3])?$
    prefix: P563
    uri_format: https://codes.iarc.fr/search.php?cx=009987501641899931167%3A2_7lsevqpdm&cof=FORID%3A9&ie=UTF-8&ie=ISO-8859-1&oe=ISO-8859-1&sa=&q=$1
iceberg.cime:
  contact:
    email: hyou@sjtu.edu.cn
    github: null
    name: Hong-Yu Ou
    orcid: 0000-0001-9439-1660
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: ICEs have also been reported capable to mobilize other genetic elements,
    such as the chromosome-borne integrative and mobilizable elements (IMEs), cis-mobilizable
    elements (CIMEs), plasmids and etc. IMEs and CIMEs are also important vehicles
    for the spread of antiobiotic resistances and virulence factors. However, unlike
    ICE, IMEs and CIMEs are commonly devoid of conjugal apparatus, thus have to hijack
    the machinery of other conjugative elements.
  example: '6'
  homepage: https://bioinfo-mml.sjtu.edu.cn/ICEberg2/browse_CIME.php?type=alpha&alpha=100
  keywords:
  - biology
  - genomics
  name: ICEberg cis-integrative and mobilizable element
  part_of_database: iceberg
  pattern: ^\d+$
  prefix: iceberg.cime
  publications:
  - doi: 10.1093/nar/gky1123
    pmc: PMC6323972
    pubmed: '30407568'
    title: 'ICEberg 2.0: an updated database of bacterial integrative and conjugative
      elements'
    year: 2019
  - doi: 10.1093/nar/gkr846
    pmc: PMC3244999
    pubmed: '22009673'
    title: 'ICEberg: a web-based resource for integrative and conjugative elements
      found in Bacteria'
    year: 2011
  uri_format: https://bioinfo-mml.sjtu.edu.cn/ICEberg2/feature_page_CIME.php?cime_id=$1_CIME
iceberg.element:
  biocontext:
    prefix: ICEBERG.ELEMENT
  homepage: https://bioinfo-mml.sjtu.edu.cn/ICEberg2/browse_result.php?type=alpha&alpha=100
  mappings:
    biocontext: ICEBERG.ELEMENT
    miriam: iceberg.element
    n2t: iceberg.element
  miriam:
    deprecated: false
    description: ICEberg (Integrative and conjugative elements) is a database of integrative
      and conjugative elements (ICEs) found in bacteria. ICEs are conjugative self-transmissible
      elements that can integrate into and excise from a host chromosome, and can
      carry likely virulence determinants, antibiotic-resistant factors and/or genes
      coding for other beneficial traits. It contains details of ICEs found in representatives
      bacterial species, and which are organised as families. This collection references
      ICE elements.
    homepage: https://bioinfo-mml.sjtu.edu.cn/ICEberg2
    id: 00000469
    name: ICEberg element
    namespaceEmbeddedInLui: false
    pattern: ^\d+$
    prefix: iceberg.element
    sampleId: '100'
    uri_format: https://bioinfo-mml.sjtu.edu.cn/ICEberg2/feature_page.php?ice_id=$1
  n2t:
    description: ICEberg (Integrative and conjugative elements) is a database of integrative
      and conjugative elements (ICEs) found in bacteria. ICEs are conjugative self-transmissible
      elements that can integrate into and excise from a host chromosome, and can
      carry likely virulence determinants, antibiotic-resistant factors and/or genes
      coding for other beneficial traits. It contains details of ICEs found in representatives
      bacterial species, and which are organised as families. This collection references
      ICE elements.
    example: '100'
    homepage: http://db-mml.sjtu.edu.cn/ICEberg/
    name: ICEberg element at Shanghai Jiaotong University
    namespaceEmbeddedInLui: false
    pattern: ^\d+$
    prefix: iceberg.element
    uri_format: http://db-mml.sjtu.edu.cn/ICEberg/feature_page.php?ice_id=$1
  name: ICEberg integrative and conjugative element
  part_of_database: iceberg
  prefix: iceberg.element
  publications:
  - doi: 10.1093/nar/gky1123
    pmc: PMC6323972
    pubmed: '30407568'
    title: 'ICEberg 2.0: an updated database of bacterial integrative and conjugative
      elements'
    year: 2019
  - doi: 10.1093/nar/gkr846
    pmc: PMC3244999
    pubmed: '22009673'
    title: 'ICEberg: a web-based resource for integrative and conjugative elements
      found in Bacteria'
    year: 2011
  synonyms:
  - iceberg.ice
  uri_format: https://bioinfo-mml.sjtu.edu.cn/ICEberg2/feature_page.php?ice_id=$1
iceberg.family:
  biocontext:
    prefix: ICEBERG.FAMILY
  contact:
    email: hyou@sjtu.edu.cn
    github: null
    name: Hong-Yu Ou
    orcid: 0000-0001-9439-1660
  homepage: https://bioinfo-mml.sjtu.edu.cn/ICEberg2/browse_fam.php
  mappings:
    biocontext: ICEBERG.FAMILY
    miriam: iceberg.family
    n2t: iceberg.family
  miriam:
    deprecated: false
    description: ICEberg (Integrative and conjugative elements) is a database of integrative
      and conjugative elements (ICEs) found in bacteria. ICEs are conjugative self-transmissible
      elements that can integrate into and excise from a host chromosome, and can
      carry likely virulence determinants, antibiotic-resistant factors and/or genes
      coding for other beneficial traits. It contains details of ICEs found in representatives
      bacterial species, and which are organised as families. This collection references
      ICE families.
    homepage: https://bioinfo-mml.sjtu.edu.cn/ICEberg2
    id: '00000470'
    name: ICEberg family
    namespaceEmbeddedInLui: false
    pattern: ^\d+$
    prefix: iceberg.family
    sampleId: '1'
    uri_format: https://bioinfo-mml.sjtu.edu.cn/ICEberg2/browse_result.php?type=fam&fam_id=$1
  n2t:
    description: ICEberg (Integrative and conjugative elements) is a database of integrative
      and conjugative elements (ICEs) found in bacteria. ICEs are conjugative self-transmissible
      elements that can integrate into and excise from a host chromosome, and can
      carry likely virulence determinants, antibiotic-resistant factors and/or genes
      coding for other beneficial traits. It contains details of ICEs found in representatives
      bacterial species, and which are organised as families. This collection references
      ICE families.
    example: '1'
    homepage: http://db-mml.sjtu.edu.cn/ICEberg/
    name: ICEberg family at Shanghai Jiaotong University
    namespaceEmbeddedInLui: false
    pattern: ^\d+$
    prefix: iceberg.family
    uri_format: http://db-mml.sjtu.edu.cn/ICEberg/browse_result.php?type=fam&fam_id=$1
  part_of_database: iceberg
  prefix: iceberg.family
  publications:
  - doi: 10.1093/nar/gky1123
    pmc: PMC6323972
    pubmed: '30407568'
    title: 'ICEberg 2.0: an updated database of bacterial integrative and conjugative
      elements'
    year: 2019
  - doi: 10.1093/nar/gkr846
    pmc: PMC3244999
    pubmed: '22009673'
    title: 'ICEberg: a web-based resource for integrative and conjugative elements
      found in Bacteria'
    year: 2011
  uri_format: https://bioinfo-mml.sjtu.edu.cn/ICEberg2/browse_result.php?type=fam&fam_id=$1
iceberg.ime:
  contact:
    email: hyou@sjtu.edu.cn
    github: null
    name: Hong-Yu Ou
    orcid: 0000-0001-9439-1660
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: ICEs have also been reported capable to mobilize other genetic elements,
    such as the chromosome-borne integrative and mobilizable elements (IMEs), cis-mobilizable
    elements (CIMEs), plasmids and etc. IMEs and CIMEs are also important vehicles
    for the spread of antiobiotic resistances and virulence factors. However, unlike
    ICE, IMEs and CIMEs are commonly devoid of conjugal apparatus, thus have to hijack
    the machinery of other conjugative elements.
  example: '1'
  homepage: https://bioinfo-mml.sjtu.edu.cn/ICEberg2/browse_IME.php?type=alpha&alpha=100
  keywords:
  - biology
  - genomics
  name: ICEberg integrative and mobilizable element
  part_of_database: iceberg
  pattern: ^\d+$
  prefix: iceberg.ime
  publications:
  - doi: 10.1093/nar/gky1123
    pmc: PMC6323972
    pubmed: '30407568'
    title: 'ICEberg 2.0: an updated database of bacterial integrative and conjugative
      elements'
    year: 2019
  - doi: 10.1093/nar/gkr846
    pmc: PMC3244999
    pubmed: '22009673'
    title: 'ICEberg: a web-based resource for integrative and conjugative elements
      found in Bacteria'
    year: 2011
  uri_format: https://bioinfo-mml.sjtu.edu.cn/ICEberg2/feature_page_IME.php?ime_id=$1_IME
icechem:
  mappings:
    miriam: ice.chem
  miriam:
    deprecated: false
    description: 'The Integrated Chemical Environment (ICE) provides high-quality
      curated data and appropriate tools to support development and evaluation of
      new, revised, and alternative methods. ICE provides free online access to curated
      in vivo and in vitro test data, in silico toxicity predictions and chemical
      property data, reference chemical lists, and computational tools for chemical
      characterization and predicting toxicity.

      ICE supports the following: (i) Data integration: brings together available
      data, including data on formulations; (ii) Results exploration: enables dynamic,
      graphical exploration with publication-quality graphics; (iii) Data analysis:
      allows characterization of data using online workflows, and (iv) FAIR data access:
      data are findable, accessible, interoperable, and reusable.'
    homepage: https://ice.ntp.niehs.nih.gov
    id: 00001082
    name: Integrated Chemical Environment - Chemical data
    namespaceEmbeddedInLui: false
    pattern: ^\d{2,7}-\d{2}-\d|DTXSID\d{7,9}|[A-Z]{14}-[A-Z]{8}[SN][A-Z]-[A-Z]$
    prefix: ice.chem
    sampleId: DTXSID7032004
    uri_format: https://ice.ntp.niehs.nih.gov/api/v1/search?chemid=$1
  prefix: icechem
iceo:
  aberowl:
    description: ICEO is an integrated biological ontology for the description of
      bacterial integrative and conjugative elements (ICEs).
    download_owl: http://aber-owl.net/media/ontologies/ICEO/22/iceo.owl
    homepage: https://github.com/ontoice/ICEO
    name: Integrative and Conjugative Element Ontology
    prefix: ICEO
  bioportal:
    contact:
      email: noreply@bioontology.org
      name: Unknown
    homepage: https://github.com/ontoice/ICEO
    name: Integrative and Conjugative Element Ontology
    prefix: ICEO
    version: '2.1'
  comment: ICEO is not consistent about its identfiers like ICEO:0000595:1  and ICEO:0000595_1
  example: '0000712_1'
  example_extras:
  - '0000712'
  mappings:
    aberowl: ICEO
    bioportal: ICEO
    obofoundry: iceo
    ols: iceo
    ontobee: ICEO
    wikidata.entity: Q81661661
  obofoundry:
    contact: liumeng94@sjtu.edu.cn
    contact.github: Lemon-Liu
    contact.label: Meng LIU
    contact.orcid: 0000-0003-3781-6962
    deprecated: false
    description: ICEO is an integrated biological ontology for the description of
      bacterial integrative and conjugative elements (ICEs).
    domain: microbiology
    download.owl: http://purl.obolibrary.org/obo/iceo.owl
    homepage: https://github.com/ontoice/ICEO
    license: CC BY 4.0
    license.url: http://creativecommons.org/licenses/by/4.0/
    name: Integrative and Conjugative Element Ontology
    preferredPrefix: ICEO
    prefix: iceo
    publications:
    - id: https://www.ncbi.nlm.nih.gov/pubmed/35058462
      title: ICEO, a biological ontology for representing and analyzing bacterial
        integrative and conjugative elements
    repository: https://github.com/ontoice/ICEO
  ols:
    description: A biological ontology to standardize and integrate Integrative and
      Conjugative Element (ICE) information and to support computer-assisted reasoning.
    download_owl: http://purl.obolibrary.org/obo/iceo.owl
    homepage: https://github.com/ontoice/ICEO
    name: 'ICEO: Ontology of Integrative and Conjugative Elements'
    prefix: iceo
    tracker: https://github.com/ontoice/ICEO/issues
    version: '2.1'
  ontobee:
    library: Library
    name: Integrative and Conjugative Element Ontology
    prefix: ICEO
  pattern: ^\d{7}(_\d)?$
  prefix: iceo
  publications:
  - doi: 10.1038/s41597-021-01112-5
    pmc: PMC8776819
    pubmed: '35058462'
    title: ICEO, a biological ontology for representing and analyzing bacterial integrative
      and conjugative elements
    year: 2022
  uri_format: http://purl.obolibrary.org/obo/ICEO_$1
icepo:
  contact:
    email: pascale.gaudet@isb-sib.ch
    github: pgaudet
    name: Pascale Gaudet
    orcid: 0000-0003-1813-6857
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: The Ion Channel Electrophysiology Ontology supports the capture of
    voltage-gated ion channel electrophysiological data from the literature in a structured
    manner and thus enables other applications such as querying and reasoning tools.
  download_obo: https://download.nextprot.org/pub/current_release/controlled_vocabularies/icepo.obo
  example: '0000002'
  homepage: https://download.nextprot.org/pub/current_release/controlled_vocabularies/
  name: Ion Channel Electrophysiology Ontology
  pattern: ^\d{7}$
  prefix: icepo
  publications:
  - doi: null
    pmc: PMC4823818
    pubmed: null
    title: 'ICEPO: the ion channel electrophysiology ontology'
    year: null
  twitter: neXtProt_news
  uri_format: https://biopragmatics.github.io/providers/icepo/$1
icf:
  aberowl:
    description: 'The International Classification of Functioning, Disability and
      Health, known more commonly as ICF, is a classification of health and health-related
      domains. These domains are classified from body, individual and societal perspectives
      by means of two lists: a list of body functions and structure, and a list of
      domains of activity and participation. Since an individual''s functioning and
      disability occurs in a context, the ICF also includes a list of environmental
      factors. <br><br> Source: <a href="http://www.who.int/classifications/icf/en/">http://www.who.int/classifications/icf/en/</a>'
    download_owl: http://aber-owl.net/media/ontologies/ICF/3/icf.owl
    homepage: http://www.who.int/classifications/icf/en/
    name: International Classification of Functioning, Disability and Health
    prefix: ICF
    version: 1.0.2
  bioportal:
    contact:
      email: info@who.int
      name: The World Health Organization
    description: 'The International Classification of Functioning, Disability and
      Health, known more commonly as ICF, is a classification of health and health-related
      domains. These domains are classified from body, individual and societal perspectives
      by means of two lists: a list of body functions and structure, and a list of
      domains of activity and participation. Since an individual''s functioning and
      disability occurs in a context, the ICF also includes a list of environmental
      factors. <br><br> Source: <a href="http://www.who.int/classifications/icf/en/">http://www.who.int/classifications/icf/en/</a>'
    homepage: http://www.who.int/classifications/icf/en/
    name: International Classification of Functioning, Disability and Health
    prefix: ICF
    version: 1.0.2
  comment: This might be possible to roll directly into ICD11
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: The International Classification of Functioning, Disability and Health,
    known more commonly as ICF, is a classification of health and health-related domains.
    As the functioning and disability of an individual occurs in a context, ICF also
    includes a list of environmental factors. ICF is the WHO framework for measuring
    health and disability at both individual and population levels.
  example: '326705068'
  fairsharing:
    abbreviation: ICF
    description: The International Classification of Functioning, Disability and Health
      (ICF) is a classification of health and health-related domains. As the functioning
      and disability of an individual occurs in a context, ICF also includes a list
      of environmental factors. ICF is the WHO framework for measuring health and
      disability at both individual and population levels. ICF was officially endorsed
      by all 191 WHO Member States in the Fifty-fourth World Health Assembly on 22
      May 2001 (resolution WHA 54.21) as the international standard to describe and
      measure health and disability.
    domains:
    - Electronic Health Record
    homepage: https://www.who.int/standards/classifications/international-classification-of-functioning-disability-and-health
    license: https://creativecommons.org/licenses/by-nc-sa/3.0/igo
    name: International Classification of Functioning, Disability and Health
    prefix: FAIRsharing.7rngj0
    subjects:
    - Biomedical Science
    - Health Science
    - Medicine
    - Primary Health Care
  hl7:
    description: ICF describes how people live with their health condition. ICF is
      a classification of health and health related domains that describe body functions
      and structures, activities and participation. The domains are classified from
      body, individual and societal perspectives. Since an individual's functioning
      and disability occurs in a context, ICF also includes a list of environmental
      factors. ICF  is useful to understand and measure health outcomes. It can be
      used in clinical settings, health services or surveys at the individual or population
      level. Thus ICF complements ICD-10 , The International Statistical Classification
      of Diseases and Related Health Problems and therefore is looking beyond mortality
      and disease.
    homepage: http://www.who.int/classifications/icf/en/
    name: International Classification of Function
    organization: World Health Organisation
    preferred_prefix: icf
    prefix: 2.16.840.1.113883.6.254
    status: Complete
  homepage: https://icd.who.int/dev11/l-icf/en
  mappings:
    aberowl: ICF
    bioportal: ICF
    fairsharing: FAIRsharing.7rngj0
    hl7: 2.16.840.1.113883.6.254
  name: International Classification of Functioning, Disability and Health
  pattern: ^\d+$
  prefix: icf
  uri_format: https://icd.who.int/dev11/l-icf/en#/http://id.who.int/icd/entity/$1
iclc:
  cellosaurus:
    category: Cell line collections (Providers)
    homepage: http://www.iclc.it
    name: Interlab Cell Line Collection
    prefix: ICLC
    uri_format: http://www.iclc.it/details/det_list.php?line_id=$1
  example: ATL98012
  mappings:
    cellosaurus: ICLC
  pattern: ^\w{3}\d+$
  prefix: iclc
icldb:
  cellosaurus:
    category: Cell line databases/resources
    homepage: https://entomology.ca.uky.edu/aginsectcellsdatabase
    name: Insect Cell Lines DataBase
    prefix: ICLDB
    uri_format: https://entomology.ca.uky.edu/content/$1
  contact:
    email: surjeet.arya@uky.edu
    github: null
    name: Surjeet Kumar Arya
    orcid: 0000-0002-2212-4771
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: We have developed an online database describing the known cell lines
    from Coleoptera, Diptera, Hemiptera, Hymenoptera, and Lepidoptera that originated
    from crop pest insects. Cell line information has been primarily obtained from
    previous compilations of insect cell lines. (from homepage)
  example: 64ba
  homepage: https://entomology.ca.uky.edu/aginsectcellsdatabase
  mappings:
    cellosaurus: ICLDB
  name: Insect Cell Line Database
  prefix: icldb
  uri_format: https://entomology.ca.uky.edu/content/$1
ico:
  aberowl:
    description: An ontology of clinical informed consents
    download_owl: http://aber-owl.net/media/ontologies/ICO/17/ico.owl
    homepage: https://github.com/ICO-ontology/ICO
    name: Informed Consent Ontology
    prefix: ICO
  biocontext:
    prefix: ICO
  bioportal:
    contact:
      email: yongqunh@med.umich.edu
      name: Oliver He
    description: Informed Consent Ontology (ICO) is a community-based ontology in
      the domain of informed consent. It is an OBO library ontology and developed
      by following the OBO Foundry principles.
    homepage: https://github.com/ICO-ontology/ICO
    name: Informed Consent Ontology
    prefix: ICO
    publications:
    - http://ceur-ws.org/Vol-1327/icbo2014_paper_54.pdf
    version: '2025-03-15'
  example: '0000066'
  fairsharing:
    abbreviation: ICO
    contact:
      email: yongqunh@med.umich.edu
      name: Yongqun He
      orcid: 0000-0001-9189-9661
    description: Informed Consent Ontology (ICO) represents the documentations and
      processes involved in informed consent. ICO aims to support informed consent
      data integration and reasoning in the clinical research space. The core terms
      of ICO covers informed consent forms, the component inside the informed consent
      form, and various informed consent processes.
    homepage: https://github.com/ICO-ontology/ICO
    name: Informed Consent Ontology
    prefix: FAIRsharing.b9znd5
    repository: https://github.com/ICO-ontology/ICO/issues
    subjects:
    - Biomedical Science
    - Clinical Studies
    - Health Science
    - Medicine
  mappings:
    aberowl: ICO
    biocontext: ICO
    bioportal: ICO
    fairsharing: FAIRsharing.b9znd5
    obofoundry: ico
    ols: ico
    ontobee: ICO
    wikidata.entity: Q55118417
  obofoundry:
    appears_in:
    - scdo
    contact: yongqunh@med.umich.edu
    contact.github: yongqunh
    contact.label: Yongqun Oliver He
    contact.orcid: 0000-0001-9189-9661
    deprecated: false
    description: An ontology of clinical informed consents
    domain: investigations
    download.owl: http://purl.obolibrary.org/obo/ico.owl
    homepage: https://github.com/ICO-ontology/ICO
    license: CC BY 4.0
    license.url: http://creativecommons.org/licenses/by/4.0/
    name: Informed Consent Ontology
    preferredPrefix: ICO
    prefix: ico
    repository: https://github.com/ICO-ontology/ICO
  ols:
    description: The Informed Consent Ontology (ICO) is an ontology for the informed
      consent and informed consent process in the medical field.
    download_owl: http://purl.obolibrary.org/obo/ico.owl
    homepage: https://github.com/ICO-ontology/ICO
    name: Informed Consent Ontology (ICO)
    prefix: ico
    tracker: https://github.com/ICO-ontology/ICO/issues
    version: '2025-03-15'
    version.iri: http://purl.obolibrary.org/obo/ico/releases/2025-03-15/ico.owl
  ontobee:
    library: Library
    name: Informed Consent Ontology
    prefix: ICO
  pattern: ^\d{7}$
  prefix: ico
  uri_format: http://purl.obolibrary.org/obo/ICO_$1
iconclass:
  bartoc:
    abbreviation: ICONCLASS
    description: 'Iconclass is a subject-specific classification system. It is a hierarchically
      ordered collection of definitions of objects, people, events and abstract ideas
      that serve as the subject of an image. Art historians, researchers and curators
      use it to describe, classify and examine the subject of images represented in
      various media such as paintings, drawings and photographs. Numerous institutions
      across the world use Iconclass to describe and classify their collections in
      a standardized manner. In turn, users ranging from art historians to museum
      visitors use Iconclass to search and retrieve images from these collections.
      And as a research tool, Iconclass is also used to identify the significance
      of entire scenes or individual elements represented within an image. ICONCLASS
      applications used around the world have made it the most widely accepted classification
      system for visual documents. The three main components of Iconclass are: Classification
      System: 28,000 hierarchically ordered definitions divided into ten main divisions.
      Each definition consists of an alphanumeric classification code (notation) and
      the description of the iconographic subject (textual correlate). The definitions
      are used to index, catalogue and describe the subjects of images represented
      in works of art, reproductions, photographs and other sources. Alphabetical
      Index: 14,000 keywords used for locating the notation and its textual correlate
      needed to describe and/or index an image. Bibliography: 40,000 references to
      books and articles of iconographical interest (not yet online).'
    homepage: https://iconclass.org/
    license: ODBL
    name: Iconclass
    prefix: '459'
    wikidata_database: Q1502787
  contact:
    email: ep@epoz.org
    github: epoz
    name: Etienne Posthumus
    orcid: 0000-0002-0006-7542
  contact_group_email: info@iconclass.org
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: A classification system for the subject matter of works of art, originating
    from work from Henri van de Waal in the 1940.
  domain: multiple
  example: '3'
  example_extras:
  - 98C
  - 49E3932
  - 11HH(ELISABETH)35
  - 98C(ZENOBIA%20SEPTIMIA)2
  - 98C(...)(%2B1)
  homepage: https://iconclass.org
  mappings:
    bartoc: '459'
    wikidata.entity: Q1502787
  name: Iconclass Classification
  prefix: iconclass
  uri_format: https://iconclass.org/$1
icpd.project:
  contact:
    email: sonia.balyan@ibdc.rcb.res.in
    github: soniabalyan24
    name: Sonia Balyan
    orcid: 0000-0003-2136-4519
  contributor:
    email: sonia.balyan@ibdc.rcb.res.in
    github: soniabalyan24
    name: Sonia Balyan
    orcid: 0000-0003-2136-4519
  description: This resource is about projects in the Indian Crop Phenome Database
    (ICPD). The ICPD is a domain of the Indian Biological Data Center (IBDC), Regional
    Centre for Biotechnology, Faridabad, developed for the digitization of crop phenome
    data. Being the global agricultural powerhouse, the bulk of biological data generated
    in India is associated with agricultural trials. Ironically most of the trial
    data has been inaccessible to other researchers, and remains unpublished, and
    is lost as time passes. Therefore, ICPD would act as single-stop user-friendly
    platform for freely archiving, organizing, analyzing, and sharing the multi-crop
    phenome data following FAIR (Findable, Accessible, Interoperable and Re-usable)
    data principles. [from homepage]
  example: PPJ_100024
  github_request_issue: 1570
  homepage: https://ibdc.dbtindia.gov.in/icpd
  license: CC BY-NC-SA 4.0
  logo: https://ibdc.dbtindia.gov.in/icpd/static/image/ICPD-log.jpg
  name: Indian Crop Phenome Database Project
  part_of_database: icpd
  pattern: ^PPJ_\d+$
  prefix: icpd.project
  reviewer:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
icpd.study:
  contact:
    email: sonia.balyan@ibdc.rcb.res.in
    github: soniabalyan24
    name: Sonia Balyan
    orcid: 0000-0003-2136-4519
  contributor:
    email: sonia.balyan@ibdc.rcb.res.in
    github: soniabalyan24
    name: Sonia Balyan
    orcid: 0000-0003-2136-4519
  description: This resource is about studies in the Indian Crop Phenome Database
    (ICPD). The ICPD is a domain of the Indian Biological Data Center (IBDC), Regional
    Centre for Biotechnology, Faridabad, developed for the digitization of crop phenome
    data. Being the global agricultural powerhouse, the bulk of biological data generated
    in India is associated with agricultural trials. Ironically most of the trial
    data has been inaccessible to other researchers, and remains unpublished, and
    is lost as time passes. Therefore, ICPD would act as single-stop user-friendly
    platform for freely archiving, organizing, analyzing, and sharing the multi-crop
    phenome data following FAIR (Findable, Accessible, Interoperable and Re-usable)
    data principles. [from homepage]
  example: PST_100013
  github_request_issue: 1570
  homepage: https://ibdc.dbtindia.gov.in/icpd
  license: CC BY-NC-SA 4.0
  logo: https://ibdc.dbtindia.gov.in/icpd/static/image/ICPD-log.jpg
  name: Indian Crop Phenome Database Study
  part_of_database: icpd
  pattern: ^PST_\d+$
  prefix: icpd.study
  reviewer:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  uri_format: https://ibdc.dbtindia.gov.in/icpd/study-view-home/$1
ictv:
  bartoc:
    abbreviation: ICTV
    description: Taxonomy lies at the uneasy interface between biology and logic.
      The processing of information follows somewhat different rules in these two
      systems and the role of taxonomy is to reconcile them as tidily as possible.
      To this end, the Virology Division of the International Union of Microbiological
      Societies (IUMS) charged the International Committee on Taxonomy of Viruses
      (ICTV) with the task of developing, refining, and maintaining a universal virus
      taxonomy. The goal of this undertaking is to categorize the multitude of known
      viruses into a single classification scheme that reflects their evolutionary
      relationships, i.e. their individual phylogenies.
    homepage: https://talk.ictvonline.org/taxonomy
    name: Virus Taxonomy
    prefix: '507'
  description: Ontology representation of the [International Committee on Taxonomy
    of Viruses (ICTV)](https://ictv.global/) for the [EVORA project](https://evora-project.eu/)
  example: ICTV19990991
  homepage: https://github.com/EVORA-project/ictv-ontology
  mappings:
    bartoc: '507'
    ols: ictv
  name: International Committee on Taxonomy of Viruses Ontology
  ols:
    prefix: ictv
    version: MSL40
  prefix: ictv
  repository: https://github.com/EVORA-project/ictv-ontology
  uri_format: http://ictv.global/id/MSL40/$1
ideal:
  biocontext:
    prefix: IDEAL
  contact:
    email: sfukuchi@maebashi-it.ac.jp
    github: sfukuchi
    name: Satoshi Fukuchi
    orcid: 0000-0002-5705-3061
  fairsharing:
    abbreviation: IDEAL
    description: IDEAL (Intrinsically Disordered proteins with Extensive Annotations
      and Literature) is a collection of experimentally-verified intrinsically disordered
      proteins (IDPs) that cannot adopt stable globular structures under physiological
      conditions. IDEAL contains manually curated annotations on IDPs in locations,
      structures, and functional sites such as protein binding regions and post-translational
      modification sites together with references and structural domain assignments.
    homepage: http://www.ideal.force.cs.is.nagoya-u.ac.jp/IDEAL/
    license: CC-BY-4.0
    name: Intrinsically Disordered proteins with Extensive Annotations and Literature
    prefix: FAIRsharing.h3y42f
    publications:
    - doi: 10.1093/nar/gkt1010
      pubmed_id: 24178034
      title: IDEAL in 2014 illustrates interaction networks composed of intrinsically
        disordered proteins and their binding partners.
    subjects:
    - Biology
  homepage: https://www.ideal-db.org
  integbio:
    alt_name: Intrinsically Disordered proteins with Exten sive Annotations and Literatures
    description: This is a collection of knowledge on experimentally verified intrinsically
      disordered proteins. It contains manual annotations by curators on intrinsically
      disordered regions, interaction regions to other molecules, post-translational
      modification sites, references, and structural domain assignment. This database
      allows to browse by a list or search using keywords or BLAST. Data are downloadable
      with a XML file.
    fairsharing: biodbcore-000052
    homepage: https://www.ideal-db.org
    information_keywords:
    - Interaction/Pathway
    - Image/Movie
    - 3D structure
    maintainer: IDEAL Development Team
    name: IDEAL
    prefix: nbdc01456
    pubmeds:
    - '22067451'
    status: Active
    target_keywords:
    - Protein
  mappings:
    biocontext: IDEAL
    fairsharing: FAIRsharing.h3y42f
    integbio: nbdc01456
    miriam: ideal
    n2t: ideal
    pathguide: '701'
    uniprot: DB-0251
  miriam:
    deprecated: false
    description: IDEAL provides a collection of knowledge on experimentally verified
      intrinsically disordered proteins. It contains manual annotations by curators
      on intrinsically disordered regions, interaction regions to other molecules,
      post-translational modification sites, references and structural domain assignments.
    homepage: http://www.ideal.force.cs.is.nagoya-u.ac.jp/IDEAL/
    id: 00000398
    name: IDEAL
    namespaceEmbeddedInLui: false
    pattern: ^IID\d+$
    prefix: ideal
    sampleId: IID00001
    uri_format: http://idp1.force.cs.is.nagoya-u.ac.jp/IDEAL/ideal.php?id=$1
  n2t:
    description: IDEAL provides a collection of knowledge on experimentally verified
      intrinsically disordered proteins. It contains manual annotations by curators
      on intrinsically disordered regions, interaction regions to other molecules,
      post-translational modification sites, references and structural domain assignments.
    example: IID00001
    homepage: http://www.ideal.force.cs.is.nagoya-u.ac.jp/IDEAL/
    name: IDEAL at Maebashi Institute of Technology
    namespaceEmbeddedInLui: false
    pattern: ^IID\d+$
    prefix: ideal
    uri_format: http://idp1.force.cs.is.nagoya-u.ac.jp/IDEAL/idealItem.php?id=$1
  name: Intrinsically Disordered proteins with Extensive Annotations and Literature
  pathguide:
    abbreviation: IDEAL
    homepage: http://www.ideal.force.cs.is.nagoya-u.ac.jp/IDEAL/
    name: Intrinsically Disordered proteins with Extensive Annotations and Literature
    prefix: '701'
  prefix: ideal
  publications:
  - doi: 10.1093/nar/gkt1010
    pmc: PMC3965115
    pubmed: '24178034'
    title: IDEAL in 2014 illustrates interaction networks composed of intrinsically
      disordered proteins and their binding partners
    year: 2013
  - doi: 10.1093/nar/gkt1010
    pmc: null
    pubmed: null
    title: IDEAL in 2014 illustrates interaction networks composed of intrinsically
      disordered proteins and their binding partners.
    year: null
  - doi: 10.1093/nar/gkt1010
    pmc: null
    pubmed: '24178034'
    title: null
    year: null
  uniprot:
    abbreviation: IDEAL
    category: Family and domain databases
    homepage: https://www.ideal-db.org/
    name: Intrinsically Disordered proteins with Extensive Annotations and Literature
    prefix: DB-0251
    publications:
    - doi: 10.1093/nar/gkt1010
      pubmed: '24178034'
    uri_format: https://www.ideal-db.org/ideal.php?id=$1
ido:
  aberowl:
    download_owl: http://aber-owl.net/media/ontologies/IDO/12/ido.owl
    homepage: http://www.bioontology.org/wiki/index.php/Infectious_Disease_Ontology
    name: Infectious Disease Ontology
    prefix: IDO
  biocontext:
    prefix: IDO
  bioportal:
    contact:
      email: johnbeverley2021@u.northwestern.edu
      name: John Beverley
    description: 'The IDO ontologies are designed as a set of interoperable ontologies
      that will together provide coverage of the infectious disease domain. At the
      core of the set is a general Infectious Disease Ontology (IDO-Core) of entities
      relevant to both biomedical and clinical aspects of most infectious diseases.
      Sub-domain specific extensions of IDO-Core complete the set providing ontology
      coverage of entities relevant to specific pathogens or diseases. <br><br> To
      import,<br> Latest version: <a href="http://purl.obolibrary.org/obo/ido.owl">http://purl.obolibrary.org/obo/ido.owl</a><br>
      This version (2010-12-02): <a href="http://purl.obolibrary.org/obo/ido/2010-12-02/ido.owl">http://purl.obolibrary.org/obo/ido/2010-12-02/ido.owl</a><br>
      Previous versions:<br> 2010-05-26 <a href="http://purl.obolibrary.org/obo/ido/2010-05-26/ido.owl">http://purl.obolibrary.org/obo/ido/2010-05-26/ido.owl</a><br>
      2009-08-14 <a href="http://purl.obolibrary.org/obo/ido/2009-08-14/ido.owl">http://purl.obolibrary.org/obo/ido/2009-08-14/ido.owl</a><br>
      <br> <br> Latest release notes at <a href="http://infectiousdiseaseontology.org/page/Download">http://infectiousdiseaseontology.org/page/Download</a><br>
      Please note: The ontology metrics displayed by BioPortal do not distinguish
      IDO-developed terms from terms imported from other ontologies.'
    homepage: http://infectiousdiseaseontology.org
    name: Infectious Disease Ontology
    prefix: IDO
    publications:
    - http://infectiousdiseaseontology.org/page/Publications
    version: 8-3-20
  contributor_extras:
  - email: github@yohannparis.com
    github: YohannParis
    name: Yohann Paris
    orcid: 0009-0006-6049-1392
  fairsharing:
    abbreviation: IDO
    contact:
      email: Lindsay.Cowell@utsouthwestern.edu
      name: Lindsay Cowell
      orcid: 0000-0003-1617-8244
    description: 'The IDO ontologies are designed as a set of interoperable ontologies
      that will together provide coverage of the infectious disease domain. At the
      core of the set is a general Infectious Disease Ontology (IDO-Core) of entities
      relevant to both biomedical and clinical aspects of most infectious diseases.
      Sub-domain specific extensions of IDO-Core complete the set providing ontology
      coverage of entities relevant to specific pathogens or diseases. '
    domains:
    - disease
    - disease course
    - Classification
    homepage: https://github.com/infectious-disease-ontology
    license: https://creativecommons.org/licenses/by/3.0/us
    name: Infectious Disease Ontology Core
    prefix: FAIRsharing.aae3v6
    publications:
    - doi: 10.1186/s13326-021-00245-1
      pubmed: '34275487'
      title: The Infectious Disease Ontology in the age of COVID-19
      year: 2021
    repository: https://github.com/infectious-disease-ontology/infectious-disease-ontology
    subjects:
    - Preclinical Studies
    - Biomedical Science
    - Molecular Infection Biology
  mappings:
    aberowl: IDO
    biocontext: IDO
    bioportal: IDO
    fairsharing: FAIRsharing.aae3v6
    miriam: ido
    n2t: ido
    obofoundry: ido
    ols: ido
    ontobee: IDO
  miriam:
    deprecated: false
    description: Infectious Disease Ontology holds entities relevant to both biomedical
      and clinical aspects of most infectious diseases.
    homepage: https://www.ebi.ac.uk/ols4/ontologies/ido
    id: '00000677'
    name: Infectious Disease Ontology
    namespaceEmbeddedInLui: false
    pattern: ^[0-9]+$
    prefix: ido
    sampleId: '0000504'
    uri_format: https://www.ebi.ac.uk/ols4/ontologies/ido/terms?obo_id=IDO:$1
  n2t:
    description: Infectious Disease Ontology holds entities relevant to both biomedical
      and clinical aspects of most infectious diseases.
    example: '0000504'
    homepage: https://www.ebi.ac.uk/ols/ontologies/ido
    name: IDO through OLS
    namespaceEmbeddedInLui: false
    pattern: ^[0-9]+$
    prefix: ido
    uri_format: https://www.ebi.ac.uk/ols/ontologies/ido/terms?obo_id=IDO:$1
  obofoundry:
    appears_in:
    - scdo
    contact: Lindsay.Cowell@utsouthwestern.edu
    contact.github: lgcowell
    contact.label: Lindsay Cowell
    contact.orcid: 0000-0003-1617-8244
    deprecated: false
    description: A set of interoperable ontologies that will together provide coverage
      of the infectious disease domain. IDO core is the upper-level ontology that
      hosts terms of general relevance across the domain, while extension ontologies
      host terms to specific to a particular part of the domain.
    domain: health
    download.owl: http://purl.obolibrary.org/obo/ido.owl
    homepage: http://www.bioontology.org/wiki/index.php/Infectious_Disease_Ontology
    license: CC BY 3.0
    license.url: https://creativecommons.org/licenses/by/3.0/
    name: Infectious Disease Ontology
    preferredPrefix: IDO
    prefix: ido
    publications:
    - id: https://www.ncbi.nlm.nih.gov/pubmed/34275487
      title: The Infectious Disease Ontology in the age of COVID-19
    repository: https://github.com/infectious-disease-ontology/infectious-disease-ontology
  ols:
    description: A set of interoperable ontologies that will together provide coverage
      of the infectious disease domain. IDO core is the upper-level ontology that
      hosts terms of general relevance across the domain, while extension ontologies
      host terms to specific to a particular part of the domain.
    download_owl: http://purl.obolibrary.org/obo/ido.owl
    homepage: http://www.bioontology.org/wiki/index.php/Infectious_Disease_Ontology
    name: Infectious Disease Ontology
    prefix: ido
    tracker: https://github.com/infectious-disease-ontology/infectious-disease-ontology/issues
    version: '2017-11-03'
    version.iri: http://purl.obolibrary.org/obo/ido/2017-11-03/ido.owl
  ontobee:
    library: Library
    name: Infectious Disease Ontology
    prefix: IDO
  pattern: ^\d{7}$
  prefix: ido
  providers:
  - code: obo.1
    description: This incorrect encoding was found inside IDO-COVID-19
    example: null
    first_party: null
    homepage: http://purl.obolibrary.org
    name: Nonstandard OBO PURL
    publications: null
    status: null
    uri_format: http://purl.obolibrary.org/obo/ido.owl/IDO_$1
  publications:
  - doi: 10.1186/s13326-021-00245-1
    pmc: PMC8286442
    pubmed: '34275487'
    title: The Infectious Disease Ontology in the age of COVID-19
    year: 2021
  - doi: null
    pmc: null
    pubmed: '34275487'
    title: The Infectious Disease Ontology in the age of COVID-19
    year: null
  - doi: 10.1186/s13326-021-00245-1
    pmc: null
    pubmed: '34275487'
    title: The Infectious Disease Ontology in the age of COVID-19
    year: 2021
  uri_format: http://purl.obolibrary.org/obo/IDO_$1
idocovid19:
  aberowl:
    description: The COVID-19 Infectious Disease Ontology (IDO-COVID-19) is an extension
      of the Infectious Disease Ontology (IDO) and the Virus Infectious Disease Ontology
      (VIDO). IDO Virus follows OBO Foundry guidelines, employs the Basic Formal Ontology
      as its starting point, and covers epidemiology, classification, pathogenesis,
      and treatment of terms used to represent infection by the SARS-CoV-2 virus strain,
      and the associated COVID-19 disease.
    download_owl: http://aber-owl.net/media/ontologies/IDO-COVID-19/2/ido-covid-19.owl
    homepage: https://github.com/infectious-disease-ontology-extensions/ido-covid-19
    name: The COVID-19 Infectious Disease Ontology
    prefix: IDO-COVID-19
    version: 8-3-2020
  bioportal:
    contact:
      email: johnbeverley2021@u.northwestern.edu
      name: John Beverley
    description: The COVID-19 Infectious Disease Ontology (IDO-COVID-19) is an extension
      of the Infectious Disease Ontology (IDO) and the Virus Infectious Disease Ontology
      (VIDO). IDO Virus follows OBO Foundry guidelines, employs the Basic Formal Ontology
      as its starting point, and covers epidemiology, classification, pathogenesis,
      and treatment of terms used to represent infection by the SARS-CoV-2 virus strain,
      and the associated COVID-19 disease.
    homepage: https://github.com/infectious-disease-ontology-extensions/ido-covid-19
    name: The COVID-19 Infectious Disease Ontology
    prefix: IDO-COVID-19
    version: 8-3-2020
  contact:
    email: johnbeverley2021@u.northwestern.edu
    github: johnbeve
    name: John Beverly
    orcid: 0000-0002-1118-1738
  download_owl: https://raw.githubusercontent.com/infectious-disease-ontology-extensions/ido-covid-19/master/ontology/ido%20covid-19
  example: 0001191
  mappings:
    aberowl: IDO-COVID-19
    bioportal: IDO-COVID-19
    ols: idocovid19
  ols:
    contact: johnbeverley2021@u.northwestern.edu
    description: The COVID-19 Infectious Disease Ontology (IDO-COVID-19) is an extension
      of the Infectious Disease Ontology (IDO) and the Virus Infectious Disease Ontology
      (VIDO). IDO-COVID-19 follows OBO Foundry guidelines, employs the Basic Formal
      Ontology as its starting point, and covers epidemiology, classification, pathogenesis,
      and treatment of terms used to represent infection by the SARS-CoV-2 virus strain,
      and the associated COVID-19 disease.
    homepage: https://github.com/infectious-disease-ontology-extensions/ido-covid-19
    name: The COVID-19 Infectious Disease Ontology
    prefix: idocovid19
    uri_format: http://purl.obolibrary.org/obo/IDO-COVID-19$1
    version: '2020-21-07'
    version.iri: http://purl.obolibrary.org/obo/2020-21-07/ido-covid-19.owl
  pattern: ^\d{7}$
  prefix: idocovid19
  providers:
  - code: obo1
    description: This variation uses incorrect usage of dashes instead of underscores
    example: null
    first_party: null
    homepage: http://purl.obolibrary.org
    name: Incorrect OBO PURL variation 1
    publications: null
    status: null
    uri_format: http://purl.obolibrary.org/obo/IDO-COVID-19_$1
  repository: https://github.com/infectious-disease-ontology-extensions/ido-covid-19
  uri_format: http://purl.obolibrary.org/obo/COVIDO_$1
idoden:
  aberowl:
    description: An ontology for dengue fever.
    download_owl: http://aber-owl.net/media/ontologies/IDODEN/6/idoden.owl
    homepage: http://code.google.com/p/dengue-fever-ontology/
    name: Dengue Fever Ontology
    prefix: IDODEN
    version: 0.15b
  bioportal:
    contact:
      email: elvira@imbb.forth.gr
      name: Elvira Mitraka
    description: An ontology for dengue fever.
    homepage: http://code.google.com/p/dengue-fever-ontology/
    name: Dengue Fever Ontology
    prefix: IDODEN
    version: 0.15b
  contact:
    email: elvira@imbb.forth.gr
    github: null
    name: Elvira Mitraka
    orcid: 0000-0003-0719-3485
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: An ontology for dengue fever.
  example: '0003463'
  fairsharing:
    abbreviation: IDODEN
    description: 'This resource is no longer available because its underlying source
      material is not in scope for FAIRsharing.Records previously linked: [549, 720]. '
    homepage: http://code.google.com/p/dengue-fever-ontology/
    name: Dengue Fever Ontology
    prefix: FAIRsharing.askzq4
    subjects:
    - Medicine
  homepage: https://bioportal.bioontology.org/ontologies/IDODEN
  mappings:
    aberowl: IDODEN
    bioportal: IDODEN
    fairsharing: FAIRsharing.askzq4
  name: Dengue Fever Ontology
  pattern: ^\d{7}$
  prefix: idoden
  references:
  - https://journals.plos.org/plosntds/article?id=10.1371/journal.pntd.0003479
  uri_format: http://purl.bioontology.org/ontology/IDODEN_$1
idog:
  contact:
    email: baoym@big.ac.cn
    github: null
    name: Yiming Bao
    orcid: 0000-0002-9922-9723
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: Provides the worldwide dog research community a variety of data services
    including access to genes, genomes, SNPs, breed/disease Traits, gene expression
    experiments, dog-guman homology, and literatur. In addition, iDog provides online
    tools for performing genomic data visualization and analyses.
  example: '4'
  homepage: https://ngdc.cncb.ac.cn/idog/
  integbio:
    description: iDog is an integrated resource for domestic dog (Canis lupus familiaris)
      and wild canids. It includes information about Genes, Genomes, SNPs, Breed/Disease
      Traits, Gene Expressions, GO Function Annotations, Dog-Human Homolog Diseases
      and Literatures. In addition, it provides online tools for performing genomic
      data visualization and analyses.
    homepage: https://bigd.big.ac.cn/idog/
    information_keywords:
    - Sequence
    - Expression
    - Phenotype
    - Interaction/Pathway
    - Bibliography/Documents
    maintainer: National Genomics Data Center, Beijing Institute of Genomics, Chinese
      Academy of Sciences
    name: iDog
    prefix: nbdc02480
    pubmeds:
    - '30371881'
    status: Active
    target_keywords:
    - Genome/Gene
    - Genetic variation
    - Organism
    - Health/Disease
  license: CC-BY-4.0
  mappings:
    integbio: nbdc02480
    re3data: r3d100012176
  name: Integrated Resource for Domestic Dog
  pattern: ^\d+$
  prefix: idog
  publications:
  - doi: 10.1093/nar/gky1041
    pmc: PMC6323916
    pubmed: '30371881'
    title: 'iDog: an integrated resource for domestic dogs and wild canids'
    year: 2019
  re3data:
    description: iDog, an integrated resource for domestic dog (Canis lupus familiaris)
      and wild canids, provides the worldwide dog research community a variety of
      data services. This includes Genes, Genomes, SNPs, Breed/Disease Traits, Gene
      Expressions, Single Cell, Dog-Human Homolog Diseases and Literatures. In addition,
      iDog provides Online tools for performing genomic data visualization and analyses.
    doi: 10.17616/R3DH12
    homepage: https://ngdc.cncb.ac.cn/idog/
    name: iDog
    prefix: r3d100012176
    synonyms:
    - DoGSD
    - Dog Genome SNP Database
  references:
  - https://github.com/biopragmatics/bioregistry/pull/725
  uri_format: https://ngdc.cncb.ac.cn/idog/breed/getBreedDetail.action?breedId=$1
idomal:
  aberowl:
    description: An application ontology to cover all aspects of malaria as well as
      the intervention attempts to control it.
    download_owl: http://aber-owl.net/media/ontologies/IDOMAL/187/idomal.owl
    homepage: https://www.vectorbase.org/ontology-browser
    name: Malaria Ontology
    prefix: IDOMAL
  biocontext:
    prefix: IDOMAL
  bioportal:
    contact:
      email: topalis@imbb.forth.gr
      name: Pantelis Topalis
    description: An application ontology for malaria extending the infectious disease
      ontology (IDO)
    homepage: http://anobase.vectorbase.org/idomal/IDOMAL.obo
    name: Malaria Ontology
    prefix: IDOMAL
    publications:
    - http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2925367/?tool=pubmed
    version: 1.3.9
  download_obo: http://purl.obolibrary.org/obo/idomal.obo
  example: '0002350'
  example_extras:
  - '50000015'
  fairsharing:
    abbreviation: IDOMAL
    contact:
      email: topalis@imbb.forth.gr
      name: Pantelis Topalis
      orcid: 0000-0002-1635-4810
    description: An application ontology for malaria extending the infectious disease
      ontology (IDO). With about half a billion cases, of which nearly one million
      fatal ones, malaria constitutes one of the major infectious diseases worldwide.
      A recently revived effort to eliminate the disease also focuses on IT resources
      for its efficient control, which prominently includes the control of the mosquito
      vectors that transmit the Plasmodium pathogens. As part of this effort, IDOMAL
      has been developed and it is continually being updated.
    domains:
    - malaria
    - intervention design
    - disease
    - pathogen
    homepage: https://github.com/VEuPathDB-ontology/IDOMAL
    license: CC0-1.0
    name: Infection Disease Ontology Malaria
    prefix: FAIRsharing.2q8c28
    publications:
    - doi: 10.1186/2041-1480-4-16
      pubmed: '24034841'
      title: 'IDOMAL: the malaria ontology revisited'
      year: 2013
    - doi: 10.1186/1475-2875-9-230
      pubmed: '20698959'
      title: 'IDOMAL: an ontology for malaria'
      year: 2010
    subjects:
    - Life Science
    - Biomedical Science
    - Molecular Infection Biology
    twitter: VectorBase
  mappings:
    aberowl: IDOMAL
    biocontext: IDOMAL
    bioportal: IDOMAL
    fairsharing: FAIRsharing.2q8c28
    obofoundry: idomal
    ols: idomal
    ontobee: IDOMAL
  obofoundry:
    appears_in:
    - scdo
    contact: topalis@imbb.forth.gr
    contact.label: Pantelis Topalis
    deprecated: true
    description: An application ontology to cover all aspects of malaria as well as
      the intervention attempts to control it.
    domain: health
    download.obo: http://purl.obolibrary.org/obo/idomal.obo
    download.owl: http://purl.obolibrary.org/obo/idomal.owl
    homepage: https://www.vectorbase.org/ontology-browser
    license: CC0 1.0
    license.url: https://creativecommons.org/publicdomain/zero/1.0/
    name: Malaria Ontology
    prefix: idomal
    repository: https://github.com/VEuPathDB-ontology/IDOMAL
  ols:
    description: An application ontology to cover all aspects of malaria as well as
      the intervention attempts to control it.
    download_owl: http://purl.obolibrary.org/obo/idomal.owl
    homepage: https://www.vectorbase.org/ontology-browser
    name: Malaria Ontology
    prefix: idomal
    version: '2015-03-16'
    version.iri: http://purl.obolibrary.org/obo/idomal/2015-03-16/idomal.owl
  ontobee:
    library: Library
    name: Malaria Ontology
    prefix: IDOMAL
  pattern: ^(5?)\d{7}$
  prefix: idomal
  publications:
  - doi: 10.1186/2041-1480-4-16
    pmc: PMC3848731
    pubmed: '24034841'
    title: 'IDOMAL: the malaria ontology revisited'
    year: 2013
  - doi: 10.1186/1475-2875-9-230
    pmc: PMC2925367
    pubmed: '20698959'
    title: 'IDOMAL: an ontology for malaria'
    year: 2010
idoo:
  mappings:
    miriam: idoo
    n2t: idoo
  miriam:
    deprecated: false
    description: Identifiers.org Ontology
    homepage: http://registry.api.hq.identifiers.org/semanticApi/getRegistryOntology
    id: 00000683
    name: Identifiers.org Ontology
    namespaceEmbeddedInLui: false
    pattern: ^[0-9a-zA-Z]+$
    prefix: idoo
    sampleId: DataCollection
    uri_format: http://registry.api.hq.identifiers.org/semanticApi/getRegistryOntology#$1
  n2t:
    description: Identifiers.org Ontology
    example: DataCollection
    homepage: http://registry.api.hq.identifiers.org/semanticApi/getRegistryOntology
    name: Identifiers.org Ontology
    namespaceEmbeddedInLui: false
    pattern: ^[0-9a-zA-Z]+$
    prefix: idoo
    uri_format: http://registry.api.hq.identifiers.org/semanticApi/getRegistryOntology#$1
  prefix: idoo
idot:
  biocontext:
    prefix: idot
  homepage: http://biomodels.net/vocab/idot.rdf
  mappings:
    biocontext: idot
    miriam: idot
    n2t: idot
  miriam:
    deprecated: false
    description: Identifiers.org Terms (idot) is an RDF vocabulary providing useful
      terms for describing datasets.
    homepage: https://github.com/identifiers-org/ontop
    id: 00000519
    name: Identifiers.org Terms
    namespaceEmbeddedInLui: false
    pattern: ^[A-Za-z]+$
    prefix: idot
    sampleId: Namespace
    uri_format: https://github.com/identifiers-org/ontop/tree/main/idorg-ontology#idot$1
  n2t:
    description: Identifiers.org Terms (idot) is an RDF vocabulary providing useful
      terms for describing datasets.
    example: identifierPattern
    homepage: https://identifiers.org/
    name: IdoT via biomodels.net
    namespaceEmbeddedInLui: false
    pattern: ^[A-Za-z]+$
    prefix: idot
    uri_format: https://biomodels.net/vocab/idot.rdf#$1
  preferred_prefix: idot
  prefix: idot
  uri_format: https://biomodels.net/vocab/idot.rdf#$1
idpo:
  contact:
    email: f.quaglia@ibiom.cnr.it
    github: federicaquaglia
    name: Federica Quaglia
    orcid: 0000-0002-0341-4888
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: IDPO is used to describe structural aspects of an IDP/IDR, self-functions
    and functions directly associated with their disordered state. GO is used to describe
    functional aspects of an IDP/IDR.
  example: '00056'
  fairsharing:
    abbreviation: IDPO
    contact:
      email: f.quaglia@ibiom.cnr.it
      name: Federica Quaglia
      orcid: 0000-0002-0341-4888
    description: The Intrinsically Disordered Proteins Ontology (IDPO) describes the
      structural aspects of experimentally validated intrinsically disordered proteins
      (IDPs), intrinsically disordered regions (IDRs), and functions directly associated
      with protein disordered states.
    domains:
    - Protein Analysis
    homepage: https://www.disprot.org/ontology
    license: CC-BY-4.0
    name: Intrinsically Disordered Proteins Ontology
    prefix: FAIRsharing.bc973b
    publications:
    - doi: 10.1093/nar/gkad928
      pubmed: '37904585'
      title: 'DisProt in 2024: improving function annotation of intrinsically disordered
        proteins'
      year: 2024
    - doi: 10.1093/database/baae009
      title: Best practices for the manual curation of intrinsically disordered proteins
        in DisProt
      year: 2024
    subjects:
    - Structural Biology
    - Proteomics
  homepage: https://www.disprot.org/ontology
  keywords:
  - protein structure
  - proteins
  - structural biochemistry
  - structural bioinformatics
  mappings:
    fairsharing: FAIRsharing.bc973b
  name: Intrinsically Disordered Proteins Ontology
  pattern: ^\d{5}$
  prefix: idpo
  repository: https://github.com/BioComputingUP/idpo
  uri_format: https://www.disprot.org/idpo/IDPO:$1
idr:
  fairsharing:
    abbreviation: IDR
    contact:
      email: j.a.moore@dundee.ac.uk
      name: Josh Moore
      orcid: 0000-0003-4028-811X
    description: IDR is a prototype platform for publishing, mining and integrating
      bioimaging data at scale, following the Euro-BioImaging/ELIXIR imaging strategy
      using the OMERO and Bio-Formats open source software built by the Open Microscopy
      Environment. Deployed on an OpenStack cloud running on the EMBL-EBI’s Embassy
      resource, it includes image data linked to independent studies from genetic,
      RNAi, chemical, localisation and geographic high content screens, super-resolution
      microscopy, and digital pathology.
    homepage: https://idr.openmicroscopy.org
    name: Image Data Resource
    prefix: FAIRsharing.6wf1zw
    publications:
    - doi: 10.1038/nmeth.4326
      pubmed_id: 28775673
      title: 'The Image Data Resource: A Bioimage Data Integration and Publication
        Platform.'
    subjects:
    - Botany
    - Life Science
    - Biomedical Science
    twitter: openmicroscopy
  mappings:
    fairsharing: FAIRsharing.6wf1zw
    miriam: idr
    re3data: r3d100012435
  miriam:
    deprecated: false
    description: Image Data Resource (IDR) is an online, public data repository that
      seeks to store, integrate and serve image datasets from published scientific
      studies. We have collected and are continuing to receive existing and newly
      created “reference image" datasets that are valuable resources for a broad community
      of users, either because they will be frequently accessed and cited or because
      they can serve as a basis for re-analysis and the development of new computational
      tools.
    homepage: https://idr.openmicroscopy.org
    id: '00000743'
    name: Image Data Resource
    namespaceEmbeddedInLui: false
    pattern: ^[0-9]{4}$
    prefix: idr
    sampleId: '0001'
    uri_format: https://idr.openmicroscopy.org/search/?query=Name:idr$1
  prefix: idr
  publications:
  - doi: 10.1038/nmeth.4326
    pmc: PMC5536224
    pubmed: '28775673'
    title: 'The Image Data Resource: A Bioimage Data Integration and Publication Platform'
    year: 2017
  - doi: 10.1038/nmeth.4326
    pmc: null
    pubmed: null
    title: 'The Image Data Resource: A Bioimage Data Integration and Publication Platform.'
    year: null
  re3data:
    description: The IDR makes datasets that have never previously been accessible
      publicly available, allowing the community to search, view, mine and even process
      and analyze large, complex, multidimensional life sciences image data. Sharing
      data promotes the validation of experimental methods and scientific conclusions,
      the comparison with new data obtained by the global scientific community, and
      enables data reuse by developers of new analysis and processing tools.
    doi: 10.17616/R3XR0R
    homepage: https://idr.openmicroscopy.org/about/
    name: Image Data Resource
    prefix: r3d100012435
    synonyms:
    - IDR
    xrefs:
      omics: '13850'
idsa:
  deprecated: true
  mappings:
    tib: idsa
  prefix: idsa
  repository: https://github.com/International-Data-Spaces-Association/InformationModel
  tib:
    description: This ontology defines classes and properties for describing participants,
      infrastructure, data and services of the International Data Spaces (formerly
      known as Industrial Data Space).
    homepage: https://www.internationaldataspaces.org/
    keywords:
    - NFDI4ING
    - engineering
    name: International Data Spaces Information Model
    prefix: idsa
    tracker: https://github.com/International-Data-Spaces-Association/InformationModel/issues
    uri_format: https://w3id.org/idsa/core/$1
iedb.assay:
  contact:
    email: rvita@liai.org
    github: rvita
    name: Randi Vita
    orcid: 0000-0001-8957-7612
  contributor:
    email: m.naguthana@hotmail.com
    github: nagutm
    name: Mufaddal Naguthanawala
    orcid: 0009-0009-5240-7463
  description: Identifiers for specific experimental assays that serve as evidence
    for immune-related studies.
  example: '1691753'
  fairsharing:
    abbreviation: IEDB
    description: The IEDB provides the scientific community with a central repository
      of freely accessible epitope data and epitope prediction and analysis resources.
      The IEDB is a publicly accessible, comprehensive immune epitope database containing
      peptidic linear and conformational epitopes and non peptidic epitopes such as
      lipids, metals, drugs, carbohydrates, etc, with published or submitted antibody,
      T cell, MHC binding or MHC ligand elution experimental assays. Epitope data
      related to infectious diseases, allergy, autoimmunity and transplant tested
      in humans, non human primates, and any other species can be found in the IEDB.
    homepage: http://www.iedb.org/
    name: Immune Epitope Database
    prefix: FAIRsharing.c886cd
    publications:
    - doi: null
      pubmed_id: 16312048
      title: 'The immune epitope database and analysis resource: from vision to blueprint.'
    - doi: 10.1093/nar/gku938
      pubmed_id: 25300482
      title: The immune epitope database (IEDB) 3.0.
    - doi: 10.1093/nar/gkp1004
      pubmed_id: 19906713
      title: The immune epitope database 2.0.
    - doi: 10.1111/j.1365-2567.2012.03611.x
      pubmed_id: 22681406
      title: 'The immune epitope database: a historical retrospective of the first
        decade.'
    subjects:
    - Bioinformatics
    - Immunology
    - Life Science
  github_request_issue: 1204
  homepage: https://www.iedb.org/
  integbio:
    alt_name: Immune Epitope Database
    description: IEDB is a database of immunological molecules. The database contains
      entries on epitopes, MHC alleles and assays measuring immunological entities
      gathered from the literature. Users can search by epitope structure, epitope
      source, recognition context, or disease associations. Epitope prediction tools
      are available online, and some tools are available for local download and operation.
    homepage: http://www.immuneepitope.org/
    information_keywords:
    - Sequence
    - Bibliography/Documents
    maintainer: NIAID (The National Institute of Allergy and Infectious Diseases)
    name: IEDB
    prefix: nbdc00924
    pubmeds:
    - '19906713'
    status: Active
    target_keywords:
    - Protein
    - Health/Disease
  keywords:
  - immunology
  mappings:
    fairsharing: FAIRsharing.c886cd
    integbio: nbdc00924
    re3data: r3d100012702
  name: Immune Epitope Database Assays
  part_of_database: iedb
  pattern: ^\d+$
  prefix: iedb.assay
  providers:
  - code: cedar
    description: Cancer Epitope Database and Analysis Resource (CEDAR) is a specialized
      interface providing cancer-focused access to IEDB data with domain-specific
      analysis tools and workflows.
    example: null
    first_party: null
    homepage: https://cedar.iedb.org/
    name: Cancer Epitope Database and Analysis Resource
    publications:
    - doi: 10.1007/978-1-0716-4566-6_3
      pmc: null
      pubmed: '40779104'
      title: Using the Cancer Epitope Database and Analysis Resource (CEDAR)
      year: 2025
    status: null
    uri_format: https://cedar.iedb.org/assay/$1
  publications:
  - doi: 10.1093/nar/gku938
    pmc: PMC4384014
    pubmed: '25300482'
    title: The immune epitope database (IEDB) 3.0
    year: 2014
  - doi: 10.1111/j.1365-2567.2012.03611.x
    pmc: PMC3461392
    pubmed: '22681406'
    title: 'The immune epitope database: a historical retrospective of the first decade'
    year: 2012
  - doi: 10.1093/nar/gkp1004
    pmc: PMC2808938
    pubmed: '19906713'
    title: The immune epitope database 2.0
    year: 2009
  - doi: null
    pmc: null
    pubmed: '16312048'
    title: 'The immune epitope database and analysis resource: from vision to blueprint'
    year: 2004
  - doi: 10.1093/nar/gku938
    pmc: null
    pubmed: null
    title: The immune epitope database (IEDB) 3.0.
    year: null
  - doi: 10.1093/nar/gkp1004
    pmc: null
    pubmed: null
    title: The immune epitope database 2.0.
    year: null
  - doi: 10.1111/j.1365-2567.2012.03611.x
    pmc: null
    pubmed: null
    title: 'The immune epitope database: a historical retrospective of the first decade.'
    year: null
  - doi: 10.1007/978-1-0716-4566-6_3
    pmc: null
    pubmed: '40779104'
    title: Using the Cancer Epitope Database and Analysis Resource (CEDAR)
    year: 2025
  - doi: 10.1093/nar/gku938
    pmc: null
    pubmed: null
    title: The immune epitope database (IEDB) 3.0.
    year: null
  - doi: 10.1093/nar/gkp1004
    pmc: null
    pubmed: null
    title: The immune epitope database 2.0.
    year: null
  - doi: 10.1111/j.1365-2567.2012.03611.x
    pmc: null
    pubmed: null
    title: 'The immune epitope database: a historical retrospective of the first decade.'
    year: null
  - doi: 10.1007/978-1-0716-4566-6_3
    pmc: null
    pubmed: '40779104'
    title: Using the Cancer Epitope Database and Analysis Resource (CEDAR)
    year: 2025
  - doi: 10.1093/nar/gku938
    pmc: null
    pubmed: null
    title: The immune epitope database (IEDB) 3.0.
    year: null
  - doi: 10.1093/nar/gkp1004
    pmc: null
    pubmed: null
    title: The immune epitope database 2.0.
    year: null
  - doi: 10.1111/j.1365-2567.2012.03611.x
    pmc: null
    pubmed: null
    title: 'The immune epitope database: a historical retrospective of the first decade.'
    year: null
  - doi: 10.1007/978-1-0716-4566-6_3
    pmc: null
    pubmed: '40779104'
    title: Using the Cancer Epitope Database and Analysis Resource (CEDAR)
    year: 2025
  - doi: 10.1093/nar/gku938
    pmc: null
    pubmed: null
    title: The immune epitope database (IEDB) 3.0.
    year: null
  - doi: 10.1093/nar/gkp1004
    pmc: null
    pubmed: null
    title: The immune epitope database 2.0.
    year: null
  - doi: 10.1111/j.1365-2567.2012.03611.x
    pmc: null
    pubmed: null
    title: 'The immune epitope database: a historical retrospective of the first decade.'
    year: null
  - doi: 10.1007/978-1-0716-4566-6_3
    pmc: null
    pubmed: '40779104'
    title: Using the Cancer Epitope Database and Analysis Resource (CEDAR)
    year: 2025
  re3data:
    description: 'IEDB offers easy searching of experimental data characterizing antibody
      and T cell epitopes studied in humans, non-human primates, and other animal
      species. Epitopes involved in infectious disease, allergy, autoimmunity, and
      transplant are included.

      The IEDB also hosts tools to assist in the prediction and analysis of B cell
      and T cell epitopes.'
    homepage: https://www.iedb.org/
    name: Immune Epitope Database
    prefix: r3d100012702
    synonyms:
    - IEDB
    - Immune Epitope Database and Analysis Resource
    xrefs:
      ' nif': 0000-03017
      fairsharing: FAIRsharing.c886cd
      scr: '006604'
  reviewer:
    email: b.gyori@northeastern.edu
    github: bgyori
    name: Benjamin M. Gyori
    orcid: 0000-0001-9439-5346
  uri_format: https://www.iedb.org/assay/$1
iedb.epitope:
  contact:
    email: rvita@liai.org
    github: rvita
    name: Randi Vita
    orcid: 0000-0001-8957-7612
  contributor:
    email: m.naguthana@hotmail.com
    github: nagutm
    name: Mufaddal Naguthanawala
    orcid: 0009-0009-5240-7463
  description: Identifiers for epitopes, which are the specific parts of antigens
    recognized by the immune system.
  example: '117395'
  fairsharing:
    abbreviation: IEDB
    description: The IEDB provides the scientific community with a central repository
      of freely accessible epitope data and epitope prediction and analysis resources.
      The IEDB is a publicly accessible, comprehensive immune epitope database containing
      peptidic linear and conformational epitopes and non peptidic epitopes such as
      lipids, metals, drugs, carbohydrates, etc, with published or submitted antibody,
      T cell, MHC binding or MHC ligand elution experimental assays. Epitope data
      related to infectious diseases, allergy, autoimmunity and transplant tested
      in humans, non human primates, and any other species can be found in the IEDB.
    homepage: http://www.iedb.org/
    name: Immune Epitope Database
    prefix: FAIRsharing.c886cd
    publications:
    - doi: null
      pubmed_id: 16312048
      title: 'The immune epitope database and analysis resource: from vision to blueprint.'
    - doi: 10.1093/nar/gku938
      pubmed_id: 25300482
      title: The immune epitope database (IEDB) 3.0.
    - doi: 10.1093/nar/gkp1004
      pubmed_id: 19906713
      title: The immune epitope database 2.0.
    - doi: 10.1111/j.1365-2567.2012.03611.x
      pubmed_id: 22681406
      title: 'The immune epitope database: a historical retrospective of the first
        decade.'
    subjects:
    - Bioinformatics
    - Immunology
    - Life Science
  github_request_issue: 1204
  homepage: https://www.iedb.org/
  integbio:
    alt_name: Immune Epitope Database
    description: IEDB is a database of immunological molecules. The database contains
      entries on epitopes, MHC alleles and assays measuring immunological entities
      gathered from the literature. Users can search by epitope structure, epitope
      source, recognition context, or disease associations. Epitope prediction tools
      are available online, and some tools are available for local download and operation.
    homepage: http://www.immuneepitope.org/
    information_keywords:
    - Sequence
    - Bibliography/Documents
    maintainer: NIAID (The National Institute of Allergy and Infectious Diseases)
    name: IEDB
    prefix: nbdc00924
    pubmeds:
    - '19906713'
    status: Active
    target_keywords:
    - Protein
    - Health/Disease
  keywords:
  - immunology
  mappings:
    fairsharing: FAIRsharing.c886cd
    integbio: nbdc00924
    prefixcommons: tied
    re3data: r3d100012702
  name: Immune Epitope Database Epitopes
  part_of_database: iedb
  pattern: ^\d+$
  prefix: iedb.epitope
  prefixcommons:
    description: The IEDB contains data related to antibody and T cell epitopes for
      humans, non-human primates, rodents, and other animal species.
    example: '21'
    homepage: http://www.iedb.org
    keywords:
    - protein
    - small molecule
    name: The Immune Epitope Database (IEDB)
    pattern: ^\d+$
    prefix: tied
    uri_format: http://www.iedb.org/epId/$1
  providers:
  - code: cedar
    description: Cancer Epitope Database and Analysis Resource (CEDAR) is a specialized
      interface providing cancer-focused access to IEDB data with domain-specific
      analysis tools and workflows.
    example: null
    first_party: null
    homepage: https://cedar.iedb.org/
    name: Cancer Epitope Database and Analysis Resource
    publications:
    - doi: 10.1007/978-1-0716-4566-6_3
      pmc: null
      pubmed: '40779104'
      title: Using the Cancer Epitope Database and Analysis Resource (CEDAR)
      year: 2025
    status: null
    uri_format: https://cedar.iedb.org/epitope/$1
  publications:
  - doi: 10.1093/nar/gku938
    pmc: PMC4384014
    pubmed: '25300482'
    title: The immune epitope database (IEDB) 3.0
    year: 2014
  - doi: 10.1111/j.1365-2567.2012.03611.x
    pmc: PMC3461392
    pubmed: '22681406'
    title: 'The immune epitope database: a historical retrospective of the first decade'
    year: 2012
  - doi: 10.1093/nar/gkp1004
    pmc: PMC2808938
    pubmed: '19906713'
    title: The immune epitope database 2.0
    year: 2009
  - doi: null
    pmc: null
    pubmed: '16312048'
    title: 'The immune epitope database and analysis resource: from vision to blueprint'
    year: 2004
  - doi: 10.1093/nar/gku938
    pmc: null
    pubmed: null
    title: The immune epitope database (IEDB) 3.0.
    year: null
  - doi: 10.1093/nar/gkp1004
    pmc: null
    pubmed: null
    title: The immune epitope database 2.0.
    year: null
  - doi: 10.1111/j.1365-2567.2012.03611.x
    pmc: null
    pubmed: null
    title: 'The immune epitope database: a historical retrospective of the first decade.'
    year: null
  - doi: 10.1007/978-1-0716-4566-6_3
    pmc: null
    pubmed: '40779104'
    title: Using the Cancer Epitope Database and Analysis Resource (CEDAR)
    year: 2025
  re3data:
    description: 'IEDB offers easy searching of experimental data characterizing antibody
      and T cell epitopes studied in humans, non-human primates, and other animal
      species. Epitopes involved in infectious disease, allergy, autoimmunity, and
      transplant are included.

      The IEDB also hosts tools to assist in the prediction and analysis of B cell
      and T cell epitopes.'
    homepage: https://www.iedb.org/
    name: Immune Epitope Database
    prefix: r3d100012702
    synonyms:
    - IEDB
    - Immune Epitope Database and Analysis Resource
    xrefs:
      ' nif': 0000-03017
      fairsharing: FAIRsharing.c886cd
      scr: '006604'
  reviewer:
    email: b.gyori@northeastern.edu
    github: bgyori
    name: Benjamin M. Gyori
    orcid: 0000-0001-9439-5346
  uri_format: https://www.iedb.org/epitope/$1
iedb.mhc:
  contact:
    email: rvita@liai.org
    github: rvita
    name: Randi Vita
    orcid: 0000-0001-8957-7612
  contributor:
    email: m.naguthana@hotmail.com
    github: nagutm
    name: Mufaddal Naguthanawala
    orcid: 0009-0009-5240-7463
  description: Identifiers for Major Histocompatibility Complex (MHC) restrictions
    of immune cells, detailing genetic factors that influence immune recognition.
  example: '86'
  fairsharing:
    abbreviation: IEDB
    description: The IEDB provides the scientific community with a central repository
      of freely accessible epitope data and epitope prediction and analysis resources.
      The IEDB is a publicly accessible, comprehensive immune epitope database containing
      peptidic linear and conformational epitopes and non peptidic epitopes such as
      lipids, metals, drugs, carbohydrates, etc, with published or submitted antibody,
      T cell, MHC binding or MHC ligand elution experimental assays. Epitope data
      related to infectious diseases, allergy, autoimmunity and transplant tested
      in humans, non human primates, and any other species can be found in the IEDB.
    homepage: http://www.iedb.org/
    name: Immune Epitope Database
    prefix: FAIRsharing.c886cd
    publications:
    - doi: null
      pubmed_id: 16312048
      title: 'The immune epitope database and analysis resource: from vision to blueprint.'
    - doi: 10.1093/nar/gku938
      pubmed_id: 25300482
      title: The immune epitope database (IEDB) 3.0.
    - doi: 10.1093/nar/gkp1004
      pubmed_id: 19906713
      title: The immune epitope database 2.0.
    - doi: 10.1111/j.1365-2567.2012.03611.x
      pubmed_id: 22681406
      title: 'The immune epitope database: a historical retrospective of the first
        decade.'
    subjects:
    - Bioinformatics
    - Immunology
    - Life Science
  github_request_issue: 1204
  homepage: https://www.iedb.org/
  integbio:
    alt_name: Immune Epitope Database
    description: IEDB is a database of immunological molecules. The database contains
      entries on epitopes, MHC alleles and assays measuring immunological entities
      gathered from the literature. Users can search by epitope structure, epitope
      source, recognition context, or disease associations. Epitope prediction tools
      are available online, and some tools are available for local download and operation.
    homepage: http://www.immuneepitope.org/
    information_keywords:
    - Sequence
    - Bibliography/Documents
    maintainer: NIAID (The National Institute of Allergy and Infectious Diseases)
    name: IEDB
    prefix: nbdc00924
    pubmeds:
    - '19906713'
    status: Active
    target_keywords:
    - Protein
    - Health/Disease
  keywords:
  - immunology
  mappings:
    fairsharing: FAIRsharing.c886cd
    integbio: nbdc00924
    re3data: r3d100012702
  name: Immune Epitope Database MHC Restrictions
  part_of_database: iedb
  pattern: ^\d+$
  prefix: iedb.mhc
  publications:
  - doi: 10.1093/nar/gku938
    pmc: PMC4384014
    pubmed: '25300482'
    title: The immune epitope database (IEDB) 3.0
    year: 2014
  - doi: 10.1111/j.1365-2567.2012.03611.x
    pmc: PMC3461392
    pubmed: '22681406'
    title: 'The immune epitope database: a historical retrospective of the first decade'
    year: 2012
  - doi: 10.1093/nar/gkp1004
    pmc: PMC2808938
    pubmed: '19906713'
    title: The immune epitope database 2.0
    year: 2009
  - doi: null
    pmc: null
    pubmed: '16312048'
    title: 'The immune epitope database and analysis resource: from vision to blueprint'
    year: 2004
  re3data:
    description: 'IEDB offers easy searching of experimental data characterizing antibody
      and T cell epitopes studied in humans, non-human primates, and other animal
      species. Epitopes involved in infectious disease, allergy, autoimmunity, and
      transplant are included.

      The IEDB also hosts tools to assist in the prediction and analysis of B cell
      and T cell epitopes.'
    homepage: https://www.iedb.org/
    name: Immune Epitope Database
    prefix: r3d100012702
    synonyms:
    - IEDB
    - Immune Epitope Database and Analysis Resource
    xrefs:
      ' nif': 0000-03017
      fairsharing: FAIRsharing.c886cd
      scr: '006604'
  reviewer:
    email: b.gyori@northeastern.edu
    github: bgyori
    name: Benjamin M. Gyori
    orcid: 0000-0001-9439-5346
  uri_format: https://www.iedb.org/mhc/$1
iedb.receptor:
  contact:
    email: rvita@liai.org
    github: rvita
    name: Randi Vita
    orcid: 0000-0001-8957-7612
  contributor:
    email: m.naguthana@hotmail.com
    github: nagutm
    name: Mufaddal Naguthanawala
    orcid: 0009-0009-5240-7463
  description: Identifiers for immune receptors, representing receptor complexes or
    groups studied for their interactions with antigens or epitopes.
  example: '47'
  fairsharing:
    abbreviation: IEDB
    description: The IEDB provides the scientific community with a central repository
      of freely accessible epitope data and epitope prediction and analysis resources.
      The IEDB is a publicly accessible, comprehensive immune epitope database containing
      peptidic linear and conformational epitopes and non peptidic epitopes such as
      lipids, metals, drugs, carbohydrates, etc, with published or submitted antibody,
      T cell, MHC binding or MHC ligand elution experimental assays. Epitope data
      related to infectious diseases, allergy, autoimmunity and transplant tested
      in humans, non human primates, and any other species can be found in the IEDB.
    homepage: http://www.iedb.org/
    name: Immune Epitope Database
    prefix: FAIRsharing.c886cd
    publications:
    - doi: null
      pubmed_id: 16312048
      title: 'The immune epitope database and analysis resource: from vision to blueprint.'
    - doi: 10.1093/nar/gku938
      pubmed_id: 25300482
      title: The immune epitope database (IEDB) 3.0.
    - doi: 10.1093/nar/gkp1004
      pubmed_id: 19906713
      title: The immune epitope database 2.0.
    - doi: 10.1111/j.1365-2567.2012.03611.x
      pubmed_id: 22681406
      title: 'The immune epitope database: a historical retrospective of the first
        decade.'
    subjects:
    - Bioinformatics
    - Immunology
    - Life Science
  github_request_issue: 1204
  homepage: https://www.iedb.org/
  integbio:
    alt_name: Immune Epitope Database
    description: IEDB is a database of immunological molecules. The database contains
      entries on epitopes, MHC alleles and assays measuring immunological entities
      gathered from the literature. Users can search by epitope structure, epitope
      source, recognition context, or disease associations. Epitope prediction tools
      are available online, and some tools are available for local download and operation.
    homepage: http://www.immuneepitope.org/
    information_keywords:
    - Sequence
    - Bibliography/Documents
    maintainer: NIAID (The National Institute of Allergy and Infectious Diseases)
    name: IEDB
    prefix: nbdc00924
    pubmeds:
    - '19906713'
    status: Active
    target_keywords:
    - Protein
    - Health/Disease
  keywords:
  - immunology
  mappings:
    fairsharing: FAIRsharing.c886cd
    integbio: nbdc00924
    re3data: r3d100012702
  name: Immune Epitope Database Receptors
  part_of_database: iedb
  pattern: ^\d+$
  prefix: iedb.receptor
  providers:
  - code: cedar
    description: Cancer Epitope Database and Analysis Resource (CEDAR) is a specialized
      interface providing cancer-focused access to IEDB data with domain-specific
      analysis tools and workflows.
    example: null
    first_party: null
    homepage: https://cedar.iedb.org/
    name: Cancer Epitope Database and Analysis Resource
    publications:
    - doi: 10.1007/978-1-0716-4566-6_3
      pmc: null
      pubmed: '40779104'
      title: Using the Cancer Epitope Database and Analysis Resource (CEDAR)
      year: 2025
    status: null
    uri_format: https://cedar.iedb.org/receptor/$1
  publications:
  - doi: 10.1093/nar/gku938
    pmc: PMC4384014
    pubmed: '25300482'
    title: The immune epitope database (IEDB) 3.0
    year: 2014
  - doi: 10.1111/j.1365-2567.2012.03611.x
    pmc: PMC3461392
    pubmed: '22681406'
    title: 'The immune epitope database: a historical retrospective of the first decade'
    year: 2012
  - doi: 10.1093/nar/gkp1004
    pmc: PMC2808938
    pubmed: '19906713'
    title: The immune epitope database 2.0
    year: 2009
  - doi: null
    pmc: null
    pubmed: '16312048'
    title: 'The immune epitope database and analysis resource: from vision to blueprint'
    year: 2004
  re3data:
    description: 'IEDB offers easy searching of experimental data characterizing antibody
      and T cell epitopes studied in humans, non-human primates, and other animal
      species. Epitopes involved in infectious disease, allergy, autoimmunity, and
      transplant are included.

      The IEDB also hosts tools to assist in the prediction and analysis of B cell
      and T cell epitopes.'
    homepage: https://www.iedb.org/
    name: Immune Epitope Database
    prefix: r3d100012702
    synonyms:
    - IEDB
    - Immune Epitope Database and Analysis Resource
    xrefs:
      ' nif': 0000-03017
      fairsharing: FAIRsharing.c886cd
      scr: '006604'
  reviewer:
    email: b.gyori@northeastern.edu
    github: bgyori
    name: Benjamin M. Gyori
    orcid: 0000-0001-9439-5346
  uri_format: https://www.iedb.org/receptor/$1
iedb.reference:
  contact:
    email: rvita@liai.org
    github: rvita
    name: Randi Vita
    orcid: 0000-0001-8957-7612
  contributor:
    email: m.naguthana@hotmail.com
    github: nagutm
    name: Mufaddal Naguthanawala
    orcid: 0009-0009-5240-7463
  description: Identifiers for references, typically linking to sources of evidence
    such as publications that support data within IEDB.
  example: '1038233'
  fairsharing:
    abbreviation: IEDB
    description: The IEDB provides the scientific community with a central repository
      of freely accessible epitope data and epitope prediction and analysis resources.
      The IEDB is a publicly accessible, comprehensive immune epitope database containing
      peptidic linear and conformational epitopes and non peptidic epitopes such as
      lipids, metals, drugs, carbohydrates, etc, with published or submitted antibody,
      T cell, MHC binding or MHC ligand elution experimental assays. Epitope data
      related to infectious diseases, allergy, autoimmunity and transplant tested
      in humans, non human primates, and any other species can be found in the IEDB.
    homepage: http://www.iedb.org/
    name: Immune Epitope Database
    prefix: FAIRsharing.c886cd
    publications:
    - doi: null
      pubmed_id: 16312048
      title: 'The immune epitope database and analysis resource: from vision to blueprint.'
    - doi: 10.1093/nar/gku938
      pubmed_id: 25300482
      title: The immune epitope database (IEDB) 3.0.
    - doi: 10.1093/nar/gkp1004
      pubmed_id: 19906713
      title: The immune epitope database 2.0.
    - doi: 10.1111/j.1365-2567.2012.03611.x
      pubmed_id: 22681406
      title: 'The immune epitope database: a historical retrospective of the first
        decade.'
    subjects:
    - Bioinformatics
    - Immunology
    - Life Science
  github_request_issue: 1204
  homepage: https://www.iedb.org/
  integbio:
    alt_name: Immune Epitope Database
    description: IEDB is a database of immunological molecules. The database contains
      entries on epitopes, MHC alleles and assays measuring immunological entities
      gathered from the literature. Users can search by epitope structure, epitope
      source, recognition context, or disease associations. Epitope prediction tools
      are available online, and some tools are available for local download and operation.
    homepage: http://www.immuneepitope.org/
    information_keywords:
    - Sequence
    - Bibliography/Documents
    maintainer: NIAID (The National Institute of Allergy and Infectious Diseases)
    name: IEDB
    prefix: nbdc00924
    pubmeds:
    - '19906713'
    status: Active
    target_keywords:
    - Protein
    - Health/Disease
  keywords:
  - immunology
  mappings:
    fairsharing: FAIRsharing.c886cd
    integbio: nbdc00924
    miriam: iedb
    re3data: r3d100012702
  miriam:
    deprecated: false
    description: The Immune Epitope Database (IEDB) is a freely available resource
      funded by NIAID. It catalogs experimental data on antibody and T cell epitopes
      studied in humans, non-human primates, and other animal species in the context
      of infectious disease, allergy, autoimmunity and transplantation. The IEDB also
      hosts tools to assist in the prediction and analysis of epitopes.
    homepage: https://www.lji.org/
    id: 00000865
    name: Immune Epitope Database (IEDB)
    namespaceEmbeddedInLui: false
    pattern: ^[0-9]+$
    prefix: iedb
    sampleId: '1038233'
    uri_format: https://www.iedb.org/reference/$1
  name: Immune Epitope Database References
  part_of_database: iedb
  pattern: ^\d+$
  prefix: iedb.reference
  providers:
  - code: cedar
    description: Cancer Epitope Database and Analysis Resource (CEDAR) is a specialized
      interface providing cancer-focused access to IEDB data with domain-specific
      analysis tools and workflows.
    example: null
    first_party: null
    homepage: https://cedar.iedb.org/
    name: Cancer Epitope Database and Analysis Resource
    publications:
    - doi: 10.1007/978-1-0716-4566-6_3
      pmc: null
      pubmed: '40779104'
      title: Using the Cancer Epitope Database and Analysis Resource (CEDAR)
      year: 2025
    status: null
    uri_format: https://cedar.iedb.org/reference/$1
  publications:
  - doi: 10.1093/nar/gku938
    pmc: PMC4384014
    pubmed: '25300482'
    title: The immune epitope database (IEDB) 3.0
    year: 2014
  - doi: 10.1111/j.1365-2567.2012.03611.x
    pmc: PMC3461392
    pubmed: '22681406'
    title: 'The immune epitope database: a historical retrospective of the first decade'
    year: 2012
  - doi: 10.1093/nar/gkp1004
    pmc: PMC2808938
    pubmed: '19906713'
    title: The immune epitope database 2.0
    year: 2009
  - doi: null
    pmc: null
    pubmed: '16312048'
    title: 'The immune epitope database and analysis resource: from vision to blueprint'
    year: 2004
  - doi: 10.1093/nar/gku938
    pmc: null
    pubmed: null
    title: The immune epitope database (IEDB) 3.0.
    year: null
  - doi: 10.1093/nar/gkp1004
    pmc: null
    pubmed: null
    title: The immune epitope database 2.0.
    year: null
  - doi: 10.1111/j.1365-2567.2012.03611.x
    pmc: null
    pubmed: null
    title: 'The immune epitope database: a historical retrospective of the first decade.'
    year: null
  - doi: 10.1007/978-1-0716-4566-6_3
    pmc: null
    pubmed: '40779104'
    title: Using the Cancer Epitope Database and Analysis Resource (CEDAR)
    year: 2025
  re3data:
    description: 'IEDB offers easy searching of experimental data characterizing antibody
      and T cell epitopes studied in humans, non-human primates, and other animal
      species. Epitopes involved in infectious disease, allergy, autoimmunity, and
      transplant are included.

      The IEDB also hosts tools to assist in the prediction and analysis of B cell
      and T cell epitopes.'
    doi: 10.17616/R3X217
    homepage: https://www.iedb.org/
    license: CC
    name: Immune Epitope Database
    prefix: r3d100012702
    synonyms:
    - IEDB
    - Immune Epitope Database and Analysis Resource
    xrefs:
      nif: 0000-03017
  reviewer:
    email: b.gyori@northeastern.edu
    github: bgyori
    name: Benjamin M. Gyori
    orcid: 0000-0001-9439-5346
  uri_format: https://www.iedb.org/reference/$1
ieee.author:
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  homepage: https://ieeexplore.ieee.org
  keywords:
  - person
  - researcher
  mappings:
    wikidata: P6479
  prefix: ieee.author
  references:
  - https://github.com/biopragmatics/bioregistry/pull/1171
  wikidata:
    description: identifier for an author in IEEE Xplore
    example:
    - '37271072100'
    - '37274652000'
    - '37393195900'
    name: IEEE Xplore author ID
    pattern: ^[1-9]\d*$
    prefix: P6479
    uri_format: https://ieeexplore.ieee.org/author/$1
ieee.document:
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  homepage: https://ieeexplore.ieee.org
  mappings:
    wikidata: P6480
  prefix: ieee.document
  references:
  - https://github.com/biopragmatics/bioregistry/pull/1171
  wikidata:
    description: identifier for a document in IEEE Xplore
    example:
    - '1580791'
    - '668698'
    - '761722'
    name: IEEE Xplore document ID
    pattern: ^[1-9]\d*$
    prefix: P6480
    uri_format: https://ieeexplore.ieee.org/document/$1
ietf.language:
  bartoc:
    description: The IANA Language Subtag Registry contains language tags (abbreviated
      language codes) as defined by the Internet Engineering Task Force (IETF). These
      language tags are used in a number of modern computing standards, such as HTTP,
      HTML, XML, and RDF. Components of language tags are drawn from other standards
      such as ISO 639, ISO 15924 and ISO 3166-1.
    homepage: http://www.iana.org/assignments/language-subtag-registry/
    license: CC0-1.0
    name: IANA Language Subtag Registry
    prefix: '2022'
    wikidata_database: Q1059900
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: Shorthand representations of languages and their subtypes
  example: en-GB
  example_extras:
  - en
  - ar-SA
  - aaf
  homepage: http://www.iana.org/assignments/language-subtag-registry/language-subtag-registry
  mappings:
    bartoc: '2022'
    wikidata: P305
    wikidata.entity: Q1059900
  name: Internet Engineering Task Force Language Tag
  pattern: ^\w{2,3}(-\w+)?$
  prefix: ietf.language
  synonyms:
  - bcp47
  wikidata:
    description: 'identifier for language or languoid per the Internet Engineering
      Task Force; can include a primary language subtag, subtags for script, region,
      variant, extension, or private-use. Format: 2 or 3 letters, followed by "-"
      if subtags present'
    example:
    - ar-SA
    - en-GB
    - hu
    homepage: http://www.iana.org/assignments/language-subtag-registry/language-subtag-registry
    name: IETF language tag
    prefix: P305
iev:
  biocontext:
    prefix: IEV
  example: '0000000'
  mappings:
    biocontext: IEV
    obofoundry: iev
    prefixcommons: iev
  obofoundry:
    deprecated: true
    domain: chemistry and biochemistry
    homepage: http://www.inoh.org
    name: Event (INOH pathway ontology)
    prefix: iev
  pattern: ^\d{7}$
  prefix: iev
  prefixcommons:
    bioportal: '1011'
    description: The Event Ontology is an ontology of pathways. It classifies pathways,
      sub-pathways and other biological phenomena to form a DAG structure.
    example: IEV_0000913
    homepage: http://www.inoh.org
    keywords:
    - obo
    - pathway
    - structure
    name: Event (INOH pathway ontology)
    pattern: ^IEV_\d+$
    prefix: iev
    uri_format: http://www.inoh.org/ontology-viewer/cgi-bin/InohOVAttr.php?type=IEV&id=$1
igrhcellid:
  cellosaurus:
    category: Cell line databases/resources
    homepage: http://igrcid.ibms.sinica.edu.tw/cgi-bin/index.cgi
    name: Integrated Genomic Resources of human Cell Lines for Identification
    prefix: IGRhCellID
    uri_format: http://igrcid.ibms.sinica.edu.tw/cgi-bin/cell_line_view.cgi?cl_name=$1
  example: ACHN
  mappings:
    cellosaurus: IGRhCellID
  prefix: igrhcellid
igsn:
  bartoc:
    abbreviation: IGSN
    description: An IGSN ID is a globally unique and persistent identifier for material
      samples. The core purpose of the IGSN ID is to enable transparent and traceable
      connections between research activities and objects, including samples, collections,
      instruments, grants, data, publications, people, and organizations.
    homepage: https://ev.igsn.org
    name: International Generic Sample Number
    prefix: '20719'
  contact:
    email: jens.klump@csiro.au
    github: jklump
    name: Jens Klump
    orcid: 0000-0001-5911-6022
  fairsharing:
    abbreviation: IGSN (Generic)
    description: An IGSN ID is a globally unique and persistent identifier for physical
      samples in all scientific fields. An IGSN ID can be applied to an individual
      sample, an aggregation of samples, or to a feature-of-interest (the real-world
      feature that the sample is taken from). From 2021, IGSN IDs are functionally
      DOIs and are registered with metadata encoded in the DataCite Metadata Schema.
      The IGSN ID, previously known as an "International GeoSample Number", naming
      schema has changed, to reflects the expanding scope and utilization as a partnership
      agreement between DataCite and the IGSN e.V.
    domains:
    - environmental material
    - centrally registered identifier
    - Biospecimen
    homepage: https://www.igsn.org
    logo: https://api.fairsharing.org/rails/active_storage/blobs/redirect/eyJfcmFpbHMiOnsibWVzc2FnZSI6IkJBaHBBaVVDIiwiZXhwIjpudWxsLCJwdXIiOiJibG9iX2lkIn19--4d19e53906f86cdaca6a9752fde1dd82276b7f22/igsn-original.jpg?disposition=inline
    name: International Generic Sample Number
    prefix: FAIRsharing.c7f365
    publications:
    - doi: 10.5334/dsj-2017-002
      title: Utilizing the International Geo Sample Number Concept in Continental
        Scientific Drilling During ICDP Expedition COSC-1
      year: 2017
    - doi: 10.5334/dsj-2021-033
      title: 'Towards Globally Unique Identification of Physical Samples: Governance
        and Technical Implementation of the IGSN Global Sample Number'
      year: 2021
    - doi: 10.5334/dsj-2023-005
      title: 'Scaling Identifiers and their Metadata to Gigascale: An Architecture
        to Tackle the Challenges of Volume and Variety'
      year: 2023
    - doi: 10.1007/978-3-030-85040-1_162
      title: International Generic Sample Number
      year: 2023
    - doi: 10.5281/zenodo.5118289
      title: 'IGSN 2040 Summary Report: Defining the Future of the IGSN as a Global
        Persistent Identifier for Material Samples'
      year: 2021
    repository: https://igsn.github.io/
    subjects:
    - Hydrogeology
    - Geochemistry
    - Environmental Science
    - Omics
    - Archaeology
    - Geology
    - Earth Science
  mappings:
    bartoc: '20719'
    fairsharing: FAIRsharing.c7f365
    miriam: igsn
    n2t: igsn
  miriam:
    deprecated: false
    description: IGSN is a globally unique and persistent identifier for material
      samples and specimens.  IGSNs are obtained from IGSN e.V. Agents.
    homepage: https://ev.igsn.org/home
    id: 00000806
    name: International Generic Sample Number
    namespaceEmbeddedInLui: false
    pattern: ^[A-Za-z]{2,4}[A-Za-z0-9.-]{1,71}$
    prefix: igsn
    sampleId: AU124
    uri_format: http://igsn.org/$1
  n2t:
    example: SSH000SUA
    homepage: http://www.geosamples.org/
    name: International Geo Sample Number
    namespaceEmbeddedInLui: false
    prefix: igsn
    uri_format: hdl.handle.net/10273/$1
  prefix: igsn
igsr:
  cellosaurus:
    category: Biological sample resources
    homepage: https://www.internationalgenome.org/
    name: International Genome Sample Resource
    prefix: IGSR
    uri_format: https://www.internationalgenome.org/data-portal/sample/$1
  contact:
    email: flicek@ebi.ac.uk
    github: null
    name: Paul Flicek
    orcid: 0000-0002-3897-7955
  example: NA06985
  fairsharing:
    abbreviation: IGSR
    description: 'The International Genome Sample Resource (IGSR) was established
      to ensure the ongoing usability of data generated by the 1000 Genomes Project
      and to extend the data set. The 1000 Genomes Project ran between 2008 and 2015,
      creating the largest public catalogue of human variation and genotype data.
      As the project ended, the Data Coordination Centre at EMBL-EBI has received
      continued funding from the Wellcome Trust to maintain and expand the resource.
      IGSR was set up to do this and has the following aims: ensure the future access
      to and usability of the 1000 Genomes reference data; incorporate additional
      published genomic data on the 1000 Genomes samples; and expand the data collection
      to include new populations not represented in the 1000 Genomes Project.'
    homepage: https://www.internationalgenome.org/
    name: The International Genome Sample Resource
    prefix: FAIRsharing.4Vs9VM
    publications:
    - doi: 10.1038/nature15393
      pubmed_id: 26432245
      title: A global reference for human genetic variation.
    - doi: 10.1093/nar/gkz836
      pubmed_id: 31584097
      title: The International Genome Sample Resource (IGSR) collection of open human
        genomic variation resources.
    subjects:
    - Genomics
    - Comparative Genomics
    twitter: 1000genomes
  mappings:
    cellosaurus: IGSR
    fairsharing: FAIRsharing.4Vs9VM
    re3data: r3d100010180
  prefix: igsr
  publications:
  - doi: 10.1093/nar/gkz836
    pmc: PMC6943028
    pubmed: '31584097'
    title: The International Genome Sample Resource (IGSR) collection of open human
      genomic variation resources
    year: 2020
  - doi: 10.1038/nature15393
    pmc: PMC4750478
    pubmed: '26432245'
    title: A global reference for human genetic variation
    year: 2015
  re3data:
    description: 'The 1000 Genomes Project is an international collaboration to produce
      an extensive public catalog of human genetic variation, including SNPs and structural
      variants, and their haplotype contexts. This resource will support genome-wide
      association studies and other medical research studies.

      The genomes of about 2500 unidentified people from about 25 populations around
      the world will be sequenced using next-generation sequencing technologies. The
      results of the study will be freely and publicly accessible to researchers worldwide.

      The International Genome Sample Resource (IGSR) has been established at EMBL-EBI
      to continue supporting data generated by the 1000 Genomes Project, supplemented
      with new data and new analysis.'
    doi: 10.17616/R3CP4M
    homepage: https://www.internationalgenome.org/
    name: 1000 Genomes
    prefix: r3d100010180
    synonyms:
    - IGSR - International Genome Sample Resource
    - Thousand Genomes
    xrefs:
      omics: '00261'
ihw:
  cellosaurus:
    category: Cell line databases/resources
    homepage: https://www.fredhutch.org/en/research/institutes-networks-ircs/international-histocompatibility-working-group.html
    name: International Histocompatibility Workshop cell lines
    prefix: IHW
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: The International Histocompatibility Working Group provides a comprehensive
    inventory of HLA reference genes to support worldwide research in immunogenetics.
    We also offer selected cell lines and DNA from our substantial DNA Bank of more
    than 1,000 cell lines from selected families, as well as individuals with diverse
    ethnicity and immunologic characteristics.
  example: IHW09326
  homepage: https://www.fredhutch.org/en/research/institutes-networks-ircs/international-histocompatibility-working-group.html
  mappings:
    cellosaurus: IHW
  name: International Histocompatibility Workshop cell lines
  pattern: ^IHW\d+$
  prefix: ihw
iirds.core:
  description: An ontology encoding the core metadata based on the Intelligent Information
    Request and Delivery (iiRDS) standard
  example: Action
  homepage: https://github.com/iirds-consortium/models
  mappings:
    tib: iirds
  name: International Standard for Intelligent Information Request and Delivery Core
    Ontology
  prefix: iirds.core
  repository: https://github.com/iirds-consortium/models
  tib:
    contact: comment.iirds@tekom.de
    download_rdf: https://raw.githubusercontent.com/iirds-consortium/models/main/iirds-core.rdf
    homepage: https://iirds.org/index.php
    keywords:
    - NFDI4ING
    - computer science
    name: IIRDS CORE Ontology
    prefix: iirds
    tracker: https://github.com/iirds-consortium/models/issues
    uri_format: http://iirds.tekom.de/iirds#$1
iirds.mch:
  description: An ontology encoding machinery based on the Intelligent Information
    Request and Delivery (iiRDS) standard
  example: ConsumableSupply
  homepage: https://github.com/iirds-consortium/models
  mappings:
    tib: iirdsmch
  name: International Standard for Intelligent Information Request and Delivery Machinery
    Ontology
  prefix: iirds.mch
  repository: https://github.com/iirds-consortium/models
  tib:
    contact: comment.iirds@tekom.de
    download_rdf: https://raw.githubusercontent.com/iirds-consortium/models/main/iirds-machinery.rdf
    homepage: https://iirds.org/index.php
    keywords:
    - NFDI4ING
    - computer science
    name: IIRDS Machinery Ontology
    prefix: iirdsmch
    tracker: https://github.com/iirds-consortium/models/issues
    uri_format: http://iirds.tekom.de/iirds/domain/machinery#$1
iirds.sft:
  description: An ontology encoding software based on the Intelligent Information
    Request and Delivery (iiRDS) standard
  example: iirdsSoftwareDomainEntity
  homepage: https://github.com/iirds-consortium/models
  mappings:
    tib: iirdssft
  name: International Standard for Intelligent Information Request and Delivery Software
    Ontology
  prefix: iirds.sft
  repository: https://github.com/iirds-consortium/models
  tib:
    contact: comment.iirds@tekom.de
    download_rdf: https://raw.githubusercontent.com/iirds-consortium/models/main/iirds-software.rdf
    homepage: https://iirds.org/index.php
    keywords:
    - NFDI4ING
    - computer science
    name: IIRDS Software Ontology
    prefix: iirdssft
    tracker: https://github.com/iirds-consortium/models/issues
    uri_format: http://iirds.tekom.de/iirds/domain/software#$1
illumina.probe:
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: Illumina probe identifiers for microarrays, such as those in Illumina
    HumanRef-6 v2.0 expression beadchip.
  example: ILMN_129894
  homepage: https://www.ebi.ac.uk/arrayexpress/files/A-GEOD-6790/A-GEOD-6790.adf.txt
  keywords:
  - transcriptomics
  name: Illumina Probe Identifier
  pattern: ^ILMN_\d+$
  prefix: illumina.probe
  references:
  - https://www.ebi.ac.uk/arrayexpress/files/A-GEOD-9184/A-GEOD-9184_comments.txt
imanis:
  cellosaurus:
    category: Cell line collections (Providers)
    homepage: https://www.imanislife.com/collections/cell-lines/
    name: Imanis Life Sciences cell line products
    prefix: Imanis
    uri_format: https://www.imanislife.com/?s=$1
  example: CL070
  mappings:
    cellosaurus: Imanis
  prefix: imanis
imdrf:
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: The International Medical Device Regulators Forum (IMDRF) is a forum
    of voluntary medical device regulators from around the world who have come together
    to build on the strong foundational work of the Global Harmonization Task Force
    on Medical Devices (GHTF), and to accelerate international medical device regulatory
    harmonization and convergence.
  homepage: http://www.imdrf.org/
  name: International Medical Device Regulators Forum
  no_own_terms: true
  prefix: imdrf
  references:
  - https://www.fda.gov/medical-devices/mandatory-reporting-requirements-manufacturers-importers-and-device-user-facilities/mdr-adverse-event-codes
imex:
  banana: IM
  banana_peel: '-'
  biocontext:
    prefix: IMEX
  contact:
    email: orchard@ebi.ac.uk
    github: sandraorchard
    name: Sandra Orchard
    orcid: 0000-0002-8878-3972
  example: 19210-3
  example_extras:
  - '19210'
  mappings:
    biocontext: IMEX
    miriam: imex
    n2t: imex
    pathguide: '422'
    prefixcommons: imex
    re3data: r3d100010669
  miriam:
    deprecated: false
    description: The International Molecular Exchange (IMEx) is a consortium of molecular
      interaction databases which collaborate to share manual curation efforts and
      provide accessibility to multiple information sources.
    homepage: https://www.ebi.ac.uk/intact/
    id: '00000122'
    name: IMEx
    namespaceEmbeddedInLui: false
    pattern: ^IM-\d+(-?)(\d+?)$
    prefix: imex
    providers:
    - code: ebi
      description: IMEx Consortium running at EBI
      homepage: https://www.imexconsortium.org/
      name: IMEx Consortium running at EBI
      uri_format: https://www.ebi.ac.uk/intact/imex/main.xhtml?query=$1
    sampleId: IM-19210-3
    uri_format: https://www.ebi.ac.uk/intact/search?query=$1#interaction
  n2t:
    description: The International Molecular Exchange (IMEx) is a consortium of molecular
      interaction databases which collaborate to share manual curation efforts and
      provide accessibility to multiple information sources.
    example: IM-19210-3
    homepage: https://www.imexconsortium.org/
    name: IMEx Consortium running at EBI
    namespaceEmbeddedInLui: false
    pattern: ^IM-\d+(-?)(\d+?)$
    prefix: imex
    uri_format: https://www.ebi.ac.uk/intact/imex/main.xhtml?query=$1
  name: International Molecular Exchange
  owners:
  - name: European Bioinformatics Institute
    partnered: false
    ror: 02catss52
    wikidata: null
  pathguide:
    abbreviation: IMEx
    homepage: http://www.imexconsortium.org/
    keywords:
    - PSI-MI
    name: The International Molecular Exchange Consortium
    prefix: '422'
  pattern: ^\d+(-\d+)?$
  prefix: imex
  prefixcommons:
    description: The International Molecular Exchange (IMEx) is a consortium of molecular
      interaction databases which collaborate to share manual curation efforts and
      provide accessibility to multiple information sources.
    example: IM-12080-80
    homepage: http://disber.net/imexdrupal/
    keywords:
    - molecule
    - interaction
    license: http://disber.net/imexdrupal/node/5
    name: International Molecular Exchange
    pattern: ^IM-\d+(-?)(\d+?)$
    prefix: imex
    pubmed_ids:
    - '17893861'
    uri_format: http://www.ebi.ac.uk/intact/imex/main.xhtml?query=$1
  providers:
  - code: intact.search
    description: Search page on IntAct
    example: null
    first_party: null
    homepage: https://www.ebi.ac.uk/intact
    name: IntAct Search
    publications: null
    status: null
    uri_format: https://www.ebi.ac.uk/intact/search?query=IM-$1
  publications:
  - doi: 10.1002/pmic.200700286
    pmc: null
    pubmed: '17893861'
    title: 'Submit your interaction data the IMEx way: a step by step guide to trouble-free
      deposition'
    year: 2007
  re3data:
    description: The IMEx consortium is an international collaboration between a group
      of major public interaction data providers who have agreed to share curation
      effort and develop and work to a single set of curation rules when capturing
      data from both directly deposited interaction data or from publications in peer-reviewed
      journals, capture full details of an interaction in a “deep” curation model,
      perform a complete curation of all protein-protein interactions experimentally
      demonstrated within a publication, make these interaction available in a single
      search interface on a common website, provide the data in standards compliant
      download formats, make all IMEx records freely accessible under the Creative
      Commons Attribution License
    doi: 10.17616/R3090W
    homepage: https://www.imexconsortium.org/
    name: IMEx
    prefix: r3d100010669
    synonyms:
    - The International Molecular Exchange Consortium
    xrefs:
      fairsharing.legacy: '3507'
      nif: 0000-00447
  uri_format: https://www.ebi.ac.uk/intact/imex/main.xhtml?query=IM-$1
img.gene:
  biocontext:
    prefix: IMG.GENE
  contact:
    email: nckyrpides@lbl.gov
    github: null
    name: Nikos C. Kyrpides
    orcid: 0000-0002-6131-0462
  mappings:
    biocontext: IMG.GENE
    miriam: img.gene
    n2t: img.gene
    prefixcommons: img.gene
  miriam:
    deprecated: false
    description: The integrated microbial genomes (IMG) system is a data management,
      analysis and annotation platform for all publicly available genomes. IMG contains
      both draft and complete JGI (DoE Joint Genome Institute) microbial genomes integrated
      with all other publicly available genomes from all three domains of life, together
      with a large number of plasmids and viruses. This datatype refers to gene information.
    homepage: http://img.jgi.doe.gov/
    id: '00000176'
    name: Integrated Microbial Genomes Gene
    namespaceEmbeddedInLui: false
    pattern: ^\d+$
    prefix: img.gene
    sampleId: '638309541'
    uri_format: http://img.jgi.doe.gov/cgi-bin/w/main.cgi?section=GeneDetail&gene_oid=$1
  n2t:
    description: The integrated microbial genomes (IMG) system is a data management,
      analysis and annotation platform for all publicly available genomes. IMG contains
      both draft and complete JGI (DoE Joint Genome Institute) microbial genomes integrated
      with all other publicly available genomes from all three domains of life, together
      with a large number of plasmids and viruses. This datatype refers to gene information.
    example: '638309541'
    homepage: http://img.jgi.doe.gov/
    name: Integrated Microbial Genomes Taxon at Lawrence Berkeley National Laboratory
    namespaceEmbeddedInLui: false
    pattern: ^\d+$
    prefix: img.gene
    uri_format: http://img.jgi.doe.gov/cgi-bin/w/main.cgi?section=GeneDetail&gene_oid=$1
  prefix: img.gene
  prefixcommons:
    description: The integrated microbial genomes (IMG) system is a data management,
      analysis and annotation platform for all publicly available genomes. IMG contains
      both draft and complete JGI (DoE Joint Genome Institute) microbial genomes integrated
      with all other publicly available genomes from all three domains of life, together
      with a large number of plasmids and viruses. This datatype refers to gene information.
    example: '638309541'
    keywords:
    - gene
    - genome
    name: Integrated Microbial Genomes Gene
    pattern: ^\d+$
    prefix: img.gene
    pubmed_ids:
    - '17933782'
    uri_format: http://img.jgi.doe.gov/cgi-bin/w/main.cgi?section=GeneDetail&gene_oid=$1
  publications:
  - doi: 10.1093/nar/gkm846
    pmc: PMC2238897
    pubmed: '17933782'
    title: 'The integrated microbial genomes (IMG) system in 2007: data content and
      analysis tool extensions'
    year: 2007
img.taxon:
  biocontext:
    prefix: IMG.TAXON
  contact:
    email: nckyrpides@lbl.gov
    github: null
    name: Nikos C. Kyrpides
    orcid: 0000-0002-6131-0462
  mappings:
    biocontext: IMG.TAXON
    miriam: img.taxon
    n2t: img.taxon
    prefixcommons: img.taxon
  miriam:
    deprecated: false
    description: The integrated microbial genomes (IMG) system is a data management,
      analysis and annotation platform for all publicly available genomes. IMG contains
      both draft and complete JGI (DoE Joint Genome Institute) microbial genomes integrated
      with all other publicly available genomes from all three domains of life, together
      with a large number of plasmids and viruses. This datatype refers to taxon information.
    homepage: http://img.jgi.doe.gov/
    id: '00000175'
    name: Integrated Microbial Genomes Taxon
    namespaceEmbeddedInLui: false
    pattern: ^\d+$
    prefix: img.taxon
    sampleId: '648028003'
    uri_format: http://img.jgi.doe.gov/cgi-bin/w/main.cgi?section=TaxonDetail&taxon_oid=$1
  n2t:
    description: The integrated microbial genomes (IMG) system is a data management,
      analysis and annotation platform for all publicly available genomes. IMG contains
      both draft and complete JGI (DoE Joint Genome Institute) microbial genomes integrated
      with all other publicly available genomes from all three domains of life, together
      with a large number of plasmids and viruses. This datatype refers to taxon information.
    example: '648028003'
    homepage: http://img.jgi.doe.gov/
    name: Integrated Microbial Genomes Taxon at Lawrence Berkeley National Laboratory
    namespaceEmbeddedInLui: false
    pattern: ^\d+$
    prefix: img.taxon
    uri_format: http://img.jgi.doe.gov/cgi-bin/w/main.cgi?section=TaxonDetail&taxon_oid=$1
  prefix: img.taxon
  prefixcommons:
    description: The integrated microbial genomes (IMG) system is a data management,
      analysis and annotation platform for all publicly available genomes. IMG contains
      both draft and complete JGI (DoE Joint Genome Institute) microbial genomes integrated
      with all other publicly available genomes from all three domains of life, together
      with a large number of plasmids and viruses. This datatype refers to taxon information.
    example: '648028003'
    keywords:
    - genome
    - taxonomy
    name: Integrated Microbial Genomes Taxon
    pattern: ^\d+$
    prefix: img.taxon
    pubmed_ids:
    - '17933782'
    uri_format: http://img.jgi.doe.gov/cgi-bin/m/main.cgi?section=TaxonDetail&taxon_oid=$1
  publications:
  - doi: 10.1093/nar/gkm846
    pmc: PMC2238897
    pubmed: '17933782'
    title: 'The integrated microbial genomes (IMG) system in 2007: data content and
      analysis tool extensions'
    year: 2007
imgt.hla:
  biocontext:
    prefix: IMGT.HLA
  cellosaurus:
    category: Cell line databases/resources
    homepage: https://www.ebi.ac.uk/ipd/imgt/hla/
    name: IPD-IMGT/HLA database
    prefix: IPD-IMGT/HLA
    uri_format: https://www.ebi.ac.uk/ipd/imgt/hla/cells/cell/?cellid=$1
  edam:
    description: Identifier of a human major histocompatibility complex (HLA) or other
      protein from the IMGT/HLA database.
    name: IMGT/HLA
    obsolete: false
    prefix: '2773'
  fairsharing:
    abbreviation: IPD-IMGT/HLA
    contact:
      email: steven.marsh@ucl.ac.uk
      name: Steven G. E. Marsh
      orcid: 0000-0003-2855-4120
    description: The IPD-IMGT/HLA Database provides a specialist database for sequences
      of the human major histocompatibility complex (MHC) and includes the official
      sequences named by the WHO Nomenclature Committee For Factors of the HLA System.
      The IMGT/HLA Database was established to provide a locus-specific database (LSDB)
      for the allelic sequences of the genes in the HLA system, also known as the
      human MHC. The IMGT/HLA Database was first released in 1998 and subsequently
      incorporated as a module of IPD in 2012.
    homepage: https://www.ebi.ac.uk/ipd/imgt/hla/
    license: https://creativecommons.org/licenses/by-nd/4.0
    name: IPD-IMGT/HLA - Human Leukocyte Antigen Sequence Database
    prefix: FAIRsharing.e28v7g
    publications:
    - doi: 10.1093/nar/gku1161
      pubmed_id: 25414341
      title: 'The IPD and IMGT/HLA database: allele variant databases.'
    - doi: 10.1034/j.1399-0039.2000.550314.x
      pubmed_id: 10777106
      title: IMGT/HLA database--a sequence database for the human major histocompatibility
        complex.
    - doi: 10.1093/nar/29.1.210
      pubmed_id: 11125094
      title: IMGT/HLA Database--a sequence database for the human major histocompatibility
        complex.
    - doi: 10.1093/nar/gkn662
      pubmed_id: 18838392
      title: The IMGT/HLA database.
    - doi: 10.1007/978-1-60327-118-9_3
      pubmed_id: 18449991
      title: The IMGT/HLA database.
    - doi: 10.1002/humu.20406
      pubmed_id: 16944494
      title: The IMGT/HLA and IPD databases.
    - doi: 10.1093/nar/gkz950
      pubmed_id: 31667505
      title: IPD-IMGT/HLA Database.
    - doi: 10.1093/nar/gkg070
      pubmed_id: 12520010
      title: 'IMGT/HLA and IMGT/MHC: sequence databases for the study of the major
        histocompatibility complex.'
    subjects:
    - Immunogenetics
    - Immunology
    - Biomedical Science
  go:
    homepage: http://www.ebi.ac.uk/imgt/hla
    name: IMGT/HLA human major histocompatibility complex sequence database
    prefix: IMGT_HLA
  integbio:
    description: 'IMGT/HLA is a database that specializes in the human major histocompatibility
      complex and its sequences.

      There are 8,949 allele sequences that are available, and of them, 6919 are HLA
      Class I Alleles, 1,875 are HLA Class II Alleles and 155 are other non-HLA Alleles.

      Information about the source material, from which the sequences were obtained,
      is provided in detail.

      Authors of publications regularly check their data against IMGT/HLA first to
      ascertain the official name of their sequence to avoid confusion due to multiple
      names for the same product.

      An IMGT/HLA Alignment Tool is provided as well as protein and nucleotide Blast
      search options.'
    fairsharing: biodbcore-000171
    homepage: http://www.ebi.ac.uk/imgt/hla/
    information_keywords:
    - Ontology/Terminology/Nomenclature
    - Sequence
    maintainer: EMBL-EBI (European Bioinformatics Institute)
    name: IPD-IMGT/HLA
    prefix: nbdc00106
    pubmeds:
    - '31667505'
    - '26826444'
    - '25048120'
    status: Active
    target_keywords:
    - Genome/Gene
    - Cell/Organelle
  logo: https://www.ebi.ac.uk/ipd/imgt/hla/assets/images/hla_logo_2014-e4fa904dc2.svg
  mappings:
    biocontext: IMGT.HLA
    cellosaurus: IPD-IMGT/HLA
    edam: '2773'
    fairsharing: FAIRsharing.e28v7g
    go: IMGT_HLA
    integbio: nbdc00106
    miriam: imgt.hla
    n2t: imgt.hla
    ncbi: IMGT/HLA
    prefixcommons: imgthla
    re3data: r3d100010804
  miriam:
    deprecated: false
    description: IMGT, the international ImMunoGeneTics project, is a collection of
      high-quality integrated databases specialising in Immunoglobulins, T cell receptors
      and the Major Histocompatibility Complex (MHC) of all vertebrate species. IMGT/HLA
      is a database for sequences of the human MHC, referred to as HLA. It includes
      all the official sequences for the WHO Nomenclature Committee For Factors of
      the HLA System. This collection references allele information through the WHO
      nomenclature.
    homepage: https://www.ebi.ac.uk/imgt/hla/allele.html
    id: '00000331'
    name: IMGT HLA
    namespaceEmbeddedInLui: false
    pattern: ^[A-Z0-9*:]+$
    prefix: imgt.hla
    sampleId: A*01:01:01:01
    uri_format: https://www.ebi.ac.uk/ipd/imgt/hla/alleles/?query=eq(name,%22$1%22)
  n2t:
    description: IMGT, the international ImMunoGeneTics project, is a collection of
      high-quality integrated databases specialising in Immunoglobulins, T cell receptors
      and the Major Histocompatibility Complex (MHC) of all vertebrate species. IMGT/HLA
      is a database for sequences of the human MHC, referred to as HLA. It includes
      all the official sequences for the WHO Nomenclature Committee For Factors of
      the HLA System. This collection references allele information through the WHO
      nomenclature.
    example: A*01:01:01:01
    homepage: https://www.ebi.ac.uk/imgt/hla/allele.html
    name: IMGT HLA at EBI
    namespaceEmbeddedInLui: false
    pattern: ^[A-Z0-9*:]+$
    prefix: imgt.hla
    uri_format: https://www.ebi.ac.uk/cgi-bin/imgt/hla/get_allele.cgi?$1
  ncbi:
    example: HLA00031
    homepage: http://www.ebi.ac.uk/imgt/hla/
    name: Immunogenetics database, human MHC
    prefix: IMGT/HLA
  owners:
  - name: European Bioinformatics Institute
    partnered: false
    ror: 02catss52
    wikidata: null
  prefix: imgt.hla
  prefixcommons:
    description: The IMGT/HLA Database provides a specialist database for sequences
      of the human major histocompatibility complex (HLA) and includes the official
      sequences for the WHO Nomenclature Committee For Factors of the HLA System.
    example: A*01:01:01:01
    homepage: http://www.ebi.ac.uk/imgt/hla/
    keywords:
    - DNA
    - RNA
    - protein
    name: IMGT/HLA
    pattern: ^[A-Z0-9*:]+$
    prefix: imgthla
    pubmed_ids:
    - '16381979'
    uri_format: http://www.ebi.ac.uk/cgi-bin/ipd/imgt/hla/get_allele.cgi?
  publications:
  - doi: 10.1093/nar/gkz950
    pmc: PMC7145640
    pubmed: '31667505'
    title: IPD-IMGT/HLA Database
    year: 2020
  - doi: 10.1093/nar/gku1161
    pmc: PMC4383959
    pubmed: '25414341'
    title: 'The IPD and IMGT/HLA database: allele variant databases'
    year: 2014
  - doi: 10.1093/nar/gkn662
    pmc: PMC2686596
    pubmed: '18838392'
    title: The IMGT/HLA database
    year: 2008
  - doi: 10.1007/978-1-60327-118-9_3
    pmc: null
    pubmed: '18449991'
    title: The IMGT/HLA database
    year: 2007
  - doi: 10.1093/nar/gkj088
    pmc: PMC1347451
    pubmed: '16381979'
    title: IMGT/LIGM-DB, the IMGT comprehensive database of immunoglobulin and T cell
      receptor nucleotide sequences
    year: 2006
  - doi: 10.1002/humu.20406
    pmc: null
    pubmed: '16944494'
    title: The IMGT/HLA and IPD databases
    year: 2006
  - doi: 10.1093/nar/gkg070
    pmc: PMC165517
    pubmed: '12520010'
    title: 'IMGT/HLA and IMGT/MHC: sequence databases for the study of the major histocompatibility
      complex'
    year: 2003
  - doi: 10.1093/nar/29.1.210
    pmc: PMC29780
    pubmed: '11125094'
    title: IMGT/HLA Database--a sequence database for the human major histocompatibility
      complex
    year: 2001
  - doi: 10.1034/j.1399-0039.2000.550314.x
    pmc: null
    pubmed: '10777106'
    title: IMGT/HLA database--a sequence database for the human major histocompatibility
      complex
    year: 2000
  re3data:
    description: 'The IPD-IMGT/HLA Database provides a specialist database for sequences
      of the human major histocompatibility complex (MHC) and includes the official
      sequences named by the WHO Nomenclature Committee For Factors of the HLA System.
      The IPD-IMGT/HLA Database is part of the international ImMunoGeneTics project
      (IMGT).

      The database uses the 2010 naming convention for HLA alleles in all tools herein.
      To aid in the adoption of the new nomenclature, all search tools can be used
      with both the current and pre-2010 allele designations. The pre-2010 nomenclature
      designations are only used where older reports or outputs have been made available
      for download.'
    doi: 10.17616/R3T31N
    homepage: https://www.ebi.ac.uk/ipd/imgt/hla/
    license: CC
    name: IMGT/HLA Database
    prefix: r3d100010804
    synonyms:
    - IPD-IMGT/HLA
    - ImMunoGeneTics/HLA Database
    - International ImMunoGeneTics information system/Humane Leukozyten Antigene Database
    xrefs:
      nif: 0000-03014
  synonyms:
  - IPD-IMGT/HLA
imgt.ligm:
  biocontext:
    prefix: IMGT.LIGM
  contact:
    email: marie-paule.lefranc@umontpellier.fr
    github: null
    name: Marie-Paule Lefranc
    orcid: 0000-0003-0116-9353
  go:
    description: Database of immunoglobulins and T cell receptors from human and other
      vertebrates, with translation for fully annotated sequences.
    homepage: http://www.imgt.org/
    name: ImMunoGeneTics database covering immunoglobulins and T-cell receptors
    prefix: IMGT_LIGM
  mappings:
    biocontext: IMGT.LIGM
    go: IMGT_LIGM
    miriam: imgt.ligm
    n2t: imgt.ligm
    ncbi: IMGT/LIGM
    prefixcommons: imgt.ligm
  miriam:
    deprecated: false
    description: IMGT, the international ImMunoGeneTics project, is a collection of
      high-quality integrated databases specialising in Immunoglobulins, T cell receptors
      and the Major Histocompatibility Complex (MHC) of all vertebrate species. IMGT/LIGM
      is a comprehensive database of fully annotated sequences of Immunoglobulins
      and T cell receptors from human and other vertebrates.
    homepage: http://www.imgt.org/
    id: 00000287
    name: IMGT LIGM
    namespaceEmbeddedInLui: false
    pattern: ^M\d+$
    prefix: imgt.ligm
    sampleId: M94112
    uri_format: http://www.imgt.org/ligmdb/view?id=$1
  n2t:
    description: IMGT, the international ImMunoGeneTics project, is a collection of
      high-quality integrated databases specialising in Immunoglobulins, T cell receptors
      and the Major Histocompatibility Complex (MHC) of all vertebrate species. IMGT/LIGM
      is a comprehensive database of fully annotated sequences of Immunoglobulins
      and T cell receptors from human and other vertebrates.
    example: M94112
    homepage: http://www.imgt.org/
    name: IMGT LIGM at CNRS
    namespaceEmbeddedInLui: false
    pattern: ^M\d+$
    prefix: imgt.ligm
    uri_format: http://www.imgt.org/ligmdb/view?id=$1
  ncbi:
    example: U03895
    homepage: http://www.imgt.org/IMGTinformation/LIGM.html
    name: Immunogenetics database, immunoglobulins and T-cell receptors
    prefix: IMGT/LIGM
  prefix: imgt.ligm
  prefixcommons:
    description: MGT/LIGM-DB is the IMGT comprehensive database of immunoglobulin
      (IG) and T cell receptor (TR) nucleotide sequences from human and other vertebrate
      species.
    example: A68511
    homepage: http://imgt.cines.fr/cgi-bin/IMGTlect.jv
    keywords:
    - DNA
    name: IMGT/LIGM-DB
    pattern: ^[A-Z]\d+$
    prefix: imgt.ligm
    pubmed_ids:
    - '16381979'
    synonyms:
    - imgt_ligmdb
  publications:
  - doi: 10.1093/nar/gkj088
    pmc: PMC1347451
    pubmed: '16381979'
    title: IMGT/LIGM-DB, the IMGT comprehensive database of immunoglobulin and T cell
      receptor nucleotide sequences
    year: 2006
imgt.primerdb:
  mappings:
    prefixcommons: imgt.primerdb
    re3data: r3d100012535
  prefix: imgt.primerdb
  prefixcommons:
    description: The IMGT/PRIMER-DB database provides standardized information on
      oligonucleotides or primers of the immunoglobulins (IG) and T cell receptors
      (TR).
    example: IPP900099
    homepage: http://imgt.org/IMGTPrimerDB/
    keywords:
    - DNA
    name: IMGT/PRIMER-DB
    pattern: ^IPP\d+$
    prefix: imgt.primerdb
    uri_format: http://imgt.org/IMGTPrimerDB/Check_PrDB.pl?numacc0=$1&origin=view&source=PrList
  re3data:
    description: The IMGT/PRIMER-DB database provides standardized information on
      oligonucleotides or primers of the immunoglobulins (IG) and T cell receptors
      (TR).
    doi: 10.17616/R3R19C
    homepage: https://www.imgt.org/IMGTPrimerDB/
    license: Copyrights
    name: IMGT/PRIMER-DB
    prefix: r3d100012535
    synonyms:
    - ImMunoGeneTics/PRIMER-DB
    - International ImMunoGeneTics information system/PRIMER-Database
imotdb:
  comment: This resource doesn't exist on the web anymore
  deprecated: true
  mappings:
    pathguide: '207'
    prefixcommons: imotdb
  pathguide:
    abbreviation: iMOTdb
    homepage: http://caps.ncbs.res.in/imotdb/
    name: Interacting motifs in proteins database
    prefix: '207'
  prefix: imotdb
  prefixcommons:
    description: The interacting motif database or iMOTdb , lists interacting motifs
      thatare identified for all structural entries in the PDB. The conserved patterns
      or finger prints are identified for individual structural entries and also grouped
      together for reporting the common motifs shared among all superfamily members.
    example: '53784'
    homepage: http://caps.ncbs.res.in/imotdb/
    keywords:
    - interaction
    - protein
    name: Database of Spatially Interacting Motifs in Proteins
    pattern: ^\d+$
    prefix: imotdb
    uri_format: http://caps.ncbs.res.in/cgi-bin/mini/databases/imotdb/imotdb.cgi?sfcode=$1
  reviewer:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
imr:
  biocontext:
    prefix: IMR
  example: '0000001'
  mappings:
    biocontext: IMR
    obofoundry: imr
    prefixcommons: imr
  obofoundry:
    contact: curator@inoh.org
    contact.label: INOH curators
    deprecated: true
    domain: chemistry and biochemistry
    homepage: http://www.inoh.org
    name: Molecule role (INOH Protein name/family name ontology)
    prefix: imr
  pattern: ^\d{7}$
  prefix: imr
  prefixcommons:
    bioportal: '1029'
    description: MoleculeRole Ontology is an ontology for proteins/chemicals. It is
      used to annotate protein family names, generic/concrete protein names and chemical
      names in the INOH pathway data.
    example: IMR_0800118
    homepage: http://www.inoh.org
    keywords:
    - ontology
    - protein
    - small molecule
    name: MoleculeRole Ontology (INOH Protein name/family name ontology)
    pattern: ^IMR_\d+$
    prefix: imr
    synonyms:
    - molecule_role
    uri_format: http://www.inoh.org/ontology-viewer/cgi-bin/InohOVAttr.php?type=IMR&id=$1
imsr.apb:
  description: 'The NHMRC Australian PhenomeBank (APB) is a non-profit repository
    of mouse strains used in Medical Research. The database allows you to search for
    murine strains, housed or archived in Australia, carrying mutations in particular
    genes, strains with transgenic alterations and for mice with particular phenotypes.
    1876 publicly available strains, 922 genes, 439 transgenes The APB has two roles:
    Provide and maintain a central database of genetically modified mice held in Australia
    either live or as cryopreserved material; Establish and maintain a mouse strain
    archive. Strains are archived as cryopreserved sperm or embryos. [from RRID]'
  example: '7345'
  mappings:
    rrid: IMSR_APB
  pattern: ^\d+$
  prefix: imsr.apb
  rrid:
    abbreviation: APB
    homepage: https://pb.apf.edu.au/phenbank/homePage.html
    keywords:
    - allele
    - alteration
    - chromosome
    - database
    - embryo
    - gene
    - live mouse
    - murine
    - mutation
    - phenotype
    - sperm
    - strain
    - transgene
    - transgenic
    name: NHMRC Australian PhenomeBank
    prefix: IMSR_APB
    scr: 006149
  uri_format: https://pb.apf.edu.au/phenbank/strain.html?id=$1
imsr_em:
  contact:
    email: d.smedley@qmul.ac.uk
    github: null
    name: Damian Smedley
    orcid: 0000-0002-5836-9850
  description: Non-profit repository for the collection, archiving (via cryopreservation)
    and distribution of relevant mutant strains essential for basic biomedical research.
    Users may browse by strain, gene, phenotype, or human disease. Its primary objective
    is to establish and manage a unified repository for maintaining medically relevant
    mouse mutants and making them available to the scientific community. Therefore,
    EMMA archives mutant strains and distributes them to requesting researchers. EMMA
    also hosts courses in cryopreservation, to promote the use and dissemination of
    frozen embryos and spermatozoa. Dissemination of knowledge is further fostered
    by a dedicated resource database. Anybody who wants their mutant mouse strains
    cryopreserved may deposit strains with EMMA. However depositors must be aware
    that these strains become freely available to other researchers after being deposited.With
    more than 8400 mutant mouse strains and asmall but increasing number of rat mutant
    strains available, EMMA is the primary mouse repository in Europe and the third
    largest non-profit repository worldwide. [from RRID]
  example: '11478'
  mappings:
    rrid: IMSR_EM
  pattern: ^\d+$
  prefix: imsr_em
  rrid:
    abbreviation: EMMA
    homepage: https://www.infrafrontier.eu/emma/
    keywords:
    - ''
    - mouse
    - mutant mouse repository
    - mutant mouse strain
    - mutant strain
    name: European Mouse Mutant Archive
    prefix: IMSR_EM
    pubmeds:
    - '19783817'
    - '17709347'
    scr: '006136'
    twitter: InfrafrontierEU
  uri_format: https://www.infrafrontier.eu/emma/strain-search/straindetails/?q=$1
imsr_tac:
  description: Supplier of mice for research purposes. [from RRID]
  example: '1178'
  mappings:
    rrid: IMSR_TAC
  prefix: imsr_tac
  rrid:
    abbreviation: TAC, TB
    homepage: https://www.taconic.com/
    keywords:
    - gene
    - genetic engineering
    - knockout
    - mice
    - model
    - mouse
    - repository
    - research
    - strain
    - subject
    - supply
    - transgenic
    name: Taconic Biosciences
    prefix: IMSR_TAC
    scr: '016410'
  uri_format: https://scicrunch.org/resolver/RRID:IMSR_TAC_$1
inaturalist.observation:
  contributor:
    email: null
    github: oolonek
    name: Pierre-Marie Allard
    orcid: 0000-0003-3389-2191
  description: The identifier for an observation in iNaturalist
  example: '36010371'
  github_request_issue: 517
  homepage: https://www.inaturalist.org/observations
  mappings:
    wikidata: P5683
  name: iNaturalist Observation
  pattern: ^[1-9]\d*$
  prefix: inaturalist.observation
  reviewer:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  uri_format: https://www.inaturalist.org/observations/$1
  wikidata:
    description: observation identifier in iNaturalist
    name: iNaturalist observation ID
    pattern: ^[1-9]\d*$
    prefix: P5683
    uri_format: https://www.inaturalist.org/observations/$1
inaturalist.place:
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: Identifier for a place in iNaturalist
  example: '7207'
  homepage: https://www.inaturalist.org/places
  mappings:
    wikidata: P7471
  name: iNaturalist Place
  pattern: ^[1-9]\d*$
  prefix: inaturalist.place
  uri_format: https://www.inaturalist.org/places/$1
  wikidata:
    description: identifier for a place in iNaturalist
    example:
    - '13378'
    - '49955'
    - '7207'
    - '98521'
    name: iNaturalist place ID
    pattern: ^[1-9]\d*$
    prefix: P7471
    uri_format: https://www.inaturalist.org/places/$1
inaturalist.taxon:
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: Identifier for a species in iNaturalist
  example: '21723'
  homepage: https://www.inaturalist.org/taxa
  mappings:
    wikidata: P3151
  name: iNaturalist Taxonomy
  pattern: ^[1-9]\d{0,6}$
  prefix: inaturalist.taxon
  uri_format: https://www.inaturalist.org/taxa/$1
  wikidata:
    description: identifier in iNaturalist
    example:
    - '1'
    - '21723'
    - '9999'
    name: iNaturalist taxon ID
    pattern: ^[1-9]\d{0,6}$
    prefix: P3151
    uri_format: https://inaturalist.org/taxa/$1
inaturalist.user:
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: Identifier for a user in iNaturalist
  example: '1426686'
  homepage: https://www.inaturalist.org/users
  keywords:
  - person
  name: iNaturalist User
  pattern: ^[1-9]\d*$
  prefix: inaturalist.user
  uri_format: https://www.inaturalist.org/users/$1
inchi:
  biocontext:
    prefix: INCHI
  contact:
    email: jmg11@cam.ac.uk
    github: null
    name: Stephen R. Heller
    orcid: 0000-0002-5538-8482
  fairsharing:
    abbreviation: InChI
    description: Originally developed by the International Union of Pure and Applied
      Chemistry (IUPAC), the IUPAC International Chemical Identifier (InChI) is a
      machine-readable string generated from a chemical structure. InChIs are unique
      to the compound they describe and can encode absolute stereochemistry making
      chemicals and chemistry machine-readable and discoverable. A simple analogy
      is that InChI is the bar-code for chemistry and chemical structures. A hashed
      fixed-length version of the InChI, the InChIKey, is also widely used.  The InChI
      format and algorithm are non-proprietary and the software is open source, with
      ongoing development done by the community. A number of IUPAC working groups
      are working on extensions and new applications of the standard.
    domains:
    - Structure
    - Chemical structure image
    - molecular entity
    - chemical entity
    - centrally registered identifier
    homepage: https://www.inchi-trust.org/
    logo: https://api.fairsharing.org/rails/active_storage/blobs/redirect/eyJfcmFpbHMiOnsibWVzc2FnZSI6IkJBaHBBcUVFIiwiZXhwIjpudWxsLCJwdXIiOiJibG9iX2lkIn19--250afbf70b1e3f9c188231ff2fb50477040a71f5/inchi-wheel.png?disposition=inline
    name: IUPAC International Chemical Identifier
    prefix: FAIRsharing.ddk9t9
    publications:
    - doi: 10.1186/s13321-015-0068-4
      pubmed: '26136848'
      title: InChI, the IUPAC International Chemical Identifier
      year: 2015
    - doi: 10.1007/s10822-015-9854-3
      pubmed: '26081259'
      title: Many InChIs and quite some feat
      year: 2015
    - doi: 10.1186/s13321-021-00517-z
      title: 'InChI version 1.06: now more than 99.99% reliable'
      year: 2021
    - doi: 10.1186/s13321-024-00847-8
      title: InChI isotopologue and isotopomer specifications
      year: 2024
    repository: https://github.com/IUPAC-InChI/InChI
    subjects:
    - Cheminformatics
    - Chemistry
    twitter: inchi_trust
  mappings:
    biocontext: INCHI
    fairsharing: FAIRsharing.ddk9t9
    miriam: inchi
    n2t: inchi
    wikidata: P234
    wikidata.entity: Q203250
  miriam:
    deprecated: false
    description: The IUPAC International Chemical Identifier (InChI) is a non-proprietary
      identifier for chemical substances that can be used in printed and electronic
      data sources. It is derived solely from a structural representation of that
      substance, such that a single compound always yields the same identifier.
    homepage: https://www.ebi.ac.uk/chebi/
    id: 00000383
    name: InChI
    namespaceEmbeddedInLui: false
    pattern: ^InChI\=1S?\/[A-Za-z0-9\.]+(\+[0-9]+)?(\/[cnpqbtmsih][A-Za-z0-9\-\+\(\)\,\/\?\;\.]+)*$
    prefix: inchi
    providers:
    - code: um
      description: InChI through RDF Open Molecules
      homepage: http://rdf.openmolecules.net/
      name: InChI through RDF Open Molecules
      uri_format: http://rdf.openmolecules.net/?$1
    - code: ''
      description: InChI through NIST
      homepage: http://webbook.nist.gov/chemistry
      name: InChI through NIST
      uri_format: http://webbook.nist.gov/cgi/cbook.cgi?$1
    sampleId: InChI=1S/C2H6O/c1-2-3/h3H,2H2,1H3
    uri_format: https://www.ebi.ac.uk/chebi/advancedSearchFT.do?searchString=$1
  n2t:
    description: The IUPAC International Chemical Identifier (InChI) is a non-proprietary
      identifier for chemical substances that can be used in printed and electronic
      data sources. It is derived solely from a structural representation of that
      substance, such that a single compound always yields the same identifier.
    example: InChI=1S/C2H6O/c1-2-3/h3H,2H2,1H3
    homepage: http://webbook.nist.gov/chemistry
    name: InChI through NIST
    namespaceEmbeddedInLui: false
    pattern: ^InChI\=1S?\/[A-Za-z0-9\.]+(\+[0-9]+)?(\/[cnpqbtmsih][A-Za-z0-9\-\+\(\)\,\/\?\;\.]+)*$
    prefix: inchi
    uri_format: http://webbook.nist.gov/cgi/cbook.cgi?$1
  prefix: inchi
  publications:
  - doi: 10.1186/s13321-021-00517-z
    pmc: PMC8147039
    pubmed: '34030732'
    title: 'InChI version 1.06: now more than 99.99% reliable'
    year: 2021
  - doi: 10.1186/s13321-015-0068-4
    pmc: PMC4486400
    pubmed: '26136848'
    title: InChI, the IUPAC International Chemical Identifier
    year: 2015
  - doi: 10.1007/s10822-015-9854-3
    pmc: null
    pubmed: '26081259'
    title: Many InChIs and quite some feat
    year: 2015
  wikidata:
    database: Q203250
    description: International Chemical Identifier
    example:
    - InChI=1S/C10H9NO2/c12-10(13)5-7-6-11-9-4-2-1-3-8(7)9/h1-4,6,11H,5H2,(H,12,13)
    - InChI=1S/C6H6/c1-2-4-6-5-3-1/h1-6H
    miriam: inchi
    name: InChI
    pattern: ^InChI=1S?/([0-9]*[A-Z][ub]?[a-z]?[0-9]*\.?)+(/[0-9A-Za-z+\-(),.*;?]+)*$
    prefix: P234
    uri_format: https://chemapps.stolaf.edu/jmol/jmol.php?&model=$1
inchikey:
  biocontext:
    prefix: INCHIKEY
  mappings:
    biocontext: INCHIKEY
    miriam: inchikey
    n2t: inchikey
    togoid: InchiKey
    wikidata: P235
    wikidata.entity: Q21445422
  miriam:
    deprecated: false
    description: The IUPAC International Chemical Identifier (InChI, see MIR:00000383)
      is an identifier for chemical substances, and is derived solely from a structural
      representation of that substance. Since these can be quite unwieldly, particularly
      for web use, the InChIKey was developed. These are of a fixed length (25 character)
      and were created as a condensed, more web friendly, digital representation of
      the InChI.
    homepage: http://www.chemspider.com/
    id: 00000387
    name: InChIKey
    namespaceEmbeddedInLui: false
    pattern: ^[A-Z]{14}\-[A-Z]{10}(\-[A-Z])?$
    prefix: inchikey
    providers:
    - code: scholia
      description: Scholia is a service that creates visual scholarly profiles for
        topic, people, organizations, species, chemicals, etc using bibliographic
        and other information in Wikidata.
      homepage: https://scholia.toolforge.org/
      name: Scholia
      uri_format: https://scholia.toolforge.org/inchikey/$1
    sampleId: RYYVLZVUVIJVGH-UHFFFAOYSA-N
    uri_format: https://www.chemspider.com/search?params=$1
  n2t:
    description: The IUPAC International Chemical Identifier (InChI, see MIR:00000383)
      is an identifier for chemical substances, and is derived solely from a structural
      representation of that substance. Since these can be quite unwieldly, particularly
      for web use, the InChIKey was developed. These are of a fixed length (25 character)
      and were created as a condensed, more web friendly, digital representation of
      the InChI.
    example: RYYVLZVUVIJVGH-UHFFFAOYSA-N
    homepage: http://cactus.nci.nih.gov/chemical/structure
    name: InChiKey resolver at NCI
    namespaceEmbeddedInLui: false
    pattern: ^[A-Z]{14}\-[A-Z]{10}(\-[A-Z])?
    prefix: inchikey
    uri_format: http://cactus.nci.nih.gov/chemical/structure/$1/names
  prefix: inchikey
  togoid:
    examples:
    - RYYVLZVUVIJVGH-UHFFFAOYSA-N
    - RZWGTXHSYZGXKF-UHFFFAOYSA-N
    - RQQIIXFYTHWFKW-ZETCQYMHSA-N
    - RALAARQREFCZJO-UHFFFAOYSA-N
    - HVFRJJDZWVSUIB-UHFFFAOYSA-N
    - KVNZVXVZQFTXNA-UHFFFAOYSA-N
    - KVQUJTYBWCGJRS-UHFFFAOYSA-N
    - AFGLQVAJWVTAJT-UHFFFAOYSA-N
    - LHISABQPMWXWCC-UHFFFAOYSA-N
    - ZSXCHLJCWRSMMS-UHFFFAOYSA-N
    keywords:
    - Compound
    name: InChIKey
    pattern: ^(?[A-Z]{14}\-[A-Z]{10}(\-[A-Z])?)$
    prefix: InchiKey
    uri_format: http://identifiers.org/inchikey/$1
  wikidata:
    database: Q21445422
    description: a hashed version of the full standard InChI
    example:
    - LFQSCWFLJHTTHZ-UHFFFAOYSA-N
    - PCHJSUWPFVWCPO-UHFFFAOYSA-N
    miriam: inchikey
    name: InChIKey
    pattern: ^[A-Z]{14}-[A-Z]{10}-[A-Z]$
    prefix: P235
    uri_format: https://www.ncbi.nlm.nih.gov/sites/entrez?cmd=search&db=pccompound&term=%22$1%22%5BInChIKey%5D
infores:
  contact:
    email: smoxon@lbl.gov
    github: sierra-moxon
    name: Sierra Moxon
    orcid: 0000-0002-8719-7760
  contributor:
    email: nicolas.matentzoglu@gmail.com
    github: matentzn
    name: Nicolas Matentzoglu
    orcid: 0000-0002-7356-1779
  description: The information resource registry is a listing of data sources present
    in the NCATS Data Translator system. Each information resource has an identifier,
    a short description, and a URL to more information about that resource.
  example: agrkb
  github_request_issue: 1601
  homepage: https://biolink.github.io/information-resource-registry/
  license: Apache-2.0
  name: Information Resource Registry
  pattern: ^[a-z0-9-_.]+$
  prefix: infores
  repository: https://github.com/biolink/information-resource-registry
  reviewer:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  uri_format: https://w3id.org/information-resource-registry/$1
informall:
  appears_in:
  - doid
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: The InformAll database was developed to provide a credible source of
    information on allergenic food materials of both plant and animal origin.
  example: '410'
  github_request_issue: 1311
  homepage: http://research.bmh.manchester.ac.uk/informAll/
  name: InformAll Allergenic Food Database
  pattern: ^\d+$
  prefix: informall
  uri_format: http://research.bmh.manchester.ac.uk/informall/allergenic-food/?FoodId=$1
infosecsos:
  example: Accept
  mappings:
    tib: infosecsos
  prefix: infosecsos
  tib:
    description: InfoSecSoS - Ontology for Information Security Management in Systems-of-Systems
    download_rdf: https://raw.githubusercontent.com/rmbelmont/InfoSecSoS_Ontology/main/InfoSecSoS.rdf
    homepage: https://zenodo.org/record/6621882
    keywords:
    - NFDI4ING
    - engineering
    name: InfoSecSoS Ontology
    prefix: infosecsos
    uri_format: http://www.labesc.unirio.br/InfoSecSoS#$1
    version.iri: http://www.labesc.unirio.br/InfoSecSoS
inhand:
  comment: This nomenclature is available via email. Truly a disgrace.
  contact:
    email: harkemaj@msu.edu
    github: null
    name: Jack R Harkema
    orcid: 0000-0003-4682-0824
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: The standard reference for nomenclature and diagnostic criteria in
    toxicologic pathology.
  fairsharing:
    abbreviation: INHAND
    description: Standard reference for nomenclature and diagnostic criteria in toxicologic
      pathology.
    domains:
    - disease
    - toxicity
    homepage: http://www.goreni.org/
    name: International Harmonization of Nomenclature and Diagnostic criteria
    prefix: FAIRsharing.9gqfpm
    publications:
    - doi: 10.1177/0192623309353423
      pubmed: '20032296'
      title: Proliferative and nonproliferative lesions of the rat and mouse respiratory
        tract
      year: 2010
    subjects:
    - Biomedical Science
  homepage: https://www.goreni.org/gr3_nomenclature.php
  mappings:
    fairsharing: FAIRsharing.9gqfpm
  name: The International Harmonization of Nomenclature and Diagnostic criteria
  prefix: inhand
  proprietary: true
  publications:
  - doi: 10.1177/0192623309353423
    pmc: null
    pubmed: '20032296'
    title: Proliferative and nonproliferative lesions of the rat and mouse respiratory
      tract
    year: 2009
inn:
  comment: can not find a place to resolve to
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: Documentation of GO that provides a description of some of the commonly
    used relationships and conventions in GO.
  example: fluticasone
  homepage: https://www.who.int/teams/health-product-and-policy-standards/inn
  mappings:
    wikidata: P2275
    wikidata.entity: Q824258
  name: International Nonproprietary Names
  prefix: inn
  providers:
  - code: dotad
    description: Database Of Therapeutic Antibody Developability (DOTAD) provides
      comprehensive developability assessments and annotations for therapeutic antibodies
      referenced by their INN names.
    example: null
    first_party: null
    homepage: https://i.uestc.edu.cn/DOTAD/
    name: Database Of Therapeutic Antibody Developability
    publications:
    - doi: 10.1007/s12539-024-00613-2
      pmc: null
      pubmed: '38530613'
      title: 'DOTAD: A Database of Therapeutic Antibody Developability'
      year: 2025
    status: null
    uri_format: https://i.uestc.edu.cn/DOTAD/detail.html?INN=$1
  synonyms:
  - INN_ID
  uri_format: https://mednet-communities.net/inn/db/ViewINN.aspx?i=$1
  wikidata:
    database: Q824258
    description: identifier for a drug
    example:
    - amfetamine
    - amfétamine
    - anfetamina
    - anfetaminum
    - phencyclidinum
    - vemurafenibum
    - амфетамин
    - амфетамін
    - أمفيتامين
    - 苯丙胺
    homepage: https://www.who.int/teams/health-product-and-policy-standards/inn/
    name: World Health Organisation  international non-proprietary name
    prefix: P2275
innatedb:
  contact:
    email: david.lynn@flinders.edu.au
    github: null
    name: David Lynn
    orcid: 0000-0003-4664-1404
  fairsharing:
    abbreviation: InnateDB
    description: InnateDB has been developed to facilitate systems level investigations
      of the mammalian (human, mouse and bovine) innate immune response. Its goal
      is to provide a manually-curated knowledgebase of the genes, proteins, and particularly,
      the interactions and signaling responses involved in mammalian innate immunity.
      InnateDB incorporates information of the whole human, mouse and bovine interactomes
      by integrating interaction and pathway information from several of the major
      publicly available databases but aims to capture an improved coverage of the
      innate immunity interactome through manual curation.
    homepage: http://www.innatedb.com/
    license: https://www.innatedb.com
    name: InnateDB
    prefix: FAIRsharing.rb2drw
    publications:
    - doi: 10.1093/nar/gks1147
      pubmed_id: 23180781
      title: 'InnateDB: systems biology of innate immunity and beyond--recent updates
        and continuing curation.'
    subjects:
    - Immunology
    - Life Science
    twitter: innatedb
  integbio:
    description: InnateDB has been developed to facilitate systems level investigations
      of the mammalian (human, mouse and bovine) innate immune response. Its goal
      is to provide a manually-curated knowledgebase of the genes, proteins, and particularly,
      the interactions and signaling responses involved in mammalian innate immunity.
      InnateDB incorporates information of the whole human, mouse and bovine interactomes
      by integrating interaction and pathway information from several of the major
      publicly available databases but aims to capture an improved coverage of the
      innate immunity interactome through manual curation.
    fairsharing: FAIRsharing.rb2drw
    homepage: http://www.innatedb.com/
    information_keywords:
    - Interaction/Pathway
    maintainer: Brinkman Laboratory, Simon Fraser University
    name: InnateDB
    prefix: nbdc01870
    pubmeds:
    - '23180781'
    status: Active
    target_keywords:
    - Genome/Gene
    - Protein
    - Organism
    - Health/Disease
  keywords:
  - immunology
  mappings:
    fairsharing: FAIRsharing.rb2drw
    integbio: nbdc01870
    pathguide: '264'
    prefixcommons: innatedb
    re3data: r3d100010676
  pathguide:
    abbreviation: InnateDB
    homepage: http://www.innatedb.ca/
    keywords:
    - PSI-MI
    name: A Knowledge Resource for Innate Immunity Interactions and Pathways
    prefix: '264'
  prefix: innatedb
  prefixcommons:
    description: InnateDB is a publicly available database of the genes, proteins,
      experimentally-verified interactions and signaling pathways involved in the
      innate immune response of humans and mice to microbial infection. The database
      covers the innate immunity interactome by integrating known interactions and
      pathways from major public databases.
    example: '20021'
    homepage: http://www.innatedb.ca/
    keywords:
    - gene
    - protein
    - interaction
    - pathway
    name: A Knowledge Resource for Innate Immunity Interactions and Pathways
    pattern: ^\d+$
    prefix: innatedb
    uri_format: http://www.innatedb.ca/getGeneCard.do?id=$1
  publications:
  - doi: 10.1093/nar/gks1147
    pmc: PMC3531080
    pubmed: '23180781'
    title: 'InnateDB: systems biology of innate immunity and beyond--recent updates
      and continuing curation'
    year: 2012
  - doi: 10.1093/nar/gks1147
    pmc: null
    pubmed: null
    title: 'InnateDB: systems biology of innate immunity and beyond--recent updates
      and continuing curation.'
    year: null
  - doi: 10.1093/nar/gks1147
    pmc: null
    pubmed: null
    title: 'InnateDB: systems biology of innate immunity and beyond--recent updates
      and continuing curation.'
    year: null
  re3data:
    description: InnateDB is a publicly available database of the genes, proteins,
      experimentally-verified interactions and signaling pathways involved in the
      innate immune response of humans, mice and bovines to microbial infection. The
      database captures an improved coverage of the innate immunity interactome by
      integrating known interactions and pathways from major public databases together
      with manually-curated data into a centralised resource. The database can be
      mined as a knowledgebase or used with our integrated bioinformatics and visualization
      tools for the systems level analysis of the innate immune response.
    doi: 10.17616/R36S43
    homepage: https://www.innatedb.com/
    name: InnateDB
    prefix: r3d100010676
    synonyms:
    - A Knowlede Resource for Innate Immunity Interactions & Pathways
    xrefs:
      nif: 0000-20808
  reviewer:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
ino:
  aberowl:
    description: An ontology of interactions and interaction networks
    download_owl: http://aber-owl.net/media/ontologies/INO/32/ino.owl
    homepage: https://github.com/INO-ontology/ino
    name: Interaction Network Ontology
    prefix: INO
  biolink:
    is_identifiers: false
    is_obo: true
    prefix: INO
    uri_format: http://purl.obolibrary.org/obo/INO_$1
  bioportal:
    contact:
      email: yongqunh@med.umich.edu
      name: Yongqun "Oliver" He
    description: The Interaction Network Ontology (INO) is an ontology in the domain
      of interactions and interaction networks. INO represents general and species-neutral
      types of interactions and interaction networks, and their related elements and
      relations. INO is a community-driven ontology, aligns with BFO, and is developed
      by following the OBO Foundry principles.
    homepage: https://github.com/INO-ontology/ino
    name: Interaction Network Ontology
    prefix: INO
    publications:
    - https://www.ncbi.nlm.nih.gov/pubmed/25785184
    version: 1.1.13
  example: '0000003'
  fairsharing:
    abbreviation: INO
    contact:
      email: yongqunh@med.umich.edu
      name: Yongqun He
      orcid: 0000-0001-9189-9661
    description: The Interaction Network Ontology (INO) aims to standardize interaction
      network annotation, integrate various interaction network data, and support
      computer-assisted reasoning. It models general interactions (e.g., molecular
      interactions) and interaction networks (e.g., Bayesian network). INO is aligned
      with the Basic Formal Ontology (BFO) and imports terms from 10 other existing
      ontologies, and includes over 500 terms. In terms of interaction-related terms,
      INO imports and aligns PSI-MI and GO interaction terms and includes over 100
      newly generated ontology terms.
    domains:
    - molecular interaction
    homepage: https://github.com/INO-ontology/ino
    license: CC-BY-4.0
    name: Interaction Network Ontology
    prefix: FAIRsharing.mm72as
    publications:
    - doi: 10.1186/s13040-016-0118-0
      pubmed: '28031747'
      title: The Interaction Network Ontology-supported modeling and mining of complex
        interactions represented with multiple keywords in biomedical literature
      year: 2016
    - doi: 10.1186/2041-1480-6-2
      pubmed: '25785184'
      title: Development and application of an interaction network ontology for literature
        mining of vaccine-associated gene-gene interactions
      year: 2015
    - doi: 10.1186/2041-1480-2-s2-s8
      pubmed: '21624163'
      title: Mining of vaccine-associated IFN-gamma gene interaction networks using
        the Vaccine Ontology
      year: 2011
    subjects:
    - Life Science
  mappings:
    aberowl: INO
    biolink: INO
    bioportal: INO
    fairsharing: FAIRsharing.mm72as
    obofoundry: ino
    ols: ino
    ontobee: INO
    wikidata.entity: Q55118418
  obofoundry:
    contact: yongqunh@med.umich.edu
    contact.github: yongqunh
    contact.label: Yongqun Oliver He
    contact.orcid: 0000-0001-9189-9661
    deprecated: false
    description: An ontology of interactions and interaction networks
    domain: biological systems
    download.owl: http://purl.obolibrary.org/obo/ino.owl
    homepage: https://github.com/INO-ontology/ino
    license: CC BY 3.0
    license.url: http://creativecommons.org/licenses/by/3.0/
    name: Interaction Network Ontology
    preferredPrefix: INO
    prefix: ino
    publications:
    - id: https://doi.org/10.1186/2041-1480-6-2
      title: Development and application of an Interaction Network Ontology for literature
        mining of vaccine-associated gene-gene interactions
    repository: https://github.com/INO-ontology/ino
  ols:
    description: he Interaction Network Ontology (INO) is an ontology in the domain
      of interactions and interaction networks. INO represents general and species-neutral
      types of interactions and interaction networks, and their related elements and
      relations. INO is a community-driven ontology, aligns with BFO, and is developed
      by following the OBO Foundry principles.
    download_owl: http://purl.obolibrary.org/obo/ino.owl
    homepage: https://github.com/INO-ontology/ino
    name: 'INO: Interaction Network Ontology'
    prefix: ino
    tracker: https://github.com/INO-ontology/ino/issues
    version: 1.1.13
  ontobee:
    library: Library
    name: Interaction Network Ontology
    prefix: INO
  pattern: ^\d{7}$
  prefix: ino
  publications:
  - doi: 10.1186/s13040-016-0118-0
    pmc: PMC5168857
    pubmed: '28031747'
    title: The Interaction Network Ontology-supported modeling and mining of complex
      interactions represented with multiple keywords in biomedical literature
    year: 2016
  - doi: 10.1186/2041-1480-6-2
    pmc: PMC4362819
    pubmed: '25785184'
    title: Development and application of an interaction network ontology for literature
      mining of vaccine-associated gene-gene interactions
    year: 2015
  - doi: 10.1186/2041-1480-2-s2-s8
    pmc: PMC3102897
    pubmed: '21624163'
    title: Mining of vaccine-associated IFN-γ gene interaction networks using the
      Vaccine Ontology
    year: 2011
  uri_format: http://purl.obolibrary.org/obo/INO_$1
insdc:
  biocontext:
    prefix: INSDC
  integbio:
    alt_name: International Nucleotide Sequence Database Collaboration
    description: It is a portal site for the INSDC(International Nucleotide Sequence
      Database Collaboration), which is an initiative operated between DDBJ, EMBL-EBI
      and NCBI.  Each organization operates DNA databases in close coordination and
      cooperation with each other to achieve common accession numbers, and standardize
      data format (INSD-XML). The databases are called the International Nucleotide
      Sequence Databases (INSD).
    homepage: http://www.insdc.org/
    information_keywords:
    - Sequence
    - Portal
    maintainer: EMBL-EBI (European Bioinformatics Institute)||NCBI (National Center
      for Biotechnology Information)||Bioinformation and DDBJ Center, National Institute
      of Genetics, Research Organization of Information and Systems
    name: INSDC
    prefix: nbdc02567
    pubmeds: []
    status: Active
    target_keywords:
    - Genome/Gene
  mappings:
    biocontext: INSDC
    integbio: nbdc02567
    miriam: insdc
    n2t: insdc
    prefixcommons: insdc
    togoid: Insdc
  miriam:
    deprecated: false
    description: The International Nucleotide Sequence Database Collaboration (INSDC)
      consists of a joint effort to collect and disseminate databases containing DNA
      and RNA sequences.
    homepage: https://www.ebi.ac.uk/ena/
    id: 00000029
    name: Nucleotide Sequence Database
    namespaceEmbeddedInLui: false
    pattern: ^([A-Z]\d{5}|[A-Z]{2}\d{6}|[A-Z]{4,6}\d{8,10}|[A-J][A-Z]{2}\d{5})(\.\d+)?$
    prefix: insdc
    providers:
    - code: ncbi
      description: INSDC through Nucleotide database at NCBI
      homepage: https://www.ncbi.nlm.nih.gov/nuccore/
      name: INSDC through Nucleotide database at NCBI
      uri_format: https://www.ncbi.nlm.nih.gov/nuccore/$1
    - code: ''
      description: INSDC through GenBank
      homepage: https://www.ncbi.nlm.nih.gov/Genbank/
      name: INSDC through GenBank
      uri_format: https://www.ncbi.nlm.nih.gov/nuccore/$1
    - code: ''
      description: INSDC through DDBJ
      homepage: http://www.ddbj.nig.ac.jp/
      name: INSDC through DDBJ
      uri_format: https://getentry.ddbj.nig.ac.jp/getentry?database=ddbj&accession_number=$1
    sampleId: X58356
    uri_format: https://www.ebi.ac.uk/ena/data/view/$1
  n2t:
    description: The International Nucleotide Sequence Database Collaboration (INSDC)
      consists of a joint effort to collect and disseminate databases containing DNA
      and RNA sequences.
    example: X58356
    homepage: https://www.ncbi.nlm.nih.gov/nuccore/
    name: INSDC through Nucleotide database at NCBI
    namespaceEmbeddedInLui: false
    pattern: ^([A-Z]\d{5}|[A-Z]{2}\d{6}|[A-Z]{4}\d{8}|[A-J][A-Z]{2}\d{5})(\.\d+)?$
    prefix: insdc
    uri_format: https://www.ncbi.nlm.nih.gov/nuccore/$1
  part_of_database: insdc
  prefix: insdc
  prefixcommons:
    description: The International Nucleotide Sequence Databases (INSD) have been
      developed and maintained collaboratively between DDBJ, EMBL, and GenBank for
      over 18 years.
    example: X58356
    homepage: http://www.insdc.org/
    keywords:
    - DNA
    name: International Nucleotide Sequence Database Collaboration (GenBank, EMBL,
      DDBJ)
    pattern: ^\w+(\_)?\d+(\.\d+)?$
    prefix: insdc
    pubmed_ids:
    - '17148479'
    - '17202161'
    - '2326192'
    - '12436968'
    synonyms:
    - ddbj/embl/genbank
    - insd
  publications:
  - doi: 10.1093/nar/gkae1058
    pmc: null
    pubmed: '39535044'
    title: 'The international nucleotide sequence database collaboration (INSDC):
      enhancing global participation'
    year: 2024
  - doi: 10.1093/nar/gkl986
    pmc: PMC1781245
    pubmed: '17202161'
    title: GenBank
    year: 2007
  - doi: 10.1093/nar/gkl913
    pmc: PMC1897316
    pubmed: '17148479'
    title: EMBL Nucleotide Sequence Database in 2006
    year: 2006
  - doi: 10.1126/science.298.5597.1333b
    pmc: null
    pubmed: '12436968'
    title: Nucleotide sequence database policies
    year: 2002
  - doi: 10.1093/nar/18.6.1517
    pmc: PMC330520
    pubmed: '2326192'
    title: Recent changes in the GenBank On-line Service
    year: 1990
  togoid:
    catalog: nbdc02567
    description: It is a portal site for the INSDC(International Nucleotide Sequence
      Database Collaboration), which is an initiative operated between DDBJ, EMBL-EBI
      and NCBI.  Each organization operates DNA databases in close coordination and
      cooperation with each other to achieve common accession numbers, and standardize
      data format (INSD-XML). The databases are called the International Nucleotide
      Sequence Databases (INSD).
    examples:
    - U10991
    - AF116914
    - AK056978
    - DQ440258
    - U91725
    - AY301270
    - U32907
    - AY261360
    - AK001332
    - U13261
    keywords:
    - Gene
    name: GenBank/ENA/DDBJ
    pattern: ^(?:insdc:)?(?[A-Z]\d{5}|[A-Z]{2}\d{6}|[A-Z]{4}\d{8}|[A-J][A-Z]{2}\d{5}|[A-Z]{4,}\d{9})(?:\.\d+)?$
    prefix: Insdc
    uri_format: http://identifiers.org/insdc/$1
insdc.cds:
  biocontext:
    prefix: INSDC.CDS
  has_canonical: ncbiprotein
  mappings:
    biocontext: INSDC.CDS
    miriam: insdc.cds
    n2t: insdc.cds
  miriam:
    deprecated: false
    description: The coding sequence or protein identifiers as maintained in INSDC.
    homepage: http://getentry.ddbj.nig.ac.jp
    id: '00000606'
    name: INSDC CDS
    namespaceEmbeddedInLui: false
    pattern: ^([A-Z]\d{5}|[A-Z]{2}\d{6}|[A-Z]{4}\d{8}|[A-J][A-Z]{2}\d{5})(\.\d+)?$
    prefix: insdc.cds
    providers:
    - code: ''
      description: INSDC CDS through ENA
      homepage: https://www.ebi.ac.uk/ena
      name: INSDC CDS through ENA
      uri_format: https://www.ebi.ac.uk/ena/data/view/$1
    - code: ''
      description: INSDC CDS through NCBI
      homepage: https://www.ncbi.nlm.nih.gov/protein/
      name: INSDC CDS through NCBI
      uri_format: https://www.ncbi.nlm.nih.gov/protein/$1
    sampleId: AAA35559
    uri_format: http://getentry.ddbj.nig.ac.jp/getentry/dad/$1
  n2t:
    description: The coding sequence or protein identifiers as maintained in INSDC.
    example: AAA35559
    homepage: https://www.ncbi.nlm.nih.gov/protein/
    name: INSDC CDS through NCBI
    namespaceEmbeddedInLui: false
    pattern: ^([A-Z]\d{5}|[A-Z]{2}\d{6}|[A-Z]{4}\d{8}|[A-J][A-Z]{2}\d{5})(\.\d+)?$
    prefix: insdc.cds
    uri_format: https://www.ncbi.nlm.nih.gov/protein/$1
  part_of_database: insdc
  prefix: insdc.cds
insdc.gca:
  biocontext:
    prefix: INSDC.GCA
  has_canonical: ncbi.assembly
  mappings:
    biocontext: INSDC.GCA
    miriam: insdc.gca
    n2t: insdc.gca
  miriam:
    deprecated: false
    description: The genome assembly database contains detailed information about
      genome assemblies for eukaryota, bacteria and archaea. The scope of the genome
      collections database does not extend to viruses, viroids and bacteriophage.
    homepage: https://www.ncbi.nlm.nih.gov/datasets/genome/
    id: '00000607'
    name: Genome assembly database - INSDC accessions
    namespaceEmbeddedInLui: false
    pattern: ^GCA_[0-9]{9}(\.[0-9]+)?$
    prefix: insdc.gca
    providers:
    - code: ''
      description: Genome assembly database through ENA
      homepage: https://www.ebi.ac.uk/ena/browse/genome-assembly-database
      name: Genome assembly database through ENA
      uri_format: https://www.ebi.ac.uk/ena/data/view/$1
    sampleId: GCA_000155495.1
    uri_format: https://www.ncbi.nlm.nih.gov/datasets/genome/$1
  n2t:
    description: The genome assembly database contains detailed information about
      genome assemblies for eukaryota, bacteria and archaea. The scope of the genome
      collections database does not extend to viruses, viroids and bacteriophage.
    example: GCA_000155495.1
    homepage: https://www.ncbi.nlm.nih.gov/assembly/
    name: Genome assembly database NCBI
    namespaceEmbeddedInLui: false
    pattern: ^GCA_[0-9]{9}\.[0-9]$
    prefix: insdc.gca
    uri_format: https://www.ncbi.nlm.nih.gov/assembly/$1
  part_of_database: insdc
  prefix: insdc.gca
insdc.gcf:
  has_canonical: ncbi.assembly
  mappings:
    miriam: refseq.gcf
  miriam:
    deprecated: false
    description: The genome assembly database contains detailed information about
      genome assemblies for eukaryota, bacteria and archaea. The scope of the genome
      collections database RefSeq accessions does not extend to viroids and bacteriophage.
    homepage: https://www.ncbi.nlm.nih.gov/
    id: '00001030'
    name: Genome assembly database - RefSeq accessions
    namespaceEmbeddedInLui: false
    pattern: ^GCF_[0-9]{9}(\.[0-9]+)?$
    prefix: refseq.gcf
    sampleId: GCF_000001405
    uri_format: https://www.ncbi.nlm.nih.gov/datasets/genome/$1
  part_of_database: insdc
  prefix: insdc.gcf
  synonyms:
  - insdc.gcf
insdc.run:
  comment: https://www.insdc.org/ is the authoritative source for INSDC. However,
    confusingly, they don't mention runs in this table. I think we should ask them
    to include. ENA is a partner and they have documentation [here](https://ena-docs.readthedocs.io/en/latest/submit/general-guide/accessions.html).
    Runs | (E\|D\|S)RR[0-9]{6,} | ERR123456 -- | -- | --
  contributor:
    email: cjmungall@lbl.gov
    github: cmungall
    name: Chris Mungall
    orcid: 0000-0002-6601-2165
  description: An experimental run, served thrugh the ENA
  example: ERR436051
  github_request_issue: 131
  homepage: https://www.insdc.org/
  name: International Nucleotide Sequence Database Collaboration (INSDC) Run
  pattern: ^(E|D|S)RR[0-9]{6,}$
  prefix: insdc.run
  reviewer:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  uri_format: https://www.ebi.ac.uk/ena/browser/view/$1
insdc.sra:
  biocontext:
    prefix: INSDC.SRA
  contact:
    email: Hugh.Shanahan@rhul.ac.uk
    github: hughshanahan
    name: Hugh P Shanahan
    orcid: 0000-0003-1374-6015
  fairsharing:
    abbreviation: SRA
    description: The SRA is NIH's primary archive of high-throughput sequencing data
      and is part of the International Nucleotide Sequence Database Collaboration
      (INSDC) that includes at the NCBI Sequence Read Archive (SRA), the European
      Bioinformatics Institute (EBI), and the DNA Database of Japan (DDBJ). Data submitted
      to any of the three organizations are shared among them. SRA accepts data from
      all kinds of sequencing projects including clinically important studies that
      involve human subjects or their metagenomes, which may contain human sequences.
      These data often have a controlled access via dbGaP (the database of Genotypes
      and Phenotypes).
    homepage: http://www.ncbi.nlm.nih.gov/sra
    license: http://opendatacommons.org/licenses/pddl/1.0
    name: Sequence Read Archive
    prefix: FAIRsharing.g7t2hv
    publications:
    - doi: 10.1093/nar/gkm1000
      pubmed_id: 18045790
      title: Database resources of the National Center for Biotechnology Information
    - doi: 10.1093/nar/gkr854
      pubmed_id: 22009675
      title: 'The Sequence Read Archive: explosive growth of sequencing data.'
    - doi: 10.1186/s13742-015-0064-7
      pubmed_id: 25960871
      title: Investigation into the annotation of protocol sequencing steps in the
        sequence read archive.
    subjects:
    - Genomics
    - Virology
    - Biology
    - Epidemiology
  mappings:
    biocontext: INSDC.SRA
    fairsharing: FAIRsharing.g7t2hv
    miriam: insdc.sra
    n2t: insdc.sra
    re3data: r3d100010775
  miriam:
    deprecated: false
    description: 'The Sequence Read Archive (SRA) stores raw sequencing data from
      the next generation of sequencing platforms Data submitted to SRA. It is organized
      using a metadata model consisting of six objects: study, sample, experiment,
      run, analysis and submission. The SRA study contains high-level information
      including goals of the study and literature references, and may be linked to
      the INSDC BioProject database.'
    homepage: https://www.ncbi.nlm.nih.gov/sra
    id: '00000243'
    name: Sequence Read Archive
    namespaceEmbeddedInLui: false
    pattern: ^[SED]R[APRSXZ]\d+$
    prefix: insdc.sra
    providers:
    - code: ebi
      description: European Nucleotide Archive (ENA)
      homepage: https://www.ebi.ac.uk/ena
      name: European Nucleotide Archive (ENA)
      uri_format: https://www.ebi.ac.uk/ena/data/view/$1
    - code: ddbj
      description: DDBJ Sequence Read Archive (DRA)
      homepage: https://www.ddbj.nig.ac.jp/dra/index-e.html
      name: DDBJ Sequence Read Archive (DRA)
      uri_format: https://ddbj.nig.ac.jp/resource/sra-experiment/$1
    sampleId: SRX000007
    uri_format: https://www.ncbi.nlm.nih.gov/sra/$1
  n2t:
    description: 'The Sequence Read Archive (SRA) stores raw sequencing data from
      the next generation of sequencing platforms Data submitted to SRA. It is organized
      using a metadata model consisting of six objects: study, sample, experiment,
      run, analysis and submission. The SRA study contains high-level information
      including goals of the study and literature references, and may be linked to
      the INSDC BioProject database.'
    example: SRX000007
    homepage: https://www.ncbi.nlm.nih.gov/sra
    name: Sequence Read Archive at NCBI
    namespaceEmbeddedInLui: false
    pattern: ^[SED]R[APRSXZ]\d+$
    prefix: insdc.sra
    uri_format: https://www.ncbi.nlm.nih.gov/sra/$1
  part_of_database: insdc
  prefix: insdc.sra
  publications:
  - doi: 10.1186/s13742-015-0064-7
    pmc: PMC4425880
    pubmed: '25960871'
    title: Investigation into the annotation of protocol sequencing steps in the sequence
      read archive
    year: 2015
  - doi: 10.1093/nar/gkr854
    pmc: PMC3245110
    pubmed: '22009675'
    title: 'The Sequence Read Archive: explosive growth of sequencing data'
    year: 2011
  - doi: 10.1093/nar/gkm1000
    pmc: PMC2238880
    pubmed: '18045790'
    title: Database resources of the National Center for Biotechnology Information
    year: 2007
  - doi: 10.1093/nar/gkm1000
    pmc: null
    pubmed: null
    title: Database resources of the National Center for Biotechnology Information
    year: null
  - doi: 10.1093/nar/gkr854
    pmc: null
    pubmed: null
    title: 'The Sequence Read Archive: explosive growth of sequencing data.'
    year: null
  - doi: 10.1186/s13742-015-0064-7
    pmc: null
    pubmed: null
    title: Investigation into the annotation of protocol sequencing steps in the sequence
      read archive.
    year: null
  - doi: 10.1093/nar/gkm1000
    pmc: null
    pubmed: null
    title: Database resources of the National Center for Biotechnology Information
    year: null
  - doi: 10.1093/nar/gkr854
    pmc: null
    pubmed: null
    title: 'The Sequence Read Archive: explosive growth of sequencing data.'
    year: null
  - doi: 10.1186/s13742-015-0064-7
    pmc: null
    pubmed: null
    title: Investigation into the annotation of protocol sequencing steps in the sequence
      read archive.
    year: null
  re3data:
    description: The Sequence Read Archive stores the raw sequencing data from such
      sequencing platforms as the Roche 454 GS System, the Illumina Genome Analyzer,
      the Applied Biosystems SOLiD System, the Helicos Heliscope, and the Complete
      Genomics. It archives the sequencing data associated with RNA-Seq, ChIP-Seq,
      Genomic and Transcriptomic assemblies, and 16S ribosomal RNA data.
    doi: 10.17616/R31S69
    homepage: https://www.ncbi.nlm.nih.gov/sra
    license: Copyrights
    name: Sequence Read Archive
    prefix: r3d100010775
    synonyms:
    - SRA
    xrefs:
      omics: '01031'
inspire.theme:
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: The INSPIRE theme register contains all spatial data themes, as defined
    in the Annexes of the INSPIRE Directive ( Directive 2007/2/EC of the European
    Parliament and of the Council of 14 March 2007 establishing an Infrastructure
    for Spatial Information in the European Community (INSPIRE)). The descriptions
    of the themes are based on version 3.0 of the "Definition of Annex Themes and
    Scope (D 2.3)" by the data specifications drafting team and subsequent updates
    by the INSPIRE Thematic Working Groups (TWGs). (from homepage)
  download_rdf: http://inspire.ec.europa.eu/theme/theme.en.rdf
  example: mr
  homepage: https://inspire.ec.europa.eu/theme
  name: INSPIRE theme register
  prefix: inspire.theme
  uri_format: https://inspire.ec.europa.eu/theme/$1
intact:
  biocontext:
    prefix: INTACT
  contact:
    email: kalpanap@ebi.ac.uk
    github: Kalpanapanneerselvam
    name: Kalpana Panneerselvam
    orcid: 0000-0003-2534-198X
  contact_extras:
  - email: jmedina@ebi.ac.uk
    github: jmedinaebi
    name: Juan Jose Medina Reyes
    orcid: 0009-0004-6468-260X
  contributor_extras:
  - email: sbalu@ebi.ac.uk
    github: CP-SB
    name: Sucharitha Balu
    orcid: 0000-0001-7456-0594
  domain: relationship
  fairsharing:
    abbreviation: IntAct
    contact:
      email: orchard@ebi.ac.uk
      name: Sandra Orchard
      orcid: 0000-0002-8878-3972
    description: IntAct provides a freely available, open source database system and
      analysis tools for protein interaction data. All interactions are derived from
      literature curation or direct user submissions and are freely available.
    homepage: https://www.ebi.ac.uk/intact/home
    license: CC-BY-4.0
    name: IntAct molecular interaction database
    prefix: FAIRsharing.d05nwx
    publications:
    - doi: 10.1093/nar/gkh052
      pubmed_id: 14681455
      title: 'IntAct: an open source molecular interaction database.'
    - doi: 10.1093/nar/gkp878
      pubmed_id: 19850723
      title: The IntAct molecular interaction database in 2010.
    - doi: 10.1186/1741-7007-5-44
      pubmed_id: 17925023
      title: Broadening the horizon--level 2.5 of the HUPO-PSI format for molecular
        interactions.
    - doi: 10.1038/nmeth.1637
      pubmed_id: 21716279
      title: 'PSICQUIC and PSISCORE: accessing and scoring molecular interactions.'
    - doi: 10.1093/nar/gkt1115
      pubmed_id: 24234451
      title: The MIntAct project--IntAct as a common curation platform for 11 molecular
        interaction databases.
    subjects:
    - Biology
    twitter: intact_project
  go:
    homepage: https://www.ebi.ac.uk/intact/
    name: IntAct protein interaction database
    prefix: IntAct
  integbio:
    description: IntAct is a database of molecular interactions. The database contains
      information on more than 400,000 interactions gathered from primary literature.
      Users can search by gene, protein, or publication, among others, and the database
      includes manually annotated data from several other interaction databases. Software
      and bulk data, updoated weekly, are also available for download.
    fairsharing: biodbcore-000054
    homepage: http://www.ebi.ac.uk/intact/main.xhtml
    information_keywords:
    - Interaction/Pathway
    - Repository
    maintainer: EMBL-EBI (European Bioinformatics Institute)
    name: IntAct
    prefix: nbdc00507
    pubmeds:
    - '19850723'
    - '22121220'
    status: Active
    target_keywords:
    - Protein
    - Metabolite
  license: CC-BY-4.0
  logo: https://raw.githubusercontent.com/intact-portal/intact-portal-documentation/master/assets/logo_gradient_250x82_transparentbg_300dpi.png
  mappings:
    biocontext: INTACT
    fairsharing: FAIRsharing.d05nwx
    go: IntAct
    integbio: nbdc00507
    miriam: intact
    n2t: intact
    pathguide: '111'
    prefixcommons: intact
    re3data: r3d100010671
    togoid: Intact
    uniprot: DB-0051
  miriam:
    deprecated: false
    description: IntAct provides a freely available, open source database system and
      analysis tools for protein interaction data.
    homepage: https://www.ebi.ac.uk/intact/
    id: '00000010'
    name: IntAct
    namespaceEmbeddedInLui: false
    pattern: ^EBI\-[0-9]+$
    prefix: intact
    sampleId: EBI-2307691
    uri_format: https://www.ebi.ac.uk/intact/interaction/$1
  n2t:
    description: IntAct provides a freely available, open source database system and
      analysis tools for protein interaction data.
    example: EBI-2307691
    homepage: https://www.ebi.ac.uk/intact/
    name: IntAct at EBI
    namespaceEmbeddedInLui: false
    pattern: ^EBI\-[0-9]+$
    prefix: intact
    uri_format: https://www.ebi.ac.uk/intact/interaction/$1
  name: IntAct protein interaction
  owners:
  - name: European Bioinformatics Institute
    partnered: false
    ror: 02catss52
    wikidata: null
  part_of_database: intact
  pathguide:
    abbreviation: IntAct
    homepage: http://www.ebi.ac.uk/intact
    keywords:
    - PSI-MI
    name: IntAct Molecular Interaction Database
    prefix: '111'
  prefix: intact
  prefixcommons:
    description: IntAct provides a freely available, open source database system and
      analysis tools for protein interaction data. All interactions are derived from
      literature curation or direct user submissions and are freely available.
    example: EBI-2307691
    homepage: http://www.ebi.ac.uk/intact
    keywords:
    - protein
    - interaction
    license: http://www.ebi.ac.uk/Information/termsofuse.html
    name: The IntAct molecular interaction database
    pattern: ^EBI\-\d+$
    prefix: intact
    pubmed_ids:
    - '14681455'
    uri_format: http://www.ebi.ac.uk/intact/pages/details/details.xhtml?interactionAc=$1
  publications:
  - doi: 10.1002/cpz1.70018
    pmc: null
    pubmed: '39401100'
    title: IntAct Database for Accessing IMEx's Contextual Metadata of Molecular Interactions
    year: 2024
  - doi: 10.1093/nar/gkt1115
    pmc: PMC3965093
    pubmed: '24234451'
    title: The MIntAct project--IntAct as a common curation platform for 11 molecular
      interaction databases
    year: 2013
  - doi: 10.1038/nmeth.1637
    pmc: PMC3246345
    pubmed: '21716279'
    title: 'PSICQUIC and PSISCORE: accessing and scoring molecular interactions'
    year: 2011
  - doi: 10.1093/nar/gkp878
    pmc: PMC2808934
    pubmed: '19850723'
    title: The IntAct molecular interaction database in 2010
    year: 2009
  - doi: 10.1186/1741-7007-5-44
    pmc: PMC2189715
    pubmed: '17925023'
    title: Broadening the horizon--level 2.5 of the HUPO-PSI format for molecular
      interactions
    year: 2007
  - doi: 10.1093/nar/gkh052
    pmc: PMC308786
    pubmed: '14681455'
    title: 'IntAct: an open source molecular interaction database'
    year: 2004
  - doi: 10.1093/nar/gkh052
    pmc: null
    pubmed: null
    title: 'IntAct: an open source molecular interaction database.'
    year: null
  - doi: 10.1093/nar/gkp878
    pmc: null
    pubmed: null
    title: The IntAct molecular interaction database in 2010.
    year: null
  - doi: 10.1186/1741-7007-5-44
    pmc: null
    pubmed: null
    title: Broadening the horizon--level 2.5 of the HUPO-PSI format for molecular
      interactions.
    year: null
  - doi: 10.1038/nmeth.1637
    pmc: null
    pubmed: null
    title: 'PSICQUIC and PSISCORE: accessing and scoring molecular interactions.'
    year: null
  - doi: 10.1093/nar/gkt1115
    pmc: null
    pubmed: null
    title: The MIntAct project--IntAct as a common curation platform for 11 molecular
      interaction databases.
    year: null
  - doi: null
    pmc: null
    pubmed: '14681455'
    title: null
    year: null
  - doi: 10.1093/nar/gkt1115
    pmc: null
    pubmed: '24234451'
    title: null
    year: null
  re3data:
    description: IntAct provides a freely available, open source database system and
      analysis tools for molecular interaction data. All interactions are derived
      from literature curation or direct user submissions and are freely available.
    doi: 10.17616/R3QS4R
    homepage: https://www.ebi.ac.uk/intact/home
    license: Apache License 2.0
    name: IntAct
    prefix: r3d100010671
    synonyms:
    - IntAct Molecular Interaction Database
    xrefs:
      nif: 0000-03026
      omics: 01918
  togoid:
    catalog: nbdc00507
    description: IntAct is a database of molecular interactions. The database contains
      information on more than 400,000 interactions gathered from primary literature.
      Users can search by gene, protein, or publication, among others, and the database
      includes manually annotated data from several other interaction databases. Software
      and bulk data, updoated weekly, are also available for download.
    examples:
    - EBI-7947422
    - EBI-15714708
    - EBI-16225271
    - EBI-4406290
    - EBI-9026465
    - EBI-6403471
    - EBI-1113651
    - EBI-562824
    - EBI-9014072
    - EBI-1784742
    keywords:
    - Interaction
    name: IntAct
    pattern: ^(?EBI\-[0-9]+)$
    prefix: Intact
    uri_format: http://identifiers.org/intact/$1
  uniprot:
    abbreviation: IntAct
    category: Protein-protein interaction databases
    homepage: https://www.ebi.ac.uk/intact/
    name: Protein interaction database and analysis system
    prefix: DB-0051
    publications:
    - doi: 10.1093/nar/gkt1115
      pubmed: '24234451'
    uri_format: https://www.ebi.ac.uk/intact/interactors/id:$1*
intact.molecule:
  biocontext:
    prefix: INTACT.MOLECULE
  mappings:
    biocontext: INTACT.MOLECULE
    miriam: intact.molecule
    n2t: intact.molecule
  miriam:
    deprecated: false
    description: IntAct provides a freely available, open source database system and
      analysis tools for protein interaction data. This collection references interactor
      molecules.
    homepage: https://www.ebi.ac.uk/intact/
    id: '00000427'
    name: IntAct Molecule
    namespaceEmbeddedInLui: false
    pattern: ^EBI\-[0-9]+$
    prefix: intact.molecule
    sampleId: EBI-366083
    uri_format: https://www.ebi.ac.uk/intact/molecule/$1
  n2t:
    description: IntAct provides a freely available, open source database system and
      analysis tools for protein interaction data. This collection references interactor
      molecules.
    example: EBI-366083
    homepage: https://www.ebi.ac.uk/intact/
    name: IntAct Molecule at EBI
    namespaceEmbeddedInLui: false
    pattern: ^EBI\-[0-9]+$
    prefix: intact.molecule
    uri_format: https://www.ebi.ac.uk/intact/molecule/$1
  part_of_database: intact
  prefix: intact.molecule
  publications:
  - doi: 10.1002/cpz1.70018
    pmc: null
    pubmed: '39401100'
    title: IntAct Database for Accessing IMEx's Contextual Metadata of Molecular Interactions
    year: 2024
  uri_format: https://www.ebi.ac.uk/intact/search?query=$1
integbio:
  contact:
    email: kwsm@dbcls.rois.ac.jp
    github: skwsm
    name: Shuichi Kawashima
    orcid: 0000-0001-7883-3756
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: 'Integbio Database Catalog provides whereabouts information (URL),
    database description, biological species and other attributes (metadata) of Japanese
    and international life science databases to make it easier for users to find databases
    they need. This catalog has been developed as a part of the integration of life
    science databases promoted by four ministries in Japan: the Ministry of Education,
    Culture, Sports, Science, and Technology (MEXT), The Ministry of Health, Labor,
    and Welfare (MHLW), the Ministry of Agriculture, Forestry, and Fisheries (MAFF),
    and the Ministry of Economy, Trade, and Industry of Japan (METI). (from https://integbio.jp/dbcatalog/en/about)'
  example: nbdc01071
  homepage: https://integbio.jp/en/
  license: CC0-1.0
  logo: https://integbio.jp/templates/integbio/images/logo/logo.png
  name: Integbio
  pattern: ^nbdc\d+$
  prefix: integbio
  uri_format: https://catalog.integbio.jp/dbcatalog/en/record/$1
interfil:
  mappings:
    prefixcommons: interfil
  prefix: interfil
  prefixcommons:
    description: The Intermediate Filament Database functions as a continuously updated
      review of the intermediate filament field and it is hoped that users will contribute
      to the development and expansion of the database on a regular basis. Contributions
      may include novel variants, new patients with previously discovered sequence
      and allelic variants.
    example: NM_006262
    homepage: http://www.interfil.org
    keywords:
    - genome
    name: Human Intermediate Filament Database
    pattern: ^N[A-Z]_\d+$
    prefix: interfil
    synonyms:
    - intermediate_filament_db
    uri_format: http://www.interfil.org/details.php?id=$1
  reviewer:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
interlex:
  contact:
    email: mmartone@ucsd.edu
    github: memartone
    name: Maryann Elizabeth Martone
    orcid: 0000-0002-8406-3871
  fairsharing:
    abbreviation: InterLex
    description: The InterLex terminology is a lexicon of biomedical terms built on
      the foundation of NeuroLex and contains all of the existing NeuroLex terms.
      The initial entries in NeuroLex were built from the NIFSTD ontologies and BIRNLex
      (Biomedical Informatics Research Network Project Lexicon). Final content review
      from NeuroLex is still ongoing.
    domains:
    - Imaging
    - brain
    homepage: https://scicrunch.org/scicrunch/interlex/dashboard
    license: CC-BY-3.0
    name: InterLex
    prefix: FAIRsharing.67sssf
    publications:
    - doi: 10.3389/fninf.2013.00018
      pubmed: '24009581'
      title: 'NeuroLex.org: an online framework for neuroscience knowledge'
      year: 2013
    subjects:
    - Anatomy
    - Neurobiology
    - Biomedical Science
  mappings:
    fairsharing: FAIRsharing.67sssf
    miriam: ilx
    wikidata: P696
  miriam:
    deprecated: false
    description: 'InterLex is a dynamic lexicon, initially built on the foundation
      of NeuroLex (PMID: 24009581), of biomedical terms and common data elements designed
      to help improve the way that biomedical scientists communicate about their data,
      so that information systems can find data more easily and provide more powerful
      means of integrating data across distributed resources and datasets. InterLex
      allows for the association of data fields and data values to common data elements
      and terminologies enabling the crowdsourcing of data-terminology mappings within
      and across communities. InterLex provides a stable layer on top of the many
      other existing terminologies, lexicons, ontologies, and common data element
      collections and provides a set of inter-lexical and inter-data-lexical mappings. '
    homepage: https://www.fdilab.org
    id: 00000814
    name: InterLex
    namespaceEmbeddedInLui: false
    pattern: ^[0-9]+$
    prefix: ilx
    sampleId: 0101963
    uri_format: https://scicrunch.org/scicrunch/interlex/view/ilx_$1
  name: InterLex
  prefix: interlex
  publications:
  - doi: 10.3389/fninf.2013.00018
    pmc: PMC3757470
    pubmed: '24009581'
    title: 'NeuroLex.org: an online framework for neuroscience knowledge'
    year: 2013
  - doi: 10.3389/fninf.2013.00018
    pmc: null
    pubmed: '24009581'
    title: 'NeuroLex.org: an online framework for neuroscience knowledge'
    year: 2013
  - doi: 10.3389/fninf.2013.00018
    pmc: null
    pubmed: '24009581'
    title: 'NeuroLex.org: an online framework for neuroscience knowledge'
    year: 2013
  references:
  - https://github.com/AllenInstitute/nomenclature
  synonyms:
  - ILX
  wikidata:
    description: identifier in the Interlex database (used to be Neurolex)
    example:
    - nlx_anat_090801
    - sao1103104164
    homepage: http://interlex.org
    name: Interlex ID
    pattern: ^[0-9A-Za-z_]+$
    prefix: P696
interpro:
  biocontext:
    prefix: IPR
  biolink:
    is_identifiers: false
    is_obo: false
    prefix: interpro
    uri_format: https://www.ebi.ac.uk/interpro/entry/$1
  contact:
    email: agb@ebi.ac.uk
    github: bateman-research
    name: Alex Bateman
    orcid: 0000-0002-6982-4660
  contact_group_email: interhelp@ebi.ac.uk
  domain: protein family
  edam:
    description: Primary accession number of an InterPro entry.
    name: InterPro
    obsolete: false
    prefix: '1133'
  example: IPR016380
  fairsharing:
    abbreviation: InterPro
    description: InterPro is a resource that provides functional analysis of protein
      sequences by classifying them into families and predicting the presence of domains
      and important sites. To classify proteins in this way, InterPro uses predictive
      models, known as signatures, provided by several different databases (referred
      to as member databases) that make up the InterPro consortium.
    homepage: https://www.ebi.ac.uk/interpro
    license: http://opendatacommons.org/licenses/pddl/1.0
    name: Integrated resource of protein families, domains and functional sites
    prefix: FAIRsharing.pda11d
    publications:
    - doi: 10.1093/nar/gky1100
      pubmed_id: 30398656
      title: 'InterPro in 2019: improving coverage, classification and access to protein
        sequence annotations.'
    - doi: 10.1093/nar/gki106
      pubmed_id: 15608177
      title: InterPro, progress and status in 2005.
    repository: https://proteinswebteam.github.io/interpro-blog/
    subjects:
    - Bioinformatics
    - Biology
    twitter: InterProDB
  go:
    homepage: http://www.ebi.ac.uk/interpro/
    name: InterPro database of protein domains and motifs
    prefix: InterPro
    synonyms:
    - INTERPRO
    - IPR
    uri_format: http://www.ebi.ac.uk/interpro/entry/$1
  integbio:
    alt_name: Integrated documentation resource for protein families, domains and
      functional sites
    description: 'InterPro is a database that analyses proteins functionally and classifies
      them into families as well as predicts their domain and sites in the genome.

      This repository harvests its content from a large number of related databases
      and consolidates its findings into a single searchable resource avoiding the
      occurrence of redundant entries.

      InterPro aims to update their content every 8 weeks.

      A keyword search is available and an option is provided where a protein sequence
      can be entered for analysis.'
    fairsharing: biodbcore-000315
    homepage: http://www.ebi.ac.uk/interpro/
    information_keywords:
    - Sequence
    - Classification
    maintainer: EMBL-EBI (European Bioinformatics Institute)
    name: InterPro
    prefix: nbdc00108
    pubmeds:
    - '22096229'
    - '22301074'
    - '15980438'
    - '21785143'
    - '18836194'
    status: Active
    target_keywords:
    - Protein
  license: CC0-1.0
  logo: https://content.embl.org/sites/default/files/03-2025/interpro_newlogo-2-scaled-1.jpg
  mappings:
    biocontext: IPR
    biolink: interpro
    edam: '1133'
    fairsharing: FAIRsharing.pda11d
    go: InterPro
    integbio: nbdc00108
    miriam: interpro
    n2t: interpro
    ncbi: InterPro
    obofoundry: ipr
    prefixcommons: interpro
    re3data: r3d100010798
    togoid: Interpro
    uniprot: DB-0052
    wikidata: P2926
    wikidata.entity: Q114677890
  miriam:
    deprecated: false
    description: InterPro is a database of protein families, domains and functional
      sites in which identifiable features found in known proteins can be applied
      to unknown protein sequences.
    homepage: https://www.ebi.ac.uk/interpro/
    id: '00000011'
    name: InterPro
    namespaceEmbeddedInLui: false
    pattern: ^IPR\d{6}$
    prefix: interpro
    providers:
    - code: ''
      description: Bio2RDF
      homepage: http://bio2rdf.org/
      name: Bio2RDF
      uri_format: http://bio2rdf.org/interpro:$1
    sampleId: IPR000100
    uri_format: https://www.ebi.ac.uk/interpro/entry/$1
  n2t:
    description: InterPro is a database of protein families, domains and functional
      sites in which identifiable features found in known proteins can be applied
      to unknown protein sequences.
    example: IPR000100
    homepage: https://www.ebi.ac.uk/interpro/
    name: InterPro
    namespaceEmbeddedInLui: false
    pattern: ^IPR\d{6}$
    prefix: interpro
    uri_format: https://www.ebi.ac.uk/interpro/entry/$1
  name: InterPro
  ncbi:
    example: IPR002928
    homepage: http://www.ebi.ac.uk/interpro/
    name: InterPro protein sequence database
    prefix: InterPro
  obofoundry:
    contact: interhelp@ebi.ac.uk
    contact.label: InterPro Help
    deprecated: true
    domain: chemistry and biochemistry
    homepage: http://www.ebi.ac.uk/interpro/index.html
    name: Protein Domains
    prefix: ipr
  preferred_prefix: interpro
  prefix: interpro
  prefixcommons:
    description: InterPro is an integrated database of predictive protein "signatures"
      used for the classification and automatic annotation of proteins and genomes.
      InterPro classifies sequences at superfamily, family and subfamily levels, predicting
      the occurrence of functional domains, repeats and important sites.
    example: IPR000100
    homepage: http://www.ebi.ac.uk/interpro
    keywords:
    - domain
    - protein
    license: http://www.ebi.ac.uk/Information/termsofuse.html
    name: Integrated resource of protein families, domains and functional sites
    pattern: ^IPR\d{6}$
    prefix: interpro
    pubmed_ids:
    - '15608177'
    synonyms:
    - ipr
    uri_format: http://www.ebi.ac.uk/interpro/IEntry?ac=$1
  publications:
  - doi: 10.1093/nar/gkae1082
    pmc: null
    pubmed: '39565202'
    title: 'InterPro: the protein sequence classification resource in 2025'
    year: 2024
  - doi: 10.1093/nar/gkac993
    pmc: PMC9825450
    pubmed: '36350672'
    title: InterPro in 2022
    year: 2023
  - doi: 10.1093/nar/gkaa977
    pmc: PMC7778928
    pubmed: '33156333'
    title: 'The InterPro protein families and domains database: 20 years on'
    year: 2021
  - doi: 10.1093/nar/gky1100
    pmc: PMC6323941
    pubmed: '30398656'
    title: 'InterPro in 2019: improving coverage, classification and access to protein
      sequence annotations'
    year: 2019
  - doi: 10.1093/nar/gki106
    pmc: PMC540060
    pubmed: '15608177'
    title: InterPro, progress and status in 2005
    year: 2005
  - doi: 10.1093/nar/gky1100
    pmc: null
    pubmed: null
    title: 'InterPro in 2019: improving coverage, classification and access to protein
      sequence annotations.'
    year: null
  - doi: 10.1093/nar/gki106
    pmc: null
    pubmed: null
    title: InterPro, progress and status in 2005.
    year: null
  - doi: null
    pmc: null
    pubmed: '15608177'
    title: null
    year: null
  - doi: 10.1093/nar/gkac993
    pmc: null
    pubmed: '36350672'
    title: null
    year: null
  rdf_uri_format: http://purl.obolibrary.org/obo/IPR_$1
  re3data:
    description: InterPro collects information about protein sequence analysis and
      classification, providing access to a database of predictive protein signatures
      used for the classification and automatic annotation of proteins and genomes.
      Sequences in InterPro are classified at superfamily, family, and subfamily.
      InterPro predicts the occurrence of functional domains, repeats, and important
      sites, and adds in-depth annotation such as GO terms to the protein signatures.
    doi: 10.17616/R3FS61
    homepage: https://www.ebi.ac.uk/interpro/
    license: Public Domain
    name: InterPro
    prefix: r3d100010798
    synonyms:
    - protein sequence analysis & classification
    xrefs:
      nif: 0000-03035
      omics: 01694
  synonyms:
  - IP
  - IPR
  - InterPro
  togoid:
    catalog: nbdc00108
    description: InterPro is a database that analyses proteins functionally and classifies
      them into families as well as predicts their domain and sites in the genome.
      This repository harvests its content from a large number of related databases
      and consolidates its findings into a single searchable resource avoiding the
      occurrence of redundant entries. InterPro aims to update their content every
      8 weeks. A keyword search is available and an option is provided where a protein
      sequence can be entered for analysis.
    examples:
    - IPR038152
    - IPR040448
    - IPR036748
    - IPR034266
    - IPR005479
    - IPR036365
    - IPR000174
    - IPR001334
    - IPR000731
    - IPR001767
    keywords:
    - Domain
    name: InterPro
    pattern: ^(?IPR\d{6})$
    prefix: Interpro
    uri_format: http://identifiers.org/interpro/$1
  uniprot:
    abbreviation: InterPro
    category: Family and domain databases
    homepage: https://www.ebi.ac.uk/interpro/
    name: Integrated resource of protein families, domains and functional sites
    prefix: DB-0052
    publications:
    - doi: 10.1093/nar/gkac993
      pubmed: '36350672'
    uri_format: https://www.ebi.ac.uk/interpro/entry/$1
  uri_format: https://www.ebi.ac.uk/interpro/entry/InterPro/$1
  wikidata:
    description: InterPro unique identifier
    example:
    - IPR000455
    - IPR001807
    - IPR039030
    homepage: https://www.ebi.ac.uk/interpro/
    name: InterPro ID
    pattern: ^IPR\d{6}$
    prefix: P2926
    uri_format: http://www.ebi.ac.uk/interpro/entry/$1
iobc:
  aberowl:
    description: 'Interlinking Ontology for Biological Concepts (IOBC) contains approximately
      80,000 biological concepts such as biological phenomena, diseases, molecular
      functions, gene products, chemicals, and medical cares, and approximately 20,000
      related concepts such as earth science and environmental science. The concepts
      are structured by thirty-five relations such as has function, has role, has
      quality, and precedes. Each concept has both of English and Japanese labels.
      For further information including the developmental method, see papers in the
      PUBLICATIONS PAGE. The license for this ontology is specified in the Creative
      Commons Attribution-NonCommercial 4.0 International. If you use data from this
      ontology, please be sure attribute this ontology as follows: "Interlinking Ontology
      for Biological Concepts © National Bioscience Database Center licensed under
      CC Attribution-NonCommercial 4.0 International".'
    download_owl: http://aber-owl.net/media/ontologies/IOBC/25/iobc.owl
    homepage: https://github.com/kushidat/IOBC
    name: Interlinking Ontology for Biological Concepts
    prefix: IOBC
    version: version 1.6.0
  bioportal:
    contact:
      email: kushida@biosciencedbc.jp
      name: Tatsuya Kushida
    description: 'Interlinking Ontology for Biological Concepts (IOBC) contains approximately
      80,000 biological concepts such as biological phenomena, diseases, molecular
      functions, gene products, chemicals, and medical cares, and approximately 20,000
      related concepts such as earth science and environmental science. The concepts
      are structured by thirty-five relations such as has function, has role, has
      quality, and precedes. Each concept has both of English and Japanese labels.
      For further information including the developmental method, see papers in the
      PUBLICATIONS PAGE. The license for this ontology is specified in the Creative
      Commons Attribution-NonCommercial 4.0 International. If you use data from this
      ontology, please be sure attribute this ontology as follows: "Interlinking Ontology
      for Biological Concepts © National Bioscience Database Center licensed under
      CC Attribution-NonCommercial 4.0 International".'
    homepage: https://github.com/kushidat/IOBC
    name: Interlinking Ontology for Biological Concepts
    prefix: IOBC
    publications:
    - http://purl.jp/bio/4/publications/iobc
    version: version 1.6.0
  contact:
    email: kushida@biosciencedbc.jp
    github: kushidatatsuya
    name: Tatsuya Kushida
    orcid: 0000-0002-0784-4113
  example: '200906038218908385'
  example_extras:
  - AC21_cat
  - AC21
  - OWLClass_00000000000000000321
  homepage: https://github.com/kushidat/IOBC
  license: CC-BY-NC-4.0
  mappings:
    aberowl: IOBC
    bioportal: IOBC
  prefix: iobc
  publications:
  - doi: 10.1007/s00354-019-00074-y
    pmc: null
    pubmed: null
    title: Interconnection of Biological Knowledge Using NikkajiRDF and Interlinking
      Ontology for Biological Concepts
    year: 2019
  repository: https://github.com/kushidat/IOBC
  uri_format: http://purl.jp/bio/4/id/$1
iofcore:
  download_owl: https://github.com/iofoundry/ontology/raw/refs/heads/master/core/Core.rdf
  example: hasSpecifiedOutput
  mappings:
    tib: iofcore
  prefix: iofcore
  repository: https://github.com/iofoundry/ontology
  tib:
    description: The IOF Core Ontology contains notions found to be common across
      multiple manufacturing domains. This file is an RDF implementation of these
      notions. The ontology utilizes the Basic Formal Ontology or BFO as a top-level
      ontology but also borrows terms from various domain-independent or mid-level
      ontologies. The purpose of the ontology is to serve as a foundation for ensuring
      consistency and interoperability across various domain-specific reference ontologies
      the IOF publishes.
    homepage: https://oagi.org/pages/Released-Ontologies
    keywords:
    - NFDI4ING
    - engineering
    name: Industrial Ontology Foundry (IOF) Core Ontology
    prefix: iofcore
    tracker: https://github.com/iofoundry/ontology/issues
    uri_format: https://spec.industrialontologies.org/ontology/core/Core/$1
    version.iri: https://spec.industrialontologies.org/ontology/202401/core/Core/
ioio:
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: An ontology of information entities about an individual
  download_owl: https://github.com/OpenLHS/IOIO/raw/refs/heads/main/IOIO.owl
  example: '0000001'
  homepage: https://openlhs.github.io/IOIO/
  name: Individual Organism Information Ontology
  pattern: ^\d{7}$
  prefix: ioio
  repository: https://github.com/OpenLHS/IOIO
  uri_format: http://purl.obolibrary.org/obo/IOIO_$1
ipi:
  biocontext:
    prefix: IPI
  deprecated: true
  integbio:
    alt_name: International Protein Index
    homepage: http://www.ebi.ac.uk/IPI/
    information_keywords:
    - Sequence
    maintainer: EMBL-EBI (European Bioinformatics Institute)
    name: IPI
    prefix: nbdc00911
    pubmeds:
    - '15221759'
    target_keywords:
    - Protein
  mappings:
    biocontext: IPI
    integbio: nbdc00911
    prefixcommons: ipi
  prefix: ipi
  prefixcommons:
    description: IPI provides a top level guide to the main databases that describe
      the proteomes of higher eukaryotic organisms. IPI maintaisn a database of cross
      references between the primary data sources, it provides minimally redundant
      but complete sets of proteins for featured species, and it maintains stable
      and unique identifiers.
    example: IPI00000001
    homepage: http://www.ebi.ac.uk/IPI
    keywords:
    - protein
    license: http://www.ebi.ac.uk/Information/termsofuse.html
    name: International Protein Index
    pattern: ^IPI\d{8}$
    prefix: ipi
    pubmed_ids:
    - '15221759'
    uri_format: http://www.ebi.ac.uk/cgi-bin/dbfetch?db=IPI&id=$1&format=default
  publications:
  - doi: 10.1002/pmic.200300721
    pmc: null
    pubmed: '15221759'
    title: 'The International Protein Index: an integrated database for proteomics
      experiments'
    year: 2004
  - doi: null
    pmc: null
    pubmed: '15221759'
    title: null
    year: null
  - doi: null
    pmc: null
    pubmed: '15221759'
    title: null
    year: null
irct:
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: 'Iranian Registry of Clinical Trials. This is a Primary Registry in
    the WHO Registry Network set up with the help from the Ministry of Health and
    Medical Education (MOHME) and hosted by Iran University of Medical Sciences (IUMS).
    (from homepage)

    Note that the website uses a different identifier then the one reported in this
    semantic space.'
  example: IRCT20080904001199N7
  homepage: https://en.irct.ir/
  name: Iranian Registry of Clinical Trials
  pattern: ^IRCT\d+N\d+$
  prefix: irct
  references:
  - https://en.irct.ir/trial/65035
ird.segment:
  biocontext:
    prefix: IRD.SEGMENT
  contact:
    email: richard.scheuermann@nih.gov
    github: scheuerm
    name: Richard H. Scheuermann
    orcid: 0000-0003-1355-892X
  mappings:
    biocontext: IRD.SEGMENT
    miriam: ird.segment
    n2t: ird.segment
    prefixcommons: ird.segment
  miriam:
    deprecated: false
    description: Influenza Research Database (IRD) contains information related to
      influenza virus, including genomic sequence, strain, protein, epitope  and bibliographic
      information. The Segment Details page contains descriptive information and annotation
      data about a particular genomic segment and its encoded product(s).
    homepage: http://www.fludb.org/
    id: '00000172'
    name: IRD Segment Sequence
    namespaceEmbeddedInLui: false
    pattern: ^\w+(\_)?\d+(\.\d+)?$
    prefix: ird.segment
    sampleId: CY077097
    uri_format: http://www.fludb.org/brc/fluSegmentDetails.do?ncbiGenomicAccession=$1
  n2t:
    description: Influenza Research Database (IRD) contains information related to
      influenza virus, including genomic sequence, strain, protein, epitope  and bibliographic
      information. The Segment Details page contains descriptive information and annotation
      data about a particular genomic segment and its encoded product(s).
    example: CY077097
    homepage: http://www.fludb.org/
    name: IRD at BioHealthBase
    namespaceEmbeddedInLui: false
    pattern: ^\w+(\_)?\d+(\.\d+)?$
    prefix: ird.segment
    uri_format: http://www.fludb.org/brc/fluSegmentDetails.do?ncbiGenomicAccession=$1
  prefix: ird.segment
  prefixcommons:
    description: Influenza Research Database (IRD) contains information related to
      influenza virus, including genomic sequence, strain, protein, epitope  and bibliographic
      information. The Segment Details page contains descriptive information and annotation
      data about a particular genomic segment and its encoded product(s).
    example: CY077097
    keywords:
    - gene
    - protein
    name: IRD Segment Sequence
    pattern: ^\w+(\_)?\d+(\.\d+)?$
    prefix: ird.segment
    pubmed_ids:
    - '17965094'
    uri_format: http://www.fludb.org/brc/fluSegmentDetails.do?ncbiGenomicAccession=$1
  publications:
  - doi: 10.1093/nar/gkm905
    pmc: PMC2238987
    pubmed: '17965094'
    title: 'BioHealthBase: informatics support in the elucidation of influenza virus
      host pathogen interactions and virulence'
    year: 2007
  - doi: null
    pmc: null
    pubmed: '17965094'
    title: null
    year: null
irefweb:
  biocontext:
    prefix: IREFWEB
  contact:
    email: shoshana@sickkids.ca
    github: null
    name: Shoshana J. Wodak
    orcid: 0000-0002-0701-6545
  fairsharing:
    abbreviation: iRefWeb
    description: 'iRefWeb is an interface to a relational database containing the
      latest build of the interaction Reference Index (iRefIndex) which integrates
      protein interaction data from ten different interaction databases: BioGRID,
      BIND, CORUM, DIP, HPRD, INTACT, MINT, MPPI, MPACT and OPHID.'
    homepage: http://wodaklab.org/iRefWeb/
    name: Interaction Reference Index Web Interface
    prefix: FAIRsharing.t31wcb
    publications:
    - doi: 10.1093/database/baq023
      pubmed_id: 20940177
      title: 'iRefWeb: interactive analysis of consolidated protein interaction data
        and their supporting evidence.'
    subjects:
    - Life Science
    twitter: wodaklab
  mappings:
    biocontext: IREFWEB
    fairsharing: FAIRsharing.t31wcb
    miriam: irefweb
    n2t: irefweb
    pathguide: '300'
    prefixcommons: irefweb
    re3data: r3d100012725
  miriam:
    deprecated: true
    description: 'iRefWeb is an interface to a relational database containing the
      latest build of the interaction Reference Index (iRefIndex) which integrates
      protein interaction data from ten different interaction databases: BioGRID,
      BIND, CORUM, DIP, HPRD, INTACT, MINT, MPPI, MPACT and OPHID. In addition, iRefWeb
      associates interactions with the PubMed record from which they are derived.'
    homepage: http://wodaklab.org/iRefWeb/
    id: '00000123'
    name: iRefWeb
    namespaceEmbeddedInLui: false
    pattern: ^\d+$
    prefix: irefweb
    sampleId: '617102'
    uri_format: http://wodaklab.org/iRefWeb/interaction/show/$1
  n2t:
    description: 'iRefWeb is an interface to a relational database containing the
      latest build of the interaction Reference Index (iRefIndex) which integrates
      protein interaction data from ten different interaction databases: BioGRID,
      BIND, CORUM, DIP, HPRD, INTACT, MINT, MPPI, MPACT and OPHID. In addition, iRefWeb
      associates interactions with the PubMed record from which they are derived.'
    example: '617102'
    homepage: http://wodaklab.org/iRefWeb/
    name: iRefWeb Protein Interaction Reference Index
    namespaceEmbeddedInLui: false
    pattern: ^\d+$
    prefix: irefweb
    uri_format: http://wodaklab.org/iRefWeb/interaction/show/$1
  pathguide:
    abbreviation: iRefWeb
    homepage: http://wodaklab.org/iRefWeb/
    keywords:
    - PSI-MI
    name: Interaction Reference Index Web Interface
    prefix: '300'
  prefix: irefweb
  prefixcommons:
    description: 'iRefWeb is an interface to a relational database containing the
      latest build of the interaction Reference Index (iRefIndex) which integrates
      protein interaction data from ten different interaction databases: BioGRID,
      BIND, CORUM, DIP, HPRD, INTACT, MINT, MPPI, MPACT and OPHID.'
    example: '617102'
    homepage: http://wodaklab.org/iRefWeb/
    keywords:
    - interaction
    - protein
    name: Interaction Reference Index Web Interface
    pattern: ^\d+$
    prefix: irefweb
    uri_format: http://wodaklab.org/iRefWeb/interaction/show/$1
  publications:
  - doi: 10.1093/database/baq023
    pmc: PMC2963317
    pubmed: '20940177'
    title: 'iRefWeb: interactive analysis of consolidated protein interaction data
      and their supporting evidence'
    year: 2010
  - doi: 10.1093/database/baq023
    pmc: null
    pubmed: null
    title: 'iRefWeb: interactive analysis of consolidated protein interaction data
      and their supporting evidence.'
    year: null
  - doi: 10.1093/database/baq023
    pmc: null
    pubmed: null
    title: 'iRefWeb: interactive analysis of consolidated protein interaction data
      and their supporting evidence.'
    year: null
  re3data:
    description: 'iRefWeb is an interface to a relational database containing the
      latest build of the interaction Reference Index (iRefIndex) which integrates
      protein interaction data from ten different interaction databases: BioGRID,
      BIND, CORUM, DIP, HPRD, INTACT, MINT, MPPI, MPACT and OPHID.'
    doi: 10.17616/R31B8K
    homepage: https://wodaklab.org/iRefWeb/
    name: iRefWeb
    prefix: r3d100012725
    synonyms:
    - Interaction Reference Index Web Interface
    xrefs:
      nif: 0000-20861
      omics: 02922
iresite:
  contact:
    email: martin.pospisek@natur.cuni.cz
    github: null
    name: Martin Pospíšek
    orcid: 0000-0002-9490-8911
  fairsharing:
    abbreviation: IRESite
    description: The IRESite database presents information about experimentally studied
      IRES (Internal Ribosome Entry Site) segments. IRES regions are known to attract
      the eukaryotic ribosomal translation initiation complex and thus promote translation
      initiation independently of the presence of the commonly utilized 5'-terminal
      7mG cap structure.
    homepage: http://www.iresite.org
    name: IRESite
    prefix: FAIRsharing.kd39j4
    publications:
    - doi: 10.1093/nar/gkj081
      pubmed_id: 16381829
      title: 'IRESite: the database of experimentally verified IRES structures (www.iresite.org).'
    - doi: 10.1093/nar/gkp981
      pubmed_id: 19917642
      title: IRESite--a tool for the examination of viral and cellular internal ribosome
        entry sites.
    subjects:
    - Life Science
  integbio:
    description: The IRESite database presents information about experimentally studied
      IRES (Internal Ribosome Entry Site) segments. IRES regions are known to attract
      the eukaryotic ribosomal translation initiation complex and thus promote translation
      initiation independently of the presence of the commonly utilized 5'-terminal
      7mG cap structure.
    fairsharing: FAIRsharing.kd39j4
    homepage: http://www.iresite.org
    information_keywords:
    - Sequence
    - Interaction/Pathway
    maintainer: Charles University
    name: IRESite
    prefix: nbdc01752
    pubmeds:
    - '16381829'
    - '19917642'
    status: Active
    target_keywords:
    - DNA
    - Protein
    - RNA
  mappings:
    fairsharing: FAIRsharing.kd39j4
    integbio: nbdc01752
    prefixcommons: iresite
  name: Database of experimentally verified IRES structures
  prefix: iresite
  prefixcommons:
    description: The IRESite database presents information about the experimentally
      studied IRES (Internal Ribosome Entry Site) segments. IRES regions are known
      to attract eukaryotic ribosomal translation initiation complex and thus promote
      translation initiation independently of the presence of the commonly utilized
      5'-terminal 7mG cap structure.
    example: '322'
    homepage: http://www.iresite.org
    keywords:
    - RNA
    - regulation
    name: 'IRESite: The database of experimentally verified IRES structures'
    pattern: ^\d+$
    prefix: iresite
    uri_format: http://www.iresite.org/IRESite_web.php?page=view&entry_id=$1
  publications:
  - doi: 10.1093/nar/gkp981
    pmc: PMC2808886
    pubmed: '19917642'
    title: IRESite--a tool for the examination of viral and cellular internal ribosome
      entry sites
    year: 2009
  - doi: 10.1093/nar/gkj081
    pmc: PMC1347444
    pubmed: '16381829'
    title: 'IRESite: the database of experimentally verified IRES structures (www.iresite.org)'
    year: 2006
  - doi: 10.1093/nar/gkj081
    pmc: null
    pubmed: null
    title: 'IRESite: the database of experimentally verified IRES structures (www.iresite.org).'
    year: null
  - doi: 10.1093/nar/gkp981
    pmc: null
    pubmed: null
    title: IRESite--a tool for the examination of viral and cellular internal ribosome
      entry sites.
    year: null
  reviewer:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
iro:
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  deprecated: true
  example: 0000008
  name: Insect Resistance Ontology
  pattern: ^\d{7}$
  prefix: iro
  uri_format: https://legacy.vectorbase.org/ontology-browser?cv=MIRO&t=IRO:$1
isbn:
  biocontext:
    prefix: ISBN-13
    uri_format: https://monarchinitiative.org/ISBN13_$1
  biolink:
    is_identifiers: false
    is_obo: false
    prefix: isbn
    uri_format: https://www.isbn-international.org/identifier/$1
  edam:
    description: The International Standard Book Number (ISBN) is for identifying
      printed books.
    name: ISBN
    obsolete: false
    prefix: '2634'
  example: '9789211613865'
  example_extras:
  - 978-92-1-161386-5
  go:
    homepage: https://www.worldcat.org
    name: International Standard Book Number
    prefix: ISBN
    uri_format: https://www.worldcat.org/search?q=bn%3A$1
  mappings:
    biocontext: ISBN-13
    biolink: isbn
    edam: '2634'
    go: ISBN
    miriam: isbn
    n2t: isbn
    prefixcommons: isbn
  miriam:
    deprecated: false
    description: The International Standard Book Number (ISBN) is for identifying
      printed books.
    homepage: http://www.worldcat.org/
    id: '00000064'
    name: ISBN
    namespaceEmbeddedInLui: false
    pattern: ^(ISBN)?(-13|-10)?[:]?[ ]?(\d{2,3}[ -]?)?\d{1,5}[ -]?\d{1,7}[ -]?\d{1,6}[
      -]?(\d|X)$
    prefix: isbn
    providers:
    - code: ''
      description: ISBNDB - ISBN Database
      homepage: http://isbndb.com/
      name: ISBNDB - ISBN Database
      uri_format: http://isbndb.com/search-all.html?kw=$1
    sampleId: '9781584885658'
    uri_format: http://www.worldcat.org/isbn/$1
  n2t:
    description: The International Standard Book Number (ISBN) is for identifying
      printed books.
    example: '9781584885658'
    homepage: http://isbndb.com/
    name: ISBNDB - ISBN Database
    namespaceEmbeddedInLui: false
    pattern: ^(ISBN)?(-13|-10)?[:]?[ ]?(\d{2,3}[ -]?)?\d{1,5}[ -]?\d{1,7}[ -]?\d{1,6}[
      -]?(\d|X)$
    prefix: isbn
    uri_format: http://isbndb.com/search-all.html?kw=$1
  prefix: isbn
  prefixcommons:
    description: The International Standard Book Number (ISBN) is for identifying
      printed books.
    example: '9781584885658'
    homepage: http://isbndb.com/
    keywords:
    - bibliography
    name: International Standard Book Number
    pattern: ^\d+$
    prefix: isbn
    uri_format: http://isbndb.com/search-all.html?kw=$1
  providers:
  - code: google.isbn
    description: Google Books provider for ISBN numbers
    example: null
    first_party: null
    homepage: https://books.google.com
    name: Google Books
    publications: null
    status: null
    uri_format: https://books.google.com/books?isbn=$1
  - code: isbnsearch
    description: ISBN Search is an unofficial search engine for ISBNs.
    example: null
    first_party: null
    homepage: https://isbnsearch.org
    name: ISBN Search
    publications: null
    status: null
    uri_format: https://isbnsearch.org/isbn/$1
  synonyms:
  - ISBN-10
  - ISBN-13
  uri_format: https://www.worldcat.org/isbn/$1
isced1997:
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: ISCED is designed to serve as a framework to classify educational activities
    as defined in programmes and the resulting qualifications into internationally
    agreed categories. The basic concepts and definitions of ISCED are therefore intended
    to be internationally valid and comprehensive of the full range of education systems.
  download_rdf:
    rdf_format: ttl
    url: https://github.com/dini-ag-kim/vocabs-edu/raw/refs/heads/master/isced-1997.ttl
  example: '1'
  github_request_issue: 1625
  homepage: https://ec.europa.eu/eurostat/statistics-explained/index.php?title=International_Standard_Classification_of_Education_(ISCED)
  keywords:
  - education level
  - open educational resources
  name: International Standard Classification of Education, 1997 Edition
  prefix: isced1997
  references:
  - https://uis.unesco.org/sites/default/files/documents/international-standard-classification-of-education-1997-en_0.pdf
  uri_format: https://w3id.org/kim/isced-1997/level$1
isced2011:
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: ISCED is designed to serve as a framework to classify educational activities
    as defined in programmes and the resulting qualifications into internationally
    agreed categories. The basic concepts and definitions of ISCED are therefore intended
    to be internationally valid and comprehensive of the full range of education systems.
  download_rdf:
    rdf_format: ttl
    url: https://github.com/dini-ag-kim/vocabs-edu/raw/refs/heads/master/isced-2011.ttl
  example: '1'
  github_request_issue: 1625
  homepage: https://ec.europa.eu/eurostat/statistics-explained/index.php?title=International_Standard_Classification_of_Education_(ISCED)
  keywords:
  - education level
  - open educational resources
  name: International Standard Classification of Education, 2011 Edition
  prefix: isced2011
  references:
  - https://uis.unesco.org/sites/default/files/documents/international-standard-classification-of-education-isced-2011-en.pdf
  uri_format: https://w3id.org/kim/isced-2011/level$1
isced2013:
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: ISCED is designed to serve as a framework to classify educational activities
    as defined in programmes and the resulting qualifications into internationally
    agreed categories. The basic concepts and definitions of ISCED are therefore intended
    to be internationally valid and comprehensive of the full range of education systems.
  download_rdf: https://github.com/dini-ag-kim/vocabs-edu/raw/refs/heads/master/isced-2013.ttl
  example: n0021
  github_request_issue: 1625
  homepage: https://ec.europa.eu/eurostat/statistics-explained/index.php?title=International_Standard_Classification_of_Education_(ISCED)
  keywords:
  - education level
  - open educational resources
  mappings:
    tib: isced
  name: International Standard Classification of Education, 2013 Edition
  prefix: isced2013
  references:
  - http://www.uis.unesco.org/Education/Documents/isced-fields-of-education-training-2013.pdf
  tib:
    description: 'The International Standard Classification of Education (ISCED) is
      a framework for assembling, compiling and analysing cross-nationally comparable
      statistics on education. ISCED Fields of Education and Training classifies education
      programmes and related qualifications by fields of study: A field is the `broad
      domain, branch or area of content covered by an education programme or qualification''.
      The International Standard Classification of Education is maintained by DG EMPL
      and published by the Publications Office of the European Union on the EU Vocabularies
      website.'
    homepage: https://op.europa.eu/de/home
    keywords:
    - Educational Resources
    name: 'International Standard Classification of Education: Fields of Education
      and Training 2013'
    prefix: isced
    uri_format: http://data.europa.eu/snb/isced-f/$1
  uri_format: https://w3id.org/kim/isced-2013/$1
ised:
  mappings:
    prefixcommons: ised
  prefix: ised
  prefixcommons:
    description: ISED catalogues the influenza sequence and epitope information obtained
      in countries worldwide and currently hosts a total of 49368 influenza A and
      4761 influenza B virus sequence data including pandemic A/H1N1 2009 virus sequences
      collected in 42 countries, and a total of 545 amantadine-resistant influenza
      virus sequences collected in Korea.
    example: AY209920
    homepage: http://influenza.korea.ac.kr
    keywords:
    - protein
    name: Influenza Sequence and Epitope Database
    pattern: ^[A-Z]+\d+$
    prefix: ised
isfinder:
  biocontext:
    prefix: ISFINDER
  contact:
    email: patricia.siguier@univ-tlse3.fr
    github: null
    name: Patricia Siguier
    orcid: 0000-0003-1620-6495
  fairsharing:
    abbreviation: IS Finder
    description: This database provides a list of insertion sequences (IS) isolated
      from bacteria and archae. It is organized into individual files containing their
      general features (name, size, origin, family.....) as well as their DNA and
      potential protein sequences. Some of the entries have been identified as individual
      elements by their insertion activities but a growing number are included from
      their description in sequenced bacterial genomes. It also includes certain transposons,
      in particular, members of the Tn3 family of replicative transposons.
    homepage: http://www-is.biotoul.fr
    name: Insertion Sequence Finder
    prefix: FAIRsharing.xhpc3h
    publications:
    - doi: 10.1093/nar/gkj014
      pubmed_id: 16381877
      title: 'ISfinder: the reference centre for bacterial insertion sequences'
    subjects:
    - Life Science
  integbio:
    description: IS FINDER is a database of bacterial and archaeal insertion sequences.
      The database contains sequence and position information on insertion elements.
      Links to external databases are provided for each entry.
    fairsharing: biodbcore-000296
    homepage: http://www-is.biotoul.fr/
    information_keywords:
    - Sequence
    - Taxonomy
    maintainer: Laboratoire de Microbiologie et Genetique Moleculaire
    name: IS FINDER
    prefix: nbdc00510
    pubmeds:
    - '16381877'
    status: Active
    target_keywords:
    - DNA
  mappings:
    biocontext: ISFINDER
    fairsharing: FAIRsharing.xhpc3h
    integbio: nbdc00510
    miriam: isfinder
    n2t: isfinder
    ncbi: ISFinder
    prefixcommons: isfinder
  miriam:
    deprecated: true
    description: ISfinder is a database of bacterial insertion sequences (IS). It
      assigns IS nomenclature and acts as a repository for ISs. Each IS is annotated
      with information such as the open reading frame DNA sequence, the sequence of
      the ends of the element and target sites, its origin and distribution together
      with a bibliography, where available.
    homepage: http://www-is.biotoul.fr/i
    id: '00000173'
    name: ISFinder
    namespaceEmbeddedInLui: false
    pattern: ^IS\w+(\-\d)?$
    prefix: isfinder
    sampleId: ISA1083-2
    uri_format: https://www-is.biotoul.fr/scripts/ficheIS.php?name=$1
  n2t:
    description: ISfinder is a database of bacterial insertion sequences (IS). It
      assigns IS nomenclature and acts as a repository for ISs. Each IS is annotated
      with information such as the open reading frame DNA sequence, the sequence of
      the ends of the element and target sites, its origin and distribution together
      with a bibliography, where available.
    example: ISA1083-2
    homepage: http://www-is.biotoul.fr/i
    name: IS Finder at CNRS
    namespaceEmbeddedInLui: false
    pattern: ^IS\w+(\-\d)?$
    prefix: isfinder
    uri_format: https://www-is.biotoul.fr/scripts/ficheIS.php?name=$1
  ncbi:
    example: ISA1083-2
    homepage: http://www-is.biotoul.fr/
    name: Insertion sequence elements database
    prefix: ISFinder
  prefix: isfinder
  prefixcommons:
    description: ISfinder is a database of bacterial insertion sequences (IS). It
      assigns IS nomenclature and acts as a repository for ISs. Each IS is annotated
      with information such as the open reading frame DNA sequence, the sequence of
      the ends of the element and target sites, its origin and distribution together
      with a bibliography, where available.
    example: ISA1083-2
    homepage: http://www-is.biotoul.fr
    keywords:
    - gene
    - sequence
    name: IS Finder
    pattern: ^IS\w+(\-\d)?$
    prefix: isfinder
    pubmed_ids:
    - '16381877'
    uri_format: http://www-is.biotoul.fr/index.html?is_special_name=$1
  publications:
  - doi: 10.1093/nar/gkj014
    pmc: PMC1347377
    pubmed: '16381877'
    title: 'ISfinder: the reference centre for bacterial insertion sequences'
    year: 2006
isni:
  bartoc:
    abbreviation: ISNI
    description: 'ISNI is the ISO certified global standard number for identifying
      the millions of contributors to creative works and those active in their distribution,
      including researchers, inventors, writers, artists, visual creators, performers,
      producers, publishers, aggregators, and more. As ISO 27729, it is part of a
      family of international standard identifiers that includes identifiers of works,
      recordings, products and right holders in all repertoires, e.g. DOI, ISAN, ISBN,
      ISRC, ISSN, and ISWC.


      The mission of the ISNI International Agency (ISNI-IA) is to assign to the public
      name(s) of a researcher, inventor, writer, artist, performer, publisher, etc.
      a persistent unique identifying number in order to resolve the problem of name
      ambiguity in search and discovery; and diffuse each assigned ISNI across all
      repertoires in the global supply chain so that every published work can be unambiguously
      attributed to its creator wherever that work is described.


      By achieving these goals, the ISNI will act as a bridge identifier across multiple
      domains and become a critical component in Linked Data and Semantic Web applications.'
    homepage: https://isni.org/
    license: http://rightsstatements.org/vocab/InC/1.0
    name: International Standard Name Identifier
    prefix: '20464'
  biolink:
    is_identifiers: false
    is_obo: false
    prefix: isni
    uri_format: https://isni.org/isni/$1
  mappings:
    bartoc: '20464'
    biolink: isni
    miriam: isni
    n2t: isni
    wikidata: P213
    wikidata.entity: Q423048
  miriam:
    deprecated: false
    description: "ISNI is the ISO certified global standard number for identifying\
      \ the millions of contributors to creative works and those active in their distribution,\
      \ including researchers, inventors, writers, artists, visual creators, performers,\
      \ producers, publishers, aggregators, and more. It is part of a family of international\
      \ standard identifiers that includes identifiers of works, recordings, products\
      \ and right holders in all repertoires, e.g. DOI, ISAN, ISBN, ISRC, ISSN, ISTC,\
      \ and ISWC.\r\n\r\nThe mission of the ISNI International Authority (ISNI-IA)\
      \ is to assign to the public name(s) of a researcher, inventor, writer, artist,\
      \ performer, publisher, etc. a persistent unique identifying number in order\
      \ to resolve the problem of name ambiguity in search and discovery; and diffuse\
      \ each assigned ISNI across all repertoires in the global supply chain so that\
      \ every published work can be unambiguously attributed to its creator wherever\
      \ that work is described."
    homepage: http://www.isni.org
    id: 00000684
    name: International Standard Name Identifier
    namespaceEmbeddedInLui: false
    pattern: ^[0-9]{15}[0-9X]{1}$
    prefix: isni
    sampleId: 000000012281955X
    uri_format: http://www.isni.org/isni/$1
  n2t:
    description: ISNI is the ISO certified global standard number for identifying
      the millions of contributors to creative works and those active in their distribution,
      including researchers, inventors, writers, artists, visual creators, performers,
      producers, publishers, aggregators, and more. It is part of a family of international
      standard identifiers that includes identifiers of works, recordings, products
      and right holders in all repertoires, e.g. DOI, ISAN, ISBN, ISRC, ISSN, ISTC,
      and ISWC.  The mission of the ISNI International Authority (ISNI-IA) is to assign
      to the public name(s) of a researcher, inventor, writer, artist, performer,
      publisher, etc. a persistent unique identifying number in order to resolve the
      problem of name ambiguity in search and discovery; and diffuse each assigned
      ISNI across all repertoires in the global supply chain so that every published
      work can be unambiguously attributed to its creator wherever that work is described.
    example: 000000012281955X
    homepage: http://www.isni.org
    name: International Standard Name Identifier
    namespaceEmbeddedInLui: false
    pattern: ^[0-9]{15}[0-9X]{1}$
    prefix: isni
    uri_format: http://www.isni.org/isni/$1
  name: International Standard Name Identifier
  prefix: isni
  providers:
  - code: isni.short
    description: Unqualified ISNI URI
    example: null
    first_party: null
    homepage: http://www.isni.org
    name: ISNI short
    publications: null
    status: null
    uri_format: http://www.isni.org/$1
  wikidata:
    database: Q423048
    description: International Standard Name Identifier for an identity. Starting
      with 0000.
    example:
    - 000000006629310X
    - '0000000103545207'
    - 0000000109397559
    - 0000000121430569
    - 0000000122974701
    - 0000000123317789
    - 0000000403855362
    name: ISNI
    pattern: ^[0]{7}[0-9]{8}[0-9X]$
    prefix: P213
    uri_format: https://isni.org/isni/$1
iso.3166:
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: An identifier for a country in numeric format per ISO 3166-1
  example: '554'
  homepage: https://www.iso.org/iso-3166-country-codes.html
  mappings:
    wikidata: P299
  name: ISO 3166-1 Country Code
  pattern: ^\d+$
  prefix: iso.3166
  wikidata:
    description: identifier for a country in numeric format per ISO 3166-1
    example:
    - '276'
    - '554'
    name: ISO 3166-1 numeric code
    prefix: P299
    uri_format: https://data.who.int/countries/$1
iso.639-3:
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: Since the introduction of ISO 639-3 in 2007, access to language information
    has increased tremendously. The code set initially adopted as ISO639-3:2007 was
    based on a harmonization of ISO 639-2 with the code set of SIL’s Ethnologue 15th
    edition and languages from Linguist List to form a comprehensive set of code elements
    for world languages.  SIL International, the Language Coding Agency for 639-3,
    relies on the contributions of linguists, language coding experts, and language
    users around the world to maintain and improve the code set through the change
    request process defined in the ISO 639 standard. [from homepage]
  example: spa
  fairsharing:
    abbreviation: ISO 639-3
    description: 'ISO 639-3 provides a comprehensive set of identifiers for all languages
      for use in a wide range of applications, including linguistics, lexicography
      and internationalization of information systems. It attempts to represent all
      known full languages. ISO 639 provides three language code sets: one is a two-letter
      code (ISO 639-1) and two others are three-letter codes (ISO 639-2 and ISO 639-3)
      for the representation of names of languages.  The three-letter codes in ISO
      639-2 and ISO 639-3 are complementary and compatible. The two codes have been
      devised for different purposes. The set of individual languages listed in ISO
      639-2 is a subset of those listed in ISO 639-3. The codes differ in that ISO
      639-2 includes code elements representing some individual languages and also
      collections of languages, while ISO 639-3 includes code elements for all known
      individual languages but not for collections of languages. Overall, the set
      of individual languages listed in ISO 639-3 is much larger than the set of individual
      languages listed in ISO 639-2.'
    homepage: https://www.iso.org/standard/39534.html
    name: 'ISO 639-3 Codes for the representation of names of languages - Part 3:
      Alpha-3 code for comprehensive coverage of languages'
    prefix: FAIRsharing.33aa85
    subjects:
    - Linguistics
    - Informatics
    - Computer Science
    user_defined_tags:
    - Language
  github_request_issue: 1614
  hl7:
    description: 'ISO 639-3 is a code that aims to define three-letter identifiers
      for all known human languages. At the core of ISO 639-3 are the individual languages
      already accounted for in ISO 639-2. The large number of living languages in
      the initial inventory of ISO 639-3 beyond those already included in ISO 639-2
      was derived primarily from Ethnologue (15th edition). Additional extinct, ancient,
      historic, and constructed languages have been obtained from Linguist List.SIL
      International has been designated as the ISO 639-3/RA for the purpose of processing
      requests for alpha-3 language codes comprising the International Standard, Codes
      for the representation of names of languages - Part 3: Alpha-3 code for comprehensive
      coverage of languages. The ISO 639-3/RA receives and reviews applications for
      requesting new language codes and for the change of existing ones according
      to criteria indicated in the standard. It maintains an accurate list of information
      associated with registered language codes which can be viewed on or downloaded
      from this website, and processes updates of registered language codes. Notification
      of pending and adopted updates are also distributed on a regular basis to subscribers
      and other parties.'
    homepage: http://www.sil.org/ISO639-3/
    name: ISO 639-3 Language Codes Alpha 3
    organization: SIL International
    preferred_prefix: iso639-3
    prefix: 1.0.639.3
    status: Complete
  homepage: https://iso639-3.sil.org/
  mappings:
    fairsharing: FAIRsharing.33aa85
    hl7: 1.0.639.3
  name: ISO 639 3-Letter Language Code
  prefix: iso.639-3
  providers:
  - code: loc
    description: ISO 639-2 is part of the ISO 639 language code family, which provides
      also a two-character code set (ISO 639-1) for the representation of names of
      languages. ISO 639-2 contains codes for all languages contained in ISO 639-1
      and several hundred additional languages. The ISO 639-2 (Bibliographic) codes
      were devised for use in bibliographic metadata, e.g., for libraries, information
      services, and publishers, and ISO 639-2 (Terminology) targets terminology, lexicography,
      and linguistic applications. The lists are the same except for 20 languages
      that have different Bibliographic and Terminology codes. The list contains over
      500 discrete codes. The ISO 639-2 (Bibliographic) codes are equivalent to the
      MARC Language Codes. The ISO 639-2 codes are linked to two-character codes for
      the same language in ISO 639-1, to the MARC Language Codes, and to equivalent
      codes for language groups in ISO 639-5. [from homepage]
    example: null
    first_party: null
    homepage: http://id.loc.gov/vocabulary/iso639-2
    name: 'ISO 639-2: Codes for the Representation of Names of Languages - Part 2:
      Alpha-3 Code for the Names of Languages'
    publications: null
    status: null
    uri_format: http://id.loc.gov/vocabulary/iso639-2/$1
  uri_format: https://iso639-3.sil.org/code/$1
iso15926:
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: The primary purpose of ISO 15926 is to provide a foundation ontology
    to support the integration and sharing of data related to the lifecycle of a process
    plant in such a way that it is consistent, unambiguous, and minimizing the number
    of ways something could be expressed. Further purpose of ISO 15926-14 is to meet
    needs for OWL 2 ontologies that are based on ISO 15926-2, that enable efficient
    reasoning and that capture lifecycle information. A specific purpose is to demonstrate
    lifecycle modelling through a representation of the lifecycle model of ISO/IEC
    81346-1. Another specific purpose is to exemplify how this standard can be used
    to develop industrial ontologies through various real-world use cases from industry.
    (from https://nfdi4cat.org/services/ontologie-sammlung/)
  download_rdf: https://github.com/uwasystemhealth/modular_ontologies/raw/master/LIS-14.ttl
  example: activityBoundOf
  homepage: https://15926.org/home/
  name: ISO 15926-14
  prefix: iso15926
  uri_format: http://standards.iso.org/iso/15926/part14/$1
isrctn:
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: The International Clinical Trials Registry Platform, originally called
    International Standard Randomised Controlled Trial Number (ISRCTN) registry, is
    a primary clinical study registry recognised by the World Health Organisation
    (WHO) and the International Committee of Medical Journal Editors (ICMJE) that
    accepts all clinical research studies (whether proposed, ongoing or completed),
    providing content validation and curation and the unique identification number
    necessary for publication. All study records in the database are freely accessible
    and searchable. (from homepage)
  domain: clinical trial
  example: ISRCTN10175490
  homepage: https://www.isrctn.com
  name: International Clinical Trials Registry Platform
  pattern: ^ISRCTN\d+$
  prefix: isrctn
  providers:
  - code: doi
    description: DOI resolution of ISRCTN
    example: null
    first_party: null
    homepage: https://doi.org/10.1186
    name: DOI
    publications: null
    status: null
    uri_format: https://doi.org/10.1186/$1
  - code: who
    description: WHO Clinical Trials Search
    example: null
    first_party: null
    homepage: https://trialsearch.who.int
    name: WHO Clinical Trials Search
    publications: null
    status: null
    uri_format: https://trialsearch.who.int/Trial2.aspx?TrialID=$1
  uri_format: https://www.isrctn.com/$1
issn:
  biocontext:
    prefix: ISSN
  biolink:
    is_identifiers: false
    is_obo: false
    prefix: issn
    uri_format: https://portal.issn.org/resource/ISSN/$1
  go:
    homepage: http://www.issn.org/
    name: International Standard Serial Number
    prefix: ISSN
  mappings:
    biocontext: ISSN
    biolink: issn
    go: ISSN
    miriam: issn
    n2t: issn
  miriam:
    deprecated: false
    description: The International Standard Serial Number (ISSN) is a unique eight-digit
      number used to identify a print or electronic periodical publication, rather
      than individual articles or books.
    homepage: https://portal.issn.org
    id: '00000301'
    name: ISSN
    namespaceEmbeddedInLui: false
    pattern: ^\d{4}-\d{3}[\dX]$
    prefix: issn
    providers:
    - code: ''
      description: ISSN at Library of Congress
      homepage: http://catalog.loc.gov
      name: ISSN at Library of Congress
      uri_format: https://search.catalog.loc.gov/search?option=keyword&query=$1
    sampleId: 0745-4570
    uri_format: https://portal.issn.org/resource/ISSN/$1
  n2t:
    description: The International Standard Serial Number (ISSN) is a unique eight-digit
      number used to identify a print or electronic periodical publication, rather
      than individual articles or books.
    example: 1776-3045
    homepage: https://portal.issn.org
    name: ISSN Portal
    namespaceEmbeddedInLui: false
    pattern: ^\d{4}-\d{3}[\dX]$
    prefix: issn
    uri_format: https://portal.issn.org/resource/ISSN/$1
  prefix: issn
istransbase:
  contact:
    email: oriental-cds@163.com
    github: null
    name: Dongsheng Cao
    orcid: null
  contributor:
    email: shah.tanay2@northeastern.edu
    github: tanayshah2
    name: Tanay Shah
    orcid: 0009-0001-1912-5132
  description: ISTransbase is a highly reliable and accessible database that focuses
    on inhibitors and substrates of drug transporters, offering a wealth of vital
    information encompassing experimental methods, transport parameters, and references.
  example: IST028
  github_request_issue: 1145
  homepage: https://istransbase.scbdd.com/
  name: ISTransbase
  prefix: istransbase
  publications:
  - doi: 10.1093/database/baae053
    pmc: PMC11214160
    pubmed: '38943608'
    title: 'ISTransbase: an online database for inhibitor and substrate of drug transporters'
    year: 2024
  reviewer:
    email: b.gyori@northeastern.edu
    github: bgyori
    name: Benjamin M. Gyori
    orcid: 0000-0001-9439-5346
  uri_format: https://istransbase.scbdd.com/database/trans/$1
itis:
  bartoc:
    description: ITIS is an easily accessible database with reliable information on
      species names and their hierarchical classification that is publicly accessible
      with unlimited free use. The database is reviewed periodically to ensure high
      quality with valid classifications, revisions, and additions of newly described
      species. The ITIS includes documented taxonomic information of flora and fauna
      from both aquatic and terrestrial habitats. For each scientific name, ITIS includes
      the authority, taxonomic rank, a unique taxonomic serial number, data source
      information, data quality indicators, and associated synonyms and vernacular
      names where available. Geographic coverage is worldwide, with an emphasis on
      North American taxa. The ITIS Web Services provide the ability to search and
      retrieve data from ITIS by providing access to the data behind the ITIS web
      site (http://www.itis.gov/web_service.html#). There is also web interface for
      viewing reports, and several options for text downloads. Each part of the basic
      WSDL web services is provided by a web service API, which defines the name,
      input to, and output from the service for a particular data request.
    homepage: https://www.itis.gov/
    name: Integrated Taxonomic Information System
    prefix: '17791'
    wikidata_database: Q82575
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: Information system with taxonomic data on plants, animals, fungi, and
    microbes of North America and the world.
  domain: taxonomy
  example: '589462'
  fairsharing:
    abbreviation: ITIS
    contact:
      email: itiswebmaster@itis.gov
      name: Gerald Guala
      orcid: 0000-0002-4972-3782
    description: The Integrated Taxonomic Information System (ITIS) provides taxonomic
      information on plants, animals, fungi, and microbes of North America and the
      world. The goal is to create an easily accessible database with reliable information
      on species names and their hierarchical classification. The database will be
      reviewed periodically to ensure high quality with valid classifications, revisions,
      and additions of newly described species. The ITIS includes documented taxonomic
      information of flora and fauna from both aquatic and terrestrial habitats.
    homepage: https://www.itis.gov/
    name: Integrated Taxonomic Information System
    prefix: FAIRsharing.t19hpa
    publications: []
    subjects:
    - Taxonomy
    - Biodiversity
    - Life Science
  homepage: https://www.itis.gov/
  integbio:
    description: ITIS is a database of taxonomic nomenclature and information used
      in biodiversity and ecosystem preservation programs. The database contains information
      on species and serves as a respository for biodiversity information for US government
      programs. The database can be searched by taxon or hierarchically, and taxonomic
      data can be downloaded.
    fairsharing: biodbcore-000597
    homepage: http://www.itis.gov
    information_keywords:
    - Ontology/Terminology/Nomenclature
    - Bibliography/Documents
    - Taxonomy
    - Repository
    maintainer: Integrated Taxonomic Information System
    name: ITIS
    prefix: nbdc00916
    status: Active
    target_keywords:
    - Organism
  license: CC0-1.0
  logo: https://www.itis.gov/Static/images/ITIS-Logo.jpg
  mappings:
    bartoc: '17791'
    fairsharing: FAIRsharing.t19hpa
    integbio: nbdc00916
    re3data: r3d100011213
    wikidata: P815
    wikidata.entity: Q82575
  name: Integrated Taxonomic Information System
  pattern: ^\d+$
  prefix: itis
  re3data:
    description: Here you will find authoritative taxonomic information on plants,
      animals, fungi, and microbes of North America and the world.
    doi: 10.17616/R32W4W
    homepage: https://www.itis.gov/
    name: ITIS
    prefix: r3d100011213
    synonyms:
    - Integrated Taxonomic Information System
  uri_format: https://www.itis.gov/servlet/SingleRpt/SingleRpt?search_topic=TSN&search_value=$1
  wikidata:
    description: identifier for a taxon in the Integrated Taxonomic Information System
    example:
    - '160330'
    - '162003'
    homepage: https://www.itis.gov
    name: ITIS TSN
    pattern: ^[1-9]\d{1,6}$
    prefix: P815
    uri_format: https://www.itis.gov/servlet/SingleRpt/SingleRpt?search_topic=TSN&search_value=$1
itmctr:
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: The International Traditional Medicine Clinical Trial Registry (ITMCTR)
    is a non-profit online register of clinical trials being conducted in the field
    of traditional medicine. It isoperated by the China Academy of Chinese Medical
    Sciences and The China Center For Evidence Based Traditional Chinese Medicine.
    It is recognized as a Primary Registry of WHO, and contributes data to the WHO
    ICTRP. (from website)
  domain: clinical trial
  example: ITMCTR2023000002
  homepage: http://itmctr.ccebtcm.org.cn
  logo: http://itmctr.ccebtcm.org.cn/Content/images/ny_logo.png
  name: International Traditional Medicine Clinical Trial Registry
  pattern: ^ITMCTR\d+$
  prefix: itmctr
ito:
  aberowl:
    description: 'The Intelligence Task Ontology and Knowledge Graph (ITO) provides
      a comprehensive, curated model of artificial intelligence tasks, benchmarks
      and benchmark results, including the biomedical domain. NOTE: The version uploaded
      to BioPortal has all instances and benchmark data removed because of performance
      issues with the BioPortal class browser. Please refer to https://github.com/OpenBioLink/ITO/
      for downloading the full version of the ontology and dataset.'
    download_owl: http://aber-owl.net/media/ontologies/ITO/17/ito.owl
    homepage: https://github.com/OpenBioLink/ITO/
    name: Intelligence Task Ontology
    prefix: ITO
    version: 1.12 (PWC export dated 2022-07-30) - internal, just a minor fix
  banana: ITO
  banana_peel: _
  bioportal:
    description: 'The Intelligence Task Ontology and Knowledge Graph (ITO) provides
      a comprehensive, curated model of artificial intelligence tasks, benchmarks
      and benchmark results, including the biomedical domain. NOTE: The version uploaded
      to BioPortal has all instances and benchmark data removed because of performance
      issues with the BioPortal class browser. Please refer to https://github.com/OpenBioLink/ITO/
      for downloading the full version of the ontology and dataset.'
    homepage: https://github.com/OpenBioLink/ITO/
    name: Intelligence Task Ontology
    prefix: ITO
    version: 1.12 (PWC export dated 2022-07-30) - internal, just a minor fix
  example: '01625'
  fairsharing:
    abbreviation: ITO
    contact:
      email: matthias.samwald@meduniwien.ac.at
      name: Matthias Samwald
      orcid: 0000-0002-4855-2571
    description: 'The Intelligence Task Ontology and Knowledge Graph (ITO) provides
      comprehensive, curated and interlinked data of artificial intelligence tasks,
      benchmarks, AI performance metrics, benchmark results and research papers. ITO
      ontology aims to support 1) Manual curation of AI task classification hierarchies
      and performance metrics, enabling more precise analyses; 2) Representing data
      as a graph, facilitating network-based query and analysis; 3) Allowing for easy
      integration and enrichment with external data, as well as simple extensibility
      for modeling related knowledge domains from other domains; 4) Allowing for automated
      deductive inference and automated knowledge base consistency checking; 5) Allowing
      for ongoing, collaborative expert curation of underlying ontological models.
      ITO aims to enable precise and network-based analyses of the global landscape
      of AI tasks and capabilities based on technologies that allow for easy integration
      and enrichment with external data, automated inference and continuous, collaborative
      expert curation of underlying ontological models. '
    domains:
    - Machine Learning
    - Natural Language Processing
    homepage: https://github.com/OpenBioLink/ITO
    license: CC-BY-4.0
    name: Intelligence Task Ontology and Knowledge Graph
    prefix: FAIRsharing.89e853
    publications:
    - doi: 10.48550/arxiv.2110.01434
      title: A curated, ontology-based, large-scale knowledge graph of artificial
        intelligence tasks and benchmarks
      year: 2021
    - doi: 10.1038/s41597-022-01435-x
      title: A curated, ontology-based, large-scale knowledge graph of artificial
        intelligence tasks and benchmarks
      year: 2022
    - doi: 10.5281/zenodo.5561989
      title: Intelligence Task Ontology and Knowledge Graph (ITO)
      year: 2022
    subjects:
    - Artificial Intelligence
  homepage: https://openbiolink.github.io/ITOExplorer/
  mappings:
    aberowl: ITO
    bioportal: ITO
    fairsharing: FAIRsharing.89e853
    miriam: ito
  miriam:
    deprecated: false
    description: The Intelligence Task Ontology (ITO) provides a comprehensive map
      of machine intelligence tasks, as well as broader human intelligence or hybrid
      human/machine intelligence tasks.
    homepage: https://bioportal.bioontology.org/
    id: 00000802
    name: Intelligence Task Ontology
    namespaceEmbeddedInLui: false
    pattern: ^.+$
    prefix: ito
    sampleId: ITO_01625
    uri_format: https://bioportal.bioontology.org/ontologies/ITO/?p=classes&conceptid=https://identifiers.org/ito:$1
  pattern: ^\d+$
  prefix: ito
  publications:
  - doi: 10.1038/s41597-022-01435-x
    pmc: PMC9205953
    pubmed: '35715466'
    title: A curated, ontology-based, large-scale knowledge graph of artificial intelligence
      tasks and benchmarks
    year: 2022
  - doi: 10.5281/zenodo.5561989
    pmc: null
    pubmed: null
    title: Intelligence Task Ontology and Knowledge Graph (ITO)
    year: 2022
  - doi: 10.48550/arxiv.2110.01434
    pmc: null
    pubmed: null
    title: A curated, ontology-based, large-scale knowledge graph of artificial intelligence
      tasks and benchmarks
    year: 2021
  repository: https://github.com/OpenBioLink/ITO
  uri_format: https://bioportal.bioontology.org/ontologies/ITO/?p=classes&conceptid=https://identifiers.org/ito:ITO_$1
iuphar.family:
  biocontext:
    prefix: IUPHAR.FAMILY
  license: CC-BY-SA-4.0
  mappings:
    biocontext: IUPHAR.FAMILY
    miriam: iuphar.family
    n2t: iuphar.family
    prefixcommons: iuphar.family
  miriam:
    deprecated: false
    description: The IUPHAR Compendium details the molecular, biophysical and pharmacological
      properties of identified mammalian sodium, calcium and potassium channels, as
      well as the related cyclic nucleotide-modulated ion channels and the recently
      described transient receptor potential channels. It includes information on
      nomenclature systems, and on inter and intra-species molecular structure variation.
      This collection references families of receptors or subunits.
    homepage: http://www.guidetopharmacology.org/
    id: '00000317'
    name: IUPHAR family
    namespaceEmbeddedInLui: false
    pattern: ^\d+$
    prefix: iuphar.family
    sampleId: '78'
    uri_format: http://www.guidetopharmacology.org/GRAC/FamilyDisplayForward?familyId=$1
  n2t:
    description: The IUPHAR Compendium details the molecular, biophysical and pharmacological
      properties of identified mammalian sodium, calcium and potassium channels, as
      well as the related cyclic nucleotide-modulated ion channels and the recently
      described transient receptor potential channels. It includes information on
      nomenclature systems, and on inter and intra-species molecular structure variation.
      This collection references families of receptors or subunits.
    example: '78'
    homepage: http://www.guidetopharmacology.org/
    name: The IUPHAR/BPS Guide to PHARMACOLOGY
    namespaceEmbeddedInLui: false
    pattern: ^\d+$
    prefix: iuphar.family
    uri_format: http://www.guidetopharmacology.org/GRAC/FamilyDisplayForward?familyId=$1
  prefix: iuphar.family
  prefixcommons:
    description: IUPHAR G protein-coupled receptors database
    example: '78'
    homepage: http://www.iuphar-db.org/DATABASE/ReceptorFamiliesForward?type=GPCR
    keywords:
    - protein
    name: G protein-coupled receptors database
    pattern: ^\d+$
    prefix: iuphar.family
    synonyms:
    - iuphar.gpcr
    uri_format: http://www.iuphar-db.org/DATABASE/FamilyIntroductionForward?familyId=$1
  synonyms:
  - IUPHARfam
iuphar.ligand:
  biocontext:
    prefix: IUPHAR.LIGAND
  biolink:
    is_identifiers: false
    is_obo: false
    prefix: GTOPDB
    uri_format: https://www.guidetopharmacology.org/GRAC/LigandDisplayForward?ligandId=$1
  license: CC-BY-SA-4.0
  mappings:
    biocontext: IUPHAR.LIGAND
    biolink: GTOPDB
    miriam: iuphar.ligand
    n2t: iuphar.ligand
    togoid: IupharLigand
    wikidata: P595
  miriam:
    deprecated: false
    description: The IUPHAR Compendium details the molecular, biophysical and pharmacological
      properties of identified mammalian sodium, calcium and potassium channels, as
      well as the related cyclic nucleotide-modulated ion channels and the recently
      described transient receptor potential channels. It includes information on
      nomenclature systems, and on inter and intra-species molecular structure variation.
      This collection references ligands.
    homepage: http://www.guidetopharmacology.org/GRAC/LigandListForward?database=all
    id: '00000457'
    name: IUPHAR ligand
    namespaceEmbeddedInLui: false
    pattern: ^\d+$
    prefix: iuphar.ligand
    sampleId: '1755'
    uri_format: http://www.guidetopharmacology.org/GRAC/LigandDisplayForward?ligandId=$1
  n2t:
    description: The IUPHAR Compendium details the molecular, biophysical and pharmacological
      properties of identified mammalian sodium, calcium and potassium channels, as
      well as the related cyclic nucleotide-modulated ion channels and the recently
      described transient receptor potential channels. It includes information on
      nomenclature systems, and on inter and intra-species molecular structure variation.
      This collection references ligands.
    example: '1755'
    homepage: http://www.guidetopharmacology.org/GRAC/LigandListForward?database=all
    name: IUPHAR ligand at University of Edinburgh
    namespaceEmbeddedInLui: false
    pattern: ^\d+$
    prefix: iuphar.ligand
    uri_format: http://www.guidetopharmacology.org/GRAC/LigandDisplayForward?ligandId=$1
  name: Guide to Pharmacology Ligand
  prefix: iuphar.ligand
  synonyms:
  - IUPHAR_LIGAND
  - IUPHAR_LIGAND_ID
  togoid:
    examples:
    - '11152'
    - '2355'
    - '2870'
    - '4047'
    - '50'
    - '5714'
    - '6382'
    - '7792'
    - '8339'
    - '965'
    keywords:
    - Compound
    name: IUPHAR ligand
    pattern: ^(?\d+)$
    prefix: IupharLigand
    uri_format: http://identifiers.org/iuphar.ligand/$1
  wikidata:
    description: ligand identifier of the Guide to Pharmacology database
    example:
    - '1627'
    - '2286'
    - '5'
    homepage: https://www.guidetopharmacology.org/
    name: Guide to Pharmacology Ligand ID
    pattern: ^\d{1,4}$
    prefix: P595
    uri_format: https://www.guidetopharmacology.org/GRAC/LigandDisplayForward?ligandId=$1
iuphar.receptor:
  biocontext:
    prefix: IUPHAR.RECEPTOR
  contact:
    email: simon.harding@igmm.ed.ac.uk
    github: simondharding
    name: Simon Douglas Harding
    orcid: 0000-0002-9262-8318
  go:
    homepage: http://www.iuphar.org/
    name: International Union of Pharmacology
    prefix: IUPHAR_RECEPTOR
    uri_format: https://www.guidetopharmacology.org/GRAC/ObjectDisplayForward?objectId=$1
  license: CC-BY-SA-4.0
  mappings:
    biocontext: IUPHAR.RECEPTOR
    go: IUPHAR_RECEPTOR
    miriam: iuphar.receptor
    n2t: iuphar.receptor
    uniprot: DB-0182
    wikidata: P5458
  miriam:
    deprecated: false
    description: The IUPHAR Compendium details the molecular, biophysical and pharmacological
      properties of identified mammalian sodium, calcium and potassium channels, as
      well as the related cyclic nucleotide-modulated ion channels and transient receptor
      potential channels. It includes information on nomenclature systems, and on
      inter and intra-species molecular structure variation. This collection references
      individual receptors or subunits.
    homepage: http://www.guidetopharmacology.org/targets.jsp
    id: 00000281
    name: IUPHAR receptor
    namespaceEmbeddedInLui: false
    pattern: ^\d+$
    prefix: iuphar.receptor
    sampleId: '101'
    uri_format: http://www.guidetopharmacology.org/GRAC/ObjectDisplayForward?objectId=$1
  n2t:
    description: The IUPHAR Compendium details the molecular, biophysical and pharmacological
      properties of identified mammalian sodium, calcium and potassium channels, as
      well as the related cyclic nucleotide-modulated ion channels and transient receptor
      potential channels. It includes information on nomenclature systems, and on
      inter and intra-species molecular structure variation. This collection references
      individual receptors or subunits.
    example: '101'
    homepage: http://www.guidetopharmacology.org/targets.jsp
    name: IUPHAR Receptor at University of Edinburgh
    namespaceEmbeddedInLui: false
    pattern: ^\d+$
    prefix: iuphar.receptor
    uri_format: http://www.guidetopharmacology.org/GRAC/ObjectDisplayForward?objectId=$1
  name: Guide to Pharmacology Target
  prefix: iuphar.receptor
  publications:
  - doi: 10.1093/nar/gkab1010
    pmc: PMC8689838
    pubmed: '34718737'
    title: 'The IUPHAR/BPS guide to PHARMACOLOGY in 2022: curating pharmacology for
      COVID-19, malaria and antibacterials'
    year: 2022
  - doi: 10.1111/j.1476-5381.2012.02141.x
    pmc: PMC3575771
    pubmed: '23003568'
    title: GuideToPharmacology.org--an update
    year: 2012
  synonyms:
  - IUPHAR_GPCR
  - IUPHARobj
  uniprot:
    abbreviation: GuidetoPHARMACOLOGY
    category: Chemistry databases
    homepage: https://www.guidetopharmacology.org
    name: IUPHAR/BPS Guide to PHARMACOLOGY
    prefix: DB-0182
    publications:
    - doi: 10.1093/nar/gkab1010
      pubmed: '34718737'
    uri_format: https://www.guidetopharmacology.org/GRAC/ObjectDisplayForward?objectId=$1
  wikidata:
    description: target identifier of the Guide to Pharmacology database
    example:
    - '1'
    - '214'
    - '620'
    homepage: https://www.guidetopharmacology.org/GRAC/
    name: Guide to Pharmacology Target ID
    pattern: ^[1-9]\d{0,3}$
    prefix: P5458
    uri_format: https://www.guidetopharmacology.org/GRAC/ObjectDisplayForward?objectId=$1
ivdb:
  mappings:
    prefixcommons: ivdb
  prefix: ivdb
  prefixcommons:
    description: IVDB hosts complete genome sequences of influenza A virus generated
      by BGI and curates all other published influenza virus sequences after expert
      annotations. IVDB provides a series of tools and viewers for analyzing the viral
      genomes, genes, genetic polymorphisms and phylogenetic relationships comparatively.
    example: E13035
    homepage: http://influenza.psych.ac.cn/
    keywords:
    - genome
    - DNA
    - gene
    name: Influenza Virus Database
    pattern: ^[A-Z]+\d+$
    prefix: ivdb
    uri_format: http://influenza.psych.ac.cn/search/detail.jsp?segment.gb_id=$1
jaxmice:
  biocontext:
    prefix: JAXMICE
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: A catalogue of mouse strains supplied by The Jackson Laboratory. Each
    identifier corresponds to a mouse strain.
  example: '004435'
  fairsharing:
    abbreviation: JAX
    description: JAX® Mice are the industry standard for animal model research, using
      precise genome solutions to better understand human disease. Our rigorous Animal
      Health Programs and stringent genetic quality standards ensure the reproducibility
      and validity of your experimental data.
    homepage: http://jaxmice.jax.org/
    license: http://opendatacommons.org/licenses/pddl/1.0
    name: JAX Mice Database
    prefix: FAIRsharing.5701h1
    publications: []
    subjects:
    - Life Science
  homepage: https://mice.jax.org
  mappings:
    biocontext: JAXMICE
    fairsharing: FAIRsharing.5701h1
    miriam: jaxmice
    n2t: jaxmice
    rrid: IMSR_JAX
  miriam:
    deprecated: false
    description: JAX Mice is a catalogue of mouse strains supplied by the Jackson
      Laboratory.
    homepage: http://jaxmice.jax.org/
    id: '00000337'
    name: JAX Mice
    namespaceEmbeddedInLui: false
    pattern: ^\d+$
    prefix: jaxmice
    sampleId: '005012'
    uri_format: http://jaxmice.jax.org/strain/$1.html
  n2t:
    description: JAX Mice is a catalogue of mouse strains supplied by the Jackson
      Laboratory.
    example: '005012'
    homepage: http://jaxmice.jax.org/
    name: JAX Mice at Jackson Laboratory
    namespaceEmbeddedInLui: false
    pattern: ^\d+$
    prefix: jaxmice
    uri_format: http://jaxmice.jax.org/strain/$1.html
  name: Jackson Laboratories Mouse Strain
  pattern: ^\d{6}$
  prefix: jaxmice
  rrid:
    abbreviation: JAX, JAX MS, JMS,IMSR_JAX
    homepage: https://www.jax.org/jax-mice-and-services
    keywords:
    - gene
    - genetic engineering
    - knockout
    - mice
    - model
    - mouse
    - repository
    - research
    - strain
    - subject
    - supply
    name: JAX Mice and Services
    prefix: IMSR_JAX
    scr: 016408
    twitter: jacksonlab
  synonyms:
  - jax
  - jaxMiceUID
  uri_format: https://www.jax.org/strain/$1
jcggdb:
  biocontext:
    prefix: JCGGDB
  integbio:
    description: This site is a search tool of JCGGDB which is a database of glycan-related
      data in Japan. It allows to search glycan structures using the monosaccharide
      symbol defined by the Consortium for Functional Glycomics (CFG) in U.S.A.
    homepage: https://jcggdb.jp/idb/flash/GlycoEditor.jsp
    information_keywords:
    - Image/Movie
    - Chemical structure
    maintainer: AIST (National Institute of Advanced Industrial Science and Technology)
    name: JCGGDB
    prefix: nbdc01164
    status: Active
    target_keywords:
    - Carbohydrate
  mappings:
    biocontext: JCGGDB
    integbio: nbdc01164
    miriam: jcggdb
    n2t: jcggdb
  miriam:
    deprecated: true
    description: JCGGDB (Japan Consortium for Glycobiology and Glycotechnology DataBase)
      is a database that aims to integrate all glycan-related data held in various
      repositories in Japan. This includes databases for large-quantity synthesis
      of glycogenes and glycans, analysis and detection of glycan structure and glycoprotein,
      glycan-related differentiation markers, glycan functions, glycan-related diseases
      and transgenic and knockout animals, etc.
    homepage: http://jcggdb.jp/index_en.html
    id: 00000479
    name: JCGGDB
    namespaceEmbeddedInLui: false
    pattern: ^JCGG-STR\d{6}$
    prefix: jcggdb
    sampleId: JCGG-STR008690
    uri_format: http://jcggdb.jp/idb/jcggdb/$1
  n2t:
    description: JCGGDB (Japan Consortium for Glycobiology and Glycotechnology DataBase)
      is a database that aims to integrate all glycan-related data held in various
      repositories in Japan. This includes databases for large-quantity synthesis
      of glycogenes and glycans, analysis and detection of glycan structure and glycoprotein,
      glycan-related differentiation markers, glycan functions, glycan-related diseases
      and transgenic and knockout animals, etc.
    example: JCGG-STR008690
    homepage: http://jcggdb.jp/index_en.html
    name: JCGGDB at Advanced Science Institute (Japan)
    namespaceEmbeddedInLui: false
    pattern: ^JCGG-STR\d{6}$
    prefix: jcggdb
    uri_format: http://jcggdb.jp/idb/jcggdb/$1
  name: Japan Consortium for Glycobiology and Glycotechnology Database
  prefix: jcggdb
jcm:
  biocontext:
    prefix: JCM
  fairsharing:
    abbreviation: JCM
    description: The Japan Collection of Microorganisms (JCM) collects, catalogues,
      and distributes cultured microbial strains, restricted to those classified in
      Risk Group 1 or 2.
    homepage: http://www.jcm.riken.go.jp/
    name: Japan Collection of Microorganisms
    prefix: FAIRsharing.h2wrt2
    publications: []
    subjects:
    - Life Science
  mappings:
    biocontext: JCM
    fairsharing: FAIRsharing.h2wrt2
    miriam: jcm
    n2t: jcm
    ncbi: JCM
    prefixcommons: jcm
  miriam:
    deprecated: false
    description: The Japan Collection of Microorganisms (JCM) collects, catalogues,
      and distributes cultured microbial strains, restricted to those classified in
      Risk Group 1 or 2.
    homepage: http://www.jcm.riken.go.jp/
    id: '00000174'
    name: Japan Collection of Microorganisms
    namespaceEmbeddedInLui: false
    pattern: ^\d+$
    prefix: jcm
    sampleId: '17254'
    uri_format: http://www.jcm.riken.go.jp/cgi-bin/jcm/jcm_number?JCM=$1
  n2t:
    description: The Japan Collection of Microorganisms (JCM) collects, catalogues,
      and distributes cultured microbial strains, restricted to those classified in
      Risk Group 1 or 2.
    example: '17254'
    homepage: http://www.jcm.riken.go.jp/
    name: JCM at RIKEN BioResource Center
    namespaceEmbeddedInLui: false
    pattern: ^\d+$
    prefix: jcm
    uri_format: http://www.jcm.riken.go.jp/cgi-bin/jcm/jcm_number?JCM=$1
  ncbi:
    example: '1339'
    homepage: http://www.jcm.riken.go.jp/
    name: Japan Collection of Microorganisms
    prefix: JCM
  prefix: jcm
  prefixcommons:
    description: The Japan Collection of Microorganisms (JCM) collects, catalogues,
      and distributes cultured microbial strains, restricted to those classified in
      Risk Group 1 or 2.
    example: '17254'
    homepage: http://www.jcm.riken.go.jp/
    keywords:
    - microbial
    - taxonomy
    name: Japan Collection of Microorganisms
    pattern: ^\d+$
    prefix: jcm
    uri_format: http://www.jcm.riken.go.jp/cgi-bin/jcm/jcm_number?JCM=$1
jcrb:
  cellosaurus:
    category: Cell line collections (Providers)
    homepage: https://cellbank.nibiohn.go.jp/english/
    name: Japanese Collection of Research Bioresources Cell Bank
    prefix: JCRB
    uri_format: https://cellbank.nibiohn.go.jp//~cellbank/en/search_res_det.cgi?RNO=$1
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  example: JCRB1355
  homepage: https://cellbank.nibiohn.go.jp
  mappings:
    cellosaurus: JCRB
  name: JRBC Cell Bank
  pattern: ^JCRB\d+$
  prefix: jcrb
  uri_format: https://cellbank.nibiohn.go.jp/~cellbank/en/search_res_det.cgi?RNO=$1
jcsd:
  biocontext:
    prefix: JCSD
  contributor_extras:
  - email: b.gyori@northeastern.edu
    github: bgyori
    name: Benjamin M. Gyori
    orcid: 0000-0001-9439-5346
  mappings:
    biocontext: JCSD
    miriam: jcsd
    n2t: jcsd
    prefixcommons: nikkaji
  miriam:
    deprecated: false
    description: The Japan Chemical Substance Dictionary is an organic compound dictionary
      database prepared by the Japan Science and Technology Agency (JST).
    homepage: http://jglobal.jst.go.jp/en/
    id: '00000241'
    name: Japan Chemical Substance Dictionary
    namespaceEmbeddedInLui: false
    pattern: ^J\d{1,3}(\.\d{3})?(\.\d{1,3})?[A-Za-z]$
    prefix: jcsd
    sampleId: J55.713G
    uri_format: http://jglobal.jst.go.jp/en/redirect?Nikkaji_No=$1
  n2t:
    description: The Japan Chemical Substance Dictionary is an organic compound dictionary
      database prepared by the Japan Science and Technology Agency (JST).
    example: J55.713G
    homepage: http://jglobal.jst.go.jp/en/
    name: Japan Chemical Substance Dictionary
    namespaceEmbeddedInLui: false
    pattern: ^J\d{1,3}(\.\d{3})?(\.\d{1,3})?[A-Za-z]$
    prefix: jcsd
    uri_format: http://jglobal.jst.go.jp/en/redirect?Nikkaji_No=$1
  prefix: jcsd
  prefixcommons:
    description: an organic compound dictionary database prepared by the Japan Science
      and Technology Agency (JST).
    example: J818D
    homepage: http://nikkajiweb.jst.go.jp/nikkaji_web/pages/top_e.jsp
    keywords:
    - drug
    license: http://nikkajiweb.jst.go.jp/nikkaji_web/pages/top_e.jsp
    name: Japan Chemical Substance Dictionary (Nikkaji)
    pattern: ^J\d+$
    prefix: nikkaji
  providers:
  - code: stirdf
    description: Appears in iobc
    example: null
    first_party: null
    homepage: http://stirdf.jst.go.jp
    name: Unknown
    publications: null
    status: null
    uri_format: http://stirdf.jst.go.jp/cde/nikkaji/$1
  synonyms:
  - Nikkaji number
  - nikkaji
jecfa:
  contact:
    email: kpetersen@who.int
    github: null
    name: Kim Petersen
    orcid: null
  contributor:
    email: m.naguthana@hotmail.com
    github: nagutm
    name: Mufaddal Naguthanawala
    orcid: 0009-0009-5240-7463
  description: JECFA provides identifiers for flavors, food additives, contaminants,
    toxicants, and veterinary drugs. Each entry includes chemical details, acceptable
    or tolerable intake limits, and links to related reports and monographs.
  example: '2116'
  github_request_issue: 1247
  homepage: https://apps.who.int/food-additives-contaminants-jecfa-database
  mappings:
    wikidata: P9557
  name: Joint FAO/WHO Expert Committee on Food Additives
  pattern: ^\d+$
  prefix: jecfa
  reviewer:
    email: b.gyori@northeastern.edu
    github: bgyori
    name: Benjamin M. Gyori
    orcid: 0000-0001-9439-5346
  wikidata:
    description: identifier for food additives assigned by Joint FAO/WHO Expert Committee
      on Food Additives
    example:
    - '1'
    - '1851'
    - '2'
    - '3'
    - '4'
    name: JECFA number
    pattern: ^[1-9]\d*$
    prefix: P9557
jgi.proposal:
  contact:
    email: sewilson@lbl.gov
    github: null
    name: Steven E. Wilson
    orcid: 0000-0002-8489-208X
  contributor:
    email: cjmungall@lbl.gov
    github: cmungall
    name: Chris Mungall
    orcid: 0000-0002-6601-2165
  contributor_extras:
  - email: aclum@lbl.gov
    github: aclum
    name: Alicia Clum
    orcid: 0000-0002-5004-3362
  description: Identifiers for proposals/projects at the Joint Genome Institute
  example: '502930'
  github_request_issue: 853
  homepage: https://genome.jgi.doe.gov/portal/
  name: Joint Genome Institute Proposals
  pattern: ^\d+$
  prefix: jgi.proposal
  publications:
  - doi: 10.1128/msystems.00804-20
    pmc: PMC8269246
    pubmed: '34006627'
    title: DOE JGI Metagenome Workflow
    year: 2021
  reviewer:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  uri_format: https://genome.jgi.doe.gov/portal/lookup?keyName=proposalId&groupOnly=1&app=Info&keyValue=$1
jrct:
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: This system submits an implementation plan to the Minister of Health,
    Labor and Welfare for clinical research conducted at medical institutions, etc.
    based on the provisions of the 'Clinical Research Act' and the 'Act on Ensuring
    Safety of Regenerative Medicine, etc.' It is a system for performing notification
    procedures such as In addition, based on the clinical research practice standards
    stipulated in the same law, we disclose information that the World Health Organization
    (WHO) requires to be disclosed, information that ensures the transparency of the
    research process, and information that contributes to the selection of participation
    in clinical research by the public. (translated from website)
  example: jRCTs041220087
  homepage: https://jrct.niph.go.jp
  name: Japan Registry of Clinical Trials
  pattern: ^jRCT\w?\d+$
  prefix: jrct
  providers:
  - code: detail
    description: Japan Registry of Clinical Trials (Details)
    example: null
    first_party: null
    homepage: https://jrct.niph.go.jp
    name: Japan Registry of Clinical Trials (Details)
    publications: null
    status: null
    uri_format: https://jrct.niph.go.jp/latest-detail/$1
  uri_format: https://jrct.niph.go.jp/en-latest-detail/$1
jstor:
  biocontext:
    prefix: JSTOR
  go:
    homepage: https://www.jstor.org/
    name: Digital archive of scholarly articles
    prefix: JSTOR
    uri_format: https://www.jstor.org/stable/$1
  mappings:
    biocontext: JSTOR
    go: JSTOR
    miriam: jstor
    n2t: jstor
  miriam:
    deprecated: false
    description: JSTOR (Journal Storage) is a digital library containing digital versions
      of historical academic journals, as well as books, pamphlets and current issues
      of journals. Some public domain content is free to access, while other articles
      require registration.
    homepage: http://www.jstor.org/
    id: '00000444'
    name: JSTOR
    namespaceEmbeddedInLui: false
    pattern: ^\d+$
    prefix: jstor
    sampleId: '3075966'
    uri_format: http://www.jstor.org/stable/$1
  n2t:
    description: JSTOR (Journal Storage) is a digital library containing digital versions
      of historical academic journals, as well as books, pamphlets and current issues
      of journals. Some public domain content is free to access, while other articles
      require registration.
    example: '3075966'
    homepage: http://www.jstor.org/
    name: JSTOR Online
    namespaceEmbeddedInLui: false
    pattern: ^\d+$
    prefix: jstor
    uri_format: http://www.jstor.org/stable/$1
  prefix: jstor
jws:
  biocontext:
    prefix: JWS
  contact:
    email: brettolivier@gmail.com
    github: bgoli
    name: Brett G. Olivier
    orcid: 0000-0002-5293-5321
  example: achcar11
  mappings:
    biocontext: JWS
    miriam: jws
    n2t: jws
    prefixcommons: jws
  miriam:
    deprecated: false
    description: JWS Online is a repository of curated biochemical pathway models,
      and additionally provides the ability to run simulations of these models in
      a web browser.
    homepage: http://jjj.bio.vu.nl/models/
    id: '00000130'
    name: JWS Online
    namespaceEmbeddedInLui: false
    pattern: ^\w+$
    prefix: jws
    providers:
    - code: ''
      description: JWS Online Model Repository at Stellenbosch
      homepage: http://jjj.biochem.sun.ac.za/models/
      name: JWS Online Model Repository at Stellenbosch
      uri_format: http://jjj.biochem.sun.ac.za/models/$1/
    - code: ''
      description: JWS Online Model Repository at Manchester
      homepage: http://jjj.mib.ac.uk/models
      name: JWS Online Model Repository at Manchester
      uri_format: http://jjj.mib.ac.uk/models/$1
    sampleId: curien1
    uri_format: http://jjj.bio.vu.nl/models/$1/
  n2t:
    description: JWS Online is a repository of curated biochemical pathway models,
      and additionally provides the ability to run simulations of these models in
      a web browser.
    example: curien
    homepage: http://jjj.mib.ac.uk/index.html
    name: JWS Online Model Repository at Manchester
    namespaceEmbeddedInLui: false
    pattern: ^\w+$
    prefix: jws
    uri_format: http://jjj.mib.ac.uk/models/$1
  prefix: jws
  prefixcommons:
    description: JWS Online is a repository of curated biochemical pathway models,
      and additionally provides the ability to run simulations of these models in
      a web browser.
    example: curien
    homepage: http://jjj.mib.ac.uk/index.html
    keywords:
    - model
    - pathway
    name: JWS Online Model Repository
    pattern: ^\w+$
    prefix: jws
    pubmed_ids:
    - '15072998'
    uri_format: http://jjj.mib.ac.uk/cgi-bin/processModelSelection.py?keytype=modelname&keyword=$1
  publications:
  - doi: 10.1093/bioinformatics/bth200
    pmc: null
    pubmed: '15072998'
    title: Web-based kinetic modelling using JWS Online
    year: 2004
  - doi: null
    pmc: null
    pubmed: '15072998'
    title: null
    year: null
  uri_format: https://jjj.bio.vu.nl/models/$1
kaggle:
  mappings:
    miriam: kaggle
    n2t: kaggle
    re3data: r3d100012705
  miriam:
    deprecated: false
    description: Kaggle is a platform for sharing data, performing reproducible analyses,
      interactive data analysis tutorials, and machine learning competitions.
    homepage: https://kaggle.com
    id: 00000682
    name: Kaggle
    namespaceEmbeddedInLui: false
    pattern: ^[0-9a-zA-Z\-]+\/[0-9a-zA-Z\-]+$
    prefix: kaggle
    sampleId: nasa/kepler-exoplanet-search-results
    uri_format: https://www.kaggle.com/$1
  n2t:
    description: Kaggle is a platform for sharing data, performing reproducible analyses,
      interactive data analysis tutorials, and machine learning competitions.
    example: nasa/kepler-exoplanet-search-results
    homepage: https://kaggle.com
    name: Kaggle
    namespaceEmbeddedInLui: false
    pattern: ^[0-9a-zA-Z\-]+\/[0-9a-zA-Z\-]+$
    prefix: kaggle
    uri_format: https://www.kaggle.com/$1
  prefix: kaggle
  re3data:
    description: Kaggle is a platform for predictive modelling and analytics competitions
      in which statisticians and data miners compete to produce the best models for
      predicting and describing the datasets uploaded by companies and users. This
      crowdsourcing approach relies on the fact that there are countless strategies
      that can be applied to any predictive modelling task and it is impossible to
      know beforehand which technique or analyst will be most effective.
    doi: 10.17616/R32N5V
    homepage: https://www.kaggle.com/datasets
    name: Kaggle
    prefix: r3d100012705
    synonyms:
    - Your home for data science
kaken:
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  keywords:
  - person
  - researcher
  mappings:
    wikidata: P9776
  prefix: kaken
  references:
  - https://github.com/biopragmatics/bioregistry/pull/1171
  wikidata:
    database: Q107428430
    description: identifier for researchers in Japan used in government-based research
      funding (from 1980s)
    example:
    - '00011461'
    - '10295694'
    - '90050426'
    homepage: https://nrid.nii.ac.jp/ja/search/?kw=
    name: e-Rad researcher number
    pattern: ^\d{8}$
    prefix: P9776
    uri_format: https://nrid.nii.ac.jp/ja/nrid/10000$1
kclb:
  cellosaurus:
    category: Cell line collections (Providers)
    homepage: https://cellbank.snu.ac.kr/en
    name: Korean Cell Line Bank
    prefix: KCLB
    uri_format: https://cellbank.snu.ac.kr/cellline/search?sc=y&q=$1
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  example: '10020.2'
  homepage: https://cellbank.snu.ac.kr/english
  mappings:
    cellosaurus: KCLB
  name: Korean Cell Line Bank
  prefix: kclb
  uri_format: https://cellbank.snu.ac.kr/english/sub/catalog.php?s_cellid=464&page=detail_info&CatNo=59&strQ=$1
kcris:
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: 'The Clinical Research Information Service (CRIS) is a non-profit online
    registration system for clinical trials (researches) to be conducted in Korea.
    It has been established at the Korea Disease Control and Prevention Agency (KDCA)
    with support from the Ministry of Health and Welfare (MOHW). It joined the WHO
    International Clinical Trials Registry Platform (ICTRP) as 11th member of Primary
    Registry. (from about page)

    Note that the web page that resolves this trial does not correspond to the semantic
    space'
  example: KCT0008394
  homepage: https://cris.nih.go.kr
  name: Korean Clinical Research Information Service
  pattern: ^KCT\d+$
  prefix: kcris
  references:
  - https://cris.nih.go.kr/cris/search/detailSearchEn.do?seq=23973
kdbirp:
  contact:
    email: zengxian@fudan.edu.cn
    github: null
    name: Xian Zeng
    orcid: 0000-0002-1397-554X
  contributor:
    email: ji.kang@northeastern.edu
    github: kanghosaeyo
    name: Kangho Ji
    orcid: 0009-0009-3402-8013
  description: Identifiers represent RNA-protein interaction entries with quantitative
    kinetic data in the Kinetic Data of Biomolecular Interactions for RNA-Protein
    database (KDBI-RP), which is an open-access database cataloging association rates,
    dissociation rates, and equilibrium dissociation constants for RNA-protein interactions.
  domain: relationship
  example: '183'
  github_request_issue: 1717
  homepage: http://www.kdbirp.aiddlab.com
  keywords:
  - binding affinity
  - kinetics
  - rna-protein interactions
  logo: http://www.kdbirp.aiddlab.com/static/images/logo2.png
  name: Kinetic Data of RNA-Protein Interactions Database
  pattern: ^\d+$
  prefix: kdbirp
  publications:
  - doi: 10.1016/j.jmb.2025.169357
    pmc: null
    pubmed: '40716733'
    title: 'KDBI-RP: Kinetic Data of RNA-Protein Interactions Database'
    year: 2025
  reviewer:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  uri_format: http://www.kdbirp.aiddlab.com/detail/$1
kdsf.ffk:
  bartoc:
    abbreviation: kdsf-ffk
    homepage: https://w3id.org/kdsf-ffk/
    license: CC BY-SA 4.0
    prefix: '20288'
  example: ErdeUndKosmos
  example_extras:
  - '111'
  homepage: https://github.com/KDSF-FFK/kdsf-ffk
  mappings:
    bartoc: '20288'
    tib: kdsfffk
  prefix: kdsf.ffk
  repository: https://github.com/KDSF-FFK/kdsf-ffk
  tib:
    description: Klassifikation für interdisziplinäre Forschungsfelder im Rahmen des
      Kerndatensatz Forschung
    download_rdf: https://raw.githubusercontent.com/KDSF-FFK/kdsf-ffk/main/FFK.ttl
    keywords:
    - NFDI4ING
    - FID move
    - Digital Planning and Construction
    - FID BAUdigital
    - computer science
    name: Interdisziplinäre Forschungsfeldklassifikation
    prefix: kdsfffk
    tracker: https://github.com/KDSF-FFK/kdsf-ffk/issues
    uri_format: https://w3id.org/kdsf-ffk/$1
kegg:
  biocontext:
    prefix: KEGG
  biolink:
    is_identifiers: false
    is_obo: false
    prefix: KEGG
    uri_format: http://www.kegg.jp/entry/$1
  cheminf:
    description: Database identifier used by KEGG.
    name: KEGG
    obsolete: false
    prefix: 000409
  comment: KEGG prefix has been split into several others
  deprecated: true
  go:
    homepage: http://www.genome.ad.jp/kegg/
    name: Kyoto Encyclopedia of Genes and Genomes
    prefix: KEGG
  integbio:
    alt_name: Kyoto Encyclopedia of Genes and Genomes
    description: KEGG is an integrated database for interpretation of biological systems
      from genomic and molecular-level information. KEGG consists of 16 main databases
      categorized into systems information, genomic information and chemical information.
      This database features to map elementary datasets (genes, small molecules, etc)
      in each KEGG database to network datasets (pathway maps, hierarchical lists,
      etc). Users can perform keyword search against the entire KEGG database, as
      well as BLAST/FASTA search and SIMCOMP search.
    fairsharing: biodbcore-000663
    homepage: http://www.kegg.jp/kegg/
    information_keywords:
    - Portal
    maintainer: Kyoto University Institute for Chemical Research Bioinformatics Center
    name: KEGG
    prefix: nbdc00530
    pubmeds:
    - '9287494'
    - '16381885'
    - '14681412'
    - '24214961'
    status: Active
  logo: https://www.kegg.jp/Fig/kegg128.gif
  mappings:
    biocontext: KEGG
    biolink: KEGG
    cheminf: 000409
    go: KEGG
    integbio: nbdc00530
    miriam: kegg
    n2t: kegg
    pathguide: '16'
    uniprot: DB-0053
  miriam:
    deprecated: false
    description: Kyoto Encyclopedia of Genes and Genomes (KEGG) is a database resource
      for understanding high-level functions and utilities of the biological system,
      such as the cell, the organism and the ecosystem, from molecular-level information,
      especially large-scale molecular datasets generated by genome sequencing and
      other high-throughput experimental technologies.
    homepage: http://www.kegg.jp/
    id: 00000578
    name: Kyoto Encyclopedia of Genes and Genomes
    namespaceEmbeddedInLui: false
    pattern: ^([CHDEGTMKR]\d+)|(\w+:[\w\d\.-]*)|([a-z]{3,5})|(\w{2,4}\d{5})$
    prefix: kegg
    sampleId: hsa00190
    uri_format: http://www.kegg.jp/entry/$1
  n2t:
    description: Kyoto Encyclopedia of Genes and Genomes (KEGG) is a database resource
      for understanding high-level functions and utilities of the biological system,
      such as the cell, the organism and the ecosystem, from molecular-level information,
      especially large-scale molecular datasets generated by genome sequencing and
      other high-throughput experimental technologies.
    example: hsa00190
    homepage: http://www.kegg.jp/
    name: KEGG at Kyoto University Bioinformatics Center
    namespaceEmbeddedInLui: false
    pattern: ^([CHDEGTMKR]\d+)|(\w+:[\w\d\.-]*)|([a-z]{3,5})|(\w{2,4}\d{5})$
    prefix: kegg
    uri_format: http://www.kegg.jp/entry/$1
  pathguide:
    abbreviation: KEGG
    homepage: http://www.genome.jp/kegg/
    keywords:
    - BioPAX
    name: Kyoto Encyclopedia of Genes and Genomes
    prefix: '16'
  prefix: kegg
  publications:
  - doi: 10.1093/nar/gkw1092
    pmc: PMC5210567
    pubmed: '27899662'
    title: 'KEGG: new perspectives on genomes, pathways, diseases and drugs'
    year: 2016
  - doi: 10.1093/nar/gkae909
    pmc: null
    pubmed: '39417505'
    title: null
    year: null
  synonyms:
  - KEGG
  uniprot:
    abbreviation: KEGG
    category: Genome annotation databases
    homepage: https://www.genome.jp/kegg/
    name: KEGG
    prefix: DB-0053
    publications:
    - doi: 10.1093/nar/gkae909
      pubmed: '39417505'
    uri_format: https://www.genome.jp/dbget-bin/www_bget?$1
kegg.brite:
  biolink:
    is_identifiers: false
    is_obo: false
    prefix: KEGG.BRITE
    uri_format: https://bioregistry.io/kegg.brite:$1
  example: ko00002
  homepage: https://www.genome.jp/kegg/brite.html
  integbio:
    alt_name: Functional hierarchies and binary relationships of biological entities
    description: The KEGG BRITE database contains functional hierarchies and binary
      relationships of biological entities, and includes many types of relationships.
      KEGG BRITE maps large-scale molecular datasets in genomics, transcriptomics,
      proteomics, and metabolomics to BRITE functional hierarchies, and allows biological
      interpretation of higher-level systemic functions.
    homepage: http://www.genome.jp/kegg/brite.html
    information_keywords:
    - Ontology/Terminology/Nomenclature
    - Classification
    maintainer: Kyoto University Institute for Chemical Research Bioinformatics Center
    name: KEGG BRITE
    prefix: nbdc00115
    status: Active
  logo: https://www.genome.jp/Fig/kegg128.gif
  mappings:
    biolink: KEGG.BRITE
    integbio: nbdc00115
    prefixcommons: kegg.brite
  prefix: kegg.brite
  prefixcommons:
    description: KEGG BRITE is a collection of hierarchical classifications (see new
      hierarchies and last updates) representing our knowledge on various aspects
      of biological systems. In contrast to KEGG PATHWAY, which is limited to molecular
      interactions and reactions, KEGG BRITE incorporates many different types of
      relationships.
    example: ko00071
    homepage: http://www.genome.jp/kegg/brite.html
    keywords:
    - pathway
    - classification
    - ontology
    name: KEGG BRITE
    pattern: ^[ko/br]\d+$
    prefix: kegg.brite
    synonyms:
    - br
    - brite
    uri_format: http://www.genome.jp/kegg-bin/get_htext?-p+/kegg/brite/br+br$1
  uri_format: https://www.kegg.jp/brite/$1
kegg.compound:
  biocontext:
    prefix: KEGG.COMPOUND
  contact:
    email: kanehisa@kuicr.kyoto-u.ac.jp
    github: null
    name: Minoru Kanehisa
    orcid: 0000-0001-6123-540X
  edam:
    description: Unique identifier of a chemical compound from the KEGG database.
    name: Compound ID (KEGG)
    obsolete: false
    prefix: '2605'
  integbio:
    alt_name: Metabolome informatics resource integrating genomics and chemistry
    description: KEGG COMPOUND is a database of biologically relevant compounds, including
      chemical structures and associated information for compounds in the KEGG database
      such as small molecules, biopolymers, and other related substances. The site
      also has a collection of links to other relevant KEGG resources such as GLYCAN.
    homepage: http://www.genome.jp/kegg/compound/
    information_keywords:
    - Interaction/Pathway
    - Chemical structure
    maintainer: Kyoto University Institute for Chemical Research Bioinformatics Center
    name: KEGG COMPOUND
    prefix: nbdc00814
    pubmeds:
    - '19327755'
    - '17921532'
    - '17400247'
    - '14505407'
    - '20460463'
    status: Active
    target_keywords:
    - DNA
    - RNA
    - Protein
    - Chemical compound
  logo: https://www.genome.jp/Fig/kegg128.gif
  mappings:
    biocontext: KEGG.COMPOUND
    edam: '2605'
    integbio: nbdc00814
    miriam: kegg.compound
    n2t: kegg.compound
    prefixcommons: kegg.compound
    wikidata: P665
  miriam:
    deprecated: false
    description: KEGG compound contains our knowledge on the universe of chemical
      substances that are relevant to life.
    homepage: https://www.genome.jp/kegg/ligand.html
    id: '00000013'
    name: KEGG Compound
    namespaceEmbeddedInLui: false
    pattern: ^C\d+$
    prefix: kegg.compound
    sampleId: C12345
    uri_format: https://www.kegg.jp/entry/$1
  n2t:
    description: KEGG compound contains our knowledge on the universe of chemical
      substances that are relevant to life.
    example: C12345
    homepage: https://www.genome.jp/kegg/ligand.html
    name: KEGG LIGAND Database
    namespaceEmbeddedInLui: false
    pattern: ^C\d+$
    prefix: kegg.compound
    uri_format: https://www.kegg.jp/entry/$1
  part_of: kegg
  prefix: kegg.compound
  prefixcommons:
    description: KEGG COMPOUND is a chemical structure database for metabolic compounds
      and other chemical substances that are relevant to biological systems.
    example: C12345
    homepage: http://www.genome.jp/kegg/compound/
    keywords:
    - small molecule
    name: KEGG Compound
    pattern: ^C\d+$
    prefix: kegg.compound
    pubmed_ids:
    - '22700311'
    synonyms:
    - cpd
    - kegg.compounds
    uri_format: http://www.genome.jp/dbget-bin/www_bget?cpd:$1
  publications:
  - doi: 10.1002/0471250953.bi0112s38
    pmc: null
    pubmed: '22700311'
    title: Using the KEGG database resource
    year: 2012
  - doi: null
    pmc: null
    pubmed: '22700311'
    title: null
    year: null
  synonyms:
  - KEGG COMPOUND
  - KEGG.COMPOUND
  wikidata:
    prefix: P665
kegg.dgroup:
  biolink:
    is_identifiers: false
    is_obo: false
    prefix: KEGG.DGROUP
    uri_format: http://www.kegg.jp/entry/$1
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: "KEGG DGROUP contains structurally and functionally related groups\
    \ of D number entries in KEGG DRUG. There are five types of drug groups.\n\n \
    \   Chemical - grouped as identical chemical structures with minor variations\
    \ of salts, hydration states, etc.\n    Structure - grouped as similar chemical\
    \ structures having the same skeleton, etc.\n    Target - grouped by drug targets\n\
    \    Class - drug classes often representing similar mechanisms of action\n  \
    \  Metabolism - grouped by substrates, inhibitors and inducers of drug metabolizing\
    \ enzymes and transporters\n\nChemical groups are often used for identifying essentially\
    \ the same active ingredients of drugs in different countries."
  example: DG00301
  homepage: http://www.genome.jp/kegg/reaction/
  logo: https://www.genome.jp/Fig/kegg128.gif
  mappings:
    biolink: KEGG.DGROUP
  name: KEGG Drug Group
  part_of: kegg
  pattern: ^DG\d+$
  prefix: kegg.dgroup
  references:
  - https://github.com/prefixcommons/prefixes/pull/4
  synonyms:
  - KEGG_DGROUP
  - KEGG_DRUG_GROUP
kegg.disease:
  biocontext:
    prefix: KEGG.DISEASE
  integbio:
    alt_name: Diseases viewed as perturbed states of the molecular system
    description: KEGG DISEASE is a database of human diseases with information on
      perturbed molecular networks. Each disease entry contains a list of known disease
      genes, environmental factors (carcinogens, pathogens, etc), diagnostic markers
      and therapeutic drugs with reference information. This database provides maps
      of molecular networks associated with diseases through links to the KEGG PATHWAY
      database. Users can search human diseases by names, description, categories,
      pathways, and known causative genes.
    homepage: http://www.genome.jp/kegg/disease/
    information_keywords:
    - Interaction/Pathway
    maintainer: Kyoto University Institute for Chemical Research Bioinformatics Center
    name: KEGG DISEASE
    prefix: nbdc00813
    status: Active
    target_keywords:
    - Genome/Gene
    - Health/Disease
    - Drug
  logo: https://www.genome.jp/Fig/kegg128.gif
  mappings:
    biocontext: KEGG.DISEASE
    integbio: nbdc00813
    miriam: kegg.disease
    n2t: kegg.disease
    prefixcommons: kegg.disease
  miriam:
    deprecated: false
    description: The KEGG DISEASE database is a collection of disease entries capturing
      knowledge on genetic and environmental perturbations. Each disease entry contains
      a list of known genetic factors (disease genes), environmental factors, diagnostic
      markers, and therapeutic drugs. Diseases are viewed as perturbed states of the
      molecular system, and drugs as perturbants to the molecular system.
    homepage: http://www.genome.jp/kegg/disease/
    id: '00000475'
    name: KEGG Disease
    namespaceEmbeddedInLui: false
    pattern: ^H\d+$
    prefix: kegg.disease
    sampleId: H00076
    uri_format: http://www.kegg.jp/entry/$1
  n2t:
    description: The KEGG DISEASE database is a collection of disease entries capturing
      knowledge on genetic and environmental perturbations. Each disease entry contains
      a list of known genetic factors (disease genes), environmental factors, diagnostic
      markers, and therapeutic drugs. Diseases are viewed as perturbed states of the
      molecular system, and drugs as perturbants to the molecular system.
    example: H00076
    homepage: http://www.genome.jp/kegg/disease/
    name: KEGG Disease at Kyoto University Bioinformatics Center
    namespaceEmbeddedInLui: false
    pattern: ^H\d+$
    prefix: kegg.disease
    uri_format: http://www.kegg.jp/entry/$1
  part_of: kegg
  prefix: kegg.disease
  prefixcommons:
    description: The KEGG DISEASE database is a new collection of disease entries
      capturing knowledge on genetic and environmental perturbations. Each disease
      entry is identified by the H number and contains a list of known genetic factors
      (disease genes), environmental factors, diagnostic markers, and therapeutic
      drugs.
    example: H00047
    homepage: http://www.genome.jp/kegg/disease/
    keywords:
    - classification
    name: KEGG Disease
    pattern: ^H\d+$
    prefix: kegg.disease
    synonyms:
    - ds
    - kegg.diseases
    uri_format: http://www.genome.jp/dbget-bin/www_bget?ds:$1
kegg.drug:
  biocontext:
    prefix: KEGG.DRUG
  contact:
    email: kanehisa@kuicr.kyoto-u.ac.jp
    github: null
    name: Minoru Kanehisa
    orcid: 0000-0001-6123-540X
  edam:
    description: Unique identifier of a drug from the KEGG Drug database.
    name: Drug ID (KEGG)
    obsolete: false
    prefix: '2609'
  integbio:
    alt_name: Drugs viewed as perturbants to the molecular system
    description: KEGG DRUG is a comprehensive database of drug information about all
      marketed drugs in Japan, as well as many prescription drugs in USA and Europe.
      KEGG DRUG is based on chemical structure or component, and each entry contains
      information about drug targets (pathways), metabolizing enzymes and other interacting
      molecules. This database also includes crude drugs and TCM (Tradictional Chinese
      Medicine). Users can check for drug-drug interaction, view structure maps representing
      the history of drug development and search drugs by generic names, trade names,
      and components.
    homepage: http://www.genome.jp/kegg/drug/
    information_keywords:
    - Interaction/Pathway
    - Chemical structure
    maintainer: Kyoto University Institute for Chemical Research Bioinformatics Center
    name: KEGG DRUG
    prefix: nbdc00812
    status: Active
    target_keywords:
    - Drug
  logo: https://www.genome.jp/Fig/kegg128.gif
  mappings:
    biocontext: KEGG.DRUG
    edam: '2609'
    integbio: nbdc00812
    miriam: kegg.drug
    n2t: kegg.drug
    prefixcommons: kegg.drug
    wikidata: P665
  miriam:
    deprecated: false
    description: KEGG DRUG contains chemical structures of drugs and additional information
      such as therapeutic categories and target molecules.
    homepage: https://www.genome.jp/kegg/drug/
    id: '00000025'
    name: KEGG Drug
    namespaceEmbeddedInLui: false
    pattern: ^D\d+$
    prefix: kegg.drug
    sampleId: D00123
    uri_format: https://www.kegg.jp/entry/$1
  n2t:
    description: KEGG DRUG contains chemical structures of drugs and additional information
      such as therapeutic categories and target molecules.
    example: D00123
    homepage: https://www.genome.jp/kegg/drug/
    name: KEGG DRUG Database
    namespaceEmbeddedInLui: false
    pattern: ^D\d+$
    prefix: kegg.drug
    uri_format: https://www.kegg.jp/entry/$1
  part_of: kegg
  prefix: kegg.drug
  prefixcommons:
    description: KEGG DRUG is a unified drug information resource that contains chemical
      structures and/or chemical components of all prescription and OTC drugs in Japan,
      most prescription drugs in the USA, and many prescription drugs in Europe.
    example: D00123
    homepage: http://www.genome.jp/kegg/drug/
    keywords:
    - small molecule
    name: KEGG Drug
    pattern: ^D\d+$
    prefix: kegg.drug
    pubmed_ids:
    - '16381885'
    synonyms:
    - dr
    - kegg.drugs
    uri_format: http://www.genome.jp/dbget-bin/www_bget?dr:$1
  publications:
  - doi: 10.1093/nar/gkj102
    pmc: PMC1347464
    pubmed: '16381885'
    title: 'From genomics to chemical genomics: new developments in KEGG'
    year: 2006
  synonyms:
  - KEGG DRUG
  - KEGG.DRUG
  wikidata:
    prefix: P665
kegg.environ:
  biocontext:
    prefix: KEGG.ENVIRON
  deprecated: true
  integbio:
    description: KEGG ENVIRON is a database of crude drugs, essential oils, and medicinal
      harbs, all of which are mostly natural products of plants. Each entry is associated
      with the chemical component, efficacy information, and source species information
      whenever applicable.
    homepage: http://www.genome.jp/kegg/drug/environ.html
    maintainer: Kyoto University Institute for Chemical Research Bioinformatics Center
    name: KEGG ENVIRON
    prefix: nbdc01059
    target_keywords:
    - Health/Disease
    - Chemical compound
    - Drug
  logo: https://www.genome.jp/Fig/kegg128.gif
  mappings:
    biocontext: KEGG.ENVIRON
    integbio: nbdc01059
    miriam: kegg.environ
    n2t: kegg.environ
  miriam:
    deprecated: false
    description: KEGG ENVIRON (renamed from EDRUG) is a collection of crude drugs,
      essential oils, and other health-promoting substances, which are mostly natural
      products of plants. It will contain environmental substances and other health-damagine
      substances as well. Each KEGG ENVIRON entry is identified by the E number and
      is associated with the chemical component, efficacy information, and source
      species information whenever applicable.
    homepage: http://www.genome.jp/kegg/drug/environ.html
    id: 00000389
    name: KEGG Environ
    namespaceEmbeddedInLui: false
    pattern: ^(ev\:)?E\d+$
    prefix: kegg.environ
    sampleId: ev:E00032
    uri_format: http://www.kegg.jp/entry/$1
  n2t:
    description: KEGG ENVIRON (renamed from EDRUG) is a collection of crude drugs,
      essential oils, and other health-promoting substances, which are mostly natural
      products of plants. It will contain environmental substances and other health-damagine
      substances as well. Each KEGG ENVIRON entry is identified by the E number and
      is associated with the chemical component, efficacy information, and source
      species information whenever applicable.
    example: ev:E00032
    homepage: http://www.genome.jp/kegg/drug/environ.html
    name: KEGG ENVIRON Database
    namespaceEmbeddedInLui: false
    pattern: ^(ev\:)?E\d+$
    prefix: kegg.environ
    uri_format: http://www.kegg.jp/entry/$1
  part_of: kegg
  prefix: kegg.environ
  synonyms:
  - KEGG.EDRUG
kegg.enzyme:
  biolink:
    is_identifiers: false
    is_obo: false
    prefix: KEGG.ENZYME
    uri_format: http://www.kegg.jp/entry/$1
  description: KEGG ENZYME is an implementation of the Enzyme Nomenclature (EC number
    system) produced by the IUBMB/IUPAC Biochemical Nomenclature Committee. KEGG ENZYME
    is based on the ExplorEnz database at Trinity College Dublin, and is maintained
    in the KEGG relational database with additional annotation of reaction hierarchy
    and sequence data links.
  go:
    homepage: http://www.genome.jp/dbget-bin/www_bfind?enzyme
    name: KEGG Enzyme Database
    prefix: KEGG_ENZYME
    uri_format: http://www.genome.jp/dbget-bin/www_bget?ec:$1
  logo: https://www.genome.jp/Fig/kegg128.gif
  mappings:
    biolink: KEGG.ENZYME
    go: KEGG_ENZYME
  name: KEGG Enzyme
  part_of: kegg
  prefix: kegg.enzyme
  provides: ec
kegg.genes:
  biocontext:
    prefix: KEGG.GENES
  biolink:
    is_identifiers: false
    is_obo: false
    prefix: KEGG.GENES
    uri_format: https://bioregistry.io/kegg.genes:bsu:$1
  contact:
    email: kanehisa@kuicr.kyoto-u.ac.jp
    github: null
    name: Minoru Kanehisa
    orcid: 0000-0001-6123-540X
  domain: gene
  example: bsu:BSU01340
  logo: https://www.genome.jp/Fig/kegg128.gif
  mappings:
    biocontext: KEGG.GENES
    biolink: KEGG.GENES
    miriam: kegg.genes
    n2t: kegg.genes
    prefixcommons: kegg.gene
    wikidata: P665
  miriam:
    deprecated: false
    description: KEGG GENES is a collection of gene catalogs for all complete genomes
      and some partial genomes, generated from publicly available resources.
    homepage: http://www.genome.jp/kegg/genes.html
    id: '00000070'
    name: KEGG Genes
    namespaceEmbeddedInLui: false
    pattern: ^\w+:[\w\d\.-]*$
    prefix: kegg.genes
    sampleId: syn:ssr3451
    uri_format: http://www.kegg.jp/entry/$1
  n2t:
    description: KEGG GENES is a collection of gene catalogs for all complete genomes
      and some partial genomes, generated from publicly available resources.
    example: syn:ssr3451
    homepage: http://www.genome.jp/kegg/genes.html
    name: KEGG GENES Database
    namespaceEmbeddedInLui: false
    pattern: ^\w+:[\w\d\.-]*$
    prefix: kegg.genes
    uri_format: http://www.kegg.jp/entry/$1
  name: KEGG gene
  part_of: kegg
  prefix: kegg.genes
  prefixcommons:
    description: KEGG GENES is a collection of gene catalogs for all complete genomes
      generated from publicly available resources, mostly NCBI RefSeq. They are subject
      to SSDB computation and KO assignment (gene annotation) by KOALA tool
    example: syn:ssr3451
    homepage: http://www.genome.jp/kegg/genes.html
    keywords:
    - gene
    - DNA
    - protein
    name: KEGG Genes
    pattern: ^\w+:[\w\d\.-]*$
    prefix: kegg.gene
    pubmed_ids:
    - '16381885'
    synonyms:
    - gene
    - kegg.genes
    uri_format: http://www.genome.jp/dbget-bin/www_bget?[?species]:$1
  publications:
  - doi: 10.1093/nar/gkj102
    pmc: PMC1347464
    pubmed: '16381885'
    title: 'From genomics to chemical genomics: new developments in KEGG'
    year: 2006
  wikidata:
    prefix: P665
kegg.genome:
  biocontext:
    prefix: KEGG.GENOME
  contact:
    email: kanehisa@kuicr.kyoto-u.ac.jp
    github: null
    name: Minoru Kanehisa
    orcid: 0000-0001-6123-540X
  domain: taxonomy
  example: T06648
  integbio:
    alt_name: Organisms and ecosystems with genome sequence information
    description: KEGG GENOME is a database of full genome sequence information for
      multiple species. The database is a collection of references to descriptive
      genome literature and has links to reaction pathways in each organism, comparative
      tools, and taxonomy based on KEGG information and provides KEGG pathway information
      and links to outside resources including primary literature.
    homepage: http://www.genome.jp/kegg/genome.html
    information_keywords:
    - Bibliography/Documents
    maintainer: Kyoto University Institute for Chemical Research Bioinformatics Center
    name: KEGG GENOME
    prefix: nbdc00816
    status: Active
    target_keywords:
    - Genome/Gene
  keywords:
  - genome
  license: https://www.kegg.jp/kegg/legal.html
  logo: https://www.genome.jp/Fig/kegg128.gif
  mappings:
    biocontext: KEGG.GENOME
    integbio: nbdc00816
    miriam: kegg.genome
    n2t: kegg.genome
    prefixcommons: kegg.genome
    wikidata: P665
  miriam:
    deprecated: false
    description: KEGG Genome is a collection of organisms whose genomes have been
      completely sequenced.
    homepage: http://www.genome.jp/kegg/catalog/org_list.html
    id: 00000238
    name: KEGG Genome
    namespaceEmbeddedInLui: false
    pattern: ^(T0\d+|\w{3,5})$
    prefix: kegg.genome
    sampleId: eco
    uri_format: http://www.kegg.jp/entry/$1
  n2t:
    description: KEGG Genome is a collection of organisms whose genomes have been
      completely sequenced.
    example: eco
    homepage: http://www.genome.jp/kegg/catalog/org_list.html
    name: KEGG Genome Database
    namespaceEmbeddedInLui: false
    pattern: ^(T0\d+|\w{3,5})$
    prefix: kegg.genome
    uri_format: http://www.kegg.jp/entry/$1
  name: KEGG genome
  part_of: kegg
  prefix: kegg.genome
  prefixcommons:
    description: Complete organism genomes
    example: T00047
    homepage: http://www.genome.jp/kegg/catalog/org_list.html
    name: KEGG Genome
    pattern: ^T\d+$
    prefix: kegg.genome
    pubmed_ids:
    - '22080510'
    synonyms:
    - gn
    - kegg.genomes
    uri_format: http://www.genome.jp/dbget-bin/www_bget?gn:$1
  publications:
  - doi: 10.1093/nar/gkr988
    pmc: PMC3245020
    pubmed: '22080510'
    title: KEGG for integration and interpretation of large-scale molecular data sets
    year: 2011
  synonyms:
  - kegg_genome
  - kegg_genomes
  wikidata:
    prefix: P665
kegg.glycan:
  biocontext:
    prefix: KEGG.GLYCAN
  contact:
    email: kanehisa@kuicr.kyoto-u.ac.jp
    github: null
    name: Minoru Kanehisa
    orcid: 0000-0001-6123-540X
  edam:
    description: Unique identifier of a glycan ligand from the KEGG GLYCAN database
      (a subset of KEGG LIGAND).
    name: KEGG Glycan
    obsolete: false
    prefix: '2613'
  integbio:
    alt_name: Glycome informatics resource integrating genomics and chemistry
    description: KEGG GLYCAN is a database of glycan structures. The database contains
      structures of glycans involved in KEGG reactions and specifies several parameters
      of the glycans, as well as collecting links to other glycan-relevant databases.
      The database is searchable by KEGG G-index ID.
    homepage: http://www.genome.jp/kegg/glycan/
    information_keywords:
    - Interaction/Pathway
    - Chemical structure
    maintainer: Kyoto University Institute for Chemical Research Bioinformatics Center
    name: KEGG GLYCAN
    prefix: nbdc00533
    pubmeds:
    - '16014746'
    - '16362924'
    - '19327755'
    - '15215393'
    - '16159923'
    - '18546491'
    status: Active
    target_keywords:
    - RNA
    - Protein
    - Carbohydrate
  logo: https://www.genome.jp/Fig/kegg128.gif
  mappings:
    biocontext: KEGG.GLYCAN
    edam: '2613'
    integbio: nbdc00533
    miriam: kegg.glycan
    n2t: kegg.glycan
    prefixcommons: kegg.glycan
  miriam:
    deprecated: false
    description: KEGG GLYCAN, a part of the KEGG LIGAND database, is a collection
      of experimentally determined glycan structures. It contains all unique structures
      taken from CarbBank, structures entered from recent publications, and structures
      present in KEGG pathways.
    homepage: https://www.genome.jp/kegg/glycan/
    id: '00000026'
    name: KEGG Glycan
    namespaceEmbeddedInLui: false
    pattern: ^G\d+$
    prefix: kegg.glycan
    sampleId: G00123
    uri_format: https://www.kegg.jp/entry/$1
  n2t:
    description: KEGG GLYCAN, a part of the KEGG LIGAND database, is a collection
      of experimentally determined glycan structures. It contains all unique structures
      taken from CarbBank, structures entered from recent publications, and structures
      present in KEGG pathways.
    example: G00123
    homepage: https://www.genome.jp/kegg/glycan/
    name: KEGG GLYCAN Database
    namespaceEmbeddedInLui: false
    pattern: ^G\d+$
    prefix: kegg.glycan
    uri_format: https://www.kegg.jp/entry/$1
  part_of: kegg
  prefix: kegg.glycan
  prefixcommons:
    description: The KEGG GLYCAN structure database is a collection of experimentally
      determined glycan structures [1]. It contains all unique structures taken from
      CarbBank, structures entered from recent publications, and structures present
      in KEGG pathways.
    example: G00123
    homepage: http://www.genome.jp/kegg/glycan/
    keywords:
    - small molecule
    name: KEGG Glycan
    pattern: ^G\d+$
    prefix: kegg.glycan
    pubmed_ids:
    - '16014746'
    synonyms:
    - gl
    - kegg.glycans
    uri_format: http://www.genome.jp/dbget-bin/www_bget?gl:$1
  publications:
  - doi: 10.1093/glycob/cwj010
    pmc: null
    pubmed: '16014746'
    title: KEGG as a glycome informatics resource
    year: 2005
  - doi: null
    pmc: null
    pubmed: '16014746'
    title: null
    year: null
  - doi: null
    pmc: null
    pubmed: '16014746'
    title: null
    year: null
kegg.ligand:
  comment: This database has been discontinued by KEGG. It now lives inside the compound
    database
  deprecated: true
  go:
    homepage: http://www.genome.ad.jp/kegg/docs/upd_ligand.html
    name: KEGG LIGAND Database
    prefix: KEGG_LIGAND
    uri_format: http://www.genome.jp/dbget-bin/www_bget?cpd:$1
  logo: https://www.genome.jp/Fig/kegg128.gif
  mappings:
    go: KEGG_LIGAND
  name: KEGG LIGAND
  part_of: kegg
  prefix: kegg.ligand
kegg.metagenome:
  biocontext:
    prefix: KEGG.METAGENOME
  contact:
    email: kanehisa@kuicr.kyoto-u.ac.jp
    github: null
    name: Minoru Kanehisa
    orcid: 0000-0001-6123-540X
  logo: https://www.genome.jp/Fig/kegg128.gif
  mappings:
    biocontext: KEGG.METAGENOME
    miriam: kegg.metagenome
    n2t: kegg.metagenome
    prefixcommons: kegg.metagenome
  miriam:
    deprecated: false
    description: The KEGG Metagenome Database collection information on environmental
      samples (ecosystems) of genome sequences for multiple species.
    homepage: http://www.genome.jp/kegg/catalog/org_list3.html
    id: 00000239
    name: KEGG Metagenome
    namespaceEmbeddedInLui: false
    pattern: ^T3\d+$
    prefix: kegg.metagenome
    sampleId: T30002
    uri_format: http://www.kegg.jp/entry/$1
  n2t:
    description: The KEGG Metagenome Database collection information on environmental
      samples (ecosystems) of genome sequences for multiple species.
    example: T30002
    homepage: http://www.genome.jp/kegg/catalog/org_list3.html
    name: KEGG Metagenome Database
    namespaceEmbeddedInLui: false
    pattern: ^T3\d+$
    prefix: kegg.metagenome
    uri_format: http://www.kegg.jp/entry/$1
  part_of: kegg
  prefix: kegg.metagenome
  prefixcommons:
    description: The KEGG Metagenome Database collection information on environmental
      samples (ecosystems) of genome sequences for multiple species.
    example: T30002
    keywords:
    - genome
    name: KEGG Metagenome
    pattern: ^T3\d+$
    prefix: kegg.metagenome
    pubmed_ids:
    - '22080510'
    synonyms:
    - kegg.metagenomes
    uri_format: http://www.genome.jp/kegg-bin/show_organism?org=$1
  publications:
  - doi: 10.1093/nar/gkr988
    pmc: PMC3245020
    pubmed: '22080510'
    title: KEGG for integration and interpretation of large-scale molecular data sets
    year: 2011
kegg.module:
  biocontext:
    prefix: KEGG.MODULE
  integbio:
    description: 'KEGG MODULE is a database of manually defined functional units called
      KEGG modules identified by M numbers, used for annotation and biological interpretation
      of sequenced genomes. It contains four types of KEGG modules;

      1) pathway modules - representing tight functional units in KEGG metabolic pathway
      maps

      2) structural complexes - often forming molecular machineries

      3) functional sets - for other types of essential sets, such as Aminoacyl-tRNA
      synthases, prokaryotes, etc.

      4) signature modules - as markers of phenotypes, such as EHEC pathogenicity
      signature, Shiga toxin, etc.'
    homepage: http://www.genome.jp/kegg/module.html
    information_keywords:
    - Phenotype
    - Interaction/Pathway
    maintainer: Kyoto University Institute for Chemical Research Bioinformatics Center
    name: KEGG MODULE
    prefix: nbdc01428
    pubmeds:
    - '23384306'
    status: Active
    target_keywords:
    - Metabolite
  logo: https://www.genome.jp/Fig/kegg128.gif
  mappings:
    biocontext: KEGG.MODULE
    integbio: nbdc01428
    miriam: kegg.module
    n2t: kegg.module
  miriam:
    deprecated: false
    description: KEGG Modules are manually defined functional units used in the annotation
      and biological interpretation of sequenced genomes. Each module corresponds
      to a set of 'KEGG Orthology' (MIR:00000116) entries. KEGG Modules can represent
      pathway, structural, functional or signature modules.
    homepage: http://www.kegg.jp/kegg/module.html
    id: '00000474'
    name: KEGG Module
    namespaceEmbeddedInLui: false
    pattern: ^([a-z]{3,5}_)?M\d{5}$
    prefix: kegg.module
    sampleId: M00002
    uri_format: http://www.kegg.jp/entry/$1
  n2t:
    description: KEGG Modules are manually defined functional units used in the annotation
      and biological interpretation of sequenced genomes. Each module corresponds
      to a set of 'KEGG Orthology' (MIR:00000116) entries. KEGG Modules can represent
      pathway, structural, functional or signature modules.
    example: M00002
    homepage: http://www.kegg.jp/kegg/module.html
    name: KEGG Module at Kyoto University Bioinformatics Center
    namespaceEmbeddedInLui: false
    pattern: ^([a-z]{3,5}_)?M\d{5}$
    prefix: kegg.module
    uri_format: http://www.kegg.jp/entry/$1
  part_of: kegg
  prefix: kegg.module
kegg.orthology:
  biocontext:
    prefix: KEGG.ORTHOLOGY
  logo: https://www.genome.jp/Fig/kegg128.gif
  mappings:
    biocontext: KEGG.ORTHOLOGY
    miriam: kegg.orthology
    n2t: kegg.orthology
    prefixcommons: kegg.orthology
  miriam:
    deprecated: false
    description: KEGG Orthology (KO) consists of manually defined, generalised ortholog
      groups that correspond to KEGG pathway nodes and BRITE hierarchy nodes in all
      organisms.
    homepage: http://www.genome.jp/kegg/ko.html
    id: '00000116'
    name: KEGG Orthology
    namespaceEmbeddedInLui: false
    pattern: ^K\d+$
    prefix: kegg.orthology
    sampleId: K00001
    uri_format: http://www.kegg.jp/entry/$1
  n2t:
    description: KEGG Orthology (KO) consists of manually defined, generalised ortholog
      groups that correspond to KEGG pathway nodes and BRITE hierarchy nodes in all
      organisms.
    example: K00001
    homepage: http://www.genome.jp/kegg/ko.html
    name: KEGG Orthology Database
    namespaceEmbeddedInLui: false
    pattern: ^K\d+$
    prefix: kegg.orthology
    uri_format: http://www.kegg.jp/entry/$1
  part_of: kegg
  prefix: kegg.orthology
  prefixcommons:
    description: The KEGG reference pathway maps and BRITE functional hierarchies
      are represented in a general way to be applicable to all organisms. KEGG Orthology
      (KO) is the basis for this representation, consisting of manually defined ortholog
      groups that correspond to KEGG pathway nodes and BRITE hierarchy nodes.
    example: K00001
    homepage: http://www.genome.jp/kegg/ko.html
    keywords:
    - classification
    - pathway
    name: KEGG Orthology
    pattern: ^K\d+$
    prefix: kegg.orthology
    synonyms:
    - ko
    uri_format: http://www.genome.jp/dbget-bin/www_bget?ko:$1
kegg.pathway:
  biocontext:
    prefix: KEGG.PATHWAY
  biolink:
    is_identifiers: false
    is_obo: false
    prefix: KEGG.PATHWAY
    uri_format: https://bioregistry.io/kegg.pathway:$1
  contact:
    email: kanehisa@kuicr.kyoto-u.ac.jp
    github: null
    name: Minoru Kanehisa
    orcid: 0000-0001-6123-540X
  domain: pathway
  edam:
    description: Identifier of a pathway from the KEGG pathway database.
    name: Pathway ID (KEGG)
    obsolete: false
    prefix: '2343'
  example: rsk00410
  go:
    homepage: http://www.genome.jp/kegg/pathway.html
    name: KEGG Pathways Database
    prefix: KEGG_PATHWAY
    uri_format: http://www.genome.jp/dbget-bin/www_bget?path:$1
  logo: https://www.genome.jp/Fig/kegg128.gif
  mappings:
    biocontext: KEGG.PATHWAY
    biolink: KEGG.PATHWAY
    edam: '2343'
    go: KEGG_PATHWAY
    miriam: kegg.pathway
    n2t: kegg.pathway
    prefixcommons: kegg.pathway
    wikidata: P665
  miriam:
    deprecated: false
    description: KEGG PATHWAY is a collection of manually drawn pathway maps representing
      our knowledge on the molecular interaction and reaction networks.
    homepage: https://www.genome.jp/kegg/pathway.html
    id: '00000012'
    name: KEGG Pathway
    namespaceEmbeddedInLui: false
    pattern: ^\w{2,4}\d{5}$
    prefix: kegg.pathway
    sampleId: hsa00620
  n2t:
    description: KEGG PATHWAY is a collection of manually drawn pathway maps representing
      our knowledge on the molecular interaction and reaction networks.
    example: hsa00620
    homepage: https://www.genome.jp/kegg/pathway.html
    name: KEGG PATHWAY Database
    namespaceEmbeddedInLui: false
    pattern: ^\w{2,4}\d{5}$
    prefix: kegg.pathway
  name: KEGG pathway
  part_of_database: kegg
  prefix: kegg.pathway
  prefixcommons:
    alt_uri_formats:
    - http://www.genome.jp/kegg-bin/show_pathway?#$1
    description: KEGG PATHWAY is a collection of manually drawn pathway maps (see
      new maps, change history, and last updates) representing our knowledge on the
      molecular interaction and reaction networks
    example: map00071
    homepage: http://www.genome.jp/kegg/pathway.html
    keywords:
    - pathway
    name: KEGG Pathway
    pattern: ^map\d+$
    prefix: kegg.pathway
    pubmed_ids:
    - '22700311'
    synonyms:
    - path
    - kegg.pathways
    uri_format: http://www.genome.jp/dbget-bin/www_bget?map$1
  publications:
  - doi: 10.1002/0471250953.bi0112s38
    pmc: null
    pubmed: '22700311'
    title: Using the KEGG database resource
    year: 2012
  - doi: null
    pmc: null
    pubmed: '22700311'
    title: null
    year: null
  synonyms:
  - KEGG-path
  - KEGG_PATHWAY
  uri_format: https://www.kegg.jp/pathway/$1
  wikidata:
    prefix: P665
kegg.rclass:
  biolink:
    is_identifiers: false
    is_obo: false
    prefix: KEGG.RCLASS
    uri_format: https://www.genome.jp/dbget-bin/www_bget?rc:$1
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: KEGG RCLASS contains classification of reactions based on the chemical
    structure transformation patterns of substrate-product pairs (reactant pairs),
    which are represented by the so-called RDM patterns.
  example: RC00001
  homepage: http://www.genome.jp/kegg/reaction/
  integbio:
    alt_name: KEGG Reaction Class
    description: KEGG RCLASS is a database of enzymatic reactions as organized by
      the KEGG system and contains an expandable list of all reaction types organized
      hierarchically. A search function for reaction class is also available. Users
      can obtain the compounds and enzymes involved for each specified reaction pathway.
    homepage: http://www.genome.jp/kegg-bin/get_htext?br08204.keg
    information_keywords:
    - Interaction/Pathway
    - Chemical structure
    maintainer: Kyoto University Institute for Chemical Research Bioinformatics Center
    name: KEGG RCLASS
    prefix: nbdc00860
    status: Active
    target_keywords:
    - RNA
    - Protein
  logo: https://www.genome.jp/Fig/kegg128.gif
  mappings:
    biolink: KEGG.RCLASS
    integbio: nbdc00860
  name: KEGG Reaction Class
  part_of: kegg
  pattern: ^RC\d+$
  prefix: kegg.rclass
  references:
  - https://github.com/prefixcommons/prefixes/pull/2
  synonyms:
  - KEGG_RCLASS
  - KEGG_REACTION_CLASS
kegg.reaction:
  biocontext:
    prefix: KEGG.REACTION
  contact:
    email: kanehisa@kuicr.kyoto-u.ac.jp
    github: null
    name: Minoru Kanehisa
    orcid: 0000-0001-6123-540X
  edam:
    description: Identifier of a biological reaction from the KEGG reactions database.
    name: Reaction ID (KEGG)
    obsolete: false
    prefix: '2608'
  go:
    homepage: http://www.genome.jp/kegg/reaction/
    name: KEGG Reaction Database
    prefix: KEGG_REACTION
    uri_format: http://www.genome.jp/dbget-bin/www_bget?rn:$1
  integbio:
    alt_name: Knowledge base for predicting biodegradation and biosynthesis
    description: KEGG REACTION is a database of enzymatic reactions. The database
      contains all KEGG enzyme interactions and KEGG pathway metabolic reactions,
      including related pathways, and uses IUBMB nomenclature. Users can also find
      the reaction pathway of individual enzymes.
    homepage: http://www.genome.jp/kegg/reaction/
    information_keywords:
    - Interaction/Pathway
    - Chemical structure
    - Classification
    maintainer: Kyoto University Institute for Chemical Research Bioinformatics Center
    name: KEGG REACTION
    prefix: nbdc00818
    pubmeds:
    - '14505407'
    - '15600352'
    - '19477985'
    - '17516640'
    - '20435670'
    status: Active
    target_keywords:
    - RNA
    - Protein
  logo: https://www.genome.jp/Fig/kegg128.gif
  mappings:
    biocontext: KEGG.REACTION
    edam: '2608'
    go: KEGG_REACTION
    integbio: nbdc00818
    miriam: kegg.reaction
    n2t: kegg.reaction
    prefixcommons: kegg.reaction
    wikidata: P665
  miriam:
    deprecated: false
    description: KEGG reaction contains our knowledge on the universe of reactions
      that are relevant to life.
    homepage: https://www.genome.jp/kegg/reaction/
    id: '00000014'
    name: KEGG Reaction
    namespaceEmbeddedInLui: false
    pattern: ^R\d+$
    prefix: kegg.reaction
    sampleId: R00100
    uri_format: https://www.kegg.jp/entry/$1
  n2t:
    description: KEGG reaction contains our knowledge on the universe of reactions
      that are relevant to life.
    example: R00100
    homepage: https://www.genome.jp/kegg/reaction/
    name: KEGG Reaction Database
    namespaceEmbeddedInLui: false
    pattern: ^R\d+$
    prefix: kegg.reaction
    uri_format: https://www.kegg.jp/entry/$1
  name: KEGG Reaction
  part_of: kegg
  prefix: kegg.reaction
  prefixcommons:
    description: KEGG REACTION contains all reactions taken from KEGG ENZYME and additional
      reactions taken from the metabolic pathway maps in KEGG PATHWAY.
    example: R00047
    homepage: http://www.genome.jp/kegg/reaction/
    keywords:
    - enzyme
    - pathway
    name: KEGG Reaction
    pattern: ^R\d+$
    prefix: kegg.reaction
    pubmed_ids:
    - '22700311'
    synonyms:
    - rn
    - kegg.reactions
    uri_format: http://www.genome.jp/dbget-bin/www_bget?rn:$1
  publications:
  - doi: 10.1002/0471250953.bi0112s38
    pmc: null
    pubmed: '22700311'
    title: Using the KEGG database resource
    year: 2012
  - doi: null
    pmc: null
    pubmed: '22700311'
    title: null
    year: null
  synonyms:
  - KEGG_REACTION
  wikidata:
    description: identifier from databases dealing with genomes, enzymatic pathways,
      and biological chemicals
    example:
    - D00018
    - D05961
    homepage: https://www.kegg.jp/
    miriam: kegg
    name: KEGG ID
    pattern: ^[A-Z]\d+$
    prefix: P665
    uri_format: https://www.kegg.jp/entry/$1
    uri_format_rdf: http://www.kegg.jp/entry/$1
kerafast:
  cellosaurus:
    category: Cell line collections (Providers)
    homepage: https://www.kerafast.com/
    name: Kerafast cell lines
    prefix: Kerafast
    uri_format: https://www.kerafast.com/Search?SearchTerm=&quot;$1&quot;
  example: EJH014
  mappings:
    cellosaurus: Kerafast
  prefix: kerafast
kestrelo:
  contact:
    email: lindsey.anderson@pnnl.gov
    github: lnanderson
    name: Lindsey N. Anderson
    orcid: 0000-0002-8741-7823
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: An ontology for harmonizing and extending severeral existing resources
    in the vaccine and immunology domains
  example: '0000001'
  homepage: https://gitlab.pnnl.gov/kestrel/kestrel_ontology
  name: KESTREL Ontology
  pattern: ^\d{7}$
  prefix: kestrelo
  uri_format: http://purl.obolibrary.org/obo/kestrelo_$1
kim.amb:
  contact:
    email: null
    github: acka47
    name: Adrian Pohl
    orcid: 0000-0001-9083-7442
  contributor:
    email: m.voigt@hzdr.de
    github: eilmiv
    name: Martin Voigt
    orcid: 0000-0001-5556-838X
  description: A cross-sectoral metadata profile for describing teaching and learning
    resources, primarily based on [schema.org](https://schema.org) and the Learning
    Resource Metadata Initiative LRMI, and additionally utilizing elements of the
    Simple Knowledge Organization System SKOS. A JSON-LD11-compliant data structure
    is defined in the form of this HTML specification, including a JSON schema against
    which data can be automatically checked for conformity with the profile.
  example: conditionsofaccess
  github_request_issue: 1780
  homepage: https://dini-ag-kim.github.io/amb/20231019/
  keywords:
  - learning material
  - learning materials
  - open educational resource
  - open educational resources
  - schema
  license: CC0-1.0
  name: Allgemeines Metadatenprofil für Bildungsressourcen
  pattern: ^[a-z]\w+$
  prefix: kim.amb
  repository: https://gitub.com/dini-ag-kim/amb
  reviewer:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  uri_format: https://dini-ag-kim.github.io/amb/20231019/#$1
kim.conditionsofaccess:
  contributor:
    email: null
    github: eilmiv
    name: Martin Voigt
    orcid: 0000-0001-5556-838X
  description: Identifiers describing conditions of access to an object (login) as
    defined by the [OER metadata group](https://oerworldmap.org/resource/urn:uuid:fd06253e-fe67-4910-b923-51db9d27e59f).
  example: no_login
  example_decoys:
  - nope
  example_extras:
  - login
  github_request_issue: 1782
  homepage: https://skohub.io/dini-ag-kim/value-lists/heads/main/w3id.org/kim/conditionsOfAccess/index.html
  keywords:
  - learning material
  - learning materials
  - open educational resource
  - open educational resources
  license: CC0-1.0
  name: Conditions of Access
  pattern: ^login|no_login$
  prefix: kim.conditionsofaccess
  reviewer:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  uri_format: https://skohub.io/dini-ag-kim/value-lists/heads/main/w3id.org/kim/conditionsOfAccess/$1.html
kim.educationlevel:
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: A controlled vocabulary for education levels, such as primary eduation,
    secondary education, and post-secondary education
  download_rdf: https://github.com/dini-ag-kim/educationalLevel/raw/refs/heads/main/educationalLevel.ttl
  example: '6'
  example_extras:
  - B
  homepage: https://w3id.org/kim/educationalLevel/
  keywords:
  - education level
  - open educational resources
  mappings:
    tib: educationallevel
  name: KIM Education Level
  prefix: kim.educationlevel
  repository: https://github.com/dini-ag-kim/educationalLevel
  tib:
    description: Eine Wertelliste für die Stufe im Bildungssystem als Lehr-/Lernkontext,
      für den Lernobjekt ausgewiesen ist.
    download_rdf: https://raw.githubusercontent.com/dini-ag-kim/educationalLevel/main/educationalLevel.ttl
    homepage: https://github.com/dini-ag-kim/educationalLevel
    keywords:
    - Educational Resources
    - educational science
    name: Educational level
    prefix: educationallevel
    tracker: https://github.com/dini-ag-kim/educationalLevel/issues/
    uri_format: https://w3id.org/kim/educationalLevel/$1
  uri_format: https://w3id.org/kim/educationalLevel/level_$1
kim.esv:
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: This is a vocabulary for educational sectors as used in the OER World
    Map (https://oerworldmap.org)
  download_rdf: https://github.com/dini-ag-kim/vocabs-edu/raw/refs/heads/master/sectors.ttl
  example: earlyChildhood
  homepage: https://w3id.org/kim/educationalLevel/
  name: Educational Sectors Vocabulary
  prefix: kim.esv
  repository: https://github.com/dini-ag-kim/vocabs-edu
  uri_format: https://w3id.org/class/sectors/$1
kim.hcrt:
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: A controlled vocbualry of higher education resource types
  download_skos: https://github.com/dini-ag-kim/hcrt/raw/refs/heads/master/hcrt.ttl
  example: simulation
  homepage: https://w3id.org/kim/hcrt/scheme.html
  mappings:
    tib: hcrt
  name: Higher Education Resource Types
  prefix: kim.hcrt
  rdf_uri_format: https://w3id.org/kim/hcrt/$1
  repository: https://github.com/dini-ag-kim/hcrt
  tib:
    description: Eine Wertelliste für Typen von Lernressourcen (Learning Resource
      Type), entstanden im Kontext des Metadatenschemas \"LOM for Higher Education
      OER Repositories\" (https://w3id.org/dini-ag-kim/hs-oer-lom-profil/latest/).
    download_rdf: https://raw.githubusercontent.com/dini-ag-kim/hcrt/master/hcrt.ttl
    homepage: https://skohub.io/dini-ag-kim/hcrt/heads/master/w3id.org/kim/hcrt/scheme.en.html
    keywords:
    - Educational Resources
    - educational science
    name: Hochschulcampus Ressourcentypen
    prefix: hcrt
    tracker: https://github.com/dini-ag-kim/hcrt/issues
    uri_format: https://w3id.org/kim/hcrt/$1
  uri_format: https://w3id.org/kim/hcrt/$1
kim.hochschulfaechersystematik:
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: A classification of subjects in Hochschule (universities of applied
    sciences)
  download_rdf: https://github.com/dini-ag-kim/hochschulfaechersystematik/raw/refs/heads/master/hochschulfaechersystematik.ttl
  example: n2
  homepage: https://w3id.org/kim/hochschulfaechersystematik/scheme
  mappings:
    tib: hfs
  name: German University Subject Classification System
  prefix: kim.hochschulfaechersystematik
  rdf_uri_format: https://w3id.org/kim/hochschulfaechersystematik/$1
  repository: https://github.com/dini-ag-kim/hochschulfaechersystematik
  tib:
    description: Diese Hochschulfächersystematik basiert auf der Destatis-Systematik
      der Fächergruppen, Studienbereiche und Studienfächer (http://bartoc.org/node/18919)
      und wird gepflegt von der OER-Metadatengruppe der DINI-AG KIM. Die Systematik
      ist Bestandteil der Spezifikationen LOM for Higher Education OER Repositories
      und LRMI-Profil (Entwurf).
    download_rdf: https://raw.githubusercontent.com/dini-ag-kim/hochschulfaechersystematik/master/hochschulfaechersystematik.ttl
    homepage: https://bartoc.org/en/node/18919
    keywords:
    - Educational Resources
    - educational science
    name: Hochschulfächersystematik
    prefix: hfs
    uri_format: https://w3id.org/kim/hochschulfaechersystematik/$1
  uri_format: https://w3id.org/kim/hochschulfaechersystematik/$1
kim.license:
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: A vocabulary describing licenses for data and code
  download_rdf: https://github.com/dini-ag-kim/license/raw/refs/heads/main/license.ttl
  example: nonCommercial
  homepage: https://w3id.org/kim/license/
  keywords:
  - license
  name: KIM License
  prefix: kim.license
  rdf_uri_format: https://w3id.org/kim/license/$1
  repository: https://github.com/dini-ag-kim/license
  uri_format: https://w3id.org/kim/license/$1
kim.lp:
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: This ontology is a formal representation that captures the fundamental
    concepts and their relationships to one another in the field of curriculum design
    and implementation of the German school system.
  download_owl: https://github.com/dini-ag-kim/school-curriculum-pg/raw/refs/heads/main/lp.owl
  example: '0000141'
  homepage: https://github.com/dini-ag-kim/school-curriculum-pg
  name: Lehrplan Ontology
  pattern: ^\d{7}$
  prefix: kim.lp
  repository: https://github.com/dini-ag-kim/school-curriculum-pg
  uri_format: https://w3id.org/lehrplan/ontology/LP_$1
kim.schularten:
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: This SKOS vocabulary describes types of primary and secondary schools
    in Germany, such as Grundschule, Gymnasium, and Realschule. This does not include
    post-secondary education such as universities or hochschulen.
  download_rdf: https://github.com/dini-ag-kim/schularten/raw/refs/heads/main/schularten.ttl
  example: s02
  github_request_issue: 1626
  homepage: https://github.com/dini-ag-kim/schularten
  keywords:
  - primary school type
  - school type
  - seconary school type
  license: CC0-1.0
  name: KIM German School Types
  prefix: kim.schularten
  rdf_uri_format: https://w3id.org/kim/schularten/$1
  repository: https://github.com/dini-ag-kim/schularten
  uri_format: https://w3id.org/kim/schularten/$1
kim.schulfaecher:
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: A vocabulary describing subjects taught in German primary and secondary
    school (not university/hochschulen), such as German, math, and art.
  download_rdf: https://github.com/dini-ag-kim/schulfaecher/raw/refs/heads/main/schulfaecher.ttl
  example: s1000
  github_request_issue: 1626
  homepage: https://github.com/dini-ag-kim/schulfaecher
  keywords:
  - discipline
  - school subject
  - subject
  name: KIM School Subjects
  prefix: kim.schulfaecher
  rdf_uri_format: http://w3id.org/kim/schulfaecher/$1
  repository: https://github.com/dini-ag-kim/schulfaecher
  uri_format: http://w3id.org/kim/schulfaecher/$1
kit.mtxx:
  example: 002_xxx_xxx-a228d7e065dc45b4b5ab48876aab7228-vp
  mappings:
    tib: kitmtxx
  prefix: kit.mtxx
  tib:
    description: Objects of this class contain a self-bound collection of mass bearing
      particles.
    download_rdf: https://gitlab.com/linked-tribological-data/vocabulary-materials-tribology-lab-at-kit/-/raw/main/SKOS_Vocabulary_Materials%20Tribology%20Lab%20at%20KIT.ttl
    homepage: https://gitlab.com/linked-tribological-data/vocabulary-materials-tribology-lab-at-kit
    keywords:
    - NFDI4ING
    - material science
    name: Vocabulary of Materials Tribology Lab at KIT
    prefix: kitmtxx
    uri_format: https://purls.helmholtz-metadaten.de/vp/kitmtxx-41732562-vp$1
  uri_format: https://purls.helmholtz-metadaten.de/vp/kitmtxx-41732562-vp/$1
knapsack:
  biocontext:
    prefix: KNAPSACK
  integbio:
    alt_name: A Comprehensive Species-Metabolite Relationship Database
    description: 'This database provides information on how species and metabolites
      relate to each other.

      Searches can be done on the Web by entering the organism''s name or that of
      the metabolite or its molecular weight or formula.

      The site also offers the option to download the database and work offline.'
    homepage: http://www.knapsackfamily.com/KNApSAcK/
    information_keywords:
    - Bibliography/Documents
    - Chemical structure
    maintainer: Nara Institute of Science and Technology
    name: KNApSAcK
    prefix: nbdc00545
    pubmeds:
    - '22123792'
    status: Active
    target_keywords:
    - Metabolite
    - Chemical compound
  mappings:
    biocontext: KNAPSACK
    integbio: nbdc00545
    miriam: knapsack
    n2t: knapsack
    wikidata: P2064
  miriam:
    deprecated: false
    description: 'KNApSAcK provides information on metabolites and the

      taxonomic class with which they are associated.'
    homepage: http://www.knapsackfamily.com/KNApSAcK/
    id: '00000271'
    name: KNApSAcK
    namespaceEmbeddedInLui: false
    pattern: ^C\d{8}$
    prefix: knapsack
    sampleId: C00000001
    uri_format: http://www.knapsackfamily.com/knapsack_core/information.php?word=$1
  n2t:
    description: Knapsack provides information on metabolites and  the taxonomic class
      with which they are associated.
    example: C00000001
    homepage: http://kanaya.aist-nara.ac.jp/KNApSAcK/
    name: KnapSack at Nara Institute
    namespaceEmbeddedInLui: false
    pattern: ^C\d{8}
    prefix: knapsack
    uri_format: http://kanaya.naist.jp/knapsack_jsp/information.jsp?word=$1
  name: KNApSAcK
  prefix: knapsack
  synonyms:
  - KNApSAcK
  wikidata:
    description: identifier in the KNApSAcK Core System
    example:
    - C00000001
    - C00035015
    name: KNApSAcK ID
    pattern: ^C\d{8}$
    prefix: P2064
    uri_format: https://www.knapsackfamily.com/knapsack_core/information.php?sname=C_ID&word=$1
kpio:
  example: Goal
  mappings:
    tib: kpi
  prefix: kpio
  tib:
    description: The Key Performance Indicator module aims to model the metrics defined
      at the beginning of building renovation activities to monitor the conformance
      with typical requirements related to energy efficient buildings.
    download_rdf: https://bimerr.iot.linkeddata.es/def/key-performance-indicator/ontology.ttl
    homepage: http://bimerr.iot.linkeddata.es/def/key-performance-indicator
    keywords:
    - FID BAUdigital
    - Digital Planning and Construction
    - NFDI4ING
    - civil engineering
    - computer science
    name: Key Performance Indicator ontology
    prefix: kpi
    uri_format: http://bimerr.iot.linkeddata.es/def/key-performance-indicator#$1
kupo:
  appears_in:
  - cl
  comment: Website is down, now it redirects to something else that is not related
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  deprecated: true
  example: 0001009
  homepage: http://www.kupkb.org/
  name: Kidney and Urinary Pathway Ontology
  pattern: ^\d{7}$
  prefix: kupo
  references:
  - https://jbiomedsem.biomedcentral.com/articles/10.1186/2041-1480-2-S2-S7
kyinno:
  cellosaurus:
    category: Cell line collections (Providers)
    homepage: https://www.kyinno.com/
    name: KYinno cell lines
    prefix: KYinno
    uri_format: https://www.kyinno.com/?s=$1
  example: KC-0979
  mappings:
    cellosaurus: KYinno
  prefix: kyinno
labo:
  aberowl:
    description: LABO is an ontology of informational entities formalizing clinical
      laboratory tests prescriptions and reporting documents.
    download_owl: http://aber-owl.net/media/ontologies/LABO/3/labo.owl
    homepage: https://github.com/OpenLHS/LABO
    name: clinical LABoratory Ontology
    prefix: LABO
  bioportal:
    contact:
      email: paul.fabry@usherbrooke.ca
      name: Paul Fabry
    description: LABO is an ontology of informational entities describing laboratory
      tests prescriptions and reporting documents. LABO is a component of a core ontological
      model, along with the ontology of drug prescriptions PDRO, that aims to enable
      interoperability between various clinical data sources in the context of a Learning
      Health System.
    homepage: https://github.com/OpenLHS/LABO
    name: clinical LABoratory Ontology
    prefix: LABO
  example: '0000124'
  mappings:
    aberowl: LABO
    bioportal: LABO
    obofoundry: labo
    ols: labo
    ontobee: LABO
    wikidata.entity: Q81661673
  obofoundry:
    contact: paul.fabry@usherbrooke.ca
    contact.github: pfabry
    contact.label: Paul Fabry
    contact.orcid: 0000-0002-3336-2476
    depends_on:
    - iao
    - obi
    - ogms
    - omiabis
    - omrse
    - opmi
    deprecated: false
    description: LABO is an ontology of informational entities formalizing clinical
      laboratory tests prescriptions and reporting documents.
    domain: information
    download.owl: http://purl.obolibrary.org/obo/labo.owl
    homepage: https://github.com/OpenLHS/LABO
    license: CC BY 4.0
    license.url: https://creativecommons.org/licenses/by/4.0/
    name: clinical LABoratory Ontology
    preferredPrefix: LABO
    prefix: labo
    publications:
    - id: https://doi.org/10.5281/zenodo.6522019
      title: 'LABO: An Ontology for Laboratory Test Prescription and Reporting'
    repository: https://github.com/OpenLHS/LABO
  ols:
    description: LABO is an ontology of informational entities formalizing clinical
      laboratory tests prescriptions and reporting documents.
    download_owl: http://purl.obolibrary.org/obo/labo.owl
    homepage: https://github.com/OpenLHS/LABO
    name: clinical LABoratory Ontology
    prefix: labo
    tracker: https://github.com/OpenLHS/LABO/issues
    version: '2021-06-08'
    version.iri: http://purl.obolibrary.org/obo/labo/2021-06-08/labo.owl
  ontobee:
    library: Library
    name: clinical LABoratory Ontology
    prefix: LABO
  pattern: ^\d{7}$
  prefix: labo
  publications:
  - doi: 10.5281/zenodo.6522019
    pmc: null
    pubmed: null
    title: 'LABO: An ontology for laboratory test prescription and reporting'
    year: 2019
  uri_format: http://purl.obolibrary.org/obo/LABO_$1
langual:
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: 'Langual stands for "langua alimentaria" or "language of food". it
    is an automated method for describing, capturing and retrieving data about food.
    the work on langual was started in the late 1970''s by the center for food safety
    and applied nutrition (cfsan) of the united states food and drug administration
    as an ongoing co-operative effort of specialists in food technology, information
    science and nutrition. the thesaurus provides a standardized language for describing
    foods, specifically for classifying food products for information retrieval. langual
    is based on the concept that: - any food (or food product) can be systematically
    described by a combination of characteristics - these characteristics can be categorized
    into viewpoints and coded for computer processing - the resulting viewpoint/characteristic
    codes can be used to retrieve data about the food from external databases'
  example: B2067
  github_request_issue: 507
  homepage: https://www.langual.org
  name: Langua aLimentaria Thesaurus
  pattern: ^B\d+$
  prefix: langual
  uri_format: https://www.langual.org/langual_thesaurus.asp?termid=$1
lattes:
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  homepage: https://lattes.cnpq.br
  keywords:
  - person
  - researcher
  mappings:
    wikidata: P1007
  prefix: lattes
  references:
  - https://github.com/biopragmatics/bioregistry/pull/1171
  wikidata:
    description: number for the Lattes Platform entry on the person or group. Relationship
      between entry and subject must be supported by a source.
    example:
    - 0061106995455595
    - '9975840620597737'
    name: Lattes Platform number
    pattern: ^\d{16}$
    prefix: P1007
    uri_format: https://lattes.cnpq.br/$1
lbctr:
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: The Lebanese Clinical Trials Registry is an online register of clinical
    trials being undertaken in Lebanon. It includes trials that target humans from
    the full spectrum of therapeutic areas of pharmaceuticals, surgical procedures,
    preventive measures, lifestyle, devices, treatment and rehabilitation strategies
    and complementary therapies. (from homepage)
  example: LBCTR2023015204
  homepage: https://lbctr.moph.gov.lb/
  name: Lebanon Clinical Trials Registry
  pattern: ^LBCTR\d+$
  prefix: lbctr
  references:
  - https://lbctr.moph.gov.lb/Trials/Details/5204
lbo:
  aberowl:
    description: A vocabulary for buffalo, cattle, chicken, goat, horse, pig, and
      sheep breeds.
    download_obo: http://aber-owl.net/media/ontologies/LBO/9/lbo.obo
    name: Livestock Breed Ontology
    prefix: LBO
    version: '2.2'
  agroportal:
    contact:
      email: jreecy@iastate.edu
      name: Jim Reecy
    description: A vocabulary for buffalo, cattle, chicken, goat, horse, pig, and
      sheep breeds., The Livestock Breed Ontology is a controlled vocabulary for buffalo
    example_uri: http://purl.obolibrary.org/obo/LBO_0000700
    license: CC-BY-4.0
    name: Livestock Breed Ontology
    prefix: LBO
    repository: https://github.com/AnimalGenome/livestock-breed-ontology
    version: '2025-10-08'
  bioportal:
    contact:
      email: caripark@iastate.edu
      name: Cari Park
    description: A vocabulary for buffalo, cattle, chicken, goat, horse, pig, and
      sheep breeds., The Livestock Breed Ontology is a controlled vocabulary for buffalo
    license: CC-BY-4.0
    name: Livestock Breed Ontology
    prefix: LBO
    version: '2025-10-08'
  contact:
    email: caripark@iastate.edu
    github: caripark
    name: Carissa Park
    orcid: 0000-0002-2346-5201
  download_obo: https://github.com/AnimalGenome/livestock-breed-ontology/raw/master/current_release/lbo.obo
  download_owl: https://github.com/AnimalGenome/livestock-breed-ontology/raw/master/current_release/lbo.owl
  example: 0000487
  fairsharing:
    abbreviation: LBO
    description: 'The Livestock Breed Ontology (LBO) is a controlled vocabulary for
      the unambiguous description of breeds. Its utility include proper identification
      of inherited variation sources in genetics/genomic studies. '
    homepage: https://www.animalgenome.org/bioinfo/projects/lbo/
    license: CC BY-NC 4.0
    name: Livestock Breed Ontology
    prefix: FAIRsharing.309v57
    repository: https://github.com/AnimalGenome/livestock-breed-ontology
    subjects:
    - Animal Breeding
    - Animal Husbandry
    - Genetics
    - Genomics
  mappings:
    aberowl: LBO
    agroportal: LBO
    bioportal: LBO
    fairsharing: FAIRsharing.309v57
    ols: lbo
  ols:
    contact: jreecy@iastate.edu
    description: A vocabulary for cattle, chicken, horse, pig, and sheep breeds.
    download: http://data.bioontology.org/ontologies/LBO/download?apikey=8b5b7825-538d-40e0-9e9e-5ab9274a9aeb
    homepage: http://bioportal.bioontology.org/ontologies/LBO
    name: Livestock Breed Ontology
    prefix: lbo
  pattern: ^\d{7}$
  prefix: lbo
  rdf_uri_format: http://purl.obolibrary.org/obo/LBO_$1
  repository: https://github.com/AnimalGenome/livestock-breed-ontology
  uri_format: https://bioportal.bioontology.org/ontologies/LBO/?p=classes&conceptid=http://purl.obolibrary.org/obo/LBO_$1
lccn:
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: LCCN Permalinks are persistent URLs for bibliographic records in the
    LC Catalog and authority records in LC Authorities. These links are constructed
    using the record's LCCN (or Library of Congress Control Number), an identifier
    assigned by the Library of Congress to bibliographic and authority records. LCCN
    Permalinks are also available for citation records in the Handbook for Latin American
    Studies (HLAS). [from homepage]
  example: '2011488555'
  github_request_issue: 1310
  homepage: https://lccn.loc.gov
  name: Library of Congress Control Number
  pattern: ^\d+$
  prefix: lccn
  uri_format: https://lccn.loc.gov/$1
lcsh:
  bartoc:
    abbreviation: LCSH
    description: 'LCSH in this service includes all Library of Congress Subject Headings,
      free-floating subdivisions (topical and form), Genre/Form headings, Children''s
      (AC) headings, and validation strings for which authority records have been
      created. The content includes a few name headings (personal and corporate),
      such as William Shakespeare, Jesus Christ, and Harvard University, and geographic
      headings that are added to LCSH as they are needed to establish subdivisions,
      provide a pattern for subdivision practice, or provide reference structure for
      other terms. This content is expanded beyond the print issue of LCSH (the ''red
      books'') with inclusion of validation strings. *Validation strings: Some authority
      records are for headings that have been built by adding subdivisions. These
      records are the result of an ongoing project to programmatically create authority
      records for valid subject strings from subject heading strings found in bibliographic
      records. The authority records for these subject strings were created so the
      entire string could be machine-validated. The strings do not have broader, narrower,
      or related terms. Library of Congress Subject Headings (LCSH) has been actively
      maintained since 1898 to catalog materials held at the Library of Congress.
      By virtue of cooperative cataloging other libraries around the United States
      also use LCSH to provide subject access to their collections. In addition LCSH
      is used internationally, often in translation.'
    homepage: http://id.loc.gov/authorities/subjects.html
    license: CC0-1.0
    name: Library of Congress Subject Headings
    prefix: '454'
    wikidata_database: Q1823134
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: Library of Congress Subject Headings (LCSH) has been actively maintained
    since 1898 to catalog materials held at the Library of Congress. (from homepage)
  example: nb2018006591
  fairsharing:
    abbreviation: LCSH
    description: The Library of Congress Subject Headings (LCSH) provides catalog
      headings for materials held at the Library of Congress. Libraries throughout
      the United States use LCSH to provide subject access to their collections. LCSH
      is also used internationally, often in translation. The LCSH online resource
      includes all Library of Congress Subject Headings, free-floating subdivisions
      (topical and form), Genre/Form headings, Children's (AC) headings, and validation
      strings for which authority records have been created.
    homepage: https://id.loc.gov/authorities/subjects.html
    license: https://www.loc.gov/legal
    name: Library of Congress Subject Headings
    prefix: FAIRsharing.d31795
    subjects:
    - Subject Agnostic
  homepage: https://id.loc.gov/authorities
  mappings:
    bartoc: '454'
    fairsharing: FAIRsharing.d31795
    wikidata: P244
    wikidata.entity: Q17109002
  name: Library of Congress Subject Headings
  pattern: ^\w{1,2}\d{8,10}$
  prefix: lcsh
  providers:
  - code: subject
    description: a subspace
    example: null
    first_party: null
    homepage: https://id.loc.gov/authorities/subjects.html
    name: LOC Subject
    publications: null
    status: null
    uri_format: http://id.loc.gov/authorities/subjects/$1
  synonyms:
  - lcnaf
  - lcnafid
  uri_format: https://id.loc.gov/authorities/$1
  wikidata:
    database: Q620946
    description: 'Library of Congress name authority (persons, families, corporate
      bodies, events, places, works and expressions) and subject authority identifier
      [Format: 1-2 specific letters followed by 8-10 digits (see regex). For manifestations,
      use P1144]'
    example:
    - n79022935
    - n81082970
    - n81092084
    - n84023326
    - sh2008005914
    - sh2020006558
    - sh85037527
    homepage: https://id.loc.gov
    name: Library of Congress authority ID
    pattern: ^(cf|ct|gf|n|nb|nr|no|ns|sh|sj)([4-9][0-9]|00|01|20[0-2][0-9])[0-9]{6}$
    prefix: P244
    short_name:
    - LC authority ID
    - LCAuth
    uri_format: https://id.loc.gov/authorities/$1
    uri_format_rdf: http://id.loc.gov/authorities/names/$1
lcsh.genreforms:
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: A subset of Library of Congress (LOC) subject headings
  example: gf2018026088
  homepage: https://id.loc.gov/authorities
  name: Library of Congress Subject Headings - Genre Forms
  part_of: lcsh
  prefix: lcsh.genreforms
  uri_format: http://id.loc.gov/authorities/genreForms/$1
ldp:
  example: Resource
  lov:
    description: A set of best practices and simple approach for a read-write Linked
      Data architecture, based on HTTP access to web resources that describe their
      state using the RDF data model.
    homepage: http://www.w3.org/TR/ldp/
    keywords:
    - API
    modified: '2015-02-26'
    name: Linked Data Platform
    prefix: ldp
    uri_prefix: http://www.w3.org/ns/ldp#$1
  mappings:
    lov: ldp
    zazuko: ldp
  name: Linked Data Platform Vocabulary
  prefix: ldp
  zazuko:
    prefix: ldp
    uri_format: http://www.w3.org/ns/ldp#$1
leafsnap:
  mappings:
    wikidata: P10538
  name: Leafsnap
  prefix: leafsnap
  wikidata:
    description: identifier for a tree species of the United States and Canada on
      the Leafsnap electronic field guide
    example:
    - Amelanchier laevis
    - Crataegus crus-galli
    homepage: http://leafsnap.com/
    name: Leafsnap ID
    prefix: P10538
    uri_format: http://leafsnap.com/species/$1/
lei:
  mappings:
    miriam: lei
    n2t: lei
  miriam:
    deprecated: false
    description: Established by the Financial Stability Board in June 2014, the Global
      Legal Entity Identifier Foundation (GLEIF) is tasked to support the implementation
      and use of the Legal Entity Identifier (LEI). The foundation is backed and overseen
      by the LEI Regulatory Oversight Committee, representing public authorities from
      around the globe that have come together to jointly drive forward transparency
      within the global financial markets. GLEIF is a supra-national not-for-profit
      organization headquartered in Basel, Switzerland.
    homepage: https://www.gleif.org/
    id: 00000686
    name: Global LEI Index
    namespaceEmbeddedInLui: false
    pattern: ^[0-9A-Z]{4}[0-9A-Z]{14}[0-9A-Z]{2}$
    prefix: lei
    sampleId: HWUPKR0MPOU8FGXBT394
    uri_format: https://www.gleif.org/lei/$1
  n2t:
    description: Established by the Financial Stability Board in June 2014, the Global
      Legal Entity Identifier Foundation (GLEIF) is tasked to support the implementation
      and use of the Legal Entity Identifier (LEI). The foundation is backed and overseen
      by the LEI Regulatory Oversight Committee, representing public authorities from
      around the globe that have come together to jointly drive forward transparency
      within the global financial markets. GLEIF is a supra-national not-for-profit
      organization headquartered in Basel, Switzerland.
    example: HWUPKR0MPOU8FGXBT394
    homepage: https://www.gleif.org/
    name: Global LEI Index
    namespaceEmbeddedInLui: false
    pattern: ^[0-9A-Z]{4}[0-9A-Z]{14}[0-9A-Z]{2}$
    prefix: lei
    uri_format: https://www.gleif.org/lei/$1
  prefix: lei
lepao:
  aberowl:
    description: The Lepidoptera Anatomy Ontology contains terms used for describing
      the anatomy and phenotype of moths and butterflies in biodiversity research.
      LEPAO is developed in part by BIOfid (The Specialised Information Service Biodiversity
      Research).
    download_owl: http://aber-owl.net/media/ontologies/LEPAO/2/lepao.owl
    homepage: https://github.com/insect-morphology/lepao
    name: Lepidoptera Anatomy Ontology
    prefix: LEPAO
  bioportal:
    contact:
      email: lagonzalezmo@unal.edu.co
      name: Luis A. Gonzalez-Montana
    description: The Lepidoptera Anatomy Ontology contains terms used for describing
      the anatomy and phenotype of moths and butterflies in biodiversity research.
      LEPAO is developed in part by BIOfid (The Specialised Information Service Biodiversity
      Research).
    homepage: https://github.com/insect-morphology/lepao
    name: Lepidoptera Anatomy Ontology
    prefix: LEPAO
    version: '2023-02-18'
  example: '0000005'
  mappings:
    aberowl: LEPAO
    bioportal: LEPAO
    obofoundry: lepao
    ols: lepao
    ontobee: LEPAO
    wikidata.entity: Q113012667
  obofoundry:
    contact: lagonzalezmo@unal.edu.co
    contact.github: luis-gonzalez-m
    contact.label: Luis A. Gonzalez-Montana
    contact.orcid: 0000-0002-9136-9932
    depends_on:
    - aism
    - bfo
    - bspo
    - caro
    - pato
    - ro
    - uberon
    deprecated: false
    description: The Lepidoptera Anatomy Ontology contains terms used for describing
      the anatomy and phenotype of moths and butterflies in biodiversity research.
      LEPAO is developed in part by BIOfid (The Specialised Information Service Biodiversity
      Research).
    domain: anatomy and development
    download.obo: http://purl.obolibrary.org/obo/lepao.obo
    download.owl: http://purl.obolibrary.org/obo/lepao.owl
    homepage: https://github.com/insect-morphology/lepao
    license: CC BY 4.0
    license.url: https://creativecommons.org/licenses/by/4.0/
    name: Lepidoptera Anatomy Ontology
    preferredPrefix: LEPAO
    prefix: lepao
    repository: https://github.com/insect-morphology/lepao
  ols:
    description: The Lepidoptera Anatomy Ontology contains terms used for describing
      the anatomy and phenotype of moths and butterflies in biodiversity research.
    download_owl: http://purl.obolibrary.org/obo/lepao.owl
    homepage: https://github.com/insect-morphology/lepao
    name: Lepidoptera Anatomy Ontology
    prefix: lepao
    tracker: https://github.com/insect-morphology/lepao/issues
    version: '2023-02-18'
    version.iri: http://purl.obolibrary.org/obo/lepao/releases/2023-02-18/lepao.owl
  ontobee:
    library: Library
    name: Lepidoptera Anatomy Ontology
    prefix: LEPAO
  pattern: ^\d{7}$
  prefix: lepao
  uri_format: http://purl.obolibrary.org/obo/LEPAO_$1
lexvo.ontology:
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: The data model underlying lexvo
  domain: data model
  download_owl: http://lexvo.org/ontology
  example: Language
  homepage: http://lexvo.org
  lov:
    description: An ontology for natural language terms description, including scripts,
      languages and meanings. The Lexvo.org ontology is still under development and
      may not be able to address all needs. Please also consider using the Lingvoj
      Ontology and the GOLD ontology, whereever appropriate.
    homepage: http://www.lexvo.org/
    keywords:
    - Vocabularies
    modified: '2014-01-29'
    name: Lexvo.org Ontology
    prefix: lvont
    uri_prefix: http://lexvo.org/ontology#$1
  mappings:
    lov: lvont
    zazuko: lvont
  name: Lexvo Ontology
  prefix: lexvo.ontology
  synonyms:
  - lvont
  uri_format: http://lexvo.org/ontology#$1
  zazuko:
    prefix: lvont
    uri_format: http://lexvo.org/ontology#$1
lgai.cede:
  mappings:
    miriam: lgai.cede
  miriam:
    deprecated: false
    description: LG Chemical Entity Detection Dataset (LGCEDe) is only available open-dataset
      with molecular instance level annotations (i.e. atom-bond level position annotations
      within an image) for molecular structure images. This dataset was designed to
      encourage research on detection-based pipelines for Optical Chemical Structure
      Recognition (OCSR).
    homepage: https://www.lgresearch.ai
    id: 00000867
    name: LG Chemical Entity Detection Dataset (LGCEDe)
    namespaceEmbeddedInLui: false
    pattern: ^LGCEDe-S-\d{9}$
    prefix: lgai.cede
    sampleId: LGCEDe-S-000002244
    uri_format: https://s3.us-east-2.amazonaws.com/lg.cede/$1
  prefix: lgai.cede
lgic:
  biocontext:
    prefix: LGIC
  comment: Website is gone
  deprecated: true
  mappings:
    biocontext: LGIC
    miriam: lgic
    n2t: lgic
    prefixcommons: lgicdb
  miriam:
    deprecated: true
    description: The Ligand-Gated Ion Channel database provides nucleic and proteic
      sequences of the subunits of ligand-gated ion channels. These transmembrane
      proteins can exist under different conformations, at least one of which forms
      a pore through the membrane connecting two neighbouring compartments. The database
      can be used to generate multiple sequence alignments from selected subunits,
      and gives the atomic coordinates of subunits, or portion of subunits, where
      available.
    homepage: https://www.ebi.ac.uk/compneur-srv/LGICdb/LGICdb.php
    id: 00000087
    name: Ligand-Gated Ion Channel database
    namespaceEmbeddedInLui: false
    pattern: ^\w+$
    prefix: lgic
    sampleId: 5HT3Arano
    uri_format: https://www.ebi.ac.uk/compneur-srv/LGICdb/HTML/$1.php
  n2t:
    description: The Ligand-Gated Ion Channel database provides nucleic and proteic
      sequences of the subunits of ligand-gated ion channels. These transmembrane
      proteins can exist under different conformations, at least one of which forms
      a pore through the membrane connecting two neighbouring compartments. The database
      can be used to generate multiple sequence alignments from selected subunits,
      and gives the atomic coordinates of subunits, or portion of subunits, where
      available.
    example: 5HT3Arano
    homepage: https://www.ebi.ac.uk/compneur-srv/LGICdb/LGICdb.php
    name: Ligand-Gated Ion Channel database at EBI
    namespaceEmbeddedInLui: false
    pattern: ^\w+$
    prefix: lgic
    uri_format: https://www.ebi.ac.uk/compneur-srv/LGICdb/HTML/$1.php
  prefix: lgic
  prefixcommons:
    description: The Ligand-Gated Ion Channel database provides nucleic and proteic
      sequences of the subunits of ligand-gated ion channels. These transmembrane
      proteins can exist under different conformations, at least one of which forms
      a pore through the membrane connecting two neighbouring compartments. The database
      can be used to generate multiple sequence alignments from selected subunits,
      and gives the atomic coordinates of subunits, or portion of subunits, where
      available.
    example: 5HT3Arano
    homepage: http://www.ebi.ac.uk/compneur-srv/LGICdb/
    keywords:
    - gene
    - protein
    - sequence
    license: http://www.ebi.ac.uk/Information/termsofuse.html
    name: Ligand-Gated Ion Channel database
    pattern: ^\w+$
    prefix: lgicdb
    pubmed_ids:
    - '9847222'
    synonyms:
    - lgic
    uri_format: http://www.ebi.ac.uk/compneur-srv/LGICdb/HTML/$1.php
  publications:
  - doi: 10.1093/nar/27.1.340
    pmc: PMC148177
    pubmed: '9847222'
    title: The Ligand Gated Ion Channel Database
    year: 1999
  - doi: null
    pmc: null
    pubmed: '9847222'
    title: null
    year: null
  - doi: null
    pmc: null
    pubmed: '9847222'
    title: null
    year: null
licebase:
  biocontext:
    prefix: LICEBASE
  fairsharing:
    abbreviation: LiceBase
    contact:
      email: Inge.Jonassen@uib.no
      name: Inge Jonassen
      orcid: 0000-0003-4110-0748
    description: LiceBase is a database for sea lice genomics. LiceBase provides the
      genome annotation of the Atlantic salmon louse Lepeophtheirus salmonis, a genome
      browser, Blast functionality and access to related high-thoughput genomics data.
    homepage: https://licebase.org/
    name: LiceBase
    prefix: FAIRsharing.c7w81a
    publications: []
    subjects:
    - Life Science
  integbio:
    description: LiceBase is a genomics database for sea lice (Lepeophtheirus salmonis
      and Caligus spp.), which are major pathogens affecting the global salmon farming
      industry. The database is designed to help researchers, industry professionals,
      and other interested parties access and share information about these parasites,
      with the goal of developing new treatment methods and tools to ensure a sustainable
      salmon farming industry. LiceBase provides genome annotation reports, genome
      browsing, RNA interference (RNAi) experiment browsing, BLAST search, and in-situ
      images. The database homepage posts news updates and recent publications related
      to sea lice and salmonid species.
    fairsharing: FAIRsharing.c7w81a
    homepage: https://licebase.org/
    information_keywords:
    - Sequence
    - Image/Movie
    maintainer: Sea Lice Research Centre
    name: LiceBase
    prefix: nbdc02217
    status: Active
    target_keywords:
    - Genome/Gene
    - RNA
    - Organism
  mappings:
    biocontext: LICEBASE
    fairsharing: FAIRsharing.c7w81a
    integbio: nbdc02217
    miriam: licebase
    n2t: licebase
    re3data: r3d100013547
  miriam:
    deprecated: false
    description: Sea lice (Lepeophtheirus salmonis and Caligus species) are the major
      pathogens of salmon,  significantly impacting upon the global salmon farming
      industry. Lice control is primarily accomplished through chemotherapeutants,
      though emerging resistance necessitates the development of new treatment methods
      (biological agents, prophylactics and new drugs). LiceBase is a database for
      sea lice genomics, providing genome annotation of the Atlantic salmon louse
      Lepeophtheirus salmonis, a genome browser, and access to related high-thoughput
      genomics data. LiceBase also mines and stores data from related genome sequencing
      and functional genomics projects.
    homepage: https://licebase.org
    id: 00000628
    name: LiceBase
    namespaceEmbeddedInLui: false
    pattern: ^[A-Za-z0-9\-\/]+$
    prefix: licebase
    sampleId: EMLSAT00000003403
    uri_format: https://licebase.org/?q=$1
  n2t:
    description: Sea lice (Lepeophtheirus salmonis and Caligus species) are the major
      pathogens of salmon,  significantly impacting upon the global salmon farming
      industry. Lice control is primarily accomplished through chemotherapeutants,
      though emerging resistance necessitates the development of new treatment methods
      (biological agents, prophylactics and new drugs). LiceBase is a database for
      sea lice genomics, providing genome annotation of the Atlantic salmon louse
      Lepeophtheirus salmonis, a genome browser, and access to related high-thoughput
      genomics data. LiceBase also mines and stores data from related genome sequencing
      and functional genomics projects.
    example: EMLSAT00000003403
    homepage: https://licebase.org
    name: LiceBase
    namespaceEmbeddedInLui: false
    pattern: ^[A-Za-z0-9\-\/]+$
    prefix: licebase
    uri_format: https://licebase.org/?q=$1
  prefix: licebase
  re3data:
    description: LiceBase is a database for sea lice genomics. LiceBase provides the
      genome annotation of the Atlantic salmon louse Lepeophtheirus salmonis, a genome
      browser, Blast functionality and access to related high-thoughput genomics data.
    doi: 10.17616/R31NJMY3
    homepage: https://licebase.org/
    name: LiceBase
    prefix: r3d100013547
lifestylefactors:
  bioportal:
    contact:
      email: lars.juhl.jensen@cpr.ku.dk
      name: Lars Juhl Jensen
    description: "In this ontology, we defined nine distinct categories that encompass\
      \ various aspects of lifestyle factors (LSFs), creating a unified Lifestyle\
      \ Factors Ontology (LSFO) across these categories. Within the context of lifestyle,\
      \ we have identified nine categories that can collectively describe all LSFs,\
      \ namely: \t1-Nutrition, a category that covers different branches such as dietary\
      \ habits, food groups, food processing and preparation, macronutrients, and\
      \ micronutrients, among others. \t2-Socioeconomic factors, which includes social\
      \ and economic conditions such as income, wealth, education and socioeconomic\
      \ status. \t3-Environmental exposures, includes exposure to various environmental\
      \ factors, such as air pollution, water quality, and workplace hazards, that\
      \ can impact an individual’s health. \t4-Substance use, covers concepts such\
      \ as smoking, as well as illicit drug use. \t5-Physical activities, includes\
      \ regular exercise and physically demanding activities like leisure time, occupational,\
      \ and household physical activities. \t6-Non-physical leisure time activities,\
      \ describes any activity an individual might engage in during their free time\
      \ that is not a physical activity. \t7-Personal care products and cosmetic procedures,\
      \ covers activities related to hygiene, use of cosmetic and cleaning products\
      \ as well as invasive procedures that people undergo to improve their appearance,\
      \ such as cosmetic surgery. \t8-Sleep, covers sleep quality, stages, and habits.\
      \ \t9-Mental health practices, includes the behaviors and habits related to\
      \ maintaining good mental health and emotional well-being such as meditation,\
      \ and psychotherapy. This ontology is released under the Creative Commons Attribution\
      \ 4.0 International (CC BY 4.0) license."
    name: Lifestyle Factor Ontology
    prefix: LSFO
    publications:
    - https://www.biorxiv.org/content/10.1101/2024.06.13.598816v2
    version: '1.01'
  example: '0000015'
  mappings:
    bioportal: LSFO
    ols: lifestylefactors
  ols:
    description: 'In this ontology, we defined nine distinct categories that encompass
      various aspects of lifestyle factors (LSFs), creating a unified Lifestyle Factors
      Ontology (LSFO) across these categories. Within the context of lifestyle, we
      have identified nine categories that can collectively describe all LSFs, namely:
      1-Nutrition, a category that covers different branches such as dietary habits,
      food groups, food processing and preparation, macronutrients, and micronutrients,
      among others. 2-Socioeconomic factors, which includes social and economic conditions
      such as income, wealth, education and socioeconomic status. 3-Environmental
      exposures, includes exposure to various environmental factors, such as air pollution,
      water quality, and workplace hazards, that can impact an individual’s health.
      4-Substance use, covers concepts such as smoking, as well as illicit drug use.
      5-Physical activities, includes regular exercise and physically demanding activities
      like leisure time, occupational, and household physical activities. 6-Non-physical
      leisure time activities, describes any activity an individual might engage in
      during their free time that is not a physical activity. 7-Personal care products
      and cosmetic procedures, covers activities related to hygiene, use of cosmetic
      and cleaning products as well as invasive procedures that people undergo to
      improve their appearance, such as cosmetic surgery. 8-Sleep, covers sleep quality,
      stages, and habits. 9-Mental health practices, includes the behaviors and habits
      related to maintaining good mental health and emotional well-being such as meditation,
      and psychotherapy.'
    download_owl: https://raw.githubusercontent.com/EsmaeilNourani/Lifestyle-factors-ontology/main/LSFO/owl/LSFO.owl
    homepage: https://bioportal.bioontology.org/ontologies/LSFO
    name: Lifestyle Factors Ontology
    prefix: lifestylefactors
  prefix: lifestylefactors
  uri_format: http://purl.obolibrary.org/obo/LFID_$1
ligandbook:
  mappings:
    miriam: ligandbook
    n2t: ligandbook
  miriam:
    deprecated: false
    description: Ligandbook is a public repository for force field parameters with
      a special emphasis on small molecules and known ligands of proteins. It acts
      as a warehouse for parameter files that are supplied by the community.
    homepage: https://ligandbook.org/
    id: 00000681
    name: LigandBook
    namespaceEmbeddedInLui: false
    pattern: ^[0-9]+$
    prefix: ligandbook
    sampleId: '785'
    uri_format: https://ligandbook.org/package/$1
  n2t:
    description: Ligandbook is a public repository for force field parameters with
      a special emphasis on small molecules and known ligands of proteins. It acts
      as a warehouse for parameter files that are supplied by the community.
    example: '785'
    homepage: https://ligandbook.org/
    name: LigandBook
    namespaceEmbeddedInLui: false
    pattern: ^[0-9]+$
    prefix: ligandbook
    uri_format: https://ligandbook.org/package/$1
  prefix: ligandbook
ligandbox:
  biocontext:
    prefix: LIGANDBOX
  integbio:
    alt_name: LIGANDs Data Base Open and eXtensible
    description: LigandBox is a database of small chemical compounds for drug screening
      on computer docking studies. This database contains 3D molecular structures
      produced by calculation based on 2D structural data of chemicals those are provided
      by companies and KEGG databases. Users can search chemical compounds by structural
      information, physical quantity, as well as keywords.
    homepage: http://www.mypresto5.com/ligandbox/cgi-bin/index.cgi?LANG=en
    information_keywords:
    - 3D structure
    maintainer: Osaka University Institute for Protein Research
    name: LigandBox
    prefix: nbdc00551
    pubmeds:
    - '27493549'
    status: Active
    target_keywords:
    - Chemical compound
  mappings:
    biocontext: LIGANDBOX
    integbio: nbdc00551
    miriam: ligandbox
    n2t: ligandbox
  miriam:
    deprecated: false
    description: LigandBox is a database of 3D compound structures.  Compound information
      is collected from the catalogues of various commercial suppliers, with approved
      drugs and biochemical compounds taken from KEGG and PDB databases. Each chemical
      compound in the database has several 3D conformers with hydrogen atoms and atomic
      charges, which are ready to be docked into receptors using docking programs.
      Various physical properties, such as aqueous solubility (LogS) and carcinogenicity
      have also been calculated to characterize the ADME-Tox properties of the compounds.
    homepage: http://www.mypresto5.com/ligandbox/cgi-bin/index.cgi?LANG=en
    id: '00000477'
    name: LigandBox
    namespaceEmbeddedInLui: false
    pattern: ^(HTS|KSH)[0-9]{4}-[0-9]{8}|PDB_[0-9,A-Z]{2,3}|[CD][0-9]{5}$
    prefix: ligandbox
    sampleId: D00001
    uri_format: http://www.mypresto5.com/ligandbox/cgi-bin/liginf.cgi?id=$1
  n2t:
    description: LigandBox is a database of 3D compound structures.  Compound information
      is collected from the catalogues of various commercial suppliers, with approved
      drugs and biochemical compounds taken from KEGG and PDB databases. Each chemical
      compound in the database has several 3D conformers with hydrogen atoms and atomic
      charges, which are ready to be docked into receptors using docking programs.
      Various physical properties, such as aqueous solubility (LogS) and carcinogenicity
      have also been calculated to characterize the ADME-Tox properties of the compounds.
    example: D00001
    homepage: http://ligandbox.protein.osaka-u.ac.jp/ligandbox//cgi-bin/index.cgi?LANG=en
    name: LigandBox at
    namespaceEmbeddedInLui: false
    pattern: ^D\d{5}
    prefix: ligandbox
    uri_format: http://ligandbox.protein.osaka-u.ac.jp/ligandbox/cgi-bin/liginf.cgi?id=$1
  prefix: ligandbox
ligandexpo:
  biocontext:
    prefix: LIGANDEXPO
  fairsharing:
    abbreviation: Ligand Expo
    contact:
      email: jwest@rcsb.rutgers.edu
      name: John Westbrook
      orcid: 0000-0002-6686-5475
    description: Ligand Expo is a data resource for finding information about small
      molecules bound to proteins and nucleic acids. Tools are provided to search
      the PDB dictionary for chemical components, to identify structure entries containing
      particular small molecules, and to download the 3D structures of the small molecule
      components in the PDB entry.
    homepage: http://ligand-depot.rutgers.edu/
    name: Ligand Expo
    prefix: FAIRsharing.2ma4gq
    publications:
    - doi: 10.1093/bioinformatics/bth214
      pubmed_id: 15059838
      title: 'Ligand Depot: a data warehouse for ligands bound to macromolecules.'
    subjects:
    - Life Science
  integbio:
    description: Ligand Expo is a data resource for finding information about small
      molecules bound to proteins and nucleic acids. Tools are provided to search
      the PDB dictionary for chemical components, to identify structure entries containing
      particular small molecules, and to download the 3D structures of the small molecule
      components in the PDB entry.
    fairsharing: FAIRsharing.2ma4gq
    homepage: http://ligand-depot.rutgers.edu/
    information_keywords:
    - Sequence
    - Interaction/Pathway
    - 3D structure
    maintainer: Rutgers, The State University of New Jersey
    name: Ligand Expo
    prefix: nbdc01864
    pubmeds:
    - '15059838'
    status: Active
    target_keywords:
    - DNA
    - Protein
    - Chemical compound
  mappings:
    biocontext: LIGANDEXPO
    fairsharing: FAIRsharing.2ma4gq
    integbio: nbdc01864
    miriam: ligandexpo
    n2t: ligandexpo
    pathguide: '154'
    prefixcommons: ligandexpo
  miriam:
    deprecated: false
    description: Ligand Expo is a data resource for finding information about small
      molecules bound to proteins and nucleic acids.
    homepage: http://ligand-depot.rutgers.edu/index.html
    id: '00000062'
    name: Ligand Expo
    namespaceEmbeddedInLui: false
    pattern: ^(\w){3}$
    prefix: ligandexpo
    providers:
    - code: ''
      description: Ligand Expo at Rutgers
      homepage: http://ligand-expo.rcsb.org/
      name: Ligand Expo at Rutgers
      uri_format: http://ligand-expo.rcsb.org/pyapps/ldHandler.py?formid=cc-index-search&target=$1&operation=ccid
    sampleId: ABC
    uri_format: http://ligand-depot.rutgers.edu/pyapps/ldHandler.py?formid=cc-index-search&target=$1&operation=ccid
  n2t:
    description: Ligand Expo is a data resource for finding information about small
      molecules bound to proteins and nucleic acids.
    example: ABC
    homepage: http://ligand-expo.rcsb.org/
    name: Ligand Expo at Rutgers
    namespaceEmbeddedInLui: false
    pattern: ^(\w){3}$
    prefix: ligandexpo
    uri_format: http://ligand-expo.rcsb.org/pyapps/ldHandler.py?formid=cc-index-search&target=$1&operation=ccid
  pathguide:
    abbreviation: Ligand Expo
    homepage: http://ligand-depot.rutgers.edu/
    name: Ligand Expo
    prefix: '154'
  prefix: ligandexpo
  prefixcommons:
    description: Ligand Expo is a data resource for finding information about small
      molecules bound to proteins and nucleic acids.
    example: ABC
    homepage: http://ligand-depot.rutgers.edu/
    keywords:
    - interaction
    - structure
    - protein
    - chemical
    - nucleic acid
    license: http://ligand-depot.rutgers.edu/acknowledgements.html
    name: Ligand Expo
    pattern: ^(\w){3}$
    prefix: ligandexpo
    pubmed_ids:
    - '15059838'
    uri_format: http://ligand-depot.rutgers.edu/pyapps/ldHandler.py?formid=cc-index-search&target=$1&operation=ccid
  publications:
  - doi: 10.1093/bioinformatics/bth214
    pmc: null
    pubmed: '15059838'
    title: 'Ligand Depot: a data warehouse for ligands bound to macromolecules'
    year: 2004
  - doi: 10.1093/bioinformatics/bth214
    pmc: null
    pubmed: null
    title: 'Ligand Depot: a data warehouse for ligands bound to macromolecules.'
    year: null
  - doi: null
    pmc: null
    pubmed: '15059838'
    title: null
    year: null
  - doi: 10.1093/bioinformatics/bth214
    pmc: null
    pubmed: null
    title: 'Ligand Depot: a data warehouse for ligands bound to macromolecules.'
    year: null
  - doi: null
    pmc: null
    pubmed: '15059838'
    title: null
    year: null
ligea:
  cellosaurus:
    category: Polymorphism and mutation databases
    homepage: http://hpc-bioinformatics.cineca.it/fusion/main
    name: Cancer cell LInes GEne fusions portAl
    prefix: LiGeA
    uri_format: http://hpc-bioinformatics.cineca.it/fusion/cell_line/$1
  comment: This might just be a provider for CCLE
  example: CCLE_867
  mappings:
    cellosaurus: LiGeA
  prefix: ligea
limore:
  cellosaurus:
    category: Cell line databases/resources
    homepage: https://www.picb.ac.cn/limore/home
    name: Liver Cancer Model Repository
    prefix: LIMORE
    uri_format: https://www.picb.ac.cn/limore/cellLines/single?para=$1
  example: Li7
  mappings:
    cellosaurus: LIMORE
  prefix: limore
lincs.cell:
  biocontext:
    prefix: LINCS.CELL
  cellosaurus:
    category: Cell line databases/resources
    homepage: http://lincsportal.ccs.miami.edu/cells/
    name: LINCS Data Portal
    prefix: LINCS_LDP
    uri_format: http://lincsportal.ccs.miami.edu/cells/#/view/$1
  mappings:
    biocontext: LINCS.CELL
    cellosaurus: LINCS_LDP
    miriam: lincs.cell
    n2t: lincs.cell
  miriam:
    deprecated: false
    description: 'The Library of Network-Based Cellular Signatures (LINCS) Program
      aims to  create a network-based understanding of biology by cataloging changes
      in gene expression and other cellular processes that occur when cells are exposed
      to a variety of perturbing agents. The LINCS cell model system can have the
      following cell categories: cell lines, primary cells, induced pluripotent stem
      cells, differentiated cells, and embryonic stem cells. The metadata contains
      information provided by each LINCS Data and Signature Generation Center (DSGC)
      and the association with a tissue or organ from which the cells were derived,
      in many cases are also associated to a disease.'
    homepage: http://lincsportal.ccs.miami.edu/cells/
    id: '00000544'
    name: LINCS Cell
    namespaceEmbeddedInLui: false
    pattern: ^(LCL-\d+)|(LDC-\d+)|(ES-\d+)|(LSC-\d+)|(LPC-\d+)$
    prefix: lincs.cell
    sampleId: LCL-2085
    uri_format: http://lincsportal.ccs.miami.edu/cells/#/view/$1
  n2t:
    description: 'The Library of Network-Based Cellular Signatures (LINCS) Program
      aims to  create a network-based understanding of biology by cataloging changes
      in gene expression and other cellular processes that occur when cells are exposed
      to a variety of perturbing agents. The LINCS cell model system can have the
      following cell categories: cell lines, primary cells, induced pluripotent stem
      cells, differentiated cells, and embryonic stem cells. The metadata contains
      information provided by each LINCS Data and Signature Generation Center (DSGC)
      and the association with a tissue or organ from which the cells were derived,
      in many cases are also associated to a disease.'
    example: LCL-2085
    homepage: http://lincsportal.ccs.miami.edu/cells/
    name: LINCS Portal
    namespaceEmbeddedInLui: false
    pattern: (^LCL-\d+$)|(^LDC-\d+$)|(^ES-\d+$)|(^LSC-\d+$)|(^LPC-\d+$)
    prefix: lincs.cell
    uri_format: http://lincsportal.ccs.miami.edu/cells/#/view/$1
  pattern: ^(LCL|LDC|ES|LSC|LPC)-\d+$
  prefix: lincs.cell
  synonyms:
  - LINCS_LDP
lincs.data:
  biocontext:
    prefix: LINCS.DATA
  mappings:
    biocontext: LINCS.DATA
    miriam: lincs.data
    n2t: lincs.data
  miriam:
    deprecated: false
    description: The Library of Network-Based Cellular Signatures (LINCS) Program
      aims to create a network-based understanding of biology by cataloguing changes
      in gene expression and other cellular processes that occur when cells are exposed
      to perturbing agents. The data is organized and available as datasets, each
      including experimental data, metadata and a description of the dataset and assay.
      The dataset group comprises datasets for the same experiment but with different
      data level results (data processed to a different level).
    homepage: http://lincsportal.ccs.miami.edu/datasets/
    id: 00000588
    name: LINCS Data
    namespaceEmbeddedInLui: false
    pattern: ^[EL]D[SG]-\d+$
    prefix: lincs.data
    providers:
    - code: omicsdi
      description: Lincs through OmicsDI
      homepage: https://www.omicsdi.org/
      name: Lincs through OmicsDI
      uri_format: https://www.omicsdi.org/dataset/lincs/$1
    sampleId: LDS-1110
    uri_format: http://lincsportal.ccs.miami.edu/datasets/#/view/$1
  n2t:
    description: The Library of Network-Based Cellular Signatures (LINCS) Program
      aims to create a network-based understanding of biology by cataloguing changes
      in gene expression and other cellular processes that occur when cells are exposed
      to perturbing agents. The data is organized and available as datasets, each
      including experimental data, metadata and a description of the dataset and assay.
      The dataset group comprises datasets for the same experiment but with different
      data level results (data processed to a different level).
    example: LDS-1110
    homepage: http://lincsportal.ccs.miami.edu/datasets/
    name: LINCS Data at University of Miami
    namespaceEmbeddedInLui: false
    pattern: ^[EL]D[SG]-\d+$
    prefix: lincs.data
    uri_format: http://lincsportal.ccs.miami.edu/datasets/#/view/$1
  prefix: lincs.data
lincs.protein:
  biocontext:
    prefix: LINCS.PROTEIN
  mappings:
    biocontext: LINCS.PROTEIN
    miriam: lincs.protein
    n2t: lincs.protein
  miriam:
    deprecated: false
    description: The HMS LINCS Database currently contains information on experimental
      reagents (small molecule perturbagens, cells, and proteins). It aims to collect
      and disseminate information relating to the fundamental principles of cellular
      response in humans to perturbation. This collection references proteins.
    homepage: http://lincs.hms.harvard.edu/db/proteins/
    id: '00000545'
    name: LINCS Protein
    namespaceEmbeddedInLui: false
    pattern: ^\d+$
    prefix: lincs.protein
    sampleId: '200282'
    uri_format: http://lincs.hms.harvard.edu/db/proteins/$1/
  n2t:
    description: The HMS LINCS Database currently contains information on experimental
      reagents (small molecule perturbagens, cells, and proteins). It aims to collect
      and disseminate information relating to the fundamental principles of cellular
      response in humans to perturbation. This collection references proteins.
    example: '200282'
    homepage: http://lincs.hms.harvard.edu/db/proteins/
    name: LINCS Protein at Harvard Medical School
    namespaceEmbeddedInLui: false
    pattern: ^\d+$
    prefix: lincs.protein
    uri_format: http://lincs.hms.harvard.edu/db/proteins/$1/
  prefix: lincs.protein
  uri_format: https://lincs.hms.harvard.edu/db/proteins/$1
lincs.smallmolecule:
  biocontext:
    prefix: LINCS.SMALLMOLECULE
  mappings:
    biocontext: LINCS.SMALLMOLECULE
    miriam: lincs.smallmolecule
    n2t: lincs.smallmolecule
  miriam:
    deprecated: false
    description: The Library of Network-Based Cellular Signatures (LINCS) Program
      aims to create a network-based understanding of biology by cataloging changes
      in gene expression and other cellular processes that occur when cells are exposed
      to a variety of perturbing agents. The LINCS small molecule collection is used
      as perturbagens in LINCS experiments. The small molecule metadata includes substance-specific
      batch information provided by each LINCS Data and Signature Generation Center
      (DSGC).
    homepage: http://lincsportal.ccs.miami.edu/SmallMolecules/
    id: '00000546'
    name: LINCS Small Molecule
    namespaceEmbeddedInLui: false
    pattern: ^LSM-\d+$
    prefix: lincs.smallmolecule
    sampleId: LSM-6306
    uri_format: http://lincsportal.ccs.miami.edu/SmallMolecules/#/view/$1
  n2t:
    description: The Library of Network-Based Cellular Signatures (LINCS) Program
      aims to create a network-based understanding of biology by cataloging changes
      in gene expression and other cellular processes that occur when cells are exposed
      to a variety of perturbing agents. The LINCS small molecule collection is used
      as perturbagens in LINCS experiments. The small molecule metadata includes substance-specific
      batch information provided by each LINCS Data and Signature Generation Center
      (DSGC).
    example: LSM-6306
    homepage: http://lincsportal.ccs.miami.edu/SmallMolecules/
    name: LINCS Portal
    namespaceEmbeddedInLui: false
    pattern: ^LSM-\d+$
    prefix: lincs.smallmolecule
    uri_format: http://lincsportal.ccs.miami.edu/SmallMolecules/#/view/$1
  prefix: lincs.smallmolecule
  synonyms:
  - lincs
linguist:
  homepage: https://github.com/github/linguist
  mappings:
    miriam: linguist
  miriam:
    deprecated: false
    description: Registry of programming languages for the Linguist program for detecting
      and highlighting programming languages.
    homepage: https://github.com/
    id: 00000849
    name: Linguist
    namespaceEmbeddedInLui: false
    pattern: ^[a-zA-Z0-9 +#'*]+$
    prefix: linguist
    sampleId: Python
    uri_format: https://raw.githubusercontent.com/github/linguist/master/lib/linguist/languages.yml#$1
  prefix: linguist
  repository: https://github.com/github/linguist
linguist.gold:
  comment: This resource has been deprecated and was last released in 2010. The homepage
    links to a zip folder that includes an OWL artifact, but it doesn't follow any
    typical standards. The ontology browser is not perfect, it only works for classes.
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  deprecated: true
  example: Term
  github_request_issue: 1310
  homepage: https://linguistlist.org/gold/
  name: Genderal Ontology for Linguistic Description
  prefix: linguist.gold
  rdf_uri_format: http://purl.org/linguistics/gold/$1
  uri_format: https://lambdamusic.github.io/ontospy-examples/gold-2010owl/class-gold$1.html
linkedin:
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  homepage: https://www.linkedin.com
  keywords:
  - person
  - researcher
  mappings:
    wikidata: P6634
  pattern: ^[\w0-9\-&_'’\.]+$
  prefix: linkedin
  references:
  - https://github.com/biopragmatics/bioregistry/pull/1171
  uri_format: https://www.linkedin.com/in/$1
  wikidata:
    description: identifier for a person, on the LinkedIn website
    example:
    - deborahlehr
    - filipposfragkogiannis
    - hélène-gasnault-a2543562
    - ursula-von-der-leyen
    name: LinkedIn personal profile ID
    pattern: ^[\p{L}0-9\-&_'’\.]+$
    prefix: P6634
    short_name:
    - LinkedIn
    uri_format: https://www.linkedin.com/in/$1/
linkml:
  biolink:
    is_identifiers: false
    is_obo: false
    prefix: linkml
    uri_format: https://w3id.org/linkml/$1
  comment: 'Closes #508'
  contact:
    email: cjmungall@lbl.gov
    github: cmungall
    name: Chris Mungall
    orcid: 0000-0002-6601-2165
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: Linkml is a flexible modeling language that allows you to author schemas
    in yaml that describe the structure of your data. additionally, it is a framework
    for working with and validating data in a variety of formats (json, rdf, tsv),
    with generators for compiling linkml schemas to other frameworks.
  example: SchemaDefinition
  fairsharing:
    abbreviation: LinkML
    contact:
      email: cjmungall@lbl.gov
      name: Chris Mungall
      orcid: 0000-0002-6601-2165
    description: LinkML is a flexible modeling language that allows you to author
      schemas in YAML that describe the structure of your data. Additionally, it is
      a framework for working with and validating data in a variety of formats (JSON,
      RDF, TSV), with generators for compiling LinkML schemas to other frameworks.
    homepage: https://linkml.io/linkml/schemas/
    license: https://creativecommons.org/licenses/by/1.0
    name: Linked (Open) Data Modeling Language
    prefix: FAIRsharing.cb7086
    publications:
    - doi: 10.5281/zenodo.5598314
      pubmed_id: null
      title: LinkML Model (v1.3.0rc7)
    repository: https://github.com/linkml/
    subjects:
    - Data Integration
    - Ontology and Terminology
    twitter: linkml_data
  github_request_issue: 512
  homepage: https://linkml.io/linkml-model/docs/SchemaDefinition/
  mappings:
    biolink: linkml
    fairsharing: FAIRsharing.cb7086
  name: LinkML
  preferred_prefix: linkml
  prefix: linkml
  publications:
  - doi: 10.5281/zenodo.5598314
    pmc: null
    pubmed: null
    title: 'linkml/linkml-model: v1.5.2'
    year: 2023
  - doi: 10.5281/zenodo.5598314
    pmc: null
    pubmed: null
    title: LinkML Model (v1.3.0rc7)
    year: null
  uri_format: https://w3id.org/linkml/$1
lipidbank:
  biocontext:
    prefix: LIPIDBANK
  contact:
    email: e-yasugi@umin.ac.jp
    github: null
    name: Etsuko Yasugi
    orcid: 0000-0003-1898-4426
  edam:
    description: Identifier of an entry from the LipidBank database.
    name: LipidBank
    obsolete: false
    prefix: '2665'
  fairsharing:
    abbreviation: LipidBank
    description: LipidBank is an open, publicly free database of natural lipids including
      fatty acids, glycerolipids, sphingolipids, steroids, and various vitamins.
    homepage: http://lipidbank.jp/index.html
    license: http://opendatacommons.org/licenses/pddl/1.0
    name: LipidBank
    prefix: FAIRsharing.bdn9br
    publications:
    - doi: null
      pubmed_id: 12058481
      title: '[LIPIDBANK for Web, the newly developed lipid database].'
    subjects:
    - Life Science
  integbio:
    description: Lipidbank is the official database of the Japanese Conference on
      the Biochemistry of Lipids (JCBL). Natural lipids including fatty acids, glycerolipids,
      sphingolipids, steroids, and various vitamins can be freely searched. It also
      provides more than 6000 unique molecular structures (ChemDraw cdx format, MDL
      MOL format) with their lipid names (common name, IUPAC), spectral information
      (mass, UV, IR, NMR and others), and links to published information.
    fairsharing: biodbcore-000581
    homepage: http://lipidbank.jp/
    information_keywords:
    - Image/Movie
    - Chemical structure
    maintainer: The Japanese Conference on the Biochemistry of Lipids
    name: LipidBank
    prefix: nbdc00126
    pubmeds:
    - '12058481'
    status: Active
    target_keywords:
    - Lipid
  mappings:
    biocontext: LIPIDBANK
    edam: '2665'
    fairsharing: FAIRsharing.bdn9br
    integbio: nbdc00126
    miriam: lipidbank
    n2t: lipidbank
    prefixcommons: lipidbank
  miriam:
    deprecated: true
    description: LipidBank is an open, publicly free database of natural lipids including
      fatty acids, glycerolipids, sphingolipids, steroids, and various vitamins.
    homepage: http://lipidbank.jp/index.html
    id: '00000115'
    name: LipidBank
    namespaceEmbeddedInLui: false
    pattern: ^\w+\d+$
    prefix: lipidbank
    sampleId: BBA0001
    uri_format: https://lipidbank.jp/data/$1.cdx
  n2t:
    description: LipidBank is an open, publicly free database of natural lipids including
      fatty acids, glycerolipids, sphingolipids, steroids, and various vitamins.
    example: BBA0001
    homepage: http://lipidbank.jp/index.html
    name: LipidBank the Lipid database
    namespaceEmbeddedInLui: false
    pattern: ^\w+\d+$
    prefix: lipidbank
    uri_format: http://lipidbank.jp/cgi-bin/detail.cgi?id=$1
  prefix: lipidbank
  prefixcommons:
    description: LipidBank is an open, publicly free database of natural lipids including
      fatty acids, glycerolipids, sphingolipids, steroids, and various vitamins.
    example: BBA0001
    homepage: http://lipidbank.jp/index.html
    keywords:
    - lipid
    - molecule
    - structure
    name: LipidBank
    pattern: ^\w+\d+$
    prefix: lipidbank
    pubmed_ids:
    - '12058481'
    uri_format: http://lipidbank.jp/cgi-bin/detail.cgi?id=$1
  publications:
  - doi: null
    pmc: null
    pubmed: '12058481'
    title: '[LIPIDBANK for Web, the newly developed lipid database]'
    year: 2002
lipidmaps:
  biocontext:
    prefix: LIPIDMAPS
  cheminf:
    description: Identifier used by the LipidMaps database, http://www.lipidmaps.org/.
    name: LipidMaps
    obsolete: false
    prefix: '000564'
  contact:
    email: edennis@ucsd.edu
    github: null
    name: Edward A Dennis
    orcid: 0000-0003-3738-3140
  edam:
    description: Identifier of an entry from the LIPID MAPS database.
    name: LIPID MAPS
    obsolete: false
    prefix: '2625'
  fairsharing:
    abbreviation: LIPID MAPS
    description: The LIPID MAPS Lipid Classification System is comprised of eight
      lipid categories, each with its own subclassification hierarchy. All lipids
      in the LIPID MAPS Structure Database (LMSD) have been classified using this
      system and have been assigned LIPID MAPS ID's which reflects their position
      in the classification hierarchy.
    homepage: http://www.lipidmaps.org
    license: http://opendatacommons.org/licenses/pddl/1.0
    name: LIPID MAPS
    prefix: FAIRsharing.cpneh8
    publications:
    - doi: 10.1093/nar/gkl838
      pubmed_id: 17098933
      title: 'LMSD: LIPID MAPS structure database.'
    - doi: 10.1093/nar/gkm324
      pubmed_id: 17584797
      title: LIPID MAPS online tools for lipid research.
    - doi: 10.1194/jlr.R800095-JLR200
      pubmed_id: 19098281
      title: Update of the LIPID MAPS comprehensive classification system for lipids.
    subjects:
    - Endocrinology
    - Life Science
    - Biomedical Science
    - Systems Biology
    twitter: lipidmaps
  logo: https://www.lipidmaps.org/assets/images/logos/lipid_maps_transparent_sm.png
  mappings:
    biocontext: LIPIDMAPS
    cheminf: '000564'
    edam: '2625'
    fairsharing: FAIRsharing.cpneh8
    miriam: lipidmaps
    n2t: lipidmaps
    ols: lipidmaps
    pathguide: '503'
    prefixcommons: lipidmaps
    re3data: r3d100012315
    togoid: Lipidmaps
    wikidata: P2063
  miriam:
    deprecated: false
    description: The LIPID MAPS Lipid Classification System is comprised of eight
      lipid categories, each with its own subclassification hierarchy. All lipids
      in the LIPID MAPS Structure Database (LMSD) have been classified using this
      system and have been assigned LIPID MAPS ID's which reflects their position
      in the classification hierarchy.
    homepage: http://www.lipidmaps.org
    id: '00000052'
    name: LIPID MAPS
    namespaceEmbeddedInLui: false
    pattern: ^LM(FA|GL|GP|SP|ST|PR|SL|PK)[0-9]{4}([0-9a-zA-Z]{4,6})?$
    prefix: lipidmaps
    providers:
    - code: scholia
      description: Scholia is a service that creates visual scholarly profiles for
        topic, people, organizations, species, chemicals, etc using bibliographic
        and other information in Wikidata.
      homepage: https://scholia.toolforge.org/
      name: Scholia
      uri_format: https://scholia.toolforge.org/lipidmaps/$1
    sampleId: LMPR0102010012
    uri_format: http://www.lipidmaps.org/data/LMSDRecord.php?LMID=$1
  n2t:
    description: The LIPID MAPS Lipid Classification System is comprised of eight
      lipid categories, each with its own subclassification hierarchy. All lipids
      in the LIPID MAPS Structure Database (LMSD) have been classified using this
      system and have been assigned LIPID MAPS ID's which reflects their position
      in the classification hierarchy.
    example: LMPR0102010012
    homepage: http://www.lipidmaps.org
    name: Department of Bioengineering and the San Diego Supercomputer Center
    namespaceEmbeddedInLui: false
    pattern: ^LM(FA|GL|GP|SP|ST|PR|SL|PK)[0-9]{4}([0-9a-zA-Z]{4,6})?$
    prefix: lipidmaps
    uri_format: http://www.lipidmaps.org/data/LMSDRecord.php?LMID=$1
  name: LIPID MAPS
  ols:
    homepage: https://lipidmaps.org
    name: LIPID MAPS
    prefix: lipidmaps
    uri_format: https://www.lipidmaps.org/rdf/$1
  pathguide:
    abbreviation: LIPID MAPS
    homepage: http://www.lipidmaps.org/
    name: LIPID Metabolites and Pathways Strategy
    prefix: '503'
  prefix: lipidmaps
  prefixcommons:
    description: The LIPID MAPS Lipid Classification System is comprised of eight
      lipid categories, each with its own subclassification hierarchy. All lipids
      in the LIPID MAPS Structure Database (LMSD) have been classified using this
      system and have been assigned LIPID MAPS ID's which reflects their position
      in the classification hierarchy.
    example: LMPR0102010012
    homepage: http://www.lipidmaps.org
    keywords:
    - lipid
    - structure
    - taxonomy
    license: http://www.lipidmaps.org/about/terms_of_use.html
    name: LIPID MAPS
    pattern: ^LM(FA|GL|GP|SP|ST|PR|SL|PK)[0-9]{4}([0-9a-zA-Z]{4,6})?$
    prefix: lipidmaps
    pubmed_ids:
    - '17098933'
    - '15722563'
    uri_format: http://www.lipidmaps.org/data/get_lm_lipids_dbgif.php?LM_ID=$1
  publications:
  - doi: 10.1194/jlr.r800095-jlr200
    pmc: PMC2674711
    pubmed: '19098281'
    title: Update of the LIPID MAPS comprehensive classification system for lipids
    year: 2008
  - doi: 10.1093/nar/gkm324
    pmc: PMC1933166
    pubmed: '17584797'
    title: LIPID MAPS online tools for lipid research
    year: 2007
  - doi: 10.1093/nar/gkl838
    pmc: PMC1669719
    pubmed: '17098933'
    title: 'LMSD: LIPID MAPS structure database'
    year: 2006
  - doi: 10.1194/jlr.e400004-jlr200
    pmc: null
    pubmed: '15722563'
    title: A comprehensive classification system for lipids
    year: 2005
  re3data:
    description: 'Tthe Lipidomics Gateway -  a free, comprehensive website for researchers
      interested in lipid biology, provided by the LIPID MAPS (Lipid Metabolites and
      Pathways Strategy) Consortium. The LIPID MAPS Lipidomics Gateway provides a
      rich collection of information and resources to help you stay abreast of the
      latest developments in this rapidly expanding field. LIPID Metabolites And Pathways
      Strategy (LIPID MAPS®) is a multi-institutional effort created in 2003 to identify
      and quantitate, using a systems biology approach and sophisticated mass spectrometers,
      all of the major — and many minor — lipid species in mammalian cells, as well
      as to quantitate the changes in these species in response to perturbation.

      The ultimate goal of our research is to better understand lipid metabolism and
      the active role lipids play in diabetes, stroke, cancer, arthritis, Alzheimer''s
      and other lipid-based diseases in order to facilitate development of more effective
      treatments.

      Since our inception, we have made great strides toward defining the "lipidome"
      (an inventory of the thousands of individual lipid molecular species) in the
      mouse macrophage. We have also worked to make lipid analysis easier and more
      accessible for the broader scientific community and to advance a robust research
      infrastructure for the international research community. We share new lipidomics
      findings and methods, hold annual meetings open to all interested investigators,
      and are exploring joint efforts to extend the use of these powerful new methods
      to new applications'
    doi: 10.17616/R3WW7G
    homepage: https://www.lipidmaps.org/
    name: LIPID MAPS
    prefix: r3d100012315
    synonyms:
    - LIPID MAPS Lipidomics Gateway
    - LIPID Metabolites And Pathways Strategy
    xrefs:
      nif: 0000-00368
      omics: 02529
  synonyms:
  - LIPID MAPS
  - LIPID_MAPS_class
  - LIPID_MAPS_instance
  togoid:
    examples:
    - LMST01060010
    - LMFA01020229
    - LMFA03020019
    - LMGP01010915
    - LMSP03010080
    - LMFA07070005
    - LMFA06000216
    - LMGP01030144
    - LMFA01170119
    - LMGP02011194
    keywords:
    - Lipid
    name: LIPID MAPS
    pattern: ^(?LM(FA|GL|GP|SP|ST|PR|SL|PK)[0-9]{4}([0-9a-zA-Z]{4,6})?)$
    prefix: Lipidmaps
    uri_format: http://identifiers.org/lipidmaps/$1
  wikidata:
    database: Q20968889
    description: identifier used in the LIPID MAPS database for lipids
    example:
    - LMFA07010511
    - LMPR0102010003
    miriam: lipidmaps
    name: LIPID MAPS ID
    pattern: ^LM[A-Z][A-Z]\d+([A-Z][A-Z]?\d+)?$
    prefix: P2063
    uri_format: https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessClassSearch&LMID=$1
lipro:
  aberowl:
    description: Lipid research is increasingly integrated within systems level biology
      such as lipidomics where lipid classification is required before appropriate
      annotation of chemical functions can be applied. The ontology describes the
      LIPIDMAPS nomenclature classification explicitly using description logics (OWL-DL).
      Lipid classes are organized hierarchically with the super-classes restricted
      by generic necessary conditions. More specific necessary conditions are used
      to define membership requirements for sub classes of lipid according to appropriate
      functional groups.
    download_owl: http://aber-owl.net/media/ontologies/LIPRO/4/lipro.owl
    name: Lipid Ontology
    prefix: LIPRO
    version: See Remote Site
  biocontext:
    prefix: LIPRO
  bioportal:
    contact:
      email: bakerc@unb.ca
      name: Christipher Baker
    description: Lipid research is increasingly integrated within systems level biology
      such as lipidomics where lipid classification is required before appropriate
      annotation of chemical functions can be applied. The ontology describes the
      LIPIDMAPS nomenclature classification explicitly using description logics (OWL-DL).
      Lipid classes are organized hierarchically with the super-classes restricted
      by generic necessary conditions. More specific necessary conditions are used
      to define membership requirements for sub classes of lipid according to appropriate
      functional groups.
    name: Lipid Ontology
    prefix: LIPRO
    version: See Remote Site
  mappings:
    aberowl: LIPRO
    biocontext: LIPRO
    bioportal: LIPRO
    obofoundry: lipro
    wikidata.entity: Q114677891
  obofoundry:
    contact: bakerc@unb.ca
    contact.label: Christopher Baker
    contact.orcid: 0000-0003-4004-6479
    deprecated: true
    description: An ontology representation of the LIPIDMAPS nomenclature classification.
    domain: chemistry and biochemistry
    name: Lipid Ontology
    prefix: lipro
  prefix: lipro
listdb.onto:
  example: C0000000001
  mappings:
    tib: listdb
  name: ListDB Ontology
  prefix: listdb.onto
  repository: https://gitlab.com/listdb
  tib:
    description: "This is an ontology draft for the description of metadata of traffic\
      \ observations, in particular video recordings of road traffic. The traffic\
      \ observations are e.g. used to design test scenarios for the effectiveness\
      \ assessment of automated driving systems. \n\nThe ontology draft resulted from\
      \ an exchange of the Chair of Automobile Engineering at TU Dresden (https://tu-dresden.de/bu/verkehr/iad/kft?set_language=en)\
      \ with representatives of NFDI4Ing (Community Cluster 4.4, Archetype Golo, Base\
      \ Services S3) and FID move in NFDI4Ing's Special Interest Group \"Metadata\
      \ and Ontologies\". An essential part of that meeting was the presentation of\
      \ the reseaerch data management approach at the Chair of Automobile Engineering,\
      \ in particular its tooling, its metadata approach and its workflow.\n\nTraffic\
      \ observations are managed with ListDB, a solution combined of a SharePoint\
      \ instance and a virtual machine for data servicing . An accompanying Codebook\
      \ defines relevant metadata that should be provided for each road traffic observation.\
      \ ListDB is currently used internally within TU Dresden, but is intentended\
      \ to be hosted publicly until spring 2023. \n\nThe ontology draft is, in fact,\
      \ based on the Codebook (v. 1.0.0.) and an attempt to make a machine-readable\
      \ document out of it, applying standards from the Semantic Web Stack (RDF(S)\
      \ and OWL). The draft is constantly being developed further in this context."
    homepage: https://w3id.org/listdb/onto
    keywords:
    - FID move
    - NFDI4ING
    - traffic engineering
    name: ListDB Ontology 0.0.1 (Draft)
    prefix: listdb
    tracker: https://gitlab.com/listdb/onto/-/issues
    uri_format: https://w3id.org/listdb/onto#$1
    version.iri: https://w3id.org/listdb/onto/0.0.1
lncbook:
  integbio:
    description: LncBook is a curated knowledgebase of human lncRNAs that features
      a comprehensive collection of human lncRNAs and systematic curation of lncRNAs
      by multi-omics data integration, functional annotation and disease association.
      It integrates multi-omics data from expression, methylation, genome variation
      and lncRNA-miRNA interaction. A core component of LncBook is the community-curated
      LncRNAWiki portal, which a wiki-based, publicly editable and open-content platform
      for community curation of human long non-coding RNAs (lncRNAs).
    fairsharing: biodbcore-001262/
    homepage: https://ngdc.cncb.ac.cn/lncbook/
    information_keywords:
    - Sequence
    - Expression
    - Interaction/Pathway
    maintainer: BIGD (Big Data Center, Beijing Institute of Genomics)
    name: LncBook
    prefix: nbdc02541
    pubmeds:
    - '30329098'
    status: Active
    target_keywords:
    - Genome/Gene
    - Genetic variation
    - RNA
    - Health/Disease
  mappings:
    integbio: nbdc02541
    miriam: lncbook
  miriam:
    deprecated: false
    description: 'LncBook accommodates a high-quality collection of human lncRNA genes
      and transcripts, and incorporates their abundant annotations at different omics
      levels, thereby enabling users to decipher functional signatures of lncRNAs
      in human diseases and different biological contexts.


      '
    homepage: https://ngdc.cncb.ac.cn/?lang=en
    id: 00001109
    name: LncBook
    namespaceEmbeddedInLui: false
    pattern: ^HSALNG\d{7}$
    prefix: lncbook
    sampleId: HSALNG0006197
    uri_format: https://ngdc.cncb.ac.cn/lncbook/gene?geneid=$1
  prefix: lncbook
lncipedia:
  contact:
    email: pieter.mestdagh@ugent.be
    github: OncoRNALab
    name: Pieter Mestdagh
    orcid: 0000-0001-7821-9684
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: A comprehensive compendium of human long non-coding RNAs
  example: SNHG3
  fairsharing:
    abbreviation: LNCipedia
    description: LNCipedia is a database for human long non-coding RNA (lncRNA) transcripts
      and genes. In addition to basic transcript information and gene structure, several
      statistics are determined for each entry in the database, such as secondary
      structure information, protein coding potential and microRNA binding sites.
      Available literature on specific lncRNAs is linked, and users or authors can
      submit articles through a web interface. LNCipedia is publicly available and
      allows users to query and download lncRNA sequences and structures based on
      different search criteria.
    homepage: https://lncipedia.org/
    name: LNCipedia
    prefix: FAIRsharing.84c1a7
    publications:
    - doi: 10.1093/nar/gku1060
      pubmed_id: 25378313
      title: 'An update on LNCipedia: a database for annotated human lncRNA sequences.'
    - doi: 10.1093/nar/gkv295
      pubmed_id: 25829178
      title: 'An update on LNCipedia: a database for annotated human lncRNA sequences.'
    - doi: 10.1093/nar/gks915
      pubmed_id: 23042674
      title: 'LNCipedia: a database for annotated human lncRNA transcript sequences
        and structures.'
    subjects:
    - Life Science
  homepage: https://lncipedia.org
  mappings:
    fairsharing: FAIRsharing.84c1a7
  name: LNCipedia
  prefix: lncipedia
  publications:
  - doi: 10.1093/nar/gkv295
    pmc: PMC4417186
    pubmed: '25829178'
    title: 'An update on LNCipedia: a database for annotated human lncRNA sequences'
    year: 2015
  - doi: 10.1093/nar/gku1060
    pmc: PMC4383901
    pubmed: '25378313'
    title: 'An update on LNCipedia: a database for annotated human lncRNA sequences'
    year: 2014
  - doi: 10.1093/nar/gks915
    pmc: PMC3531107
    pubmed: '23042674'
    title: 'LNCipedia: a database for annotated human lncRNA transcript sequences
      and structures'
    year: 2012
  - doi: 10.1093/nar/gku1060
    pmc: null
    pubmed: null
    title: 'An update on LNCipedia: a database for annotated human lncRNA sequences.'
    year: null
  - doi: 10.1093/nar/gkv295
    pmc: null
    pubmed: null
    title: 'An update on LNCipedia: a database for annotated human lncRNA sequences.'
    year: null
  - doi: 10.1093/nar/gks915
    pmc: null
    pubmed: null
    title: 'LNCipedia: a database for annotated human lncRNA transcript sequences
      and structures.'
    year: null
loc.fdd:
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: 'The digital content format descriptions accessible here provide specific
    information about individual formats and their characteristics. Each description
    provides moderately detailed information and citations. Planned for inclusion
    are a wide variety of formats: file formats, file-format classes, bitstream structures
    and encodings, and the mechanisms used to compress files or bitstreams. Inclusion
    of a description for a format does not imply that the format is preferred or acceptable
    for Library of Congress collections. [from homepage]'
  domain: semantic web
  example: fdd000613
  github_request_issue: 1725
  homepage: https://www.loc.gov/preservation/digital/formats/fdd/
  keywords:
  - file format
  - media type
  name: Library of Congress Format Description Document
  pattern: ^fdd\d+$
  prefix: loc.fdd
  providers:
  - code: xml
    description: LOC FDD XML
    example: null
    first_party: null
    homepage: https://www.loc.gov/preservation/digital/formats/fddXML/fddXMLreadme.txt
    name: LOC FDD XML
    publications: null
    status: null
    uri_format: https://www.loc.gov/preservation/digital/formats/fddXML/$1
  references:
  - https://www.loc.gov/preservation/digital/formats/fddXML/fddXMLreadme.txt
  uri_format: https://www.loc.gov/preservation/digital/formats/fdd/$1
loc.relator:
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: Relator terms and their associated codes designate the relationship
    between an agent and a bibliographic resource.
  download_rdf: https://id.loc.gov/download/vocabulary/relators.skosrdf.ttl.gz
  example: arc
  homepage: http://id.loc.gov/vocabulary/relators
  name: Library of Congress Relator
  prefix: loc.relator
  rdf_uri_format: http://id.loc.gov/vocabulary/relators/$1
  uri_format: https://id.loc.gov/vocabulary/relators/$1
loc.resourcetype:
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  contributor_extras:
  - email: null
    github: petrasteiner
    name: Petra C. Steiner
    orcid: 0000-0001-8997-2620
  description: A controlled vocabulary of media resources, such as audio, cartographic,
    manuscript, multimedia, etc.
  download_rdf: http://id.loc.gov/vocabulary/resourceTypes.skos.rdf
  example: dig
  homepage: https://id.loc.gov/vocabulary/resourceTypes.html
  keywords:
  - data classification
  name: Library of Congress Resource Types Scheme
  prefix: loc.resourcetype
  uri_format: http://id.loc.gov/vocabulary/resourceTypes/$1
locn:
  example: Address
  lov:
    description: The ISA Programme Location Core Vocabulary provides a minimum set
      of classes and properties for describing any place in terms of its name, address
      or geometry. The vocabulary is specifically designed to aid the publication
      of data that is interoperable with EU INSPIRE Directive.
    homepage: http://www.w3.org/ns/locn
    keywords:
    - Geography
    - Geometry
    modified: '2015-03-23'
    name: ISA Programme Location Core Vocabulary
    prefix: locn
    uri_prefix: http://www.w3.org/ns/locn#$1
  mappings:
    lov: locn
    zazuko: locn
  prefix: locn
  zazuko:
    prefix: locn
    uri_format: http://www.w3.org/ns/locn#$1
log:
  example: dtlit
  lov:
    description: Une ontologie "historique" utilisée par l'outil en ligne de commande
      cwm, au temps des balbutiements du web sémantique (~ 2000 - 2003 ?)
    homepage: http://www.w3.org/2000/10/swap/doc/CwmBuiltins
    keywords:
    - RDF
    modified: '2000-10-01'
    name: SWAP Logic Ontology
    prefix: log
    uri_prefix: http://www.w3.org/2000/10/swap/log#$1
  mappings:
    lov: log
    zazuko: log
  prefix: log
  zazuko:
    prefix: log
    uri_format: http://www.w3.org/2000/10/swap/log#$1
loggerhead:
  biocontext:
    prefix: LOGGERHEAD
  mappings:
    biocontext: LOGGERHEAD
    obofoundry: loggerhead
    wikidata.entity: Q114677892
  obofoundry:
    contact: peteremidford@yahoo.com
    contact.label: Peter Midford
    contact.orcid: 0000-0001-6512-3296
    deprecated: true
    domain: organisms
    homepage: http://www.mesquiteproject.org/ontology/Loggerhead/index.html
    name: Loggerhead nesting
    prefix: loggerhead
  prefix: loggerhead
loinc:
  aberowl:
    description: Logical Observation Identifier Names and Codes (LOINC)
    homepage: http://loinc.org/downloads
    name: Logical Observation Identifier Names and Codes
    prefix: LOINC
    version: 2016AB
  bartoc:
    description: 'LOINC was initiated in 1994 by Clem McDonald, an investigator at
      the Regenstrief Institute, which is an internationally respected non-profit
      medical research organization associated with Indiana University. Regenstrief
      organized the LOINC committee to develop a common terminology for laboratory
      and clinical observations because there was a growing trend to send clinical
      data electronically from laboratories and other data producers to hospitals,
      physician''s offices, and payers who use the data for clinical care and management
      purposes.


      At the time, and still today, most laboratories and clinical services use HL7
      to send their results electronically from their reporting systems to their care
      systems. However, the tests in these messages are identified by means of their
      internal, idiosyncratic code values. As a result, receiving care system cannot
      fully "understand" and properly file the results they receive unless they either
      adopt the producer''s test codes (which is impossible if they receive results
      from multiple sources), or invest in the work to map each result producer''s
      code system to their internal code system.


      Here''s the problem that LOINC solves: LOINC provides universal codes and names
      that provide the global lingua franca for identifying tests and observations.'
    homepage: http://loinc.org/
    name: LOINC
    prefix: '1897'
    wikidata_database: Q502480
  biolink:
    is_identifiers: false
    is_obo: false
    prefix: LOINC
    uri_format: http://loinc.org/rdf/$1
  bioportal:
    contact:
      email: loinc@regenstrief.org
      name: LOINC Support
    description: Logical Observation Identifier Names and Codes (LOINC) provides formal
      names and standardized codes for laboratory and other clinical observations.
      The data cover laboratory terminology, vital signs, hemodynamics intake/output,
      EKG, obstetric ultrasound, cardiac echo, urologic, imaging, gastroendoscopic
      procedures, pulmonary ventilator management, and selected survey instruments.
    homepage: http://loinc.org/downloads
    name: Logical Observation Identifier Names and Codes
    prefix: LOINC
    publications:
    - http://loinc.org/downloads
    version: LNC278
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: The international standard for identifying health measurements, observations,
    and documents.
  example: LL379-9
  fairsharing:
    abbreviation: LOINC
    description: LOINC is a common language (set of identifiers, names, and codes)
      for clinical and laboratory observations. LOINC is a catalog of measurements,
      including laboratory tests, clinical measures like vital signs and anthropomorphic
      measures, standardized survey instruments, and more. LOINC enables the exchange
      and aggregation of clinical results for care delivery, outcomes management,
      and research by providing a set of universal codes and structured names to unambiguously
      identify things you can measure or observe.
    domains:
    - Genetic Polymorphism
    - assay
    - phenotype
    - diagnosis
    - genetic disorder
    homepage: https://loinc.org/
    license: https://loinc.org/terms-of-use
    name: Logical Observation Identifier Names and Codes
    prefix: FAIRsharing.2mk2zb
    publications:
    - doi: 10.1016/s1386-5056(98)00089-6
      pubmed: '9749897'
      title: Combining laboratory data sets from multiple institutions using the logical
        observation identifier names and codes (LOINC)
      year: 1998
    - doi: 10.1016/j.jbi.2012.01.005
      pubmed: '22285984'
      title: Enabling international adoption of LOINC through translation
      year: 2012
    - doi: 10.1093/jamia/ocu012
      pubmed: '25656513'
      title: Supporting interoperability of genetic data with LOINC
      year: 2015
    subjects:
    - Life Science
    - Preclinical Studies
    - Biomedical Science
    twitter: LOINC
  hl7:
    description: Logical Observation Identifiers Names and Codes (LOINC&#174;) provides
      a set of universal codes and names for identifying laboratory and other clinical
      observations. One of the main goals of LOINC is to facilitate the exchange and
      pooling of results for clinical care, outcomes management, and research. LOINC
      was initiated by Regenstrief Institute research scientists who continue to develop
      it with the collaboration of the LOINC Committee. The LOINC table, LOINC codes,
      and LOINC panels and forms file are copyright &#169; 1995-2010, Regenstrief
      Institute, Inc. and the LOINC Committee and available at no cost (http://loinc.org)
      under the license at http://loinc.org/terms-of-use.The laboratory portion of
      the LOINC database contains the usual clinical laboratory categories of chemistry,
      hematology, serology, microbiology (including parasitology and virology), toxicology;
      as well as categories for drugs and the cell counts, antibiotic susceptibilities,
      and more. The clinical portion of the LOINC database includes entries for vital
      signs, hemodynamics, intake/output, EKG, obstetric ultrasound, cardiac echo,
      radiology report titles, pulmonary ventilator management, document and section
      titles, patient assessment instruments (e.g. Glascow Coma Score, PHQ-9 depression
      scale, CMS-required patient assessment instruments), and other clinical observations.LOINC
      may be accessed at http://loinc.org
    homepage: http://www.regenstrief.org
    name: Logical Observation Identifier Names and Codes
    organization: Regenstrief Institute
    preferred_prefix: loinc
    prefix: 2.16.840.1.113883.6.1
    status: Complete
  homepage: https://loinc.org/
  license: https://uts.nlm.nih.gov/uts/assets/LicenseAgreement.pdf
  mappings:
    aberowl: LOINC
    bartoc: '1897'
    biolink: LOINC
    bioportal: LOINC
    fairsharing: FAIRsharing.2mk2zb
    hl7: 2.16.840.1.113883.6.1
    wikidata: P4338
    wikidata.entity: Q502480
  name: Logical Observation Identifiers Names and Codes
  pattern: ^(\d|\w)+-\d$
  prefix: loinc
  publications:
  - doi: 10.1093/jamia/ocu012
    pmc: PMC5566197
    pubmed: '25656513'
    title: Supporting interoperability of genetic data with LOINC
    year: 2015
  - doi: 10.1016/j.jbi.2012.01.005
    pmc: PMC3376691
    pubmed: '22285984'
    title: Enabling international adoption of LOINC through translation
    year: 2012
  - doi: 10.1016/s1386-5056(98)00089-6
    pmc: null
    pubmed: '9749897'
    title: Combining laboratory data sets from multiple institutions using the logical
      observation identifier names and codes (LOINC)
    year: 1998
  synonyms:
  - LNC
  uri_format: https://loinc.org/$1
  wikidata:
    description: identifier for medical observations, measurements, and documents
      in the Regenstrief Institute's Logical Observation Identifiers Names and Codes
      (LOINC), a database of internationalized medical terminology
    example:
    - 41995-2
    - 69723-5
    homepage: https://loinc.org/
    name: LOINC ID
    pattern: ^\d+-\d$
    prefix: P4338
    uri_format: https://loinc.org/$1
    uri_format_rdf: http://loinc.org/rdf/$1
lonza:
  cellosaurus:
    category: Cell line databases/resources
    homepage: https://knowledge.lonza.com
    name: Lonza Cell and Transfection Database
    prefix: Lonza
    uri_format: https://knowledge.lonza.com/cell?id=$1
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: Contains information about cells and data sheets related to transfection.
  example: '968'
  homepage: https://knowledge.lonza.com
  mappings:
    cellosaurus: Lonza
  name: Lonza
  pattern: ^\d+$
  prefix: lonza
  uri_format: https://knowledge.lonza.com/cell?id=$1
loop:
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  keywords:
  - person
  - researcher
  mappings:
    wikidata: P2798
  prefix: loop
  references:
  - https://github.com/biopragmatics/bioregistry/pull/1171
  wikidata:
    description: identifier for a person, in the Loop database of researcher impact
    example:
    - '1859'
    - '2187'
    - '82461'
    homepage: https://loop.frontiersin.org/
    name: Loop ID
    pattern: ^[1-9]\d*$
    prefix: P2798
    uri_format: https://loop.frontiersin.org/people/$1/overview
loqate:
  contact:
    email: maya.schuldiner@weizmann.ac.il
    github: Maya-Schuldiner-lab
    name: Maya Schuldiner
    orcid: 0000-0001-9947-115X
  mappings:
    prefixcommons: loqate
  prefix: loqate
  prefixcommons:
    description: The data presented here is a result of systematically tracking the
      localization and abundance of 5330 yeast proteins at single-cell resolution
      under three different stress conditions (DTT, H2O2 and nitrogen starvation)
      using the GFP-tagged yeast library
    example: '1001'
    homepage: http://www.weizmann.ac.il/molgen/loqate/
    license: http://www.weizmann.ac.il/molgen/loqate/downloads
    name: The localization and quantitation atlas of the yeast proteome
    pattern: ^\d+$
    prefix: loqate
    pubmed_ids:
    - '24150937'
    uri_format: http://www.weizmann.ac.il/molgen/loqate/gene/view/$1
  publications:
  - doi: 10.1093/nar/gkt933
    pmc: PMC3965041
    pubmed: '24150937'
    title: LoQAtE--Localization and Quantitation ATlas of the yeast proteomE. A new
      tool for multiparametric dissection of single-protein behavior in response to
      biological perturbations in yeast
    year: 2013
  - doi: null
    pmc: null
    pubmed: '24150937'
    title: null
    year: null
  - doi: null
    pmc: null
    pubmed: '24150937'
    title: null
    year: null
  reviewer:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
lotus:
  comment: IDs are actually leading to the structural part of LOTUS only, which might
    change in the future. Will adapt the regexp in case.
  contact:
    email: adriano.rutz@ik.me
    github: adafede
    name: Adriano Rutz
    orcid: 0000-0003-0443-9902
  contributor:
    email: adriano.rutz@ik.me
    github: adafede
    name: Adriano Rutz
    orcid: 0000-0003-0443-9902
  description: LOTUS, actually, represents the most exhaustive resource of documented
    structure-organism pairs. Within the frame of current computational approaches
    in Natural Produts’s research and related fields, these documented structure-organism
    pairs should allow a more complete understanding of organisms and their chemistry.
  example: LTS0004651
  github_request_issue: 222
  homepage: https://lotus.naturalproducts.net
  keywords:
  - chemistry
  - drugs
  - metabolites
  logo: https://upload.wikimedia.org/wikipedia/commons/6/64/Lotus_initiative_logo.svg
  mappings:
    wikidata.entity: Q104225190
  name: LOTUS Initiative for Open Natural Products Research
  pattern: ^LTS\d{7}$
  prefix: lotus
  reviewer:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  uri_format: https://lotus.naturalproducts.net/compound/lotus_id/$1
  wikidata:
    database: Q104225190
lpt:
  aberowl:
    description: The Livestock Product Trait Ontology is a controlled vocabulary for
      the description of traits (measurable or observable characteristics) pertaining
      to products produced by or obtained from the body of an agricultural animal
      or bird maintained for use and profit.
    download_obo: http://aber-owl.net/media/ontologies/LPT/3/lpt.obo
    name: Livestock Product Trait Ontology
    prefix: LPT
    version: '1.4'
  agroportal:
    contact:
      email: jreecy@iastate.edu
      name: Jim Reecy
    description: The Livestock Product Trait (LPT) Ontology is a controlled vocabulary
      for the description of traits (measurable or observable characteristics) pertaining
      to products produced by or obtained from the body of an agricultural animal
      or bird maintained for use and profit., The Livestock Product Trait Ontology
      is a controlled vocabulary for the description of traits (measurable or observable
      characteristics) pertaining to products produced by or obtained from the body
      of an agricultural animal or bird maintained for use and profit.
    example_uri: http://purl.obolibrary.org/obo/LPT_0000156
    homepage: https://www.animalgenome.org/bioinfo/projects/lpt/
    license: CC-BY-4.0
    name: Livestock Product Trait Ontology
    prefix: LPT
    repository: https://github.com/AnimalGenome/livestock-product-trait-ontology
    version: '2025-08-14'
  biocontext:
    prefix: LPT
  bioportal:
    contact:
      email: caripark@iastate.edu
      name: Cari Park
    description: The Livestock Product Trait Ontology is a controlled vocabulary for
      the description of traits (measurable or observable characteristics) pertaining
      to products produced by or obtained from the body of an agricultural animal
      or bird maintained for use and profit. , The Livestock Product Trait Ontology
      is a controlled vocabulary for the description of traits (measurable or observable
      characteristics) pertaining to products produced by or obtained from the body
      of an agricultural animal or bird maintained for use and profit.
    homepage: https://www.animalgenome.org/bioinfo/projects/lpt/
    license: CC-BY-4.0
    name: Livestock Product Trait Ontology
    prefix: LPT
    version: '2025-08-14'
  contact:
    email: caripark@iastate.edu
    github: caripark
    name: Carissa Park
    orcid: 0000-0002-2346-5201
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: The Livestock Product Trait Ontology (LPT) is a controlled vocabulary
    for the description of traits (measurable or observable characteristics) pertaining
    to products produced by or obtained from the body of an agricultural animal or
    bird maintained for use and profit.
  download_obo: https://github.com/AnimalGenome/livestock-product-trait-ontology/raw/master/current_release/lpt.obo
  download_owl: https://github.com/AnimalGenome/livestock-product-trait-ontology/raw/master/current_release/lpt.owl
  example: '0000156'
  fairsharing:
    abbreviation: LPT
    description: The Livestock Product Trait Ontology is a controlled vocabulary for
      the description of traits (measurable or observable characteristics) pertaining
      to products produced by or obtained from the body of an agricultural animal
      or bird maintained for use and profit.
    domains:
    - phenotype
    homepage: https://www.animalgenome.org/bioinfo/projects/lpt/
    name: Livestock Product Trait Ontology
    prefix: FAIRsharing.g78mbm
    repository: 'https://github.com/AnimalGenome/livestock-product-trait-ontology '
    subjects:
    - Animal Husbandry
  homepage: https://github.com/AnimalGenome/livestock-product-trait-ontology
  mappings:
    aberowl: LPT
    agroportal: LPT
    biocontext: LPT
    bioportal: LPT
    fairsharing: FAIRsharing.g78mbm
  name: Livestock Product Trait Ontology
  pattern: ^\d+$
  prefix: lpt
  repository: https://github.com/AnimalGenome/livestock-product-trait-ontology
  uri_format: http://purl.obolibrary.org/obo/LPT_$1
lrg:
  banana: LRG
  banana_peel: _
  biocontext:
    prefix: LRG
  example: '1'
  hl7:
    description: 'In collaboration with NCBI, the European Bioinformatics Institute
      (EBI) is developing the Locus Reference Genomic Sequences (LRG) database, which
      is a database of reference sequences. LRG is a system for providing a genomic
      DNA sequence representation of a single gene that is idealized, has a permanent
      ID (with no versioning), and core content that never changes. LRG is not a nomenclature
      system. More than one LRG could be created for a region of interest, should
      that need arise.  Additional annotations will be present that may change with
      time (each item carrying its own date stamp), so that the latest ancillary knowledge
      about a gene is directly available.  In other words, an LRG sequence and its
      core annotation are not meant to represent current biology knowledge, but to
      provide a standard for reporting variation in a stable coordinate system.  The
      combination of the LRG plus the updatable-annotation layer will be used to support
      the biological interpretation of variants.LRG identifiers can be used with the
      HL7 coded data type (code data type that accepts expression data, or a coded
      expression data type).  This coded data type will be  gene symbols can be used
      with the HL7 coded data type.  For example, in the HL7 messages specified according
      to the HL7 V2 Clinical Genomics Fully LOINC-Qualified Genetic Variation Model,
      LRG identifiers can be used to as the observation values for Genomic Reference
      Sequence Identifier (LOINC code: 48013-7).  LRG is a database that can be used
      freely by the public.'
    homepage: http://ebi.ac.uk
    name: Locus Reference Genomic Sequences (LRG)
    organization: Wellcome Trust
    preferred_prefix: lrg
    prefix: 2.16.840.1.113883.6.283
    status: Complete
  integbio:
    alt_name: Locus Reference Genomic
    description: LRG is a database of stable genomic, transcript and protein reference
      sequences for reporting clinically relevant sequence variants. NCBI (RefSeq)
      and EMBL-EBI (Ensembl/GENCODE) are working together to rationalise differences
      in their gene sets. Records contain information about genomic, transcript and
      protein sequences, annotations, maps about the genome assembly, etc. This database
      allows users to search using LRG identifier, HGNC gene name, NCBI and Ensembl
      accession numbers (gene or transcript), gene synonym or LRG status (public or
      pending). Genome browsers on Ensembl, NCBI and UCSC are available.
    homepage: http://www.lrg-sequence.org/
    information_keywords:
    - Sequence
    maintainer: EMBL-EBI (European Bioinformatics Institute)||NCBI (National Center
      for Biotechnology Information)
    name: LRG
    prefix: nbdc02566
    pubmeds:
    - '24285302'
    status: Active
    target_keywords:
    - Genome/Gene
    - Protein
    - Health/Disease
  mappings:
    biocontext: LRG
    hl7: 2.16.840.1.113883.6.283
    integbio: nbdc02566
    miriam: lrg
    n2t: lrg
    togoid: Lrg
  miriam:
    deprecated: false
    description: A Locus Reference Genomic (LRG) is a manually curated record that
      contains stable genomic, transcript and protein reference sequences for reporting
      clinically relevant sequence variants. All LRGs are generated and maintained
      by the NCBI and EMBL-EBI.
    homepage: http://www.lrg-sequence.org/
    id: '00000376'
    name: Locus Reference Genomic
    namespaceEmbeddedInLui: false
    pattern: ^LRG_\d+$
    prefix: lrg
    providers:
    - code: ''
      description: Locus Reference Genomic through Ensembl
      homepage: http://www.ensembl.org/
      name: Locus Reference Genomic through Ensembl
      uri_format: http://www.ensembl.org/Homo_sapiens/LRG/Summary?lrg=$1
    - code: ''
      description: Locus Reference Genomic through Ensembl mirror (asia)
      homepage: http://asia.ensembl.org/
      name: Locus Reference Genomic through Ensembl mirror (asia)
      uri_format: http://asia.ensembl.org/Homo_sapiens/LRG/Summary?lrg=$1
    - code: ''
      description: Locus Reference Genomic through Ensembl mirror (US east)
      homepage: http://useast.ensembl.org/
      name: Locus Reference Genomic through Ensembl mirror (US east)
      uri_format: http://useast.ensembl.org/Homo_sapiens/LRG/Summary?lrg=$1
    sampleId: LRG_1
    uri_format: http://ftp.ebi.ac.uk/pub/databases/lrgex/$1.xml
  n2t:
    description: Locus Reference Genomic (LRG) provides identifiers to stable genomic
      DNA sequences for regions of the human genome, providing a recognized reference-sequence
      standard for reporting sequence variants. LRG is maintained by the NCBI and
      the European Bioinformatics Institute (EBI).
    example: LRG_1
    homepage: http://uswest.ensembl.org/
    name: Locus Reference Genomic through Ensembl mirror (US west)
    namespaceEmbeddedInLui: false
    pattern: ^LRG_\d+$
    prefix: lrg
    uri_format: http://uswest.ensembl.org/Homo_sapiens/LRG/Summary?lrg=$1
  pattern: ^\d+$
  prefix: lrg
  togoid:
    catalog: nbdc02566
    description: LRG is a database of stable genomic, transcript and protein reference
      sequences for reporting clinically relevant sequence variants. NCBI (RefSeq)
      and EMBL-EBI (Ensembl/GENCODE) are working together to rationalise differences
      in their gene sets. Records contain information about genomic, transcript and
      protein sequences, annotations, maps about the genome assembly, etc. This database
      allows users to search using LRG identifier, HGNC gene name, NCBI and Ensembl
      accession numbers (gene or transcript), gene synonym or LRG status (public or
      pending). Genome browsers on Ensembl, NCBI and UCSC are available.
    examples:
    - LRG_41
    - LRG_356
    - LRG_147
    - LRG_660
    - LRG_498
    - LRG_364
    - LRG_203
    - LRG_162
    - LRG_1271
    - LRG_884
    keywords:
    - Gene
    name: LRG
    pattern: ^(?LRG_\d+)$
    prefix: Lrg
    uri_format: http://identifiers.org/lrg/$1
lrmi:
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: The Learning Resource Metadata Innovation (LRMI) specification is a
    collection of classes and properties for markup and description of educational
    resources. The specification builds on the extensive vocabulary provided by Schema.org
    and other standards. LRMI terms not included in schema.org may nevertheless be
    used to augment and enrich Schema.org markup. (from homepage)
  download_rdf: https://www.dublincore.org/specifications/lrmi/lrmi_terms/2022-06-14/lrmi-terms.ttl
  example: AlignmentObject
  github_request_issue: 1677
  homepage: https://www.dublincore.org/specifications/lrmi/lrmi_terms/2022-06-14/
  keywords:
  - education
  - educational resource
  - open educational resources
  license: CC-BY-4.0
  name: Learning Resource Metadata Innovation Terms
  prefix: lrmi
  rdf_uri_format: http://purl.org/dcx/lrmi-terms/$1
  uri_format: http://purl.org/dcx/lrmi-terms/$1
lrmi.alignmenttype:
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: A concept scheme that defines the types of relationships between a
    learning resource and a node in an educational framework.
  download_skos: https://www.dublincore.org/vocabs/alignmentType.ttl
  example: assesses
  github_request_issue: 1750
  homepage: https://www.dublincore.org/specifications/lrmi/concept_schemes/alignmentType/
  keywords:
  - learning resource
  - open educational resource
  license: CC-BY-4.0
  name: LRMI Alignment Type Vocabulary
  prefix: lrmi.alignmenttype
  repository: https://github.com/dcmi/lrmi
  uri_format: http://purl.org/dcx/lrmi-vocabs/alignmentType/$1
lrmi.educationalaudiencerole:
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: A concept scheme that defines the primary or intended roles of the
    audience (beneficiary) of the resource being described.
  download_skos: https://www.dublincore.org/vocabs/educationalAudienceRole.ttl
  example: mentor
  github_request_issue: 1750
  homepage: https://www.dublincore.org/specifications/lrmi/concept_schemes/alignmentType/
  keywords:
  - learning resource
  - open educational resource
  license: CC-BY-4.0
  name: LRMI Educational Audience Role Vocabulary
  prefix: lrmi.educationalaudiencerole
  repository: https://github.com/dcmi/lrmi
  uri_format: http://purl.org/dcx/lrmi-vocabs/educationalAudienceRole/$1
lrmi.eduse:
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: A concept scheme that enumerates the educational uses of a learning
    resource.
  download_skos: https://www.dublincore.org/vocabs/educationalUse.ttl
  example: instruction
  github_request_issue: 1750
  homepage: https://www.dublincore.org/specifications/lrmi/concept_schemes/educationalUse/
  keywords:
  - learning resource
  - open educational resource
  license: CC-BY-4.0
  name: LRMI Educational Use Vocabulary
  prefix: lrmi.eduse
  repository: https://github.com/dcmi/lrmi
  uri_format: http://purl.org/dcx/lrmi-vocabs/educationalUse/$1
lrmi.interact:
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: A concept scheme that defines the predominate interact mode of the
    learning resource being described.
  download_skos: https://www.dublincore.org/vocabs/interactivityType.ttl
  example: active
  github_request_issue: 1750
  homepage: https://www.dublincore.org/specifications/lrmi/concept_schemes/interactivityType/
  keywords:
  - learning resource
  - open educational resource
  license: CC-BY-4.0
  name: LRMI Interact Type Vocabulary
  prefix: lrmi.interact
  repository: https://github.com/dcmi/lrmi
  uri_format: http://purl.org/dcx/lrmi-vocabs/interactivityType/$1
lrmi.resourcetype:
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: A top-level concept scheme that enumerates different types of Learning
    Resource, designed to supplement existing more generic resource type schemes and
    which can support local extensions.
  download_skos: https://www.dublincore.org/vocabs/learningResourceType.ttl
  example: activityPlan
  github_request_issue: 1750
  homepage: https://www.dublincore.org/specifications/lrmi/concept_schemes/learningResourceType/
  keywords:
  - learning resource
  - open educational resource
  license: CC-BY-4.0
  name: LRMI Learning Resource Type Concept Scheme
  prefix: lrmi.resourcetype
  repository: https://github.com/dcmi/lrmi
  uri_format: http://purl.org/dcx/lrmi-vocabs/learningResourceType/$1
lspci:
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: Internal identifiers form the LSP for ChEBML compound classes (e.g.,
    combining various salts and ions)
  example: '1'
  homepage: https://labsyspharm.github.io/lspci/
  keywords:
  - chemistry
  - drugs
  - metabolites
  name: Laboratory of Systems Pharmacology Compound
  pattern: ^\d+$
  prefix: lspci
  uri_format: https://labsyspharm.github.io/lspci/$1
lter:
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: Ecological terms
  example: '182'
  homepage: https://vocab.lternet.edu/vocab/vocab/index.php
  name: Long Term Ecological Research Controlled Vocabulary
  pattern: ^\d+$
  prefix: lter
  uri_format: https://vocab.lternet.edu/vocab/vocab/index.php?tema=$1
lw:
  mappings:
    miriam: lw
  miriam:
    deprecated: false
    description: The LifeWatch Metadata Catalogues plays a crucial role in managing
      metadata for digital objects, including Datasets, Services, Workflows and Virtual
      Research Environments. This catalogue serves as the central repository, ensuring
      that resources are accessible and reusable by stakeholders.
    homepage: https://metadatacatalogue.lifewatch.eu/
    id: 00001084
    name: LifeWatch Metadata Catalogue
    namespaceEmbeddedInLui: false
    pattern: ^[a-fA-F0-9]{8}-[a-fA-F0-9]{4}-[a-fA-F0-9]{4}-[a-fA-F0-9]{4}-[a-fA-F0-9]{12}$
    prefix: lw
    sampleId: 6e3b1371-59d7-481a-9db4-cd0d0de98436
    uri_format: https://metadatacatalogue.lifewatch.eu/srv/eng/catalog.search#/metadata/$1
  prefix: lw
m4i:
  bartoc:
    abbreviation: m4i
    description: The ontology Metadata4Ing is developed within the NFDI Consortium
      NFDI4Ing with the aim of providing a thorough framework for the semantic description
      of research data, with a particular focus on engineering sciences and neighbouring
      disciplines. This ontology allows a description of the whole data generation
      process (experiment, observation, simulation), embracing the object of investigation,
      all sample and data manipulation procedures, a summary of the data files and
      the informaton contained, and all personal and institutional roles. The subordinate
      classes and relations can be built according to the two principles of inheritance
      and modularity. "Inheritance" means that a subclass inherits all properties
      of its superordinate class, possibly adding some new ones. Modularity means
      that all expansions are independent of each other; this makes possible for instance
      to generate expanded ontologies for any possible combinations of method × object
      of research."
    homepage: https://w3id.org/nfdi4ing/metadata4ing
    license: CC-BY-4.0
    name: Metadata4Ing
    prefix: '20402'
  contact:
    email: dorothea.iglezakis@ub.uni-stuttgart.de
    github: doigl
    name: Dorothea Iglezakis
    orcid: 0000-0002-8524-0569
  contributor:
    email: giacomo.lanza@ptb.de
    github: Zack-83
    name: Giacomo Lanza
    orcid: 0000-0002-2239-3955
  description: The ontology Metadata4Ing is developed within the NFDI Consortium NFDI4Ing
    with the aim of providing a thorough framework for the semantic description of
    research data, with a particular focus on engineering sciences and neighbouring
    disciplines. This ontology allows a description of the whole data generation process
    (experiment, observation, simulation), embracing the object of investigation,
    all sample and data manipulation procedures, a summary of the data files and the
    information contained, and all personal and institutional roles. The subordinate
    classes and relations can be built according to the two principles of inheritance
    and modularity. "Inheritance" means that a subclass inherits all properties of
    its superordinate class, possibly adding some new ones. Modularity means that
    all expansions are independent of each other; this makes possible for instance
    to generate expanded ontologies for any possible combinations of method × object
    of research.
  download_rdf: https://nfdi4ing.pages.rwth-aachen.de/metadata4ing/metadata4ing/ontology.ttl
  example: Method
  fairsharing:
    abbreviation: m4i
    description: The ontology Metadata4Ing is developed within the NFDI Consortium
      NFDI4Ing with the aim of providing a framework for the semantic description
      of research data, with a particular focus on engineering sciences and neighbouring
      disciplines. This ontology allows a thorough description of the whole data generation
      process (experiment, observation, simulation), embracing the object of investigation,
      all sample and data manipulation procedures, a summary of the data files and
      the information contained, and all personal and institutional roles. The subordinate
      classes and relations can be built according to the two principles of inheritance
      and modularity. "Inheritance" means that a subclass inherits all properties
      of its superordinate class, possibly adding some new ones. Modularity means
      that all expansions are independent of each other; this makes possible for instance
      to generate expanded ontologies for any possible combinations of method × object
      of research.
    homepage: https://metadata4ing.org
    license: CC-BY-4.0
    logo: https://api.fairsharing.org/rails/active_storage/blobs/redirect/eyJfcmFpbHMiOnsibWVzc2FnZSI6IkJBaHBBaWNHIiwiZXhwIjpudWxsLCJwdXIiOiJibG9iX2lkIn19--6435da59153a976c6b09d30ac0ee96286c50a32c/Logo.png?disposition=inline
    name: Metadata4Ing
    prefix: FAIRsharing.f8b3ec
    repository: https://git.rwth-aachen.de/nfdi4ing/metadata4ing/metadata4ing
    subjects:
    - Engineering Science
  github_request_issue: 970
  homepage: https://w3id.org/nfdi4ing/metadata4ing/
  license: CC-BY-4.0
  lov:
    description: "Metadata4Ing defines classes and properties or reuses such classes\
      \ and properties from other ontologies to describe research processes and research\
      \ data management in NFDI4Ing. \nNew concepts and properties are located in\
      \ the namespace of Metadata4Ing.\nMetadata4Ing does not import complete ontologies\
      \ for the sake of relevance, readability, understandability and usability by\
      \ and for engineers.\nInstead, it tries to make re-use of existing identifiers\
      \ for classes and properties by re-using all or a relevant subset of the axioms\
      \ from the original ontology.\nThese statements have been extracted in different\
      \ ways, e.g. by using Protégé tools importing an ontology and copying axioms\
      \ of relevant items to Metadata4Ing or by download from data services or raw\
      \ files of ontologies and manual copypasting.\nIn some cases there was a need\
      \ to extend or modify the original set of statements about an entity, e.g. because\
      \ labels and definitions were expressed with a different owl:AnnotationProperty\
      \ than the rest of Metadata4Ing, or because a skos:preflabel or a skos:definition\
      \ in any of the languages we would like to support was missing.\nAny editorial\
      \ changes on elements from external ontologies are declared in Metadata4Ing\
      \ by an annotation with skos:editorialNote at item-level.\nTo get the original\
      \ set of statements we encourage to visit the original namespace of the respective\
      \ item.\nMetadata4Ing reuses elements from the following ontologies:\n- BIBO\
      \ = Bibliographic Ontology  \n- BIRO = Bibliographic Reference Ontology  \n\
      - DCAT = Data Catalog  \n- DCTERMS = Dublin Core Terms  \n- FOAF = Friend of\
      \ a Friend  \n- OWL = Web Ontology Language  \n- PROV = Provenance Namespace\
      \  \n- QUDT = Quantities, Units, Dimensions and Types  \n- RDF = Resource Description\
      \ Framework  \n- RDFS = RDF Schema  \n- SCHEMA = schema.org  \n- SKOS = Simple\
      \ Knowledge Organization System  \n- SSN = Semantic Sensor Network Ontology\
      \  \n- VANN = Vocabulary for Annotating vocabulary descriptions  \n- XSD = XML\
      \ Schema Definition  \n- EMMO = European Materials and Modelling Ontology  \n\
      - BFO = Basic Formal Ontology  \n- RO = Relation Ontology  \n- PIMS-II = PIMS\
      \ Interoperability Infrastructure  \n- D-SI = Digital System of Units"
    homepage: https://nfdi4ing.pages.rwth-aachen.de/metadata4ing/metadata4ing/
    keywords:
    - Academy
    - Metadata
    modified: '2025-03-10'
    name: 'Metadata4Ing: An ontology for describing the generation of research data
      within a scientific activity.'
    prefix: m4i
    uri_prefix: http://w3id.org/nfdi4ing/metadata4ing#$1
  mappings:
    bartoc: '20402'
    fairsharing: FAIRsharing.f8b3ec
    lov: m4i
    miriam: m4i
    tib: m4i
    wikidata.entity: Q111516803
    zazuko: m4i
  mastodon: nfdi4ing@nfdi.social
  miriam:
    deprecated: false
    description: The ontology Metadata4Ing provides a framework for the semantic description
      of research data and of the whole data generation process, embracing the object
      of investigation, all sample and data manipulation methods and tools, the data
      files themselves, and the roles of persons and institutions. The structure and
      application of the ontology are based on the principles of modularity and inheritance.
    homepage: http://www.rwth-aachen.de/cms/~a/root/lidx/1/
    id: 00001008
    name: Metadata4Ing
    namespaceEmbeddedInLui: false
    pattern: '[A-Za-z_0-9]*'
    prefix: m4i
    sampleId: ProcessingStep
    uri_format: http://w3id.org/nfdi4ing/metadata4ing#$1
  name: Metadata4Ing
  owners:
  - name: Nationale Forschungsdateninfrastruktur
    partnered: false
    ror: 05qj6w324
    wikidata: null
  prefix: m4i
  repository: https://git.rwth-aachen.de/nfdi4ing/metadata4ing/metadata4ing
  reviewer:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  tib:
    contact: metadata4ing@nfdi4ing.de
    description: The ontology Metadata4Ing is developed within the NFDI Consortium
      NFDI4Ing with the aim of providing a thorough framework for the semantic description
      of research data, with a particular focus on engineering sciences and neighbouring
      disciplines. This ontology allows a thorough description of the whole data generation
      process (experiment, observation, simulation), embracing the object of investigation,
      all sample and data manipulation procedures, a summary of the data files and
      the information contained, and all personal and institutional roles. The subordinate
      classes and relations can be built according to the two principles of _inheritance_
      and _modularity_. _Inheritance_ means that a subclass inherits all properties
      of its superordinate class, possibly adding some new ones. _Modularity_ means
      that all expansions are independent of each other; this makes possible for instance
      to generate expanded ontologies for any possible combinations of method × object
      of research.
    keywords:
    - NFDI4ING
    - Digital Planning and Construction
    - FID BAUdigital
    - NFDI4CAT
    - engineering
    name: 'Metadata4Ing: An ontology for describing the generation of research data
      within a scientific activity'
    prefix: m4i
    tracker: https://git.rwth-aachen.de/nfdi4ing/metadata4ing/metadata4ing/-/issues
    uri_format: http://w3id.org/nfdi4ing/metadata4ing#$1
    version.iri: http://w3id.org/nfdi4ing/metadata4ing/1.3.1
  uri_format: http://w3id.org/nfdi4ing/metadata4ing#$1
  zazuko:
    prefix: m4i
    uri_format: http://w3id.org/nfdi4ing/metadata4ing#$1
ma:
  aberowl:
    description: A structured controlled vocabulary of the adult anatomy of the mouse
      (Mus).
    download_owl: http://aber-owl.net/media/ontologies/MA/127/ma.owl
    homepage: https://github.com/obophenotype/mouse-anatomy-ontology
    name: Mouse adult gross anatomy
    prefix: MA
  bartoc:
    abbreviation: MA
    description: The Classification scheme of Literature of the Middle Ages from the
      University of Geneva is an internal classification system. It is employed by
      the Department of German Language and Literature.
    name: Classification Literature Middle Ages
    prefix: '1143'
  biocontext:
    prefix: MA
  bioportal:
    contact:
      email: Terry.Hayamizu@jax.org
      name: Terry Hayamizu
    description: A structured controlled vocabulary of the adult anatomy of the mouse
      (Mus).
    homepage: http://www.informatics.jax.org/searches/AMA_form.shtml
    name: Mouse Adult Gross Anatomy Ontology
    prefix: MA
    version: releases/2017-02-07
  fairsharing:
    abbreviation: MA
    description: 'The Anatomy Ontology for the Adult Mouse is organized spatially
      and functionally, using "is a" and "part of" relationships to describe the anatomy
      of the postnatal mouse. Anatomical terms are arranged as a hierarchy from body
      region or organ system to tissue substructure. Modeling the anatomy hierarchically
      makes it possible to record expression results from assays with differing spatial
      resolution in a consistent and integrated manner. Organizing the anatomical
      terms as a Directed Acyclic Graph (DAG), i.e., in which a term can have more
      than one parent, allows presentation of the anatomy from multiple perspectives.
      In various locations, this ontology is also referred to as:  ''Mouse Adult Gross
      Anatomy ontology'', ''Adult Mouse Anatomy'',  ''Mouse Anatomy'' or ''Mouse anatomical
      entity''. '
    domains:
    - organ
    - tissue
    homepage: http://www.informatics.jax.org/vocab/gxd/ma_ontology/
    license: CC-BY-4.0
    name: Mouse Adult Gross Anatomy Ontology
    prefix: FAIRsharing.pdwqcr
    publications:
    - doi: 10.1186/gb-2005-6-3-r29
      pubmed: '15774030'
      title: 'The Adult Mouse Anatomical Dictionary: a tool for annotating and integrating
        data'
      year: 2005
    repository: https://github.com/obophenotype/mouse-anatomy-ontology
    subjects:
    - Anatomy
  go:
    description: Adult Mouse Anatomical Dictionary; part of Gene Expression Database
    homepage: http://www.informatics.jax.org/
    name: Adult Mouse Anatomical Dictionary
    prefix: MA
    uri_format: http://www.informatics.jax.org/searches/AMA.cgi?id=MA:$1
  mappings:
    aberowl: MA
    bartoc: '1143'
    biocontext: MA
    bioportal: MA
    fairsharing: FAIRsharing.pdwqcr
    go: MA
    miriam: ma
    n2t: ma
    obofoundry: ma
    ols: ma
    ontobee: MA
    prefixcommons: ma
    wikidata.entity: Q81661674
  miriam:
    deprecated: false
    description: A structured controlled vocabulary of the adult anatomy of the mouse
      (Mus)
    homepage: http://www.informatics.jax.org/
    id: '00000445'
    name: Mouse Adult Gross Anatomy
    namespaceEmbeddedInLui: true
    pattern: ^MA:\d+$
    prefix: ma
    sampleId: '0002502'
    uri_format: http://www.informatics.jax.org/searches/AMA.cgi?id=MA:$1
  n2t:
    description: A structured controlled vocabulary of the adult anatomy of the mouse
      (Mus)
    example: '0002502'
    homepage: http://www.informatics.jax.org/
    name: Mouse Adult Gross Anatomy at The Jackson Laboratory
    namespaceEmbeddedInLui: true
    pattern: ^MA:\d+$
    prefix: ma
    uri_format: http://www.informatics.jax.org/searches/AMA.cgi?id=MA:$1
  obofoundry:
    contact: Terry.Hayamizu@jax.org
    contact.github: tfhayamizu
    contact.label: Terry Hayamizu
    contact.orcid: 0000-0002-0956-8634
    deprecated: false
    description: A structured controlled vocabulary of the adult anatomy of the mouse
      (Mus).
    domain: anatomy and development
    download.obo: http://purl.obolibrary.org/obo/ma.obo
    download.owl: http://purl.obolibrary.org/obo/ma.owl
    homepage: https://github.com/obophenotype/mouse-anatomy-ontology
    license: CC BY 4.0
    license.url: https://creativecommons.org/licenses/by/4.0/
    name: Mouse adult gross anatomy
    preferredPrefix: MA
    prefix: ma
    repository: https://github.com/obophenotype/mouse-anatomy-ontology
  ols:
    description: A structured controlled vocabulary of the adult anatomy of the mouse
      (Mus).
    download_owl: http://purl.obolibrary.org/obo/ma.owl
    homepage: https://github.com/obophenotype/mouse-anatomy-ontology
    name: Mouse adult gross anatomy
    prefix: ma
    tracker: https://github.com/obophenotype/mouse-anatomy-ontology/issues
  ontobee:
    library: Library
    name: Mouse adult gross anatomy
    prefix: MA
  pattern: ^\d+$
  prefix: ma
  prefixcommons:
    alt_uri_formats:
    - http://purl.org/obo/owl/MA#$1
    bioportal: '1000'
    description: A structured controlled vocabulary of the adult anatomy of the mouse
      (Mus).
    example: MA:0000021
    homepage: http://www.informatics.jax.org/searches/AMA_form.shtml
    keywords:
    - obo
    - anatomy
    - mouse
    name: Mouse adult gross anatomy
    pattern: ^MA:\d+$
    prefix: ma
  publications:
  - doi: 10.1186/gb-2005-6-3-r29
    pmc: PMC1088948
    pubmed: '15774030'
    title: 'The Adult Mouse Anatomical Dictionary: a tool for annotating and integrating
      data'
    year: 2005
  uri_format: http://purl.obolibrary.org/obo/MA_$1
macie:
  biocontext:
    prefix: MACIE
  contact:
    email: gemma.l.holliday@gmail.com
    github: GLHolliday79
    name: Gemma L. Holliday
    orcid: 0000-0002-6731-6398
  edam:
    description: Identifier of an enzyme reaction mechanism from the MACie database.
    name: Reaction ID (MACie)
    obsolete: false
    prefix: '2641'
  fairsharing:
    abbreviation: MACiE
    description: MACiE is an electronic database of well-characterised enzymatic reactions.
      MACiE is the result of more than three years' collaboration between the Mitchell
      and Murray-Rust groups in the Unilever Centre and Prof. Janet Thornton at the
      European Bioinformatics Institute. The database contains the reaction mechanisms
      for 100 individual enzymes; this includes the overall reactions and the multiple
      steps that constitute them.
    homepage: http://www.ebi.ac.uk/thornton-srv/databases/MACiE
    name: Mechanism, Annotation and Classification in Enzymes
    prefix: FAIRsharing.7xkx69
    publications:
    - doi: 10.1093/bioinformatics/bti693
      pubmed_id: 16188925
      title: 'MACiE: a database of enzyme reaction mechanisms.'
    - doi: 10.1093/nar/gkl774
      pubmed_id: 17082206
      title: 'MACiE (Mechanism, Annotation and Classification in Enzymes): novel tools
        for searching catalytic mechanisms.'
    subjects:
    - Life Science
  mappings:
    biocontext: MACIE
    edam: '2641'
    fairsharing: FAIRsharing.7xkx69
    miriam: macie
    n2t: macie
    prefixcommons: macie
  miriam:
    deprecated: false
    description: MACiE (Mechanism, Annotation and Classification in Enzymes) is a
      database of enzyme reaction mechanisms. Each entry in MACiE consists of an overall
      reaction describing the chemical compounds involved, as well as the species
      name in which the reaction occurs. The individual reaction stages for each overall
      reaction are listed with mechanisms, alternative mechanisms, and amino acids
      involved.
    homepage: https://www.ebi.ac.uk/thornton-srv/m-csa/about/
    id: '00000077'
    name: MACiE
    namespaceEmbeddedInLui: false
    pattern: ^M\d{4}$
    prefix: macie
    sampleId: M0001
    uri_format: https://www.ebi.ac.uk/thornton-srv/m-csa/search/?s=$1
  n2t:
    description: MACiE (Mechanism, Annotation and Classification in Enzymes) is a
      database of enzyme reaction mechanisms. Each entry in MACiE consists of an overall
      reaction describing the chemical compounds involved, as well as the species
      name in which the reaction occurs. The individual reaction stages for each overall
      reaction are listed with mechanisms, alternative mechanisms, and amino acids
      involved.
    example: M0001
    homepage: https://www.ebi.ac.uk/thornton-srv/databases/MACiE/index.html
    name: MACiE database of mechanisms, annotation and classification in enzymes
    namespaceEmbeddedInLui: false
    pattern: ^M\d{4}$
    prefix: macie
    uri_format: https://www.ebi.ac.uk/thornton-srv/databases/cgi-bin/MACiE/entry/getPage.pl?id=$1
  name: Mechanism, Annotation and Classification in Enzymes
  prefix: macie
  prefixcommons:
    description: MACiE is an electronic database of well-characterised enzymatic reactions.
      MACiE is the result of more than three years' collaboration between the Mitchell
      and Murray-Rust groups in the Unilever Centre and Prof. Janet Thornton at the
      European Bioinformatics Institute. The database contains the reaction mechanisms
      for 100 individual enzymes; this includes the overall reactions and the multiple
      steps that constitute them.
    example: M0001
    homepage: http://www.ebi.ac.uk/thornton-srv/databases/MACiE/
    keywords:
    - enzyme
    - pathway
    license: http://www.ebi.ac.uk/Information/termsofuse.html
    name: MACiE
    pattern: ^M\d{4}$
    prefix: macie
    pubmed_ids:
    - '17082206'
    uri_format: http://www.ebi.ac.uk/thornton-srv/databases/cgi-bin/MACiE/getPage.pl?id=$1
  publications:
  - doi: 10.1093/nar/gkl774
    pmc: PMC1634735
    pubmed: '17082206'
    title: 'MACiE (Mechanism, Annotation and Classification in Enzymes): novel tools
      for searching catalytic mechanisms'
    year: 2006
  - doi: 10.1093/bioinformatics/bti693
    pmc: PMC2748267
    pubmed: '16188925'
    title: 'MACiE: a database of enzyme reaction mechanisms'
    year: 2005
maggot:
  mappings:
    miriam: maggot
  miriam:
    deprecated: false
    description: Sharing descriptive Metadata is the first essential step towards
      Open Scientific Data. With this in mind, Maggot was specifically designed to
      annotate datasets by creating a metadata file to attach to the storage space.
      Indeed, it allows users to easily add descriptive metadata to datasets produced
      within a collective of people (research unit, platform, multi-partner project,
      etc.). This approach fits perfectly into a data management plan as it addresses
      the issues of data organization and documentation, data storage and frictionless
      metadata sharing within this same collective and beyond.
    homepage: https://eng-bfp.bordeaux-aquitaine.hub.inrae.fr/resources/metabolome-platform
    id: 00001038
    name: Maggot
    namespaceEmbeddedInLui: false
    pattern: ^[A-Za-z0-9]+$
    prefix: maggot
    sampleId: frim1
    uri_format: https://pmb-bordeaux.fr/maggot/metadata/$1
  prefix: maggot
maizegdb.locus:
  biocontext:
    prefix: MAIZEGDB.LOCUS
  contact:
    email: margaret.woodhouse@usda.gov
    github: margaretwoodhouse
    name: Margaret R. Woodhouse
    orcid: 0000-0003-2164-8300
  fairsharing:
    abbreviation: MaizeGDB
    description: MaizeGDB is the maize research community's central repository for
      genetics and genomics information.
    homepage: https://www.maizegdb.org
    name: Maize Genetics and Genomics Database
    prefix: FAIRsharing.aq280w
    publications:
    - doi: 10.1155/2008/496957
      pubmed_id: 18769488
      title: 'MaizeGDB: The maize model organism database for basic, translational,
        and applied research.'
    - doi: 10.1007/978-1-4939-3167-5_9
      pubmed_id: 26519406
      title: 'MaizeGDB: The Maize Genetics and Genomics Database'
    - doi: 10.1093/nar/gkv1007
      pubmed_id: 26432828
      title: 'MaizeGDB update: new tools, data and interface for the maize model organism
        database'
    - doi: 10.3389/fpls.2019.01050
      pubmed_id: 31555312
      title: 'MaizeDIG: Maize Database of Images and Genomes.'
    - doi: 10.1093/nar/gky1046
      pubmed_id: 30407532
      title: 'MaizeGDB 2018: the maize multi-genome genetics and genomics database'
    subjects:
    - Genomics
    - Genetics
    - Life Science
  go:
    homepage: https://www.maizegdb.org/
    name: MaizeGDB
    prefix: MaizeGDB_Locus
    uri_format: https://www.maizegdb.org/gene_center/gene/$1
  integbio:
    alt_name: Maize Genetics and Genomics Database
    description: MaizeGDB is a integrated database of the crop plant and model organism
      Zea mays. It contains maps, gene product information, loci and their various
      alleles, phenotypes (both naturally occurring and as a result of directed mutagenesis),
      stocks, sequences, molecular markers, references and contact information for
      maize researchers on worldwide. Moreover, users are able to obtain various community
      support service bulletin boards including the Editorial Board's list of high-impact
      papers, information about the Annual Maize genetics Conference and the Jobs
      board where employment opportunities are posted.
    fairsharing: biodbcore-000414
    homepage: http://www.maizegdb.org/
    information_keywords:
    - Bioresource
    - Sequence
    - Expression
    - Interaction/Pathway
    - Image/Movie
    - Portal
    maintainer: MaizeGDB (Maize Genetics and Genomoics Database) Working Group
    name: MaizeGDB
    prefix: nbdc00129
    pubmeds:
    - '17202174'
    - '14681441'
    - '21565781'
    status: Active
    target_keywords:
    - Genome/Gene
    - cDNA/EST
    - Genetic variation
    - Protein
    - Organism
  mappings:
    biocontext: MAIZEGDB.LOCUS
    fairsharing: FAIRsharing.aq280w
    go: MaizeGDB_Locus
    integbio: nbdc00129
    miriam: maizegdb.locus
    n2t: maizegdb.locus
    ncbi: MaizeGDB
    prefixcommons: maizegdb
    re3data: r3d100010795
    uniprot: DB-0058
  miriam:
    deprecated: false
    description: MaizeGDB is the maize research community's central repository for
      genetics and genomics information.
    homepage: http://www.maizegdb.org/
    id: '00000177'
    name: MaizeGDB Locus
    namespaceEmbeddedInLui: false
    pattern: ^\d+$
    prefix: maizegdb.locus
    sampleId: '25011'
    uri_format: http://www.maizegdb.org/cgi-bin/displaylocusrecord.cgi?id=$1
  n2t:
    description: MaizeGDB is the maize research community's central repository for
      genetics and genomics information.
    example: '25011'
    homepage: http://www.maizegdb.org/
    name: MaizeGDB at Missouri
    namespaceEmbeddedInLui: false
    pattern: ^\d+$
    prefix: maizegdb.locus
    uri_format: http://www.maizegdb.org/cgi-bin/displaylocusrecord.cgi?id=$1
  name: MaizeGDB Locus
  ncbi:
    example: '635633'
    homepage: http://www.maizegdb.org/
    name: Maize Genome Database unique identifiers
    prefix: MaizeGDB
  prefix: maizegdb.locus
  prefixcommons:
    description: MaizeGDB is the maize research community's central repository for
      genetics and genomics information.
    example: '25011'
    homepage: http://www.maizegdb.org
    keywords:
    - genome
    - DNA
    name: Maize Genetics and Genomics Database
    pattern: ^\d+$
    prefix: maizegdb
    pubmed_ids:
    - '18769488'
    synonyms:
    - maizegdb.locus
    - maizegdb_qtl
    uri_format: http://www.maizegdb.org/cgi-bin/displaylocusrecord.cgi?id=$1
  publications:
  - doi: 10.3389/fpls.2019.01050
    pmc: PMC6724615
    pubmed: '31555312'
    title: 'MaizeDIG: Maize Database of Images and Genomes'
    year: 2019
  - doi: 10.1093/nar/gky1046
    pmc: PMC6323944
    pubmed: '30407532'
    title: 'MaizeGDB 2018: the maize multi-genome genetics and genomics database'
    year: 2019
  - doi: 10.1007/978-1-4939-3167-5_9
    pmc: null
    pubmed: '26519406'
    title: 'MaizeGDB: The Maize Genetics and Genomics Database'
    year: 2016
  - doi: 10.1093/nar/gkv1007
    pmc: PMC4702771
    pubmed: '26432828'
    title: 'MaizeGDB update: new tools, data and interface for the maize model organism
      database'
    year: 2015
  - doi: 10.1155/2008/496957
    pmc: PMC2518694
    pubmed: '18769488'
    title: 'MaizeGDB: The maize model organism database for basic, translational,
      and applied research'
    year: 2008
  - doi: 10.1093/nar/gkl1048
    pmc: PMC1899092
    pubmed: '17202174'
    title: MaizeGDB's new data types, resources and activities
    year: 2007
  - doi: 10.1155/2008/496957
    pmc: null
    pubmed: null
    title: 'MaizeGDB: The maize model organism database for basic, translational,
      and applied research.'
    year: null
  - doi: 10.1007/978-1-4939-3167-5_9
    pmc: null
    pubmed: null
    title: 'MaizeGDB: The Maize Genetics and Genomics Database'
    year: null
  - doi: 10.1093/nar/gkv1007
    pmc: null
    pubmed: null
    title: 'MaizeGDB update: new tools, data and interface for the maize model organism
      database'
    year: null
  - doi: 10.3389/fpls.2019.01050
    pmc: null
    pubmed: null
    title: 'MaizeDIG: Maize Database of Images and Genomes.'
    year: null
  - doi: 10.1093/nar/gky1046
    pmc: null
    pubmed: null
    title: 'MaizeGDB 2018: the maize multi-genome genetics and genomics database'
    year: null
  - doi: null
    pmc: null
    pubmed: '18769488'
    title: null
    year: null
  - doi: 10.1186/s12870-021-03173-5
    pmc: null
    pubmed: '34416864'
    title: null
    year: null
  re3data:
    description: 'The Maize Genetics and Genomics Database focuses on collecting data
      related to the crop plant and model organism Zea mays. The project''s goals
      are to synthesize, display, and provide access to maize genomics and genetics
      data, prioritizing mutant and phenotype data and tools, structural and genetic
      map sets, and gene models. MaizeGDB also aims to make the Maize Newsletter available,
      and provide support services to the community of maize researchers.

      MaizeGDB is working with the Schnable lab, the Panzea project, The Genome Reference
      Consortium, and iPlant Collaborative to create a plan for archiving, dessiminating,
      visualizing, and analyzing diversity data.

      MMaizeGDB is short for Maize Genetics/Genomics Database. It is a USDA/ARS funded
      project to integrate the data found in MaizeDB and ZmDB into a single schema,
      develop an effective interface to access this data, and develop additional tools
      to make data analysis easier. Our goal in the long term is a true next-generation
      online maize database.aize genetics and genomics database.'
    doi: 10.17616/R3V32B
    homepage: https://www.maizegdb.org/
    license: Public Domain
    name: MaizeGDB
    prefix: r3d100010795
    synonyms:
    - Maize Genetics and Genomics Database
    xrefs:
      nif: 0000-03096
  synonyms:
  - MaizeGDB
  uniprot:
    abbreviation: MaizeGDB
    category: Organism-specific databases
    homepage: https://www.maizegdb.org/
    name: Maize Genetics and Genomics Database
    prefix: DB-0058
    publications:
    - doi: 10.1186/s12870-021-03173-5
      pubmed: '34416864'
    uri_format: https://www.maizegdb.org/data_center/gene_product?id=$1
mamo:
  aberowl:
    description: The Mathematical Modelling Ontology (MAMO) is a classification of
      the types of mathematical models used mostly in the life sciences, their variables,
      relationships and other relevant features.
    download_owl: http://aber-owl.net/media/ontologies/MAMO/17/mamo.owl
    homepage: http://sourceforge.net/p/mamo-ontology/wiki/Home/
    name: Mathematical modeling ontology
    prefix: MAMO
  banana: MAMO
  banana_peel: _
  biocontext:
    prefix: MAMO
  bioportal:
    contact:
      email: mamo-ontology-discuss@lists.sourceforge.net
      name: mamo-ontology-discuss
    description: The Mathematical Modelling Ontology (MAMO) is a classification of
      the types of mathematical models used mostly in the life sciences, their variables,
      relationships and other relevant features.
    homepage: http://co.mbine.org/standards/mamo
    name: Mathematical Modelling Ontology
    prefix: MAMO
    version: '2023-02-03'
  example: '0000026'
  fairsharing:
    abbreviation: MAMO
    contact:
      email: n.lenovere@gmail.com
      name: Nicolas Le Novere
      orcid: 0000-0002-6309-7327
    description: Classification of the types of mathematical models used mostly in
      the life sciences, the types of variables, the types of readout and other relevant
      features.
    homepage: https://sourceforge.net/p/mamo-ontology/wiki/Home/
    name: Mathematical Modelling Ontology
    prefix: FAIRsharing.kbz5jh
    subjects:
    - Systems Biology
    - Computational Biology
    - Mathematics
  mappings:
    aberowl: MAMO
    biocontext: MAMO
    bioportal: MAMO
    fairsharing: FAIRsharing.kbz5jh
    miriam: mamo
    n2t: mamo
    obofoundry: mamo
    ols: mamo
    ontobee: MAMO
    wikidata.entity: Q113014441
  miriam:
    deprecated: false
    description: The Mathematical Modelling Ontology (MAMO) is a classification of
      the types of mathematical models used mostly in the life sciences, their variables,
      relationships and other relevant features.
    homepage: http://bioportal.bioontology.org/ontologies/MAMO
    id: '00000517'
    name: Mathematical Modelling Ontology
    namespaceEmbeddedInLui: false
    pattern: ^MAMO_\d{7}$
    prefix: mamo
    sampleId: MAMO_0000026
    uri_format: http://bioportal.bioontology.org/ontologies/MAMO/?p=classes&conceptid=http://identifiers.org/mamo/$1
  n2t:
    description: The Mathematical Modelling Ontology (MAMO) is a classification of
      the types of mathematical models used mostly in the life sciences, their variables,
      relationships and other relevant features.
    example: MAMO_0000026
    homepage: http://bioportal.bioontology.org/ontologies/MAMO
    name: MAMO through BioPortal
    namespaceEmbeddedInLui: false
    pattern: ^MAMO_\d{7}$
    prefix: mamo
    uri_format: http://bioportal.bioontology.org/ontologies/MAMO/?p=classes&conceptid=http://identifiers.org/mamo/$1
  obofoundry:
    deprecated: true
    description: The Mathematical Modelling Ontology (MAMO) is a classification of
      the types of mathematical models used mostly in the life sciences, their variables,
      relationships and other relevant features.
    domain: simulation
    download.owl: http://purl.obolibrary.org/obo/mamo.owl
    homepage: http://sourceforge.net/p/mamo-ontology/wiki/Home/
    license: Artistic License 2.0
    license.url: http://opensource.org/licenses/Artistic-2.0
    name: Mathematical modeling ontology
    preferredPrefix: MAMO
    prefix: mamo
    repository: http://sourceforge.net/p/mamo-ontology
  ols:
    description: The Mathematical Modelling Ontology (MAMO) is a classification of
      the types of mathematical models used mostly in the life sciences, their variables,
      relationships and other relevant features.
    download_rdf: https://raw.githubusercontent.com/EBISPOT/mamo/main/mamo.rdf
    homepage: http://sourceforge.net/p/mamo-ontology/wiki/Home/
    name: Mathematical Modelling Ontology
    prefix: mamo
    tracker: http://sourceforge.net/p/mamo-ontology/tickets/
    version: '2023-02-03'
  ontobee:
    library: Library
    name: Mathematical modeling ontology
    prefix: MAMO
  pattern: ^\d{7}$
  prefix: mamo
  uri_format: http://bioportal.bioontology.org/ontologies/MAMO/?p=classes&conceptid=http://identifiers.org/mamo/MAMO_$1
mampol:
  mappings:
    prefixcommons: mampol
  prefix: mampol
  prefixcommons:
    description: The Mammalia Polymorphism Database is a secondary database designed
      to provide a collection of all the existing polymorphic sequences in the MammaliaOnline
      query interfaces facilitate data interrogation by different polymorphism parameter
      values and keyword queries (based on SQL searches).
    example: MAMpol005339
    homepage: http://mampol.uab.es
    keywords:
    - DNA
    name: Mammalia Polymorphism Database
    pattern: ^MAMpol\d+$
    prefix: mampol
    uri_format: http://mampol.uab.es/cgi-bin/MamPol_s2.pl?Accession=$1
  reviewer:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
mao:
  biocontext:
    prefix: MAO
  example: '0000061'
  mappings:
    biocontext: MAO
    obofoundry: mao
    prefixcommons: mao
    wikidata.entity: Q114677893
  obofoundry:
    contact: julie@igbmc.u-strasbg.fr
    contact.label: Julie Thompson
    deprecated: true
    domain: chemistry and biochemistry
    homepage: http://www-igbmc.u-strasbg.fr/BioInfo/MAO/mao.html
    name: Multiple alignment
    prefix: mao
  pattern: ^\d{7}$
  prefix: mao
  prefixcommons:
    bioportal: '1026'
    description: An ontology for data retrieval and exchange in the fields of multiple
      DNA/RNA  alignment, protein sequence and protein structure alignment.
    example: MAO:0000061
    homepage: http://bips.u-strasbg.fr/LBGI/MAO/mao.html
    keywords:
    - obo
    - sequence
    - alignment
    name: Multiple Alignment Ontology
    pattern: ^MAO_\d+$
    prefix: mao
marc21:
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: 'MARC List for Languages provides three-character lowercase alphabetic
    strings that serve as the identifiers of languages and language groups. The codes
    are usually based on the first three letters of the English form or, in some cases,
    vernacular form of the corresponding language name. The codes are varied where
    necessary to resolve conflicts and are not intended to be abbreviations of a language
    name. When the name of a language is changed in the list, the original code is
    generally retained. The codes in this list are equivalent to those of ISO 639-2
    (Bibliographic) codes and some codes from ISO 639-5, although the language name
    labels may differ. They are linked to the equivalent codes in ISO 639-2 and ISO
    639-5 and the corresponding two-character codes in ISO 639-1. The list contains
    over 480 discrete codes. It is also searchable at: MARC Code List for Languages.'
  download_rdf: https://id.loc.gov/vocabulary/languages.skos.rdf
  example: amh
  homepage: https://id.loc.gov/vocabulary/languages.html
  name: Machine-readable Cataloging (MARC) List for Languages
  prefix: marc21
  rdf_uri_format: http://id.loc.gov/vocabulary/languages/$1
  uri_format: https://id.loc.gov/vocabulary/languages/$1
markerdb:
  contact:
    email: dwishart@ualberta.ca
    github: DavidWishartLab
    name: David S. Wishart
    orcid: 0000-0002-3207-2434
  contributor:
    email: m.naguthana@hotmail.com
    github: nagutm
    name: Mufaddal Naguthanawala
    orcid: 0009-0009-5240-7463
  description: MarkerDB is a freely available electronic database that attempts to
    consolidate information on all known clinical and pre-clinical biomarkers into
    a single resource. It provides identifiers for known clinical and pre-clinical
    biomarkers. Each entry provides detailed annotations, including biomarker descriptions,
    associated conditions, specificity, sensitivity, molecular structures, chromosomal
    locations, and clinical approval status.
  example: MDB00000001
  github_request_issue: 1330
  homepage: https://markerdb.ca
  name: MarkerDB
  pattern: ^MDB\d{8}$
  prefix: markerdb
  publications:
  - doi: 10.1093/nar/gkae1056
    pmc: null
    pubmed: '39535054'
    title: 'MarkerDB 2.0: a comprehensive molecular biomarker database for 2025'
    year: 2024
  - doi: 10.1093/nar/gkaa1067
    pmc: PMC7778954
    pubmed: '33245771'
    title: 'MarkerDB: an online database of molecular biomarkers'
    year: 2021
  reviewer:
    email: benjamin_gyori@hms.harvard.edu
    github: bgyori
    name: Benjamin M. Gyori
    orcid: 0000-0001-9439-5346
massbank:
  biocontext:
    prefix: MASSBANK
  contact:
    email: tobias.schulze@ufz.de
    github: tsufz
    name: Tobias Schulze
    orcid: 0000-0002-9744-8914
  fairsharing:
    abbreviation: MassBank
    description: MassBank is the first public repository of mass spectral data for
      sharing them among scientific research community.  MassBank data are useful
      for the chemical identification and structure elucidation of chemical compounds
      detected by mass spectrometry.
    homepage: https://massbank.eu/MassBank/
    license: https://creativecommons.org
    name: MassBank Europe
    prefix: FAIRsharing.dk451a
    publications:
    - doi: 10.1002/jms.1777
      pubmed_id: 20623627
      title: 'MassBank: a public repository for sharing mass spectral data for life
        sciences.'
    repository: https://github.com/MassBank
    subjects:
    - Chemistry
    - Life Science
    - Physics
  integbio:
    alt_name: High Resolution Mass Spectral Database
    description: MassBank is a high-resolution mass spectral database that involves
      the JST-BIRD project, and was developed by the Institute for Advanced Biosciences,
      Keio University (IAB) Analytical Chemistry Group, and the RIKEN Plant Science
      Center (PSC) Metabolomics Research Group. MassBank is used to search chemical
      compounds that have been detected by mass spectrometry for chemical identification,
      structure detail, similar spectrum search, etc. MassBank was recognized as the
      official mass spectral database of the Mass Spectrometry Society of Japan in
      2008. It also contains the results of the NEDO project.
    homepage: http://www.massbank.jp/Index
    information_keywords:
    - Method
    - Chemical structure
    maintainer: The Mass Spectrometry Society of Japan
    name: MassBank
    prefix: nbdc00298
    pubmeds:
    - '20623627'
    status: Active
    target_keywords:
    - Metabolite
  mappings:
    biocontext: MASSBANK
    fairsharing: FAIRsharing.dk451a
    integbio: nbdc00298
    miriam: massbank
    n2t: massbank
    wikidata: P6689
  miriam:
    deprecated: false
    description: MassBank is a federated database of reference spectra from different
      instruments, including high-resolution mass spectra of small metabolites (<3000
      Da).
    homepage: http://www.massbank.jp
    id: '00000273'
    name: MassBank
    namespaceEmbeddedInLui: false
    pattern: ^MSBNK-[0-9a-zA-Z_]+-[A-Z0-9_]+$
    prefix: massbank
    providers:
    - code: massbankeu
      description: MassBank in Europe
      homepage: https://massbank.eu/
      name: MassBank in Europe
      uri_format: https://massbank.eu/MassBank/RecordDisplay?id=$1
    sampleId: MSBNK-IPB_Halle-PB000166
    uri_format: https://massbank.jp/MassBank/RecordDisplay?id=$1
  n2t:
    description: MassBank is a federated database of reference spectra from different
      instruments, including high-resolution mass spectra of small metabolites (<3000
      Da).
    example: PB000166
    homepage: http://www.massbank.jp
    name: MassBank in Japan
    namespaceEmbeddedInLui: false
    pattern: ^[A-Z]{2}[A-Z0-9][0-9]{5}$
    prefix: massbank
    uri_format: http://www.massbank.jp/jsp/FwdRecord.jsp?id=$1
  name: MassBank
  prefix: massbank
  publications:
  - doi: 10.1002/jms.1777
    pmc: null
    pubmed: '20623627'
    title: 'MassBank: a public repository for sharing mass spectral data for life
      sciences'
    year: 2010
  wikidata:
    description: accession number for entries in the MassBank database (records of
      mass spectrometry)
    example:
    - MSBNK-Athens_Univ-AU112601
    - MSBNK-Eawag-EA030311
    - SMI00011
    homepage: https://massbank.eu/
    name: MassBank accession ID
    pattern: ^MSBNK-[A-Za-z0-9_]{1,32}-[A-Za-z0-9_]{1,64}$
    prefix: P6689
    uri_format: https://massbank.eu/MassBank/RecordDisplay?id=$1
massive:
  biocontext:
    prefix: MASSIVE
  fairsharing:
    abbreviation: MassIVE
    contact:
      email: miw023@ucsd.edu
      name: Mingxun Wang
      orcid: 0000-0001-7647-6097
    description: MassIVE is a worldwide mass spectrometry data repository integrated
      into a flexible, scalable, user-friendly framework offering a diverse set of
      data analysis algorithms and tools. MassIVE is a  mass spectrometry community
      resource data repository, developed the Center for Computational Mass Spectrometry
      (CCMS), designed to store, browse, redistribute, re-analyze and integrate all
      publicly available mass spectrometry data in promoting globally accessible and
      free exchange of mass spectrometry data. The MassIVE data repository provides
      reliable sharing of primary data in addition to offering user-friendly tools
      for advanced data analysis and visualization.
    homepage: https://massive.ucsd.edu/ProteoSAFe/static/massive.jsp
    license: CC0-1.0
    name: Mass Spectrometry Interactive Virtual Environment
    prefix: FAIRsharing.LYsiMd
    publications:
    - doi: 10.1038/nbt.3597
      pubmed_id: 27504778
      title: Sharing and community curation of mass spectrometry data with Global
        Natural Products Social Molecular Networking.
    - doi: 10.1093/nar/gkw936
      pubmed_id: 27924013
      title: 'The ProteomeXchange consortium in 2017: supporting the cultural change
        in proteomics public data deposition.'
    - doi: 10.1038/s41592-020-0955-0
      pubmed_id: 32929271
      title: 'MassIVE.quant: a community resource of quantitative mass spectrometry-based
        proteomics datasets.'
    - doi: 10.1093/nar/gkz984
      pubmed_id: 31686107
      title: 'The ProteomeXchange consortium in 2020: enabling ''big data'' approaches
        in proteomics.'
    repository: https://ccms-ucsd.github.io/MassIVEDocumentation
    subjects:
    - Functional Genomics
    - Metaproteomics
    - Proteomics
    - Metabolomics
    - Phenomics
    - Omics
  mappings:
    biocontext: MASSIVE
    fairsharing: FAIRsharing.LYsiMd
    miriam: massive
    n2t: massive
    uniprot: DB-0241
  miriam:
    deprecated: false
    description: MassIVE is a community resource developed by the NIH-funded Center
      for Computational Mass Spectrometry to promote the global, free exchange of
      mass spectrometry data.
    homepage: https://www.omicsdi.org/
    id: '00000650'
    name: MassIVE
    namespaceEmbeddedInLui: false
    pattern: ^MSV\d+$
    prefix: massive
    providers:
    - code: ''
      description: MassIVE
      homepage: https://massive.ucsd.edu/ProteoSAFe/static/massive.jsp
      name: MassIVE
      uri_format: https://massive.ucsd.edu/ProteoSAFe/QueryMSV?id=$1
    sampleId: MSV000082131
    uri_format: https://www.omicsdi.org/dataset/massive/$1
  n2t:
    description: MassIVE is a community resource developed by the NIH-funded Center
      for Computational Mass Spectrometry to promote the global, free exchange of
      mass spectrometry data.
    example: MSV000082131
    homepage: https://massive.ucsd.edu/ProteoSAFe/static/massive.jsp
    name: MassIVE
    namespaceEmbeddedInLui: false
    pattern: ^MSV\d+$
    prefix: massive
    uri_format: https://massive.ucsd.edu/ProteoSAFe/QueryMSV?id=$1
  prefix: massive
  publications:
  - doi: 10.1038/s41592-020-0955-0
    pmc: PMC7541731
    pubmed: '32929271'
    title: 'MassIVE.quant: a community resource of quantitative mass spectrometry-based
      proteomics datasets'
    year: 2020
  - doi: 10.1093/nar/gkz984
    pmc: PMC7145525
    pubmed: '31686107'
    title: 'The ProteomeXchange consortium in 2020: enabling ''big data'' approaches
      in proteomics'
    year: 2020
  - doi: 10.1016/j.cels.2018.08.004
    pmc: PMC6279426
    pubmed: '30172843'
    title: Assembling the Community-Scale Discoverable Human Proteome
    year: 2018
  - doi: 10.1038/nbt.3597
    pmc: PMC5321674
    pubmed: '27504778'
    title: Sharing and community curation of mass spectrometry data with Global Natural
      Products Social Molecular Networking
    year: 2016
  - doi: 10.1093/nar/gkw936
    pmc: PMC5210636
    pubmed: '27924013'
    title: 'The ProteomeXchange consortium in 2017: supporting the cultural change
      in proteomics public data deposition'
    year: 2016
  uniprot:
    abbreviation: MassIVE
    category: Proteomic databases
    homepage: https://massive.ucsd.edu/
    name: MassIVE - Mass Spectrometry Interactive Virtual Environment
    prefix: DB-0241
    publications:
    - doi: 10.1016/j.cels.2018.08.004
      pubmed: '30172843'
    uri_format: https://massive.ucsd.edu/ProteoSAFe/protein_explorer.jsp?libraries=2&protein_name=$1
mastodon:
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  homepage: https://mastodon.social
  mappings:
    wikidata: P4033
  name: Mastodon
  prefix: mastodon
  wikidata:
    database: Q27986619
    description: address on the Mastodon decentralized social network (the form is
      'user@server.domain' without a leading '@')
    example:
    - jz@mamot.fr
    - libreoffice@fosstodon.org
    name: Mastodon address
    pattern: ^[A-Za-z0-9_]+([A-Za-z0-9_\.]+[A-Za-z0-9_]+)?@[\d\w\.\-]+[0-9a-z]+$
    prefix: P4033
    short_name:
    - Mastodon
    uri_format: https://fedirect.toolforge.org/?id=$1
mat:
  aberowl:
    description: Minimal set of terms for anatomy
    download_obo: http://aber-owl.net/media/ontologies/MAT/3/mat.obo
    name: Minimal Anatomical Terminology
    prefix: MAT
    version: '1.1'
  biocontext:
    prefix: MAT
  bioportal:
    contact:
      email: J.Bard@ed.ac.uk
      name: Jonathan Bard
    description: A minimal set of terms for anatomy.
    name: Minimal Anatomical Terminology
    prefix: MAT
    version: '1.1'
  example: '0000000'
  mappings:
    aberowl: MAT
    biocontext: MAT
    bioportal: MAT
    obofoundry: mat
    wikidata.entity: Q114677894
  name: Minimal Anatomical Terminology
  obofoundry:
    contact: j.bard@ed.ac.uk
    contact.label: Jonathan Bard
    deprecated: true
    domain: anatomy and development
    name: Minimal anatomical terminology
    prefix: mat
  pattern: ^\d{7}$
  prefix: mat
mathmoddb:
  example: ComputationalTask
  homepage: https://github.com/mardi4nfdi/MathModDB
  mappings:
    tib: mathmoddb
  prefix: mathmoddb
  repository: https://github.com/mardi4nfdi/MathModDB
  tib:
    description: This is the MathModDB Ontology for documenting mathematical models.
    download_owl: https://mardi4nfdi.github.io/MathModDB/ontology.owl
    keywords:
    - NFDI4ING
    - computer science
    - mathematics
    - engineering
    name: MathModDB Ontology
    prefix: mathmoddb
    tracker: https://github.com/MaRDI4NFDI/MathModDB/issues
    uri_format: https://mardi4nfdi.de/mathmoddb#$1
matrixdb:
  appears_in:
  - complexportal
  contact:
    email: sylvie.ricard-blum@univ-lyon1.fr
    github: ricardblum
    name: Sylvie Ricard-Blum
    orcid: 0000-0001-9263-1851
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  contributor_extras:
  - email: sbalu@ebi.ac.uk
    github: CP-SB
    name: Sucharitha Balu
    orcid: 0000-0001-7456-0594
  description: MatrixDB is a freely available database focused on interactions established
    by extracellular matrix proteins, proteoglycans and polysaccharides
  example: MULT_4_VAR1_bovine
  fairsharing:
    abbreviation: MatrixDB
    description: MatrixDB stores experimental data established by full-length proteins,
      matricryptins, glycosaminoglycans, lipids and cations. MatrixDB reports interactions
      with individual polypeptide chains or with multimers (e.g. collagens, laminins,
      thrombospondins) when appropriate. Multimers are treated as permanent complexes,
      referencing EBI identifiers when possible. Human interactions were inferred
      from non-human homologous interactions when available.
    homepage: http://matrixdb.univ-lyon1.fr
    license: CC-BY-4.0
    name: Extracellular Matrix Interaction Database
    prefix: FAIRsharing.91yrz6
    publications:
    - doi: 10.1093/bioinformatics/btp025
      pubmed_id: 19147664
      title: MatrixDB, a database focused on extracellular protein-protein and protein-carbohydrate
        interactions.
    - doi: 10.1093/nar/gku1091
      pubmed_id: 25378329
      title: 'MatrixDB, the extracellular matrix interaction database: updated content,
        a new navigator and expanded functionalities.'
    - doi: 10.1093/nar/gkq830
      pubmed_id: 20852260
      title: MatrixDB, the extracellular matrix interaction database.
    - doi: 10.1093/nar/gky1035
      pubmed_id: 30371822
      title: 'MatrixDB: integration of new data with a focus on glycosaminoglycan
        interactions.'
    subjects:
    - Biology
  homepage: http://matrixdb.univ-lyon1.fr/
  integbio:
    alt_name: Extracellular Matrix interactions DataBase
    description: 'MatrixDB is a database focused on interactions established by extracellular
      proteins and polysaccharides. This database takes into account the multimeric
      nature of the extracellular proteins, for example, collagens, laminins and thrombospondins
      which are multimers.This database includes interaction data extracted from the
      literature by manual curation, and this database offers access to relevant data
      involving extracellular proteins provided by thier IMEx partner databases through
      the PSICQUIC webservice, as well as data from the Human Protein Reference Database.

      MatrixDB is an active member of the International Molecular Exchange (IMEx)
      consortium.'
    homepage: http://matrixdb.univ-lyon1.fr
    information_keywords:
    - Interaction/Pathway
    maintainer: ICBMS (Institute for Molecular and Supramolecular Chemistry and Biochemistry,
      University of Lyon 1)
    name: MatrixDB
    prefix: nbdc01222
    pubmeds:
    - '20852260'
    - '20213321'
    - '19147664'
    status: Active
    target_keywords:
    - Protein
    - Carbohydrate
    - Metabolite
  mappings:
    fairsharing: FAIRsharing.91yrz6
    integbio: nbdc01222
    pathguide: '298'
    prefixcommons: matrixdb
    re3data: r3d100010672
  name: MatrixDB
  part_of_database: matrixdb
  pathguide:
    abbreviation: MatrixDB
    homepage: http://matrixdb.univ-lyon1.fr/
    keywords:
    - PSI-MI
    name: Extracellular Matrix Interactions Database
    prefix: '298'
  prefix: matrixdb
  prefixcommons:
    description: MatrixDB is a database reporting mammalian protein-protein and protein-carbohydrate
      interactions involving extracellular molecules.  Interactions with lipids and
      cations are also reported.  Full-length molecules, fragments and multimers present
      in the extracellular matrix are all included in the database.
    example: P00747_P07355
    homepage: http://matrixdb.ibcp.fr
    keywords:
    - protein
    - small molecule
    - interaction
    license: http://dip.doe-mbi.ucla.edu/dip/termsofuse.html
    name: 'MatrixDB: Extracellular Matrix interactions database'
    pattern: ^[A-Z]\d+_[A-Z]\d+$
    prefix: matrixdb
    pubmed_ids:
    - '19147664'
    synonyms:
    - matrixdb.association
    uri_format: http://matrixdb.ibcp.fr/cgi-bin/model/report/default?name=$1&class=Association
  publications:
  - doi: 10.1093/nar/gky1035
    pmc: PMC6324007
    pubmed: '30371822'
    title: 'MatrixDB: integration of new data with a focus on glycosaminoglycan interactions'
    year: 2019
  - doi: 10.1093/nar/gku1091
    pmc: PMC4383919
    pubmed: '25378329'
    title: 'MatrixDB, the extracellular matrix interaction database: updated content,
      a new navigator and expanded functionalities'
    year: 2014
  - doi: 10.1093/nar/gkq830
    pmc: PMC3013758
    pubmed: '20852260'
    title: MatrixDB, the extracellular matrix interaction database
    year: 2010
  - doi: 10.1093/bioinformatics/btp025
    pmc: PMC2647840
    pubmed: '19147664'
    title: MatrixDB, a database focused on extracellular protein-protein and protein-carbohydrate
      interactions
    year: 2009
  - doi: 10.1093/bioinformatics/btp025
    pmc: null
    pubmed: null
    title: MatrixDB, a database focused on extracellular protein-protein and protein-carbohydrate
      interactions.
    year: null
  - doi: 10.1093/nar/gku1091
    pmc: null
    pubmed: null
    title: 'MatrixDB, the extracellular matrix interaction database: updated content,
      a new navigator and expanded functionalities.'
    year: null
  - doi: 10.1093/nar/gkq830
    pmc: null
    pubmed: null
    title: MatrixDB, the extracellular matrix interaction database.
    year: null
  - doi: 10.1093/nar/gky1035
    pmc: null
    pubmed: null
    title: 'MatrixDB: integration of new data with a focus on glycosaminoglycan interactions.'
    year: null
  - doi: null
    pmc: null
    pubmed: '19147664'
    title: null
    year: null
  re3data:
    description: 'MatrixDB is a freely available database focused on interactions
      established by extracellular proteins and polysaccharides.

      MatrixDB takes into account the multimetric nature of the extracellular proteins
      (e.g. collagens, laminins and thrombospondins are multimers). MatrixDB includes
      interaction data extracted from the literature by manual curation in our lab,
      and offers access to relevant data involving extracellular proteins provided
      by our IMEx partner databases through the PSICQUIC webservice, as well as data
      from the Human Protein Reference Database. MatrixDB is in charge of the curation
      of papers published in Matrix Biology since January 2009'
    doi: 10.17616/R3M03H
    homepage: https://matrixdb.univ-lyon1.fr/
    name: MatrixDB
    prefix: r3d100010672
    synonyms:
    - Extracellular Matrix interactions DataBase
    xrefs:
      nif: 0000-10226
      omics: 01918
  uri_format: http://matrixdb.univ-lyon1.fr/cgi-bin/current/newPort?type=biomolecule&value=$1
matrixdb.association:
  biocontext:
    prefix: MATRIXDB.ASSOCIATION
  mappings:
    biocontext: MATRIXDB.ASSOCIATION
    miriam: matrixdb.association
    n2t: matrixdb.association
  miriam:
    deprecated: false
    description: MatrixDB stores experimentally determined interactions involving
      at least one extracellular biomolecule. It includes mostly protein-protein and
      protein-glycosaminoglycan interactions, as well as interactions with lipids
      and cations.
    homepage: https://matrixdb.univ-lyon1.fr/
    id: 00000068
    name: MatrixDB
    namespaceEmbeddedInLui: false
    pattern: ^([A-N,R-Z][0-9][A-Z][A-Z, 0-9][A-Z, 0-9][0-9])_.*|([O,P,Q][0-9][A-Z,
      0-9][A-Z, 0-9][A-Z, 0-9][0-9]_.*)|(GAG_.*)|(MULT_.*)|(PFRAG_.*)|(LIP_.*)|(CAT_.*)$
    prefix: matrixdb.association
    sampleId: P00747__P07355
    uri_format: https://matrixdb.univ-lyon1.fr/association/$1
  n2t:
    description: MatrixDB stores experimentally determined interactions involving
      at least one extracellular biomolecule. It includes mostly protein-protein and
      protein-glycosaminoglycan interactions, as well as interactions with lipids
      and cations.
    example: P00747__P07355
    homepage: http://matrixdb.univ-lyon1.fr/
    name: MatrixDB Association
    namespaceEmbeddedInLui: false
    pattern: ^([A-N,R-Z][0-9][A-Z][A-Z, 0-9][A-Z, 0-9][0-9])_.*|([O,P,Q][0-9][A-Z,
      0-9][A-Z, 0-9][A-Z, 0-9][0-9]_.*)|(GAG_.*)|(MULT_.*)|(PFRAG_.*)|(LIP_.*)|(CAT_.*)$
    prefix: matrixdb.association
    uri_format: http://matrixdb.univ-lyon1.fr//cgi-bin/current/newPort?type=association&value=$1&class=Association
  name: MatrixDB Association
  part_of_database: matrixdb
  prefix: matrixdb.association
mavedb:
  comment: This is an interesting one as the full IDs as they appear on the page are
    of the form `urn:mavedb:00000011-a` suggesting this is the preferred URI expansion
    for identification purposes. However, mavedb hasn't been registered with IANA
    https://www.iana.org/assignments/urn-namespaces/urn-namespaces.xhtml
  contact:
    email: alan.rubin@wehi.edu.au
    github: afrubin
    name: Alan Rubin
    orcid: 0000-0003-1474-605X
  contributor:
    email: cjmungall@lbl.gov
    github: cmungall
    name: Chris Mungall
    orcid: 0000-0002-6601-2165
  description: Some IDs may represent experiment sets, e.g. https://www.mavedb.org/#/experiment-sets/urn:mavedb:00000011
    Others represent genomic regions (specifically deep mutational scans thereof)
    e.g. https://www.mavedb.org/#/experiment-sets/urn:mavedb:00000011-a
  example: 00000011-a
  example_extras:
  - '00000011'
  github_request_issue: 1045
  homepage: https://www.mavedb.org
  name: Multiplexed Assays of Variant Effect Database
  pattern: ^\S+$
  prefix: mavedb
  publications:
  - doi: 10.1186/s13059-025-03476-y
    pmc: PMC11753097
    pubmed: '39838450'
    title: 'MaveDB 2024: a curated community database with over seven million variant
      effects from multiplexed functional assays'
    year: 2025
  - doi: 10.1186/s13059-019-1845-6
    pmc: PMC6827219
    pubmed: '31679514'
    title: 'MaveDB: an open-source platform to distribute and interpret data from
      multiplexed assays of variant effect'
    year: 2019
  repository: https://github.com/VariantEffect/mavedb-api
  reviewer:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  uri_format: https://www.mavedb.org/#/experiments/urn:mavedb:$1
maxo:
  aberowl:
    description: The Medical Action Ontology (MAxO) provides a broad view of medical
      actions and includes terms for medical procedures, interventions, therapies,
      treatments, and recommendations.
    download_owl: http://aber-owl.net/media/ontologies/MAXO/45/maxo.owl
    homepage: https://github.com/monarch-initiative/MAxO
    name: Medical Action Ontology
    prefix: MAXO
  biolink:
    is_identifiers: false
    is_obo: true
    prefix: MAXO
    uri_format: http://purl.obolibrary.org/obo/MAXO_$1
  bioportal:
    contact:
      email: Leigh.Carmody@jax.org
      name: Leigh Carmody
    description: The Medical Action Ontology (MAxO) provides a structured vocabulary
      for medical procedures, interventions, therapies, and treatments for disease
      with an emphasis on rare disease (RD). It is often difficult to find relevant
      clinical literature about strategies to manage RD patients. Responding to this
      need, MAxO provides a vocabulary to annotate diseases and phenotypes with recommended
      treatments and interventions.
    homepage: https://github.com/monarch-initiative/MAxO
    name: Medical Action Ontology
    prefix: MAXO
    version: '2025-04-24'
  example: 0000008
  fairsharing:
    abbreviation: MAxO
    contact:
      email: Leigh.Carmody@jax.org
      name: Leigh Carmody
      orcid: 0000-0001-7941-2961
    description: The Medical Action Ontology (MAxO) is being developed to provide
      a structured vocabulary for medical procedures, interventions, therapies, and
      treatments for rare diseases.
    domains:
    - Rare Disorder
    homepage: https://github.com/monarch-initiative/MAxO
    license: CC-BY-4.0
    name: Medical Action Ontology
    prefix: FAIRsharing.945c78
    publications:
    - doi: 10.1101/2023.07.13.23292612
      pubmed: '37503136'
      title: 'The Medical Action Ontology: A Tool for Annotating and Analyzing Treatments
        and Clinical Management of Human Disease'
      year: 2023
    subjects:
    - Medicine
  mappings:
    aberowl: MAXO
    biolink: MAXO
    bioportal: MAXO
    fairsharing: FAIRsharing.945c78
    miriam: maxo
    obofoundry: maxo
    ols: maxo
    ontobee: MAXO
    wikidata.entity: Q113012668
  miriam:
    deprecated: false
    description: An ontology to represent medically relevant actions, procedures,
      therapies, interventions, and recommendations.
    homepage: https://www.ebi.ac.uk/ols4/ontologies/maxo
    id: '00001032'
    name: Medical Action Ontology
    namespaceEmbeddedInLui: false
    pattern: ^\d{7}$
    prefix: maxo
    sampleId: '0001073'
    uri_format: https://www.ebi.ac.uk/ols4/ontologies/maxo/terms?obo_id=MAXO:$1
  obofoundry:
    appears_in:
    - ecto
    contact: Leigh.Carmody@jax.org
    contact.github: LCCarmody
    contact.label: Leigh Carmody
    contact.orcid: 0000-0001-7941-2961
    depends_on:
    - chebi
    - foodon
    - go
    - hp
    - iao
    - nbo
    - obi
    - ro
    - uberon
    deprecated: false
    description: The Medical Action Ontology (MAxO) provides a broad view of medical
      actions and includes terms for medical procedures, interventions, therapies,
      treatments, and recommendations.
    domain: health
    download.json: http://purl.obolibrary.org/obo/maxo.json
    download.obo: http://purl.obolibrary.org/obo/maxo.obo
    download.owl: http://purl.obolibrary.org/obo/maxo.owl
    homepage: https://github.com/monarch-initiative/MAxO
    license: CC BY 4.0
    license.url: http://creativecommons.org/licenses/by/4.0/
    logo: https://raw.githubusercontent.com/jmcmurry/closed-illustrations/master/logos/maxo-logos/maxo_logo_black-banner.png
    name: Medical Action Ontology
    preferredPrefix: MAXO
    prefix: maxo
    repository: https://github.com/monarch-initiative/MAxO
  ols:
    description: An ontology to represent medically relevant actions, procedures,
      therapies, interventions, and recommendations.
    download_owl: http://purl.obolibrary.org/obo/maxo.owl
    homepage: https://github.com/monarch-initiative/MAxO
    name: Medical Action Ontology
    prefix: maxo
    tracker: https://github.com/monarch-initiative/MAxO/issues
    version: '2025-04-24'
    version.iri: http://purl.obolibrary.org/obo/maxo/releases/2025-04-24/maxo.owl
  ontobee:
    library: Library
    name: Medical Action Ontology
    prefix: MAXO
  pattern: ^\d{7}$
  prefix: maxo
  twitter: MonarchInit
  uri_format: http://purl.obolibrary.org/obo/MAXO_$1
mba:
  bioportal:
    contact:
      email: chinhda@alleninstitute.org
      name: Allen Institute for Brain Science
    description: Allen Brain Atlas P56 Mouse Ontology
    homepage: http://www.brain-map.org
    name: Allen Brain Atlas (ABA) Adult Mouse Brain Ontology
    prefix: ABA-AMB
    publications:
    - http://www.wiley.com/WileyCDA/WileyTitle/productCd-0470054085.html
    version: '1'
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: A controlled vocabulary to support the study of transcription in the
    mouse brain
  download_obo: https://raw.githubusercontent.com/obophenotype/uberon/master/source-ontologies/allen-mba.obo
  example: '688'
  homepage: https://mouse.brain-map.org
  mappings:
    bioportal: ABA-AMB
    ols: mba
  name: Mouse Brain Atlas
  ols:
    contact: cellsemantics@gmail.com
    description: An application ontology built by combining ontologised versions of
      the Allen Institute Mouse Brain Atlas (MBA) StructureGraph mapped to Uberon.
    download_owl: https://purl.brain-bican.org/ontology/mbao/mbao.owl
    homepage: https://purl.brain-bican.org/ontology/mbao
    name: Mouse Brain Atlas Ontology
    prefix: mba
    uri_format: https://purl.brain-bican.org/ontology/mbao/MBA_$1
    version: '2025-10-29'
    version.iri: https://purl.brain-bican.org/ontology/mbao/releases/2025-10-29/mbao.owl
  pattern: ^\d+$
  preferred_prefix: MBA
  prefix: mba
  providers:
  - code: biopragmatics
    description: Biopragmatics provider for MBA
    example: null
    first_party: null
    homepage: https://biopragmatics.github.io/providers/mba
    name: MBA from Biopragmatics
    publications: null
    status: null
    uri_format: https://biopragmatics.github.io/providers/mba/$1
  repository: https://github.com/brain-bican/mouse_brain_atlas_ontology
  uri_format: https://purl.brain-bican.org/ontology/mbao/MBA_$1
mcc:
  bioportal:
    contact:
      email: usha@molecularconnections.com
      name: Usha Mahadevan
    description: Ontologies provide a common platform of controlled vocabulary for
      researchers who need to share information across a particular domain, inclusive
      of machine-interpretable definitions of basic concepts in the domain and relations
      among them. The need for ontologies that provide a systematic arrangement of
      available data and allow cross talk across various related domains is gaining
      momentum. In this backdrop, we have developed a comprehensive ontology on primary
      and established cell lines-both normal and pathologic. It covers around 400
      cell lines. This ontology has been built to include the major domains in the
      field of biology like anatomy, bio-molecules, chemicals and drugs, pathological
      conditions and genetic variations around the cell lines. An extensive network
      of relations has been built across these concepts to enable different combinations
      of queries. The ontology covers all cell lines from major sources like ATCC,
      DSMZ, ECACC, ICLC etc. and is built in OWL format.
    homepage: http://www.molecularconnections.com
    name: Cell Line Ontology [by Mahadevan]
    prefix: MCCL
    version: '2'
  deprecated: true
  example: ThoracicArtery
  mappings:
    bioportal: MCCL
  name: Cell Line Ontology [derivative]
  prefix: mcc
  uri_format: http://www.semanticweb.org/pallabi.d/ontologies/2014/2/untitled-ontology-11#$1
mco:
  aberowl:
    description: Microbial Conditions Ontology is an ontology...
    download_owl: http://aber-owl.net/media/ontologies/MCO/2/mco.owl
    homepage: https://github.com/microbial-conditions-ontology/microbial-conditions-ontology
    name: Microbial Conditions Ontology
    prefix: MCO
  bioportal:
    contact:
      email: citlalli.mejiaalmonte@gmail.com
      name: Citlalli Mejía-Almonte
    description: Microbial Conditions Ontology contains terms to describe growth conditions
      in microbiological experiments. The first version is based on gene regulation
      experiments in Escherichia coli K-12. It is being used in RegulonDB to link
      growth conditions to gene regulation data.
    homepage: https://github.com/microbial-conditions-ontology/microbial-conditions-ontology
    name: Microbial Conditions Ontology
    prefix: MCO
  example: 0000858
  mappings:
    aberowl: MCO
    bioportal: MCO
    obofoundry: mco
    ols: mco
    ontobee: MCO
    wikidata.entity: Q81661676
  obofoundry:
    contact: citlalli.mejiaalmonte@gmail.com
    contact.github: citmejia
    contact.label: Citlalli Mejía-Almonte
    contact.orcid: 0000-0002-0142-5591
    depends_on:
    - bfo
    - chebi
    - cl
    - clo
    - micro
    - ncbitaxon
    - ncit
    - obi
    - omit
    - omp
    - pato
    - peco
    - uberon
    - zeco
    deprecated: false
    description: Microbial Conditions Ontology is an ontology...
    domain: investigations
    download.obo: http://purl.obolibrary.org/obo/mco.obo
    download.owl: http://purl.obolibrary.org/obo/mco.owl
    homepage: https://github.com/microbial-conditions-ontology/microbial-conditions-ontology
    license: CC BY 3.0
    license.url: http://creativecommons.org/licenses/by/3.0/
    name: Microbial Conditions Ontology
    preferredPrefix: MCO
    prefix: mco
    repository: https://github.com/microbial-conditions-ontology/microbial-conditions-ontology
  ols:
    description: Microbial Conditions Ontology is an ontology...
    download_owl: http://purl.obolibrary.org/obo/mco.owl
    homepage: https://github.com/microbial-conditions-ontology/microbial-conditions-ontology
    name: Microbial Conditions Ontology
    prefix: mco
    tracker: https://github.com/microbial-conditions-ontology/microbial-conditions-ontology/issues
    version: '2019-05-15'
    version.iri: http://purl.obolibrary.org/obo/mco/releases/2019-05-15/mco.owl
  ontobee:
    library: Library
    name: Microbial Conditions Ontology
    prefix: MCO
  pattern: ^\d+$
  prefix: mco
  uri_format: http://purl.obolibrary.org/obo/MCO_$1
mcro:
  aberowl:
    description: An ontology representing the structure of model card reports - reports
      that describe basic characteristics of machine learning models for the public
      and consumers.
    download_owl: http://aber-owl.net/media/ontologies/MCRO/3/mcro.owl
    homepage: https://github.com/UTHealth-Ontology/MCRO
    name: Model Card Report Ontology
    prefix: MCRO
  bioportal:
    contact:
      email: muamith@utmb.edu
      name: Tuan Amith
    description: An ontology representing the structure of model card reports - reports
      that describe basic characteristics of machine learning models for the public
      and consumers., An ontology representing the model card structure
    homepage: https://github.com/UTHealth-Ontology/MCRO
    license: CC-BY-3.0
    name: Model Card Report Ontology
    prefix: MCRO
    version: '2023-03-07'
  example: '0000001'
  mappings:
    aberowl: MCRO
    bioportal: MCRO
    miriam: mcro
    obofoundry: mcro
    ols: mcro
    ontobee: MCRO
  miriam:
    deprecated: false
    description: 'An ontology representing the model card structure, he aim of this
      work is to describe machine learning models to communicate information about
      specific details about the model (trade offs, intended users, licensing, etc.). '
    homepage: https://www.ebi.ac.uk/ols4/ontologies/mcro
    id: 00001049
    name: Model Card Ontology
    namespaceEmbeddedInLui: true
    pattern: ^MCRO:\d+$
    prefix: mcro
    sampleId: '0000027'
    uri_format: https://www.ebi.ac.uk/ols4/ontologies/mcro/classes?obo_id=MCRO:$1
  obofoundry:
    contact: muamith@utmb.edu
    contact.github: ProfTuan
    contact.label: Tuan Amith
    contact.orcid: 0000-0003-4333-1857
    depends_on:
    - iao
    - swo
    deprecated: false
    description: An ontology representing the structure of model card reports - reports
      that describe basic characteristics of machine learning models for the public
      and consumers.
    domain: information technology
    download.owl: http://purl.obolibrary.org/obo/mcro.owl
    homepage: https://github.com/UTHealth-Ontology/MCRO
    license: CC BY 4.0
    license.url: https://creativecommons.org/licenses/by/4.0/
    name: Model Card Report Ontology
    preferredPrefix: MCRO
    prefix: mcro
    publications:
    - id: https://doi.org/10.1186/s12859-022-04797-6
      title: Toward a standard formal semantic representation of the model card report
    repository: https://github.com/UTHealth-Ontology/MCRO
  ols:
    description: An ontology representing the structure of model card reports - reports
      that describe basic characteristics of machine learning models for the public
      and consumers.
    download_owl: http://purl.obolibrary.org/obo/mcro.owl
    homepage: https://github.com/UTHealth-Ontology/MCRO
    name: Model Card Report Ontology
    prefix: mcro
    tracker: https://github.com/UTHealth-Ontology/MCRO/issues
    version: '2023-03-07'
    version.iri: http://purl.obolibrary.org/obo/mcro/releases/2023-03-07/mcro.owl
  ontobee:
    library: Library
    name: Model Card Report Ontology
    prefix: MCRO
  pattern: ^\d{7}$
  prefix: mcro
mdl:
  appears_in:
  - xlmod
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: The MDL number contains a unique identification number for each reaction
    and variation. The format is RXXXnnnnnnnn. R indicates a reaction, XXX indicates
    which database contains the reaction record. The numeric portion, nnnnnnnn, is
    an 8-digit number. [wikipedia]
  example: MFCD00011659
  github_request_issue: 1311
  homepage: https://en.wikipedia.org/wiki/Chemical_file_format#MDL_number
  name: Molecular Design Limited Hash
  pattern: ^\w{4}\d{8}$
  prefix: mdl
  references:
  - https://en.wikipedia.org/wiki/Chemical_file_format#MDL_number
mdm:
  aberowl:
    description: 'The Mapping of Drug Names and MeSH 2022 (MDM) provides owl:sameAs
      relationships of similar concepts for Drug Names from the DrugBank vocabulary
      (released 2022-01-03 under version 5.1.9: https://go.drugbank.com/releases/latest#open-data)
      and the Medical Subject Headings (2022 version: http://id.nlm.nih.gov/mesh/).
      Two concepts are considered similar if they share the same concept name or a
      common synonym. Additional synonyms are generated using the Snowball stemming
      algorithm. The software implementation is available on github within the Maven
      project SNoKE in the module snoke.ontology: https://github.com/bernd-mueller/snoke/tree/master/snoke.ontology'
    download_owl: http://aber-owl.net/media/ontologies/MDM/4/mdm.owl
    homepage: https://www.zbmed.de/
    name: Mapping of Drug Names and MeSH 2022
    prefix: MDM
    version: '0.33'
  biocontext:
    prefix: MDM
  bioportal:
    contact:
      email: bernd.mueller@zbmed.de
      name: Bernd Müller
    description: 'The Mapping of Drug Names and MeSH 2022 (MDM) provides owl:sameAs
      relationships as well as owl:equivalentClass of similar concepts for Drug Names
      from the DrugBank vocabulary (released 2022-01-03 under version 5.1.9: https://go.drugbank.com/releases/latest#open-data)
      and the Medical Subject Headings (2022 version: http://id.nlm.nih.gov/mesh/).
      Two concepts are considered similar if they share the same concept name or a
      common synonym. Additional synonyms are generated using the Snowball stemming
      algorithm. The software implementation is available on github within the Maven
      project SNoKE in the module snoke.ontology: https://github.com/bernd-mueller/snoke/tree/master/snoke.ontology'
    homepage: https://www.zbmed.de/
    name: Mapping of Drug Names and MeSH 2022
    prefix: MDM
    version: '0.330'
  contact:
    email: bernd.mueller@zbmed.de
    github: null
    name: Bernd Müller
    orcid: 0000-0003-3062-8192
  fairsharing:
    abbreviation: MDM
    contact:
      email: dugas@uni-muenster.de
      name: Martin Dugas
      orcid: 0000-0001-9740-0788
    description: MDM-Portal (Medical Data-Models) is a meta-data registry for creating,
      analysing, sharing and reusing medical forms, developed by the Institute of
      Medical Informatics, University of Muenster in Germany. see also http://www.ncbi.nlm.nih.gov/pubmed/26868052
      Electronic forms for documentation of patient data are an integral part within
      the workflow of physicians. A huge amount of data is collected either through
      routine documentation forms (EHRs) for electronic health records or as case
      report forms (CRFs) for clinical trials. This raises major scientific challenges
      for health care, since different health information systems are not necessarily
      compatible with each other and thus information exchange of structured data
      is hampered. Software vendors provide a variety of individual documentation
      forms according to their standard contracts, which function as isolated applications.
      Furthermore, free availability of those forms is rarely the case. Currently
      less than 5 % of medical forms are freely accessible. Based on this lack of
      transparency harmonization of data models in health care is extremely cumbersome,
      thus work and know-how of completed clinical trials and routine documentation
      in hospitals are hard to be re-used. The MDM-Portal serves as an infrastructure
      for academic (non-commercial) medical research to contribute a solution to this
      problem. It already contains more than 6,000 system-independent forms (CDISC
      ODM Format, www.cdisc.org, Operational Data Model) with more than 470,000 data-elements.
      This enables researchers to view, discuss, download and export forms in most
      common technical formats such as PDF, CSV, Excel, SQL, SPSS, R, etc. A growing
      user community will lead to a growing database of medical forms. In this matter,
      we would like to encourage all medical researchers to register and add forms
      and discuss existing forms.
    homepage: https://medical-data-models.org
    license: CC BY-NC 4.0
    name: Medical Data Models
    prefix: FAIRsharing.wnk2eq
    publications:
    - doi: 10.1093/database/bav121
      pubmed_id: 26868052
      title: 'Portal of medical data models: information infrastructure for medical
        research and healthcare'
    subjects:
    - Medicine
    - Biomedical Science
    - Translational Medicine
  mappings:
    aberowl: MDM
    biocontext: MDM
    bioportal: MDM
    fairsharing: FAIRsharing.wnk2eq
    miriam: mdm
    n2t: mdm
    re3data: r3d100013816
  miriam:
    deprecated: false
    description: The MDM (Medical Data Models) Portal is a meta-data registry for
      creating, analysing, sharing and reusing medical forms. Electronic forms are
      central in numerous processes involving data, including the collection of data
      through electronic health records (EHRs), Electronic Data Capture (EDC), and
      as case report forms (CRFs) for clinical trials. The MDM Portal provides medical
      forms in numerous export formats, facilitating the sharing and reuse of medical
      data models and exchange between information systems.
    homepage: https://medical-data-models.org/
    id: '00000574'
    name: MDM
    namespaceEmbeddedInLui: false
    pattern: ^\d+$
    prefix: mdm
    sampleId: '4776'
    uri_format: https://medical-data-models.org/forms/$1
  n2t:
    description: The MDM (Medical Data Models) Portal is a meta-data registry for
      creating, analysing, sharing and reusing medical forms. Electronic forms are
      central in numerous processes involving data, including the collection of data
      through electronic health records (EHRs), Electronic Data Capture (EDC), and
      as case report forms (CRFs) for clinical trials. The MDM Portal provides medical
      forms in numerous export formats, facilitating the sharing and reuse of medical
      data models and exchange between information systems.
    example: '4776'
    homepage: https://medical-data-models.org/
    name: MDM at University of Muenster
    namespaceEmbeddedInLui: false
    pattern: ^\d+$
    prefix: mdm
    uri_format: https://medical-data-models.org/forms/$1
  name: Medical Data Models
  prefix: mdm
  publications:
  - doi: 10.1093/database/bav121
    pmc: PMC4750548
    pubmed: '26868052'
    title: 'Portal of medical data models: information infrastructure for medical
      research and healthcare'
    year: 2016
  - doi: 10.1093/database/bav121
    pmc: null
    pubmed: null
    title: 'Portal of medical data models: information infrastructure for medical
      research and healthcare'
    year: null
  re3data:
    description: MDM-Portal (Medical Data Models) is a meta-data registry for creating,
      analyzing, sharing and reusing medical forms. It serves as an infrastructure
      for academic (non-commercial) medical research to contribute a solution to this
      problem. It contains forms in the system-independent CDISC Operational Data
      Model (ODM) format with more than 500,000 data-elements. The Portal provides
      numerous core data sets, common data elements or data standards, code lists
      and value sets. This enables researchers to view, discuss, download and export
      forms in most common technical formats such as PDF, CSV, Excel, SQL, SPSS, R,
      etc.
    doi: 10.17616/R31NJN5K
    homepage: https://medical-data-models.org/
    name: Portal of Medical Data Models
    prefix: r3d100013816
    synonyms:
    - MDM Portal
meddra:
  aberowl:
    description: Medical Dictionary for Regulatory Activities Terminology (MedDRA)
    homepage: http://www.meddramsso.com/MSSOWeb/contact_us/index.htm
    name: Medical Dictionary for Regulatory Activities Terminology (MedDRA)
    prefix: MEDDRA
    version: 2016AB
  bartoc:
    description: In the late 1990s, the International Conference on Harmonisation
      of Technical Requirements for Registration of Pharmaceuticals for Human Use
      (ICH) developed MedDRA, a rich and highly specific standardised medical terminology
      to facilitate sharing of regulatory information internationally for medical
      products used by humans. ICH’s powerful tool, MedDRA is available to all for
      use in the registration, documentation and safety monitoring of medical products
      both before and after a product has been authorised for sale. Products covered
      by the scope of MedDRA include pharmaceuticals, biologics, vaccines and drug-device
      combination products. Today, its growing use worldwide by regulatory authorities,
      pharmaceutical companies, clinical research organisations and health care professionals
      allows better global protection of patient health.
    homepage: http://www.meddra.org/
    name: MedDRA
    prefix: '1237'
    wikidata_database: Q1539689
  biocontext:
    prefix: MEDDRA
    uri_format: http://purl.bioontology.org/ontology/MEDDRA/$1
  bioportal:
    contact:
      email: mssohelp@meddra.org
      name: MedDRA MSSO
    description: MedDRA is an international medical terminology with an emphasis on
      use for data entry, retrieval, analysis, and display. It applies to all phases
      of drug development, excluding animal toxicology, and to the health effects
      and malfunction of devices. An appendix includes concept descriptions which
      describe how a medical concept is interpreted, used, and classified within the
      MedDRA terminology. It is not intended as a medical definition. The concept
      descriptions are intended to aid the consistent and accurate use of MedDRA in
      coding, retrieval, and analysis.
    homepage: https://www.meddra.org/
    name: Medical Dictionary for Regulatory Activities Terminology (MedDRA)
    prefix: MEDDRA
    publications:
    - https://www.meddra.org/msso-presentations
    version: MDR27_0
  fairsharing:
    abbreviation: MedDRA
    description: 'MedDRA is a multilingual terminology allowing most users to operate
      in their native languages. MedDRA can be used to analyse individual medical
      events (e.g., “Influenza”) or issues involving a system, organ or etiology (e.g.,
      infections) using its hierarchical structure. MedDRA can be used for signal
      detection and monitoring of clinical syndromes whose symptoms encompass numerous
      systems or organs using its multi-axial hierarchy or through the special feature
      of Standardised MedDRA Queries. The ability to communicate adverse event data
      is another strength of MedDRA and has lead to MedDRA being an integral part
      of the ICH e-submission standards: eCTD (ICH M8) and ICSRs (ICH E2B).'
    domains:
    - disease
    homepage: http://www.meddra.org/
    name: Medical Dictionary for Regulatory Activities Terminology
    prefix: FAIRsharing.ad3137
    publications:
    - doi: 10.2165/00002018-199920020-00002
      pubmed: '10082069'
      title: The medical dictionary for regulatory activities (MedDRA)
      year: 1999
    - doi: 10.1016/s1386-5056(00)00062-9
      pubmed: '10961570'
      title: The use of a medical dictionary for regulatory activities terminology
        (MedDRA) in prescription-event monitoring in Japan (J-PEM)
      year: 2000
    subjects:
    - Preclinical Studies
    - Biomedical Science
    - Medicine
  hl7:
    description: "MedDRA is a five-level hierarchy of terms.  MedDRA was developed\
      \ as an ICH initiative and is maintained and distributed by the MedDRA Maintenance\
      \ and Support Services Organization (MSSO).\tVersions \x13 Versions are released\
      \ twice per year and are identified by 2 numbers separated by a decimal point\
      \ (e.g., 7.0, 7.1, 8.0, and 8.1).  \x1C.0\x1D releases may contain changes to\
      \ the hierarchy.  \x1C.1\x1D releases will only contain additions, moves, and\
      \ modifications of medical concept terms (Preferred Terms) and coding level\
      \ terms (Lowest Level Terms).\tConcepts \x13 Concepts are represented by a MedDRA\
      \ code and a MedDRA term name.  The MedDRA code is an eight digit numeric code.\
      \  MedDRA codes are unique and are never reused.  The MedDRA term name is a\
      \ 100 character alphanumeric field used to describe the concept or term.\tHierarchies\
      \ \x13 MedDRA is structured as a five level hierarchy.  System Organ Classes\
      \ (SOCs) are the broadest terms (e.g., Cardiac disorders, Investigations). \
      \ The lowest level of the terminology is the Lowest Level Term (LLT) level.\
      \  There are 26 SOCs and over 60,000 LLTs"
    homepage: www.meddramsso.com
    name: MedDRA
    organization: MedDRA MSSO/ Northrop Grumman,MedDRA MSSO/ Northrop Grumman
    preferred_prefix: mdr
    prefix: 2.16.840.1.113883.6.163
    status: Complete
  integbio:
    alt_name: Medical Dictionary for Regulatory Activities
    description: MedDRA is a standardized medical terminology for regulatory information
      of medical products. It is available for use in the registration, documentation
      and safety monitoring of medical products. It is provided in many languages,
      which are Chinese, Czech, Dutch, French, German, Hungarian, Italian, Japanese,
      Korean, Portuguese, Portuguese - Brazilian, Russian, and Spanish in addition
      to English Master.
    fairsharing: FAIRsharing.ad3137
    homepage: https://www.meddra.org/
    information_keywords:
    - Ontology/Terminology/Nomenclature
    maintainer: ICH (The International Council for Harmonisation of Technical Requirements
      for Pharmaceuticals for Human Use)
    name: MedDRA
    prefix: nbdc02564
    status: Active
    target_keywords:
    - Drug
    - Health/Disease
  mappings:
    aberowl: MEDDRA
    bartoc: '1237'
    biocontext: MEDDRA
    bioportal: MEDDRA
    fairsharing: FAIRsharing.ad3137
    hl7: 2.16.840.1.113883.6.163
    integbio: nbdc02564
    miriam: meddra
    n2t: meddra
    togoid: Meddra
    wikidata: P3201
    wikidata.entity: Q1539689
  miriam:
    deprecated: false
    description: The Medical Dictionary for Regulatory Activities (MedDRA) was developed
      by the International Council for Harmonisation of Technical Requirements for
      Registration of Pharmaceuticals for Human Use (ICH)to provide a standardised
      medical terminology to facilitate sharing of regulatory information internationally
      for medical products used by humans. It is used within regulatory processes,
      safety monitoring, as well as for marketing activities. Products covered by
      the scope of MedDRA include pharmaceuticals, biologics, vaccines and drug-device
      combination products. The MedDRA dictionary is organized by System Organ Class
      (SOC), divided into High-Level Group Terms (HLGT), High-Level Terms (HLT), Preferred
      Terms (PT) and finally into Lowest Level Terms (LLT).
    homepage: http://bioportal.bioontology.org/ontologies/MEDDRA
    id: '00000563'
    name: MedDRA
    namespaceEmbeddedInLui: false
    pattern: ^\d+$
    prefix: meddra
    sampleId: '10015919'
    uri_format: http://purl.bioontology.org/ontology/MEDDRA/$1
  n2t:
    description: The Medical Dictionary for Regulatory Activities (MedDRA) was developed
      by the International Council for Harmonisation of Technical Requirements for
      Registration of Pharmaceuticals for Human Use (ICH)to provide a standardised
      medical terminology to facilitate sharing of regulatory information internationally
      for medical products used by humans. It is used within regulatory processes,
      safety monitoring, as well as for marketing activities. Products covered by
      the scope of MedDRA include pharmaceuticals, biologics, vaccines and drug-device
      combination products. The MedDRA dictionary is organized by System Organ Class
      (SOC), divided into High-Level Group Terms (HLGT), High-Level Terms (HLT), Preferred
      Terms (PT) and finally into Lowest Level Terms (LLT).
    example: '10015919'
    homepage: http://bioportal.bioontology.org/ontologies/MEDDRA
    name: MedDRA through BioPortal
    namespaceEmbeddedInLui: false
    pattern: ^\d+$
    prefix: meddra
    uri_format: http://purl.bioontology.org/ontology/MEDDRA/$1
  name: Medical Dictionary for Regulatory Activities Terminology
  prefix: meddra
  publications:
  - doi: 10.1016/s1386-5056(00)00062-9
    pmc: null
    pubmed: '10961570'
    title: The use of a medical dictionary for regulatory activities terminology (MedDRA)
      in prescription-event monitoring in Japan (J-PEM)
    year: 2000
  - doi: 10.2165/00002018-199920020-00002
    pmc: null
    pubmed: '10082069'
    title: The medical dictionary for regulatory activities (MedDRA)
    year: 1999
  - doi: 10.2165/00002018-199920020-00002
    pmc: null
    pubmed: '10082069'
    title: The medical dictionary for regulatory activities (MedDRA)
    year: 1999
  - doi: 10.1016/s1386-5056(00)00062-9
    pmc: null
    pubmed: '10961570'
    title: The use of a medical dictionary for regulatory activities terminology (MedDRA)
      in prescription-event monitoring in Japan (J-PEM)
    year: 2000
  - doi: 10.2165/00002018-199920020-00002
    pmc: null
    pubmed: '10082069'
    title: The medical dictionary for regulatory activities (MedDRA)
    year: 1999
  - doi: 10.1016/s1386-5056(00)00062-9
    pmc: null
    pubmed: '10961570'
    title: The use of a medical dictionary for regulatory activities terminology (MedDRA)
      in prescription-event monitoring in Japan (J-PEM)
    year: 2000
  - doi: 10.2165/00002018-199920020-00002
    pmc: null
    pubmed: '10082069'
    title: The medical dictionary for regulatory activities (MedDRA)
    year: 1999
  - doi: 10.1016/s1386-5056(00)00062-9
    pmc: null
    pubmed: '10961570'
    title: The use of a medical dictionary for regulatory activities terminology (MedDRA)
      in prescription-event monitoring in Japan (J-PEM)
    year: 2000
  - doi: 10.2165/00002018-199920020-00002
    pmc: null
    pubmed: '10082069'
    title: The medical dictionary for regulatory activities (MedDRA)
    year: 1999
  - doi: 10.1016/s1386-5056(00)00062-9
    pmc: null
    pubmed: '10961570'
    title: The use of a medical dictionary for regulatory activities terminology (MedDRA)
      in prescription-event monitoring in Japan (J-PEM)
    year: 2000
  synonyms:
  - MEDRA
  - MeDRA
  - MedDRA
  - Medical Dictionary for Regulatory Activities
  togoid:
    catalog: nbdc02564
    description: MedDRA is a standardized medical terminology for regulatory information
      of medical products. It is available for use in the registration, documentation
      and safety monitoring of medical products. It is provided in many languages,
      which are Chinese, Czech, Dutch, French, German, Hungarian, Italian, Japanese,
      Korean, Portuguese, Portuguese - Brazilian, Russian, and Spanish in addition
      to English Master.
    examples:
    - '10008033'
    - '10027710'
    - '10062506'
    - '10040493'
    - '10013611'
    - '10065857'
    - '10063143'
    - '10022599'
    - '10042342'
    - '10047883'
    keywords:
    - Phenotype
    name: MedDRA
    pattern: ^(?:(?:MedDRA|meddra):)?(?\d+)$
    prefix: Meddra
    uri_format: http://identifiers.org/meddra/$1
  wikidata:
    description: identifier in the Medical Dictionary for Regulatory Activities
    example:
    - '10000304'
    - '10014021'
    - '10067326'
    name: Medical Dictionary for Regulatory Activities ID
    prefix: P3201
    uri_format: https://bioportal.bioontology.org/ontologies/MEDDRA?p=classes&conceptid=$1
    uri_format_rdf: http://purl.bioontology.org/ontology/MDRFRE/$1
medgen:
  biocontext:
    prefix: MedGen
    uri_format: http://www.ncbi.nlm.nih.gov/medgen/$1
  biolink:
    is_identifiers: false
    is_obo: false
    prefix: medgen
    uri_format: https://www.ncbi.nlm.nih.gov/medgen/$1
  contact:
    email: megan.kane@nih.gov
    github: kanems
    name: Megan S. Kane
    orcid: 0000-0001-5493-2602
  contributor_extras:
  - email: nicolas.matentzoglu@gmail.com
    github: matentzn
    name: Nicolas Matentzoglu
    orcid: 0000-0002-7356-1779
  example: '760050'
  example_decoys:
  - N1849341
  - C1849341
  example_extras:
  - '610'
  - CN970821
  integbio:
    description: 'MedGen is a portal database about conditions and phenotypes related
      to Medical Genetics. It aggregates terms from the NIH Genetic Testing Registry
      (GTR), UMLS, HPO, Orphanet, ClinVar and other sources into concepts, and assigns
      a unique identifier and a preferred name and symbol. Each entry includes names,
      identifiers used by other databases, mode of inheritance, clinical features,
      and map location of the loci affecting the disorder. This database provides
      links to such resources as:

      Genetic tests registered in the NIH Genetic Testing Registry (GTR), GeneReviews,
      ClinVar, OMIM, Related genes, Disorders with similar clinical features, Medical
      and research literature, Practice guidelines, Consumer resources, Ontologies
      such as HPO and ORDO.'
    homepage: https://www.ncbi.nlm.nih.gov/medgen/
    information_keywords:
    - Phenotype
    - Ontology/Terminology/Nomenclature
    - Bibliography/Documents
    maintainer: NCBI (National Center for Biotechnology Information)
    name: MedGen
    prefix: nbdc02560
    status: Active
    target_keywords:
    - Genome/Gene
    - Health/Disease
  mappings:
    biocontext: MedGen
    biolink: medgen
    integbio: nbdc02560
    miriam: medgen
    n2t: medgen
    ncbi: MedGen
    togoid: Medgen
  miriam:
    deprecated: false
    description: MedGen is a portal for information about conditions and phenotypes
      related to Medical Genetics. Terms from multiple sources are aggregated into
      concepts, each of which is assigned a unique identifier and a preferred name
      and symbol. The core content of the record may include names, identifiers used
      by other databases, mode of inheritance, clinical features, and map location
      of the loci affecting the disorder.
    homepage: https://www.ncbi.nlm.nih.gov/medgen/
    id: 00000594
    name: MedGen
    namespaceEmbeddedInLui: false
    pattern: ^[CN]*\d{4,7}$
    prefix: medgen
    sampleId: '760050'
    uri_format: https://www.ncbi.nlm.nih.gov/medgen/$1
  n2t:
    description: MedGen is a portal for information about conditions and phenotypes
      related to Medical Genetics. Terms from multiple sources are aggregated into
      concepts, each of which is assigned a unique identifier and a preferred name
      and symbol. The core content of the record may include names, identifiers used
      by other databases, mode of inheritance, clinical features, and map location
      of the loci affecting the disorder.
    example: '760050'
    homepage: https://www.ncbi.nlm.nih.gov/medgen/
    name: MedGen at NCBI
    namespaceEmbeddedInLui: false
    pattern: ^[CN]*\d{4,7}$
    prefix: medgen
    uri_format: https://www.ncbi.nlm.nih.gov/medgen/$1
  ncbi:
    example: C0010674
    homepage: https://www.ncbi.nlm.nih.gov/medgen
    name: Human Medical Genetics
    prefix: MedGen
  pattern: ^(CN)?\d{2,7}$
  prefix: medgen
  references:
  - https://github.com/biopragmatics/bioregistry/pull/1567
  synonyms:
  - medgen.uid
  togoid:
    catalog: nbdc02560
    description: 'MedGen is a portal database about conditions and phenotypes related
      to Medical Genetics. It aggregates terms from the NIH Genetic Testing Registry
      (GTR), UMLS, HPO, Orphanet, ClinVar and other sources into concepts, and assigns
      a unique identifier and a preferred name and symbol. Each entry includes names,
      identifiers used by other databases, mode of inheritance, clinical features,
      and map location of the loci affecting the disorder. This database provides
      links to such resources as: Genetic tests registered in the NIH Genetic Testing
      Registry (GTR), GeneReviews, ClinVar, OMIM, Related genes, Disorders with similar
      clinical features, Medical and research literature, Practice guidelines, Consumer
      resources, Ontologies such as HPO and ORDO.'
    examples:
    - C0264897
    - C0028860
    - C0018818
    - C1848392
    - C0006389
    - C0020517
    - C0000364
    - CN227118
    - CN203043
    - CN292950
    keywords:
    - Phenotype
    name: MedGen
    pattern: ^(?CN?\d{4,7})$
    prefix: Medgen
    uri_format: http://identifiers.org/medgen/$1
medgen.cid:
  contact:
    email: megan.kane@nih.gov
    github: kanems
    name: Megan S. Kane
    orcid: 0000-0001-5493-2602
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: This vocabulary is used internally inside MedGen to assign temporary
    identifiers to terms that will later get put in UMLS. Mappings between MedGen,
    MedGen CIDs, and UMLS can be found [here](https://ftp.ncbi.nlm.nih.gov/pub/medgen/MedGenIDMappings.txt.gz).
  example: CN970821
  github_request_issue: 1576
  homepage: https://www.ncbi.nlm.nih.gov/medgen
  name: MedGen Concept Unique ID
  pattern: ^CN\d+$
  prefix: medgen.cid
  references:
  - https://github.com/biopragmatics/bioregistry/pull/1567
mediadive.ingredient:
  contact:
    email: joerg.overmann@dsmz.de
    github: null
    name: Jörg Overmann
    orcid: 0000-0003-3909-7201
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: The mission of MediaDive is to transform poorly structured media recipes
    into a standardized database. The contents of the database include mined thousands
    of PDF and HTML documents. To ensure the quality of the media and continous improvement
    of the database, we developed an internal editor interface. Experts at the DSMZ
    are creating new media and curating the existing media using this interface. [adapted
    from https://mediadive.dsmz.de/about]
  example: '13'
  github_request_issue: 941
  homepage: https://mediadive.dsmz.de/solutions
  license: CC-BY-4.0
  name: MediaDive Ingredient
  pattern: ^\d+$
  prefix: mediadive.ingredient
  uri_format: https://mediadive.dsmz.de/ingredients/$1
mediadive.medium:
  contact:
    email: joerg.overmann@dsmz.de
    github: null
    name: Jörg Overmann
    orcid: 0000-0003-3909-7201
  contributor:
    email: cjmungall@lbl.gov
    github: cmungall
    name: Chris Mungall
    orcid: 0000-0002-6601-2165
  description: The mission of MediaDive is to transform poorly structured media recipes
    into a standardized database. The contents of the database include mined thousands
    of PDF and HTML documents. To ensure the quality of the media and continous improvement
    of the database, we developed an internal editor interface. Experts at the DSMZ
    are creating new media and curating the existing media using this interface. [adapted
    from https://mediadive.dsmz.de/about]
  example: '77'
  example_extras:
  - 54b
  github_request_issue: 941
  homepage: https://mediadive.dsmz.de/media
  license: CC-BY-4.0
  mappings:
    miriam: mediadive.medium
  miriam:
    deprecated: false
    description: MediaDive is a manually curated collection of cultivation media and
      growth conditions. This namespace specifically references mediums.
    homepage: https://www.dsmz.de/
    id: 00001078
    name: MediaDive mediums
    namespaceEmbeddedInLui: false
    pattern: ^[A-Z]?[0-9]{1,5}[a-z]?$
    prefix: mediadive.medium
    sampleId: 1011c
    uri_format: https://mediadive.dsmz.de/medium/$1
  name: MediaDive Medium
  pattern: ^\d+\w?$
  prefix: mediadive.medium
  reviewer:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  uri_format: https://mediadive.dsmz.de/medium/$1
mediadive.solution:
  contact:
    email: joerg.overmann@dsmz.de
    github: null
    name: Jörg Overmann
    orcid: 0000-0003-3909-7201
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: The mission of MediaDive is to transform poorly structured media recipes
    into a standardized database. The contents of the database include mined thousands
    of PDF and HTML documents. To ensure the quality of the media and continous improvement
    of the database, we developed an internal editor interface. Experts at the DSMZ
    are creating new media and curating the existing media using this interface. [adapted
    from https://mediadive.dsmz.de/about]
  example: S6
  github_request_issue: 941
  homepage: https://mediadive.dsmz.de/solutions
  license: CC-BY-4.0
  name: MediaDive Solution
  pattern: ^S\d+$
  prefix: mediadive.solution
  uri_format: https://mediadive.dsmz.de/solutions/$1
medlineplus:
  aberowl:
    description: MedlinePlus Health Topics;National Library of Medicine;June 14, 2008;Bethesda,
      MD
    homepage: http://www.nlm.nih.gov/medlineplus/xmldescription.html
    name: MedlinePlus Health Topics
    prefix: MEDLINEPLUS
    version: 2016AB
  biocontext:
    prefix: MEDLINEPLUS
  bioportal:
    contact:
      email: custserv@nlm.nih.gov
      name: NLM Customer Service
    description: MedlinePlus Health Topics;National Library of Medicine;June 14, 2008;Bethesda,
      MD
    homepage: http://medlineplus.gov/
    name: MedlinePlus Health Topics
    prefix: MEDLINEPLUS
    publications:
    - http://www.nlm.nih.gov/medlineplus/xmldescription.html
    version: MEDLINEPLUS_20231101
  fairsharing:
    abbreviation: MEDLINEPLUS
    description: This resource provides information on the symptoms, causes, treatment
      and prevention for a wide range of diseases, illnesses, health conditions and
      wellness issues. MedlinePlus health topics are regularly reviewed, and links
      are updated daily.
    domains:
    - disease
    homepage: https://medlineplus.gov/xmldescription.html
    logo: https://api.fairsharing.org/rails/active_storage/blobs/redirect/eyJfcmFpbHMiOnsibWVzc2FnZSI6IkJBaHBBaEFGIiwiZXhwIjpudWxsLCJwdXIiOiJibG9iX2lkIn19--611e307f6ed5ae6a6f06017953d913cdcacc490b/Screenshot%20from%202024-10-04%2017-49-50.png?disposition=inline
    name: MedlinePlus Health Topics
    prefix: FAIRsharing.bf8dsb
    subjects:
    - Biomedical Science
    - Health Science
    - Medicine
  hl7:
    description: 'MedlinePlus Health Topics. Bethesda (MD): National Library of Medicine,
      August 14, 2004.'
    name: MedlinePlus
    preferred_prefix: MEDLINEPLUS
    prefix: 2.16.840.1.113883.6.173
    status: Pending
  integbio:
    description: MedlinePlus is the patient-forward site of the US NIH National Library
      of Medicine. The database contains information on a variety of health topics,
      from diseases to drugs, presented for the general public. The database is curated
      and updated by NLM staff and seeks to provide users with straightforward, unbiased
      explanations and information.
    homepage: http://www.nlm.nih.gov/medlineplus/
    information_keywords:
    - Bibliography/Documents
    maintainer: NLM (National Library of Medicine)
    name: MedlinePlus
    prefix: nbdc00836
    status: Active
    target_keywords:
    - Health/Disease
  mappings:
    aberowl: MEDLINEPLUS
    biocontext: MEDLINEPLUS
    bioportal: MEDLINEPLUS
    fairsharing: FAIRsharing.bf8dsb
    hl7: 2.16.840.1.113883.6.173
    integbio: nbdc00836
    miriam: medlineplus
    n2t: medlineplus
  miriam:
    deprecated: false
    description: MedlinePlus is the National Institutes of Health's Web site for patients
      and their families and friends. Produced by the National Library of Medicine,
      it provides information about diseases, conditions, and wellness issues using
      non-technical terms and language.
    homepage: http://www.nlm.nih.gov/medlineplus/
    id: '00000476'
    name: MedlinePlus
    namespaceEmbeddedInLui: false
    pattern: ^\d+$
    prefix: medlineplus
    sampleId: 002804
    uri_format: http://www.nlm.nih.gov/medlineplus/ency/article/$1.htm
  n2t:
    description: MedlinePlus is the National Institutes of Health's Web site for patients
      and their families and friends. Produced by the National Library of Medicine,
      it provides information about diseases, conditions, and wellness issues using
      non-technical terms and language.
    example: 002804
    homepage: http://www.nlm.nih.gov/medlineplus/
    name: MedlinePlus at NCBI
    namespaceEmbeddedInLui: false
    pattern: ^\d+$
    prefix: medlineplus
    uri_format: http://www.nlm.nih.gov/medlineplus/ency/article/$1.htm
  prefix: medlineplus
  providers:
  - code: medlineplus.fp
    description: First-party version of medline plus.
    example: null
    first_party: null
    homepage: https://medlineplus.gov
    name: MedLine Plus home page
    publications: null
    status: null
    uri_format: https://medlineplus.gov/ency/article/$1.htm
meno:
  contact:
    email: mirjam.stappel@uni-osnabrueck.de
    github: stap-m
    name: Mirjam Stappel
    orcid: 0000-0003-3722-5564
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: The midlevel energy ontology (MENO) is a BFO-based midlevel ontology.
    It comprises the concepts for energy qualities, energy-based dispositions and
    energy-driven transformation and transfer processes and their interrelations.
    It has the goal to provide an upper level structure for these concepts for energy-related
    domain ontologies.
  download_owl: https://github.com/stap-m/midlevel-energy-ontology/raw/refs/heads/dev/ontology/src/midlevel-energy.owl
  example: '01013'
  homepage: https://github.com/stap-m/midlevel-energy-ontology
  license: CC-BY-4.0
  name: Mid-level Energy Ontology
  pattern: ^\d+$
  prefix: meno
  references:
  - https://www.utwente.nl/en/eemcs/fois2024/resources/papers/stappel-neuhaus-representing-energy-in-the-midlevel-energy-ontology-meno.pdf
  repository: https://github.com/stap-m/midlevel-energy-ontology
merckindex.monograph:
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: A semantic space of small molecules
  example: M2871
  github_request_issue: 1554
  homepage: https://merckindex.rsc.org
  name: Merck Index Monograph
  prefix: merckindex.monograph
  uri_format: https://merckindex.rsc.org/monographs/$1
merckindex.reaction:
  appears_in:
  - rxno
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  deprecated: true
  description: Chemical reactions in the Merck Index. This website doesn't exist anymore
  example: r376
  github_request_issue: 1554
  homepage: https://merckindex.rsc.org
  name: Merck Index Reaction
  pattern: ^r\d+$
  prefix: merckindex.reaction
  uri_format: https://www.rsc.org/Merck-Index/reaction/$1
merops.clan:
  contact:
    email: ndr@ebi.ac.uk
    github: null
    name: Neil D Rawlings
    orcid: 0000-0001-5557-7665
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: The MEROPS database is an information resource for peptidases (also
    termed proteases, proteinases and proteolytic enzymes) and the proteins that inhibit
    them.
  example: IA
  homepage: https://www.ebi.ac.uk/merops
  name: MEROPS Clan
  part_of_database: merops
  prefix: merops.clan
  publications:
  - doi: 10.1093/nar/gkx1134
    pmc: PMC5753285
    pubmed: '29145643'
    title: The MEROPS database of proteolytic enzymes, their substrates and inhibitors
      in 2017 and a comparison with peptidases in the PANTHER database
    year: 2018
  references:
  - https://github.com/biopragmatics/bioregistry/issues/439
  uri_format: https://www.ebi.ac.uk/merops/cgi-bin/clansum?clan=$1
merops.entry:
  biocontext:
    prefix: MEROPS.INHIBITOR
  contact:
    email: ndr@ebi.ac.uk
    github: null
    name: Neil D Rawlings
    orcid: 0000-0001-5557-7665
  edam:
    description: Unique identifier of a peptidase enzyme from the MEROPS database.
    name: Enzyme ID (MEROPS)
    obsolete: false
    prefix: '2629'
  example: I31.952
  example_extras:
  - S01.001
  - XM02.001
  fairsharing:
    abbreviation: MEROPS
    description: The MEROPS database is an information resource for peptidases (also
      termed proteases, proteinases and proteolytic enzymes) and the proteins that
      inhibit them.
    homepage: http://www.ebi.ac.uk/merops/
    name: MEROPS
    prefix: FAIRsharing.2s4n8r
    publications:
    - doi: 10.1093/nar/gkm954
      pubmed_id: 17991683
      title: 'MEROPS: the peptidase database.'
    - doi: 10.1093/nar/gkx1134
      pubmed_id: 29145643
      title: The MEROPS database of proteolytic enzymes, their substrates and inhibitors
        in 2017 and a comparison with peptidases in the PANTHER database.
    - doi: 10.1042/bj2900205
      pubmed_id: 8439290
      title: Evolutionary families of peptidases.
    - doi: 10.1093/nar/27.1.325
      pubmed_id: 9847218
      title: 'MEROPS: the peptidase database.'
    - doi: 10.1093/nar/gkr987
      pubmed_id: 22086950
      title: 'MEROPS: the database of proteolytic enzymes, their substrates and inhibitors.'
    - doi: 10.1093/nar/gkv1118
      pubmed_id: 26527717
      title: Twenty years of the MEROPS database of proteolytic enzymes, their substrates
        and inhibitors.
    - doi: 10.1016/j.biochi.2015.10.003
      pubmed_id: 26455268
      title: Peptidase specificity from the substrate cleavage collection in the MEROPS
        database and a tool to measure cleavage site conservation.
    subjects:
    - Life Science
    - Biomedical Science
  go:
    homepage: https://www.ebi.ac.uk/merops/
    name: MEROPS peptidase database
    prefix: MEROPS
    uri_format: https://www.ebi.ac.uk/merops/cgi-bin/pepsum?id=$1
  mappings:
    biocontext: MEROPS.INHIBITOR
    edam: '2629'
    fairsharing: FAIRsharing.2s4n8r
    go: MEROPS
    miriam: merops.inhibitor
    n2t: merops.inhibitor
    prefixcommons: merops
  miriam:
    deprecated: false
    description: The MEROPS database is an information resource for peptidases (also
      termed proteases, proteinases and proteolytic enzymes) and the proteins that
      inhibit them. This collections references inhibitors.
    homepage: https://www.ebi.ac.uk/merops
    id: 00000491
    name: MEROPS Inhibitor
    namespaceEmbeddedInLui: false
    pattern: ^I\d{2}\.\d{3}$
    prefix: merops.inhibitor
    sampleId: I31.952
    uri_format: https://www.ebi.ac.uk/merops/cgi-bin/pepsum?id=$1
  n2t:
    description: The MEROPS database is an information resource for peptidases (also
      termed proteases, proteinases and proteolytic enzymes) and the proteins that
      inhibit them. This collections references inhibitors.
    example: I31.952
    homepage: http://merops.sanger.ac.uk/index.htm
    name: MEROPS Inhibitor at Sanger Institute
    namespaceEmbeddedInLui: false
    pattern: ^I\d{2}\.\d{3}$
    prefix: merops.inhibitor
    uri_format: http://merops.sanger.ac.uk/cgi-bin/pepsum?id=$1
  name: MEROPS Entry
  pattern: ^[SCTAGMNUIX]{1,2}\d{2}\.([AB]\d{2}|\d{3})$
  prefix: merops.entry
  prefixcommons:
    description: The MEROPS database is an information resource for peptidases (also
      termed proteases, proteinases and proteolytic enzymes) and the proteins that
      inhibit them.
    example: S01.001
    homepage: http://merops.sanger.ac.uk/
    keywords:
    - protein
    - enzyme
    - structure
    license: http://merops.sanger.ac.uk/about/availability.shtml
    name: MEROPS - the Peptidase Database
    pattern: ^S\d{2}\.\d{3}$
    prefix: merops
    pubmed_ids:
    - '17991683'
    uri_format: http://merops.sanger.ac.uk/cgi-bin/pepsum?id=$1
  publications:
  - doi: 10.1093/nar/gkx1134
    pmc: PMC5753285
    pubmed: '29145643'
    title: The MEROPS database of proteolytic enzymes, their substrates and inhibitors
      in 2017 and a comparison with peptidases in the PANTHER database
    year: 2018
  - doi: 10.1016/j.biochi.2015.10.003
    pmc: PMC4756867
    pubmed: '26455268'
    title: Peptidase specificity from the substrate cleavage collection in the MEROPS
      database and a tool to measure cleavage site conservation
    year: 2015
  - doi: 10.1093/nar/gkv1118
    pmc: PMC4702814
    pubmed: '26527717'
    title: Twenty years of the MEROPS database of proteolytic enzymes, their substrates
      and inhibitors
    year: 2015
  - doi: 10.1093/nar/gkr987
    pmc: PMC3245014
    pubmed: '22086950'
    title: 'MEROPS: the database of proteolytic enzymes, their substrates and inhibitors'
    year: 2011
  - doi: 10.1093/nar/gkm954
    pmc: PMC2238837
    pubmed: '17991683'
    title: 'MEROPS: the peptidase database'
    year: 2007
  - doi: 10.1093/nar/27.1.325
    pmc: PMC148173
    pubmed: '9847218'
    title: 'MEROPS: the peptidase database'
    year: 1999
  - doi: 10.1042/bj2900205
    pmc: PMC1132403
    pubmed: '8439290'
    title: Evolutionary families of peptidases
    year: 1993
  references:
  - https://github.com/biopragmatics/bioregistry/issues/439
  synonyms:
  - merops.inhibitor
  uri_format: https://www.ebi.ac.uk/merops/cgi-bin/pepsum?id=$1
merops.family:
  biocontext:
    prefix: MEROPS.FAMILY
  contact:
    email: ndr@ebi.ac.uk
    github: null
    name: Neil D Rawlings
    orcid: 0000-0001-5557-7665
  mappings:
    biocontext: MEROPS.FAMILY
    miriam: merops.family
    n2t: merops.family
  miriam:
    deprecated: false
    description: The MEROPS database is an information resource for peptidases (also
      termed proteases, proteinases and proteolytic enzymes) and the proteins that
      inhibit them. These are hierarchically classified and assigned to a Family on
      the basis of statistically significant similarities in amino acid sequence.
      Families thought to be homologous are grouped together in a Clan. This collection
      references peptidase families.
    homepage: https://www.ebi.ac.uk/merops/
    id: '00000302'
    name: MEROPS Family
    namespaceEmbeddedInLui: false
    pattern: ^[SCTAGMNU]\d+$
    prefix: merops.family
    sampleId: S1
    uri_format: https://www.ebi.ac.uk/merops/cgi-bin/famsum?family=$1
  n2t:
    description: The MEROPS database is an information resource for peptidases (also
      termed proteases, proteinases and proteolytic enzymes) and the proteins that
      inhibit them. These are hierarchically classified and assigned to a Family on
      the basis of statistically significant similarities in amino acid sequence.
      Families thought to be homologous are grouped together in a Clan. This collection
      references peptidase families.
    example: S1
    homepage: http://merops.sanger.ac.uk/index.htm
    name: Merops Family at Sanger Institute
    namespaceEmbeddedInLui: false
    pattern: ^[SCTAGMNU]\d+$
    prefix: merops.family
    uri_format: http://merops.sanger.ac.uk/cgi-bin/famsum?family=$1
  part_of_database: merops
  prefix: merops.family
  publications:
  - doi: 10.1093/nar/gkx1134
    pmc: PMC5753285
    pubmed: '29145643'
    title: The MEROPS database of proteolytic enzymes, their substrates and inhibitors
      in 2017 and a comparison with peptidases in the PANTHER database
    year: 2018
  references:
  - https://github.com/biopragmatics/bioregistry/issues/439
  uri_format: https://www.ebi.ac.uk/merops/cgi-bin/famsum?family=$1
merriamwebster:
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: Online Dictionary
  example: buccal_gland
  github_request_issue: 1310
  homepage: https://www.merriam-webster.com
  name: Merriam Webster Dictionary
  prefix: merriamwebster
  synonyms:
  - merriam_webster
  uri_format: https://www.merriam-webster.com/dictionary/$1
mesh:
  aberowl:
    description: Medical Subject Headings (MeSH);National Library of Medicine; 2011
    homepage: http://www.nlm.nih.gov/mesh/meshhome.html
    name: Medical Subject Headings
    prefix: MESH
    version: 2016AB
  bartoc:
    abbreviation: MeSH
    description: MeSH is the National Library of Medicine's controlled vocabulary
      thesaurus. It consists of sets of terms naming descriptors in a hierarchical
      structure that permits searching at various levels of specificity. MeSH descriptors
      are arranged in both an alphabetic and a hierarchical structure. At the most
      general level of the hierarchical structure are very broad headings such as
      'Anatomy' or 'Mental Disorders'. More specific headings are found at more narrow
      levels of the twelve-level hierarchy, such as 'Ankle' and 'Conduct Disorder'.
      There are 26,142 descriptors in 2011 MeSH. There are also over 177,000 entry
      terms that assist in finding the most appropriate MeSH Heading, for example,
      'Vitamin C' is an entry term to 'Ascorbic Acid'. In addition to these headings,
      there are more than 199,000 headings called Supplementary Concept Records (formerly
      Supplementary Chemical Records) within a separate thesaurus. The MeSH thesaurus
      is used by NLM for indexing articles from 5,400 of the world's leading biomedical
      journals for the MEDLINE®/PubMED® database. It is also used for the NLM-produced
      database that includes cataloging of books, documents, and audiovisuals acquired
      by the Library. Each bibliographic reference is associated with a set of MeSH
      terms that describe the content of the item. Similarly, search queries use MeSH
      vocabulary to find items on a desired topic.
    homepage: http://www.nlm.nih.gov/mesh/
    name: Medical Subject Headings
    prefix: '391'
    wikidata_database: Q199897
  biocontext:
    prefix: MESH
  biolink:
    is_identifiers: false
    is_obo: false
    prefix: MESH
    uri_format: http://id.nlm.nih.gov/mesh/$1
  bioportal:
    contact:
      email: custserv@nlm.nih.gov
      name: NLM Customer Service
    description: Medical Subject Headings (MeSH);National Library of Medicine; 2011
    homepage: http://www.nlm.nih.gov/mesh
    name: Medical Subject Headings
    prefix: MESH
    publications:
    - http://www.nlm.nih.gov/mesh
    version: MSH2025_2024_08_19
  cellosaurus:
    category: Medical resources
    homepage: https://www.ncbi.nlm.nih.gov/mesh
    name: Medical Subject Headings
    prefix: MeSH
    uri_format: https://www.nlm.nih.gov/cgi/mesh/2013/MB_cgi?field=uid&term=$1
  contributor_extras:
  - email: baum@zbmed.de
    github: rombaum
    name: Roman Baum
    orcid: 0000-0001-5246-9351
  domain: multiple
  edam:
    description: An identifier of a concept from the MeSH vocabulary.
    name: MeSH concept
    obsolete: false
    prefix: '1177'
  example: C063233
  example_extras:
  - D000001
  - Q000473
  fairsharing:
    abbreviation: MESH
    description: 'The Medical Subject Headings (MeSH®) thesaurus is a controlled vocabulary
      produced by the National Library of Medicine and used for indexing, cataloging,
      and searching for biomedical and health-related information and documents. MeSH
      includes the subject descriptors appearing in MEDLINE®/PubMed® and other NLM
      databases. MeSH provides a consistent way to find content with different terminology
      but the same concepts. Many synonyms, near-synonyms, and closely related concepts
      are included as entry terms to help users find the most relevant MeSH descriptor
      for the concept they are seeking. In NLM''s online databases, many terms entered
      by searchers are automatically mapped to MeSH descriptors to facilitate retrieval
      of relevant information. Various online systems provide access to MeSH and the
      vocabulary is available in several NLM online systems. These include the MeSH
      Browser, containing the complete contents of the MeSH vocabulary; the MeSH Entrez
      databases, which are designed to assist those searching MEDLINE®/PubMed®; and
      the UMLS Metathesaurus® with links to many other controlled vocabularies. MeSH
      Records contain three types: Descriptors, Qualifiers, and Supplementary Concept
      Records (SCRs).'
    domains:
    - Data retrieval
    - literature curation
    homepage: http://www.nlm.nih.gov/mesh/
    name: Medical Subject Headings
    prefix: FAIRsharing.qnkw45
    publications:
    - pubmed: '13982385'
      title: Medical subject headings
      year: 1963
    subjects:
    - Life Science
    - Biomedical Science
    - Bioinformatics
  go:
    homepage: https://meshb.nlm.nih.gov
    name: Medical Subject Headings
    prefix: MeSH
    synonyms:
    - MESH
    - MSH
    uri_format: http://id.nlm.nih.gov/mesh/$1
  hl7:
    description: 'Medical Subject Headings (MeSH). Bethesda (MD): National Library
      of Medicine, 2004'
    name: MeSH
    preferred_prefix: MSH
    prefix: 2.16.840.1.113883.6.177
    status: Pending
  integbio:
    alt_name: Medical Subject Headings
    description: This is a database of keywords representing the content of articles
      and biological information. The keywords are structured in layers to allow users
      to find more detailed information or perform abstract searches.
    homepage: https://www.nlm.nih.gov/mesh/meshhome.html
    information_keywords:
    - Ontology/Terminology/Nomenclature
    maintainer: NCBI (National Center for Biotechnology Information)
    name: MeSH
    prefix: nbdc00132
    pubmeds:
    - '20623263'
    - '15360776'
    - '15360776'
    status: Active
  keywords:
  - metascience
  - topics
  license: CC0-1.0
  logo: https://meshb.nlm.nih.gov/public/img/meshLogo.jpg
  mappings:
    aberowl: MESH
    bartoc: '391'
    biocontext: MESH
    biolink: MESH
    bioportal: MESH
    cellosaurus: MeSH
    edam: '1177'
    fairsharing: FAIRsharing.qnkw45
    go: MeSH
    hl7: 2.16.840.1.113883.6.177
    integbio: nbdc00132
    miriam: mesh
    n2t: mesh
    ols: mesh
    prefixcommons: mesh
    togoid: Mesh
    wikidata: P486
    wikidata.entity: Q199897
  miriam:
    deprecated: false
    description: MeSH (Medical Subject Headings) is the National Library of Medicine's
      controlled vocabulary thesaurus. It consists of sets of terms naming descriptors
      in a hierarchical structure that permits searching at various levels of specificity.
      This thesaurus is used by NLM for indexing articles from biomedical journals,
      cataloguing of books, documents, etc.
    homepage: https://www.nlm.nih.gov/
    id: '00000560'
    name: MeSH
    namespaceEmbeddedInLui: false
    pattern: ^(C|D|M)\d{6,9}$
    prefix: mesh
    providers:
    - code: ''
      description: MeSH Linked Data at National Library of Medicine
      homepage: http://id.nlm.nih.gov/mesh/
      name: MeSH Linked Data at National Library of Medicine
      uri_format: http://id.nlm.nih.gov/mesh/$1
    sampleId: C000100
    uri_format: https://www.ncbi.nlm.nih.gov/mesh/?term=$1
  n2t:
    description: MeSH (Medical Subject Headings) is the National Library of Medicine's
      controlled vocabulary thesaurus. It consists of sets of terms naming descriptors
      in a hierarchical structure that permits searching at various levels of specificity.
      This thesaurus is used by NLM for indexing articles from biomedical journals,
      cataloguing of books, documents, etc.
    example: C000100
    homepage: http://id.nlm.nih.gov/mesh/
    name: MeSH Linked Data at National Library of Medicine
    namespaceEmbeddedInLui: false
    pattern: ^(C|D)\d{6}$
    prefix: mesh
    uri_format: http://id.nlm.nih.gov/mesh/$1
  name: Medical Subject Headings
  ols:
    contact: custserv@nlm.nih.gov
    description: MeSH (Medical Subject Headings) is the National Library of Medicine's
      controlled vocabulary thesaurus. It consists of sets of terms naming descriptors
      in a hierarchical structure that permits searching at various levels of specificity.
      This thesaurus is used by NLM for indexing articles from biomedical journals,
      cataloguing of books, documents, etc.
    homepage: https://www.nlm.nih.gov/
    name: Medical Subject Headings
    prefix: mesh
    uri_format: http://id.nlm.nih.gov/mesh/$1
    version.iri: https://w3id.org/biopragmatics/resources/mesh/2025/mesh.ofn
  pattern: ^(C|D|Q)\d+$
  prefix: mesh
  prefixcommons:
    alt_uri_formats:
    - http://bioonto.de/mesh.owl#$1
    bioportal: '1351'
    description: MeSH is the National Library of Medicine's controlled vocabulary
      thesaurus. It consists of sets of terms naming descriptors in a hierarchical
      structure that permits searching at various levels of specificity
    example: D018377
    homepage: http://www.nlm.nih.gov/mesh/meshhome.html
    keywords:
    - classification
    name: Medical Subject Headings
    pattern: ^[A-Za-z0-9]+$
    prefix: mesh
    rdf_uri_format: http://purl.bioontology.org/ontology/MSH/$1
    synonyms:
    - msh
    - bionto.mesh
    - mesh_cui
  providers:
  - code: bioportal.purl
    description: The BioPortal version of MeSH. Should be re-coded to `bioportal`,
      see https://github.com/biopragmatics/bioregistry/pull/1066.
    example: null
    first_party: null
    homepage: https://bioportal.bioontology.org/ontologies/MESH
    name: BioPortal
    publications: null
    status: null
    uri_format: http://purl.bioontology.org/ontology/MESH/$1
  - code: mesh.json-ld
    description: The MeSH version in JSON-LD.
    example: null
    first_party: true
    homepage: http://id.nlm.nih.gov/mesh/
    name: Medical Subject Headings (JSON-LD)
    publications: null
    status: null
    uri_format: https://id.nlm.nih.gov/mesh/$1.json-ld
  - code: mesh.ttl
    description: The MeSH version in TTL.
    example: null
    first_party: true
    homepage: http://id.nlm.nih.gov/mesh/
    name: Medical Subject Headings (TTL)
    publications: null
    status: null
    uri_format: https://id.nlm.nih.gov/mesh/$1.ttl
  - code: mesh.n3
    description: The MeSH version in N3.
    example: null
    first_party: true
    homepage: http://id.nlm.nih.gov/mesh/
    name: Medical Subject Headings (N3)
    publications: null
    status: null
    uri_format: https://id.nlm.nih.gov/mesh/$1.n3
  - code: mesh.2008
    description: Appears in birnlex
    example: null
    first_party: null
    homepage: http://id.nlm.nih.gov/mesh/
    name: Legacy 2008 MeSH URL
    publications: null
    status: null
    uri_format: http://www.nlm.nih.gov/cgi/mesh/2008/MB_cgi?field=uid&term=$1
  publications:
  - doi: null
    pmc: PMC197951
    pubmed: '13982385'
    title: Medical subject headings
    year: 1963
  - doi: null
    pmc: null
    pubmed: '13982385'
    title: Medical subject headings
    year: 1963
  - doi: null
    pmc: null
    pubmed: '13982385'
    title: Medical subject headings
    year: 1963
  synonyms:
  - MESH
  - MESHA
  - MESHC
  - MESHCS
  - MESHD
  - MESHPP
  - MESH_DESCRIPTOR_UI
  - MESH_SUPPLEMENTAL_RECORD_UI
  - MSH
  - MSH2010_2010_02_22
  - MeSH
  - meshUID
  togoid:
    catalog: nbdc00132
    description: This is a database of keywords representing the content of articles
      and biological information. The keywords are structured in layers to allow users
      to find more detailed information or perform abstract searches.
    examples:
    - D002065
    - C562829
    - C566582
    - D010623
    - D003327
    - D001715
    - D000453
    - D010260
    - C537322
    - C563418
    keywords:
    - Phenotype
    name: MeSH
    pattern: ^(?[CD]\d{6,9})$
    prefix: Mesh
    uri_format: http://id.nlm.nih.gov/mesh/$1
  uri_format: https://meshb.nlm.nih.gov/record/ui?ui=$1
  wikidata:
    description: identifier for Descriptor or Supplementary concept in the Medical
      Subject Headings controlled vocabulary
    example:
    - C004931
    - D008180
    - D014583
    homepage: http://www.nlm.nih.gov
    miriam: mesh
    name: MeSH descriptor ID
    pattern: ^[CD]\w{6}(\w{3}|)$
    prefix: P486
    uri_format: https://meshb.nlm.nih.gov/record/ui?ui=$1
    uri_format_rdf: http://id.nlm.nih.gov/mesh/$1
mesh.2012:
  biocontext:
    prefix: MESH.2012
  mappings:
    biocontext: MESH.2012
    miriam: mesh.2012
    n2t: mesh.2012
  miriam:
    deprecated: false
    description: MeSH (Medical Subject Headings) is the National Library of Medicine's
      controlled vocabulary thesaurus. It consists of sets of terms naming descriptors
      in a hierarchical structure that permits searching at various levels of specificity.
      This thesaurus is used by NLM for indexing articles from biomedical journals,
      cataloging of books, documents, etc. This collection references MeSH terms published
      in 2012.
    id: '00000270'
    name: MeSH 2012
    namespaceEmbeddedInLui: false
    pattern: ^[A-Za-z0-9]+$
    prefix: mesh.2012
    sampleId: '17186'
  n2t:
    description: MeSH (Medical Subject Headings) is the National Library of Medicine's
      controlled vocabulary thesaurus. It consists of sets of terms naming descriptors
      in a hierarchical structure that permits searching at various levels of specificity.
      This thesaurus is used by NLM for indexing articles from biomedical journals,
      cataloging of books, documents, etc. This collection references MeSH terms published
      in 2012.
    example: '17186'
    homepage: http://www.nlm.nih.gov/mesh/
    name: MeSH at National Library of Medicine
    namespaceEmbeddedInLui: false
    pattern: ^[A-Za-z0-9]+$
    prefix: mesh.2012
    uri_format: http://www.nlm.nih.gov/cgi/mesh/2012/MB_cgi?mode=&index=$1&view=expanded
  part_of_database: mesh
  prefix: mesh.2012
  provides: mesh
mesh.2013:
  biocontext:
    prefix: MESH.2013
  mappings:
    biocontext: MESH.2013
    miriam: mesh.2013
    n2t: mesh.2013
  miriam:
    deprecated: false
    description: MeSH (Medical Subject Headings) is the National Library of Medicine's
      controlled vocabulary thesaurus. It consists of sets of terms naming descriptors
      in a hierarchical structure that permits searching at various levels of specificity.
      This thesaurus is used by NLM for indexing articles from biomedical journals,
      cataloging of books, documents, etc. This collection references MeSH terms published
      in 2013.
    id: '00000473'
    name: MeSH 2013
    namespaceEmbeddedInLui: false
    pattern: ^[A-Za-z0-9]+$
    prefix: mesh.2013
    sampleId: '17165'
  n2t:
    description: MeSH (Medical Subject Headings) is the National Library of Medicine's
      controlled vocabulary thesaurus. It consists of sets of terms naming descriptors
      in a hierarchical structure that permits searching at various levels of specificity.
      This thesaurus is used by NLM for indexing articles from biomedical journals,
      cataloging of books, documents, etc. This collection references MeSH terms published
      in 2013.
    example: '17165'
    homepage: http://www.nlm.nih.gov/mesh/
    name: MeSH 2013 at National Library of Medicine
    namespaceEmbeddedInLui: false
    pattern: ^[A-Za-z0-9]+$
    prefix: mesh.2013
    uri_format: http://www.nlm.nih.gov/cgi/mesh/2013/MB_cgi?mode=&index=$1&view=expanded
  part_of_database: mesh
  prefix: mesh.2013
  provides: mesh
mesh.vocab:
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: Medical Subject Headings vocabulary is the set of predicates used in
    the MeSH RDF dump
  example: term
  homepage: https://hhs.github.io/meshrdf/
  name: Medical Subject Headings Vocabulary
  part_of_database: mesh
  prefix: mesh.vocab
  references:
  - https://id.nlm.nih.gov/mesh/query
  repository: https://github.com/HHS/meshrdf
  uri_format: http://id.nlm.nih.gov/mesh/vocab#$1
metabolights:
  biocontext:
    prefix: METABOLIGHTS
  cellosaurus:
    category: Metabolomic databases
    homepage: https://www.ebi.ac.uk/metabolights/
    name: MetaboLights database for metabolomics experiments and derived information
    prefix: MetaboLights
    uri_format: https://www.ebi.ac.uk/metabolights/$1
  integbio:
    alt_name: MTBLS
    description: MetaboLights is a database is a collection of metabolite structures.
      This resource provides information on the compound origins,the biological roles,
      locations and concentrations, as well as experimental data from metabolic experiments.
      The tools and capabilities of this database is firmly routed in collaborative
      working worldwie with the metabolomics community such as the Metabolomics Society
      and the associated Metabolomics Standards Initiative (MSI).
    fairsharing: FAIRsharing.kkdpxe
    homepage: https://www.ebi.ac.uk/metabolights/
    information_keywords:
    - Method
    - Chemical structure
    - Bibliography/Documents
    maintainer: Cambridge Systems Biology Centre, University of Cambridge||EMBL (European
      Molecular Biology Laboratory)
    name: MetaboLights
    prefix: nbdc02124
    pubmeds:
    - '23109552'
    - '23630246'
    - '23060735'
    - '23683662'
    - '27010336'
    - '28830114'
    status: Active
    target_keywords:
    - Metabolite
  mappings:
    biocontext: METABOLIGHTS
    cellosaurus: MetaboLights
    integbio: nbdc02124
    miriam: metabolights
    n2t: metabolights
    re3data: r3d100011556
    wikidata: P3890
  miriam:
    deprecated: false
    description: MetaboLights is a database for Metabolomics experiments and derived
      information. The database is cross-species, cross-technique and covers metabolite
      structures and their reference spectra as well as their biological roles, locations
      and concentrations, and experimental data from metabolic experiments. This collection
      references individual metabolomics studies.
    homepage: https://www.ebi.ac.uk/metabolights/
    id: 00000380
    name: MetaboLights
    namespaceEmbeddedInLui: false
    pattern: ^MTBL[CS]\d+$
    prefix: metabolights
    providers:
    - code: omicsdi
      description: MataboLights through OmicsDI
      homepage: https://www.omicsdi.org/
      name: MataboLights through OmicsDI
      uri_format: https://www.omicsdi.org/dataset/metabolights_dataset/$1
    sampleId: MTBLS1
    uri_format: https://www.ebi.ac.uk/metabolights/$1
  n2t:
    description: MetaboLights is a database for Metabolomics experiments and derived
      information. The database is cross-species, cross-technique and covers metabolite
      structures and their reference spectra as well as their biological roles, locations
      and concentrations, and experimental data from metabolic experiments. This collection
      references individual metabolomics studies.
    example: MTBLS1
    homepage: https://www.ebi.ac.uk/metabolights/
    name: MetaboLights at EBI
    namespaceEmbeddedInLui: false
    pattern: ^MTBLS\d+$
    prefix: metabolights
    uri_format: https://www.ebi.ac.uk/metabolights/$1
  name: MetaboLights Compound
  prefix: metabolights
  re3data:
    description: MetaboLights is a database for Metabolomics experiments and derived
      information. The database is cross-species, cross-technique and covers metabolite
      structures and their reference spectra as well as their biological roles, locations
      and concentrations, and experimental data from metabolic experiments.
    doi: 10.17616/R31P7N
    homepage: https://www.ebi.ac.uk/metabolights/
    license: Apache License 2.0
    name: MetaboLights
    prefix: r3d100011556
  wikidata:
    description: identifiers for compound entries in the MetaboLights databases.
    example:
    - MTBLC16704
    - MTBLC17170
    - MTBLC72802
    name: MetaboLights Compound ID
    pattern: ^MTBLC\d+$
    prefix: P3890
    uri_format: https://www.ebi.ac.uk/metabolights/$1
metacyc.compound:
  biocontext:
    prefix: METACYC.COMPOUND
  biolink:
    is_identifiers: false
    is_obo: false
    prefix: MetaCyc
    uri_format: http://translator.ncats.nih.gov/MetaCyc_$1
  contact:
    email: pkarp@ai.sri.com
    github: pkarp111
    name: Peter D. Karp
    orcid: 0000-0002-5876-6418
  fairsharing:
    abbreviation: null
    description: 'MetaCyc is the largest curated collection of metabolic pathways
      currently available. It provides a comprehensive resource for metabolic pathways
      and enzymes from all domains of life. The pathways in MetaCyc are experimentally
      determined, small-molecule metabolic pathways, and are curated from the primary
      scientific literature. Most reactions in MetaCyc pathways are linked to one
      or more well-characterized enzymes, and both pathways and enzymes are annotated
      with reviews, evidence codes, and literature citations.  As of 2022 MetaCyc
      describes 3,000 pathways and 17,000 reactions curated from 71,000 publications.

      '
    homepage: http://metacyc.org/
    name: MetaCyc
    prefix: FAIRsharing.yytevr
    publications:
    - doi: 10.1093/nar/gkr1014
      pubmed_id: 22102576
      title: The MetaCyc database of metabolic pathways and enzymes and the BioCyc
        collection of pathway/genome databases.
    - doi: 10.1093/nar/gkt1103
      pubmed_id: 24225315
      title: The MetaCyc database of metabolic pathways and enzymes and the BioCyc
        collection of Pathway/Genome Databases
    - doi: 10.1093/nar/gkv1164
      pubmed_id: 26527732
      title: The MetaCyc database of metabolic pathways and enzymes and the BioCyc
        collection of pathway/genome databases.
    subjects:
    - Life Science
    - Metabolomics
    - Systems Biology
    twitter: BioCyc
  go:
    homepage: https://metacyc.org/
    name: Metabolic Encyclopedia of metabolic and other pathways
    prefix: MetaCyc
    synonyms:
    - METACYC
    uri_format: https://biocyc.org/META/NEW-IMAGE?type=NIL&object=$1
  integbio:
    description: MetaCyc is a database of metabolic pathways. The database contains
      hundreds of curated pathways from hundreds of organisms acorss all kingdoms
      of life. Users can search by gene, protein, enzyme, or keyword, and explore
      pathways across related species.
    fairsharing: biodbcore-000136
    homepage: http://metacyc.org/
    information_keywords:
    - Interaction/Pathway
    - Image/Movie
    maintainer: SRI International
    name: MetaCyc
    prefix: nbdc00907
    pubmeds:
    - '17965431'
    - '16381923'
    - '14681452'
    - '11752254'
    - '10592180'
    status: Active
    target_keywords:
    - Genome/Gene
    - RNA
    - Protein
    - Metabolite
  logo: https://metacyc.org/graphics2021/MetaCyc-logo-color.svg
  mappings:
    biocontext: METACYC.COMPOUND
    biolink: MetaCyc
    fairsharing: FAIRsharing.yytevr
    go: MetaCyc
    integbio: nbdc00907
    miriam: metacyc.compound
    n2t: metacyc.compound
    pathguide: '10'
    re3data: r3d100011294
  miriam:
    deprecated: false
    description: MetaCyc is a curated database of experimentally elucidated metabolic
      pathways from all domains of life. MetaCyc contains 2526 pathways from 2844
      different organisms. MetaCyc contains pathways involved in both primary and
      secondary metabolism, as well as associated metabolites, reactions, enzymes,
      and genes. The goal of MetaCyc is to catalog the universe of metabolism by storing
      a representative sample of each experimentally elucidated pathway.
    homepage: https://metacyc.org
    id: 00000609
    name: MetaCyc Compound
    namespaceEmbeddedInLui: false
    pattern: ^[A-Za-z0-9+_.%-:]+$
    prefix: metacyc.compound
    sampleId: CPD-10330
    uri_format: https://metacyc.org/compound?orgid=META&id=$1
  n2t:
    description: MetaCyc is a curated database of experimentally elucidated metabolic
      pathways from all domains of life. MetaCyc contains 2526 pathways from 2844
      different organisms. MetaCyc contains pathways involved in both primary and
      secondary metabolism, as well as associated metabolites, reactions, enzymes,
      and genes. The goal of MetaCyc is to catalog the universe of metabolism by storing
      a representative sample of each experimentally elucidated pathway.
    example: CPD-10330
    homepage: https://metacyc.org
    name: MetaCyc Metabolic Pathway Database
    namespaceEmbeddedInLui: false
    pattern: ^CPD-\d{5}$
    prefix: metacyc.compound
    uri_format: https://metacyc.org/compound?orgid=META&id=$1
  pathguide:
    abbreviation: MetaCyc
    homepage: http://metacyc.org/
    keywords:
    - BioPAX
    - SBML
    name: Metabolic Pathway Database
    prefix: '10'
  prefix: metacyc.compound
  publications:
  - doi: 10.1093/nar/gkv1164
    pmc: PMC4702838
    pubmed: '26527732'
    title: The MetaCyc database of metabolic pathways and enzymes and the BioCyc collection
      of pathway/genome databases
    year: 2015
  - doi: 10.1093/nar/gkt1103
    pmc: PMC3964957
    pubmed: '24225315'
    title: The MetaCyc database of metabolic pathways and enzymes and the BioCyc collection
      of Pathway/Genome Databases
    year: 2013
  - doi: 10.1093/nar/gkr1014
    pmc: PMC3245006
    pubmed: '22102576'
    title: The MetaCyc database of metabolic pathways and enzymes and the BioCyc collection
      of pathway/genome databases
    year: 2011
  re3data:
    description: "MetaCyc is a curated database of experimentally elucidated metabolic\
      \ pathways from all domains of life. \nMetaCyc contains pathways involved in\
      \ both primary and secondary metabolism, as well as associated metabolites,\
      \ reactions, enzymes, and genes. The goal of MetaCyc is to catalog the universe\
      \ of metabolism by storing a representative sample of each experimentally elucidated\
      \ pathway.\nMetaCyc applications include: Online encyclopedia of metabolism,\
      \ Prediction of metabolic pathways in sequenced genomes, Support metabolic engineering\
      \ via enzyme database, Metabolite database aids. metabolomics research."
    doi: 10.17616/R32K7X
    homepage: https://metacyc.org/
    license: other
    name: MetaCyc
    prefix: r3d100011294
    synonyms:
    - Metabolic Pathway Database
    - a member of the BioCyc database collection
    xrefs:
      nif: 0000-03114
      omics: 02718
  synonyms:
  - MetaCyc
metacyc.pathway:
  contact:
    email: pkarp@ai.sri.com
    github: pkarp111
    name: Peter D. Karp
    orcid: 0000-0002-5876-6418
  contributor:
    email: null
    github: hrshdhgd
    name: Harshad Hegde
    orcid: 0000-0002-2411-565X
  description: 'MetaCyc is a database of non-redundant, experimentally elucidated
    metabolic pathways and enzymes. It also contains reactions, chemical compounds,
    and genes. It stores predominantly qualitative information rather than quantitative
    data, although it does contain some quantitative data such as enzyme kinetics
    data.


    MetaCyc is [curated](http://www.biocyc.org/glossary.shtml?sid=biocyc14-3908554027#Curation)
    from the scientific experimental literature according to an [extensive process](https://metacyc.org/MetaCycUserGuide.shtml#TAG:__tex2page_sec_4)].
    The majority of pathways occurring in it are from microorganisms and plants. MetaCyc
    stores thousands of additional enzyme-catalyzed reactions that have not yet been
    assigned an EC number'
  example: 12DICHLORETHDEG-PWY
  github_request_issue: 1012
  homepage: https://metacyc.org
  name: Metabolic Encyclopedia for Pathway/Genome Databases
  prefix: metacyc.pathway
  publications:
  - doi: null
    pmc: null
    pubmed: '31586394'
    title: The MetaCyc database of metabolic pathways and enzymes - a 2019 update
    year: 2019
  - doi: null
    pmc: null
    pubmed: '23746312'
    title: The challenge of constructing, classifying, and representing metabolic
      pathways
    year: 2013
  - doi: null
    pmc: null
    pubmed: '21523460'
    title: A survey of metabolic databases emphasizing the MetaCyc family
    year: 2011
  reviewer:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  uri_format: https://metacyc.org/META/NEW-IMAGE?object=$1
metacyc.reaction:
  biocontext:
    prefix: METACYC.REACTION
  biolink:
    is_identifiers: true
    is_obo: false
    prefix: metacyc.reaction
    uri_format: http://identifiers.org/metacyc.reaction:$1
  contact:
    email: pkarp@ai.sri.com
    github: pkarp111
    name: Peter D. Karp
    orcid: 0000-0002-5876-6418
  mappings:
    biocontext: METACYC.REACTION
    biolink: metacyc.reaction
    miriam: metacyc.reaction
    n2t: metacyc.reaction
  miriam:
    deprecated: false
    description: MetaCyc is a curated database of experimentally elucidated metabolic
      pathways from all domains of life. MetaCyc contains 2526 pathways from 2844
      different organisms. MetaCyc contains pathways involved in both primary and
      secondary metabolism, as well as associated metabolites, reactions, enzymes,
      and genes. The goal of MetaCyc is to catalog the universe of metabolism by storing
      a representative sample of each experimentally elucidated pathway.
    homepage: https://metacyc.org
    id: '00000610'
    name: MetaCyc Reaction
    namespaceEmbeddedInLui: false
    pattern: ^[A-Za-z0-9+_.%-:]+$
    prefix: metacyc.reaction
    sampleId: RXN-14904
    uri_format: https://metacyc.org/META/NEW-IMAGE?type=REACTION&object=$1
  n2t:
    description: MetaCyc is a curated database of experimentally elucidated metabolic
      pathways from all domains of life. MetaCyc contains 2526 pathways from 2844
      different organisms. MetaCyc contains pathways involved in both primary and
      secondary metabolism, as well as associated metabolites, reactions, enzymes,
      and genes. The goal of MetaCyc is to catalog the universe of metabolism by storing
      a representative sample of each experimentally elucidated pathway.
    example: RXN-14904
    homepage: https://metacyc.org
    name: MetaCyc Metabolic Pathway Database - Reaction
    namespaceEmbeddedInLui: false
    pattern: ^RXN-\d{5}$
    prefix: metacyc.reaction
    uri_format: https://metacyc.org/META/NEW-IMAGE?type=REACTION&object=$1
  prefix: metacyc.reaction
metanetx.chemical:
  biocontext:
    prefix: METANETX.CHEMICAL
  mappings:
    biocontext: METANETX.CHEMICAL
    miriam: metanetx.chemical
    n2t: metanetx.chemical
  miriam:
    deprecated: false
    description: MetaNetX/MNXref integrates various information from genome-scale
      metabolic network reconstructions such as information on reactions, metabolites
      and compartments. This information undergoes a reconciliation process to minimise
      for discrepancies between different data sources, and makes the data accessible
      under a common namespace. This collection references chemical or metabolic components.
    homepage: https://www.metanetx.org/
    id: '00000567'
    name: MetaNetX chemical
    namespaceEmbeddedInLui: false
    pattern: ^(MNXM\d+|BIOMASS|WATER)$
    prefix: metanetx.chemical
    sampleId: MNXM1723
    uri_format: https://www.metanetx.org/chem_info/$1
  n2t:
    description: MetaNetX/MNXref integrates various information from genome-scale
      metabolic network reconstructions such as information on reactions, metabolites
      and compartments. This information undergoes a reconciliation process to minimise
      for discrepancies between different data sources, and makes the data accessible
      under a common namespace. This collection references chemical or metabolic components.
    example: MNXM1723
    homepage: http://www.metanetx.org/
    name: MetaNetX chemical at SIB Swiss Institute of Bioinformatics
    namespaceEmbeddedInLui: false
    pattern: ^(MNXM\d+|BIOMASS)$
    prefix: metanetx.chemical
    uri_format: https://www.metanetx.org/chem_info/$1
  prefix: metanetx.chemical
metanetx.compartment:
  biocontext:
    prefix: METANETX.COMPARTMENT
  mappings:
    biocontext: METANETX.COMPARTMENT
    miriam: metanetx.compartment
    n2t: metanetx.compartment
  miriam:
    deprecated: false
    description: MetaNetX/MNXref integrates various information from genome-scale
      metabolic network reconstructions such as information on reactions, metabolites
      and compartments. This information undergoes a reconciliation process to minimise
      for discrepancies between different data sources, and makes the data accessible
      under a common namespace. This collection references cellular compartments.
    homepage: https://www.metanetx.org/
    id: 00000569
    name: MetaNetX compartment
    namespaceEmbeddedInLui: false
    pattern: ^(MNX[CD]\d+|BOUNDARY|IN|OUT)$
    prefix: metanetx.compartment
    sampleId: MNXC15
    uri_format: https://www.metanetx.org/comp_info/$1
  n2t:
    description: MetaNetX/MNXref integrates various information from genome-scale
      metabolic network reconstructions such as information on reactions, metabolites
      and compartments. This information undergoes a reconciliation process to minimise
      for discrepancies between different data sources, and makes the data accessible
      under a common namespace. This collection references cellular compartments.
    example: MNXC15
    homepage: http://www.metanetx.org/
    name: MetaNetX compartment at SIB Swiss Institute of Bioinformatics
    namespaceEmbeddedInLui: false
    pattern: ^(MNX[CD]\d+|BOUNDARY)$
    prefix: metanetx.compartment
    uri_format: http://www.metanetx.org/comp_info/$1
  prefix: metanetx.compartment
metanetx.reaction:
  biocontext:
    prefix: METANETX.REACTION
  biolink:
    is_identifiers: false
    is_obo: false
    prefix: METANETX.REACTION
    uri_format: https://www.metanetx.org/equa_info/$1
  mappings:
    biocontext: METANETX.REACTION
    biolink: METANETX.REACTION
    miriam: metanetx.reaction
    n2t: metanetx.reaction
  miriam:
    deprecated: false
    description: MetaNetX/MNXref integrates various information from genome-scale
      metabolic network reconstructions such as information on reactions, metabolites
      and compartments. This information undergoes a reconciliation process to minimise
      for discrepancies between different data sources, and makes the data accessible
      under a common namespace. This collection references reactions.
    homepage: https://www.metanetx.org/
    id: 00000568
    name: MetaNetX reaction
    namespaceEmbeddedInLui: false
    pattern: ^(MNXR\d+|EMPTY)$
    prefix: metanetx.reaction
    sampleId: MNXR101574
    uri_format: https://www.metanetx.org/equa_info/$1
  n2t:
    description: MetaNetX/MNXref integrates various information from genome-scale
      metabolic network reconstructions such as information on reactions, metabolites
      and compartments. This information undergoes a reconciliation process to minimise
      for discrepancies between different data sources, and makes the data accessible
      under a common namespace. This collection references reactions.
    example: MNXR101574
    homepage: http://www.metanetx.org/
    name: MetaNetX reaction at SIB Swiss Institute of Bioinformatics
    namespaceEmbeddedInLui: false
    pattern: ^MNXR\d+$
    prefix: metanetx.reaction
    uri_format: http://www.metanetx.org/equa_info/$1
  prefix: metanetx.reaction
metatlas:
  contact:
    email: mihail.anton@chalmers.se
    github: mihai-sysbio
    name: Mihail Anton
    orcid: 0000-0002-7753-9042
  contributor:
    email: mihail.anton@chalmers.se
    github: mihai-sysbio
    name: Mihail Anton
    orcid: 0000-0002-7753-9042
  description: A resource for exploring metabolism, starting with a set of of community-curated
    genome-scale metabolic models of human and model organisms, enriched with pathway
    maps and other tools for easy browsing and analysis.
  example: MAM01234c
  example_decoys:
  - MAR11851c
  example_extras:
  - MAR11851
  github_request_issue: 495
  homepage: https://metabolicatlas.org
  keywords:
  - chemistry
  - metabolites
  - reactions
  mappings:
    miriam: metatlas
  miriam:
    deprecated: false
    description: Metabolic Atlas facilitates metabolic modelling by presenting open
      source genome-scale metabolic models for easy browsing and analysis.
    homepage: https://metabolicatlas.org
    id: 00000959
    name: Metabolic Atlas
    namespaceEmbeddedInLui: false
    pattern: ^MA[MR]\d{5}[a-z]?$
    prefix: metatlas
    sampleId: MAR01234
    uri_format: https://metabolicatlas.org/identifier/MetabolicAtlas/$1
  name: Metabolic Atlas
  part_of_database: metatlas
  pattern: ^(MAM\d{5}\w)|(MAR\d{5})$
  prefix: metatlas
  reviewer:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  uri_format: https://metabolicatlas.org/identifier/MetabolicAtlas/$1
metatlas.metabolite:
  contact:
    email: mihail.anton@chalmers.se
    github: mihai-sysbio
    name: Mihail Anton
    orcid: 0000-0002-7753-9042
  contributor:
    email: mihail.anton@chalmers.se
    github: mihai-sysbio
    name: Mihail Anton
    orcid: 0000-0002-7753-9042
  description: A subspace of Metabolic Atlas for compartment-specific records for
    metabolites.
  example: MAM01234c
  github_request_issue: 495
  homepage: https://metabolicatlas.org
  keywords:
  - chemistry
  - metabolites
  name: Metabolic Atlas Metabolite
  part_of: metatlas
  pattern: ^MAM\d{5}\w$
  prefix: metatlas.metabolite
  reviewer:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  uri_format: https://metabolicatlas.org/identifier/MetabolicAtlas/$1
metatlas.reaction:
  contact:
    email: mihail.anton@chalmers.se
    github: mihai-sysbio
    name: Mihail Anton
    orcid: 0000-0002-7753-9042
  contributor:
    email: mihail.anton@chalmers.se
    github: mihai-sysbio
    name: Mihail Anton
    orcid: 0000-0002-7753-9042
  description: A subspace of Metabolic Atlas for reactions.
  example: MAR11851
  github_request_issue: 495
  homepage: https://metabolicatlas.org
  keywords:
  - chemistry
  - reactions
  name: Metabolic Atlas Reaction
  part_of: metatlas
  pattern: ^MAR\d{5}$
  prefix: metatlas.reaction
  reviewer:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  uri_format: https://metabolicatlas.org/identifier/MetabolicAtlas/$1
metlin:
  biocontext:
    prefix: METLIN
  mappings:
    biocontext: METLIN
    miriam: metlin
    n2t: metlin
    re3data: r3d100012311
  miriam:
    deprecated: true
    description: The METLIN (Metabolite and Tandem Mass Spectrometry) Database is
      a repository of metabolite information as well as tandem mass spectrometry data,
      providing public access to its comprehensive MS and MS/MS metabolite data. An
      annotated list of known metabolites and their mass, chemical formula, and structure
      are available, with each metabolite linked to external resources for further
      reference and inquiry.
    homepage: http://masspec.scripps.edu/
    id: '00000322'
    name: METLIN
    namespaceEmbeddedInLui: false
    pattern: ^\d{4}$
    prefix: metlin
    sampleId: '1455'
    uri_format: http://metlin.scripps.edu/metabo_info.php?molid=$1
  n2t:
    description: The METLIN (Metabolite and Tandem Mass Spectrometry) Database is
      a repository of metabolite information as well as tandem mass spectrometry data,
      providing public access to its comprehensive MS and MS/MS metabolite data. An
      annotated list of known metabolites and their mass, chemical formula, and structure
      are available, with each metabolite linked to external resources for further
      reference and inquiry.
    example: '1455'
    homepage: http://masspec.scripps.edu/
    name: METLIN at Scripps Center, Molecular Biology and Center for Mass Spectrometry,
      La Jolla
    namespaceEmbeddedInLui: false
    pattern: ^\d{4}$
    prefix: metlin
    uri_format: http://metlin.scripps.edu/metabo_info.php?molid=$1
  name: Metabolite and Tandem Mass Spectrometry Database
  prefix: metlin
  re3data:
    description: METLIN represents the largest MS/MS collection of data with the database
      generated at multiple collision energies and in positive and negative ionization
      modes. The data is generated on multiple instrument types including SCIEX, Agilent,
      Bruker and Waters QTOF mass spectrometers.
    doi: 10.17616/R3RD3W
    homepage: https://metlin.scripps.edu/landing_page.php?pgcontent=mainPage
    name: Metlin
    prefix: r3d100012311
    synonyms:
    - The original and most comprehensive MS/MS metabolite database
    xrefs:
      omics: '02633'
metnetdb:
  mappings:
    pathguide: '234'
    prefixcommons: metnetdb
  name: Metabolic Network Exchange Database
  pathguide:
    abbreviation: MetNetDB
    homepage: http://metnetweb.gdcb.iastate.edu/MetNet_db.htm
    keywords:
    - SBML
    name: Metabolic Network Exchange
    prefix: '234'
  prefix: metnetdb
  prefixcommons:
    description: The MetNet database (MetNetDB) contains information on networks of
      metabolic and regulatory and interactions in Arabidopsis. Types of interactions
      in MetNetDB include transcription, translation, protein modification, assembly,
      allosteric regulation, translocation from one subcellular compartment to another.
    example: '377369'
    homepage: http://www.metnetdb.org/MetNet_db.htm
    keywords:
    - pathway
    - interaction
    - regulation
    - protein
    - small molecule
    - DNA
    - RNA
    name: Metabolic Network Exchange
    pattern: ^\d+$
    prefix: metnetdb
    uri_format: http://metnetonline.org/browse_pathway2.php?pthID=$1
  reviewer:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
mex:
  biocontext:
    prefix: MEX
  mappings:
    biocontext: MEX
    miriam: mex
    n2t: mex
  miriam:
    deprecated: false
    description: A public place to process, interpret and share GC/MS metabolomics
      datasets.
    homepage: https://www.metabolome-express.org/
    id: 00000648
    name: Metabolome Express
    namespaceEmbeddedInLui: false
    pattern: ^\d+$
    prefix: mex
    providers:
    - code: omicsdi
      description: Metabolome Express through OmicsDI
      homepage: https://www.omicsdi.org/
      name: Metabolome Express through OmicsDI
      uri_format: https://www.omicsdi.org/dataset/metabolome_express/MEX$1
    sampleId: '36'
    uri_format: https://www.metabolome-express.org/datasetview.php?datasetid=$1
  n2t:
    description: A public place to process, interpret and share GC/MS metabolomics
      datasets.
    example: '36'
    homepage: https://www.metabolome-express.org/
    name: Metabolome Express
    namespaceEmbeddedInLui: false
    pattern: ^\d+$
    prefix: mex
    uri_format: https://www.metabolome-express.org/datasetview.php?datasetid=$1
  prefix: mex
mf:
  aberowl:
    description: The Mental Functioning Ontology is an overarching ontology for all
      aspects of mental functioning.
    download_owl: http://aber-owl.net/media/ontologies/MF/30/mf.owl
    homepage: https://github.com/jannahastings/mental-functioning-ontology
    name: Mental Functioning Ontology
    prefix: MF
  biocontext:
    prefix: MF
  bioportal:
    contact:
      email: noreply@bioontology.org
      name: Unknown
    description: The Mental Functioning Ontology is an ontology for mental functioning,
      including mental processes such as cognition and traits such as intelligence,
      and related diseases and disorders. It is developed in the context of the Ontology
      for General Medical Science and the Basic Formal Ontology. The project is being
      developed in collaboration between the University of Geneva, Switzerland, and
      the University at Buffalo, USA.\r\n\r\nThe project is being developed with full
      involvement of all relevant communities, following best practices laid out by
      the OBO Foundry. Efforts are currently underway to align with related projects
      including the Behaviour Ontology, the Cognitive Atlas, the Cognitive Paradigm
      Ontology and the Neural Electro Magnetic Ontologies.
    homepage: https://github.com/jannahastings/mental-functioning-ontology/
    name: Mental Functioning Ontology
    prefix: MF
    publications:
    - https://github.com/jannahastings/mental-functioning-ontology/
    version: '2025-07-08'
  example: 0000091
  fairsharing:
    abbreviation: MF
    contact:
      email: janna.hastings@uzh.ch
      name: Janna Hastings
      orcid: 0000-0002-3469-4923
    description: The Mental Functioning Ontology is an ontology for mental functioning,
      including mental processes such as cognition and traits such as intelligence,
      and related diseases and disorders. It is developed in the context of the Ontology
      for General Medical Science and the Basic Formal Ontology. The project is being
      developed in collaboration between the University of Geneva, Switzerland, and
      the University at Buffalo, USA. The project is being developed with full involvement
      of all relevant communities, following best practices laid out by the OBO Foundry.
      Efforts are currently underway to align with related projects including the
      Behaviour Ontology, the Cognitive Atlas, the Cognitive Paradigm Ontology and
      the Neural Electro Magnetic Ontologies.
    domains:
    - cognition
    - mental health
    homepage: https://github.com/jannahastings/mental-functioning-ontology
    license: CC-BY-3.0
    name: Mental Functioning Ontology
    prefix: FAIRsharing.4gm9gt
    repository: https://github.com/jannahastings/mental-functioning-ontology
    subjects:
    - Biomedical Science
    - Cognitive Neuroscience
  mappings:
    aberowl: MF
    biocontext: MF
    bioportal: MF
    fairsharing: FAIRsharing.4gm9gt
    obofoundry: mf
    ols: mf
    ontobee: MF
    wikidata.entity: Q55118443
  obofoundry:
    contact: janna.hastings@gmail.com
    contact.github: jannahastings
    contact.label: Janna Hastings
    contact.orcid: 0000-0002-3469-4923
    deprecated: false
    description: The Mental Functioning Ontology is an overarching ontology for all
      aspects of mental functioning.
    domain: health
    download.owl: http://purl.obolibrary.org/obo/mf.owl
    homepage: https://github.com/jannahastings/mental-functioning-ontology
    license: CC BY 3.0
    license.url: http://creativecommons.org/licenses/by/3.0/
    name: Mental Functioning Ontology
    preferredPrefix: MF
    prefix: mf
    repository: https://github.com/jannahastings/mental-functioning-ontology
  ols:
    description: The Mental Functioning Ontology is an overarching ontology for all
      aspects of mental functioning.
    download_owl: http://purl.obolibrary.org/obo/mf.owl
    homepage: https://github.com/jannahastings/mental-functioning-ontology
    name: Mental Functioning Ontology
    prefix: mf
    tracker: https://github.com/jannahastings/mental-functioning-ontology/issues
    version: '2025-07-08'
    version.iri: http://purl.obolibrary.org/obo/MF/2025-07-08/MF.owl
  ontobee:
    library: Library
    name: Mental Functioning Ontology
    prefix: MF
  pattern: ^\d{7}$
  prefix: mf
  uri_format: http://purl.obolibrary.org/obo/MF_$1
mfmo:
  aberowl:
    description: The Mammalian Feeding Muscle Ontology is an antomy ontology for the
      muscles of the head and neck that participate in feeding, swallowing, and other
      oral-pharyngeal behaviors.
    download_owl: http://aber-owl.net/media/ontologies/MFMO/2/mfmo.owl
    homepage: http://feedexp.org
    name: Mammalian Feeding Muscle Ontology
    prefix: MFMO
  biocontext:
    prefix: MFMO
  bioportal:
    contact:
      email: druzinsk@uic.edu
      name: Robert Druzinsky
    description: An antomy ontology for the muscles of the head and neck that participate
      in feeding, swallowing, and other oral-pharyngeal behaviors.
    homepage: http://feedexp.org/
    name: Mammalian Feeding Muscle Ontology
    prefix: MFMO
  example: 0000208
  fairsharing:
    abbreviation: MFMO
    description: This resource is no longer available because its underlying source
      material is not in scope for FAIRsharing.
    homepage: http://feedexp.org/
    name: Mammalian Feeding Muscle Ontology
    prefix: FAIRsharing.669cnk
    subjects:
    - Anatomy
  mappings:
    aberowl: MFMO
    biocontext: MFMO
    bioportal: MFMO
    fairsharing: FAIRsharing.669cnk
    obofoundry: mfmo
    ols: mfmo
    ontobee: MFMO
    wikidata.entity: Q81661681
  obofoundry:
    contact: druzinsk@uic.edu
    contact.github: RDruzinsky
    contact.label: Robert Druzinsky
    contact.orcid: 0000-0002-1572-1316
    depends_on:
    - uberon
    deprecated: true
    description: The Mammalian Feeding Muscle Ontology is an antomy ontology for the
      muscles of the head and neck that participate in feeding, swallowing, and other
      oral-pharyngeal behaviors.
    domain: anatomy and development
    download.owl: http://purl.obolibrary.org/obo/mfmo.owl
    homepage: https://github.com/rdruzinsky/feedontology
    license: CC BY 3.0
    license.url: http://creativecommons.org/licenses/by/3.0/
    name: Mammalian Feeding Muscle Ontology
    preferredPrefix: MFMO
    prefix: mfmo
    repository: https://github.com/RDruzinsky/feedontology
  ols:
    description: The Mammalian Feeding Muscle Ontology is an antomy ontology for the
      muscles of the head and neck that participate in feeding, swallowing, and other
      oral-pharyngeal behaviors.
    download_owl: http://purl.obolibrary.org/obo/mfmo.owl
    homepage: https://github.com/rdruzinsky/feedontology
    name: Mammalian Feeding Muscle Ontology
    prefix: mfmo
    tracker: https://github.com/RDruzinsky/feedontology/issues
    version: '2013-11-16'
    version.iri: http://purl.obolibrary.org/obo/mfmo/2013-11-16/mfmo.owl
  ontobee:
    library: Library
    name: Mammalian Feeding Muscle Ontology
    prefix: MFMO
  pattern: ^\d{7}$
  prefix: mfmo
  providers:
  - code: conflated
    description: A conflated URL with parts.
    example: null
    first_party: null
    homepage: http://purl.obolibrary.org
    name: OBO PURL Parts
    publications: null
    status: null
    uri_format: http://purl.obolibrary.org/obo/mfmo.owl#MFMO_$1
  uri_format: http://purl.obolibrary.org/obo/MFMO_$1
mfo:
  aberowl:
    description: A structured controlled vocabulary of the anatomy and development
      of the Japanese medaka fish, <i>Oryzias latipes</i>.
    download_obo: http://aber-owl.net/media/ontologies/MFO/14/mfo.obo
    name: Medaka Fish Anatomy and Development Ontology
    prefix: MFO
    version: unknown
  biocontext:
    prefix: MFO
  bioportal:
    contact:
      email: Thorsten.Henrich@embl-heidelberg.de
      name: Medaka_ontology Administrators
    description: A structured controlled vocabulary of the anatomy and development
      of the Japanese medaka fish, <i>Oryzias latipes</i>.
    name: Medaka Fish Anatomy and Development Ontology
    prefix: MFO
  example: '0000001'
  mappings:
    aberowl: MFO
    biocontext: MFO
    bioportal: MFO
    obofoundry: mfo
    prefixcommons: mfo
    wikidata.entity: Q114677896
  obofoundry:
    contact: henrich@embl.de
    contact.github: ThorstenHen
    contact.label: Thorsten Henrich
    contact.orcid: 0000-0002-1548-3290
    deprecated: true
    description: A structured controlled vocabulary of the anatomy and development
      of the Japanese medaka fish, <i>Oryzias latipes</i>.
    domain: anatomy and development
    download.owl: http://purl.obolibrary.org/obo/mfo.owl
    name: Medaka fish anatomy and development
    prefix: mfo
  pattern: ^\d{7}$
  prefix: mfo
  prefixcommons:
    bioportal: '1027'
    description: A structured controlled vocabulary of the anatomy and development
      of the Japanese medaka fish, <i>Oryzias latipes</i>.
    example: MFO_0000001
    homepage: http://ani.embl.de:8080/mepd/
    keywords:
    - obo
    - anatomy
    - development
    - fish
    name: Medaka fish anatomy and development
    pattern: ^MFO_\d+$
    prefix: mfo
mfoem:
  aberowl:
    description: An ontology of affective phenomena such as emotions, moods, appraisals
      and subjective feelings.
    download_owl: http://aber-owl.net/media/ontologies/MFOEM/44/mfoem.owl
    homepage: https://github.com/jannahastings/emotion-ontology
    name: Emotion Ontology
    prefix: MFOEM
  biocontext:
    prefix: MFOEM
  bioportal:
    contact:
      email: janna.hastings@gmail.com
      name: Janna Hastings
    description: An ontology of affective phenomena such as emotions, moods, appraisals
      and subjective feelings, designed to support interdisciplinary research by providing
      unified annotations. The ontology is a domain specialisation of the broader
      Mental Functioning Ontology.
    homepage: https://github.com/jannahastings/emotion-ontology
    name: Emotion Ontology
    prefix: MFOEM
    publications:
    - https://github.com/jannahastings/emotion-ontology
    version: '2025-07-31'
  example: '000204'
  fairsharing:
    abbreviation: MFOEM
    contact:
      email: janna.hastings@uzh.ch
      name: Janna Hastings
      orcid: 0000-0002-3469-4923
    description: An ontology of affective phenomena such as emotions, moods, appraisals
      and subjective feelings, designed to support interdisciplinary research by providing
      unified annotations. The ontology is a domain specialisation of the broader
      Mental Functioning Ontology.
    domains:
    - emotion process
    - mental health
    homepage: https://github.com/jannahastings/emotion-ontology
    license: CC-BY-3.0
    name: Emotion Ontology
    prefix: FAIRsharing.dx30m8
    publications:
    - doi: 10.1186/2041-1480-5-38
      pubmed: '25937879'
      title: Evaluating the Emotion Ontology through use in the self-reporting of
        emotional responses at an academic conference
      year: 2014
    repository: https://github.com/jannahastings/emotion-ontology
    subjects:
    - Biomedical Science
  mappings:
    aberowl: MFOEM
    biocontext: MFOEM
    bioportal: MFOEM
    fairsharing: FAIRsharing.dx30m8
    obofoundry: mfoem
    ols: mfoem
    ontobee: MFOEM
    wikidata.entity: Q55118370
  obofoundry:
    contact: janna.hastings@gmail.com
    contact.github: jannahastings
    contact.label: Janna Hastings
    contact.orcid: 0000-0002-3469-4923
    deprecated: false
    description: An ontology of affective phenomena such as emotions, moods, appraisals
      and subjective feelings.
    domain: health
    download.owl: http://purl.obolibrary.org/obo/mfoem.owl
    homepage: https://github.com/jannahastings/emotion-ontology
    license: CC BY 3.0
    license.url: http://creativecommons.org/licenses/by/3.0/
    name: Emotion Ontology
    preferredPrefix: MFOEM
    prefix: mfoem
    repository: https://github.com/jannahastings/emotion-ontology
  ols:
    description: An ontology of affective phenomena such as emotions, moods, appraisals
      and subjective feelings.
    download_owl: http://purl.obolibrary.org/obo/mfoem.owl
    homepage: https://github.com/jannahastings/emotion-ontology
    name: Emotion Ontology
    prefix: mfoem
    tracker: https://github.com/jannahastings/emotion-ontology/issues
    version: '2025-07-31'
    version.iri: http://purl.obolibrary.org/obo/MFOEM/2025-07-31/MFOEM.owl
  ontobee:
    library: Library
    name: Emotion Ontology
    prefix: MFOEM
  pattern: ^\d{6}$
  prefix: mfoem
  publications:
  - doi: 10.1186/2041-1480-5-38
    pmc: PMC4417517
    pubmed: '25937879'
    title: Evaluating the Emotion Ontology through use in the self-reporting of emotional
      responses at an academic conference
    year: 2014
  uri_format: http://purl.obolibrary.org/obo/MFOEM_$1
mfomd:
  aberowl:
    description: An ontology to describe and classify mental diseases such as schizophrenia,
      annotated with DSM-IV and ICD codes where applicable
    download_owl: http://aber-owl.net/media/ontologies/MFOMD/3/mfomd.owl
    homepage: https://github.com/jannahastings/mental-functioning-ontology
    name: Mental Disease Ontology
    prefix: MFOMD
  biocontext:
    prefix: MFOMD
  bioportal:
    contact:
      email: janna.hastings@gmail.com
      name: Janna Hastings
    description: An ontology to describe and classify mental diseases such as schizophrenia,
      annotated with DSM-IV and ICD codes where applicable.
    homepage: https://github.com/jannahastings/mental-functioning-ontology
    name: MFO Mental Disease Ontology
    prefix: MFOMD
    version: '2020-04-26'
  example: '0000046'
  fairsharing:
    abbreviation: MFOMD
    description: 'The Mental Functioning Ontology (MF) is an ontology for mental functioning,
      including mental processes such as cognition and traits such as intelligence.
      There is a module (MFO-MD) which covers mental disorders, within which the IDs
      are reused from the Disease Ontology as far as is possible. It is developed
      in the context of the Ontology for General Medical Science (OGMS) and the Basic
      Formal Ontology (BFO). '
    domains:
    - disease
    homepage: https://github.com/jannahastings/mental-functioning-ontology
    name: MFO Mental Disease Ontology
    prefix: FAIRsharing.q053vb
    subjects:
    - Psychiatry
  mappings:
    aberowl: MFOMD
    biocontext: MFOMD
    bioportal: MFOMD
    fairsharing: FAIRsharing.q053vb
    obofoundry: mfomd
    ols: mfomd
    ontobee: MFOMD
    wikidata.entity: Q55118439
  obofoundry:
    contact: janna.hastings@gmail.com
    contact.github: jannahastings
    contact.label: Janna Hastings
    contact.orcid: 0000-0002-3469-4923
    deprecated: false
    description: An ontology to describe and classify mental diseases such as schizophrenia,
      annotated with DSM-IV and ICD codes where applicable
    domain: health
    download.owl: http://purl.obolibrary.org/obo/mfomd.owl
    homepage: https://github.com/jannahastings/mental-functioning-ontology
    license: CC BY 3.0
    license.url: http://creativecommons.org/licenses/by/3.0/
    name: Mental Disease Ontology
    preferredPrefix: MFOMD
    prefix: mfomd
    repository: https://github.com/jannahastings/mental-functioning-ontology
  ols:
    description: The Mental Disease Ontology is developed to facilitate representation
      for all aspects of mental disease. It is an extension of the Ontology for General
      Medical Science (OGMS) and Mental Functioning Ontology (MF).
    download_owl: http://purl.obolibrary.org/obo/mfomd.owl
    homepage: https://github.com/jannahastings/mental-functioning-ontology
    name: Mental Disease Ontology
    prefix: mfomd
    tracker: https://github.com/jannahastings/mental-functioning-ontology/issues
    version: '2020-04-26'
    version.iri: http://purl.obolibrary.org/obo/MFOMD/2020-04-26/MFOMD.owl
  ontobee:
    library: Library
    name: Mental Disease Ontology
    prefix: MFOMD
  pattern: ^\d{7}$
  prefix: mfomd
  uri_format: http://purl.obolibrary.org/obo/MFOMD_$1
mge:
  banana: mge
  biocontext:
    prefix: ACLAME
  edam:
    description: An identifier of a mobile genetic element from the Aclame database.
    name: ACLAME
    obsolete: false
    prefix: '2631'
  fairsharing:
    abbreviation: ACLAME
    description: ACLAME is a database dedicated to the collection and classification
      of mobile genetic elements (MGEs) from various sources, comprising all known
      phage genomes, plasmids and transposons.
    homepage: http://aclame.ulb.ac.be/
    license: http://opendatacommons.org/licenses/pddl/1.0
    name: A CLAssification of Mobile genetic Elements
    prefix: FAIRsharing.5tfcy8
    publications:
    - doi: 10.1093/nar/gkh084
      pubmed_id: 14681355
      title: 'ACLAME: a CLAssification of Mobile genetic Elements.'
    - doi: 10.1093/nar/gkp938
      pubmed_id: 19933762
      title: 'ACLAME: a CLAssification of Mobile genetic Elements, update 2010.'
    subjects:
    - Life Science
  integbio:
    alt_name: A CLAssification of Mobile genetic Elements
    description: 'ACLAME Version 4 is a database of the mobile genetic elements (MGEs)
      as found in the genomes of all phages, plasmids and transposons known at present
      - 811 hosts in total.

      Information on 122,154 proteins, discovered to be present in 2,326 MGEs, is
      provided.

      The proteins were grouped in families as follows:

      The prophages contained 6,822 clusters, the plasmids 18,228 groups, the viruses
      and prophages 16,057 groups and the viruses 11,503 clusters.

      The database is in the process of developing a classification system of the
      functional modules of these MGEs at the protein level, gene level, and higher.

      Keyword and Blast search options are available.

      An option is also offered whereby host-specific groups of MGEs can be viewed.'
    fairsharing: biodbcore-000549
    homepage: http://aclame.ulb.ac.be/
    information_keywords:
    - Ontology/Terminology/Nomenclature
    maintainer: Universite Libre de Bruxelles
    name: ACLAME
    prefix: nbdc00355
    pubmeds:
    - '19933762'
    - '18238785'
    - '18234706'
    - '17614261'
    - '17482656'
    - '17064288'
    - '14681355'
    status: Inactive
    target_keywords:
    - Genome/Gene
    - DNA
    - Protein
  mappings:
    biocontext: ACLAME
    edam: '2631'
    fairsharing: FAIRsharing.5tfcy8
    integbio: nbdc00355
    miriam: mge
    n2t: mge
    prefixcommons: aclame
  miriam:
    deprecated: true
    description: ACLAME is a database dedicated to the collection and classification
      of mobile genetic elements (MGEs) from various sources, comprising all known
      phage genomes, plasmids and transposons.
    homepage: http://aclame.ulb.ac.be/
    id: '00000063'
    name: Aclame
    namespaceEmbeddedInLui: true
    pattern: ^mge:\d+$
    prefix: mge
    sampleId: '2'
    uri_format: http://aclame.ulb.ac.be/perl/Aclame/Genomes/mge_view.cgi?view=info&id=mge:$1
  n2t:
    description: ACLAME is a database dedicated to the collection and classification
      of mobile genetic elements (MGEs) from various sources, comprising all known
      phage genomes, plasmids and transposons.
    example: '2'
    homepage: http://aclame.ulb.ac.be/
    name: Aclame database of mobile genetic elements
    namespaceEmbeddedInLui: true
    pattern: ^mge:\d+$
    prefix: mge
    uri_format: http://aclame.ulb.ac.be/perl/Aclame/Genomes/mge_view.cgi?view=info&id=mge:$1
  pattern: ^\d+$
  prefix: mge
  prefixcommons:
    description: ACLAME is a database dedicated to the collection and classification
      of mobile genetic elements (MGEs) from various sources, comprising all known
      phage genomes, plasmids and transposons.
    example: mge:2
    homepage: http://aclame.ulb.ac.be
    keywords:
    - genome
    - gene
    miriam: mge
    name: A CLAssification of Mobile genetic Elements
    pattern: ^mge:\d+$
    prefix: aclame
    pubmed_ids:
    - '14681355'
    uri_format: http://aclame.ulb.ac.be/perl/Aclame/Genomes/mge_view.cgi?view=info&id=$1
  publications:
  - doi: 10.1093/nar/gkp938
    pmc: PMC2808911
    pubmed: '19933762'
    title: 'ACLAME: a CLAssification of Mobile genetic Elements, update 2010'
    year: 2009
  - doi: 10.1093/nar/gkh084
    pmc: PMC308818
    pubmed: '14681355'
    title: 'ACLAME: a CLAssification of Mobile genetic Elements'
    year: 2004
  - doi: 10.1093/nar/gkh084
    pmc: null
    pubmed: null
    title: 'ACLAME: a CLAssification of Mobile genetic Elements.'
    year: null
  - doi: 10.1093/nar/gkp938
    pmc: null
    pubmed: null
    title: 'ACLAME: a CLAssification of Mobile genetic Elements, update 2010.'
    year: null
  - doi: null
    pmc: null
    pubmed: '14681355'
    title: null
    year: null
  - doi: 10.1093/nar/gkh084
    pmc: null
    pubmed: null
    title: 'ACLAME: a CLAssification of Mobile genetic Elements.'
    year: null
  - doi: 10.1093/nar/gkp938
    pmc: null
    pubmed: null
    title: 'ACLAME: a CLAssification of Mobile genetic Elements, update 2010.'
    year: null
  - doi: null
    pmc: null
    pubmed: '14681355'
    title: null
    year: null
  synonyms:
  - aclame
mgi:
  banana: MGI
  biocontext:
    prefix: MGI
    uri_format: http://www.informatics.jax.org/accession/MGI:$1
  cellosaurus:
    category: Organism-specific databases
    homepage: http://www.informatics.jax.org
    name: Mouse Genome Database (MGD) from Mouse Genome Informatics
    prefix: MGI
    uri_format: http://www.informatics.jax.org/marker/$1
  contact:
    email: joel.richardson@jax.org
    github: JoelRichardson
    name: Joel Richardson
    orcid: 0000-0003-3342-5753
  domain: gene
  edam:
    description: Identifier of an object from the MGI database.
    name: MGI
    obsolete: false
    prefix: '3274'
  example: '6017782'
  fairsharing:
    abbreviation: MGI
    description: MGI is the international database resource for the laboratory mouse,
      providing integrated genetic, genomic, and biological data to facilitate the
      study of human health and disease. Data includes gene characterization, nomenclature,
      mapping, gene homologies among mammals, sequence links, phenotypes, allelic
      variants and mutants, and strain data.
    homepage: http://www.informatics.jax.org/
    license: http://opendatacommons.org/licenses/pddl/1.0
    name: Mouse Genome Database - a Mouse Genome Informatics (MGI) Resource
    prefix: FAIRsharing.fcwyhz
    publications:
    - doi: 10.1093/nar/gkt1225
      pubmed_id: 24285300
      title: 'The Mouse Genome Database: integration of and access to knowledge about
        the laboratory mouse.'
    - doi: 10.1093/nar/gks1115
      pubmed_id: 23175610
      title: 'The Mouse Genome Database: Genotypes, Phenotypes, and Models of Human
        Disease'
    - doi: 10.1007/978-1-4939-6427-7_3
      pubmed_id: 27933520
      title: 'Mouse Genome Informatics (MGI): Resources for Mining Mouse Genetic,
        Genomic, and Biological Data in Support of Primary and Translational Research.'
    - doi: 10.1093/ilar/ilx013
      pubmed_id: 28838066
      title: 'Mouse Genome Informatics (MGI) Resource: Genetic, Genomic, and Biological
        Knowledgebase for the Laboratory Mouse.'
    - doi: 10.1093/nar/gkr974
      pubmed_id: 22075990
      title: 'The Mouse Genome Database (MGD): comprehensive resource for genetics
        and genomics of the laboratory mouse'
    - doi: 10.1093/nar/gkw1040
      pubmed_id: 27899570
      title: 'Mouse Genome Database (MGD)-2017: community knowledge resource for the
        laboratory mouse.'
    - doi: 10.1126/science.8091224
      pubmed_id: 8091224
      title: A database for mouse development.
    - doi: 10.1093/nar/gki113
      pubmed_id: 15608240
      title: 'The Mouse Genome Database (MGD): from genes to mice--a community resource
        for mouse biology.'
    - doi: 10.1093/nar/gky922
      pubmed_id: 30335138
      title: 'The mouse Gene Expression Database (GXD): 2019 update.'
    - doi: 10.1093/nar/gky1056
      pubmed_id: 30407599
      title: Mouse Genome Database (MGD) 2019.
    subjects:
    - Life Science
    - Ontology and Terminology
    twitter: mgi_mouse
  go:
    homepage: http://www.informatics.jax.org/
    name: Mouse Genome Informatics
    prefix: MGI
  integbio:
    alt_name: Medaka Genome Initiative
    description: MGI is a website of Medaka genome studies. The site has links to
      various projects, some of which are published papers and some of which can be
      searched and browsed further to obtain sequence and genome mapping information.
    homepage: http://park.itc.u-tokyo.ac.jp/K-medaka/MGI2/MGI.html
    maintainer: The University of Tokyo Graduate School of Frontier Sciences
    name: MGI
    prefix: nbdc00568
    pubmeds:
    - '15602912'
    status: Active
    target_keywords:
    - Genome/Gene
  license: CC-BY-4.0
  logo: https://www.informatics.jax.org/webshare/images/mgi_logo.gif
  mappings:
    biocontext: MGI
    cellosaurus: MGI
    edam: '3274'
    fairsharing: FAIRsharing.fcwyhz
    go: MGI
    integbio: nbdc00568
    miriam: mgi
    n2t: mgi
    ncbi: MGI
    prefixcommons: mgi
    re3data: r3d100010266
    rrid: MGI
    uniprot: DB-0060
    wikidata: P671
  miriam:
    deprecated: false
    description: The Mouse Genome Database (MGD) project includes data on gene characterization,
      nomenclature, mapping, gene homologies among mammals, sequence links, phenotypes,
      allelic variants and mutants, and strain data.
    homepage: http://www.informatics.jax.org/
    id: '00000037'
    name: Mouse Genome Database
    namespaceEmbeddedInLui: true
    pattern: ^MGI:\d+$
    prefix: mgi
    providers:
    - code: agr
      description: MGI through the Alliance of Genome Resources
      homepage: https://www.alliancegenome.org
      name: MGI through the Alliance of Genome Resources
      uri_format: https://www.alliancegenome.org/gene/MGI:$1
    sampleId: '2442292'
    uri_format: http://www.informatics.jax.org/accession/MGI:$1
  n2t:
    description: The Mouse Genome Database (MGD) project includes data on gene characterization,
      nomenclature, mapping, gene homologies among mammals, sequence links, phenotypes,
      allelic variants and mutants, and strain data.
    example: '2442292'
    homepage: http://www.informatics.jax.org/
    name: Mouse Genome Informatics Database
    namespaceEmbeddedInLui: true
    pattern: ^MGI:\d+$
    prefix: mgi
    uri_format: http://www.informatics.jax.org/accession/MGI:$1
  name: Mouse Genome Informatics
  ncbi:
    example: MGI:1894891
    homepage: http://www.informatics.jax.org/
    name: Mouse Genome Informatics
    prefix: MGI
  pattern: ^\d+$
  preferred_prefix: MGI
  prefix: mgi
  prefixcommons:
    description: The Mouse Genome Database (MGD) project includes data on gene characterization,
      nomenclature, mapping, gene homologies among mammals, sequence links, phenotypes,
      allelic variants and mutants, and strain data.
    example: '95484'
    homepage: http://www.informatics.jax.org/
    keywords:
    - expression
    - phenotype
    - sequence
    name: Mouse genome database (MGD) from Mouse Genome Informatics (MGI)
    pattern: ^\d+$
    prefix: mgi
    pubmed_ids:
    - '15608240'
    synonyms:
    - mgd
    uri_format: http://www.informatics.jax.org/searches/accession_report.cgi?id=mgi:$1
  providers:
  - code: mgi.marker
    description: MGI Marker
    example: null
    first_party: null
    homepage: http://www.informatics.jax.org/marker
    name: MGI Marker
    publications: null
    status: null
    uri_format: http://www.informatics.jax.org/marker/MGI:$1
  publications:
  - doi: 10.1093/nar/gky1056
    pmc: PMC6323923
    pubmed: '30407599'
    title: Mouse Genome Database (MGD) 2019
    year: 2019
  - doi: 10.1093/nar/gky922
    pmc: PMC6324054
    pubmed: '30335138'
    title: 'The mouse Gene Expression Database (GXD): 2019 update'
    year: 2019
  - doi: 10.1093/ilar/ilx013
    pmc: PMC5886341
    pubmed: '28838066'
    title: 'Mouse Genome Informatics (MGI) Resource: Genetic, Genomic, and Biological
      Knowledgebase for the Laboratory Mouse'
    year: 2017
  - doi: 10.1007/978-1-4939-6427-7_3
    pmc: null
    pubmed: '27933520'
    title: 'Mouse Genome Informatics (MGI): Resources for Mining Mouse Genetic, Genomic,
      and Biological Data in Support of Primary and Translational Research'
    year: 2017
  - doi: 10.1093/nar/gkw1040
    pmc: PMC5210536
    pubmed: '27899570'
    title: 'Mouse Genome Database (MGD)-2017: community knowledge resource for the
      laboratory mouse'
    year: 2016
  - doi: 10.1093/nar/gkt1225
    pmc: PMC3964950
    pubmed: '24285300'
    title: 'The Mouse Genome Database: integration of and access to knowledge about
      the laboratory mouse'
    year: 2013
  - doi: 10.1093/nar/gks1115
    pmc: PMC3531104
    pubmed: '23175610'
    title: 'The mouse genome database: genotypes, phenotypes, and models of human
      disease'
    year: 2012
  - doi: 10.1093/nar/gkr974
    pmc: PMC3245042
    pubmed: '22075990'
    title: 'The Mouse Genome Database (MGD): comprehensive resource for genetics and
      genomics of the laboratory mouse'
    year: 2011
  - doi: 10.1093/nar/gki113
    pmc: PMC540067
    pubmed: '15608240'
    title: 'The Mouse Genome Database (MGD): from genes to mice--a community resource
      for mouse biology'
    year: 2005
  - doi: 10.1126/science.8091224
    pmc: null
    pubmed: '8091224'
    title: A database for mouse development
    year: 1994
  - doi: 10.1093/nar/gkt1225
    pmc: null
    pubmed: null
    title: 'The Mouse Genome Database: integration of and access to knowledge about
      the laboratory mouse.'
    year: null
  - doi: 10.1093/nar/gks1115
    pmc: null
    pubmed: null
    title: 'The Mouse Genome Database: Genotypes, Phenotypes, and Models of Human
      Disease'
    year: null
  - doi: 10.1007/978-1-4939-6427-7_3
    pmc: null
    pubmed: null
    title: 'Mouse Genome Informatics (MGI): Resources for Mining Mouse Genetic, Genomic,
      and Biological Data in Support of Primary and Translational Research.'
    year: null
  - doi: 10.1093/ilar/ilx013
    pmc: null
    pubmed: null
    title: 'Mouse Genome Informatics (MGI) Resource: Genetic, Genomic, and Biological
      Knowledgebase for the Laboratory Mouse.'
    year: null
  - doi: 10.1093/nar/gkr974
    pmc: null
    pubmed: null
    title: 'The Mouse Genome Database (MGD): comprehensive resource for genetics and
      genomics of the laboratory mouse'
    year: null
  - doi: 10.1093/nar/gkw1040
    pmc: null
    pubmed: null
    title: 'Mouse Genome Database (MGD)-2017: community knowledge resource for the
      laboratory mouse.'
    year: null
  - doi: 10.1126/science.8091224
    pmc: null
    pubmed: null
    title: A database for mouse development.
    year: null
  - doi: 10.1093/nar/gki113
    pmc: null
    pubmed: null
    title: 'The Mouse Genome Database (MGD): from genes to mice--a community resource
      for mouse biology.'
    year: null
  - doi: 10.1093/nar/gky922
    pmc: null
    pubmed: null
    title: 'The mouse Gene Expression Database (GXD): 2019 update.'
    year: null
  - doi: 10.1093/nar/gky1056
    pmc: null
    pubmed: null
    title: Mouse Genome Database (MGD) 2019.
    year: null
  - doi: null
    pmc: null
    pubmed: '15608240'
    title: null
    year: null
  - doi: null
    pmc: null
    pubmed: '19274630'
    title: null
    year: null
  - doi: null
    pmc: null
    pubmed: '18428715'
    title: null
    year: null
  - doi: 10.1093/genetics/iyae031
    pmc: null
    pubmed: '38531069'
    title: null
    year: null
  - doi: 10.1093/nar/gkt1225
    pmc: null
    pubmed: null
    title: 'The Mouse Genome Database: integration of and access to knowledge about
      the laboratory mouse.'
    year: null
  - doi: 10.1093/nar/gks1115
    pmc: null
    pubmed: null
    title: 'The Mouse Genome Database: Genotypes, Phenotypes, and Models of Human
      Disease'
    year: null
  - doi: 10.1007/978-1-4939-6427-7_3
    pmc: null
    pubmed: null
    title: 'Mouse Genome Informatics (MGI): Resources for Mining Mouse Genetic, Genomic,
      and Biological Data in Support of Primary and Translational Research.'
    year: null
  - doi: 10.1093/ilar/ilx013
    pmc: null
    pubmed: null
    title: 'Mouse Genome Informatics (MGI) Resource: Genetic, Genomic, and Biological
      Knowledgebase for the Laboratory Mouse.'
    year: null
  - doi: 10.1093/nar/gkr974
    pmc: null
    pubmed: null
    title: 'The Mouse Genome Database (MGD): comprehensive resource for genetics and
      genomics of the laboratory mouse'
    year: null
  - doi: 10.1093/nar/gkw1040
    pmc: null
    pubmed: null
    title: 'Mouse Genome Database (MGD)-2017: community knowledge resource for the
      laboratory mouse.'
    year: null
  - doi: 10.1126/science.8091224
    pmc: null
    pubmed: null
    title: A database for mouse development.
    year: null
  - doi: 10.1093/nar/gki113
    pmc: null
    pubmed: null
    title: 'The Mouse Genome Database (MGD): from genes to mice--a community resource
      for mouse biology.'
    year: null
  - doi: 10.1093/nar/gky922
    pmc: null
    pubmed: null
    title: 'The mouse Gene Expression Database (GXD): 2019 update.'
    year: null
  - doi: 10.1093/nar/gky1056
    pmc: null
    pubmed: null
    title: Mouse Genome Database (MGD) 2019.
    year: null
  - doi: null
    pmc: null
    pubmed: '15608240'
    title: null
    year: null
  - doi: null
    pmc: null
    pubmed: '19274630'
    title: null
    year: null
  - doi: null
    pmc: null
    pubmed: '18428715'
    title: null
    year: null
  - doi: 10.1093/genetics/iyae031
    pmc: null
    pubmed: '38531069'
    title: null
    year: null
  re3data:
    description: 'MGI is the international database resource for the laboratory mouse,
      providing integrated genetic, genomic, and biological data to facilitate the
      study of human health and disease. The projects contributing to this resource
      are: Mouse Genome Database (MGD) Project, Gene Expression Database (GXD) Project,
      Mouse Tumor Biology (MTB) Database Project, Gene Ontology (GO) Project at MGI,
      MouseMine Project, MouseCyc Project at MGI'
    doi: 10.17616/R35P54
    homepage: https://www.informatics.jax.org/
    license: Copyrights
    name: Mouse Genome Informatics
    prefix: r3d100010266
    synonyms:
    - MGI
    xrefs:
      nif: 0000-00096
      omics: '01656'
  rrid:
    homepage: http://www.informatics.jax.org
    keywords:
    - animal model
    - blast
    - data analysis service
    - function
    - gene
    - gene expression
    - genetics
    - genome
    - genotype
    - gold standard
    - human disease
    - human health
    - image
    - model
    - molecular neuroanatomy resource
    - orthology
    - pathology
    - pathway
    - phenotype
    - recombinase
    - single nucleotide polymorphism
    - strain
    - tumor
    name: Mouse Genome Informatics (MGI)
    prefix: MGI
    pubmeds:
    - '19274630'
    - '18428715'
    scr: '006460'
  synonyms:
  - MGD
  - MGI
  uniprot:
    abbreviation: MGI
    category: Organism-specific databases
    homepage: https://www.informatics.jax.org/
    name: Mouse genome database (MGD) from Mouse Genome Informatics (MGI)
    prefix: DB-0060
    publications:
    - doi: 10.1093/genetics/iyae031
      pubmed: '38531069'
    uri_format: https://www.informatics.jax.org/marker/$1
  wikidata:
    database: Q1951035
    description: identifier for a gene in the Mouse Genome Informatics database
    example:
    - MGI:2148705
    - MGI:95674
    - MGI:96922
    homepage: http://www.informatics.jax.org/
    name: Mouse Genome Informatics ID
    pattern: ^MGI:\d{1,7}$
    prefix: P671
    uri_format: http://www.informatics.jax.org/accession/$1
mgnify.analysis:
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: Analyses of microbiome data within MGnify
  example: MGYA00002270
  homepage: https://www.ebi.ac.uk/metagenomics/
  mappings:
    miriam: mgnify.analysis
  miriam:
    deprecated: false
    description: 'The free-to-use MGnify platform provides assembly, analysis and
      archiving of microbiome-derived nucleic acid sequence data from a wide range
      of biomes, with analysis results providing taxonomic and functional

      profiles. The platform also includes MGnify Proteins, a database of protein
      sequences derived from the analysis of metagenomic assemblies, and MGnify Genomes,
      a resource of biome-specific catalogues of microbial genomes, including extensive
      functional annotations.'
    homepage: https://www.ebi.ac.uk/metagenomics
    id: 00001094
    name: MGnify Analysis
    namespaceEmbeddedInLui: false
    pattern: ^MGYA\d{8}$
    prefix: mgnify.analysis
    sampleId: MGYA00791518
    uri_format: https://www.ebi.ac.uk/metagenomics/analyses/$1
  name: MGnify Analysis
  pattern: ^MGYA\d+$
  prefix: mgnify.analysis
  uri_format: https://www.ebi.ac.uk/metagenomics/analyses/$1
mgnify.proj:
  mappings:
    miriam: mgnify.proj
    n2t: mgnify.proj
  miriam:
    deprecated: false
    description: MGnify is a resource for the analysis and archiving of microbiome
      data to help determine the taxonomic diversity and functional & metabolic potential
      of environmental samples. Users can submit their own data for analysis or freely
      browse all of the analysed public datasets held within the repository. In addition,
      users can request analysis of any appropriate dataset within the European Nucleotide
      Archive (ENA). User-submitted or ENA-derived datasets can also be assembled
      on request, prior to analysis.
    homepage: https://www.ebi.ac.uk/metagenomics
    id: '00000535'
    name: MGnify Project
    namespaceEmbeddedInLui: false
    pattern: ^[A-Z]+[0-9]+$
    prefix: mgnify.proj
    sampleId: ERP004492
    uri_format: https://www.ebi.ac.uk/metagenomics/projects/$1
  n2t:
    description: MGnify is a resource for the analysis and archiving of microbiome
      data to help determine the taxonomic diversity and functional & metabolic potential
      of environmental samples. Users can submit their own data for analysis or freely
      browse all of the analysed public datasets held within the repository. In addition,
      users can request analysis of any appropriate dataset within the European Nucleotide
      Archive (ENA). User-submitted or ENA-derived datasets can also be assembled
      on request, prior to analysis.
    example: ERP004492
    homepage: https://www.ebi.ac.uk/metagenomics
    name: MGnify Project
    namespaceEmbeddedInLui: false
    pattern: ^[A-Z]+[0-9]+$
    prefix: mgnify.proj
    uri_format: https://www.ebi.ac.uk/metagenomics/projects/$1
  prefix: mgnify.proj
mgnify.samp:
  mappings:
    miriam: mgnify.samp
    n2t: mgnify.samp
  miriam:
    deprecated: false
    description: The EBI Metagenomics service is an automated pipeline for the analysis
      and archiving of metagenomic data that aims to provide insights into the phylogenetic
      diversity as well as the functional and metabolic potential of a sample. Metagenomics
      is the study of all genomes present in any given environment without the need
      for prior individual identification or amplification. This collection references
      samples.
    homepage: https://www.ebi.ac.uk/metagenomics
    id: '00000510'
    name: MGnify Sample
    namespaceEmbeddedInLui: false
    pattern: ^[A-Z]+[0-9]+$
    prefix: mgnify.samp
    sampleId: SRS086444
    uri_format: https://www.ebi.ac.uk/metagenomics/samples/$1
  n2t:
    description: The EBI Metagenomics service is an automated pipeline for the analysis
      and archiving of metagenomic data that aims to provide insights into the phylogenetic
      diversity as well as the functional and metabolic potential of a sample. Metagenomics
      is the study of all genomes present in any given environment without the need
      for prior individual identification or amplification. This collection references
      samples.
    example: SRS086444
    homepage: https://www.ebi.ac.uk/metagenomics
    name: MGnify Sample
    namespaceEmbeddedInLui: false
    pattern: ^[A-Z]+[0-9]+$
    prefix: mgnify.samp
    uri_format: https://www.ebi.ac.uk/metagenomics/samples/$1
  prefix: mgnify.samp
mgnifygenome:
  mappings:
    miriam: mgnify.genome
  miriam:
    deprecated: false
    description: 'The free-to-use MGnify platform provides assembly, analysis and
      archiving of microbiome-derived nucleic acid sequence data from a wide range
      of biomes, with analysis results providing taxonomic and functional

      profiles. The platform also includes MGnify Proteins, a database of protein
      sequences derived from the analysis of metagenomic assemblies, and MGnify Genomes,
      a resource of biome-specific catalogues of microbial genomes, including extensive
      functional annotations.'
    homepage: https://www.ebi.ac.uk/metagenomics
    id: 00001092
    name: MGnify Genome
    namespaceEmbeddedInLui: false
    pattern: ^MGYG\d{9}(\.\d+)?$
    prefix: mgnify.genome
    sampleId: MGYG000004903
    uri_format: https://www.ebi.ac.uk/metagenomics/genomes/$1
  prefix: mgnifygenome
mgnifyprotein:
  mappings:
    miriam: mgnify.protein
  miriam:
    deprecated: false
    description: 'The free-to-use MGnify platform provides assembly, analysis and
      archiving of microbiome-derived nucleic acid sequence data from a wide range
      of biomes, with analysis results providing taxonomic and functional

      profiles. The platform also includes MGnify Proteins, a database of protein
      sequences derived from the analysis of metagenomic assemblies, and MGnify Genomes,
      a resource of biome-specific catalogues of microbial genomes, including extensive
      functional annotations.'
    homepage: https://www.ebi.ac.uk/metagenomics
    id: 00001098
    name: MGnify Protein
    namespaceEmbeddedInLui: false
    pattern: ^MGYP\d{12}$
    prefix: mgnify.protein
    sampleId: MGYP000261684433
    uri_format: https://www.ebi.ac.uk/metagenomics/proteins/$1
  prefix: mgnifyprotein
mgnifystudy:
  mappings:
    miriam: mgnify.study
  miriam:
    deprecated: false
    description: 'The free-to-use MGnify platform provides assembly, analysis and
      archiving of microbiome-derived nucleic acid sequence data from a wide range
      of biomes, with analysis results providing taxonomic and functional

      profiles. The platform also includes MGnify Proteins, a database of protein
      sequences derived from the analysis of metagenomic assemblies, and MGnify Genomes,
      a resource of biome-specific catalogues of microbial genomes, including extensive
      functional annotations.'
    homepage: https://www.ebi.ac.uk/metagenomics
    id: 00001096
    name: MGnify Study
    namespaceEmbeddedInLui: false
    pattern: ^MGYS\d{8}$
    prefix: mgnify.study
    sampleId: MGYS00006794
    uri_format: https://www.ebi.ac.uk/metagenomics/studies/$1
  prefix: mgnifystudy
mi:
  aberowl:
    description: A structured controlled vocabulary for the annotation of experiments
      concerned with protein-protein interactions.
    download_owl: http://aber-owl.net/media/ontologies/MI/134/mi.owl
    homepage: https://github.com/HUPO-PSI/psi-mi-CV
    name: Molecular Interactions Controlled Vocabulary
    prefix: MI
  biocontext:
    prefix: PSIMI
  biolink:
    is_identifiers: false
    is_obo: true
    prefix: MI
    uri_format: http://purl.obolibrary.org/obo/MI_$1
  bioportal:
    contact:
      email: orchard@ebi.ac.uk
      name: Sandra Orchard
    description: A structured controlled vocabulary for the annotation of experiments
      concerned with protein-protein interactions. Developed by the HUPO Proteomics
      Standards Initiative.
    homepage: https://github.com/HUPO-PSI/psi-mi-CV
    name: Molecular Interactions
    prefix: MI
  example: 0058
  fairsharing:
    abbreviation: PSI-MI CV
    description: A structured controlled vocabulary for the annotation of experiments
      concerned with protein-protein interactions. Developed by the HUPO Proteomics
      Standards Initiative. The Molecular Interactions Working group page can be found
      at http://www.psidev.info/groups/molecular-interactions.
    domains:
    - Protein interactions
    - molecular interaction
    - protein
    homepage: http://www.psidev.info/groups/molecular-interactions
    license: CC-BY-4.0
    name: PSI Molecular Interaction Controlled Vocabulary
    prefix: FAIRsharing.8qzmtr
    repository: https://github.com/HUPO-PSI/psi-mi-CV
    subjects:
    - Life Science
  go:
    homepage: http://www.psidev.info/
    name: Proteomic Standard Initiative for Molecular Interaction
    prefix: PSI-MI
    synonyms:
    - MI
  mappings:
    aberowl: MI
    biocontext: PSIMI
    biolink: MI
    bioportal: MI
    fairsharing: FAIRsharing.8qzmtr
    go: PSI-MI
    miriam: mi
    n2t: psimi
    obofoundry: mi
    ols: mi
    ontobee: MI
    prefixcommons: psi.mi
    tib: mi
    wikidata.entity: Q81661689
  miriam:
    deprecated: false
    description: The Molecular Interactions (MI) ontology forms a structured controlled
      vocabulary for the annotation of experiments concerned with protein-protein
      interactions. MI is developed by the HUPO Proteomics Standards Initiative.
    homepage: https://www.ebi.ac.uk/ols4/ontologies/mi
    id: 00000109
    name: Molecular Interactions Ontology
    namespaceEmbeddedInLui: true
    pattern: ^MI:\d{4}$
    prefix: mi
    sampleId: 0308
    uri_format: https://www.ebi.ac.uk/ols4/ontologies/mi/terms?obo_id=MI:$1
  n2t:
    description: The Molecular Interactions (MI) ontology forms a structured controlled
      vocabulary for the annotation of experiments concerned with protein-protein
      interactions. MI is developed by the HUPO Proteomics Standards Initiative.
    example: 0308
    homepage: https://www.ebi.ac.uk/ols/ontologies/mi
    name: Molecular Interactions Ontology through OLS
    namespaceEmbeddedInLui: true
    pattern: ^MI:\d{4}$
    prefix: psimi
    uri_format: https://www.ebi.ac.uk/ols/ontologies/mi/terms?obo_id=MI:$1
  obofoundry:
    contact: luana.licata@gmail.com
    contact.github: luanalicata
    contact.label: Luana Licata
    contact.orcid: 0000-0001-5084-9000
    deprecated: false
    description: A structured controlled vocabulary for the annotation of experiments
      concerned with protein-protein interactions.
    domain: investigations
    download.obo: http://purl.obolibrary.org/obo/mi.obo
    download.owl: http://purl.obolibrary.org/obo/mi.owl
    homepage: https://github.com/HUPO-PSI/psi-mi-CV
    license: CC BY 4.0
    license.url: https://creativecommons.org/licenses/by/4.0/
    name: Molecular Interactions Controlled Vocabulary
    preferredPrefix: MI
    prefix: mi
    repository: https://github.com/HUPO-PSI/psi-mi-CV
  ols:
    description: A structured controlled vocabulary for the annotation of experiments
      concerned with protein-protein interactions.
    download_owl: http://purl.obolibrary.org/obo/mi.owl
    homepage: https://github.com/HUPO-PSI/psi-mi-CV
    name: Molecular Interactions Controlled Vocabulary
    prefix: mi
    tracker: https://github.com/HUPO-PSI/psi-mi-CV/issues
  ontobee:
    library: Library
    name: Molecular Interactions Controlled Vocabulary
    prefix: MI
  pattern: ^\d{4}$
  prefix: mi
  prefixcommons:
    alt_uri_formats:
    - http://purl.org/obo/owl/PSI-MI#$1
    bioportal: '1040'
    description: The Molecular Interactions (MI) ontology forms a structured controlled
      vocabulary for the annotation of experiments concerned with protein-protein
      interactions. MI is developed by the HUPO Proteomics Standards Initiative.
    example: MI:0308
    homepage: http://psidev.sf.net
    keywords:
    - obo
    - interaction
    - molecule
    name: Proteomic Standard Initiative for Molecular Interaction
    pattern: ^MI:\d{4}$
    prefix: psi.mi
    pubmed_ids:
    - '14755292'
    synonyms:
    - mi
    - obo.mi
  publications:
  - doi: 10.1038/nbt926
    pmc: null
    pubmed: '14755292'
    title: The HUPO PSI's molecular interaction format--a community standard for the
      representation of protein interaction data
    year: 2004
  - doi: null
    pmc: null
    pubmed: '14755292'
    title: null
    year: null
  - doi: null
    pmc: null
    pubmed: '14755292'
    title: null
    year: null
  - doi: null
    pmc: null
    pubmed: '14755292'
    title: null
    year: null
  synonyms:
  - PSI-MI
  tib:
    description: A structured controlled vocabulary for the annotation of experiments
      concerned with protein-protein interactions. Developed by the HUPO Proteomics
      Standards Initiative.
    download_owl: http://purl.obolibrary.org/obo/mi.owl
    homepage: https://github.com/HUPO-PSI/psi-mi-CV
    keywords:
    - TIB
    - life sciences, biology
    name: Molecular Interactions
    prefix: mi
    tracker: https://github.com/HUPO-PSI/psi-mi-CV/issues
  uri_format: http://purl.obolibrary.org/obo/MI_$1
miaa:
  comment: same as MAT
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  deprecated: true
  name: Minimal Information About Anatomy ontology
  prefix: miaa
  references:
  - https://bioconductor.statistik.tu-dortmund.de/packages/3.1/bioc/vignettes/rols/inst/doc/rols.pdf
miapa:
  aberowl:
    description: An application ontology to formalize annotation of phylogenetic data.
    download_owl: http://aber-owl.net/media/ontologies/MIAPA/2/miapa.owl
    homepage: http://www.evoio.org/wiki/MIAPA
    name: MIAPA Ontology
    prefix: MIAPA
  biocontext:
    prefix: MIAPA
  bioportal:
    contact:
      email: hlapp@drycafe.net
      name: Hilmar Lapp
    description: An application ontology to formalize annotation of phylogenetic data
      according to the emerging Minimum Information About a Phylogenetic Analysis
      (MIAPA) metadata reporting standard.
    homepage: http://www.evoio.org/wiki/MIAPA
    name: MIAPA Ontology
    prefix: MIAPA
  example: '0000010'
  fairsharing:
    abbreviation: MIAPA
    description: The MIAPA (minimum information about a phylogenetic analysis) checklist
      details the list of metadata necessary for researchers to evaluate or reuse
      a published phylogeny.
    homepage: http://www.evoio.org/wiki/MIAPA
    name: Minimal Information About a Phylogenetic Analysis
    prefix: FAIRsharing.ca48xs
    publications:
    - doi: 10.1089/omi.2006.10.231
      pubmed_id: 16901231
      title: 'Taking the first steps towards a standard for reporting on phylogenies:
        Minimum Information About a Phylogenetic Analysis (MIAPA).'
    repository: https://github.com/miapa/miapa/blob/master/checklist/MIAPA-checklist.md
    subjects:
    - Phylogeny
    - Phylogenetics
    - Life Science
  mappings:
    aberowl: MIAPA
    biocontext: MIAPA
    bioportal: MIAPA
    fairsharing: FAIRsharing.ca48xs
    obofoundry: miapa
    ols: miapa
    ontobee: MIAPA
    wikidata.entity: Q81661690
  name: Minimum Anformation About a Phylogenetic Analysis Ontology
  obofoundry:
    contact: hilmar.lapp@duke.edu
    contact.github: hlapp
    contact.label: Hilmar Lapp
    contact.orcid: 0000-0001-9107-0714
    deprecated: false
    description: An application ontology to formalize annotation of phylogenetic data.
    domain: information
    download.owl: http://purl.obolibrary.org/obo/miapa.owl
    homepage: http://www.evoio.org/wiki/MIAPA
    license: CC0 1.0
    license.url: http://creativecommons.org/publicdomain/zero/1.0/
    name: MIAPA Ontology
    preferredPrefix: MIAPA
    prefix: miapa
    publications:
    - id: https://doi.org/10.1089/omi.2006.10.231
      title: 'Taking the First Steps towards a Standard for Reporting on Phylogenies:
        Minimum Information about a Phylogenetic Analysis (MIAPA)'
    repository: https://github.com/evoinfo/miapa
  ols:
    description: 'The MIAPA ontology is intended to be an application ontology for
      the purpose of semantic annotation of phylogenetic data according to the requirements
      and recommendations of the Minimum Information for A Phylogenetic Analysis (MIAPA)
      metadata reporting standard. The ontology leverages (imports) primarily from
      the CDAO (Comparative Data Analysis Ontology), PROV (W3C Provenance Ontology),
      and SWO (Software Ontology, which includes the EDAM ontologies) ontologies.
      It adds some assertions of its own, as well as some classes and individuals
      that may eventually get pushed down into one of the respective source ontologies.


      This ontology is maintained at http://github.com/miapa/miapa, and requests for
      changes or additions should be filed at the issue tracker there. The discussion
      list is at miapa-discuss@googlegroups.com. Further resources about MIAPA can
      be found at the project''s main page at http://evoio.org/wiki/MIAPA.'
    download_owl: http://purl.obolibrary.org/obo/miapa.owl
    homepage: http://www.evoio.org/wiki/MIAPA
    name: Minimum Information for A Phylogenetic Analysis (MIAPA) Ontology
    prefix: miapa
    tracker: https://github.com/evoinfo/miapa/issues
  ontobee:
    library: Library
    name: MIAPA Ontology
    prefix: MIAPA
  pattern: ^\d{7}$
  prefix: miapa
  publications:
  - doi: 10.1089/omi.2006.10.231
    pmc: PMC3167193
    pubmed: '16901231'
    title: 'Taking the first steps towards a standard for reporting on phylogenies:
      Minimum Information About a Phylogenetic Analysis (MIAPA)'
    year: 2006
  - doi: 10.1089/omi.2006.10.231
    pmc: null
    pubmed: null
    title: 'Taking the First Steps towards a Standard for Reporting on Phylogenies:
      Minimum Information about a Phylogenetic Analysis (MIAPA)'
    year: null
  - doi: 10.1089/omi.2006.10.231
    pmc: null
    pubmed: null
    title: 'Taking the first steps towards a standard for reporting on phylogenies:
      Minimum Information About a Phylogenetic Analysis (MIAPA).'
    year: null
  uri_format: http://purl.obolibrary.org/obo/MIAPA_$1
mibig:
  contact:
    email: kblin@biosustain.dtu.dk
    github: kblin
    name: Kai Blin
    orcid: 0000-0003-3764-6051
  contributor:
    email: zdoucmm@gmail.com
    github: mmzdouc
    name: Mitja M. Zdouc
    orcid: 0000-0001-6534-6609
  description: MIBiG (Minimum Information about a Biosynthetic Gene Cluster) is a
    data repository and associated data standard designed to describe biosynthetic
    gene clusters involved in the production of specialized metabolites. It also stores
    data on measured biological activities and links to other resources such as NCBI,
    NPAtlas, and ChEBI. MIBiG is used as a reference database, knowledgebase, and
    training dataset for machine learning.
  example: BGC0000001
  github_request_issue: 1407
  homepage: https://mibig.secondarymetabolites.org
  license: CC-BY-4.0
  name: Minimum Information about a Biosynthetic Gene Cluster data repository
  pattern: ^BGC\d{7}$
  prefix: mibig
  publications:
  - doi: 10.1093/nar/gkae1115
    pmc: PMC11701617
    pubmed: '39657789'
    title: 'MIBiG 4.0: advancing biosynthetic gene cluster curation through global
      collaboration'
    year: 2024
  repository: https://github.com/mibig-secmet/mibig-json
  reviewer:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  uri_format: https://mibig.secondarymetabolites.org/go/$1
micro:
  aberowl:
    description: An ontology of prokaryotic phenotypic and metabolic characters
    download_owl: http://aber-owl.net/media/ontologies/MICRO/3/micro.owl
    homepage: https://github.com/carrineblank/MicrO
    name: Ontology of Prokaryotic Phenotypic and Metabolic Characters
    prefix: MICRO
  biocontext:
    prefix: MICRO
  example: 0002999
  fairsharing:
    abbreviation: MicrO
    description: MicrO is an ontology of microbiological terms, including prokaryotic
      qualities and processes, material entities (such as cell components), chemical
      entities (such as microbiological culture media and medium ingredients), and
      assays. The ontology was built to support the ongoing development of a natural
      language processing algorithm, MicroPIE (or, Microbial Phenomics Information
      Extractor). FAIRsharing curators have been unable to contact the project developers,
      and as such this record has been marked as Uncertain. Please contact us if you
      have any information on this resource.
    domains:
    - assay
    - cell culture
    - phenotype
    homepage: https://github.com/carrineblank/MicrO
    license: CC BY 2.0
    name: Ontology of Prokaryotic Phenotypic and Metabolic Characters
    prefix: FAIRsharing.brhpb0
    publications:
    - doi: 10.1186/s13326-016-0060-6
      pubmed: '27076900'
      title: 'MicrO: an ontology of phenotypic and metabolic characters, assays, and
        culture media found in prokaryotic taxonomic descriptions'
      year: 2016
    repository: https://github.com/carrineblank/MicrO/issues
    subjects:
    - Microbiology
    - Bioinformatics
  mappings:
    aberowl: MICRO
    biocontext: MICRO
    fairsharing: FAIRsharing.brhpb0
    obofoundry: micro
    ols: micro
    ontobee: MICRO
    wikidata.entity: Q81661692
  obofoundry:
    appears_in:
    - mco
    contact: carrine.blank@umontana.edu
    contact.github: carrineblank
    contact.label: Carrine Blank
    contact.orcid: 0000-0002-2100-6351
    deprecated: true
    description: An ontology of prokaryotic phenotypic and metabolic characters
    domain: phenotype
    download.owl: http://purl.obolibrary.org/obo/micro.owl
    homepage: https://github.com/carrineblank/MicrO
    license: CC BY 2.0
    license.url: https://creativecommons.org/licenses/by/2.0/
    name: Ontology of Prokaryotic Phenotypic and Metabolic Characters
    preferredPrefix: MICRO
    prefix: micro
    repository: https://github.com/carrineblank/MicrO
  ols:
    description: An ontology of prokaryotic phenotypic and metabolic characters
    download_owl: http://purl.obolibrary.org/obo/micro.owl
    homepage: https://github.com/carrineblank/MicrO
    name: Ontology of Prokaryotic Phenotypic and Metabolic Characters
    prefix: micro
    tracker: https://github.com/carrineblank/MicrO/issues
    version: 1.5.1
  ontobee:
    library: Library
    name: Ontology of Prokaryotic Phenotypic and Metabolic Characters
    prefix: MICRO
  pattern: ^\d{7}$
  prefix: micro
  publications:
  - doi: 10.1186/s13326-016-0060-6
    pmc: PMC4830071
    pubmed: '27076900'
    title: 'MicrO: an ontology of phenotypic and metabolic characters, assays, and
      culture media found in prokaryotic taxonomic descriptions'
    year: 2016
microscope:
  biocontext:
    prefix: MICROSCOPE
  contact:
    email: cmedigue@genoscope.cns.fr
    github: null
    name: MEDIGUE Claudine
    orcid: 0000-0002-3905-1054
  fairsharing:
    abbreviation: MicroScope
    description: MicroScope is a web-based platform for microbial comparative genome
      analysis and manual functional annotation. Its relational database schema stores
      precalculated results of syntactic and functional annotation pipelines as well
      as Pathway Tools and metabolic analysis specific to each genome.
    homepage: http://www.genoscope.cns.fr/agc/microscope/home/
    name: Microbial Genome Annotation & Analysis Platform
    prefix: FAIRsharing.3t5qc3
    publications:
    - doi: 10.1093/nar/gks1194
      pubmed_id: 23193269
      title: MicroScope--an integrated microbial resource for the curation and comparative
        analysis of genomic and metabolic data.
    subjects:
    - Life Science
    - Comparative Genomics
  mappings:
    biocontext: MICROSCOPE
    fairsharing: FAIRsharing.3t5qc3
    miriam: microscope
    n2t: microscope
    re3data: r3d100012928
  miriam:
    deprecated: false
    description: MicroScope is an integrative resource that supports systematic and
      efficient revision of microbial genome annotation, data management and comparative
      analysis.
    homepage: http://www.genoscope.cns.fr/agc/microscope
    id: '00000631'
    name: MicroScope
    namespaceEmbeddedInLui: false
    pattern: ^\d+$
    prefix: microscope
    sampleId: '5601141'
    uri_format: http://www.genoscope.cns.fr/agc/microscope/mage/info.php?id=$1
  n2t:
    description: MicroScope is an integrative resource that supports systematic and
      efficient revision of microbial genome annotation, data management and comparative
      analysis.
    example: '5601141'
    homepage: http://www.genoscope.cns.fr/agc/microscope
    name: MicroScope
    namespaceEmbeddedInLui: false
    pattern: ^\d+$
    prefix: microscope
    uri_format: http://www.genoscope.cns.fr/agc/microscope/mage/info.php?id=$1
  prefix: microscope
  publications:
  - doi: 10.1093/nar/gks1194
    pmc: PMC3531135
    pubmed: '23193269'
    title: MicroScope--an integrated microbial resource for the curation and comparative
      analysis of genomic and metabolic data
    year: 2012
  - doi: 10.1093/nar/gks1194
    pmc: null
    pubmed: null
    title: MicroScope--an integrated microbial resource for the curation and comparative
      analysis of genomic and metabolic data.
    year: null
  - doi: 10.1093/nar/gks1194
    pmc: null
    pubmed: null
    title: MicroScope--an integrated microbial resource for the curation and comparative
      analysis of genomic and metabolic data.
    year: null
  - doi: 10.1093/nar/gks1194
    pmc: null
    pubmed: null
    title: MicroScope--an integrated microbial resource for the curation and comparative
      analysis of genomic and metabolic data.
    year: null
  re3data:
    description: The MicroScope is a web platform for the analysis of prokaryotic
      genomes and expert functional annotation.
    doi: 10.17616/R31NJMGW
    homepage: https://mage.genoscope.cns.fr/microscope/
    name: MicroScope
    prefix: r3d100012928
    synonyms:
    - Microbial Genome Annotation & Analysis Platform
microsporidia:
  biocontext:
    prefix: MICROSPORIDIA
  contact:
    email: oharb@upenn.edu
    github: ramobrah
    name: Omar S. Harb
    orcid: 0000-0003-4446-6200
  mappings:
    biocontext: MICROSPORIDIA
    miriam: microsporidia
    n2t: microsporidia
    prefixcommons: microsporidia
  miriam:
    deprecated: false
    description: MicrosporidiaDB is one of the databases that can be accessed through
      the EuPathDB (http://EuPathDB.org; formerly ApiDB) portal, covering eukaryotic
      pathogens of the genera Cryptosporidium, Giardia, Leishmania, Neospora, Plasmodium,
      Toxoplasma, Trichomonas and Trypanosoma. While each of these groups is supported
      by a taxon-specific database built upon the same infrastructure, the EuPathDB
      portal offers an entry point to all these resources, and the opportunity to
      leverage orthology for searches across genera.
    homepage: http://microsporidiadb.org/micro/
    id: '00000152'
    name: MicrosporidiaDB
    namespaceEmbeddedInLui: false
    pattern: ^\w+$
    prefix: microsporidia
    sampleId: ECU03_0820i
    uri_format: http://microsporidiadb.org/micro/showRecord.do?name=GeneRecordClasses.GeneRecordClass&source_id=$1
  n2t:
    description: MicrosporidiaDB is one of the databases that can be accessed through
      the EuPathDB (http://EuPathDB.org; formerly ApiDB) portal, covering eukaryotic
      pathogens of the genera Cryptosporidium, Giardia, Leishmania, Neospora, Plasmodium,
      Toxoplasma, Trichomonas and Trypanosoma. While each of these groups is supported
      by a taxon-specific database built upon the same infrastructure, the EuPathDB
      portal offers an entry point to all these resources, and the opportunity to
      leverage orthology for searches across genera.
    example: ECU03_0820i
    homepage: http://microsporidiadb.org/micro/
    name: MicrosporidiaDB at EuPathDB
    namespaceEmbeddedInLui: false
    pattern: ^\w+$
    prefix: microsporidia
    uri_format: http://microsporidiadb.org/micro/showRecord.do?name=GeneRecordClasses.GeneRecordClass&source_id=$1
  prefix: microsporidia
  prefixcommons:
    description: MicrosporidiaDB is one of the databases that can be accessed through
      the EuPathDB (http://EuPathDB.org; formerly ApiDB) portal, covering eukaryotic
      pathogens of the genera Cryptosporidium, Giardia, Leishmania, Neospora, Plasmodium,
      Toxoplasma, Trichomonas and Trypanosoma. While each of these groups is supported
      by a taxon-specific database built upon the same infrastructure, the EuPathDB
      portal offers an entry point to all these resources, and the opportunity to
      leverage orthology for searches across genera.
    example: ECU03_0820i
    homepage: http://microsporidiadb.org/micro/
    keywords:
    - eukaryotic
    - genome
    name: MicrosporidiaDB
    pattern: ^\w+$
    prefix: microsporidia
    pubmed_ids:
    - '19914931'
    uri_format: http://microsporidiadb.org/micro/showRecord.do?name=GeneRecordClasses.GeneRecordClass&source_id=$1
  publications:
  - doi: 10.1093/nar/gkp941
    pmc: PMC2808945
    pubmed: '19914931'
    title: 'EuPathDB: a portal to eukaryotic pathogen databases'
    year: 2009
  - doi: null
    pmc: null
    pubmed: '19914931'
    title: null
    year: null
  - doi: null
    pmc: null
    pubmed: '19914931'
    title: null
    year: null
millipore:
  cellosaurus:
    category: Cell line collections (Providers)
    homepage: https://www.merckmillipore.com/
    name: Merck Millipore (EMD Millipore)
    prefix: Millipore
    uri_format: https://www.merckmillipore.com/catalogue/item/$1
  example: SCC111
  mappings:
    cellosaurus: Millipore
  prefix: millipore
mimodb:
  biocontext:
    prefix: MIMODB
  contact:
    email: hj@uestc.edu.cn
    github: null
    name: Jian Huang
    orcid: 0000-0003-2314-7104
  fairsharing:
    abbreviation: MimoDB
    description: Mimotope database, active site-mimicking peptides selected from phage-display
      libraries. It is a database which stores information on peptides that have been
      selected from random peptide libraries based on their ability to bind small
      compounds, nucleic acids, proteins, cells, tissues, organs, and even entire
      organisms through phage display technology. Besides the peptide sequences, other
      information such as the corresponding target, template, library, and structures
      are also stored. All entries are manually extracted from published peer review
      articles and other public data sources such as Uniprot, GenBank and PDBSum.
    homepage: http://immunet.cn/mimodb
    name: Mimotope Database
    prefix: FAIRsharing.bv0zjz
    publications:
    - doi: 10.3390/molecules15118279
      pubmed_id: 21079566
      title: 'MimoDB: a new repository for mimotope data derived from phage display
        technology.'
    - doi: 10.1093/nar/gkr922
      pubmed_id: 22053087
      title: 'MimoDB 2.0: a mimotope database and beyond.'
    - doi: 10.1093/nar/gkv1100
      pubmed_id: 26503249
      title: 'BDB: biopanning data bank.'
    subjects:
    - Life Science
  mappings:
    biocontext: MIMODB
    fairsharing: FAIRsharing.bv0zjz
    miriam: mimodb
    n2t: mimodb
    prefixcommons: mimodb
  miriam:
    deprecated: false
    description: MimoDB is a database collecting peptides that have been selected
      from random peptide libraries based on their ability to bind small compounds,
      nucleic acids, proteins, cells, tissues and organs. It also stores other information
      such as the corresponding target, template, library, and structures. As of March
      2016, this database was renamed Biopanning Data Bank.
    homepage: http://immunet.cn/bdb/
    id: '00000251'
    name: MimoDB
    namespaceEmbeddedInLui: false
    pattern: ^\d+$
    prefix: mimodb
    sampleId: '1'
    uri_format: http://immunet.cn/bdb/index.php/mimoset/$1
  n2t:
    description: MimoDB is a database collecting peptides that have been selected
      from random peptide libraries based on their ability to bind small compounds,
      nucleic acids, proteins, cells, tissues and organs. It also stores other information
      such as the corresponding target, template, library, and structures. As of March
      2016, this database was renamed Biopanning Data Bank.
    example: '1'
    homepage: http://immunet.cn/bdb/
    name: BDB at University of Electronic Science and Technology of China
    namespaceEmbeddedInLui: false
    pattern: ^\d+$
    prefix: mimodb
    uri_format: http://immunet.cn/bdb/index.php/mimoset/$1
  prefix: mimodb
  prefixcommons:
    description: MimoDB is a database collecting peptides that have been selected
      from random peptide libraries based on their ability to bind small compounds,
      nucleic acids, proteins, cells, tissues and organs. It also stores other information
      such as the corresponding target, template, library, and structures.
    example: '1'
    homepage: http://immunet.cn/mimodb/
    keywords:
    - interaction
    - protein
    name: MimoDB
    pattern: ^\d+$
    prefix: mimodb
    pubmed_ids:
    - '22053087'
    uri_format: http://immunet.cn/mimodb/browse.php?table=mimoset&ID=$1
  publications:
  - doi: 10.1093/nar/gkv1100
    pmc: PMC4702802
    pubmed: '26503249'
    title: 'BDB: biopanning data bank'
    year: 2015
  - doi: 10.1093/nar/gkr922
    pmc: PMC3245166
    pubmed: '22053087'
    title: 'MimoDB 2.0: a mimotope database and beyond'
    year: 2011
  - doi: 10.3390/molecules15118279
    pmc: PMC6259156
    pubmed: '21079566'
    title: 'MimoDB: a new repository for mimotope data derived from phage display
      technology'
    year: 2010
minid:
  biocontext:
    prefix: MINID
  fairsharing:
    abbreviation: minid
    contact:
      email: foster@uchicago.edu
      name: Ian Foster
      orcid: 0000-0003-2129-5269
    description: 'A Minimal Viable Identifier (minid) provides a lightweight way of
      uniquely and unambiguously identifying research data products and is sufficiently
      simple to create and use to make data easily findable, accessible, interoperable,
      and reusable (FAIR). '
    domains:
    - Data retrieval
    homepage: https://github.com/fair-research/minid
    license: CC-BY-3.0
    name: Minimal Viable Identifier
    prefix: FAIRsharing.d099fb
    publications:
    - doi: 10.1371/journal.pone.0294883
      title: 'Correction: Reproducible big data science: A case study in continuous
        FAIRness'
      year: 2023
    - doi: 10.1371/journal.pone.0213013
      pubmed: '30973881'
      title: 'Reproducible big data science: A case study in continuous FAIRness'
      year: 2019
    subjects:
    - Subject Agnostic
  mappings:
    biocontext: MINID
    fairsharing: FAIRsharing.d099fb
    miriam: minid
    n2t: minid
  miriam:
    deprecated: false
    description: Minid are identifiers used to provide robust reference to intermediate
      data generated during the course of a research investigation.
    homepage: https://fair-research.org
    id: '00000645'
    name: Minimal Viable Identifier
    namespaceEmbeddedInLui: false
    pattern: ^[A-Za-z0-9]+$
    prefix: minid
    sampleId: b97957
    uri_format: https://hdl.handle.net/hdl:20.500.12582/$1
  n2t:
    description: Minid are identifiers used to provide robust reference to intermediate
      data generated during the course of a research investigation.
    example: b97957
    homepage: http://minid.bd2k.org
    name: Minimal Identifiers for Transient Data
    namespaceEmbeddedInLui: false
    pattern: ^[A-Za-z0-9]+$
    prefix: minid
    uri_format: http://n2t.net/ark:/57799/$1
  prefix: minid
minid.test:
  mappings:
    miriam: minid.test
  miriam:
    deprecated: false
    description: 'Minid are identifiers used to provide robust reference to intermediate
      data generated during the course of a research investigation. This is a prefix
      for referencing identifiers in the minid test namespace. '
    homepage: https://fair-research.org
    id: '00000707'
    name: MINID Test
    namespaceEmbeddedInLui: false
    pattern: ^[A-Za-z0-9]+$
    prefix: minid.test
    sampleId: 3SBPLMKKVEVR
    uri_format: https://hdl.handle.net/hdl:20.500.12633/$1
  part_of: minid
  prefix: minid.test
mint:
  banana: MINT
  banana_peel: '-'
  biocontext:
    prefix: MINT
  edam:
    description: Unique identifier of an entry from the MINT database of protein-protein
      interactions.
    name: MINT
    obsolete: false
    prefix: '2615'
  example: '6978836'
  fairsharing:
    abbreviation: MINT
    contact:
      email: luana.licata@gmail.com
      name: Luana Licata
      orcid: 0000-0001-5084-9000
    description: MINT focuses on experimentally verified protein-protein interactions
      mined from the scientific literature by expert curators. This resource uses
      the IntAct database framework to help reduce the effort of scientists and improve
      on IT development. MINT is an ELIXIR Core Resource.
    homepage: http://mint.bio.uniroma2.it
    license: https://creativecommons.org/licenses/by/2.5
    name: Molecular INTeraction Database
    prefix: FAIRsharing.2bdvmk
    publications:
    - doi: 10.1016/s0014-5793(01)03293-8
      pubmed_id: 11911893
      title: 'MINT: a Molecular INTeraction database.'
    - doi: 10.1093/nar/gkl950
      pubmed_id: 17135203
      title: 'MINT: the Molecular INTeraction database.'
    - doi: 10.1093/nar/gkp983
      pubmed_id: 19897547
      title: 'MINT, the molecular interaction database: 2009 update.'
    - doi: 10.1093/nar/gkr930
      pubmed_id: 22096227
      title: 'MINT, the molecular interaction database: 2012 update.'
    subjects:
    - Proteomics
    - Life Science
    twitter: MINT_database
  homepage: https://mint.bio.uniroma2.it
  logo: https://mint.bio.uniroma2.it/wp-content/uploads/2017/11/cropped-mint-1-e1509905882312.png
  mappings:
    biocontext: MINT
    edam: '2615'
    fairsharing: FAIRsharing.2bdvmk
    miriam: mint
    n2t: mint
    pathguide: '17'
    prefixcommons: mint
    re3data: r3d100010414
    uniprot: DB-0158
  miriam:
    deprecated: false
    description: The Molecular INTeraction database (MINT) stores, in a structured
      format, information about molecular interactions by extracting experimental
      details from work published in peer-reviewed journals.
    homepage: https://www.ebi.ac.uk/intact/
    id: '00000042'
    name: MINT
    namespaceEmbeddedInLui: false
    pattern: ^MINT\-\d{1,7}$
    prefix: mint
    providers:
    - code: ''
      description: The Molecular INTeraction database (MINT)
      homepage: http://mint.bio.uniroma2.it/mint/
      name: The Molecular INTeraction database (MINT)
      uri_format: https://mint.bio.uniroma2.it/index.php/results-interactions/?id=$1
    sampleId: MINT-10000
    uri_format: https://www.ebi.ac.uk/intact/query/interaction_id:$1
  n2t:
    description: The Molecular INTeraction database (MINT) stores, in a structured
      format, information about molecular interactions by extracting experimental
      details from work published in peer-reviewed journals.
    example: MINT-7905142
    homepage: https://www.ebi.ac.uk/intact/
    name: MINT subset through IntAct
    namespaceEmbeddedInLui: false
    pattern: ^MINT\-\d{1,7}$
    prefix: mint
    uri_format: https://www.ebi.ac.uk/intact/query/interaction_id:$1
  name: Molecular Interaction Database
  pathguide:
    abbreviation: MINT
    homepage: http://mint.bio.uniroma2.it/
    keywords:
    - PSI-MI
    name: Molecular Interaction Database
    prefix: '17'
  pattern: ^\d{1,7}$
  prefix: mint
  prefixcommons:
    description: The Molecular INTeraction database (MINT) stores, in a structured
      format, information about molecular interactions by extracting experimental
      details from work published in peer-reviewed journals.
    example: MINT-10000
    homepage: http://mint.bio.uniroma2.it/mint/
    keywords:
    - protein
    - interaction
    license: http://dip.doe-mbi.ucla.edu/dip/termsofuse.html
    name: Molecular INTeraction Database
    pattern: ^MINT\-\d{1,5}$
    prefix: mint
    pubmed_ids:
    - '17135203'
    uri_format: http://mint.bio.uniroma2.it/mint/search/interactor.do?queryType=protein&interactorAc=$1
  publications:
  - doi: 10.1093/nar/gkr930
    pmc: PMC3244991
    pubmed: '22096227'
    title: 'MINT, the molecular interaction database: 2012 update'
    year: 2011
  - doi: 10.1093/nar/gkp983
    pmc: PMC2808973
    pubmed: '19897547'
    title: 'MINT, the molecular interaction database: 2009 update'
    year: 2009
  - doi: 10.1093/nar/gkl950
    pmc: PMC1751541
    pubmed: '17135203'
    title: 'MINT: the Molecular INTeraction database'
    year: 2006
  - doi: 10.1016/s0014-5793(01)03293-8
    pmc: null
    pubmed: '11911893'
    title: 'MINT: a Molecular INTeraction database'
    year: 2002
  - doi: 10.1016/s0014-5793(01)03293-8
    pmc: null
    pubmed: null
    title: 'MINT: a Molecular INTeraction database.'
    year: null
  - doi: 10.1093/nar/gkl950
    pmc: null
    pubmed: null
    title: 'MINT: the Molecular INTeraction database.'
    year: null
  - doi: 10.1093/nar/gkp983
    pmc: null
    pubmed: null
    title: 'MINT, the molecular interaction database: 2009 update.'
    year: null
  - doi: 10.1093/nar/gkr930
    pmc: null
    pubmed: null
    title: 'MINT, the molecular interaction database: 2012 update.'
    year: null
  - doi: null
    pmc: null
    pubmed: '17135203'
    title: null
    year: null
  - doi: 10.1093/nar/gkr930
    pmc: null
    pubmed: '22096227'
    title: null
    year: null
  - doi: 10.1016/s0014-5793(01)03293-8
    pmc: null
    pubmed: null
    title: 'MINT: a Molecular INTeraction database.'
    year: null
  - doi: 10.1093/nar/gkl950
    pmc: null
    pubmed: null
    title: 'MINT: the Molecular INTeraction database.'
    year: null
  - doi: 10.1093/nar/gkp983
    pmc: null
    pubmed: null
    title: 'MINT, the molecular interaction database: 2009 update.'
    year: null
  - doi: 10.1093/nar/gkr930
    pmc: null
    pubmed: null
    title: 'MINT, the molecular interaction database: 2012 update.'
    year: null
  - doi: null
    pmc: null
    pubmed: '17135203'
    title: null
    year: null
  - doi: 10.1093/nar/gkr930
    pmc: null
    pubmed: '22096227'
    title: null
    year: null
  - doi: 10.1016/s0014-5793(01)03293-8
    pmc: null
    pubmed: null
    title: 'MINT: a Molecular INTeraction database.'
    year: null
  - doi: 10.1093/nar/gkl950
    pmc: null
    pubmed: null
    title: 'MINT: the Molecular INTeraction database.'
    year: null
  - doi: 10.1093/nar/gkp983
    pmc: null
    pubmed: null
    title: 'MINT, the molecular interaction database: 2009 update.'
    year: null
  - doi: 10.1093/nar/gkr930
    pmc: null
    pubmed: null
    title: 'MINT, the molecular interaction database: 2012 update.'
    year: null
  - doi: null
    pmc: null
    pubmed: '17135203'
    title: null
    year: null
  - doi: 10.1093/nar/gkr930
    pmc: null
    pubmed: '22096227'
    title: null
    year: null
  re3data:
    description: 'Starting September 2013, MINT uses the IntAct database infrastructure
      to limit the duplication of efforts and to optimise future software development.
      Data manually curated by the MINT curators can now be accessed from the IntAct
      homepage at the EBI. Data maintenance and release, MINT PSICQUIC and IMEx services
      are under the responsibility of the IntAct team, while curation effort will
      be carried by both groups.

      The MINT development team now focuses on two new developments: mentha that integrates
      protein interaction information curated by IMEx databases and SIGNOR a database
      of logic relationships between human proteins. MINT is a public repository for
      molecular interactions reported in peer-reviewed journals.IT is a collection
      of molecular interaction databases that can be used to search for, analyze and
      graphically display molecular interaction networks and pathways from a wide
      variety of species. MINT is comprised of separate database components. HomoMINT,
      is an inferred human protein interatction database. Domino, is database of domain
      peptide interactions. A new component has been added called VirusMINT that explores
      the interactions of viral proteins with human proteins.'
    doi: 10.17616/R38S3B
    homepage: https://mint.bio.uniroma2.it/
    license: CC
    name: Molecular INTeraction Database
    prefix: r3d100010414
    synonyms:
    - MINT
    xrefs:
      omics: 02928
  uniprot:
    abbreviation: MINT
    category: Protein-protein interaction databases
    homepage: https://mint.bio.uniroma2.it/
    name: Molecular INTeraction database
    prefix: DB-0158
    publications:
    - doi: 10.1093/nar/gkr930
      pubmed: '22096227'
    uri_format: https://mint.bio.uniroma2.it/cgi-bin/protein.py?id=$1
  uri_format: https://mint.bio.uniroma2.it/index.php/detailed-curation/?id=MINT-$1
mipmod:
  biocontext:
    prefix: MIPMOD
  contact:
    email: rsankar@iitk.ac.in
    github: null
    name: Ramasubbu Sankararamakrishnan
    orcid: 0000-0002-8527-5614
  mappings:
    biocontext: MIPMOD
    miriam: mipmod
    n2t: mipmod
    prefixcommons: mipmod
  miriam:
    deprecated: false
    description: MIPModDb is a database of comparative protein structure models of
      MIP (Major Intrinsic Protein) family of proteins, identified from complete genome
      sequence. It provides key information of MIPs based on their sequence and structures.
    homepage: http://bioinfo.iitk.ac.in/MIPModDB
    id: '00000256'
    name: MIPModDB
    namespaceEmbeddedInLui: false
    pattern: ^\w+$
    prefix: mipmod
    sampleId: HOSAPI0399
    uri_format: http://bioinfo.iitk.ac.in/MIPModDB/result.php?code=$1
  n2t:
    description: MIPModDb is a database of comparative protein structure models of
      MIP (Major Intrinsic Protein) family of proteins, identified from complete genome
      sequence. It provides key information of MIPs based on their sequence and structures.
    example: HOSAPI0399
    homepage: http://bioinfo.iitk.ac.in/MIPModDB
    name: MIPModDB at Indian Institute of Technology Kanpur
    namespaceEmbeddedInLui: false
    pattern: ^\w+$
    prefix: mipmod
    uri_format: http://bioinfo.iitk.ac.in/MIPModDB/result.php?code=$1
  prefix: mipmod
  prefixcommons:
    description: MIPModDb is a database of comparative protein structure models of
      MIP (Major Intrinsic Protein) family of proteins, identified from complete genome
      sequence. It provides key information of MIPs based on their sequence and structures.
    example: HOSAPI0399
    homepage: http://bioinfo.iitk.ac.in/MIPModDB
    keywords:
    - protein
    - structure
    name: MIPModDB
    pattern: ^\w+$
    prefix: mipmod
    pubmed_ids:
    - '22080560'
    uri_format: http://bioinfo.iitk.ac.in/MIPModDB/result.php?code=$1
  publications:
  - doi: 10.1093/nar/gkr914
    pmc: PMC3245135
    pubmed: '22080560'
    title: 'MIPModDB: a central resource for the superfamily of major intrinsic proteins'
    year: 2011
mir:
  banana: MIR
  biocontext:
    prefix: MIR
  mappings:
    biocontext: MIR
    miriam: mir
    n2t: mir
  miriam:
    deprecated: false
    description: The Identifiers.org registry contains registered namespace and provider
      prefixes with associated access URIs for a large number of high quality data
      collections. These prefixes are used in web resolution of compact identifiers
      of the form “PREFIX:ACCESSION” or "PROVIDER/PREFIX:ACCESSION” commonly used
      to specify bioinformatics and other data resources.
    homepage: https://registry.identifiers.org/registry
    id: 00000599
    name: Identifiers.org Registry
    namespaceEmbeddedInLui: true
    pattern: ^MIR:\d{8}$
    prefix: mir
    sampleId: '00100037'
    uri_format: https://resolver.api.identifiers.org/resolveMirId/MIR:$1
  n2t:
    description: The Identifiers.org registry contains registered namespace and provider
      prefixes with associated access URIs for a large number of high quality data
      collections. These prefixes are used in web resolution of compact identifiers
      of the form &#x201C;PREFIX:ACCESSION&#x201D; or "PROVIDER/PREFIX:ACCESSION&#x201D;
      commonly used to specify bioinformatics and other data resources.
    example: '00100037'
    homepage: https://identifiers.org/registry
    name: Identifiers.org Registry through EBI
    namespaceEmbeddedInLui: true
    pattern: ^MIR:\d{8}$
    prefix: mir
    uri_format: https://identifiers.org/registry?query="MIR:$1"
  pattern: ^\d{8}$
  prefix: mir
  uri_format: https://registry.identifiers.org/registry?query=MIR:$1
mirbase:
  biocontext:
    prefix: MIRBASE
  biolink:
    is_identifiers: true
    is_obo: false
    prefix: mirbase
    uri_format: http://identifiers.org/mirbase$1
  contact:
    email: sam.griffiths-jones@manchester.ac.uk
    github: samgriffithsjones
    name: Sam Griffiths-Jones
    orcid: 0000-0001-6043-807X
  domain: mirna
  edam:
    description: Identifier for a gene from the miRBase database.
    name: Gene ID (miRBase)
    obsolete: false
    prefix: '2642'
  example: MI0026471
  fairsharing:
    abbreviation: miRBase
    description: The miRBase database is a searchable database of published miRNA
      sequences and annotation. Each entry in miRBase represents a predicted hairpin
      portion of a miRNA transcript (termed mir in the database), with information
      on the location and sequence of the mature miRNA sequence (termed miR). Both
      hairpin and mature sequences are available for searching and browsing, and entries
      can also be retrieved by name, keyword, references and annotation.
    homepage: http://www.mirbase.org/
    name: miRBase
    prefix: FAIRsharing.hmgte8
    publications:
    - doi: 10.1093/nar/gkh023
      pubmed_id: 14681370
      title: The microRNA Registry.
    - doi: 10.1093/nar/gky1141
      pubmed_id: 30423142
      title: 'miRBase: from microRNA sequences to function.'
    - doi: 10.1093/nar/gkt1181
      pubmed_id: 24275495
      title: 'miRBase: annotating high confidence microRNAs using deep sequencing
        data.'
    - doi: 10.1093/nar/gkq1027
      pubmed_id: 21037258
      title: 'miRBase: integrating microRNA annotation and deep-sequencing data.'
    - doi: 10.1093/nar/gkm952
      pubmed_id: 17991681
      title: 'miRBase: tools for microRNA genomics.'
    - doi: 10.1093/nar/gkj112
      pubmed_id: 16381832
      title: 'miRBase: microRNA sequences, targets and gene nomenclature.'
    subjects:
    - Biology
  homepage: http://www.mirbase.org/
  integbio:
    alt_name: microRNA database
    description: miRBase is a database for published microRNA sequences and annotations,
      which include mature miRNA sequences (indicated by miR), and hairpin structures
      predicted by sequences that are precursors for miRNA (indicated by mir). A variety
      of search methods can be used, including by keyword, genomic position, cluster,
      expression data, and user-provided sequences. Furthermore, these sequences and
      annotations can be downloaded.
    fairsharing: biodbcore-000569
    homepage: http://mirbase.org/
    information_keywords:
    - Sequence
    maintainer: Faculty of Life Sciences, The University of Manchester
    name: miRBase
    prefix: nbdc00136
    status: Active
    target_keywords:
    - RNA
  license: public domain
  logo: https://www.mirbase.org/static/images/mirbase-logo_new.png
  mappings:
    biocontext: MIRBASE
    biolink: mirbase
    edam: '2642'
    fairsharing: FAIRsharing.hmgte8
    integbio: nbdc00136
    miriam: mirbase
    n2t: mirbase
    ncbi: miRBase
    pathguide: '210'
    prefixcommons: mirbase
    re3data: r3d100010566
    togoid: Mirbase
    wikidata: P2870
  miriam:
    deprecated: false
    description: The miRBase Sequence Database is a searchable database of published
      miRNA sequences and annotation. The data were previously provided by the miRNA
      Registry. Each entry in the miRBase Sequence database represents a predicted
      hairpin portion of a miRNA transcript (termed mir in the database), with information
      on the location and sequence of the mature miRNA sequence (termed miR).
    homepage: http://www.mirbase.org/
    id: 00000078
    name: miRBase Sequence
    namespaceEmbeddedInLui: false
    pattern: ^MI\d{7}$
    prefix: mirbase
    sampleId: MI0000001
    uri_format: http://www.mirbase.org/cgi-bin/mirna_entry.pl?acc=$1
  n2t:
    description: The miRBase Sequence Database is a searchable database of published
      miRNA sequences and annotation. The data were previously provided by the miRNA
      Registry. Each entry in the miRBase Sequence database represents a predicted
      hairpin portion of a miRNA transcript (termed mir in the database), with information
      on the location and sequence of the mature miRNA sequence (termed miR).
    example: MI0000001
    homepage: http://www.mirbase.org/
    name: miRBase Sequence Database
    namespaceEmbeddedInLui: false
    pattern: MI\d{7}
    prefix: mirbase
    uri_format: http://www.mirbase.org/cgi-bin/mirna_entry.pl?acc=$1
  name: miRBase pre-miRNA
  ncbi:
    example: MI0000681
    homepage: http://www.mirbase.org/
    name: miRNA Database
    prefix: miRBase
  part_of_database: mirbase
  pathguide:
    abbreviation: miRBase
    homepage: http://www.mirbase.org/index.shtml
    name: microRNA  Database
    prefix: '210'
  prefix: mirbase
  prefixcommons:
    description: The miRBase Sequence Database is a searchable database of published
      miRNA sequences and annotation. The data were previously provided by the miRNA
      Registry. The miRBase Registry continues to provide gene hunters with unique
      names for novel miRNA genes prior to publication of results. The miRBase Targets
      database is a new resource of predicted miRNA targets in animals
    example: MI0000001
    homepage: http://www.mirbase.org/
    keywords:
    - RNA
    - gene
    name: miRBase Sequence Database
    pattern: ^MI\d{7}$
    prefix: mirbase
    pubmed_ids:
    - '14681370'
    uri_format: http://www.mirbase.org/cgi-bin/mirna_entry.pl?acc=$1
  publications:
  - doi: 10.1093/nar/gky1141
    pmc: PMC6323917
    pubmed: '30423142'
    title: 'miRBase: from microRNA sequences to function'
    year: 2019
  - doi: 10.1093/nar/gkt1181
    pmc: PMC3965103
    pubmed: '24275495'
    title: 'miRBase: annotating high confidence microRNAs using deep sequencing data'
    year: 2013
  - doi: 10.1093/nar/gkq1027
    pmc: PMC3013655
    pubmed: '21037258'
    title: 'miRBase: integrating microRNA annotation and deep-sequencing data'
    year: 2010
  - doi: 10.1093/nar/gkm952
    pmc: PMC2238936
    pubmed: '17991681'
    title: 'miRBase: tools for microRNA genomics'
    year: 2007
  - doi: 10.1093/nar/gkj112
    pmc: PMC1347474
    pubmed: '16381832'
    title: 'miRBase: microRNA sequences, targets and gene nomenclature'
    year: 2006
  - doi: 10.1093/nar/gkh023
    pmc: PMC308757
    pubmed: '14681370'
    title: The microRNA Registry
    year: 2004
  - doi: 10.1093/nar/gkh023
    pmc: null
    pubmed: null
    title: The microRNA Registry.
    year: null
  - doi: 10.1093/nar/gky1141
    pmc: null
    pubmed: null
    title: 'miRBase: from microRNA sequences to function.'
    year: null
  - doi: 10.1093/nar/gkt1181
    pmc: null
    pubmed: null
    title: 'miRBase: annotating high confidence microRNAs using deep sequencing data.'
    year: null
  - doi: 10.1093/nar/gkq1027
    pmc: null
    pubmed: null
    title: 'miRBase: integrating microRNA annotation and deep-sequencing data.'
    year: null
  - doi: 10.1093/nar/gkm952
    pmc: null
    pubmed: null
    title: 'miRBase: tools for microRNA genomics.'
    year: null
  - doi: 10.1093/nar/gkj112
    pmc: null
    pubmed: null
    title: 'miRBase: microRNA sequences, targets and gene nomenclature.'
    year: null
  - doi: null
    pmc: null
    pubmed: '14681370'
    title: null
    year: null
  - doi: 10.1093/nar/gkh023
    pmc: null
    pubmed: null
    title: The microRNA Registry.
    year: null
  - doi: 10.1093/nar/gky1141
    pmc: null
    pubmed: null
    title: 'miRBase: from microRNA sequences to function.'
    year: null
  - doi: 10.1093/nar/gkt1181
    pmc: null
    pubmed: null
    title: 'miRBase: annotating high confidence microRNAs using deep sequencing data.'
    year: null
  - doi: 10.1093/nar/gkq1027
    pmc: null
    pubmed: null
    title: 'miRBase: integrating microRNA annotation and deep-sequencing data.'
    year: null
  - doi: 10.1093/nar/gkm952
    pmc: null
    pubmed: null
    title: 'miRBase: tools for microRNA genomics.'
    year: null
  - doi: 10.1093/nar/gkj112
    pmc: null
    pubmed: null
    title: 'miRBase: microRNA sequences, targets and gene nomenclature.'
    year: null
  - doi: null
    pmc: null
    pubmed: '14681370'
    title: null
    year: null
  re3data:
    description: The miRBase database is a searchable database of published miRNA
      sequences and annotation. Each entry in the miRBase Sequence database represents
      a predicted hairpin portion of a miRNA transcript (termed mir in the database),
      with information on the location and sequence of the mature miRNA sequence (termed
      miR). Both hairpin and mature sequences are available for searching and browsing,
      and entries can also be retrieved by name, keyword, references and annotation.
      All sequence and annotation data are also available for download. The miRBase
      Registry provides miRNA gene hunters with unique names for novel miRNA genes
      prior to publication of results.
    doi: 10.17616/R30P5K
    homepage: https://www.mirbase.org/
    name: miRBase
    prefix: r3d100010566
    synonyms:
    - microRNA database
    xrefs:
      nif: 0000-03134
  togoid:
    catalog: nbdc00136
    description: miRBase is a database for published microRNA sequences and annotations,
      which include mature miRNA sequences (indicated by miR), and hairpin structures
      predicted by sequences that are precursors for miRNA (indicated by mir). A variety
      of search methods can be used, including by keyword, genomic position, cluster,
      expression data, and user-provided sequences. Furthermore, these sequences and
      annotations can be downloaded.
    examples:
    - MI0003587
    - MI0000252
    - MI0000811
    - MI0014201
    - MI0003578
    - MI0000293
    - MI0006384
    - MI0006361
    - MI0000480
    - MI0006419
    keywords:
    - Transcript
    name: miRBase
    pattern: ^(?MI\d{7})$
    prefix: Mirbase
    uri_format: http://identifiers.org/mirbase/$1
  uri_format: http://www.mirbase.org/cgi-bin/mirna_entry.pl?acc=$1
  wikidata:
    description: identifier for pre-miRNAs in miRBase, the reference database for
      microRNAs
    example:
    - MI0000472
    - MI0016867
    - MI0024976
    homepage: http://www.mirbase.org/
    name: miRBase pre-miRNA ID
    pattern: ^MI\d{7}$
    prefix: P2870
    uri_format: http://www.mirbase.org/cgi-bin/mirna_entry.pl?acc=$1
mirbase.family:
  contact:
    email: sam.griffiths-jones@manchester.ac.uk
    github: samgriffithsjones
    name: Sam Griffiths-Jones
    orcid: 0000-0001-6043-807X
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: The miRBase database is a searchable database of published miRNA sequences
    and annotation. Each entry in the miRBase Sequence database represents a predicted
    hairpin portion of a miRNA transcript (termed mir in the database), with information
    on the location and sequence of the mature miRNA sequence (termed miR). Both hairpin
    and mature sequences are available for searching and browsing, and entries can
    also be retrieved by name, keyword, references and annotation. All sequence and
    annotation data are also available for download.
  domain: mirna
  example: MIPF0000002
  homepage: http://www.mirbase.org/
  keywords:
  - gene
  - mirna
  license: public domain
  logo: https://www.mirbase.org/static/images/mirbase-logo_new.png
  mappings:
    wikidata.entity: Q6826947
  name: miRBase Families
  part_of_database: mirbase
  prefix: mirbase.family
  synonyms:
  - MIRBASE_FAMILY
  uri_format: http://www.mirbase.org/cgi-bin/mirna_summary.pl?fam=$1
  wikidata:
    database: Q6826947
mirbase.mature:
  biocontext:
    prefix: MIRBASE.MATURE
  contact:
    email: sam.griffiths-jones@manchester.ac.uk
    github: samgriffithsjones
    name: Sam Griffiths-Jones
    orcid: 0000-0001-6043-807X
  domain: mirna
  example: MIMAT0046872
  homepage: http://www.mirbase.org/
  license: public domain
  logo: https://www.mirbase.org/static/images/mirbase-logo_new.png
  mappings:
    biocontext: MIRBASE.MATURE
    miriam: mirbase.mature
    n2t: mirbase.mature
    prefixcommons: mirbase.mature
    wikidata: P2871
  miriam:
    deprecated: false
    description: The miRBase Sequence Database is a searchable database of published
      miRNA sequences and annotation. This collection refers specifically to the mature
      miRNA sequence.
    homepage: http://www.mirbase.org/
    id: '00000235'
    name: miRBase mature sequence
    namespaceEmbeddedInLui: false
    pattern: ^MIMAT\d{7}$
    prefix: mirbase.mature
    sampleId: MIMAT0000001
    uri_format: http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=$1
  n2t:
    description: The miRBase Sequence Database is a searchable database of published
      miRNA sequences and annotation. This collection refers specifically to the mature
      miRNA sequence.
    example: MIMAT0000001
    homepage: http://www.mirbase.org/
    name: miRBase
    namespaceEmbeddedInLui: false
    pattern: MIMAT\d{7}
    prefix: mirbase.mature
    uri_format: http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=$1
  name: miRBase mature miRNA
  part_of_database: mirbase
  prefix: mirbase.mature
  prefixcommons:
    description: The miRBase Sequence Database is a searchable database of published
      miRNA sequences and annotation. This collection refers specifically to the mature
      miRNA sequence.
    example: MIMAT0000001
    keywords:
    - nucleotide
    - sequence
    name: miRBase mature sequence
    pattern: ^MIMAT\d{7}$
    prefix: mirbase.mature
    uri_format: http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=$1
  synonyms:
  - MIRBASEM
  uri_format: http://mirbase.org/cgi-bin/mature.pl?mature_acc=$1
  wikidata:
    description: identifier for mature miRNAs in miRBase, the reference database for
      microRNAs
    example:
    - MIMAT0000446
    - MIMAT0000682
    - MIMAT0003214
    homepage: http://www.mirbase.org/
    name: miRBase mature miRNA ID
    pattern: ^MIMAT\d{7}$
    prefix: P2871
    uri_format: http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=$1
mirex:
  biocontext:
    prefix: MIREX
  contact:
    email: wmk@amu.edu.pl
    github: null
    name: Wojciech M. Karlowski
    orcid: 0000-0002-8086-5404
  fairsharing:
    abbreviation: mirEX
    description: mirEX2 is a comprehensive platform for comparative analysis of primary
      microRNA expression data. RT–qPCR-based gene expression profiles are stored
      in a universal and expandable database scheme and wrapped by an intuitive user-friendly
      interface.
    homepage: http://www.comgen.pl/mirex/
    name: mirEX
    prefix: FAIRsharing.q3b39v
    publications:
    - doi: 10.1093/nar/gkr878
      pubmed_id: 22013167
      title: 'mirEX: a platform for comparative exploration of plant pri-miRNA expression
        data.'
    - doi: 10.1186/s12870-015-0533-2
      pubmed_id: 26141515
      title: mirEX 2.0 - an integrated environment for expression profiling of plant
        microRNAs.
    subjects:
    - Life Science
  integbio:
    description: mirEX2 is a comprehensive platform for comparative analysis of primary
      microRNA expression data. RT–qPCR-based gene expression profiles are stored
      in a universal and expandable database scheme and wrapped by an intuitive user-friendly
      interface.
    fairsharing: FAIRsharing.q3b39v
    homepage: http://www.comgen.pl/mirex/
    information_keywords:
    - Expression
    - Sequence
    - Localization
    maintainer: Wellcome Sanger Institute
    name: mirEX
    prefix: nbdc02064
    pubmeds:
    - '22013167'
    - '26141515'
    status: Active
    target_keywords:
    - Genome/Gene
    - RNA
  mappings:
    biocontext: MIREX
    fairsharing: FAIRsharing.q3b39v
    integbio: nbdc02064
    miriam: mirex
    n2t: mirex
  miriam:
    deprecated: false
    description: mirEX is a comprehensive platform for comparative analysis of primary
      microRNA expression data, storing RT–qPCR-based gene expression profile over
      seven development stages of Arabidopsis. It also provides RNA structural models,
      publicly available deep sequencing results and experimental procedure details.
      This collection provides profile information for a single microRNA over all
      development stages.
    homepage: http://comgen.pl/mirex/?page=home
    id: 00000329
    name: mirEX
    namespaceEmbeddedInLui: false
    pattern: ^\d+(\w+)?$
    prefix: mirex
    sampleId: 165a
    uri_format: http://comgen.pl/mirex1/?page=results/record&name=$1&exref=pp2a&limit=yes
  n2t:
    description: mirEX is a comprehensive platform for comparative analysis of primary
      microRNA expression data, storing RT&#x2013;qPCR-based gene expression profile
      over seven development stages of Arabidopsis. It also provides RNA structural
      models, publicly available deep sequencing results and experimental procedure
      details. This collection provides profile information for a single microRNA
      over all development stages.
    example: 165a
    homepage: http://comgen.pl/mirex/?page=home
    name: mirEX at Adam Mickiewicz University
    namespaceEmbeddedInLui: false
    pattern: ^\d+(\w+)?$
    prefix: mirex
    uri_format: http://comgen.pl/mirex1/?page=results/record&name=$1&exref=pp2a&limit=yes
  prefix: mirex
  publications:
  - doi: 10.1186/s12870-015-0533-2
    pmc: PMC4490709
    pubmed: '26141515'
    title: mirEX 2.0 - an integrated environment for expression profiling of plant
      microRNAs
    year: 2015
  - doi: 10.1093/nar/gkr878
    pmc: PMC3245179
    pubmed: '22013167'
    title: 'mirEX: a platform for comparative exploration of plant pri-miRNA expression
      data'
    year: 2011
mirgenedb:
  contact:
    email: BastianFromm@gmail.com
    github: null
    name: Bastian Fromm
    orcid: 0000-0003-0352-3037
  contributor:
    email: palayoor.n@northeastern.edu
    github: nalikapalayoor
    name: Nalika Palayoor
    orcid: 0009-0008-8406-631X
  description: mircoRNA Gene Database is a collection of animal microRNA genes. This
    database allows researchers to analyze mircoRNA properties like secondary structure
    and features in a phylogenetic context.
  example: Hsa-Let-7-P2a3
  github_request_issue: 1393
  homepage: https://mirgenedb.org/
  name: microRNA Gene Database
  pattern: ^[a-zA-Z0-9]+(-[a-zA-Z0-9]+)+$
  prefix: mirgenedb
  publications:
  - doi: 10.1093/nar/gkae1094
    pmc: PMC11701709
    pubmed: '39673268'
    title: 'MirGeneDB 3.0: improved taxonomic sampling, uniform nomenclature of novel
      conserved microRNA families and updated covariance models'
    year: 2025
  - doi: 10.1093/nar/gkab1101
    pmc: PMC8728216
    pubmed: '34850127'
    title: 'MirGeneDB 2.1: toward a complete sampling of all major animal phyla'
    year: 2022
  - doi: 10.1093/nar/gkz885
    pmc: PMC6943042
    pubmed: '31598695'
    title: 'MirGeneDB 2.0: the metazoan microRNA complement'
    year: 2020
  - doi: 10.1146/annurev-genet-120213-092023
    pmc: PMC4743252
    pubmed: '26473382'
    title: A Uniform System for the Annotation of Vertebrate microRNA Genes and the
      Evolution of the Human microRNAome
    year: 2015
  reviewer:
    email: b.gyori@northeastern.edu
    github: bgyori
    name: Benjamin M. Gyori
    orcid: 0000-0001-9439-5346
  uri_format: https://mirgenedb.org/browse?qtype=mgid&org=ALL&query=$1
miriam:
  edam:
    description: Unique identifier of a MIRIAM data resource.
    name: MIRIAM
    obsolete: false
    prefix: '1162'
  fairsharing:
    abbreviation: MIRIAM
    contact:
      email: n.lenovere@gmail.com
      name: Nicolas Le Novère
      orcid: 0000-0002-6309-7327
    description: The Minimal Information Required In the Annotation of Models (MIRIAM),
      initiated by the BioModels.net effort, is a set of guidelines for the consistent
      annotation and curation of computational models in biology. It is suitable for
      use with any structured format for computational models.
    homepage: http://co.mbine.org/standards/miriam
    license: CC BY-SA 4.0
    name: Minimal Information Required In the Annotation of Models
    prefix: FAIRsharing.ap169a
    publications:
    - doi: 10.1186/1752-0509-1-58
      pubmed_id: 18078503
      title: 'MIRIAM Resources: tools to generate and resolve robust cross-references
        in Systems Biology.'
    - doi: 10.1093/nar/gkr1097
      pubmed_id: 22140103
      title: 'Identifiers.org and MIRIAM Registry: community resources to provide
        persistent identification.'
    - doi: 10.1038/nbt1156
      pubmed_id: 16333295
      title: Minimum information requested in the annotation of biochemical models
        (MIRIAM).
    subjects:
    - Biochemistry
    - Life Science
    - Biomedical Science
  mappings:
    edam: '1162'
    fairsharing: FAIRsharing.ap169a
    miriam: identifiers.namespace
  miriam:
    deprecated: false
    description: Identifiers.org is an established resolving system that enables the
      referencing of data for the scientific community, with a current focus on the
      Life Sciences domain.
    homepage: https://www.ebi.ac.uk
    id: 00000859
    name: Identifiers.org namespace
    namespaceEmbeddedInLui: false
    pattern: ^[a-z_\.]+$
    prefix: identifiers.namespace
    sampleId: pubmed
    uri_format: https://registry.identifiers.org/registry/$1
  part_of_database: miriam
  pattern: ^[0-9a-z_:\.-]+$
  prefix: miriam
  publications:
  - doi: 10.1093/nar/gkr1097
    pmc: PMC3245029
    pubmed: '22140103'
    title: 'Identifiers.org and MIRIAM Registry: community resources to provide persistent
      identification'
    year: 2011
  - doi: 10.1186/1752-0509-1-58
    pmc: PMC2259379
    pubmed: '18078503'
    title: 'MIRIAM Resources: tools to generate and resolve robust cross-references
      in Systems Biology'
    year: 2007
  - doi: 10.1038/nbt1156
    pmc: null
    pubmed: '16333295'
    title: Minimum information requested in the annotation of biochemical models (MIRIAM)
    year: 2005
  synonyms:
  - identifiers.namespace
miriam.collection:
  banana: MIR
  biocontext:
    prefix: MIRIAM.COLLECTION
  deprecated: true
  example: 00000008
  mappings:
    biocontext: MIRIAM.COLLECTION
    miriam: miriam.collection
    n2t: miriam.collection
  miriam:
    deprecated: true
    description: MIRIAM Registry is an online resource created to catalogue collections
      (Gene Ontology, Taxonomy or PubMed are some examples) and the corresponding
      resources (physical locations) providing access to those data collections. The
      Registry provides unique and perennial URIs for each entity of those data collections.
    id: 00000008
    name: MIRIAM Registry collection
    namespaceEmbeddedInLui: false
    pattern: ^MIR:000\d{5}$
    prefix: miriam.collection
    sampleId: MIR:00000008
  n2t:
    description: MIRIAM Registry is an online resource created to catalogue collections
      (Gene Ontology, Taxonomy or PubMed are some examples) and the corresponding
      resources (physical locations) providing access to those data collections. The
      Registry provides unique and perennial URIs for each entity of those data collections.
    example: MIR:00000008
    homepage: https://www.ebi.ac.uk/miriam/
    name: MIRIAM Resources (data collection)
    namespaceEmbeddedInLui: false
    pattern: ^MIR:000\d{5}$
    prefix: miriam.collection
    uri_format: https://www.ebi.ac.uk/miriam/main/$1
  part_of_database: miriam
  pattern: ^000\d{5}$
  prefix: miriam.collection
miriam.resource:
  banana: MIR
  biocontext:
    prefix: MIRIAM.RESOURCE
  deprecated: true
  example: '00100005'
  mappings:
    biocontext: MIRIAM.RESOURCE
    miriam: miriam.resource
    n2t: miriam.resource
    prefixcommons: miriam.resource
  miriam:
    deprecated: false
    description: MIRIAM Registry is an online resource created to catalogue data types
      (Gene Ontology, Taxonomy or PubMed are some examples), their URIs and the corresponding
      resources (or physical locations), whether these are controlled vocabularies
      or databases.
    homepage: https://www.ebi.ac.uk/miriam/
    id: 00000188
    name: MIRIAM Registry resource
    namespaceEmbeddedInLui: false
    pattern: ^MIR:001\d{5}$
    prefix: miriam.resource
    sampleId: MIR:00100005
    uri_format: https://resolver.api.identifiers.org/resolveMirId/$1
  n2t:
    description: MIRIAM Registry is an online resource created to catalogue data types
      (Gene Ontology, Taxonomy or PubMed are some examples), their URIs and the corresponding
      resources (or physical locations), whether these are controlled vocabularies
      or databases.
    example: MIR:00100005
    homepage: https://www.ebi.ac.uk/miriam/
    name: MIRIAM Registry (resources)
    namespaceEmbeddedInLui: false
    pattern: ^MIR:001\d{5}$
    prefix: miriam.resource
    uri_format: https://www.ebi.ac.uk/miriam/main/resources/$1
  name: MIRIAM Legacy Registry Identifier
  part_of_database: miriam
  pattern: ^001\d{5}$
  prefix: miriam.resource
  prefixcommons:
    description: MIRIAM Resources is an online resource created to catalogue the data-types
      (Gene Ontology, Taxonomy or PubMed are some examples), their URIs and the corresponding
      physical URLs, whether these are controlled vocabularies or databases.
    example: MIR:00100245
    homepage: http://www.ebi.ac.uk/miriam/
    keywords:
    - registry
    license: http://www.ebi.ac.uk/Information/termsofuse.html
    name: MIRIAM Resources
    pattern: ^MIR:001\d{5}$
    prefix: miriam.resource
    pubmed_ids:
    - '18078503'
    synonyms:
    - mir
    uri_format: http://www.ebi.ac.uk/miriam/main/resources/$1
  publications:
  - doi: 10.1186/1752-0509-1-58
    pmc: PMC2259379
    pubmed: '18078503'
    title: 'MIRIAM Resources: tools to generate and resolve robust cross-references
      in Systems Biology'
    year: 2007
  - doi: null
    pmc: null
    pubmed: '18078503'
    title: null
    year: null
mirnao:
  aberowl:
    description: An application ontology for microRNAs.
    download_owl: http://aber-owl.net/media/ontologies/MIRNAO/11/mirnao.owl
    homepage: https://code.google.com/p/mirna-ontology/
    name: microRNA Ontology
    prefix: MIRNAO
    version: '1.7'
  biocontext:
    prefix: MIRNAO
  bioportal:
    contact:
      email: vdritsou@gmail.com
      name: Vicky Dritsou
    description: An application ontology for microRNAs.
    homepage: https://code.google.com/archive/p/mirna-ontology/
    name: MicroRNA Ontology
    prefix: MIRNAO
    version: '1.7'
  contact:
    email: topalis@imbb.forth.gr
    github: null
    name: Pantelis Topalis
    orcid: 0000-0002-1635-4810
  download_owl: http://aber-owl.net/media/ontologies/MIRNAO/11/mirnao.owl
  mappings:
    aberowl: MIRNAO
    biocontext: MIRNAO
    bioportal: MIRNAO
    obofoundry: mirnao
    ontobee: miRNAO
  obofoundry:
    contact: topalis@imbb.forth.gr
    contact.label: Pantelis Topalis
    deprecated: true
    description: An application ontology for use with miRNA databases.
    domain: chemistry and biochemistry
    download.owl: http://purl.obolibrary.org/obo/mirnao.owl
    homepage: http://code.google.com/p/mirna-ontology/
    license: CC0 1.0
    license.url: https://creativecommons.org/publicdomain/zero/1.0/
    name: microRNA Ontology
    prefix: mirnao
  ontobee:
    library: Library
    name: microRNA Ontology
    prefix: miRNAO
  prefix: mirnao
mirnest:
  biocontext:
    prefix: MIRNEST
  contact:
    email: miszcz@amu.edu.pl
    github: null
    name: Michael Szcześniak
    orcid: 0000-0002-6050-9525
  fairsharing:
    abbreviation: miRNEST
    description: miRNEST is an integrative collection of animal, plant and virus microRNA
      data. miRNEST is being gradually developed to create an integrative resource
      of miRNA-associated data. The data comes from our computational predictions
      (new miRNAs, targets, mirtrons, miRNA gene structures) as well as from other
      databases and publications.
    homepage: http://mirnest.amu.edu.pl
    name: miRNEST
    prefix: FAIRsharing.5pfx4r
    publications:
    - doi: 10.1093/nar/gkr1159
      pubmed_id: 22135287
      title: 'miRNEST database: an integrative approach in microRNA search and annotation.'
    - doi: 10.1093/nar/gkt1156
      pubmed_id: 24243848
      title: 'miRNEST 2.0: a database of plant and animal microRNAs.'
    subjects:
    - Genomics
    - Life Science
  integbio:
    description: miRNEST is an integrative collection of animal, plant and virus microRNA
      data. miRNEST is being gradually developed to create an integrative resource
      of miRNA-associated data. The data comes from our computational predictions
      (new miRNAs, targets, mirtrons, miRNA gene structures) as well as from other
      databases and publications.
    fairsharing: FAIRsharing.5pfx4r
    homepage: http://mirnest.amu.edu.pl
    information_keywords:
    - Expression
    - Sequence
    - 3D structure
    - Interaction/Pathway
    maintainer: Laboratory of Bioinformatics, Faculty of Biology, Adam Mickiewicz
      University
    name: miRNEST
    prefix: nbdc01703
    pubmeds:
    - '22135287'
    - '24243848'
    status: Active
    target_keywords:
    - Genome/Gene
    - Genetic variation
    - RNA
  mappings:
    biocontext: MIRNEST
    fairsharing: FAIRsharing.5pfx4r
    integbio: nbdc01703
    miriam: mirnest
    n2t: mirnest
    prefixcommons: mirnest
  miriam:
    deprecated: false
    description: miRNEST is a database of animal, plant and virus microRNAs, containing  miRNA
      predictions conducted on Expressed Sequence Tags of animal and  plant species.
    homepage: http://rhesus.amu.edu.pl/mirnest/copy/
    id: '00000246'
    name: miRNEST
    namespaceEmbeddedInLui: false
    pattern: ^MNEST\d+$
    prefix: mirnest
    sampleId: MNEST029358
    uri_format: http://rhesus.amu.edu.pl/mirnest/copy/details.php?id=$1
  n2t:
    description: miRNEST is a database of animal, plant and virus microRNAs, containing  miRNA
      predictions conducted on Expressed Sequence Tags of animal and  plant species.
    example: MNEST029358
    homepage: http://rhesus.amu.edu.pl/mirnest/copy/
    name: miRNEST at Adam Mickiewicz University
    namespaceEmbeddedInLui: false
    pattern: ^MNEST\d+$
    prefix: mirnest
    uri_format: http://rhesus.amu.edu.pl/mirnest/copy/details.php?id=$1
  prefix: mirnest
  prefixcommons:
    description: miRNEST is a database of animal, plant and virus microRNAs, containing  miRNA
      predictions conducted on Expressed Sequence Tags of animal and  plant species.
    example: MNEST029358
    homepage: http://lemur.amu.edu.pl/share/php/mirnest/
    keywords:
    - expression
    - prediction
    name: miRNEST
    pattern: ^MNEST\d+$
    prefix: mirnest
    pubmed_ids:
    - '22135287'
    uri_format: http://lemur.amu.edu.pl/share/php/mirnest/search.php?search_term=$1
  publications:
  - doi: 10.1093/nar/gkt1156
    pmc: PMC3965105
    pubmed: '24243848'
    title: 'miRNEST 2.0: a database of plant and animal microRNAs'
    year: 2013
  - doi: 10.1093/nar/gkr1159
    pmc: PMC3245016
    pubmed: '22135287'
    title: 'miRNEST database: an integrative approach in microRNA search and annotation'
    year: 2011
miro:
  aberowl:
    description: Application ontology for entities related to insecticide resistance
      in mosquitos
    download_owl: http://aber-owl.net/media/ontologies/MIRO/1/miro.owl
    homepage: http://anobase.vectorbase.org
    name: Mosquito insecticide resistance
    prefix: MIRO
  biocontext:
    prefix: MIRO
  bioportal:
    contact:
      email: louis@imbb.forth.gr
      name: C. Louis
    description: Application ontology for entities related to insecticide resistance
      in mosquitos.
    homepage: http://www.anobase.org
    name: Mosquito Insecticide Resistance
    prefix: MIRO
    version: releases/2014-05-14
  contact:
    email: louis@imbb.forth.gr
    github: null
    name: Christos Louis
    orcid: 0000-0003-2497-2210
  download_obo: http://purl.obolibrary.org/obo/miro.obo
  example: '40000617'
  fairsharing:
    abbreviation: MIRO
    description: Monitoring of insect vector populations with respect to their susceptibility
      to one or more insecticides is a crucial element of the strategies used for
      the control of arthropod-borne diseases. This management task can nowadays be
      achieved more efficiently when assisted by IT (Information Technology) tools,
      ranging from modern integrated databases to GIS (Geographic Information System).
      MIRO is an application ontology that can be used for the purpose of controlling
      mosquitoes and, thus, the diseases that they transmit.
    domains:
    - mutation
    - phenotype
    homepage: https://www.vectorbase.org/ontology-browser
    name: Mosquito Insecticide Resistance Ontology
    prefix: FAIRsharing.sjf113
    publications:
    - doi: 10.1371/journal.pntd.0000465
      pubmed: '19547750'
      title: 'MIRO and IRbase: IT tools for the epidemiological monitoring of insecticide
        resistance in mosquito disease vectors'
      year: 2009
    subjects:
    - Life Science
  mappings:
    aberowl: MIRO
    biocontext: MIRO
    bioportal: MIRO
    fairsharing: FAIRsharing.sjf113
    obofoundry: miro
    ols: miro
    ontobee: MIRO
  obofoundry:
    contact: louis@imbb.forth.gr
    contact.label: Christos (Kitsos) Louis
    deprecated: true
    description: Application ontology for entities related to insecticide resistance
      in mosquitos
    domain: environment
    download.obo: http://purl.obolibrary.org/obo/miro.obo
    download.owl: http://purl.obolibrary.org/obo/miro.owl
    homepage: https://github.com/VEuPathDB-ontology/MIRO
    name: Mosquito insecticide resistance
    prefix: miro
    repository: https://github.com/VEuPathDB-ontology/MIRO
  ols:
    description: Application ontology for entities related to insecticide resistance
      in mosquitos
    download_owl: http://purl.obolibrary.org/obo/miro.owl
    name: Mosquito insecticide resistance
    prefix: miro
    version: '2014-05-14'
    version.iri: http://purl.obolibrary.org/obo/miro/releases/2014-05-14/miro.owl
  ontobee:
    library: Library
    name: Mosquito insecticide resistance
    prefix: MIRO
  pattern: ^\d{8}$
  prefix: miro
  publications:
  - doi: 10.1371/journal.pntd.0000465
    pmc: PMC2694272
    pubmed: '19547750'
    title: 'MIRO and IRbase: IT tools for the epidemiological monitoring of insecticide
      resistance in mosquito disease vectors'
    year: 2009
mirtarbase:
  biocontext:
    prefix: MIRTARBASE
  contributor_extras:
  - email: benjamin_gyori@hms.harvard.edu
    github: bgyori
    name: Benjamin M. Gyori
    orcid: 0000-0001-9439-5346
  - email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  fairsharing:
    abbreviation: miRTarBase
    contact:
      email: ken.sd.hsu@gmail.com
      name: Sheng-Da Hsu
      orcid: 0000-0002-8214-1696
    description: As a database, miRTarBase has accumulated more than fifty thousand
      miRNA-target interactions (MTIs), which are collected by manually surveying
      pertinent literature after data mining of the text systematically to filter
      research articles related to functional studies of miRNAs. Generally, the collected
      MTIs are validated experimentally by reporter assay, western blot, microarray
      and next-generation sequencing experiments. While containing the largest amount
      of validated MTIs, the miRTarBase provides the most updated collection by comparing
      with other similar, previously developed databases.
    homepage: http://miRTarBase.mbc.nctu.edu.tw
    name: miRTarBase
    prefix: FAIRsharing.f0bxfg
    publications:
    - doi: 10.1093/nar/gkq1107
      pubmed_id: 21071411
      title: 'miRTarBase: a database curates experimentally validated microRNA-target
        interactions.'
    subjects:
    - Life Science
  homepage: https://mirtarbase.cuhk.edu.cn/
  integbio:
    description: miRTarBase Version 3.5 is a database that contains information about
      miRNA-target interactions (MTIs) obtained by manual search of scientific literature
      with data on 4867 miRNA-target interactions, 726 miRNAs and 2789 target genes
      from 17 species. The database can be browsed or searched by keyword, as well
      as downloaded.
    fairsharing: biodbcore-000615
    homepage: http://mirtarbase.cuhk.edu.cn/php/index.php
    information_keywords:
    - Sequence
    - Interaction/Pathway
    - Image/Movie
    maintainer: Institute of Bioinformatics and Systems Biology, National Chiao Tung
      University
    name: miRTarBase
    prefix: nbdc01217
    pubmeds:
    - '21071411'
    status: Active
    target_keywords:
    - Genome/Gene
    - RNA
  mappings:
    biocontext: MIRTARBASE
    fairsharing: FAIRsharing.f0bxfg
    integbio: nbdc01217
    miriam: mirtarbase
    n2t: mirtarbase
    pathguide: '715'
    wikidata: P2646
  miriam:
    deprecated: true
    description: miRTarBase is a database of miRNA-target interactions (MTIs), collected
      manually from relevant literature, following Natural Language Processing of
      the text to identify research articles related to functional studies of miRNAs.
      Generally, the collected MTIs are validated experimentally by reporter assay,
      western blot, microarray and next-generation sequencing experiments.
    homepage: http://mirtarbase.mbc.nctu.edu.tw/
    id: '00000562'
    name: miRTarBase
    namespaceEmbeddedInLui: false
    pattern: ^MIRT\d{6}$
    prefix: mirtarbase
    sampleId: MIRT000002
    uri_format: http://mirtarbase.mbc.nctu.edu.tw/php/detail.php?mirtid=$1
  n2t:
    description: miRTarBase is a database of miRNA-target interactions (MTIs), collected
      manually from relevant literature, following Natural Language Processing of
      the text to identify research articles related to functional studies of miRNAs.
      Generally, the collected MTIs are validated experimentally by reporter assay,
      western blot, microarray and next-generation sequencing experiments.
    example: MIRT000002
    homepage: http://mirtarbase.mbc.nctu.edu.tw/
    name: miRTarBase at National Chiao Tung University
    namespaceEmbeddedInLui: false
    pattern: ^MIRT\d{6}$
    prefix: mirtarbase
    uri_format: http://mirtarbase.mbc.nctu.edu.tw/php/detail.php?mirtid=$1
  name: mirTarBase
  pathguide:
    abbreviation: miRTarBase
    homepage: http://mirtarbase.mbc.nctu.edu.tw/
    name: The Experimentally Validated microRNA-target Interactions Database
    prefix: '715'
  prefix: mirtarbase
  publications:
  - doi: 10.1093/nar/gkab1079
    pmc: PMC8728135
    pubmed: '34850920'
    title: 'miRTarBase update 2022: an informative resource for experimentally validated
      miRNA–target interactions'
    year: 2022
  - doi: 10.1093/nar/gkz896
    pmc: PMC7145596
    pubmed: '31647101'
    title: 'miRTarBase 2020: updates to the experimentally validated microRNA-target
      interaction database'
    year: 2020
  - doi: 10.1093/nar/gkx1067
    pmc: PMC5753222
    pubmed: '29126174'
    title: 'miRTarBase update 2018: a resource for experimentally validated microRNA-target
      interactions'
    year: 2018
  - doi: 10.1093/nar/gkv1258
    pmc: PMC4702890
    pubmed: '26590260'
    title: 'miRTarBase 2016: updates to the experimentally validated miRNA-target
      interactions database'
    year: 2016
  - doi: 10.1093/nar/gkt1266
    pmc: PMC3965058
    pubmed: '24304892'
    title: 'miRTarBase update 2014: an information resource for experimentally validated
      miRNA-target interactions'
    year: 2014
  - doi: 10.1093/nar/gkq1107
    pmc: PMC3013699
    pubmed: '21071411'
    title: 'miRTarBase: a database curates experimentally validated microRNA-target
      interactions'
    year: 2010
  references:
  - https://github.com/biopragmatics/bioregistry/pull/940
  uri_format: https://mirtarbase.cuhk.edu.cn/~miRTarBase/miRTarBase_2022/php/detail.php?mirtid=$1
  wikidata:
    description: identifier for the mirTarBase database, a database for microRNAs
      and their targets
    example:
    - MIRT000312
    homepage: http://mirtarbase.mbc.nctu.edu.tw/php/download.php
    name: mirTarBase ID
    pattern: ^MIRT\d{6}$
    prefix: P2646
    uri_format: https://mirtarbase.cuhk.edu.cn/~miRTarBase/miRTarBase_2022/php/detail.php?mirtid=$1
mirte:
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: This website provides access to our 2003 and 2005 miRNA-Target predictions
    for Drosophila miRNAs
  example: miR-1
  homepage: http://www.russelllab.org/miRNAs/
  name: miRNA Target Prediction at EMBL
  prefix: mirte
mite:
  contact:
    email: zdoucmm@gmail.com
    github: mmzdouc
    name: Mitja M. Zdouc
    orcid: 0000-0001-6534-6609
  contributor:
    email: zdoucmm@gmail.com
    github: mmzdouc
    name: Mitja M. Zdouc
    orcid: 0000-0001-6534-6609
  description: MITE (Minimum Information about a Tailoring Enzyme) is a data repository
    and associated data standard designed to capture the reaction- and substrate-specificities
    of tailoring enzymes. Community-driven and fully expert-reviewed, it represents
    enzymatic reactions using reaction SMARTS and links to established resources such
    as UniProt, NCBI GenPept, Rhea, and MIBiG. MITE serves as a knowledgebase for
    enzyme and pathway annotation, in silico biosynthesis, and machine learning applications.
  example: MITE0000001
  github_request_issue: 1405
  homepage: https://mite.bioinformatics.nl
  license: CC0-1.0
  name: Minimum Information about a Tailoring Enzyme data repository
  pattern: ^MITE\d{7}$
  prefix: mite
  publications:
  - doi: 10.26434/chemrxiv-2024-78mtl
    pmc: null
    pubmed: null
    title: The Minimum Information about a Tailoring Enzyme/Maturase data standard
      for capturing natural product biosynthesis
    year: 2024
  repository: https://github.com/mite-standard/mite_data
  reviewer:
    email: b.gyori@northeastern.edu
    github: bgyori
    name: Benjamin M. Gyori
    orcid: 0000-0001-9439-5346
  reviewer_extras:
  - email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  uri_format: https://mite.bioinformatics.nl/repository/$1
mito:
  contact:
    email: null
    github: matteo-guenci
    name: Matteo Guenci
    orcid: 0009-0006-3139-1667
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: An ontology with predicates to formalization of the concept of mentions.
    The mentions may be either explicit (e.g. as when well stated into an article
    "Dr. Johnson's groundbreaking research on climate change") or implicit (e.g. such
    as discussing "seminal studies in the field"). MiTO contains the object property
    mito:mentions and its inverse mito:isMentionedBy.
  example: MentionType
  github_request_issue: 1663
  homepage: http://purl.org/spar/mito
  keywords:
  - mentions
  - natural language processing
  - ner
  - nlp
  - ontology
  - text mining
  name: Mention Typing Ontology
  prefix: mito
  repository: https://github.com/SPAROntologies/mito
  uri_format: http://purl.org/spar/mito/$1
mixs:
  aberowl:
    description: An RDF representation of the MIxS Family of Checklists
    download_owl: http://aber-owl.net/media/ontologies/MIXS/5/mixs.owl
    name: Minimal Information about any Sequence Ontology
    prefix: MIXS
    version: unknown
  bioportal:
    contact:
      email: mam@lbl.gov
      name: Mark Andrew Miller
    description: An OWL representation of the Minimum Information for any (x) Standard
      (MIxS), managed by the Genomic Standards Consortium.
    homepage: https://github.com/GenomicsStandardsConsortium/mixs
    name: Minimal Information about any Sequence Ontology
    prefix: MIXS
    version: v6.2.0
  comment: 'Some things to be decided before granting - [ ] should the prefix be mixs,
    gsc.mixs, MIxS, MIXS, ...? - [ ] MIxS terms are most commonly identified by a
    short computable stable label, e.g ph_regm. The GSC CIG team are creating numeric
    identifiers, e.g. MIXS:0001056 - Should we support both schemes? - If we do, should
    these be different prefixes? I would strongly recommend this. E.g. mixs.term:ph_regm,
    mixs:0001056. We can then have different regex patterns for both Additional notes:
    - It currently redirects to the tdwg wiki but this is I assume temporary'
  contact:
    email: mam@lbl.gov
    github: turbomam
    name: Mark Andrew Miller
    orcid: 0000-0001-9076-6066
  contributor:
    email: cjmungall@lbl.gov
    github: cmungall
    name: Chris Mungall
    orcid: 0000-0002-6601-2165
  contributor_extras:
  - email: chris@gigasciencejournal.com
    github: only1chunts
    name: Chris Hunter
    orcid: 0000-0002-1335-0881
  - email: lindsey.anderson@pnnl.gov
    github: lnanderson
    name: Lindsey N. Anderson
    orcid: 0000-0002-8741-7823
  - email: mam@lbl.gov
    github: turbomam
    name: Mark Andrew Miller
    orcid: 0000-0001-9076-6066
  description: The GSC family of minimum information standards (checklists) – Minimum
    Information about any (x) Sequence (MIxS). MIxS identifiers are for terms describing
    an aspect of an environmental sample.
  download_owl: https://w3id.org/mixs/mixs.owl.ttl
  example: '0001056'
  fairsharing:
    abbreviation: MIxS
    description: The minimum information about any (x) sequence (MIxS) is an overarching
      framework of sequence metadata, that includes technology-specific checklists
      from the previous MIGS and MIMS standards, provides a way of introducing additional
      checklists such as MIMARKS, and also allows annotation of sample data using
      environmental packages.
    homepage: http://gensc.org/mixs/
    name: Minimum Information about any (x) Sequence
    prefix: FAIRsharing.9aa0zp
    publications:
    - doi: 10.1038/nbt.1823
      pubmed_id: 21552244
      title: Minimum information about a marker gene sequence (MIMARKS) and minimum
        information about any (x) sequence (MIxS) specifications
    subjects: []
  github_request_issue: 151
  homepage: https://w3id.org/mixs
  mappings:
    aberowl: MIXS
    bioportal: MIXS
    fairsharing: FAIRsharing.9aa0zp
    ols: gscmixs
  name: Minimum Information about any (x) Sequence
  ols:
    contact: gensc-cig@googlegroups.com
    description: An OWL representation of the Minimum Information for any (x) Standard
      (MIxS), managed by the Genomic Standards Consortium. This file is released by
      the Genomic Standards Consortium (GSC; https://www.gensc.org/) for use by anyone
      handling data or information about biological sequences.
    download_rdf: https://w3id.org/mixs/mixs.owl.ttl
    homepage: https://w3id.org/mixs
    name: Minimum Information about any (x) Sequence (MIxS) standard
    prefix: gscmixs
    uri_format: MIXS:$1
  pattern: ^\d{7}$
  preferred_prefix: MIXS
  prefix: mixs
  providers:
  - code: github
    description: MIxS LinkML schema
    example: null
    first_party: null
    homepage: https://genomicsstandardsconsortium.github.io/mixs
    name: MIxS LinkML schema
    publications: null
    status: null
    uri_format: https://genomicsstandardsconsortium.github.io/mixs/$1
  publications:
  - doi: 10.1038/nbt.1823
    pmc: PMC3367316
    pubmed: '21552244'
    title: Minimum information about a marker gene sequence (MIMARKS) and minimum
      information about any (x) sequence (MIxS) specifications
    year: 2011
  - doi: 10.1038/nbt.1823
    pmc: null
    pubmed: null
    title: Minimum information about a marker gene sequence (MIMARKS) and minimum
      information about any (x) sequence (MIxS) specifications
    year: null
  rdf_uri_format: https://w3id.org/mixs/$1
  references:
  - https://github.com/biopragmatics/bioregistry/pull/1738
  reviewer:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  uri_format: https://w3id.org/mixs/$1
mlc:
  mappings:
    miriam: mlc
  miriam:
    deprecated: false
    description: MLCommons Association artifacts, including benchmark results, datasets,
      and saved models.
    homepage: https://mlcommons.org/en/
    id: 00000828
    name: MLCommons Association
    namespaceEmbeddedInLui: false
    pattern: ^[0-9a-zA-Z\.\-\_]+$
    prefix: mlc
    sampleId: 0.7-123
    uri_format: https://www.mlcommons.org/mlc-id/$1
  prefix: mlc
mmdb:
  biocontext:
    prefix: MMDB
  contact:
    email: siqian.he@nih.gov
    github: null
    name: Siqian He
    orcid: 0000-0002-1707-4167
  edam:
    description: An identifier of an entry from the MMDB database.
    name: MMDB
    obsolete: false
    prefix: '2667'
  mappings:
    biocontext: MMDB
    edam: '2667'
    miriam: mmdb
    n2t: mmdb
    pathguide: '508'
    prefixcommons: mmdb
  miriam:
    deprecated: false
    description: The Molecular Modeling Database (MMDB) is a database of experimentally
      determined structures obtained from the Protein Data Bank (PDB). Since structures
      are known for a large fraction of all protein families, structure homologs may
      facilitate inference of biological function, or the identification of binding
      or catalytic sites.
    homepage: http://www.ncbi.nlm.nih.gov/sites/entrez?db=structure
    id: '00000121'
    name: Molecular Modeling Database
    namespaceEmbeddedInLui: false
    pattern: ^\d{1,5}$
    prefix: mmdb
    sampleId: '50885'
    uri_format: http://www.ncbi.nlm.nih.gov/Structure/mmdb/mmdbsrv.cgi?uid=$1
  n2t:
    description: The Molecular Modeling Database (MMDB) is a database of experimentally
      determined structures obtained from the Protein Data Bank (PDB). Since structures
      are known for a large fraction of all protein families, structure homologs may
      facilitate inference of biological function, or the identification of binding
      or catalytic sites.
    example: '50885'
    homepage: http://www.ncbi.nlm.nih.gov/sites/entrez?db=structure
    name: MMDB at NCBI
    namespaceEmbeddedInLui: false
    pattern: ^\d{1,5}$
    prefix: mmdb
    uri_format: http://www.ncbi.nlm.nih.gov/Structure/mmdb/mmdbsrv.cgi?uid=$1
  pathguide:
    abbreviation: MMDB
    homepage: http://www.ncbi.nlm.nih.gov/Structure/MMDB/docs/mmdb_search.html
    name: Molecular Modeling Database
    prefix: '508'
  prefix: mmdb
  prefixcommons:
    description: The Molecular Modeling Database (MMDB), as part of the Entrez system,
      facilitates access to structure data by connecting them with associated literature,
      protein and nucleic acid sequences, chemicals, biomolecular interactions, and
      more.
    example: '50885'
    homepage: http://www.ncbi.nlm.nih.gov/Structure/
    keywords:
    - structure
    - protein
    - DNA
    - small molecule
    - interaction
    name: Molecular Modeling Database
    pattern: ^\d{1,5}$
    prefix: mmdb
    pubmed_ids:
    - '17135201'
    uri_format: http://www.ncbi.nlm.nih.gov/Structure/mmdb/mmdbsrv.cgi?uid=$1
  publications:
  - doi: 10.1093/nar/gkl952
    pmc: PMC1751549
    pubmed: '17135201'
    title: 'MMDB: annotating protein sequences with Entrez''s 3D-structure database'
    year: 2006
  - doi: null
    pmc: null
    pubmed: '17135201'
    title: null
    year: null
mmmp.biomaps:
  biocontext:
    prefix: MMMP:BIOMAPS
  biolink:
    is_identifiers: false
    is_obo: false
    prefix: mmmp.biomaps
    uri_format: https://bioregistry.io/mmmp.biomaps:$1
  mappings:
    biocontext: MMMP:BIOMAPS
    biolink: mmmp.biomaps
    miriam: mmmp.biomaps
    n2t: biomaps
    prefixcommons: mmmp
  miriam:
    deprecated: false
    description: A collection of molecular interaction maps and pathways involved
      in cancer development and progression with a focus on melanoma.
    homepage: http://www.mmmp.org/MMMP/public/biomap/listBiomap.mmmp
    id: '00000075'
    name: Melanoma Molecular Map Project Biomaps
    namespaceEmbeddedInLui: false
    pattern: ^\d+$
    prefix: mmmp.biomaps
    sampleId: '37'
    uri_format: http://www.mmmp.org/MMMP/public/biomap/viewBiomap.mmmp?id=$1
  n2t:
    description: A collection of molecular interaction maps and pathways involved
      in cancer development and progression with a focus on melanoma.
    example: '37'
    homepage: http://www.mmmp.org/MMMP/public/biomap/listBiomap.mmmp
    name: main webpage
    namespaceEmbeddedInLui: false
    pattern: ^\d+$
    prefix: biomaps
    uri_format: http://www.mmmp.org/MMMP/public/biomap/viewBiomap.mmmp?id=$1
  prefix: mmmp.biomaps
  prefixcommons:
    description: A collection of molecular interaction maps and pathways involved
      in cancer development and progression with a focus on melanoma
    example: '37'
    homepage: http://www.mmmp.org/MMMP/
    keywords:
    - interaction
    - pathway
    - molecule
    name: Melanoma Molecular Map Project
    pattern: ^\d+$
    prefix: mmmp
    synonyms:
    - biomaps
    uri_format: http://www.mmmp.org/MMMP/public/biomap/viewBiomap.mmmp?id=$1
  synonyms:
  - mmmp:biomaps
mmo:
  aberowl:
    description: A representation of the variety of methods used to make clinical
      and phenotype measurements.
    download_owl: http://aber-owl.net/media/ontologies/MMO/118/mmo.owl
    homepage: https://rgd.mcw.edu/rgdweb/ontology/view.html?acc_id=MMO:0000000
    name: Measurement method ontology
    prefix: MMO
  biocontext:
    prefix: MMO
  bioportal:
    contact:
      email: akwitek@mcw.edu
      name: Anne Kwitek
    description: The Measurement Method Ontology is designed to represent the variety
      of methods used to make qualitative and quantitative clinical and phenotype
      measurements both in the clinic and with model organisms.
    homepage: https://rgd.mcw.edu/rgdweb/ontology/view.html?acc_id=MMO:0000000
    name: Measurement Method Ontology
    prefix: MMO
    publications:
    - http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3361058/
    version: '2.109'
  example: '0000574'
  fairsharing:
    abbreviation: MMO
    contact:
      email: shimoyama@mcw.edu
      name: Mary Shimoyama
      orcid: 0000-0003-1176-0796
    description: The Measurement Method Ontology is designed to represent the variety
      of methods used to make qualitative and quantitative clinical and phenotype
      measurements both in the clinic and with model organisms.
    domains:
    - Model organisms
    - phenotype
    homepage: http://rgd.mcw.edu/rgdweb/ontology/view.html?acc_id=MMO:0000000
    name: Measurement Method Ontology
    prefix: FAIRsharing.bgkyd7
    publications:
    - doi: 10.3389/fgene.2012.00087
      pubmed: '22654893'
      title: Three ontologies to define phenotype measurement data
      year: 2012
    - doi: 10.1186/2041-1480-4-26
      pubmed: '24103152'
      title: 'The clinical measurement, measurement method and experimental condition
        ontologies: expansion, improvements and new applications'
      year: 2013
    subjects:
    - Life Science
    - Preclinical Studies
    - Biomedical Science
    twitter: ratgenome
  mappings:
    aberowl: MMO
    biocontext: MMO
    bioportal: MMO
    fairsharing: FAIRsharing.bgkyd7
    obofoundry: mmo
    ols: mmo
    ontobee: MMO
    tib: mmo
    wikidata.entity: Q81661696
  obofoundry:
    contact: jrsmith@mcw.edu
    contact.github: jrsjrs
    contact.label: Jennifer Smith
    contact.orcid: 0000-0002-6443-9376
    deprecated: false
    description: 'A representation of the variety of methods used to make clinical
      and phenotype measurements. '
    domain: health
    download.obo: http://purl.obolibrary.org/obo/mmo.obo
    download.owl: http://purl.obolibrary.org/obo/mmo.owl
    homepage: https://rgd.mcw.edu/rgdweb/ontology/view.html?acc_id=MMO:0000000
    license: CC0 1.0
    license.url: https://creativecommons.org/publicdomain/zero/1.0/
    name: Measurement method ontology
    preferredPrefix: MMO
    prefix: mmo
    publications:
    - id: https://www.ncbi.nlm.nih.gov/pubmed/22654893
      title: Three ontologies to define phenotype measurement data.
    - id: https://www.ncbi.nlm.nih.gov/pubmed/24103152
      title: 'The clinical measurement, measurement method and experimental condition
        ontologies: expansion, improvements and new applications.'
    repository: https://github.com/rat-genome-database/MMO-Measurement-Method-Ontology
  ols:
    description: A representation of the variety of methods used to make clinical
      and phenotype measurements.
    download_owl: http://purl.obolibrary.org/obo/mmo.owl
    homepage: https://rgd.mcw.edu/rgdweb/ontology/view.html?acc_id=MMO:0000000
    name: Measurement method ontology
    prefix: mmo
    tracker: https://github.com/rat-genome-database/MMO-Measurement-Method-Ontology/issues
    version: '2.168'
    version.iri: http://purl.obolibrary.org/obo/mmo/2.168/mmo.owl
  ontobee:
    library: Library
    name: Measurement method ontology
    prefix: MMO
  pattern: ^\d{7}$
  prefix: mmo
  publications:
  - doi: 10.1186/2041-1480-4-26
    pmc: PMC3882879
    pubmed: '24103152'
    title: 'The clinical measurement, measurement method and experimental condition
      ontologies: expansion, improvements and new applications'
    year: 2013
  - doi: 10.3389/fgene.2012.00087
    pmc: PMC3361058
    pubmed: '22654893'
    title: Three ontologies to define phenotype measurement data
    year: 2012
  tib:
    description: A representation of the variety of methods used to make clinical
      and phenotype measurements.
    download_owl: http://purl.obolibrary.org/obo/mmo.owl
    homepage: https://github.com/rat-genome-database/MMO-Measurement-Method-Ontology/
    keywords:
    - DataPLANT
    name: Measurement Method Ontology
    prefix: mmo
    tracker: https://github.com/rat-genome-database/MMO-Measurement-Method-Ontology/issues
    version.iri: http://purl.obolibrary.org/obo/mmo/2.164/mmo.owl
  twitter: ratgenome
  uri_format: http://purl.obolibrary.org/obo/MMO_$1
mmp.cat:
  biocontext:
    prefix: MMP.CAT
  mappings:
    biocontext: MMP.CAT
    miriam: mmp.cat
    n2t: mmp.cat
  miriam:
    deprecated: false
    description: MarCat is a gene (protein) catalogue of uncultivable and cultivable
      marine genes and proteins derived from metagenomics samples.
    homepage: https://mmp.sfb.uit.no/databases/marcat/
    id: '00000615'
    name: MarCat
    namespaceEmbeddedInLui: false
    pattern: ^MMP\d+.\d+$
    prefix: mmp.cat
    sampleId: MMP743597.11
    uri_format: https://mmp.sfb.uit.no/databases/marcat/#/records/$1
  n2t:
    description: MarCat is a gene (protein) catalogue of uncultivable and cultivable
      marine genes and proteins derived from metagenomics samples.
    example: MMP743597.11
    homepage: https://mmp.sfb.uit.no/databases/marcat/
    name: MarCat through SfB
    namespaceEmbeddedInLui: false
    pattern: ^MMP\d+.\d+$
    prefix: mmp.cat
    uri_format: https://mmp.sfb.uit.no/databases/marcat/#/records/$1
  prefix: mmp.cat
mmp.db:
  biocontext:
    prefix: MMP.DB
  mappings:
    biocontext: MMP.DB
    miriam: mmp.db
    n2t: mmp.db
  miriam:
    deprecated: false
    description: MarDB includes all sequenced marine microbial genomes regardless
      of level of completeness.
    homepage: https://mmp.sfb.uit.no/databases/mardb/
    id: '00000614'
    name: MarDB
    namespaceEmbeddedInLui: false
    pattern: ^MMP\d+.\d+$
    prefix: mmp.db
    sampleId: MMP02954345.1
    uri_format: https://mmp.sfb.uit.no/databases/mardb/#/records/$1
  n2t:
    description: MarDB includes all sequenced marine microbial genomes regardless
      of level of completeness.
    example: MMP02954345.1
    homepage: https://mmp.sfb.uit.no/databases/mardb/
    name: MarDB through SfB
    namespaceEmbeddedInLui: false
    pattern: ^MMP\d+.\d+$
    prefix: mmp.db
    uri_format: https://mmp.sfb.uit.no/databases/mardb/#/records/$1
  prefix: mmp.db
mmp.fun:
  mappings:
    miriam: mmp.fun
  miriam:
    deprecated: false
    description: MarFun is manually curated database for marine fungi which is a part
      of the MAR databases.
    homepage: https://mmp.sfb.uit.no/databases/marfun
    id: 00000729
    name: MarFun
    namespaceEmbeddedInLui: false
    pattern: ^MMP\d+.\d+$
    prefix: mmp.fun
    sampleId: MMP3888430
    uri_format: https://mmp.sfb.uit.no/databases/marfun/#/records/$1
  prefix: mmp.fun
mmp.ref:
  biocontext:
    prefix: MMP.REF
  mappings:
    biocontext: MMP.REF
    miriam: mmp.ref
    n2t: mmp.ref
  miriam:
    deprecated: false
    description: MarRef is a manually curated marine microbial reference genome database
      that contains completely sequenced genomes.
    homepage: https://mmp.sfb.uit.no/databases/marref/
    id: '00000613'
    name: MarRef
    namespaceEmbeddedInLui: false
    pattern: ^MMP\d+.\d+$
    prefix: mmp.ref
    sampleId: MMP3312982.2
    uri_format: https://mmp.sfb.uit.no/databases/marref/#/records/$1
  n2t:
    description: MarRef is a manually curated marine microbial reference genome database
      that contains completely sequenced genomes.
    example: MMP3312982.2
    homepage: https://mmp.sfb.uit.no/databases/marref/
    name: MarRef through SfB
    namespaceEmbeddedInLui: false
    pattern: ^MMP\d+.\d+$
    prefix: mmp.ref
    uri_format: https://mmp.sfb.uit.no/databases/marref/#/records/$1
  prefix: mmp.ref
mmrrc:
  biocontext:
    prefix: MMRRC
    uri_format: https://www.mmrrc.org/catalog/sds.php?mmrrc_id=$1
  cellosaurus:
    category: Cell line collections (Providers)
    homepage: https://www.mmrrc.org/
    name: Mutant Mouse Resource & Research Centers
    prefix: MMRRC
    uri_format: https://www.mmrrc.org/catalog/getSDS.php?mmrrc_id=$1
  contact:
    email: f.grieder@nih.gov
    github: null
    name: Franziska B. Grieder
    orcid: 0000-0002-3070-8224
  fairsharing:
    abbreviation: MMRRC
    description: The MMRRC distributes and cryopreserves scientifically valuable,
      genetically engineered mouse strains and mouse ES cell lines with potential
      value for the genetics and biomedical research community. The Catalog provides
      information on the strains available from the MMRRC.
    homepage: https://www.mmrrc.org/
    name: Mutant Mouse Resource and Research Centers
    prefix: FAIRsharing.9dpd18
    publications:
    - doi: null
      pubmed_id: 12102564
      title: 'Mutant Mouse Regional Resource Center Program: a resource for distribution
        of mouse models for biomedical research.'
    subjects:
    - Biology
    twitter: mmrc
  homepage: https://www.mmrrc.org
  mappings:
    biocontext: MMRRC
    cellosaurus: MMRRC
    fairsharing: FAIRsharing.9dpd18
    miriam: mmrrc
    n2t: mmrrc
    re3data: r3d100013715
    rrid: MMRRC
  miriam:
    deprecated: false
    description: The MMRRC database is a repository of available mouse stocks and
      embryonic stem cell line collections.
    homepage: http://www.mmrrc.org/
    id: '00000324'
    name: MMRRC
    namespaceEmbeddedInLui: false
    pattern: ^\d+$
    prefix: mmrrc
    sampleId: '70'
    uri_format: http://www.mmrrc.org/catalog/getSDS.php?mmrrc_id=$1
  n2t:
    description: The MMRRC database is a repository of available mouse stocks and
      embryonic stem cell line collections.
    example: '70'
    homepage: http://www.mmrrc.org/
    name: MMRRC  at University of North Carolina
    namespaceEmbeddedInLui: false
    pattern: ^\d+$
    prefix: mmrrc
    uri_format: http://www.mmrrc.org/catalog/getSDS.php?mmrrc_id=$1
  name: Mutant Mouse Resource and Research Centers
  prefix: mmrrc
  publications:
  - doi: null
    pmc: null
    pubmed: '12102564'
    title: 'Mutant Mouse Regional Resource Center Program: a resource for distribution
      of mouse models for biomedical research'
    year: 2002
  re3data:
    description: The MMRRC is the nation’s premier national public repository system
      for mutant mice. Funded by the NIH continuously since 1999, the MMRRC archives
      and distributes scientifically valuable spontaneous and induced mutant mouse
      strains and ES cell lines for use by the biomedical research community. The
      MMRRC consists of a national network of breeding and distribution repositories
      and an Informatics Coordination and Service Center located at 4 major academic
      centers across the nation. The MMRRC is committed to upholding the highest standards
      of experimental design and quality control to optimize the reproducibility of
      research studies using mutant mice.
    doi: 10.17616/R31NJN2R
    homepage: https://www.mmrrc.org
    name: Mutant Mouse Resource & Research Centers
    prefix: r3d100013715
    synonyms:
    - MMRRC
    xrefs:
      nif: 0000-00045
  rrid:
    homepage: http://www.mmrrc.org/
    keywords:
    - FASEB list
    - cryopreserved
    - database
    - embryonic stem cell
    - embryonic stem cell line
    - mouse strain
    - mutant
    - mutant mouse strain
    - stem cell
    - transgenic
    name: Mutant Mouse Regional Resource Center
    prefix: MMRRC
    scr: 002953
mmsinc:
  mappings:
    prefixcommons: mmsinc
  prefix: mmsinc
  prefixcommons:
    description: MMSsINC is a database of commercially-available compounds for virtual
      screening and chemoinformatic applications. MMsINC contains over 4 million non-redundant
      chemical compounds in 3D formats.
    example: MMs00000001
    homepage: http://mms.dsfarm.unipd.it/MMsINC
    keywords:
    - small molecule
    - structure
    name: MMsINC
    pattern: ^MMs\d+$
    prefix: mmsinc
    uri_format: http://mms.dsfarm.unipd.it/mmsinc/search/molecule.php?mmscode=$1
  reviewer:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
mmsl:
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: The Lexicon is a foundational database with comprehensive drug product
    and disease nomenclature information. It includes drug names, drug product information,
    disease names, coding systems such as ICD-9-CM and NDC, generic names, brand names
    and common abbreviations. A comprehensive list of standard or customized disease
    names and ICD-9 codes is also included.
  example: '3355'
  hl7:
    description: 'Medisource Lexicon. Multum Information Services, Inc., Denver, CO.
      Release Date: March 1, 2004. URL: http://www.multum.com/ Phone: 888-633-4772
      x1420.http://www.multum.com/Lexicon.htm'
    homepage: http://www.multum.com/
    name: Multum
    organization: Multum Information Services, Inc.
    preferred_prefix: mmsl
    prefix: 2.16.840.1.113883.6.175
    status: Complete
  homepage: https://www.nlm.nih.gov/research/umls/rxnorm/sourcereleasedocs/mmsl.html
  mappings:
    hl7: 2.16.840.1.113883.6.175
  name: Multum MediSource Lexicon
  pattern: ^\d+$
  prefix: mmsl
  synonyms:
  - MMSL_CODE
mmusdv:
  aberowl:
    description: Life cycle stages for Mus Musculus
    download_owl: http://aber-owl.net/media/ontologies/MMUSDV/12/mmusdv.owl
    homepage: https://github.com/obophenotype/developmental-stage-ontologies/wiki/MmusDv
    name: Mouse Developmental Stages
    prefix: MMUSDV
  biocontext:
    prefix: MMUSDV
  biolink:
    is_identifiers: false
    is_obo: true
    prefix: MmusDv
    uri_format: http://purl.obolibrary.org/obo/MMUSDV_$1
  bioportal:
    contact:
      email: cjmungall@lbl.gov
      name: Chris Mungall
    description: Life cycle stages for Mus Musculus. MmusDv was developed by the Bgee
      group with assistance from the core Uberon developers and the Mouse anatomy
      ontology developers. Currently it includes both embryonic stages and adult stages.
    homepage: https://github.com/obophenotype/developmental-stage-ontologies/wiki/MmusDv
    name: Mouse Developmental Stages
    prefix: MMUSDV
  example: '0000066'
  fairsharing:
    abbreviation: MMUSDV
    description: 'Life cycle stages for Mus Musculus. MmusDv was developed by the
      Bgee group with assistance from the core Uberon developers and the Mouse anatomy
      ontology developers. Currently it includes both embryonic stages and adult stages. '
    domains:
    - life cycle stage
    homepage: https://obofoundry.org/ontology/mmusdv.html
    license: CC-BY-3.0
    name: Mouse Developmental Stages
    prefix: FAIRsharing.zchb68
    repository: https://github.com/obophenotype/developmental-stage-ontologies
    subjects:
    - Embryology
    - Anatomy
    - Developmental Biology
  mappings:
    aberowl: MMUSDV
    biocontext: MMUSDV
    biolink: MmusDv
    bioportal: MMUSDV
    fairsharing: FAIRsharing.zchb68
    obofoundry: mmusdv
    ols: mmusdv
    ontobee: MmusDv
    wikidata.entity: Q81661698
  obofoundry:
    contact: frederic.bastian@unil.ch
    contact.github: fbastian
    contact.label: Frédéric Bastian
    contact.orcid: 0000-0002-9415-5104
    deprecated: false
    description: Life cycle stages for Mus Musculus
    domain: anatomy and development
    download.obo: http://purl.obolibrary.org/obo/mmusdv.obo
    download.owl: http://purl.obolibrary.org/obo/mmusdv.owl
    homepage: https://github.com/obophenotype/developmental-stage-ontologies/wiki/MmusDv
    license: CC BY 3.0
    license.url: http://creativecommons.org/licenses/by/3.0/
    name: Mouse Developmental Stages
    preferredPrefix: MmusDv
    prefix: mmusdv
    repository: https://github.com/obophenotype/developmental-stage-ontologies
  ols:
    description: Life cycle stages for Mus Musculus
    download_owl: http://purl.obolibrary.org/obo/mmusdv.owl
    homepage: https://github.com/obophenotype/developmental-stage-ontologies/wiki/MmusDv
    name: Mouse Developmental Stages
    prefix: mmusdv
    tracker: https://github.com/obophenotype/developmental-stage-ontologies/issues
    version: '2025-01-23'
    version.iri: http://purl.obolibrary.org/obo/life-stages/releases/2025-01-23/components/mmusdv.owl
  ontobee:
    library: Library
    name: Mouse Developmental Stages
    prefix: MmusDv
  pattern: ^\d{7}$
  prefix: mmusdv
  synonyms:
  - MmusDv
  uri_format: http://purl.obolibrary.org/obo/MmusDv_$1
mo:
  aberowl:
    description: Concepts, definitions, terms, and resources for standardized description
      of a microarray experiment in support of MAGE v.1.
    download_owl: http://aber-owl.net/media/ontologies/MO/1/mo.owl
    homepage: http://mged.sourceforge.net/ontologies/MGEDontology.php
    name: Microarray and Gene Expression Data Ontology
    prefix: MO
    version: 1.3.1.1
  biocontext:
    prefix: MO
  bioportal:
    contact:
      email: stoeckrt@pcbi.upenn.edu
      name: Chris Stoeckert
    description: Concepts, definitions, terms, and resources for standardized description
      of a microarray experiment in support of MAGE v.1.
    homepage: http://mged.sourceforge.net/ontologies/MGEDontology.php
    name: Microarray and Gene Expression Data Ontology
    prefix: MO
    version: 1.3.1.1
  mappings:
    aberowl: MO
    biocontext: MO
    bioportal: MO
    miriam: mo
    n2t: mo
    obofoundry: mo
    wikidata.entity: Q114677897
  miriam:
    deprecated: false
    description: The MGED Ontology (MO) provides terms for annotating all aspects
      of a microarray experiment from the design of the experiment and array layout,
      through to the preparation of the biological sample and the protocols used to
      hybridize the RNA and analyze the data.
    homepage: https://mged.sourceforge.net/ontologies/MGEDontology.php
    id: '00000303'
    name: MGED Ontology
    namespaceEmbeddedInLui: false
    pattern: ^\w+$
    prefix: mo
    sampleId: ArrayGroup
    uri_format: https://mged.sourceforge.net/ontologies/MGEDontology.php#$1
  n2t:
    description: The MGED Ontology (MO) provides terms for annotating all aspects
      of a microarray experiment from the design of the experiment and array layout,
      through to the preparation of the biological sample and the protocols used to
      hybridize the RNA and analyze the data.
    example: ArrayGroup
    homepage: http://bioportal.bioontology.org/
    name: MGED Ontology at BioPortal
    namespaceEmbeddedInLui: false
    pattern: ^\w+$
    prefix: mo
    uri_format: http://purl.bioontology.org/ontology/MO/$1
  obofoundry:
    contact: stoeckrt@pcbi.upenn.edu
    contact.label: Chris Stoeckert
    contact.orcid: 0000-0002-5714-991X
    deprecated: true
    description: A standardized description of a microarray experiment in support
      of MAGE v.1.
    domain: investigations
    download.owl: http://purl.obolibrary.org/obo/mo.owl
    homepage: http://mged.sourceforge.net/ontologies/MGEDontology.php
    name: Microarray experimental conditions
    prefix: mo
  prefix: mo
mobidb:
  biocontext:
    prefix: MOBIDB
  fairsharing:
    abbreviation: MobiDB
    contact:
      email: silvio.tosatto@unipd.it
      name: Silvio C.E. Tosatto
      orcid: 0000-0003-4525-7793
    description: 'MobiDB is a database of intrinsically disordered regions (IDRs)
      and related features from various sources and prediction tools. Different levels
      of reliability and different features are reported as different and independent
      annotations. The database features three levels of annotation: manually curated,
      indirect and predicted. MobiDB annotates the binding modes of disordered proteins,
      whether they undergo disorder-to-order transitions or remain disordered in the
      bound state. In addition, disordered regions undergoing liquid-liquid phase
      separation or post-translational modifications are defined.'
    homepage: https://mobidb.org/
    license: CC-BY-4.0
    name: MobiDB
    prefix: FAIRsharing.jwra3e
    publications:
    - doi: 10.1093/nar/gkx1071
      pubmed_id: 29136219
      title: 'MobiDB 3.0: More annotations for intrinsic disorder, conformational
        diversity and interactions in proteins'
    - doi: 10.1093/bioinformatics/bts327
      pubmed_id: 22661649
      title: 'MobiDB: a comprehensive database of intrinsic protein disorder annotations.'
    - doi: 10.1093/nar/gku982
      pubmed_id: 25361972
      title: 'MobiDB 2.0: an improved database of intrinsically disordered and mobile
        proteins.'
    - doi: 10.1093/nar/gkaa1058
      pubmed_id: 33237329
      title: 'MobiDB: intrinsically disordered proteins in 2021.'
    subjects:
    - Biomedical Science
    - Biology
  homepage: https://mobidb.org
  integbio:
    description: 'MobiDB is a database of intrinsically disordered regions (IDRs)
      and related features from various sources and prediction tools. Different levels
      of reliability and different features are reported as different and independent
      annotations. The database features three levels of annotation: manually curated,
      indirect and predicted. MobiDB annotates the binding modes of disordered proteins,
      whether they undergo disorder-to-order transitions or remain disordered in the
      bound state. In addition, disordered regions undergoing liquid-liquid phase
      separation or post-translational modifications are defined.'
    fairsharing: FAIRsharing.jwra3e
    homepage: https://mobidb.org/
    information_keywords:
    - Sequence
    - 3D structure
    maintainer: University of Padova
    name: MobiDB
    prefix: nbdc01956
    pubmeds:
    - '22661649'
    - '25361972'
    status: Active
    target_keywords:
    - Protein
  mappings:
    biocontext: MOBIDB
    fairsharing: FAIRsharing.jwra3e
    integbio: nbdc01956
    miriam: mobidb
    n2t: mobidb
    pathguide: '623'
    uniprot: DB-0183
  miriam:
    deprecated: false
    description: MobiDB is a database of protein disorder and mobility annotations.
    homepage: https://mobidb.org/
    id: '00000637'
    name: MobiDB
    namespaceEmbeddedInLui: false
    pattern: ^[OPQ][0-9][A-Z0-9]{3}[0-9]|[A-NR-Z][0-9]([A-Z][A-Z0-9]{2}[0-9]){1,2}$
    prefix: mobidb
    sampleId: P10636
    uri_format: https://mobidb.org/$1
  n2t:
    description: MobiDB is a database of protein disorder and mobility annotations.
    example: P10636
    homepage: http://mobidb.bio.unipd.it
    name: MobiDB
    namespaceEmbeddedInLui: false
    pattern: ^[OPQ][0-9][A-Z0-9]{3}[0-9]|[A-NR-Z][0-9]([A-Z][A-Z0-9]{2}[0-9]){1,2}$
    prefix: mobidb
    uri_format: http://mobidb.bio.unipd.it/$1
  pathguide:
    abbreviation: MobiDB
    homepage: http://mobidb.bio.unipd.it/
    name: a database of protein disorder and mobility annotations
    prefix: '623'
  prefix: mobidb
  provides: uniprot
  publications:
  - doi: 10.1093/nar/gkae969
    pmc: null
    pubmed: '39470701'
    title: 'MOBIDB in 2025: integrating ensemble properties and function annotations
      for intrinsically disordered proteins'
    year: 2024
  - doi: 10.1093/nar/gkaa1058
    pmc: PMC7779018
    pubmed: '33237329'
    title: 'MobiDB: intrinsically disordered proteins in 2021'
    year: 2021
  - doi: 10.1093/nar/gkx1071
    pmc: PMC5753340
    pubmed: '29136219'
    title: 'MobiDB 3.0: more annotations for intrinsic disorder, conformational diversity
      and interactions in proteins'
    year: 2018
  - doi: 10.1093/nar/gku982
    pmc: PMC4384034
    pubmed: '25361972'
    title: 'MobiDB 2.0: an improved database of intrinsically disordered and mobile
      proteins'
    year: 2014
  - doi: 10.1093/bioinformatics/bts327
    pmc: null
    pubmed: '22661649'
    title: 'MobiDB: a comprehensive database of intrinsic protein disorder annotations'
    year: 2012
  - doi: 10.1093/nar/gkx1071
    pmc: null
    pubmed: null
    title: 'MobiDB 3.0: More annotations for intrinsic disorder, conformational diversity
      and interactions in proteins'
    year: null
  - doi: 10.1093/bioinformatics/bts327
    pmc: null
    pubmed: null
    title: 'MobiDB: a comprehensive database of intrinsic protein disorder annotations.'
    year: null
  - doi: 10.1093/nar/gku982
    pmc: null
    pubmed: null
    title: 'MobiDB 2.0: an improved database of intrinsically disordered and mobile
      proteins.'
    year: null
  - doi: 10.1093/nar/gkaa1058
    pmc: null
    pubmed: null
    title: 'MobiDB: intrinsically disordered proteins in 2021.'
    year: null
  - doi: 10.1093/nar/gkac1065
    pmc: null
    pubmed: '36416266'
    title: null
    year: null
  - doi: 10.1093/nar/gkx1071
    pmc: null
    pubmed: null
    title: 'MobiDB 3.0: More annotations for intrinsic disorder, conformational diversity
      and interactions in proteins'
    year: null
  - doi: 10.1093/bioinformatics/bts327
    pmc: null
    pubmed: null
    title: 'MobiDB: a comprehensive database of intrinsic protein disorder annotations.'
    year: null
  - doi: 10.1093/nar/gku982
    pmc: null
    pubmed: null
    title: 'MobiDB 2.0: an improved database of intrinsically disordered and mobile
      proteins.'
    year: null
  - doi: 10.1093/nar/gkaa1058
    pmc: null
    pubmed: null
    title: 'MobiDB: intrinsically disordered proteins in 2021.'
    year: null
  - doi: 10.1093/nar/gkac1065
    pmc: null
    pubmed: '36416266'
    title: null
    year: null
  uniprot:
    abbreviation: MobiDB
    category: Family and domain databases
    homepage: https://mobidb.org
    name: MobiDB
    prefix: DB-0183
    publications:
    - doi: 10.1093/nar/gkac1065
      pubmed: '36416266'
    uri_format: https://mobidb.org/$1
mobio:
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: The Mobilome Ontology describes bacterial mobile genetic elements,
    their mechanisms, and associated epidemiology.
  download_obo: https://github.com/arpcard/mobio/raw/refs/heads/master/mobio.obo
  download_owl: https://github.com/arpcard/mobio/raw/refs/heads/master/mobio.owl
  example: '0000001'
  homepage: https://github.com/arpcard/mobio
  name: Mobilome Ontology
  pattern: ^\d+$
  prefix: mobio
  repository: https://github.com/arpcard/mobio
  uri_format: http://purl.obolibrary.org/obo/MOBIO_$1
mobivoc:
  example: AccessCondition
  mappings:
    tib: mv
  prefix: mobivoc
  tib:
    description: MobiVoc is an open vocabulary for future-oriented mobility solutions.
    download_rdf: https://raw.githubusercontent.com/vocol/mobivoc/develop/diagrams/mobivoc_v1.1.4.ttl
    homepage: https://www.mobivoc.org/
    keywords:
    - NFDI4ING
    - FID move
    - traffic engineering
    name: MobiVoc Open Mobility Vocabulary 1.1.4
    prefix: mv
    tracker: https://github.com/vocol/mobivoc/issues
    uri_format: http://schema.mobivoc.org/#$1
mod:
  aberowl:
    description: PSI-MOD is an ontology consisting of terms that describe protein
      chemical modifications, logically linked by an is_a relationship in such a way
      as to form a direct acyclic graph (DAG). The PSI-MOD ontology has more than
      45 top-level nodes, and provides alternative hierarchical paths for classifying
      protein modifications either by the molecular structure of the modification,
      or by the amino acid residue that is modified.
    download_obo: http://aber-owl.net/media/ontologies/PSIMOD/4/psimod.obo
    homepage: http://www.psidev.info/MOD
    name: Protein Modification Ontology
    prefix: PSIMOD
    version: 1.013.0
  biocontext:
    prefix: MOD
  bioportal:
    contact:
      email: sylvie.ricard-blum@univ-lyon1.fr
      name: Sylvie Ricard-Blum
    description: PSI-MOD is an ontology consisting of terms that describe protein
      chemical modifications, logically linked by an is_a relationship in such a way
      as to form a direct acyclic graph (DAG). The PSI-MOD ontology has more than
      45 top-level nodes, and provides alternative hierarchical paths for classifying
      protein modifications either by the molecular structure of the modification,
      or by the amino acid residue that is modified.
    homepage: http://www.psidev.info/MOD
    name: Protein Modification Ontology
    prefix: PSIMOD
    version: 1.031.6
  example: '01467'
  fairsharing:
    abbreviation: PSI-MOD
    description: The HUPO Proteomic Standards Initiative (PSI) protein modifications
      ontology (MOD) consists of terms that describe protein chemical modifications,
      logically linked by an is_a relationship in such a way as to form a direct acyclic
      graph (DAG). The PSI-MOD ontology has more than 45 top-level nodes, and provides
      alternative hierarchical paths for classifying protein modifications either
      by the molecular structure of the modification, or by the amino acid residue
      that is modified.
    domains:
    - post-translational protein modification
    - enzymatic reaction
    - protein
    homepage: https://github.com/hupo-psi/psi-mod-cv
    license: CC-BY-4.0
    name: PSI Protein Modifications Ontology
    prefix: FAIRsharing.2m4ms9
    publications:
    - doi: 10.1038/nbt0808-864
      pubmed: '18688235'
      title: The PSI-MOD community standard for representation of protein modification
        data
      year: 2008
    subjects:
    - Life Science
    - Chemical Biology
    - Proteomics
  go:
    homepage: http://www.psidev.info/groups/protein-modifications
    name: Proteomics Standards Initiative protein modification ontology
    prefix: PSI-MOD
    synonyms:
    - MOD
  mappings:
    aberowl: PSIMOD
    biocontext: MOD
    bioportal: PSIMOD
    fairsharing: FAIRsharing.2m4ms9
    go: PSI-MOD
    miriam: mod
    n2t: mod
    obofoundry: mod
    ols: mod
    ontobee: MOD
    prefixcommons: psi.mod
    tib: mod
    wikidata.entity: Q81661700
  miriam:
    deprecated: false
    description: The Proteomics Standards Initiative modification ontology (PSI-MOD)  aims
      to define a concensus nomenclature and ontology reconciling, in a hierarchical
      representation, the complementary descriptions of residue modifications.
    homepage: https://www.ebi.ac.uk/ols4/ontologies/mod
    id: '00000056'
    name: Protein Modification Ontology
    namespaceEmbeddedInLui: true
    pattern: ^MOD:\d{5}$
    prefix: mod
    sampleId: '00001'
    uri_format: https://www.ebi.ac.uk/ols4/ontologies/mod/terms?obo_id=MOD:$1
  n2t:
    description: The Proteomics Standards Initiative modification ontology (PSI-MOD)  aims
      to define a concensus nomenclature and ontology reconciling, in a hierarchical
      representation, the complementary descriptions of residue modifications.
    example: '00001'
    homepage: http://bioportal.bioontology.org/ontologies/PSIMOD
    name: Protein modifications ontology through BioPortal
    namespaceEmbeddedInLui: true
    pattern: ^MOD:\d{5}
    prefix: mod
    uri_format: http://bioportal.bioontology.org/ontologies/1041?p=terms&conceptid=MOD:$1
  obofoundry:
    contact: pierre-alain.binz@chuv.ch
    contact.github: pabinz
    contact.label: Pierre-Alain Binz
    contact.orcid: 0000-0002-0045-7698
    deprecated: false
    description: PSI-MOD is an ontology consisting of terms that describe protein
      chemical modifications
    domain: chemistry and biochemistry
    download.obo: http://purl.obolibrary.org/obo/mod.obo
    download.owl: http://purl.obolibrary.org/obo/mod.owl
    homepage: http://www.psidev.info/MOD
    license: CC BY 4.0
    license.url: https://creativecommons.org/licenses/by/4.0/
    name: Protein modification
    preferredPrefix: MOD
    prefix: mod
    publications:
    - id: https://www.ncbi.nlm.nih.gov/pubmed/18688235
      title: The PSI-MOD community standard for representation of protein modification
        data
    repository: https://github.com/HUPO-PSI/psi-mod-CV
  ols:
    description: PSI-MOD is an ontology consisting of terms that describe protein
      chemical modifications
    download_owl: http://purl.obolibrary.org/obo/mod.owl
    homepage: http://www.psidev.info/MOD
    name: Protein modification
    prefix: mod
    tracker: https://github.com/HUPO-PSI/psi-mod-CV/issues
    version: 1.032.4
    version.iri: http://purl.obolibrary.org/obo/mod/1.032.4/mod.owl
  ontobee:
    library: Library
    name: Protein modification
    prefix: MOD
  pattern: ^\d{5}$
  prefix: mod
  prefixcommons:
    alt_uri_formats:
    - http://purl.org/obo/owl/PSI-MOD#$1
    bioportal: '1041'
    description: The Proteomics Standards Initiative modification ontology (PSI-MOD)  aims
      to define a concensus nomenclature and ontology reconciling, in a hierarchical
      representation, the complementary descriptions of residue modifications.
    example: MOD:00001
    homepage: http://psidev.sourceforge.net/mod/
    keywords:
    - ontology
    - protein
    - molecule
    - structure
    name: Protein Modification ontology
    pattern: ^MOD:\d{5}$
    prefix: psi.mod
    synonyms:
    - mod
    - obo.psi-mod
  publications:
  - doi: 10.1038/nbt0808-864
    pmc: null
    pubmed: '18688235'
    title: The PSI-MOD community standard for representation of protein modification
      data
    year: 2008
  - doi: null
    pmc: null
    pubmed: '18688235'
    title: The PSI-MOD community standard for representation of protein modification
      data
    year: null
  - doi: 10.1038/nbt0808-864
    pmc: null
    pubmed: '18688235'
    title: The PSI-MOD community standard for representation of protein modification
      data
    year: 2008
  synonyms:
  - PSI-MOD
  tib:
    description: PSI-MOD is an ontology consisting of terms that describe protein
      chemical modifications, logically linked by an is_a relationship in such a way
      as to form a direct acyclic graph (DAG). The PSI-MOD ontology has more than
      45 top-level nodes, and provides alternative hierarchical paths for classifying
      protein modifications either by the molecular structure of the modification,
      or by the amino acid residue that is modified.
    download_owl: http://purl.obolibrary.org/obo/mod.owl
    homepage: http://www.psidev.info/MOD
    keywords:
    - NFDI4CHEM
    - DataPLANT
    - chemistry
    - life sciences, biology
    name: Protein Modification
    prefix: mod
    tracker: https://github.com/HUPO-PSI/psi-mod-CV/issues
    version.iri: http://purl.obolibrary.org/obo/mod/1.031.6/mod.owl
  uri_format: http://purl.obolibrary.org/obo/MOD_$1
modalia:
  bartoc:
    abbreviation: Modalia
    description: MoDalia is the basic ontology of the DALIA knowledge graph. The aim
      of the DALIA project is to establish a platform for learning materials on the
      topics of research data management (RDM) and data science. MoDalia incorporates
      several modules from EduCOR. It also includes the modeling of micro-credentials
      and certificates.
    homepage: https://dalia.pages.rwth-aachen.de/dalia-ontology/
    license: CC-BY-4.0
    name: MoDALIA Ontology
    prefix: '20825'
  contact:
    email: abdelmoneim.desouki@tu-darmstadt.de
    github: abdoudesouki
    name: Abdelmoneim Amer Desouki
    orcid: 0000-0003-2083-1277
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: The aim of DALIA project is to build a platform for learning material
    for Research Data Management (RDM) and Data Science. The platform is based on
    a knowledge graph. We introduce MoDalia, the base ontology of DALIA knowledge
    graph. Modalia inherits some modules from EduCOR. It includes also modelling of
    micro -credentials and certificates
  domain: data model
  download_obo: https://git.rwth-aachen.de/dalia/dalia-ontology/-/raw/main/modalia.obo
  download_rdf: https://git.rwth-aachen.de/dalia/dalia-ontology/-/raw/main/MoDalia.ttl
  example: belongsToCluster
  homepage: https://dalia.pages.rwth-aachen.de/dalia-ontology/
  license: CC-BY-4.0
  mappings:
    bartoc: '20825'
    tib: modalia
  name: MoDALIA Ontology
  prefix: modalia
  rdf_uri_format: https://purl.org/ontology/modalia#$1
  repository: https://git.rwth-aachen.de/dalia/dalia-ontology
  tib:
    description: An ontology encoding the data model of the DALIA knowledge graph,
      reusing/extending Schema.org, FaBIO, EduCOR, HRCT, and other ontologies/CVs
    download_rdf: https://git.rwth-aachen.de/dalia/dalia-ontology/-/raw/main/MoDalia.ttl
    homepage: https://dalia.pages.rwth-aachen.de/dalia-ontology/
    keywords:
    - TIB
    - educational science
    name: MoDalia Ontology
    prefix: modalia
    uri_format: https://purl.org/ontology/modalia#$1
    version.iri: https://purl.org/ontology/modalia#1.0.0
  uri_format: https://purl.org/ontology/modalia#$1
modeldb:
  biocontext:
    prefix: MODELDB
  contact:
    email: perry.miller@yale.edu
    github: null
    name: Perry Miller
    orcid: 0000-0002-5176-943X
  edam:
    description: Unique identifier of an entry from the ModelDB database.
    name: ModelDB
    obsolete: false
    prefix: '2669'
  fairsharing:
    abbreviation: ModelDB
    description: ModelDB provides an accessible location for storing and efficiently
      retrieving computational neuroscience models. A ModelDB entry contains a model's
      source code, concise description, and a citation of the article that published
      it. Models can be coded in any language for any environment. Model code can
      be viewed before downloading and browsers can be set to auto-launch the models.
    homepage: http://senselab.med.yale.edu/modeldb
    name: ModelDB
    prefix: FAIRsharing.5rb3fk
    publications:
    - doi: 10.1007/s10827-016-0623-7
      pubmed_id: 27629590
      title: 'Twenty years of ModelDB and beyond: building essential modeling tools
        for the future of neuroscience'
    - doi: 10.1023/B:JCNS.0000023869.22017.2e
      pubmed_id: 15218350
      title: 'ModelDB: A Database to Support Computational Neuroscience.'
    - doi: 10.1136/jamia.1996.97084512
      pubmed_id: 8930855
      title: 'ModelDB: an environment for running and storing computational models
        and their results applied to neuroscience.'
    - doi: 10.1385/NI:1:1:135
      pubmed_id: 15055399
      title: 'ModelDB: making models publicly accessible to support computational
        neuroscience.'
    subjects:
    - Neurobiology
    - Computational Biology
    - Life Science
    twitter: SenseLabProject
  integbio:
    description: ModelDB provides an accessible location for storing and efficiently
      retrieving computational neuroscience models. A ModelDB entry contains a model's
      source code, concise description, and a citation of the article that published
      it. Models can be coded in any language for any environment. Model code can
      be viewed before downloading and browsers can be set to auto-launch the models.
    fairsharing: FAIRsharing.5rb3fk
    homepage: http://senselab.med.yale.edu/modeldb
    information_keywords:
    - Method
    - Bibliography/Documents
    maintainer: Yale University||Yale University School of Medicine
    name: ModelDB
    prefix: nbdc02085
    pubmeds:
    - '15218350'
    - '8930855'
    - '15055399'
    status: Active
    target_keywords:
    - Cell/Organelle
  mappings:
    biocontext: MODELDB
    edam: '2669'
    fairsharing: FAIRsharing.5rb3fk
    integbio: nbdc02085
    miriam: modeldb
    n2t: modeldb
    prefixcommons: modeldb
    re3data: r3d100011330
  miriam:
    deprecated: false
    description: ModelDB is a curated, searchable database of published models in
      the computational neuroscience domain. It accommodates models expressed in textual
      form, including procedural or declarative languages (e.g. C++, XML dialects)
      and source code written for any simulation environment.
    homepage: https://modeldb.science
    id: '00000131'
    name: ModelDB
    namespaceEmbeddedInLui: false
    pattern: ^\d+$
    prefix: modeldb
    sampleId: '45539'
    uri_format: https://modeldb.science/$1
  n2t:
    description: ModelDB is a curated, searchable database of published models in
      the computational neuroscience domain. It accommodates models expressed in textual
      form, including procedural or declarative languages (e.g. C++, XML dialects)
      and source code written for any simulation environment.
    example: '45539'
    homepage: http://senselab.med.yale.edu/ModelDB/
    name: ModelDB at SenseLab
    namespaceEmbeddedInLui: false
    pattern: ^\d+$
    prefix: modeldb
    uri_format: http://senselab.med.yale.edu/ModelDB/ShowModel.asp?model=$1
  part_of_database: modeldb
  prefix: modeldb
  prefixcommons:
    description: ModelDB is a curated, searchable database of published models in
      the computational neuroscience domain. It accommodates models expressed in textual
      form, including procedural or declarative languages (e.g. C++, XML dialects)
      and source code written for any simulation environment.
    example: '45539'
    homepage: http://senselab.med.yale.edu/ModelDB/
    license: http://senselab.med.yale.edu/ModelDB/HowToCite.html
    name: ModelDB
    pattern: ^\d+$
    prefix: modeldb
    pubmed_ids:
    - '15055399'
    uri_format: http://senselab.med.yale.edu/ModelDB/ShowModel.asp?model=$1
  publications:
  - doi: 10.1007/s10827-016-0623-7
    pmc: PMC5279891
    pubmed: '27629590'
    title: 'Twenty years of ModelDB and beyond: building essential modeling tools
      for the future of neuroscience'
    year: 2016
  - doi: 10.1023/b:jcns.0000023869.22017.2e
    pmc: PMC3732827
    pubmed: '15218350'
    title: 'ModelDB: A Database to Support Computational Neuroscience'
    year: 2004
  - doi: 10.1385/ni:1:1:135
    pmc: PMC3728921
    pubmed: '15055399'
    title: 'ModelDB: making models publicly accessible to support computational neuroscience'
    year: 2003
  - doi: 10.1136/jamia.1996.97084512
    pmc: PMC116323
    pubmed: '8930855'
    title: 'ModelDB: an environment for running and storing computational models and
      their results applied to neuroscience'
    year: 1996
  - doi: 10.1007/s10827-016-0623-7
    pmc: null
    pubmed: null
    title: 'Twenty years of ModelDB and beyond: building essential modeling tools
      for the future of neuroscience'
    year: null
  - doi: 10.1023/B:JCNS.0000023869.22017.2e
    pmc: null
    pubmed: null
    title: 'ModelDB: A Database to Support Computational Neuroscience.'
    year: null
  - doi: 10.1136/jamia.1996.97084512
    pmc: null
    pubmed: null
    title: 'ModelDB: an environment for running and storing computational models and
      their results applied to neuroscience.'
    year: null
  - doi: 10.1385/NI:1:1:135
    pmc: null
    pubmed: null
    title: 'ModelDB: making models publicly accessible to support computational neuroscience.'
    year: null
  - doi: null
    pmc: null
    pubmed: '15055399'
    title: null
    year: null
  re3data:
    description: ModelDB is a curated database of published models in the broad domain
      of computational neuroscience. It addresses the need for access to such models
      in order to evaluate their validity and extend their use. It can handle computational
      models expressed in any textual form, including procedural or declarative languages
      (e.g. C++, XML dialects) and source code written for any simulation environment.
      The model source code doesn't even have to reside inside ModelDB; it just has
      to be available from some publicly accessible online repository or WWW site.
    doi: 10.17616/R3P61F
    homepage: https://modeldb.science/
    name: ModelDB
    prefix: r3d100011330
    xrefs:
      nif: 0000-00004
modeldb.concept:
  mappings:
    miriam: modeldb.concept
  miriam:
    deprecated: false
    description: Concept used by ModelDB, an accessible location for storing and efficiently
      retrieving computational neuroscience models.
    homepage: https://www.yale.edu
    id: 00000905
    name: ModelDB concept
    namespaceEmbeddedInLui: false
    pattern: \d+
    prefix: modeldb.concept
    sampleId: '3639'
    uri_format: https://senselab.med.yale.edu/ModelDB/ModelList?id=$1
  part_of_database: modeldb
  prefix: modeldb.concept
  uri_format: https://modeldb.science/modellist/$1
modsci:
  aberowl:
    description: 'Modern Science Ontology (ModSci), for modeling relationships between
      modern science branches and related entities, such as scientific discoveries,
      phenomena, renowned scientists, instruments, etc. ModSci is an upper ontology
      that provides a unifying framework for the various domain ontologies that make
      up the Science Knowledge Graph Ontology Suite. The Systematic Approach for Building
      Ontologies (SABiO) has been followed in the development of ModSci. ModSci is
      a poly-hierarchical ontology that can be utilized in semantic web applications.
      ModSci powers two projects for semantically representing scholarly information:
      Open Research Knowledge Graph (for the categorization of research papers) and
      OpenResearch.org (for the categorization of the information about scientific
      events, research projects, scientific papers, publishers, and journals).'
    download_owl: http://aber-owl.net/media/ontologies/ModSci/2/modsci.owl
    homepage: https://saidfathalla.github.io/Science-knowledge-graph-ontologies/doc/ModSci_doc/index-en.html
    name: Modern Science Ontology
    prefix: ModSci
    version: '1.1'
  bioportal:
    contact:
      email: sm_fathalla@yahoo.com
      name: SaidFathalla
    description: ModSci is a reference ontology for modelling different types of modern
      sciences and related entities, such as scientific discoveries, renowned scientists,
      instruments, phenomena ... etc.
    homepage: https://saidfathalla.github.io/Science-knowledge-graph-ontologies/doc/ModSci_doc/index-en.html
    name: Modern Science Ontology
    prefix: MODSCI
    version: '1.0'
  example: AcidbaseChemistry
  lov:
    description: ModSci is a reference ontology for modelling different types of modern
      sciences and related entities, such as scientific discoveries, renowned scientists,
      instruments, phenomena ... etc.
    homepage: https://w3id.org/skgo/modsci#
    keywords:
    - Academy
    - Society
    modified: '2022-12-18'
    name: ModSci, Modern Science Ontology.
    prefix: modsci
    uri_prefix: https://w3id.org/skgo/modsci#$1
  mappings:
    aberowl: ModSci
    bioportal: MODSCI
    lov: modsci
    tib: modsci
  prefix: modsci
  tib:
    description: ModSci is a reference ontology for modelling different types of modern
      sciences and related entities, such as scientific discoveries, renowned scientists,
      instruments, phenomena ... etc.
    download_rdf: https://saidfathalla.github.io/Science-knowledge-graph-ontologies/doc/ModSci_doc/ontology.ttl
    homepage: https://saidfathalla.github.io/Science-knowledge-graph-ontologies/doc/ModSci_doc/index-en.html
    keywords:
    - NFDI4ING
    name: Modern Science Ontology
    prefix: modsci
    uri_format: https://w3id.org/skgo/modsci#$1
    version.iri: https://w3id.org/skgo/modsci/1.1
moid:
  mappings:
    miriam: moid
  miriam:
    deprecated: false
    description: M3G stands for “Metadata Management and distribution system for Multiple
      GNSS Networks”. M3G allows to upload, validate, and distribute GNSS station
      metadata such as IGS-style site logs, information about local networks, DOIs,
      nominal data provision, data licenses attached to the daily RINEX data, etc...
    homepage: https://www.astro.oma.be/en/
    id: 00001068
    name: Metadata Management and distribution system for Multiple GNSS Networks
    namespaceEmbeddedInLui: false
    pattern: ^[a-zA-Z0-9]+\.[a-f0-9]{24}$
    prefix: moid
    sampleId: station.6051b2f8b9142a5b8c676342
    uri_format: https://gnss-metadata.eu/MOID/$1
  prefix: moid
molbase:
  biocontext:
    prefix: MOLBASE
  mappings:
    biocontext: MOLBASE
    miriam: molbase
    n2t: molbase
  miriam:
    deprecated: false
    description: Molbase provides compound data information for researchers as well
      as listing suppliers and price information. It can be searched by keyword or
      CAS indetifier.
    homepage: http://www.molbase.com/
    id: 00000458
    name: Molbase
    namespaceEmbeddedInLui: false
    pattern: ^(\d{1,7}\-\d{2}\-\d)|([A-Za-z0-9\+\-\_]+)$
    prefix: molbase
    sampleId: 128796-39-4
    uri_format: http://www.molbase.com/en/index.php?app=search&search_keyword=$1
  n2t:
    description: Molbase provides compound data information for researchers as well
      as listing suppliers and price information. It can be searched by keyword or
      CAS indetifier.
    example: 128796-39-4
    homepage: http://www.molbase.com/
    name: Molbase at Chinese Academy of Sciences
    namespaceEmbeddedInLui: false
    pattern: ^(\d{1,7}\-\d{2}\-\d)|([A-Za-z0-9\+\-\_]+)$
    prefix: molbase
    uri_format: http://www.molbase.com/en/index.php?app=search&search_keyword=$1
  prefix: molbase
molbase.sheffield:
  comment: Do not confuse with molbase, which is a provider. These resources are unrelated.
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  deprecated: true
  description: An online database of inorganic compounds, MolBase was constructed
    by Dr Mark Winter of the University of Sheffield with input from undergraduate
    students.
  example: '1868'
  homepage: https://winter.group.shef.ac.uk/molbase/
  name: MolBase
  pattern: ^\d+$
  prefix: molbase.sheffield
molbic.cellline:
  contact:
    email: zhufeng@zju.edu.cn
    github: null
    name: Feng Zhu
    orcid: 0000-0001-8069-0053
  contributor:
    email: m.naguthana@hotmail.com
    github: nagutm
    name: Mufaddal Naguthanawala
    orcid: 0009-0009-5240-7463
  description: MolBiC provides information about cell-based molecular bioactivities
    along with associated compounds, proteins and cell lines. This prefix maintains
    identifiers for cell lines used in assays measuring molecular bioactivity, linking
    them to associated compounds and proteins.
  example: CL000025
  github_request_issue: 1418
  homepage: https://molbic.idrblab.net
  name: MolBiC Cell Line
  pattern: ^CL\d+$
  prefix: molbic.cellline
  publications:
  - doi: 10.1093/nar/gkae868
    pmc: null
    pubmed: '39373530'
    title: 'MolBiC: the cell-based landscape illustrating molecular bioactivities'
    year: 2025
  reviewer:
    email: b.gyori@northeastern.edu
    github: bgyori
    name: Benjamin M. Gyori
    orcid: 0000-0001-9439-5346
  uri_format: https://molbic.idrblab.net/data/cellline/details/$1
molbic.compound:
  contact:
    email: zhufeng@zju.edu.cn
    github: null
    name: Feng Zhu
    orcid: 0000-0001-8069-0053
  contributor:
    email: m.naguthana@hotmail.com
    github: nagutm
    name: Mufaddal Naguthanawala
    orcid: 0009-0009-5240-7463
  description: MolBiC provides information about cell-based molecular bioactivities
    along with associated compounds, proteins and cell lines. This prefix maintains
    identifiers for chemical compounds with experimentally validated bioactivity in
    cellular contexts.
  example: CP0041613
  github_request_issue: 1418
  homepage: https://molbic.idrblab.net
  name: MolBiC Compound
  pattern: ^CP\d+$
  prefix: molbic.compound
  publications:
  - doi: 10.1093/nar/gkae868
    pmc: PMC11701603
    pubmed: '39373530'
    title: 'MolBiC: the cell-based landscape illustrating molecular bioactivities'
    year: 2024
  reviewer:
    email: b.gyori@northeastern.edu
    github: bgyori
    name: Benjamin M. Gyori
    orcid: 0000-0001-9439-5346
  uri_format: https://molbic.idrblab.net/data/compound/details/$1
molbic.protein:
  contact:
    email: zhufeng@zju.edu.cn
    github: null
    name: Feng Zhu
    orcid: 0000-0001-8069-0053
  contributor:
    email: m.naguthana@hotmail.com
    github: nagutm
    name: Mufaddal Naguthanawala
    orcid: 0009-0009-5240-7463
  description: MolBiC provides information about cell-based molecular bioactivities
    along with associated compounds, proteins and cell lines. This prefix maintains
    identifiers for proteins that serve as molecular targets in cell-based bioactivity
    measurements.
  example: PT00819
  github_request_issue: 1418
  homepage: https://molbic.idrblab.net
  name: MolBiC Protein
  pattern: ^PT\d+$
  prefix: molbic.protein
  publications:
  - doi: 10.1093/nar/gkae868
    pmc: null
    pubmed: '39373530'
    title: 'MolBiC: the cell-based landscape illustrating molecular bioactivities'
    year: 2025
  reviewer:
    email: b.gyori@northeastern.edu
    github: bgyori
    name: Benjamin M. Gyori
    orcid: 0000-0001-9439-5346
  uri_format: https://molbic.idrblab.net/data/protein/details/$1
molgluedb:
  contact:
    email: qc@ouc.edu.cn
    github: null
    name: Chong Qin
    orcid: 0000-0001-8108-1698
  contributor:
    email: ji.kang@northeastern.edu
    github: kanghosaeyo
    name: Kangho Ji
    orcid: 0009-0009-3402-8013
  description: Identifiers correspond to molecular glue compounds in the MolGlueDB
    which is a free and open-access online database dedicated to the collection and
    integration of molecular glue compound information.
  example: '1'
  github_request_issue: 1775
  homepage: https://www.molgluedb.com
  keywords:
  - compound
  - degraders
  - proteolysis
  name: MolGlueDB
  pattern: ^\d+$
  prefix: molgluedb
  publications:
  - doi: 10.1093/nar/gkaf811
    pmc: null
    pubmed: '40842115'
    title: 'MolGlueDB: an online database of molecular glues'
    year: 2025
  reviewer:
    email: b.gyori@northeastern.edu
    github: bgyori
    name: Benjamin M. Gyori
    orcid: 0000-0001-9439-5346
  uri_format: https://www.molgluedb.com/browseDB/$1
molmedb:
  contact:
    email: karel.berka@upol.cz
    github: KarelBerka
    name: Karel Berka
    orcid: 0000-0001-9472-2589
  contributor_extras:
  - email: dominik.martinat@gmail.com
    github: DominikMartinat
    name: Dominik Martinat
    orcid: 0000-0001-6611-7883
  fairsharing:
    abbreviation: MolMeDB
    contact:
      email: karel.berka@upol.cz
      name: Karel Berka
      orcid: 0000-0001-9472-2589
    description: MolMeDB is an open chemistry database concerning the interaction
      of molecules with membranes.
    homepage: https://molmedb.upol.cz
    license: CC-BY-4.0
    name: 'MolMeDB: Molecules on Membranes Database'
    prefix: FAIRsharing.CWzk3C
    publications: []
    repository: https://github.com/MolMeDB/MolMeDB
    subjects:
    - Molecular biology
    - Cheminformatics
    - Biochemistry
    - Molecular Chemistry
    - Chemistry
    - Molecular Physical Chemistry
    - Molecular Dynamics
    - Computational Chemistry
  mappings:
    fairsharing: FAIRsharing.CWzk3C
    miriam: molmedb
  miriam:
    deprecated: false
    description: 'MolMeDB is an open chemistry database about interactions of molecules
      with membranes. We collect information on how chemicals interact with individual
      membranes either from experiment or from simulations. '
    homepage: http://www.upol.cz/en/
    id: 00000768
    name: MolMeDB
    namespaceEmbeddedInLui: false
    pattern: ^[Mm]{2}[0-9]{5,}(\.[0-9]+)?$
    prefix: molmedb
    sampleId: MM00040
    uri_format: https://molmedb.upol.cz/mol/$1
  prefix: molmedb
molmovdb:
  integbio:
    alt_name: The database of molecular motions
    description: MolMovDB is a database of the motions that occur in proteins and
      other macromolecules, particularly using movies. This database classifies  macromolecular
      motions into a limited number of categories, first on the basis of size (distinguishing
      between fragment, domain and subunit motions) and then on the basis of packing.
      Moreover, it contains tools to interpolate between two conformations (the Morph
      Server) and predict possible motions in a single structure and an interface
      to a hinge prediction service, which acts on single structures and predicts
      likely residue points for flexibility.
    homepage: http://molmovdb.org/
    information_keywords:
    - Image/Movie
    - 3D structure
    maintainer: Yale University
    name: MolMovDB
    prefix: nbdc00573
    pubmeds:
    - '9722650'
    status: Inactive
    target_keywords:
    - DNA
    - RNA
    - Protein
  mappings:
    integbio: nbdc00573
    prefixcommons: molmovdb
  prefix: molmovdb
  prefixcommons:
    description: The Molecular Movements Database lists motions in proteins and other
      macromolecules. It is arranged around a multi-level classification scheme and
      includes motions of loops, domains, and subunits.
    example: f665230-5267
    homepage: http://bioinfo.mbb.yale.edu/MolMovDB/
    keywords:
    - protein
    - small molecule
    - classification
    - structure
    name: Database of Macromolecular Movements
    pattern: ^[A-Z,0-9]+$
    prefix: molmovdb
    uri_format: http://www.molmovdb.org/cgi-bin/morph.cgi?ID=$1
  reviewer:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
mondo:
  aberowl:
    description: A global community effort to harmonize multiple disease resources
      to yield a coherent merged ontology.
    download_owl: http://aber-owl.net/media/ontologies/MONDO/108/mondo.owl
    homepage: https://monarch-initiative.github.io/mondo
    name: Mondo Disease Ontology
    prefix: MONDO
  bartoc:
    abbreviation: MONDO
    description: The Mondo Disease Ontology (Mondo) aims to harmonize disease definitions
      across the world. It is a semi-automatically constructed ontology that merges
      in multiple disease resources to yield a coherent merged ontology.
    homepage: https://mondo.monarchinitiative.org/
    license: CC-BY-4.0
    name: Mondo Disease Ontology
    prefix: '20699'
  biocontext:
    prefix: MONDO
  bioportal:
    contact:
      email: nicole.a.vasilevsky@gmail.com
      name: Nicole Vasilevsky
    description: The Mondo Disease Ontology (Mondo) aims to harmonize disease definitions
      across the world. It is a semi-automatically constructed ontology that merges
      in multiple disease resources to yield a coherent merged ontology., A semi-automatically
      constructed ontology that merges in multiple disease resources to yield a coherent
      merged ontology.
    homepage: http://obofoundry.org/ontology/mondo.html
    license: CC-BY-4.0
    name: Mondo Disease Ontology
    prefix: MONDO
    publications:
    - https://mondo.monarchinitiative.org/pages/resources/
    version: '2025-11-04'
  download_obo: http://purl.obolibrary.org/obo/mondo.obo
  example: '0000001'
  fairsharing:
    abbreviation: MONDO
    description: MonDO (Monarch Disease Ontology) is a semi-automatically constructed
      ontology that merges in multiple disease resources to yield a coherent merged
      ontology.
    domains:
    - Biocuration
    homepage: https://mondo.monarchinitiative.org/
    license: CC-BY-4.0
    logo: https://api.fairsharing.org/rails/active_storage/blobs/redirect/eyJfcmFpbHMiOnsibWVzc2FnZSI6IkJBaHBBdGtDIiwiZXhwIjpudWxsLCJwdXIiOiJibG9iX2lkIn19--898bdc43b92d38a40469367c9d28eae876b63f8b/mondo_logo_black-stacked.png?disposition=inline
    name: Monarch Disease Ontology
    prefix: FAIRsharing.b2979t
    publications:
    - doi: 10.1101/2022.04.13.22273750
      title: 'Mondo: Unifying diseases for the world, by the world'
      year: 2022
    - doi: 10.1093/nar/gkw1128
      pubmed: '27899636'
      title: 'The Monarch Initiative: an integrative data and analytic platform connecting
        phenotypes to genotypes across species'
      year: 2016
    repository: https://github.com/monarch-initiative/mondo
    subjects:
    - Medicine
    - Infectious Disease Medicine
    twitter: MonarchInit
  integbio:
    alt_name: Mondo Disease Ontology
    description: Mondo is an ontology for integrating disease definitions. It collects
      disease definitions and data models from numerous sources, which include HPO,
      OMIM, SNOMED CT, ICD, PhenoDB, MedDRA, MedGen, ORDO, DO, GARD, etc. It provides
      a hierarchical structure which can be used for classification or "rolling up"
      diseases to higher level groupings.
    fairsharing: FAIRsharing.b2979t
    homepage: https://mondo.monarchinitiative.org/
    information_keywords:
    - Ontology/Terminology/Nomenclature
    maintainer: Monarch Initiative
    name: MONDO
    prefix: nbdc02563
    pubmeds:
    - '31701156'
    status: Active
    target_keywords:
    - Health/Disease
  mappings:
    aberowl: MONDO
    bartoc: '20699'
    biocontext: MONDO
    bioportal: MONDO
    fairsharing: FAIRsharing.b2979t
    integbio: nbdc02563
    miriam: mondo
    obofoundry: mondo
    ols: mondo
    ontobee: MONDO
    togoid: Mondo
    wikidata: P5270
    wikidata.entity: Q27468140
  mastodon: monarch_initiative@genomic.social
  miriam:
    deprecated: false
    description: The Mondo Disease Ontology (Mondo) aims to harmonize disease definitions
      across the world.
    homepage: https://monarchinitiative.org
    id: 00001089
    name: Mondo Disease Ontology
    namespaceEmbeddedInLui: false
    pattern: ^\d{7}$
    prefix: mondo
    sampleId: 0004994
    uri_format: http://purl.obolibrary.org/obo/MONDO_$1
  name: Mondo Disease Ontology
  obofoundry:
    contact: Sabrina@tislab.org
    contact.github: sabrinatoro
    contact.label: Sabrina Toro
    contact.orcid: 0000-0002-4142-7153
    deprecated: false
    description: A global community effort to harmonize multiple disease resources
      to yield a coherent merged ontology.
    domain: health
    download.json: http://purl.obolibrary.org/obo/mondo.json
    download.obo: http://purl.obolibrary.org/obo/mondo.obo
    download.owl: http://purl.obolibrary.org/obo/mondo.owl
    homepage: https://monarch-initiative.github.io/mondo
    license: CC BY 4.0
    license.url: http://creativecommons.org/licenses/by/4.0/
    logo: https://raw.githubusercontent.com/monarch-initiative/mondo/master/docs/images/mondo_logo_black-stacked-small.png
    name: Mondo Disease Ontology
    preferredPrefix: MONDO
    prefix: mondo
    publications:
    - id: https://doi.org/10.1093/genetics/iyaf215
      title: 'Mondo: Integrating Disease Terminology Across Communities'
    - id: https://www.medrxiv.org/content/10.1101/2022.04.13.22273750
      title: 'Mondo: Unifying diseases for the world, by the world'
    repository: https://github.com/monarch-initiative/mondo
  ols:
    description: A semi-automatically constructed ontology that merges in multiple
      disease resources to yield a coherent merged ontology.
    download_owl: https://purl.obolibrary.org/obo/mondo/mondo-international.owl
    homepage: https://monarch-initiative.github.io/mondo
    name: Mondo Disease Ontology
    prefix: mondo
    tracker: https://github.com/monarch-initiative/mondo/issues
    version: '2025-12-02'
    version.iri: http://purl.obolibrary.org/obo/mondo/releases/2025-12-02/mondo-international.owl
  ontobee:
    library: Library
    name: Mondo Disease Ontology
    prefix: MONDO
  pattern: ^\d{7}$
  prefix: mondo
  providers:
  - code: clinicalgenome
    description: Clinical genome condition
    example: null
    first_party: null
    homepage: https://search.clinicalgenome.org
    name: Clinical Genome
    publications: null
    status: null
    uri_format: https://search.clinicalgenome.org/kb/conditions/MONDO:$1
  publications:
  - doi: 10.1101/2022.04.13.22273750
    pmc: null
    pubmed: null
    title: 'Mondo: Unifying diseases for the world, by the world'
    year: 2022
  togoid:
    catalog: nbdc02563
    description: Mondo is an ontology for integrating disease definitions. It collects
      disease definitions and data models from numerous sources, which include HPO,
      OMIM, SNOMED CT, ICD, PhenoDB, MedDRA, MedGen, ORDO, DO, GARD, etc. It provides
      a hierarchical structure which can be used for classification or "rolling up"
      diseases to higher level groupings.
    examples:
    - MONDO:0000115
    - MONDO:0002345
    - MONDO:0011571
    - MONDO:0020035
    - MONDO:0020920
    - MONDO:0004627
    - MONDO:0005480
    - MONDO:0010852
    - MONDO:0002053
    - MONDO:0015758
    keywords:
    - Phenotype
    name: MONDO
    pattern: ^MONDO[:_](?\d{7})$
    prefix: Mondo
    uri_format: http://purl.obolibrary.org/obo/MONDO_$1
  twitter: MonarchInit
  uri_format: http://purl.obolibrary.org/obo/MONDO_$1
  wikidata:
    description: identifier for an entity in the Mondo Disease Ontology
    example:
    - MONDO_0005301
    - MONDO_0005344
    homepage: https://github.com/monarch-initiative/mondo
    name: Mondo ID
    pattern: ^MONDO_([0-9]{1,7})$
    prefix: P5270
    short_name:
    - MONDO
mondo.issue:
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: An issue on the MONDO GitHub issue tracker
  example: '832'
  github_request_issue: 1553
  homepage: https://github.com/monarch-initiative/mondo/issues
  name: MONDO Issue Tracker
  pattern: ^\d+$
  prefix: mondo.issue
  uri_format: https://github.com/monarch-initiative/mondo/issues/$1
mop:
  aberowl:
    description: Processes at the molecular level
    download_owl: http://aber-owl.net/media/ontologies/MOP/8/mop.owl
    homepage: https://github.com/rsc-ontologies/rxno
    name: Molecular Process Ontology
    prefix: MOP
  bartoc:
    abbreviation: MOP
    description: Instruments and/or voices, devices and other performers which make
      up a musical work.
    homepage: https://www.iflastandards.info/unimarc/terms/mop
    license: CC-BY-4.0
    name: 'UNIMARC: Medium of performance'
    prefix: '20466'
  biocontext:
    prefix: MOP
  bioportal:
    contact:
      email: batchelorc@rsc.org
      name: Colin Batchelor
    description: Processes at the molecular level.
    homepage: https://github.com/rsc-ontologies/rxno
    name: Molecular Process Ontology
    prefix: MOP
  download_obo: https://raw.githubusercontent.com/rsc-ontologies/rxno/master/mop.obo
  example: 0000079
  fairsharing:
    abbreviation: MOP
    description: The Molecular Process Ontology (MOP) was created to work together
      with the Name Reaction Ontology (RXNO). MOP describes underlying molecular processes
      in organic reactions such as cyclization, methylation and demethylation.
    domains:
    - Reaction data
    homepage: https://github.com/rsc-ontologies/rxno
    license: CC-BY-4.0
    name: Molecular Process Ontology
    prefix: FAIRsharing.mct09a
    subjects:
    - Molecular Chemistry
  mappings:
    aberowl: MOP
    bartoc: '20466'
    biocontext: MOP
    bioportal: MOP
    fairsharing: FAIRsharing.mct09a
    obofoundry: mop
    ols: mop
    ontobee: MOP
    tib: mop
    wikidata.entity: Q81661705
  name: Molecular Process Ontology
  obofoundry:
    contact: batchelorc@rsc.org
    contact.github: batchelorc
    contact.label: Colin Batchelor
    contact.orcid: 0000-0001-5985-7429
    deprecated: false
    description: Processes at the molecular level
    domain: chemistry and biochemistry
    download.owl: http://purl.obolibrary.org/obo/mop.owl
    homepage: https://github.com/rsc-ontologies/rxno
    license: CC BY 4.0
    license.url: https://creativecommons.org/licenses/by/4.0/
    name: Molecular Process Ontology
    preferredPrefix: MOP
    prefix: mop
    repository: https://github.com/rsc-ontologies/rxno
  ols:
    contact: chemistry-ontologies@googlegroups.com
    description: MOP is the molecular process ontology. It contains the molecular
      processes that underlie the name reaction ontology RXNO, for example cyclization,
      methylation and demethylation.
    download_owl: http://purl.obolibrary.org/obo/mop.owl
    homepage: https://github.com/rsc-ontologies/rxno
    name: MOP
    prefix: mop
    tracker: https://github.com/rsc-ontologies/rxno/issues
    version: '2022-05-11'
    version.iri: http://purl.obolibrary.org/obo/mop/releases/2022-05-11/mop.owl
  ontobee:
    library: Library
    name: Molecular Process Ontology
    prefix: MOP
  pattern: ^\d{7}$
  prefix: mop
  tib:
    contact: chemistry-ontologies@googlegroups.com
    description: MOP is the molecular process ontology. It contains the molecular
      processes that underlie the name reaction ontology RXNO, for example cyclization,
      methylation and demethylation.
    download_owl: http://purl.obolibrary.org/obo/mop.owl
    homepage: https://github.com/rsc-ontology/rxno
    keywords:
    - NFDI4CHEM
    - NFDI4CAT
    - chemistry
    name: MOP
    prefix: mop
    tracker: https://github.com/rsc-ontology/rxno/issues
    version.iri: http://purl.obolibrary.org/obo/mop/releases/2022-05-11/mop.owl
  uri_format: http://purl.obolibrary.org/obo/MOP_$1
morpheus:
  mappings:
    miriam: morpheus
  miriam:
    deprecated: false
    description: 'The Morpheus model repository is an open-access data resource to
      store, search and retrieve unpublished and published computational models of
      spatio-temporal and multicellular biological systems, encoded in the MorpheusML
      language and readily executable with the Morpheus software.

      '
    homepage: https://morpheus.gitlab.io/
    id: '00000725'
    name: Morpheus model repository
    namespaceEmbeddedInLui: false
    pattern: ^M[0-9]{4,}$
    prefix: morpheus
    sampleId: M0001
    uri_format: https://morpheus.gitlab.io/models/$1
  prefix: morpheus
mosaic:
  aberowl:
    description: Ontology to support Semantic Annotation of MOSAiC datasets housed
      in the Arctic Data Center (https://arcticdata.io).
    download_owl: http://aber-owl.net/media/ontologies/MOSAIC/4/mosaic.owl
    homepage: https://github.com/DataONEorg/sem-prov-ontologies
    name: The MOSAiC Ontology
    prefix: MOSAIC
    version: Version 1.0.1
  bioportal:
    contact:
      email: mecum@nceas.ucsb.edu
      name: Bryce Mecum
    description: Ontology to support Semantic Annotation of MOSAiC datasets housed
      in the Arctic Data Center (https://arcticdata.io).
    homepage: https://github.com/DataONEorg/sem-prov-ontologies
    name: The MOSAiC Ontology
    prefix: MOSAIC
    version: Version 1.0.1
  contact:
    email: brycemecum@gmail.com
    github: amoeba
    name: Bryce Mecum
    orcid: 0000-0002-0381-3766
  contributor:
    email: j.harry.caufield@gmail.com
    github: caufieldjh
    name: Harry Caufield
    orcid: 0000-0001-5705-7831
  description: An ontology used to describe data resources in the Arctic Data Center
    (https://arcticdata.io).
  download_owl: https://ontologies.dataone.org/MOSAiC.owl
  example: '00005643'
  github_request_issue: 636
  homepage: https://ontologies.dataone.org/MOSAiC.html
  license: CC-BY-4.0
  mappings:
    aberowl: MOSAIC
    bioportal: MOSAIC
  name: MOSAiC Ontology
  pattern: ^\d{8}$
  prefix: mosaic
  repository: https://github.com/DataONEorg/sem-prov-ontologies
  reviewer:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  uri_format: https://purl.dataone.org/odo/MOSAIC_$1
mp:
  aberowl:
    description: Standard terms for annotating mammalian phenotypic data.
    download_owl: http://aber-owl.net/media/ontologies/MP/134/mp.owl
    homepage: https://www.informatics.jax.org/vocab/mp_ontology/
    name: Mammalian Phenotype Ontology
    prefix: MP
  bartoc:
    abbreviation: MP
    description: The Mammalian Phenotype Ontology is being developed by Cynthia L.
      Smith, Susan M. Bello, Anna, Anagnostopoulos, Carroll W. Goldsmith and Janan
      T. Eppig, as part of the Mouse Genome Database (MGD) Project, Mouse Genome Informatics
      (MGI), The Jackson Laboratory, Bar Harbor, ME. This file contains pre-coordinated
      phenotype terms, definitions and synonyms that can be used to describe mammalian
      phenotypes. The ontology is represented as a directed acyclic graph (DAG). It
      organizes phenotype terms into major biological system headers such as nervous
      system and respiratory system. This ontology is currently under development.
      Weekly updates are available at the Mouse Genome Informatics (MGI) ftp site
      (ftp://ftp.informatics.jax.org/pub/reports/index.html#pheno) as well as the
      OBO Foundry site (http://obofoundry.org/). Japanese labels of MP were created
      by the MP Japanese Translation Project (https://github.com/dbcls/MP_Japanse).
      Questions, comments and suggestions are welcome, and should be directed to pheno@jax.org,
      Susan.Bello@jax.org or to GitHub tracker (https://github.com/mgijax/mammalian-phenotype-ontology/issues)
      MGD is funded by NIH/NHGRI grant HG000330.
    homepage: https://www.informatics.jax.org/vocab/mp_ontology
    license: CC-BY-4.0
    name: Mammalian Phenotype Ontology
    prefix: '20697'
  biocontext:
    prefix: MP
  bioportal:
    contact:
      email: pheno@jax.org
      name: JAX phenotype list
    description: Standard terms for annotating mammalian phenotypic data.
    homepage: http://www.informatics.jax.org/searches/MP_form.shtml
    name: Mammalian Phenotype Ontology
    prefix: MP
    version: '2025-11-19'
  fairsharing:
    abbreviation: MP
    contact:
      email: susan.bello@jax.org
      name: Susan M. Bello
      orcid: 0000-0003-4606-0597
    description: The observable morphological, physiological, behavioral and other
      characteristics of mammalian organisms that are manifested through development
      and lifespan.
    domains:
    - behavior
    - phenotype
    homepage: https://www.informatics.jax.org/vocab/mp_ontology/
    license: CC-BY-4.0
    name: Mammalian Phenotype Ontology
    prefix: FAIRsharing.kg1x4z
    publications:
    - doi: 10.1186/gb-2004-6-1-r7
      pubmed: '15642099'
      title: The Mammalian Phenotype Ontology as a tool for annotating, analyzing
        and comparing phenotypic information
      year: 2005
    - doi: 10.1002/wsbm.44
      pubmed: '20052305'
      title: 'The mammalian phenotype ontology: enabling robust annotation and comparative
        analysis'
      year: 2010
    - doi: 10.1007/s00335-012-9421-3
      pubmed: '22961259'
      title: The Mammalian Phenotype Ontology as a unifying standard for experimental
        and high-throughput phenotyping data
      year: 2012
    - doi: 10.1186/s13326-015-0009-1
      pubmed: '25825651'
      title: Expanding the mammalian phenotype ontology to support automated exchange
        of high throughput mouse phenotyping data generated by large-scale mouse knockout
        screens
      year: 2015
    repository: https://github.com/obophenotype/mammalian-phenotype-ontology
    subjects:
    - Life Science
    - Physiology
    - Developmental Biology
  mappings:
    aberowl: MP
    bartoc: '20697'
    biocontext: MP
    bioportal: MP
    fairsharing: FAIRsharing.kg1x4z
    miriam: mp
    n2t: mp
    obofoundry: mp
    ols: mp
    ontobee: MP
    prefixcommons: mp
    togoid: Mp
    wikidata.entity: Q81661707
  miriam:
    deprecated: false
    description: The Mammalian Phenotype Ontology (MP) classifies and organises phenotypic
      information related to the mouse and other mammalian species. This ontology
      has been applied to mouse phenotype descriptions in various databases allowing
      comparisons of data from diverse mammalian sources. It can facilitate in the
      identification of appropriate experimental disease models, and aid in the discovery
      of candidate disease genes and molecular signaling pathways.
    homepage: https://bioportal.bioontology.org/ontologies/MP
    id: 00000580
    name: Mammalian Phenotype Ontology
    namespaceEmbeddedInLui: true
    pattern: ^MP:\d{7}$
    prefix: mp
    providers:
    - code: ''
      description: Mammalian Phenotype Ontology at The Jackson Lab
      homepage: http://www.informatics.jax.org/
      name: Mammalian Phenotype Ontology at The Jackson Lab
      uri_format: http://www.informatics.jax.org/searches/Phat.cgi?id=MP:$1
    sampleId: '0005452'
    uri_format: https://bioportal.bioontology.org/ontologies/MP/MP:$1
  n2t:
    description: The Mammalian Phenotype Ontology (MP) classifies and organises phenotypic
      information related to the mouse and other mammalian species. This ontology
      has been applied to mouse phenotype descriptions in various databases allowing
      comparisons of data from diverse mammalian sources. It can facilitate in the
      identification of appropriate experimental disease models, and aid in the discovery
      of candidate disease genes and molecular signaling pathways.
    example: '0005452'
    homepage: https://bioportal.bioontology.org/ontologies/MP
    name: Mammalian Phenotype Ontology through BioPortal
    namespaceEmbeddedInLui: true
    pattern: ^MP:\d{7}$
    prefix: mp
    uri_format: https://bioportal.bioontology.org/ontologies/MP/MP:$1
  obofoundry:
    appears_in:
    - chiro
    - scdo
    contact: pheno@jax.org
    contact.github: sbello
    contact.label: Sue Bello
    contact.orcid: 0000-0003-4606-0597
    deprecated: false
    description: Standard terms for annotating mammalian phenotypic data.
    domain: phenotype
    download.json: http://purl.obolibrary.org/obo/mp.json
    download.obo: http://purl.obolibrary.org/obo/mp.obo
    download.owl: http://purl.obolibrary.org/obo/mp.owl
    homepage: https://www.informatics.jax.org/vocab/mp_ontology/
    license: CC BY 4.0
    license.url: http://creativecommons.org/licenses/by/4.0/
    logo: https://raw.githubusercontent.com/mgijax/mammalian-phenotype-ontology/main/logo/2024_MP_logo_RGB_ICON_color.png
    name: Mammalian Phenotype Ontology
    preferredPrefix: MP
    prefix: mp
    publications:
    - id: https://www.ncbi.nlm.nih.gov/pubmed/40963406
      title: Expanding and refining the Mammalian Phenotype Ontology to enhance disease
        model discovery
    - id: https://www.ncbi.nlm.nih.gov/pubmed/22961259
      title: The Mammalian Phenotype Ontology as a unifying standard for experimental
        and high-throughput phenotyping data
    - id: https://www.ncbi.nlm.nih.gov/pubmed/25825651
      title: Expanding the mammalian phenotype ontology to support automated exchange
        of high throughput mouse phenotyping data generated by large-scale mouse knockout
        screens
    repository: https://github.com/mgijax/mammalian-phenotype-ontology
  ols:
    description: The Mammalian Phenotype Ontology is being developed by Cynthia L.
      Smith, Susan M. Bello, Anna V. Anagnostopoulos, Carroll W. Goldsmith and Janan
      T. Eppig, as part of the Mouse Genome Database (MGD) Project, Mouse Genome Informatics
      (MGI), The Jackson Laboratory, Bar Harbor, ME. This file contains pre-coordinated
      phenotype terms, definitions and synonyms that can be used to describe mammalian
      phenotypes. The ontology is represented as a directed acyclic graph (DAG). It
      organizes phenotype terms into major biological system headers such as nervous
      system and respiratory system.  This ontology is currently under development.
      Weekly updates are available at the Mouse Genome Informatics (MGI) ftp site
      (ftp://ftp.informatics.jax.org/pub/reports/index.html#pheno) as well as the
      OBO Foundry site (http://obofoundry.org/). Japanese labels of MP were created
      by the MP Japanese Translation Project (https://github.com/dbcls/MP_Japanese).
      Questions, comments and suggestions are welcome, and should be directed to pheno@jax.org,
      Susan.Bello@jax.org or to GitHub tracker (https://github.com/mgijax/mammalian-phenotype-ontology/issues)
      MGD is funded by NIH/NHGRI grant HG000330.
    download_owl: http://purl.obolibrary.org/obo/mp/mp-international.owl
    homepage: https://www.informatics.jax.org/vocab/mp_ontology/
    name: The Mammalian Phenotype Ontology
    prefix: mp
    tracker: https://github.com/mgijax/mammalian-phenotype-ontology/issues
    version: '2025-11-19'
    version.iri: http://purl.obolibrary.org/obo/mp/releases/2025-11-19/mp-international.owl
  ontobee:
    library: Library
    name: Mammalian Phenotype Ontology
    prefix: MP
  pattern: ^\d{7}$
  prefix: mp
  prefixcommons:
    alt_uri_formats:
    - http://purl.org/obo/owl/MP#$1
    bioportal: '1025'
    description: The Mammalian Phenotype Ontology is under development as a community
      effort to provide standard terms for annotating mammalian phenotypic data.
    example: MP:0000001
    homepage: http://www.informatics.jax.org/searches/MP_form.shtml
    keywords:
    - obo
    - phenotype
    - mammalian
    name: Mammalian phenotype
    pattern: ^MP:\d+$
    prefix: mp
    uri_format: http://www.informatics.jax.org/searches/Phat.cgi?id=$1
  providers:
  - code: nextprot
    description: The neXtProt endpoint for exploring MP
    example: null
    first_party: null
    homepage: https://www.nextprot.org
    name: neXtProt MP Browser
    publications: null
    status: null
    uri_format: https://www.nextprot.org/term/MP:$1
  publications:
  - doi: 10.1186/s13326-015-0009-1
    pmc: PMC4378007
    pubmed: '25825651'
    title: Expanding the mammalian phenotype ontology to support automated exchange
      of high throughput mouse phenotyping data generated by large-scale mouse knockout
      screens
    year: 2015
  - doi: 10.1007/s00335-012-9421-3
    pmc: PMC3463787
    pubmed: '22961259'
    title: The Mammalian Phenotype Ontology as a unifying standard for experimental
      and high-throughput phenotyping data
    year: 2012
  - doi: 10.1002/wsbm.44
    pmc: PMC2801442
    pubmed: '20052305'
    title: 'The mammalian phenotype ontology: enabling robust annotation and comparative
      analysis'
    year: 2009
  - doi: 10.1186/gb-2004-6-1-r7
    pmc: PMC549068
    pubmed: '15642099'
    title: The Mammalian Phenotype Ontology as a tool for annotating, analyzing and
      comparing phenotypic information
    year: 2004
  togoid:
    examples:
    - MP:0000600
    - MP:0001716
    - MP:0001698
    - MP:0001092
    - MP:0000961
    - MP:0000245
    - MP:0000828
    - MP:0000826
    - MP:0005039
    - MP:0002840
    keywords:
    - Phenotype
    name: Mammalian Phenotype Ontology
    pattern: ^MP[:_](?\d{7})$
    prefix: Mp
    uri_format: http://identifiers.org/mp/MP:$1
  uri_format: http://purl.obolibrary.org/obo/MP_$1
mpath:
  aberowl:
    description: A structured controlled vocabulary of mutant and transgenic mouse
      pathology phenotypes
    download_owl: http://aber-owl.net/media/ontologies/MPATH/173/mpath.owl
    homepage: http://www.pathbase.net
    name: Mouse pathology ontology
    prefix: MPATH
  biocontext:
    prefix: MPATH
  bioportal:
    contact:
      email: pns12@cam.ac.uk
      name: Mouse_pathology Administrators
    description: A structured controlled vocabulary of mutant and transgenic mouse
      pathological lesions and processes
    homepage: http://www.pathbase.net
    name: Mouse Pathology Ontology
    prefix: MPATH
    version: '2020-05-19'
  download_obo: https://raw.githubusercontent.com/PaulNSchofield/mpath/master/mpath.obo
  example: '728'
  fairsharing:
    abbreviation: MPATH
    contact:
      email: pns12@cam.ac.uk
      name: Paul Schofield
      orcid: 0000-0002-5111-7263
    description: Mouse PATHology (MPATH) ontology is a structured controlled vocabulary
      of mutant and transgenic mouse pathology phenotypes. This resource was developed
      by the Pathology Consortium of Pathbase (www.pathbase.net).
    domains:
    - mutation
    - histological assay
    - phenotype
    - disease
    - strain
    homepage: http://eulep.pdn.cam.ac.uk/Pathology_Ontology/index.php
    name: Mouse PATHology
    prefix: FAIRsharing.3wbgm0
    publications:
    - doi: 10.1177/0300985810374845
      pubmed: '20587689'
      title: Pathbase and the MPATH ontology. Community resources for mouse histopathology
      year: 2010
    repository: https://github.com/PaulNSchofield/mpath
    subjects:
    - Anatomy
    - Biomedical Science
  integbio:
    alt_name: Navigating a Potential Metabolic Pathway
    description: M-path DB is a database of metabolic pathways calculated sets of
      compounds from the PubChem and ChEBI databases. It contains putative metabolic
      pathways for a series of chemical species, and produces networks including some
      interesting pathways.
    homepage: http://bp.scitec.kobe-u.ac.jp/m-path/db/
    information_keywords:
    - Interaction/Pathway
    - Chemical structure
    maintainer: Kobe University
    name: M-path
    prefix: nbdc01568
    pubmeds:
    - '25398612'
    status: Inactive
    target_keywords:
    - Metabolite
  mappings:
    aberowl: MPATH
    biocontext: MPATH
    bioportal: MPATH
    fairsharing: FAIRsharing.3wbgm0
    integbio: nbdc01568
    obofoundry: mpath
    ols: mpath
    ontobee: MPATH
    prefixcommons: mpath
    wikidata.entity: Q55118458
  obofoundry:
    contact: pns12@hermes.cam.ac.uk
    contact.github: PaulNSchofield
    contact.label: Paul Schofield
    contact.orcid: 0000-0002-5111-7263
    deprecated: false
    description: A structured controlled vocabulary of mutant and transgenic mouse
      pathology phenotypes
    domain: health
    download.owl: http://purl.obolibrary.org/obo/mpath.owl
    homepage: http://www.pathbase.net
    license: CC BY 3.0
    license.url: http://creativecommons.org/licenses/by/3.0/
    name: Mouse pathology ontology
    preferredPrefix: MPATH
    prefix: mpath
    repository: https://github.com/PaulNSchofield/mpath
  ols:
    description: A structured controlled vocabulary of mutant and transgenic mouse
      pathology phenotypes
    download_owl: http://purl.obolibrary.org/obo/mpath.owl
    homepage: http://www.pathbase.net
    name: Mouse pathology ontology
    prefix: mpath
    tracker: https://github.com/PaulNSchofield/mpath/issues
    version: '2020-05-19'
    version.iri: http://purl.obolibrary.org/obo/mpath/2020-05-19/mpath.owl
  ontobee:
    library: Not Specified/No
    name: Mouse pathology
    prefix: MPATH
  pattern: ^\d+$
  prefix: mpath
  prefixcommons:
    bioportal: '1031'
    description: A structured controlled vocabulary of mutant and transgenic mouse
      pathology phenotypes
    example: MPATH_606
    homepage: http://www.pathbase.net
    keywords:
    - obo
    - phenotype
    - mouse
    name: Mouse pathology
    pattern: ^MPATH_\d+$
    prefix: mpath
  publications:
  - doi: 10.1177/0300985810374845
    pmc: PMC3038412
    pubmed: '20587689'
    title: Pathbase and the MPATH ontology. Community resources for mouse histopathology
    year: 2010
  - doi: 10.1177/0300985810374845
    pmc: null
    pubmed: '20587689'
    title: Pathbase and the MPATH ontology. Community resources for mouse histopathology
    year: 2010
  synonyms:
  - MPATH
  uri_format: http://purl.obolibrary.org/obo/MPATH_$1
mpid:
  biocontext:
    prefix: MPID
  contact:
    email: jgoll@emmes.com
    github: null
    name: Johannes B. Goll
    orcid: 0000-0002-9968-4080
  fairsharing:
    abbreviation: MPIDB
    description: The microbial protein interaction database (MPIDB) provides physical
      microbial interaction data. The interactions are manually curated from the literature
      or imported from other databases, and are linked to supporting experimental
      evidence, as well as evidences based on interaction conservation, protein complex
      membership, and 3D domain contacts. This resource has been marked as Uncertain
      because its project home can no longer be found. Please get in touch if you
      have any information about this resource.
    homepage: http://www.jcvi.org/mpidb/about.php
    name: Microbial Protein Interaction Database
    prefix: FAIRsharing.eyjkws
    publications:
    - doi: 10.1093/bioinformatics/btn285
      pubmed_id: 18556668
      title: 'MPIDB: the microbial protein interaction database.'
    subjects:
    - Life Science
  mappings:
    biocontext: MPID
    fairsharing: FAIRsharing.eyjkws
    miriam: mpid
    n2t: mpid
    pathguide: '559'
    prefixcommons: mpi
  miriam:
    deprecated: false
    description: The microbial protein interaction database (MPIDB) provides physical
      microbial interaction data. The interactions are manually curated from the literature
      or imported from other databases, and are linked to supporting experimental
      evidence, as well as evidences based on interaction conservation, protein complex
      membership, and 3D domain contacts.
    homepage: https://www.ebi.ac.uk/intact/
    id: '00000124'
    name: Microbial Protein Interaction Database
    namespaceEmbeddedInLui: false
    pattern: ^\d+$
    prefix: mpid
    sampleId: '1776'
    uri_format: https://www.ebi.ac.uk/intact/query/interaction_id:MPIDB-INT-$1
  n2t:
    description: The microbial protein interaction database (MPIDB) provides physical
      microbial interaction data. The interactions are manually curated from the literature
      or imported from other databases, and are linked to supporting experimental
      evidence, as well as evidences based on interaction conservation, protein complex
      membership, and 3D domain contacts.
    example: '172'
    homepage: http://www.jcvi.org/mpidb/about.php
    name: Microbial Protein Interaction Database
    namespaceEmbeddedInLui: false
    pattern: ^\d+$
    prefix: mpid
    uri_format: http://www.jcvi.org/mpidb/experiment.php?interaction_id=$1
  pathguide:
    abbreviation: MPID
    homepage: http://bioinformatics.cau.edu.cn/cgi-bin/zzd-cgi/ppi/mpid.pl
    name: Magnaporthe grisea Protein-protein Interaction Database
    prefix: '559'
  prefix: mpid
  prefixcommons:
    description: The microbial protein interaction database (MPIDB) provides physical
      microbial interaction data. The interactions are manually curated from the literature
      or imported from other databases, and are linked to supporting experimental
      evidence, as well as evidences based on interaction conservation, protein complex
      membership, and 3D domain contacts.
    example: '172'
    homepage: http://www.jcvi.org/mpidb/
    keywords:
    - interaction
    - protein
    - small molecule
    license: http://www.jcvi.org/cms/legal/privacy-statement
    name: Microbial Protein Interaction Database
    pattern: ^\d+$
    prefix: mpi
    pubmed_ids:
    - '18556668'
    synonyms:
    - mpid
    - mpidb
    uri_format: http://www.jcvi.org/mpidb/interaction.php?pname=$1
  publications:
  - doi: 10.1093/bioinformatics/btn285
    pmc: PMC2638870
    pubmed: '18556668'
    title: 'MPIDB: the microbial protein interaction database'
    year: 2008
  - doi: 10.1093/bioinformatics/btn285
    pmc: null
    pubmed: null
    title: 'MPIDB: the microbial protein interaction database.'
    year: null
  - doi: null
    pmc: null
    pubmed: '18556668'
    title: null
    year: null
  - doi: 10.1093/bioinformatics/btn285
    pmc: null
    pubmed: null
    title: 'MPIDB: the microbial protein interaction database.'
    year: null
  - doi: null
    pmc: null
    pubmed: '18556668'
    title: null
    year: null
  synonyms:
  - mpidb
mpio:
  aberowl:
    description: An ontology of minimum information regarding potential drug-drug
      interaction information.
    download_owl: http://aber-owl.net/media/ontologies/MPIO/5/mpio.owl
    homepage: https://github.com/MPIO-Developers/MPIO
    name: Minimum PDDI Information Ontology
    prefix: MPIO
  biocontext:
    prefix: MPIO
  bioportal:
    contact:
      email: mbrochhausen@uams.edu
      name: Mathias Brochhausen
    description: MPIO (Minimum PDDI Information Ontology) is an OWL representation
      of minimum information regarding potential drug-drug interaction information.
      It is based on and meant to be use in alignment with DIDEO or DINTO.
    homepage: https://github.com/MPIO-Developers/MPIO
    name: Minimum PDDI Information Ontology
    prefix: MPIO
    version: '2023-10-17'
  example: '0000004'
  mappings:
    aberowl: MPIO
    biocontext: MPIO
    bioportal: MPIO
    obofoundry: mpio
    ols: mpio
    ontobee: MPIO
    wikidata.entity: Q81661711
  obofoundry:
    contact: mbrochhausen@uams.edu
    contact.github: mbrochhausen
    contact.label: Mathias Brochhausen
    contact.orcid: 0000-0003-1834-3856
    deprecated: false
    description: An ontology of minimum information regarding potential drug-drug
      interaction information.
    domain: health
    download.owl: http://purl.obolibrary.org/obo/mpio.owl
    homepage: https://github.com/MPIO-Developers/MPIO
    license: CC BY 4.0
    license.url: http://creativecommons.org/licenses/by/4.0/
    name: Minimum PDDI Information Ontology
    preferredPrefix: MPIO
    prefix: mpio
    repository: https://github.com/MPIO-Developers/MPIO
  ols:
    description: An ontology of minimum information regarding potential drug-drug
      interaction information.
    download_owl: http://purl.obolibrary.org/obo/mpio.owl
    homepage: https://github.com/MPIO-Developers/MPIO
    name: Minimum PDDI Information Ontology
    prefix: mpio
    tracker: https://github.com/MPIO-Developers/MPIO/issues
    version: '2023-10-17'
    version.iri: http://purl.obolibrary.org/obo/mpio/release/2023-10-17/mpio.owl
  ontobee:
    library: Library
    name: Minimum PDDI Information Ontology
    prefix: MPIO
  pattern: ^\d{7}$
  prefix: mpio
  uri_format: http://purl.obolibrary.org/obo/MPIO_$1
mro:
  aberowl:
    description: An ontology for Major Histocompatibility Complex (MHC) restriction
      in experiments
    download_owl: http://aber-owl.net/media/ontologies/MRO/64/mro.owl
    homepage: https://github.com/IEDB/MRO
    name: MHC Restriction Ontology
    prefix: MRO
  biocontext:
    prefix: MRO
  example: '0000634'
  fairsharing:
    abbreviation: MRO
    description: MHC molecules form a highly diverse family of proteins that play
      a key role in cellular immune recognition. No consistent nomenclature exists
      across different vertebrate species. To correctly represent MHC related data
      in The Immune Epitope Database (IEDB), we built upon a previously established
      MHC ontology (MaHCO) and created MRO to represent MHC molecules as they relate
      to immunological experiments. MRO models MHC protein chains from 16 species,
      deals with different approaches used to identify MHC, such as direct sequencing
      verses serotyping, relates engineered MHC molecules to naturally occurring ones,
      connects genetic loci, alleles, protein chains and multichain proteins, and
      establishes evidence codes for MHC restriction.
    domains:
    - Major Histocompatibility Complex
    - immune system
    homepage: https://github.com/IEDB/MRO
    license: CC-BY-3.0
    name: MHC Restriction Ontology
    prefix: FAIRsharing.k893xa
    publications:
    - doi: 10.1186/s13326-016-0045-5
      pubmed: '26759709'
      title: An ontology for major histocompatibility restriction
      year: 2016
    repository: https://github.com/IEDB/MRO/issues
    subjects:
    - Immunology
  mappings:
    aberowl: MRO
    biocontext: MRO
    fairsharing: FAIRsharing.k893xa
    obofoundry: mro
    ols: mro
    ontobee: MRO
    wikidata.entity: Q81661712
  obofoundry:
    contact: bpeters@lji.org
    contact.github: bpeters42
    contact.label: Bjoern Peters
    contact.orcid: 0000-0002-8457-6693
    deprecated: false
    description: An ontology for Major Histocompatibility Complex (MHC) restriction
      in experiments
    domain: chemistry and biochemistry
    download.owl: http://purl.obolibrary.org/obo/mro.owl
    homepage: https://github.com/IEDB/MRO
    license: CC BY 3.0
    license.url: https://creativecommons.org/licenses/by/3.0/
    name: MHC Restriction Ontology
    preferredPrefix: MRO
    prefix: mro
    repository: https://github.com/IEDB/MRO
  ols:
    description: The MHC Restriction Ontology is an application ontology capturing
      how Major Histocompatibility Complex (MHC) restriction is defined in experiments,
      spanning exact protein complexes, individual protein chains, serotypes, haplotypes
      and mutant molecules, as well as evidence for MHC restrictions.
    download_owl: http://purl.obolibrary.org/obo/mro.owl
    homepage: https://github.com/IEDB/MRO
    name: MHC Restriction Ontology
    prefix: mro
    tracker: https://github.com/IEDB/MRO/issues
    version: '2025-10-29'
    version.iri: http://purl.obolibrary.org/obo/mro/2025-10-29/mro.owl
  ontobee:
    library: Library
    name: MHC Restriction Ontology
    prefix: MRO
  pattern: ^\d{7}$
  prefix: mro
  publications:
  - doi: 10.1186/s13326-016-0045-5
    pmc: PMC4709943
    pubmed: '26759709'
    title: An ontology for major histocompatibility restriction
    year: 2016
  - doi: 10.1186/s13326-016-0045-5
    pmc: null
    pubmed: '26759709'
    title: An ontology for major histocompatibility restriction
    year: 2016
  uri_format: http://purl.obolibrary.org/obo/MRO_$1
ms:
  aberowl:
    description: A structured controlled vocabulary for the annotation of experiments
      concerned with proteomics mass spectrometry.
    download_owl: http://aber-owl.net/media/ontologies/MS/228/ms.owl
    homepage: http://www.psidev.info/groups/controlled-vocabularies
    name: Mass spectrometry ontology
    prefix: MS
  biocontext:
    prefix: MS
  bioportal:
    contact:
      email: gerhard.mayer@rub.de
      name: Gerhard Mayer
    description: A structured controlled vocabulary for the annotation of experiments
      concerned with proteomics mass spectrometry. Developed by the HUPO Proteomics
      Standards Initiative (PSI).
    homepage: http://www.psidev.info/groups/controlled-vocabularies
    name: Mass Spectrometry Ontology
    prefix: MS
    publications:
    - http://database.oxfordjournals.org/content/2013/bat009.long
    version: 4.1.195
  example: '1000560'
  mappings:
    aberowl: MS
    biocontext: MS
    bioportal: MS
    miriam: ms
    n2t: ms
    obofoundry: ms
    ols: ms
    ontobee: MS
    tib: ms
    wikidata.entity: Q81661714
  miriam:
    deprecated: false
    description: The PSI-Mass Spectrometry (MS) CV contains all the terms used in
      the PSI MS-related data standards. The CV contains a logical hierarchical structure
      to ensure ease of maintenance and the development of software that makes use
      of complex semantics. The CV contains terms required for a complete description
      of an MS analysis pipeline used in proteomics, including sample labeling, digestion
      enzymes, instrumentation parts and parameters, software used for identification
      and quantification of peptides/proteins and the parameters and scores used to
      determine their significance.
    homepage: https://bioportal.bioontology.org/ontologies/MS
    id: 00000590
    name: Mass Spectrometry Controlled Vocabulary
    namespaceEmbeddedInLui: true
    pattern: ^MS:\d{7}$
    prefix: ms
    sampleId: '1000001'
    uri_format: http://purl.bioontology.org/ontology/MS/MS:$1
  n2t:
    description: The PSI-Mass Spectrometry (MS) CV contains all the terms used in
      the PSI MS-related data standards. The CV contains a logical hierarchical structure
      to ensure ease of maintenance and the development of software that makes use
      of complex semantics. The CV contains terms required for a complete description
      of an MS analysis pipeline used in proteomics, including sample labeling, digestion
      enzymes, instrumentation parts and parameters, software used for identification
      and quantification of peptides/proteins and the parameters and scores used to
      determine their significance.
    example: '1000001'
    homepage: https://bioportal.bioontology.org/ontologies/MS
    name: Mass Spectrometry Controlled Vocabulary through BioPortal
    namespaceEmbeddedInLui: true
    pattern: ^MS:\d{7}$
    prefix: ms
    uri_format: http://purl.bioontology.org/ontology/MS/MS:$1
  obofoundry:
    contact: joshua.adam.klein@gmail.com
    contact.github: mobiusklein
    contact.label: Joshua Klein
    contact.orcid: 0000-0003-1279-6838
    depends_on:
    - pato
    - uo
    deprecated: false
    description: A structured controlled vocabulary for the annotation of experiments
      concerned with proteomics mass spectrometry.
    domain: investigations
    download.obo: http://purl.obolibrary.org/obo/ms.obo
    download.owl: http://purl.obolibrary.org/obo/ms.owl
    homepage: http://www.psidev.info/groups/controlled-vocabularies
    license: CC BY 3.0
    license.url: https://creativecommons.org/licenses/by/3.0/
    name: Mass spectrometry ontology
    preferredPrefix: MS
    prefix: ms
    publications:
    - id: https://www.ncbi.nlm.nih.gov/pubmed/23482073
      title: The HUPO proteomics standards initiative- mass spectrometry controlled
        vocabulary.
    repository: https://github.com/HUPO-PSI/psi-ms-CV
  ols:
    contact: psidev-ms-vocab@lists.sourceforge.net
    description: A structured controlled vocabulary for the annotation of experiments
      concerned with proteomics mass spectrometry.
    download_owl: http://purl.obolibrary.org/obo/ms.owl
    homepage: http://www.psidev.info/groups/controlled-vocabularies
    name: Mass spectrometry ontology
    prefix: ms
    tracker: https://github.com/HUPO-PSI/psi-ms-CV/issues
    version: 4.1.223
    version.iri: http://purl.obolibrary.org/obo/ms/4.1.223/ms.owl
  ontobee:
    library: Library
    name: Mass spectrometry ontology
    prefix: MS
  pattern: ^\d{7}$
  prefix: ms
  publications:
  - doi: 10.1093/database/bat009
    pmc: PMC3594986
    pubmed: '23482073'
    title: The HUPO proteomics standards initiative- mass spectrometry controlled
      vocabulary
    year: 2013
  tib:
    description: A structured controlled vocabulary for the annotation of experiments
      concerned with proteomics mass spectrometry.
    download_owl: http://purl.obolibrary.org/obo/ms.owl
    homepage: http://www.psidev.info/groups/controlled-vocabularies
    keywords:
    - NFDI4CHEM
    - DataPLANT
    - NFDI4CAT
    - chemistry
    name: Mass Spectrometry
    prefix: ms
    tracker: https://github.com/HUPO-PSI/psi-ms-CV/issues
    version.iri: http://purl.obolibrary.org/obo/ms/4.1.214/ms.owl
  uri_format: http://purl.obolibrary.org/obo/MS_$1
msigdb:
  biolink:
    is_identifiers: false
    is_obo: false
    prefix: MSigDB
    uri_format: https://www.gsea-msigdb.org/gsea/msigdb/$1
  contact:
    email: jmesirov@ucsd.edu
    github: null
    name: Jill P. Mesirov
    orcid: 0000-0002-9755-2818
  contact_group_email: gsea-team@broadinstitute.org
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: The Molecular Signatures Database (MSigDB) is a collection of annotated
    gene sets for use with GSEA software. From this web site, you can
  domain: pathway
  example: M1
  homepage: https://www.gsea-msigdb.org
  integbio:
    alt_name: Molecular Signatures Database
    description: 'MSigDB is a collection of annotated gene sets for use with Enrichment
      Analysis (GSEA) software which is a computational method that determines whether
      an a priori defined set of genes shows statistically significant, concordant
      differences between two biological states. It contains 9 major collections of
      the gene sets;

      H: hallmark gene sets

      C1: positional gene sets

      C2: curated gene sets

      C3: regulatory target gene sets

      C4: computational gene sets

      C5: ontology gene sets

      C6: oncogenic signature gene sets

      C7: immunologic signature gene sets

      C8: cell type signature gene sets'
    homepage: http://www.gsea-msigdb.org/gsea/msigdb/index.jsp
    information_keywords:
    - Expression
    - Interaction/Pathway
    maintainer: Broad Institute of Harvard and MIT||UCSD (University of California
      San Diego)
    name: MSigDB
    prefix: nbdc02550
    pubmeds:
    - '16199517'
    status: Active
    target_keywords:
    - Genome/Gene
    - Health/Disease
  keywords:
  - gene family
  - gene group
  - gene set
  - pathway
  - reaction
  license: CC-BY-4.0
  logo: https://www.gsea-msigdb.org/gsea/images/GSEA-logo.gif
  mappings:
    biolink: MSigDB
    integbio: nbdc02550
  name: Molecular Signatures Database
  pattern: ^M\d+$
  prefix: msigdb
  providers:
  - code: biopragmatics
    description: An OBO to Website of MMSigDB
    example: null
    first_party: null
    homepage: https://biopragmatics.github.io/providers/msigdb/
    name: MMSigDB from Biopragmatics
    publications: null
    status: null
    uri_format: https://biopragmatics.github.io/providers/msigdb/$1
  synonyms:
  - msig
  uri_format: https://www.gsea-msigdb.org/gsea/msigdb/human/geneset/$1
  wikidata:
    paper: Q34509167
msio:
  example: '0000111'
  fairsharing:
    abbreviation: MSIO
    contact:
      email: philippe.rocca-serra@oerc.ox.ac.uk
      name: Philippe Rocca-Serra
      orcid: 0000-0001-9853-5668
    description: The Metabolomics Standards Initiative Ontology (MSIO) aims to support
      metabolomic experimental annotations for mass spectrometry (MS) and nuclear
      magnetic resonance (NMR) spectroscopy techniques to identify, measure and quantify
      small molecules known as metabolites. MSIO covers metabolite profiling, targeted
      or untargeted, and tracer based applications.
    domains:
    - Mass spectrum
    - Experimental measurement
    - Annotation
    - Data analysis
    - nuclear magnetic resonance spectroscopy
    - Functional Magnetic Resonance Imaging
    homepage: https://github.com/MSI-Metabolomics-Standards-Initiative/MSIO
    license: CC-BY-3.0
    name: Metabolomics Standards Initiative Ontology
    prefix: FAIRsharing.4c7f91
    publications:
    - doi: 10.1007/s11306-007-0069-z
      title: 'Metabolomics standards initiative: ontology working group work in progress'
      year: 2007
    repository: https://github.com/MSI-Metabolomics-Standards-Initiative/MSIO
    subjects:
    - Metabolomics
    - Omics
  keywords:
  - nmr
  mappings:
    fairsharing: FAIRsharing.4c7f91
    ols: msio
    tib: msio
  name: Metabolomics Standards Initiative Ontology
  ols:
    description: an application ontology for supporting description and annotation
      of mass-spectrometry and nmr-spectroscopy based metabolomics experiments and
      fluxomics studies.
    download_owl: https://raw.githubusercontent.com/MSI-Metabolomics-Standards-Initiative/MSIO/master/releases/latest_release/MSIO-merged-reasoned.owl
    homepage: https://github.com/MSI-Metabolomics-Standards-Initiative/MSIO
    name: Metabolomics Standards Initiative Ontology (MSIO)
    prefix: msio
    uri_format: http://purl.obolibrary.org/obo/MSIO_$1
    version: 1.0.1
  pattern: ^\d{7}$
  prefix: msio
  repository: https://github.com/MSI-Metabolomics-Standards-Initiative/MSIO
  tib:
    description: an application ontology for supporting description and annotation
      of mass-spectrometry and nmr-spectroscopy based metabolomics experiments and
      fluxomics studies.
    download_owl: https://raw.githubusercontent.com/MSI-Metabolomics-Standards-Initiative/MSIO/master/releases/latest_release/MSIO-merged-reasoned.owl
    homepage: https://github.com/MSI-Metabolomics-Standards-Initiative/MSIO/
    keywords:
    - DataPLANT
    - life sciences, biology
    name: Metabolomics Standards Initiative Ontology (MSIO)
    prefix: msio
    tracker: https://github.com/MSI-Metabolomics-Standards-Initiative/MSIO/issues/
    uri_format: http://purl.obolibrary.org/obo/msio.owl$1
  uri_format: http://purl.obolibrary.org/obo/MSIO_$1
mtbd:
  mappings:
    prefixcommons: mtbd
  prefix: mtbd
  prefixcommons:
    description: The Mouse Tumor Biology (MTB) Database supports the use of the mouse
      as a model system of hereditary cancer by providing electronic access to Information
      on endogenous spontaneous and induced tumors in mice, including tumor frequency
      & latency data, information on genetically defined mice (inbred, hybrid, mutant,
      and genetically engineered strains of mice) in which tumors arise, and information
      on genetic factors associated with tumor susceptibility in mice and somatic
      genetic-mutations observed in the tumors.
    example: '1374'
    homepage: http://tumor.informatics.jax.org
    keywords:
    - gene expression
    - DNA
    name: Mouse Tumor Biology Database
    pattern: ^\d+$
    prefix: mtbd
    uri_format: http://tumor.informatics.jax.org/mtbwi/strainDetails.do?key=$1
  reviewer:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
mth:
  appears_in:
  - umls
  - mondo
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: The Unified Medical Language System® (UMLS®) Metathesaurus (MTH) was
    developed and is maintained by the U.S. National Library of Medicine (NLM). MTH
    contains concept names, attributes, relationships, and other data that were created
    by NLM to facilitate construction of the UMLS Metathesaurus.
  example: U001388
  github_request_issue: 1573
  hl7:
    description: 'UMLS Metathesaurus. Bethesda, MD: National Library of Medicine.'
    name: Metathesaurus Names
    preferred_prefix: MTH
    prefix: 2.16.840.1.113883.6.189
    status: Pending
  homepage: https://www.nlm.nih.gov/research/umls/sourcereleasedocs/current/MTH/index.html
  mappings:
    hl7: 2.16.840.1.113883.6.189
  name: Metathesaurus Names
  pattern: ^U\d+$
  prefix: mth
  synonyms:
  - umls.mth
  uri_format: https://uts.nlm.nih.gov/uts/umls/vocabulary/MTH/$1
multicellds:
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: MultiCellDS is data standard for multicellular simulation, experimental,
    and clinical data. A digital cell line is a hierarchical organization of quantitative
    phenotype data for a single biological cell line, including the microenvironmental
    context of the measurements and essential metadata.
  example: MCDS_S_0000000001
  fairsharing:
    abbreviation: MultiCellDS
    contact:
      email: samuel.friedman@cammlab.org
      name: Samuel Friedman
      orcid: 0000-0001-8003-6860
    description: 'MultiCellDS (Multicellular data specification), an outgrowth of
      the earlier MultiCellXML project, aims to create a data standard for sharing
      multicellular experimental, simulation, and clinical data. Our ultimate goal
      is to foster a community that develops user-friendly tools that can read, write,
      and recombine data into better simulations and analyses for multicellular biology
      and predictive medicine. As part of this effort, we are developing MultiCellDB:
      a repository for a curated library of digital cell lines and peer-reviewed simulation
      and experimental data. A novel part of MultiCellDS is the digital cell line:
      a digital analogue of experimental cell lines that will help to collect biophysical
      cell line measurements coming from many research groups and make them readily
      accessible to an ecosystem of compatible computational models. You can learn
      more about digital cell lines and other core ideas on this page. We are currently
      preparing a draft of the upcoming MultiCellDS 1.0 specification. After a multiple
      rounds of comment and review by a multidisciplinary review panel and the general
      public, we target an October 2016 release of the data specification and software
      support tools.'
    homepage: http://multicellds.org
    name: MultiCellular Data Standard
    prefix: FAIRsharing.pqzyd5
    publications: []
    subjects:
    - Life Science
  homepage: http://multicellds.org/MultiCellDB.php
  mappings:
    fairsharing: FAIRsharing.pqzyd5
  name: MultiCellDS
  prefix: multicellds
  uri_format: http://multicellds.org/MultiCellDB/$1
multicellds.cell_line:
  biocontext:
    prefix: MULTICELLDS.CELL_LINE
  mappings:
    biocontext: MULTICELLDS.CELL_LINE
    miriam: multicellds.cell_line
    n2t: multicellds.cell_line
  miriam:
    deprecated: false
    description: MultiCellDS is data standard for multicellular simulation, experimental,
      and clinical data. A digital cell line is a hierarchical organization of quantitative
      phenotype data for a single biological cell line, including the microenvironmental
      context of the measurements and essential metadata.
    homepage: http://multicellds.org/MultiCellDB.php
    id: 00000584
    name: MultiCellDS Digital Cell Line
    namespaceEmbeddedInLui: false
    pattern: ^MCDS_L_[a-zA-Z0-9]{1,10}$
    prefix: multicellds.cell_line
    sampleId: MCDS_L_0000000001
    uri_format: http://multicellds.org/MultiCellDB/$1
  n2t:
    description: MultiCellDS is data standard for multicellular simulation, experimental,
      and clinical data. A digital cell line is a hierarchical organization of quantitative
      phenotype data for a single biological cell line, including the microenvironmental
      context of the measurements and essential metadata.
    example: MCDS_L_0000000001
    homepage: http://multicellds.org/MultiCellDB.php
    name: MultiCellDS Digital Cell Line at Keck School of Medicine
    namespaceEmbeddedInLui: false
    pattern: ^MCDS_L_[a-zA-Z0-9]{1,10}$
    prefix: multicellds.cell_line
    uri_format: http://multicellds.org/MultiCellDB/$1
  part_of: multicellds
  prefix: multicellds.cell_line
multicellds.collection:
  biocontext:
    prefix: MULTICELLDS.COLLECTION
  mappings:
    biocontext: MULTICELLDS.COLLECTION
    miriam: multicellds.collection
    n2t: multicellds.collection
  miriam:
    deprecated: false
    description: MultiCellDS is data standard for multicellular simulation, experimental,
      and clinical data. A collection groups one or more individual uniquely identified
      cell lines, snapshots, or collections. Primary uses are times series (collections
      of snapshots), patient cohorts (collections of cell lines), and studies (collections
      of time series collections).
    homepage: http://multicellds.org/MultiCellDB.php
    id: 00000582
    name: MultiCellDS collection
    namespaceEmbeddedInLui: false
    pattern: ^MCDS_C_[a-zA-Z0-9]{1,10}$
    prefix: multicellds.collection
    sampleId: MCDS_C_0000000001
    uri_format: http://multicellds.org/MultiCellDB/$1
  n2t:
    description: MultiCellDS is data standard for multicellular simulation, experimental,
      and clinical data. A collection groups one or more individual uniquely identified
      cell lines, snapshots, or collections. Primary uses are times series (collections
      of snapshots), patient cohorts (collections of cell lines), and studies (collections
      of time series collections).
    example: MCDS_C_0000000001
    homepage: http://multicellds.org/MultiCellDB.php
    name: MultiCellDScollection at Keck School of Medicine
    namespaceEmbeddedInLui: false
    pattern: ^MCDS_C_[a-zA-Z0-9]{1,10}$
    prefix: multicellds.collection
    uri_format: http://multicellds.org/MultiCellDB/$1
  part_of: multicellds
  prefix: multicellds.collection
multicellds.snapshot:
  biocontext:
    prefix: MULTICELLDS.SNAPSHOT
  mappings:
    biocontext: MULTICELLDS.SNAPSHOT
    miriam: multicellds.snapshot
    n2t: multicellds.snapshot
  miriam:
    deprecated: false
    description: MultiCellDS is data standard for multicellular simulation, experimental,
      and clinical data. A digital snapshot is a single-time output of the microenvironment
      (including basement membranes and the vascular network), any cells contained
      within, and essential metadata. Cells may include phenotypic data.
    homepage: http://multicellds.org/MultiCellDB.php
    id: 00000583
    name: MultiCellDS Digital snapshot
    namespaceEmbeddedInLui: false
    pattern: ^MCDS_S_[a-zA-Z0-9]{1,10}$
    prefix: multicellds.snapshot
    sampleId: MCDS_S_0000000001
    uri_format: http://multicellds.org/MultiCellDB/$1
  n2t:
    description: MultiCellDS is data standard for multicellular simulation, experimental,
      and clinical data. A digital snapshot is a single-time output of the microenvironment
      (including basement membranes and the vascular network), any cells contained
      within, and essential metadata. Cells may include phenotypic data.
    example: MCDS_S_0000000001
    homepage: http://multicellds.org/MultiCellDB.php
    name: MultiCellDS snapshot at Keck School of Medicine
    namespaceEmbeddedInLui: false
    pattern: ^MCDS_S_[a-zA-Z0-9]{1,10}$
    prefix: multicellds.snapshot
    uri_format: http://multicellds.org/MultiCellDB/$1
  part_of: multicellds
  prefix: multicellds.snapshot
mvx:
  contributor:
    email: lindsey.anderson@pnnl.gov
    github: lnanderson
    name: Lindsey N. Anderson
    orcid: 0000-0002-8741-7823
  description: The CDC's National Center for Immunization and Respiratory Diseases
    ([NCIRD](https://www.cdc.gov/ncird/)) developed and maintains HL7 Table 0227,
    Manufacturers of Vaccines (MVX). It includes both active and inactive manufacturers
    of vaccines in the US. Inactive MVX codes allow transmission of historical immunization
    records. When [MVX code is paired with a CVX code](https://www2a.cdc.gov/vaccines/iis/iisstandards/vaccines.asp?rpt=tradename)
    (vaccine administered code), the specific trade named vaccine may be indicated.
  example: ASZ
  github_request_issue: 986
  hl7:
    description: CDC Vaccine Manufacturer CodesDO NOT USEThis OID was setup solely
      for use in the RRF research project in 1999.   The correct OID for mvx is 2.16.840.1.113883.12.227
    name: MVX
    preferred_prefix: mvx
    prefix: 2.16.840.1.113883.6.60
    status: Retired
  homepage: https://www2a.cdc.gov/vaccines/iis/iisstandards/vaccines.asp?rpt=mvx
  mappings:
    hl7: 2.16.840.1.113883.6.60
  name: Manufacturers of Vaccines
  pattern: ^\w+$
  prefix: mvx
  reviewer:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  uri_format: https://phinvads.cdc.gov/vads/ViewCodeSystemConcept.action?oid=2.16.840.1.113883.12.227&code=$1
mw.project:
  biocontext:
    prefix: MW.PROJECT
  mappings:
    biocontext: MW.PROJECT
    miriam: mw.project
    n2t: mw.project
  miriam:
    deprecated: false
    description: Metabolomics Workbench stores metabolomics data for small and large
      studies on cells, tissues and organisms for the Metabolomics Consortium Data
      Repository and Coordinating Center (DRCC).
    homepage: http://www.metabolomicsworkbench.org/
    id: '00000647'
    name: Metabolomics Workbench Project
    namespaceEmbeddedInLui: false
    pattern: ^PR[0-9]{6}$
    prefix: mw.project
    sampleId: PR000001
    uri_format: http://www.metabolomicsworkbench.org/data/DRCCMetadata.php?Mode=Project&ProjectID=$1
  n2t:
    description: Metabolomics Workbench stores metabolomics data for small and large
      studies on cells, tissues and organisms for the Metabolomics Consortium Data
      Repository and Coordinating Center (DRCC).
    example: PR000001
    homepage: http://www.metabolomicsworkbench.org/
    name: Metabolomics Workbench Project
    namespaceEmbeddedInLui: false
    pattern: ^PR[0-9]{6}$
    prefix: mw.project
    uri_format: http://www.metabolomicsworkbench.org/data/DRCCMetadata.php?Mode=Project&ProjectID=$1
  prefix: mw.project
mw.study:
  biocontext:
    prefix: MW.STUDY
  mappings:
    biocontext: MW.STUDY
    miriam: mw.study
    n2t: mw.study
  miriam:
    deprecated: false
    description: Metabolomics Workbench stores metabolomics data for small and large
      studies on cells, tissues and organisms for the Metabolomics Consortium Data
      Repository and Coordinating Center (DRCC).
    homepage: http://www.metabolomicsworkbench.org/
    id: '00000646'
    name: Metabolomics Workbench Study
    namespaceEmbeddedInLui: false
    pattern: ^ST[0-9]{6}$
    prefix: mw.study
    providers:
    - code: omicsdi
      description: Metabolomics Workbench Study through OmicsDI
      homepage: https://www.omicsdi.org/
      name: Metabolomics Workbench Study through OmicsDI
      uri_format: https://www.omicsdi.org/dataset/metabolomics_workbench/$1
    sampleId: ST000900
    uri_format: http://www.metabolomicsworkbench.org/data/DRCCMetadata.php?Mode=Study&StudyID=$1
  n2t:
    description: Metabolomics Workbench stores metabolomics data for small and large
      studies on cells, tissues and organisms for the Metabolomics Consortium Data
      Repository and Coordinating Center (DRCC).
    example: ST000900
    homepage: http://www.metabolomicsworkbench.org/
    name: Metabolomics Workbench Study
    namespaceEmbeddedInLui: false
    pattern: ^ST[0-9]{6}$
    prefix: mw.study
    uri_format: http://www.metabolomicsworkbench.org/data/DRCCMetadata.php?Mode=Study&StudyID=$1
  prefix: mw.study
mwo:
  aberowl:
    description: 'NFDI-MatWerk aims to establish a digital infrastructure for Materials
      Science and Engineering (MSE), fostering improved data sharing and collaboration.
      This repository provides comprehensive documentation for NFDI MatWerk Ontology
      (MWO) v3.0.0, a foundational framework designed to structure research data and
      enhance interoperability within the MSE community. To ensure compliance with
      top-level ontology standards, MWO v3.0.0 is aligned with the Basic Formal Ontology
      (BFO) and incorporates the modular approach of the NFDIcore mid-level ontology,
      enriching metadata through standardized classes and properties. The mwo addresses
      key aspects of MSE research data, including the NFDI-MatWerk community structure,
      covering task areas, infrastructure use cases, projects, researchers, and organizations.
      It also describes essential NFDI resources, such as software, workflows, ontologies,
      publications, datasets, metadata schemas, instruments, facilities, and educational
      materials. Additionally, mwo represents NFDI-MatWerk services, academic events,
      courses, and international collaborations. As the foundation for the MSE Knowledge
      Graph, mwo facilitates efficient data integration and retrieval, promoting collaboration
      and knowledge representation across MSE domains. This digital transformation
      enhances data discoverability, reusability, and accelerates scientific exchange,
      innovation, and discoveries by optimizing research data management and accessibility.,
      The MatWerk ontology represents research data and related activities of the
      MSE community. The mwo v3 reuses BFO2020 and NFDi core ontologies and focuses
      on: A) Consortium structure: NFDI MatWerk consortium, its structures (task areas,
      and participant projects), researches, and organizations B) NFDI resources:
      software, data portals, scientific publications, published datasets, and ontologies
      C) NFDI MatWerk services, events, educational cources, and international collabrations
      D) MSE related instruments, materials, processes, and properties. Further infomration
      can be found at GitHub: https://github.com/ISE-FIZKarlsruhe/mwo'
    download_owl: http://aber-owl.net/media/ontologies/MWO/1/mwo.owl
    name: NFDI MatWerk Ontology
    prefix: MWO
    version: 3.0.0
  bioportal:
    contact:
      email: ho_beygi@yahoo.com
      name: Hossein Beygi Nasrabadi
    description: 'NFDI-MatWerk aims to establish a digital infrastructure for Materials
      Science and Engineering (MSE), fostering improved data sharing and collaboration.
      This repository provides comprehensive documentation for NFDI MatWerk Ontology
      (MWO) v3.0.0, a foundational framework designed to structure research data and
      enhance interoperability within the MSE community. To ensure compliance with
      top-level ontology standards, MWO v3.0.0 is aligned with the Basic Formal Ontology
      (BFO) and incorporates the modular approach of the NFDIcore mid-level ontology,
      enriching metadata through standardized classes and properties. The mwo addresses
      key aspects of MSE research data, including the NFDI-MatWerk community structure,
      covering task areas, infrastructure use cases, projects, researchers, and organizations.
      It also describes essential NFDI resources, such as software, workflows, ontologies,
      publications, datasets, metadata schemas, instruments, facilities, and educational
      materials. Additionally, mwo represents NFDI-MatWerk services, academic events,
      courses, and international collaborations. As the foundation for the MSE Knowledge
      Graph, mwo facilitates efficient data integration and retrieval, promoting collaboration
      and knowledge representation across MSE domains. This digital transformation
      enhances data discoverability, reusability, and accelerates scientific exchange,
      innovation, and discoveries by optimizing research data management and accessibility.,
      The MatWerk ontology represents research data and related activities of the
      MSE community. The mwo v3 reuses BFO2020 and NFDi core ontologies and focuses
      on:

      A) Consortium structure: NFDI MatWerk consortium, its structures (task areas,
      and participant projects), researches, and organizations

      B) NFDI resources: software, data portals, scientific publications, published
      datasets, and ontologies

      C) NFDI MatWerk services, events, educational cources, and international collabrations

      D) MSE related instruments, materials, processes, and properties.

      Further infomration can be found at GitHub: https://github.com/ISE-FIZKarlsruhe/mwo'
    license: CC0-1.0
    name: NFDI MatWerk Ontology
    prefix: MWO
    version: 3.0.0
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: NFDI-MatWerk aims to establish a digital infrastructure for Materials
    Science and Engineering (MSE), fostering improved data sharing and collaboration.
    This repository provides comprehensive documentation for NFDI MatWerk Ontology
    (MWO) v3.0.0, a foundational framework designed to structure research data and
    enhance interoperability within the MSE community. To ensure compliance with top-level
    ontology standards, MWO v3.0.0 is aligned with the Basic Formal Ontology (BFO)
    and incorporates the modular approach of the NFDIcore mid-level ontology, enriching
    metadata through standardized classes and properties. The mwo addresses key aspects
    of MSE research data, including the NFDI-MatWerk community structure, covering
    task areas, infrastructure use cases, projects, researchers, and organizations.
    It also describes essential NFDI resources, such as software, workflows, ontologies,
    publications, datasets, metadata schemas, instruments, facilities, and educational
    materials. Additionally, mwo represents NFDI-MatWerk services, academic events,
    courses, and international collaborations. As the foundation for the MSE Knowledge
    Graph, mwo facilitates efficient data integration and retrieval, promoting collaboration
    and knowledge representation across MSE domains. This digital transformation enhances
    data discoverability, reusability, and accelerates scientific exchange, innovation,
    and discoveries by optimizing research data management and accessibility. (from
    repository)
  download_owl: https://github.com/ISE-FIZKarlsruhe/mwo/raw/refs/heads/main/mwo.owl
  example: 0001109
  homepage: https://github.com/ISE-FIZKarlsruhe/mwo
  mappings:
    aberowl: MWO
    bioportal: MWO
  name: NFDI MatWerk Ontology
  pattern: ^\d{7}$
  prefix: mwo
  repository: https://github.com/ISE-FIZKarlsruhe/mwo
  uri_format: http://purls.helmholtz-metadaten.de/mwo/mwo_$1
myco:
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: Mycobrowser is a resource that provides both in silico generated and
    manually reviewed information within databases dedicated to the complete genomes
    of Mycobacterium tuberculosis, Mycobacterium leprae, Mycobacterium marinum and
    Mycobacterium smegmatis. This collection references Mycobacteria leprae information.
  example: ML0224
  example_extras:
  - MMAR_2462
  - MSMEG_3769
  - Rv1908c
  homepage: https://mycobrowser.epfl.ch
  name: MycoBrowser
  prefix: myco
  uri_format: https://mycobrowser.epfl.ch/genes/$1
myco.lepra:
  biocontext:
    prefix: MYCO.LEPRA
  mappings:
    biocontext: MYCO.LEPRA
    miriam: myco.lepra
    n2t: myco.lepra
    prefixcommons: myco.lepra
  miriam:
    deprecated: false
    description: Mycobrowser is a resource that provides both in silico generated
      and manually reviewed information within databases dedicated to the complete
      genomes of Mycobacterium tuberculosis, Mycobacterium leprae, Mycobacterium marinum
      and Mycobacterium smegmatis. This collection references Mycobacteria leprae
      information.
    homepage: https://mycobrowser.epfl.ch/
    id: '00000217'
    name: MycoBrowser leprae
    namespaceEmbeddedInLui: false
    pattern: ^ML\w+$
    prefix: myco.lepra
    sampleId: ML0224
    uri_format: https://mycobrowser.epfl.ch/genes/$1
  n2t:
    description: Mycobrowser is a resource that provides both in silico generated
      and manually reviewed information within databases dedicated to the complete
      genomes of Mycobacterium tuberculosis, Mycobacterium leprae, Mycobacterium marinum
      and Mycobacterium smegmatis. This collection references Mycobacteria leprae
      information.
    example: ML0224
    homepage: http://mycobrowser.epfl.ch/leprosy.html
    name: MycoBrowser leprae at Global Health Institute
    namespaceEmbeddedInLui: false
    pattern: ^ML\w+$
    prefix: myco.lepra
    uri_format: http://mycobrowser.epfl.ch/leprosysearch.php?gene+name=$1
  part_of: myco
  prefix: myco.lepra
  prefixcommons:
    description: Mycobrowser is a resource that provides both in silico generated
      and manually reviewed information within databases dedicated to the complete
      genomes of Mycobacterium tuberculosis, Mycobacterium leprae, Mycobacterium marinum
      and Mycobacterium smegmatis. This collection references Mycobacteria leprae
      information.
    example: ML0224
    homepage: http://mycobrowser.epfl.ch/leprosy.html
    keywords:
    - genome
    - sequence
    name: MycoBrowser leprae
    pattern: ^ML\w+$
    prefix: myco.lepra
    uri_format: http://mycobrowser.epfl.ch/leprosysearch.php?gene+name=$1
myco.marinum:
  biocontext:
    prefix: MYCO.MARINUM
  mappings:
    biocontext: MYCO.MARINUM
    miriam: myco.marinum
    n2t: myco.marinum
    prefixcommons: myco.marinum
  miriam:
    deprecated: false
    description: Mycobrowser is a resource that provides both in silico generated
      and manually reviewed information within databases dedicated to the complete
      genomes of Mycobacterium tuberculosis, Mycobacterium leprae, Mycobacterium marinum
      and Mycobacterium smegmatis. This collection references Mycobacteria marinum
      information.
    homepage: https://mycobrowser.epfl.ch
    id: 00000218
    name: MycoBrowser marinum
    namespaceEmbeddedInLui: false
    pattern: ^MMAR\_\d+$
    prefix: myco.marinum
    sampleId: MMAR_2462
    uri_format: https://mycobrowser.epfl.ch/genes/$1
  n2t:
    description: Mycobrowser is a resource that provides both in silico generated
      and manually reviewed information within databases dedicated to the complete
      genomes of Mycobacterium tuberculosis, Mycobacterium leprae, Mycobacterium marinum
      and Mycobacterium smegmatis. This collection references Mycobacteria marinum
      information.
    example: MMAR_2462
    homepage: http://mycobrowser.epfl.ch/marinolist.html
    name: MycoBrowser marinum at Global Health Institute
    namespaceEmbeddedInLui: false
    pattern: ^MMAR\_\d+$
    prefix: myco.marinum
    uri_format: http://mycobrowser.epfl.ch/marinosearch.php?gene+name=$1
  part_of: myco
  prefix: myco.marinum
  prefixcommons:
    description: Mycobrowser is a resource that provides both in silico generated
      and manually reviewed information within databases dedicated to the complete
      genomes of Mycobacterium tuberculosis, Mycobacterium leprae, Mycobacterium marinum
      and Mycobacterium smegmatis. This collection references Mycobacteria marinum
      information.
    example: MMAR_2462
    homepage: http://mycobrowser.epfl.ch/marinolist.html
    keywords:
    - genome
    - sequence
    name: MycoBrowser marinum
    pattern: ^MMAR\_\d+$
    prefix: myco.marinum
    uri_format: http://mycobrowser.epfl.ch/marinosearch.php?gene+name=$1
myco.smeg:
  biocontext:
    prefix: MYCO.SMEG
  mappings:
    biocontext: MYCO.SMEG
    miriam: myco.smeg
    n2t: myco.smeg
    prefixcommons: myco.smeg
  miriam:
    deprecated: false
    description: Mycobrowser is a resource that provides both in silico generated
      and manually reviewed information within databases dedicated to the complete
      genomes of Mycobacterium tuberculosis, Mycobacterium leprae, Mycobacterium marinum
      and Mycobacterium smegmatis. This collection references Mycobacteria smegmatis
      information.
    homepage: https://mycobrowser.epfl.ch
    id: 00000219
    name: MycoBrowser smegmatis
    namespaceEmbeddedInLui: false
    pattern: ^MSMEG\w+$
    prefix: myco.smeg
    sampleId: MSMEG_3769
    uri_format: https://mycobrowser.epfl.ch/genes/$1
  n2t:
    description: Mycobrowser is a resource that provides both in silico generated
      and manually reviewed information within databases dedicated to the complete
      genomes of Mycobacterium tuberculosis, Mycobacterium leprae, Mycobacterium marinum
      and Mycobacterium smegmatis. This collection references Mycobacteria smegmatis
      information.
    example: MSMEG_3769
    homepage: http://mycobrowser.epfl.ch/smegmalist.html
    name: MycoBrowser smegmatis at Global Health Institute
    namespaceEmbeddedInLui: false
    pattern: ^MSMEG\w+$
    prefix: myco.smeg
    uri_format: http://mycobrowser.epfl.ch/smegmasearch.php?gene+name=$1
  part_of: myco
  prefix: myco.smeg
  prefixcommons:
    description: Mycobrowser is a resource that provides both in silico generated
      and manually reviewed information within databases dedicated to the complete
      genomes of Mycobacterium tuberculosis, Mycobacterium leprae, Mycobacterium marinum
      and Mycobacterium smegmatis. This collection references Mycobacteria smegmatis
      information.
    example: MSMEG_3769
    homepage: http://mycobrowser.epfl.ch/smegmalist.html
    keywords:
    - genome
    - sequence
    name: MycoBrowser smegmatis
    pattern: ^MSMEG\w+$
    prefix: myco.smeg
    uri_format: http://mycobrowser.epfl.ch/smegmasearch.php?gene+name=$1
myco.tuber:
  biocontext:
    prefix: MYCO.TUBER
  contact:
    email: stewart.cole@epfl.ch
    github: null
    name: Stewart Thomas Cole
    orcid: 0000-0003-1400-5585
  mappings:
    biocontext: MYCO.TUBER
    miriam: myco.tuber
    n2t: myco.tuber
    ncbi: TubercuList
    prefixcommons: tuberculist
    uniprot: DB-0106
  miriam:
    deprecated: false
    description: Mycobrowser is a resource that provides both in silico generated
      and manually reviewed information within databases dedicated to the complete
      genomes of Mycobacterium tuberculosis, Mycobacterium leprae, Mycobacterium marinum
      and Mycobacterium smegmatis. This collection references Mycobacteria tuberculosis
      information.
    homepage: http://tuberculist.epfl.ch/
    id: '00000216'
    name: MycoBrowser tuberculosis
    namespaceEmbeddedInLui: false
    pattern: ^Rv\d{4}(A|B|c)?$
    prefix: myco.tuber
    sampleId: Rv1908c
    uri_format: https://mycobrowser.epfl.ch/genes/$1
  n2t:
    description: Mycobrowser is a resource that provides both in silico generated
      and manually reviewed information within databases dedicated to the complete
      genomes of Mycobacterium tuberculosis, Mycobacterium leprae, Mycobacterium marinum
      and Mycobacterium smegmatis. This collection references Mycobacteria tuberculosis
      information.
    example: Rv1908c
    homepage: http://tuberculist.epfl.ch/
    name: MycoBrowser tuberculosis at Global Health Institute
    namespaceEmbeddedInLui: false
    pattern: ^Rv\d{4}(A|B|c)?$
    prefix: myco.tuber
    uri_format: http://tuberculist.epfl.ch/quicksearch.php?gene+name=$1
  ncbi:
    example: Rv3322c
    homepage: http://tuberculist.epfl.ch/
    name: TubercuList knowledge base
    prefix: TubercuList
  part_of: myco
  prefix: myco.tuber
  prefixcommons:
    description: The TubercuList knowledge base integrates genome details, protein
      information, drug and transcriptome data, mutant and operon annotation, bibliography;
      structural views and comparative genomics, in a structured manner required for
      the rational development of new diagnostic, therapeutic and prophylactic measures
      against tuberculosis.
    example: Rv0115
    homepage: http://tuberculist.epfl.ch
    keywords:
    - genome
    - protein
    - DNA
    name: Mycobacterium tuberculosis strain H37Rv genome database
    pattern: ^Rv[0-9,a-z]+$
    prefix: tuberculist
    uri_format: http://tuberculist.epfl.ch/quicksearch.php?gene+name=$1
  publications:
  - doi: 10.1016/j.tube.2010.09.006
    pmc: null
    pubmed: '20980200'
    title: 'The MycoBrowser portal: a comprehensive and manually annotated resource
      for mycobacterial genomes'
    year: 2010
  - doi: 10.1016/j.tube.2010.09.006
    pmc: null
    pubmed: '20980200'
    title: null
    year: null
  synonyms:
  - TubercuList
  uniprot:
    abbreviation: TubercuList
    category: Organism-specific databases
    homepage: https://mycobrowser.epfl.ch/
    name: Mycobacterium tuberculosis strain H37Rv genome database
    prefix: DB-0106
    publications:
    - doi: 10.1016/j.tube.2010.09.006
      pubmed: '20980200'
    uri_format: https://mycobrowser.epfl.ch/genes/$1
mycobank:
  biocontext:
    prefix: MYCOBANK
  contact:
    email: vrobert@unistra.fr
    github: null
    name: Vincent Robert
    orcid: 0000-0002-9370-4677
  contributor_extras:
  - email: carlosm@ebi.ac.uk
    github: CarMoreno
    name: Carlos Moreno
    orcid: 0000-0003-0066-1717
  fairsharing:
    abbreviation: MycoBank
    description: MycoBank was created for the mycological community (as well as scientific
      community more generally) to document new mycological names, combinations and
      associated data (such as descriptions and illustrations). Pairwise sequence
      alignments and polyphasic identifications of fungi and yeasts against curated
      references databases are available. Nomenclatural experts will be available
      to check the validity, legitimacy and linguistic correctness of the proposed
      names in order to avoid nomenclatural error. Deposited names can remain confidential
      until after publication as required. Once public, the names are accessible through
      MycoBank, Index Fungorum, GBIF and other international biodiversity initiatives,
      where they will further be linked to other databases. MycoBank will (when applicable)
      provide onward links to other databases containing, for example, living cultures,
      DNA data, reference specimens and pleomorphic names linked to the same holomorph.
      Authors intending to publish nomenclatural novelties are encouraged to contribute.
    homepage: http://www.mycobank.org
    name: MycoBank
    prefix: FAIRsharing.v8se8r
    publications:
    - doi: 10.5598/imafungus.2013.04.02.16
      pubmed_id: 24563843
      title: MycoBank gearing up for new horizons.
    subjects:
    - Taxonomy
    - Biology
  integbio:
    alt_name: MycoBank
    description: MycoBank was created for the mycological community (as well as scientific
      community more generally) to document new mycological names, combinations and
      associated data (such as descriptions and illustrations). Pairwise sequence
      alignments and polyphasic identifications of fungi and yeasts against curated
      references databases are available. Nomenclatural experts will be available
      to check the validity, legitimacy and linguistic correctness of the proposed
      names in order to avoid nomenclatural error. Deposited names can remain confidential
      until after publication as required. Once public, the names are accessible through
      MycoBank, Index Fungorum, GBIF and other international biodiversity initiatives,
      where they will further be linked to other databases. MycoBank will (when applicable)
      provide onward links to other databases containing, for example, living cultures,
      DNA data, reference specimens and pleomorphic names linked to the same holomorph.
      Authors intending to publish nomenclatural novelties are encouraged to contribute.
    fairsharing: FAIRsharing.v8se8r
    homepage: http://www.mycobank.org
    information_keywords:
    - Ontology/Terminology/Nomenclature
    - Sequence
    maintainer: IMA (International Mycological Association)||NLM (National Library
      of Medicine)
    name: MycoBank
    prefix: nbdc01815
    pubmeds:
    - '24563843'
    status: Active
    target_keywords:
    - Organism
  mappings:
    biocontext: MYCOBANK
    fairsharing: FAIRsharing.v8se8r
    integbio: nbdc01815
    miriam: mycobank
    n2t: mycobank
    ncbi: MycoBank
    prefixcommons: mycobank
    re3data: r3d100011222
  miriam:
    deprecated: false
    description: MycoBank is an online database, documenting new mycological names
      and combinations, eventually combined with descriptions and illustrations.
    homepage: http://www.mycobank.org/
    id: 00000178
    name: MycoBank
    namespaceEmbeddedInLui: false
    pattern: ^\d+$
    prefix: mycobank
    sampleId: '349124'
    uri_format: http://www.mycobank.org/Biolomics.aspx?Table=Mycobank&MycoBankNr_=$1
  n2t:
    description: MycoBank is an online database, documenting new mycological names
      and combinations, eventually combined with descriptions and illustrations.
    example: '349124'
    homepage: http://www.mycobank.org/
    name: MycoBank at Fungal Biodiversity Centre
    namespaceEmbeddedInLui: false
    pattern: ^\d+$
    prefix: mycobank
    uri_format: http://www.mycobank.org/Biolomics.aspx?Table=Mycobank&MycoBankNr_=$1
  ncbi:
    example: '8284'
    homepage: http://www.mycobank.org
    name: Fungal Nomenclature and Species Bank
    prefix: MycoBank
  prefix: mycobank
  prefixcommons:
    description: MycoBank is an online database, documenting new mycological names
      and combinations, eventually combined with descriptions and illustrations.
    example: '349124'
    homepage: http://www.mycobank.org
    keywords:
    - classification
    name: Fungal Nomenclature and Species Bank
    pattern: ^\d+$
    prefix: mycobank
    uri_format: http://www.mycobank.org/MycoTaxo.aspx?Link=T&Rec=$1
  publications:
  - doi: 10.5598/imafungus.2013.04.02.16
    pmc: PMC3905949
    pubmed: '24563843'
    title: MycoBank gearing up for new horizons
    year: 2013
  re3data:
    description: MycoBank is an on-line database aimed as a service to the mycological
      and scientific society by documenting mycological nomenclatural novelties (new
      names and combinations) and associated data, for example descriptions and illustrations.
      The nomenclatural novelties will each be allocated a unique MycoBank number
      that can be cited in the publication where the nomenclatural novelty is introduced.
      These numbers will also be used by the nomenclatural database Index Fungorum,
      with which MycoBank is associated.
    doi: 10.17616/R39D0Q
    homepage: https://www.mycobank.org/
    name: MycoBank
    prefix: r3d100011222
    synonyms:
    - Fungal databases, nomenclature and species banks
  uri_format: https://www.mycobank.org/page/Name%20details%20page/$1
mzspec:
  banana: mzspec
  biocontext:
    prefix: MZSPEC
  contact:
    email: gerhard.mayer@rub.de
    github: germa
    name: Gerhard Mayer
    orcid: 0000-0002-1767-2343
  contributor_extras:
  - email: lindsey.anderson@pnnl.gov
    github: lnanderson
    name: Lindsey N. Anderson
    orcid: 0000-0002-8741-7823
  fairsharing:
    abbreviation: USI
    contact:
      email: edeutsch@systemsbiology.org
      name: Eric Deutsch
      orcid: 0000-0001-8732-0928
    description: 'The Universal Spectrum Identifier (USI) is multi-part key identifier
      for identifying mass spectra contained in public data repositories, primarily
      focused on proteomics. The USI provides a standardized mechanism for encoding
      a virtual path to any single mass spectrum generated by a mass spectrometer
      contained/deposited to public proteomics dataset repositories for enabling greater
      transparency of spectral evidence. With more than 1 billion USI identifications
      from over 3 billion spectra already available through ProteomeXchange repositories,
      Universal Spectrum Identifier encodes the dataset, the MS Run, the scan number
      and the proposed peptidoform and charge of the ions responsible for the spectrum.
      The USI identifier is comprised of five key components (and an optional sixth
      component) in defining an abstract path to a specified spectrum. The USI core
      components include: 1) the prefix ‘mzspec’ to make clear that the following
      string is a USI and to aid in automated mapping of a USI string to a URL, 2)
      the subsequent dataset submission or dataset collection identifier assigned
      by the primary repository archive, 3) the mass spectrometry run name (or root
      name of the raw vendor format file) such as an mzML file (with or without the
      file extension), 4)  a type flag (such as ‘scan’, ‘index’ or ‘nativeId’ as defined
      in the current mzML specification) for indicating how to interpret the fifth
      component, 5) the index value (based on the flag type) within the specified
      MS run, and optionally 6) any relevant information for interpretation of the
      spectrum if available. '
    domains:
    - Mass spectrum
    - Data retrieval
    - Data analysis
    - Data identity and mapping
    homepage: http://psidev.info/usi
    license: Apache 2.0 License
    name: HUPO-PSI Universal Spectrum Identifier
    prefix: FAIRsharing.b549b8
    publications:
    - doi: 10.1038/s41592-021-01184-6
      pubmed: '34183830'
      title: Universal Spectrum Identifier for mass spectra
      year: 2021
    repository: https://github.com/HUPO-PSI/usi/tree/master/Specification
    subjects:
    - Lipidomics
    - Metabolomics
    - Proteomics
  homepage: http://www.psidev.info/usi
  mappings:
    biocontext: MZSPEC
    fairsharing: FAIRsharing.b549b8
    miriam: mzspec
    n2t: mzspec
  miriam:
    deprecated: false
    description: The Universal Spectrum Identifier (USI) is a compound identifier
      that provides an abstract path to refer to a single spectrum generated by a
      mass spectrometer, and potentially the ion that is thought to have produced
      it.
    homepage: http://proteomecentral.proteomexchange.org/
    id: '00000625'
    name: Universal Spectrum Identifier
    namespaceEmbeddedInLui: true
    pattern: ^mzspec:(PDX|USI|PXD)[0-9]{6}:[^:]+:(scan|index|nativeId):[0-9]+(:.*)?$
    prefix: mzspec
    providers:
    - code: ebi
      description: PRIDE is a database of PRoteomics IDEntifications. It contains
        protein and peptide identifications (including details of post-translational
        modifications) together with the mass spectrometric evidence supporting these
        identifications. PRIDE acts as a repository for mass spectrometry data, specifically
        the fragment ion spectra used to identify peptide sequences.
      homepage: https://www.ebi.ac.uk/pride
      name: PRIDE
      uri_format: https://www.ebi.ac.uk/pride/archive/usi?usi=mzspec:$1
    - code: ''
      description: Universal Spectrum Identifier through Peptide Atlas
      homepage: https://db.systemsbiology.net/sbeams/cgi/PeptideAtlas/ShowObservedSpectrum
      name: Universal Spectrum Identifier through Peptide Atlas
      uri_format: https://db.systemsbiology.net/sbeams/cgi/PeptideAtlas/ShowObservedSpectrum?usi=mzspec:$1
    sampleId: PXD002255:ES_XP_Ubi_97H_HCD_349:scan:9617:LAEIYVNSSFYK/2
    uri_format: http://proteomecentral.proteomexchange.org/usi/?usi=mzspec:$1
  n2t:
    description: The Universal Spectrum Identifier (USI) is a compound identifier
      that provides an abstract path to refer to a single spectrum generated by a
      mass spectrometer, and potentially the ion that is thought to have produced
      it.
    example: PXD002255::ES_XP_Ubi_97H_HCD_349:scan:9617:LAEIYVNSSFYK/2
    homepage: https://db.systemsbiology.net/sbeams/cgi/PeptideAtlas/ShowObservedSpectrum
    name: Universal Spectrum Identifier through Peptide Atlas
    namespaceEmbeddedInLui: true
    pattern: ^mzspec:.+$
    prefix: mzspec
    uri_format: https://db.systemsbiology.net/sbeams/cgi/PeptideAtlas/ShowObservedSpectrum?usi=mzspec:$1
  pattern: ^.+$
  prefix: mzspec
  publications:
  - doi: 10.1038/s41592-021-01184-6
    pmc: PMC8405201
    pubmed: '34183830'
    title: Universal Spectrum Identifier for mass spectra
    year: 2021
  repository: https://github.com/HUPO-PSI/usi
n2t:
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: An ARK resolver as well as resolver built with common prefixes as in
    Identifiers.org
  example: chebi
  homepage: https://n2t.net
  name: Name-to-Thing
  prefix: n2t
  uri_format: 'https://n2t.net/$1:'
n4e:
  example: API
  mappings:
    tib: n4e
  name: NFDI4Earth Ontology
  prefix: n4e
  tib:
    description: "The ontology and metadata schema for the NFDI4Earth Knowledge Hub.\
      \ See serializations of this schema as an OWL ontology here:\n  - [RDF/XML](https://nfdi4earth.pages.rwth-aachen.de/knowledgehub/nfdi4earth-kh-schema/ontology.owl.xml)\n\
      \  - [RDF/Turtle](https://nfdi4earth.pages.rwth-aachen.de/knowledgehub/nfdi4earth-kh-schema/ontology.owl.ttl)\n\
      \  - [RDF/JSON-LD](https://nfdi4earth.pages.rwth-aachen.de/knowledgehub/nfdi4earth-kh-schema/ontology.owl.jsonld)\n\
      \  - [RDF/N-Triples](https://nfdi4earth.pages.rwth-aachen.de/knowledgehub/nfdi4earth-kh-schema/ontology.owl.nt)"
    homepage: https://nfdi4earth.de/ontology/
    keywords:
    - ESS
    - earth sciences
    name: NFDI4EarthOntology
    prefix: n4e
    tracker: https://git.rwth-aachen.de/nfdi4earth/knowledgehub/nfdi4earth-kh-schema/-/issues
    uri_format: http://nfdi4earth.de/ontology/$1
    version.iri: https://nfdi4earth.pages.rwth-aachen.de/knowledgehub/nfdi4earth-kh-schema/ontology-v0.35.2.owl.xml
namerxn:
  contact:
    email: gregory.landrum@phys.chem.ethz.ch
    github: greglandrum
    name: Gregory Landrum
    orcid: 0000-0001-6279-4481
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: The nomenclature used for named reactions in text mining software from
    NextMove. While it's proprietary, there are a few publications listing parts.
    487/1,855 have mappings to the Reaction Ontology (RXNO).
  example: 4.2.78
  homepage: https://www.nextmovesoftware.com/namerxn.html
  keywords:
  - chemistry
  - reactions
  - text mining
  name: NameRXN
  prefix: namerxn
  proprietary: true
  publications:
  - doi: 10.1038/s42256-020-00284-w
    pmc: null
    pubmed: null
    title: Mapping the space of chemical reactions using attention-based neural networks
    year: 2021
  - doi: 10.1021/acs.jmedchem.6b00153
    pmc: null
    pubmed: '27028220'
    title: 'Big Data from Pharmaceutical Patents: A Computational Analysis of Medicinal
      Chemists'' Bread and Butter'
    year: 2016
  references:
  - https://www.nextmovesoftware.com/products/HazELNutPoster.pdf
  - https://twitter.com/cthoyt/status/1443929184745758723
nando:
  aberowl:
    description: Creating a comprehensive hierarchical controlled vocabulary for intractable
      and rare disease (i.e., nanbyo) representation in Japan.
    download_owl: http://aber-owl.net/media/ontologies/NANDO/19/nando.owl
    homepage: https://nanbyodata.jp
    name: Nanbyo Disease Ontology
    prefix: NANDO
    version: '2025-08-26'
  banana: NANDO
  bioportal:
    contact:
      email: takatter@dbcls.rois.ac.jp
      name: Terue Takatsuki
    description: Creating a comprehensive hierarchical controlled vocabulary for intractable
      and rare disease (i.e., nanbyo) representation in Japan.
    homepage: https://nanbyodata.jp
    license: CC-BY-4.0
    name: Nanbyo Disease Ontology
    prefix: NANDO
    version: '2025-08-26'
  mappings:
    aberowl: NANDO
    bioportal: NANDO
    miriam: nando
    togoid: Nando
  miriam:
    deprecated: false
    description: Nanbyo Disease Ontology (NANDO) is the ontology creating a comprehensive
      hierarchical controlled vocabulary for intractable and rare disease (i.e., nanbyo)
      representation in Japan.
    homepage: https://nanbyodata.jp/
    id: '00001010'
    name: Nanbyo Disease Ontology
    namespaceEmbeddedInLui: true
    pattern: ^NANDO:[0-9]+$
    prefix: nando
    sampleId: '1200031'
    uri_format: https://nanbyodata.jp/disease/NANDO:$1
  pattern: ^\d+$
  prefix: nando
  togoid:
    catalog: nbdc02557
    description: NanbyoData provides informative data related to intractable diseases
      using Nanbyo Disease Ontology (NANDO). Designated intractable diseases and chronic
      specific pediatric diseases in Japan are the subject diseases. NANDO, and genes
      and phenotypes related intractable diseases are downloadable.
    examples:
    - NANDO:1200461
    - NANDO:1200466
    - NANDO:1200851
    - NANDO:1200061
    - NANDO:1200315
    - NANDO:1200365
    - NANDO:1200922
    - NANDO:1200705
    - NANDO:2200074
    - NANDO:1200030
    keywords:
    - Phenotype
    name: NANDO
    pattern: ^NANDO[:_](?\d{7})$
    prefix: Nando
    uri_format: http://nanbyodata.jp/ontology/NANDO_$1
napdi:
  biocontext:
    prefix: NAPDI
  fairsharing:
    abbreviation: NaPDI
    contact:
      email: rdb20@pitt.edu
      name: Richard Boyce
      orcid: 0000-0002-2993-2085
    description: The Natural Product-Drug Interaction Research Data Repository, a
      publicly accessible database where researchers can access scientific results,
      raw data, and recommended approaches to optimally assess the clinical significance
      of pharmacokinetic natural product-drug interactions (PK-NPDIs). The repository
      is funded by the United States National Center for Complementary and Integrative
      Health.
    homepage: https://repo.napdi.org/
    license: CC BY-SA 3.0
    name: Natural Product-Drug Interaction Research Data Repository
    prefix: FAIRsharing.y9x8wk
    publications:
    - doi: 10.1186/s13326-018-0183-z
      pubmed_id: 29743102
      title: Extending the DIDEO ontology to include entities from the natural product
        drug interaction domain of discourse.
    subjects:
    - Pharmacology
    - Biomedical Science
  mappings:
    biocontext: NAPDI
    fairsharing: FAIRsharing.y9x8wk
    miriam: napdi
    n2t: napdi
  miriam:
    deprecated: false
    description: The Natural Product-Drug Interaction Research Data Repository, a
      publicly accessible database where researchers can access scientific results,
      raw data, and recommended approaches to optimally assess the clinical significance
      of pharmacokinetic natural product-drug interactions (PK-NPDIs).
    homepage: https://repo.napdi.org/
    id: '00000620'
    name: Natural Product-Drug Interaction Research Data Repository
    namespaceEmbeddedInLui: false
    pattern: ^[0-9]+$
    prefix: napdi
    sampleId: '28'
    uri_format: https://repo.napdi.org/study/$1
  n2t:
    description: The Natural Product-Drug Interaction Research Data Repository, a
      publicly accessible database where researchers can access scientific results,
      raw data, and recommended approaches to optimally assess the clinical significance
      of pharmacokinetic natural product-drug interactions (PK-NPDIs).
    example: '28'
    homepage: https://repo.napdi.org/
    name: Natural Product-Drug Interaction Research Data Repository
    namespaceEmbeddedInLui: false
    pattern: ^[0-9]+$
    prefix: napdi
    uri_format: https://repo.napdi.org/study/$1
  prefix: napdi
  publications:
  - doi: 10.1186/s13326-018-0183-z
    pmc: PMC5944177
    pubmed: '29743102'
    title: Extending the DIDEO ontology to include entities from the natural product
      drug interaction domain of discourse
    year: 2018
  - doi: 10.1186/s13326-018-0183-z
    pmc: null
    pubmed: null
    title: Extending the DIDEO ontology to include entities from the natural product
      drug interaction domain of discourse.
    year: null
  - doi: 10.1186/s13326-018-0183-z
    pmc: null
    pubmed: null
    title: Extending the DIDEO ontology to include entities from the natural product
      drug interaction domain of discourse.
    year: null
  - doi: 10.1186/s13326-018-0183-z
    pmc: null
    pubmed: null
    title: Extending the DIDEO ontology to include entities from the natural product
      drug interaction domain of discourse.
    year: null
napp:
  biocontext:
    prefix: NAPP
  fairsharing:
    abbreviation: NAPP
    contact:
      email: daniel.gautheret@u-psud.fr
      name: Daniel Gautheret
      orcid: 0000-0002-1508-8469
    description: NAPP (Nucleic Acids Phylogenetic Profile) enables users to retrieve
      RNA-rich clusters from any genome in a list of 1000+ sequenced bacterial genomes.
      RNA-rich clusters can be viewed separately or, alternatively, all tiles from
      RNA-rich clusters can be contiged into larger elements and retrieved at once
      as a CSV or GFF file for use in a genome browser or comparison with other predictions/RNA-seq
      experiments.
    homepage: http://rssf.i2bc.paris-saclay.fr/NAPP/index.php
    license: https://creativecommons.org/licenses/by/2.0/fr
    name: Nucleic Acid Phylogenetic Profile
    prefix: FAIRsharing.vr52p3
    publications:
    - doi: 10.1101/gr.089714.108
      pubmed_id: 19237465
      title: Single-pass classification of all noncoding sequences in a bacterial
        genome using phylogenetic profiles.
    - doi: 10.1093/nar/gkr807
      pubmed_id: 21984475
      title: 'NAPP: the Nucleic Acid Phylogenetic Profile Database.'
    subjects:
    - Genomics
  mappings:
    biocontext: NAPP
    fairsharing: FAIRsharing.vr52p3
    miriam: napp
    n2t: napp
    prefixcommons: napp
  miriam:
    deprecated: false
    description: NAPP (Nucleic Acids Phylogenetic Profiling) is a clustering method
      based on conserved noncoding RNA (ncRNA) elements in a bacterial genomes. Short
      intergenic regions from a reference genome are compared with other genomes to
      identify RNA rich clusters.
    homepage: http://rssf.i2bc.paris-saclay.fr/NAPP/index.php
    id: '00000247'
    name: NAPP
    namespaceEmbeddedInLui: false
    pattern: ^\d+$
    prefix: napp
    sampleId: '351'
    uri_format: http://rssf.i2bc.paris-saclay.fr/NAPP/Niveau2.php?specie=$1
  n2t:
    description: NAPP (Nucleic Acids Phylogenetic Profiling is a clustering method
      based on conserved noncoding RNA (ncRNA) elements in a bacterial genomes. Short
      intergenic regions from a reference genome are compared with other genomes to
      identify RNA rich clusters.
    example: '351'
    homepage: http://napp.u-psud.fr/
    name: NAPP at CNRS
    namespaceEmbeddedInLui: false
    pattern: ^\d+$
    prefix: napp
    uri_format: http://rna.igmors.u-psud.fr/NAPP/Niveau2.php?specie=$1
  name: Nucleic Acids Phylogenetic Profiling
  prefix: napp
  prefixcommons:
    description: NAPP (Nucleic Acids Phylogenetic Profiling) is a clustering method
      based on conserved noncoding RNA (ncRNA) elements in a bacterial genomes. Short
      intergenic regions from a reference genome are compared with other genomes to
      identify RNA rich clusters.
    example: '351'
    homepage: http://napp.u-psud.fr/
    keywords:
    - clustering
    - nucleotide
    name: 'NAPP: Nucleic Acids Phylogenetic Profiling'
    pattern: ^\d+$
    prefix: napp
    uri_format: http://napp.u-psud.fr/Niveau2.php?specie=$1
  publications:
  - doi: 10.1093/nar/gkr807
    pmc: PMC3245103
    pubmed: '21984475'
    title: 'NAPP: the Nucleic Acid Phylogenetic Profile Database'
    year: 2011
  - doi: 10.1101/gr.089714.108
    pmc: PMC2694484
    pubmed: '19237465'
    title: Single-pass classification of all noncoding sequences in a bacterial genome
      using phylogenetic profiles
    year: 2009
  - doi: 10.1101/gr.089714.108
    pmc: null
    pubmed: null
    title: Single-pass classification of all noncoding sequences in a bacterial genome
      using phylogenetic profiles.
    year: null
  - doi: 10.1093/nar/gkr807
    pmc: null
    pubmed: null
    title: 'NAPP: the Nucleic Acid Phylogenetic Profile Database.'
    year: null
narcis:
  biocontext:
    prefix: NARCIS
  fairsharing:
    abbreviation: NARCIS
    description: NARCIS provides access to scientific information, including (open
      access) publications from the repositories of all the Dutch universities, KNAW,
      NWO and a number of research institutes, which is not referenced in other citation
      databases.
    homepage: http://www.narcis.nl/?Language=en
    license: http://opendatacommons.org/licenses/pddl/1.0
    name: NARCIS
    prefix: FAIRsharing.f63h4k
    publications: []
    subjects:
    - Subject Agnostic
  homepage: http://www.narcis.nl
  integbio:
    description: NARCIS provides access to scientific information, including (open
      access) publications from the repositories of all the Dutch universities, KNAW,
      NWO and a number of research institutes, which is not referenced in other citation
      databases.
    fairsharing: FAIRsharing.f63h4k
    homepage: http://www.narcis.nl/?Language=en
    information_keywords:
    - Bibliography/Documents
    - Repository
    maintainer: VSNU (Association of Universities in the Netherlands)||DANS(Data Archiving
      and Networked Services)
    name: NARCIS
    prefix: nbdc01862
    status: Closed
  mappings:
    biocontext: NARCIS
    fairsharing: FAIRsharing.f63h4k
    integbio: nbdc01862
    miriam: narcis
    n2t: narcis
  miriam:
    deprecated: false
    description: NARCIS provides access to scientific information, including (open
      access) publications from the repositories of all the Dutch universities, KNAW,
      NWO and a number of research institutes, which is not referenced in other citation
      databases.
    homepage: http://www.narcis.nl/?Language=en
    id: '00000240'
    name: NARCIS
    namespaceEmbeddedInLui: false
    pattern: ^oai\:cwi\.nl\:\d+$
    prefix: narcis
    sampleId: oai:cwi.nl:4725
    uri_format: http://www.narcis.nl/publication/RecordID/$1
  n2t:
    description: NARCIS provides access to scientific information, including (open
      access) publications from the repositories of all the Dutch universities, KNAW,
      NWO and a number of research institutes, which is not referenced in other citation
      databases.
    example: oai:cwi.nl:4725
    homepage: http://www.narcis.nl/?Language=en
    name: NARCIS at The Hague
    namespaceEmbeddedInLui: false
    pattern: ^oai\:cwi\.nl\:\d+$
    prefix: narcis
    uri_format: http://www.narcis.nl/publication/RecordID/$1
  name: National Academic Research and Collaborations Information System
  prefix: narcis
nasaosdr.biospecimen:
  contact:
    email: sylvain.v.costes@nasa.gov
    github: null
    name: Sylvain V Costes
    orcid: 0000-0002-8542-2389
  contributor:
    email: m.naguthana@hotmail.com
    github: nagutm
    name: Mufaddal Naguthanawala
    orcid: 0009-0009-5240-7463
  description: Identifiers for biospecimens used in experiments that investigate biological
    and health responses of terrestrial life to spaceflight
  example: '7943'
  github_request_issue: 1298
  homepage: https://www.nasa.gov/osdr
  name: NASA Open Science Data Repository Biospecimen
  pattern: ^\d+$
  prefix: nasaosdr.biospecimen
  publications:
  - doi: 10.1093/nar/gkae1116
    pmc: null
    pubmed: '39558178'
    title: 'NASA open science data repository: open science for life in space'
    year: 2024
  reviewer:
    email: b.gyori@northeastern.edu
    github: bgyori
    name: Benjamin M. Gyori
    orcid: 0000-0001-9439-5346
  uri_format: https://osdr.nasa.gov/bio/repo/data/biospecimens/$1
nasaosdr.experiment:
  contact:
    email: sylvain.v.costes@nasa.gov
    github: null
    name: Sylvain V Costes
    orcid: 0000-0002-8542-2389
  contributor:
    email: m.naguthana@hotmail.com
    github: nagutm
    name: Mufaddal Naguthanawala
    orcid: 0009-0009-5240-7463
  description: Identifiers for space-related data from experiments that investigate
    biological and health responses of terrestrial life to spaceflight
  example: OS-27
  github_request_issue: 1298
  homepage: https://www.nasa.gov/osdr
  name: NASA Open Science Data Repository Experiment
  pattern: ^OS-\d+$
  prefix: nasaosdr.experiment
  publications:
  - doi: 10.1093/nar/gkae1116
    pmc: null
    pubmed: '39558178'
    title: 'NASA open science data repository: open science for life in space'
    year: 2024
  reviewer:
    email: b.gyori@northeastern.edu
    github: bgyori
    name: Benjamin M. Gyori
    orcid: 0000-0001-9439-5346
  uri_format: https://osdr.nasa.gov/bio/repo/data/experiments/$1
nasaosdr.hardware:
  contact:
    email: sylvain.v.costes@nasa.gov
    github: null
    name: Sylvain V Costes
    orcid: 0000-0002-8542-2389
  contributor:
    email: m.naguthana@hotmail.com
    github: nagutm
    name: Mufaddal Naguthanawala
    orcid: 0009-0009-5240-7463
  description: Identifiers for hardware used in experiments that investigate biological
    and health responses of terrestrial life to spaceflight
  example: '2011'
  github_request_issue: 1298
  homepage: https://www.nasa.gov/osdr
  name: NASA Open Science Data Repository Hardware
  pattern: ^\d+$
  prefix: nasaosdr.hardware
  publications:
  - doi: 10.1093/nar/gkae1116
    pmc: null
    pubmed: '39558178'
    title: 'NASA open science data repository: open science for life in space'
    year: 2024
  reviewer:
    email: b.gyori@northeastern.edu
    github: bgyori
    name: Benjamin M. Gyori
    orcid: 0000-0001-9439-5346
  uri_format: https://osdr.nasa.gov/bio/repo/data/hardware/$1
nasaosdr.mission:
  contact:
    email: sylvain.v.costes@nasa.gov
    github: null
    name: Sylvain V Costes
    orcid: 0000-0002-8542-2389
  contributor:
    email: m.naguthana@hotmail.com
    github: nagutm
    name: Mufaddal Naguthanawala
    orcid: 0009-0009-5240-7463
  description: Identifiers for missions associated with experiments that investigate
    biological and health responses of terrestrial life to spaceflight
  example: ARCBedrest
  example_extras:
  - STS-46
  - Bion 11
  github_request_issue: 1298
  homepage: https://www.nasa.gov/osdr
  name: NASA Open Science Data Repository Mission
  pattern: ^.+$
  prefix: nasaosdr.mission
  publications:
  - doi: 10.1093/nar/gkae1116
    pmc: null
    pubmed: '39558178'
    title: 'NASA open science data repository: open science for life in space'
    year: 2024
  reviewer:
    email: b.gyori@northeastern.edu
    github: bgyori
    name: Benjamin M. Gyori
    orcid: 0000-0001-9439-5346
  uri_format: https://osdr.nasa.gov/bio/repo/data/missions/$1
nasaosdr.payload:
  contact:
    email: sylvain.v.costes@nasa.gov
    github: null
    name: Sylvain V Costes
    orcid: 0000-0002-8542-2389
  contributor:
    email: m.naguthana@hotmail.com
    github: nagutm
    name: Mufaddal Naguthanawala
    orcid: 0009-0009-5240-7463
  description: Identifiers for payloads associated with experiments that investigate
    biological and health responses of terrestrial life to spaceflight
  example: VEG-03D
  example_extras:
  - NanoRacks-UF-Squids-1
  - PSE.02
  - HyperG2-SIMBA2
  github_request_issue: 1298
  homepage: https://www.nasa.gov/osdr
  name: NASA Open Science Data Repository Payload
  pattern: ^.+$
  prefix: nasaosdr.payload
  publications:
  - doi: 10.1093/nar/gkae1116
    pmc: null
    pubmed: '39558178'
    title: 'NASA open science data repository: open science for life in space'
    year: 2024
  reviewer:
    email: b.gyori@northeastern.edu
    github: bgyori
    name: Benjamin M. Gyori
    orcid: 0000-0001-9439-5346
  uri_format: https://osdr.nasa.gov/bio/repo/data/payloads/$1
nasaosdr.study:
  comment: NASA OSDR is NASA's new integrated life sciences data archive which encompasses
    NASA GeneLAB (ngl), their old database for omics data. The studies from ngl are
    relabelled with new identifier formats, thus this is curated as a new prefix
  contact:
    email: sylvain.v.costes@nasa.gov
    github: null
    name: Sylvain V Costes
    orcid: 0000-0002-8542-2389
  contributor:
    email: m.naguthana@hotmail.com
    github: nagutm
    name: Mufaddal Naguthanawala
    orcid: 0009-0009-5240-7463
  description: Identifiers for space-related data from studies that investigate biological
    and health responses of terrestrial life to spaceflight
  example: OSD-678
  github_request_issue: 1298
  homepage: https://www.nasa.gov/osdr
  name: NASA Open Science Data Repository Study
  pattern: ^OSD-\d+$
  prefix: nasaosdr.study
  publications:
  - doi: 10.1093/nar/gkae1116
    pmc: null
    pubmed: '39558178'
    title: 'NASA open science data repository: open science for life in space'
    year: 2024
  reviewer:
    email: b.gyori@northeastern.edu
    github: bgyori
    name: Benjamin M. Gyori
    orcid: 0000-0001-9439-5346
  uri_format: https://osdr.nasa.gov/bio/repo/data/studies/$1
nasaosdr.subject:
  contact:
    email: sylvain.v.costes@nasa.gov
    github: null
    name: Sylvain V Costes
    orcid: 0000-0002-8542-2389
  contributor:
    email: m.naguthana@hotmail.com
    github: nagutm
    name: Mufaddal Naguthanawala
    orcid: 0009-0009-5240-7463
  description: Identifiers for subjects of experiments that investigate biological
    and health responses of terrestrial life to spaceflight
  example: '58'
  github_request_issue: 1298
  homepage: https://www.nasa.gov/osdr
  name: NASA Open Science Data Repository Subject
  pattern: ^\d+$
  prefix: nasaosdr.subject
  publications:
  - doi: 10.1093/nar/gkae1116
    pmc: null
    pubmed: '39558178'
    title: 'NASA open science data repository: open science for life in space'
    year: 2024
  reviewer:
    email: b.gyori@northeastern.edu
    github: bgyori
    name: Benjamin M. Gyori
    orcid: 0000-0001-9439-5346
  uri_format: https://osdr.nasa.gov/bio/repo/data/subjects/$1
nasc:
  biocontext:
    prefix: NASC
  fairsharing:
    abbreviation: NASC
    contact:
      email: sean@arabidopsis.org.uk
      name: Sean May
      orcid: 0000-0001-5282-3250
    description: The Nottingham Arabidopsis Stock Centre (NASC) provides seed and
      information resources to the International Arabidopsis Genome Programme and
      the wider research community.
    homepage: http://arabidopsis.info
    name: Nottingham Arabidopsis Stock Centre Seeds Database
    prefix: FAIRsharing.2sqcxs
    publications:
    - doi: 10.1093/nar/gkh133
      pubmed_id: 14681484
      title: 'NASCArrays: a repository for microarray data generated by NASC''s transcriptomics
        service.'
    subjects:
    - Life Science
    twitter: NascArabidopsis
  mappings:
    biocontext: NASC
    fairsharing: FAIRsharing.2sqcxs
    miriam: nasc
    n2t: nasc
    prefixcommons: nasc
    re3data: r3d100010906
  miriam:
    deprecated: false
    description: The Nottingham Arabidopsis Stock Centre (NASC) provides seed and
      information resources to the International Arabidopsis Genome Programme and
      the wider research community.
    homepage: http://arabidopsis.info/
    id: '00000304'
    name: NASC code
    namespaceEmbeddedInLui: false
    pattern: ^(\w+)?\d+$
    prefix: nasc
    sampleId: N1899
    uri_format: http://arabidopsis.info/StockInfo?NASC_id=$1
  n2t:
    description: The Nottingham Arabidopsis Stock Centre (NASC) provides seed and
      information resources to the International Arabidopsis Genome Programme and
      the wider research community.
    example: N1899
    homepage: http://arabidopsis.info/
    name: NASC at University of Nottingham
    namespaceEmbeddedInLui: false
    pattern: ^(\w+)?\d+$
    prefix: nasc
    uri_format: http://arabidopsis.info/StockInfo?NASC_id=$1
  prefix: nasc
  prefixcommons:
    description: The Nottingham Arabidopsis Stock Centre (NASC) provides seed and
      information resources to the International Arabidopsis Genome Programme and
      the wider research community.
    example: '57961'
    homepage: http://arabidopsis.info
    keywords:
    - genome
    name: Nottingham Arabidopsis Stock Centre Seeds Database
    pattern: ^\d+$
    prefix: nasc
    uri_format: http://arabidopsis.info/StockInfo?NASC_id=$1
  publications:
  - doi: 10.1093/nar/gkh133
    pmc: PMC308867
    pubmed: '14681484'
    title: 'NASCArrays: a repository for microarray data generated by NASC''s transcriptomics
      service'
    year: 2004
  re3data:
    description: The Nottingham Arabidopsis Stock Centre (NASC) provides seed and
      information resources to Europe researchers.
    doi: 10.17616/R38P7T
    homepage: https://arabidopsis.info/
    name: NASC
    prefix: r3d100010906
    synonyms:
    - Nottingham Arabidopsis Stock Centre
    - The European Arabidopsis Stock Centre
    xrefs:
      omics: '28815'
nbn:
  biocontext:
    prefix: NBN
  mappings:
    biocontext: NBN
    miriam: nbn
    n2t: nbn
  miriam:
    deprecated: false
    description: The National Bibliography Number (NBN), is a URN-based publication
      identifier system employed by a variety of national libraries such as those
      of Germany, the Netherlands and Switzerland.  They are used to identify documents
      archived in national libraries, in their native format or language, and are
      typically used for documents which do not have a publisher-assigned identifier.
    homepage: http://nbn-resolving.org/resolve_urn.htm
    id: 00000381
    name: National Bibliography Number
    namespaceEmbeddedInLui: false
    pattern: ^(urn|URN):(nbn|NBN)(:[A-Za-z_0-9]+)*.+$
    prefix: nbn
    sampleId: urn:nbn:fi:tkk-004781
    uri_format: http://nbn-resolving.org/$1
  n2t:
    description: The National Bibliography Number (NBN), is a URN-based publication
      identifier system employed by a variety of national libraries such as those
      of Germany, the Netherlands and Switzerland.  They are used to identify documents
      archived in national libraries, in their native format or language, and are
      typically used for documents which do not have a publisher-assigned identifier.
    example: urn:nbn:fi:tkk-004781
    homepage: http://nbn-resolving.org/resolve_urn.htm
    name: NBN through URN Resolver at German National Library
    namespaceEmbeddedInLui: false
    pattern: ^urn\:nbn\:[A-Za-z_0-9]+\:([A-Za-z_0-9]+)-[A-Za-z_0-9]+$
    prefix: nbn
    uri_format: http://nbn-resolving.org/resolver?identifier=urn:nbn:$1&verb=redirect
  prefix: nbn
nbo:
  aberowl:
    description: An ontology of human and animal behaviours and behavioural phenotypes
    download_owl: http://aber-owl.net/media/ontologies/NBO/38/nbo.owl
    homepage: https://github.com/obo-behavior/behavior-ontology/
    name: Neuro Behavior Ontology
    prefix: NBO
  biocontext:
    prefix: NBO
  bioportal:
    contact:
      email: g.gkoutos@gmail.com
      name: George Gkoutos
    description: The Neurobehavior Ontology (NBO) consists of two main components,
      an ontology of behavioral processes and an ontology of behavioral phenotypes.
      The behavioral process branch of NBO contains a classification of behavior processes
      complementing and extending GO’s process ontology. The behavior phenotype branch
      of NBO consists of a classification of both normal and abnormal behavioral characteristics
      of organisms.
    homepage: https://github.com/obo-behavior/behavior-ontology/
    name: Neuro Behavior Ontology
    prefix: NBO
    version: '2023-07-04'
  download_obo: https://github.com/obo-behavior/behavior-ontology/raw/master/nbo.obo
  example: '0000564'
  fairsharing:
    abbreviation: NBO
    description: The Neurobehavior Ontology (NBO) consists of two main components,
      an ontology of behavioral processes and an ontology of behavioral phenotypes.
      The behavioral process branch of NBO contains a classification of behavior processes
      complementing and extending GO’s process ontology. The behavior phenotype branch
      of NBO consists of a classification of both normal and abnormal behavioral characteristics
      of organisms .
    domains:
    - behavior
    - phenotype
    homepage: https://github.com/obo-behavior/behavior-ontology/
    license: CC-BY-3.0
    name: Neuro Behavior Ontology
    prefix: FAIRsharing.pktgc6
    publications:
    - doi: 10.1016/b978-0-12-388408-4.00004-6
      pubmed: '23195121'
      title: 'The neurobehavior ontology: an ontology for annotation and integration
        of behavior and behavioral phenotypes'
      year: 2012
    repository: https://github.com/obo-behavior/behavior-ontology/issues
    subjects:
    - Social and Behavioural Science
    - Systemic Neuroscience
  mappings:
    aberowl: NBO
    biocontext: NBO
    bioportal: NBO
    fairsharing: FAIRsharing.pktgc6
    obofoundry: nbo
    ols: nbo
    ontobee: NBO
    wikidata.entity: Q81661716
  obofoundry:
    appears_in:
    - ecto
    - maxo
    - pcl
    - uberon
    - scdo
    contact: g.gkoutos@bham.ac.uk
    contact.github: gkoutos
    contact.label: George Gkoutos
    contact.orcid: 0000-0002-2061-091X
    deprecated: false
    description: An ontology of human and animal behaviours and behavioural phenotypes
    domain: biological systems
    download.owl: http://purl.obolibrary.org/obo/nbo.owl
    homepage: https://github.com/obo-behavior/behavior-ontology/
    license: CC BY 3.0
    license.url: http://creativecommons.org/licenses/by/3.0/
    name: Neuro Behavior Ontology
    preferredPrefix: NBO
    prefix: nbo
    publications:
    - id: https://www.ncbi.nlm.nih.gov/pubmed/24177753
      title: Analyzing gene expression data in mice with the Neuro Behavior Ontology
    repository: https://github.com/obo-behavior/behavior-ontology
  ols:
    description: An ontology of human and animal behaviours and behavioural phenotypes
    download_owl: http://purl.obolibrary.org/obo/nbo.owl
    homepage: https://github.com/obo-behavior/behavior-ontology/
    name: Neuro Behavior Ontology
    prefix: nbo
    tracker: https://github.com/obo-behavior/behavior-ontology/issues
    version: '2023-07-04'
    version.iri: http://purl.obolibrary.org/obo/nbo/releases/2023-07-04/nbo.owl
  ontobee:
    library: Library
    name: Neuro Behavior Ontology
    prefix: NBO
  pattern: ^\d{7}$
  prefix: nbo
  publications:
  - doi: 10.1007/s00335-013-9481-z
    pmc: null
    pubmed: '24177753'
    title: Analyzing gene expression data in mice with the Neuro Behavior Ontology
    year: 2013
  - doi: 10.1016/b978-0-12-388408-4.00004-6
    pmc: null
    pubmed: '23195121'
    title: 'The neurobehavior ontology: an ontology for annotation and integration
      of behavior and behavioral phenotypes'
    year: 2012
  uri_format: http://purl.obolibrary.org/obo/NBO_$1
nbrc:
  biocontext:
    prefix: NBRC
  fairsharing:
    abbreviation: NBRC
    description: The NITE Biological Resource Center Culture Catalogue (NBRC) collects
      potentially useful biological resources (microorganisms and cloned genes) and
      distributes them to promote basic researches as well as industrial applications.
      Information includes the source of isolation, culture conditions, literature
      and sequence by searching for strains using NBRC number or scientific name.
      Closely related strains can be discovered by performing a homology search using
      sequence data.
    homepage: https://www.nite.go.jp/nbrc/catalogue/
    name: NITE Biological Research Center Culture Catalogue
    prefix: FAIRsharing.ftamrc
    publications: []
    subjects:
    - Microbiology
  mappings:
    biocontext: NBRC
    fairsharing: FAIRsharing.ftamrc
    miriam: nbrc
    n2t: nbrc
    ncbi: NBRC
    prefixcommons: nbrc
  miriam:
    deprecated: false
    description: NITE Biological Research Center (NBRC) provides a collection of microbial
      resources, performing taxonomic characterization of individual microorganisms
      such as bacteria including actinomycetes and archaea, yeasts, fungi, algaes,
      bacteriophages and DNA resources for academic research and industrial applications.
      A catalogue is maintained which states strain nomenclature, synonyms, and culture
      and sequence information.
    homepage: http://www.nbrc.nite.go.jp/e/index.html
    id: 00000179
    name: NITE Biological Research Center Catalogue
    namespaceEmbeddedInLui: false
    pattern: ^\d+$
    prefix: nbrc
    sampleId: '00001234'
    uri_format: http://www.nbrc.nite.go.jp/NBRC2/NBRCCatalogueDetailServlet?ID=NBRC&CAT=$1
  n2t:
    description: NITE Biological Research Center (NBRC) provides a collection of microbial
      resources, performing taxonomic characterization of individual microorganisms
      such as bacteria including actinomycetes and archaea, yeasts, fungi, algaes,
      bacteriophages and DNA resources for academic research and industrial applications.
      A catalogue is maintained which states strain nomenclature, synonyms, and culture
      and sequence information.
    example: '00001234'
    homepage: http://www.nbrc.nite.go.jp/e/index.html
    name: NBRC Catalogue at National Institute of Technology Evaluation
    namespaceEmbeddedInLui: false
    pattern: ^\d+$
    prefix: nbrc
    uri_format: http://www.nbrc.nite.go.jp/NBRC2/NBRCCatalogueDetailServlet?ID=NBRC&CAT=$1
  ncbi:
    example: '3189'
    homepage: http://www.nbrc.nite.go.jp/e/catalog-e.html
    name: NITE Biological Resource Center
    prefix: NBRC
  prefix: nbrc
  prefixcommons:
    description: To provide attractive biological resources with useful information
      attached, the NITE Biological Resource Center (NBRC) actively collects potentially
      useful biological resources (microorganisms and cloned genes) and distributes
      them to promote basic researches as well as industrial applications.
    example: '00001234'
    homepage: http://www.nbrc.nite.go.jp/e/index.html
    keywords:
    - microbial
    - taxonomy
    name: NITE Biological Research Center Catalogue
    pattern: ^\d+$
    prefix: nbrc
    uri_format: http://www.nbrc.nite.go.jp/NBRC2/NBRCCatalogueDetailServlet?ID=NBRC&CAT=$1
ncats.bioplanet:
  biolink:
    is_identifiers: false
    is_obo: false
    prefix: ncats.bioplanet
    uri_format: https://tripod.nih.gov/bioplanet/detail.jsp?pid=$1
  contact:
    email: ruili.huang@nih.gov
    github: null
    name: Ruili Huang
    orcid: 0000-0001-8886-8311
  contributor:
    email: smoxon@lbl.gov
    github: sierra-moxon
    name: Sierra Moxon
    orcid: 0000-0002-8719-7760
  description: The NCATS BioPlanet is a comprehensive, publicly accessible informatics
    resource that catalogs all pathways, their healthy and disease state annotations,
    and targets within and relationships among them. The BioPlanet integrates pathway
    annotations from publicly available, manually curated sources subjected to thorough
    redundancy and consistency cross-evaluation via extensive manual curation. The
    browser supports interactive browsing, retrieval and analysis of pathways, exploration
    of pathway connections, and pathway search by gene targets, category, and availability
    of bioactivity assays.
  example: '3'
  github_request_issue: 445
  homepage: https://tripod.nih.gov/bioplanet/
  mappings:
    biolink: ncats.bioplanet
  name: National Center for Advancing Translation Sciences BioPlanet
  pattern: ^\d+$
  prefix: ncats.bioplanet
  publications:
  - doi: 10.3389/fphar.2019.00445
    pmc: PMC6524730
    pubmed: '31133849'
    title: The NCATS BioPlanet - An Integrated Platform for Exploring the Universe
      of Cellular Signaling Pathways for Toxicology, Systems Biology, and Chemical
      Genomics
    year: 2019
  reviewer:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  twitter: ncats_nih_gov
  uri_format: https://tripod.nih.gov/bioplanet/detail.jsp?pid=bioplanet_$1
ncats.drug:
  biolink:
    is_identifiers: false
    is_obo: false
    prefix: ncats.drug
    uri_format: https://drugs.ncats.io/drug/$1
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  contributor_extras:
  - email: cjmungall@lbl.gov
    github: cmungall
    name: Chris Mungall
    orcid: 0000-0002-6601-2165
  - email: null
    github: vdancik
    name: Vlado Dancik
    orcid: 0000-0002-5970-6660
  - email: smoxon@lbl.gov
    github: sierra-moxon
    name: Sierra Moxon
    orcid: 0000-0002-8719-7760
  description: 'The National Center for Advancing Translational Sciences](http://www.ncats.nih.gov/)
    (NCATS) has developed Inxight Drugs as a comprehensive portal for drug development
    information. NCATS Inxight Drugs contains information on ingredients in medicinal
    products, including:


    - US Approved Drugs

    - Marketed Drugs

    - Investigational Drugs

    - Other Substances'
  example: '44259'
  example_extras:
  - 1IJV77EI07
  homepage: https://drugs.ncats.io/
  mappings:
    biolink: ncats.drug
  name: NCATS Drugs
  prefix: ncats.drug
  synonyms:
  - inxight
  - inxight-drugs
  uri_format: https://drugs.ncats.io/drug/$1
ncbi.assembly:
  biocontext:
    prefix: NCBIAssembly
    uri_format: http://www.ncbi.nlm.nih.gov/assembly/$1
  mappings:
    biocontext: NCBIAssembly
    miriam: assembly
    re3data: r3d100012688
  miriam:
    deprecated: false
    description: A database providing information on the structure of assembled genomes,
      assembly names and other meta-data, statistical reports, and links to genomic
      sequence data.
    homepage: https://www.ncbi.nlm.nih.gov/
    id: 00000884
    name: Assembly
    namespaceEmbeddedInLui: false
    pattern: ^[a-zA-Z0-9_\.]+$
    prefix: assembly
    sampleId: GCF_000005845.2
    uri_format: https://www.ncbi.nlm.nih.gov/datasets/genome/$1
  prefix: ncbi.assembly
  re3data:
    description: '<<<!!!<<< Effective May 2024, NCBI''s Assembly resource will no
      longer be available. NCBI Assembly data can now be found on the NCBI Datasets
      genome pages. https://www.re3data.org/repository/r3d100014298 >>>!!!>>>



      A database providing information on the structure of assembled genomes, assembly
      names and other meta-data, statistical reports, and links to genomic sequence
      data.'
    doi: 10.17616/R31NJMA8
    homepage: https://www.ncbi.nlm.nih.gov/assembly
    name: NCBI Assembly
    prefix: r3d100012688
    xrefs:
      omics: '10736'
ncbi.gc:
  comment: 'see comment here: https://github.com/obophenotype/ncbitaxon/issues/47'
  contact:
    email: elzanowski@biol.uni.wroc.pl
    github: null
    name: Andrzej Elzanowski
    orcid: null
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: Genetic code, mitochontrial genetic code, and other linked information
    to NCBI taxonomy entries.
  domain: genetic code
  example: '11'
  homepage: https://www.ncbi.nlm.nih.gov/Taxonomy/taxonomyhome.html/index.cgi?chapter=cgencodes
  keywords:
  - genetic code
  - genome
  license: public domain
  logo: https://www.ncbi.nlm.nih.gov/corehtml/logo256.gif
  name: NCBI Genetic Code
  pattern: ^\d+$
  prefix: ncbi.gc
  references:
  - https://github.com/obophenotype/ncbitaxon/issues/47
  - https://www.ncbi.nlm.nih.gov/home/about/policies
  synonyms:
  - gc
  - gc_id
  uri_format: https://www.ncbi.nlm.nih.gov/Taxonomy/taxonomyhome.html/index.cgi?chapter=cgencodes#SG$1
ncbi.genome:
  biocontext:
    prefix: NCBIGenome
    uri_format: http://www.ncbi.nlm.nih.gov/genome/$1
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: This resource organizes information on genomes including sequences,
    maps, chromosomes, assemblies, and annotations.
  edam:
    description: A unique identifier of a whole genome assigned by the NCBI.
    name: NCBI genome
    obsolete: false
    prefix: '2787'
  example: '51'
  homepage: https://www.ncbi.nlm.nih.gov/genome
  mappings:
    biocontext: NCBIGenome
    edam: '2787'
    re3data: r3d100010785
  name: NCBI Genome
  pattern: ^\d+$
  prefix: ncbi.genome
  re3data:
    description: 'The Genome database contains annotations and analysis of eukaryotic
      and prokaryotic genomes, as well as tools that allow users to compare genomes
      and gene sequences from humans, microbes, plants, viruses and organelles. Users
      can browse by organism, and view genome maps and protein clusters.



      The Genome database contains annotations and analysis of eukaryotic and prokaryotic
      genomes, as well as tools that allow users to compare genomes and gene sequences
      from humans, microbes, plants, viruses and organelles. Users can browse by organism,
      and view genome maps and protein clusters.'
    doi: 10.17616/R3R89S
    homepage: https://www.ncbi.nlm.nih.gov/datasets/genome/
    license: other
    name: NCBI Genome
    prefix: r3d100010785
    xrefs:
      nif: 0000-02802
  uri_format: https://www.ncbi.nlm.nih.gov/genome/$1
ncbi.resource:
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: A database-specific registry supporting curation in the NCBI GenBank
    and related NCBI resources
  example: ECOCYC
  homepage: https://www.ncbi.nlm.nih.gov/genbank/collab/db_xref/
  name: NCBI Registry
  prefix: ncbi.resource
  uri_format: https://bioregistry.io/metaregistry/ncbi/$1
ncbibook:
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: The NCBI Bookshelf provides free online access to books and documents
    in life science and healthcare. Search, read, and discover.
  example: NBK331
  homepage: https://www.ncbi.nlm.nih.gov/books
  name: NCBI Bookshelf
  pattern: ^NBK\d+$
  prefix: ncbibook
  uri_format: https://www.ncbi.nlm.nih.gov/books/$1
ncbidrs:
  mappings:
    miriam: ncbidrs
  miriam:
    deprecated: false
    description: 'This is the namespace for the archive of sequence and other files
      provided by NCBI e.g. in SRA and dbGaP. These files are related to objects in
      the sequencing data model managed under the insdc.sra namespace. '
    homepage: https://www.ncbi.nlm.nih.gov/
    id: '00001034'
    name: NCBI Data Repository Service
    namespaceEmbeddedInLui: false
    pattern: ^[0-9a-fA-F]{32}$
    prefix: ncbidrs
    sampleId: 72ff6ff882ec447f12df018e6183de59
    uri_format: https://locate.be-md.ncbi.nlm.nih.gov/ga4gh/drs/v1/objects/$1
  prefix: ncbidrs
ncbigene:
  biocontext:
    prefix: NCBIGene
    uri_format: http://www.ncbi.nlm.nih.gov/gene/$1
  biolink:
    is_identifiers: true
    is_obo: false
    prefix: NCBIGene
    uri_format: http://identifiers.org/ncbigene/$1
  contact:
    email: murphyte@ncbi.nlm.nih.gov
    github: murphyte
    name: Terence D. Murphy
    orcid: 0000-0001-9311-9745
  contributor_extras:
  - email: rcameron@sfu.com
    github: cmrn-rhi
    name: Rhiannon Cameron
    orcid: 0000-0002-9578-0788
  domain: gene
  edam:
    description: An NCBI unique identifier of a gene.
    name: Gene ID (NCBI)
    obsolete: false
    prefix: '1027'
  fairsharing:
    abbreviation: NCBI Gene
    description: Gene supplies gene-specific connections in the nexus of map, sequence,
      expression, structure, function, citation, and homology data. Unique identifiers
      are assigned to genes with defining sequences, genes with known map positions,
      and genes inferred from phenotypic information. These gene identifiers are used
      throughout NCBI's databases and tracked through updates of annotation. Gene
      includes genomes represented by NCBI Reference Sequences (or RefSeqs) and is
      integrated for indexing and query and retrieval from NCBI's Entrez and E-Utilities
      systems. Gene comprises sequences from thousands of distinct taxonomic identifiers,
      ranging from viruses to bacteria to eukaryotes. It represents chromosomes, organelles,
      plasmids, viruses, transcripts, and millions of proteins.
    homepage: https://www.ncbi.nlm.nih.gov/gene
    name: NCBI Gene
    prefix: FAIRsharing.5h3maw
    publications:
    - doi: 10.1093/nar/gki031
      pubmed_id: 15608257
      title: 'Entrez Gene: gene-centered information at NCBI.'
    subjects:
    - Genomics
    - Genetics
  go:
    homepage: http://www.ncbi.nlm.nih.gov/
    name: NCBI Gene
    prefix: NCBIGene
    synonyms:
    - GeneID
    - LocusID
    - NCBI_Gene
    uri_format: https://www.ncbi.nlm.nih.gov/gene/$1
  hl7:
    description: Because not all genes have HGNC names and codes, NCBI has created
      gene IDs that cover the genes that are not registered by HGNC. When applicable,
      this variable identifies the gene on which the variant is located. The gene
      identifier is also carried in the transcript reference sequence database, and
      is part of a full HGVS expression.
    homepage: https://lhncbc.nlm.nih.gov/
    name: NCBI Gene Code
    organization: Lister Hill National Center for Biomedical Communications
    preferred_prefix: geneCodeNCBI
    prefix: 2.16.840.1.113883.6.340
    status: Complete
  integbio:
    description: The gene database provides information on gene sequence, structure,
      location, and function for annotated genes from the NCBI database. Users can
      search by accession ID or keyword, compare and identify sequences using BLAST,
      or submit references into function (RIFs) based on experimental results. Bulk
      download and an update mailing list are available.
    fairsharing: biodbcore-000449
    homepage: http://www.ncbi.nlm.nih.gov/gene
    information_keywords:
    - Sequence
    - Repository
    maintainer: NCBI (National Center for Biotechnology Information)
    name: NCBI Gene
    prefix: nbdc00073
    pubmeds:
    - '21115458'
    status: Active
    target_keywords:
    - Genome/Gene
  logo: https://www.ncbi.nlm.nih.gov/corehtml/logo256.gif
  mappings:
    biocontext: NCBIGene
    biolink: NCBIGene
    edam: '1027'
    fairsharing: FAIRsharing.5h3maw
    go: NCBIGene
    hl7: 2.16.840.1.113883.6.340
    integbio: nbdc00073
    miriam: ncbigene
    n2t: ncbigene
    ncbi: GeneID
    prefixcommons: ncbigene
    re3data: r3d100010650
    togoid: Ncbigene
    uniprot: DB-0118
    wikidata: P351
  miriam:
    deprecated: false
    description: Entrez Gene is the NCBI's database for gene-specific information,
      focusing on completely sequenced genomes, those with an active research community
      to contribute gene-specific information, or those that are scheduled for intense
      sequence analysis.
    homepage: https://www.ncbi.nlm.nih.gov/gene
    id: 00000069
    name: NCBI Gene
    namespaceEmbeddedInLui: false
    pattern: ^\d+$
    prefix: ncbigene
    providers:
    - code: ''
      description: Bio2RDF
      homepage: http://bio2rdf.org
      name: Bio2RDF
      uri_format: http://bio2rdf.org/ncbigene:$1
    sampleId: '100010'
    uri_format: https://www.ncbi.nlm.nih.gov/gene/$1
  n2t:
    description: Entrez Gene is the NCBI's database for gene-specific information,
      focusing on completely sequenced genomes, those with an active research community
      to contribute gene-specific information, or those that are scheduled for intense
      sequence analysis.
    example: '100010'
    homepage: https://www.ncbi.nlm.nih.gov/gene
    name: Entrez Gene (NCBI)
    namespaceEmbeddedInLui: false
    pattern: ^\d+$
    prefix: ncbigene
    uri_format: https://www.ncbi.nlm.nih.gov/gene/$1
  name: NCBI Gene
  ncbi:
    example: '3054987'
    homepage: https://www.ncbi.nlm.nih.gov/gene
    name: Entrez Gene Database (replaces NCBI Locus Link)
    prefix: GeneID
  owners:
  - name: National Center for Biotechnology Information
    partnered: false
    ror: 02meqm098
    wikidata: null
  preferred_prefix: NCBIGene
  prefix: ncbigene
  prefixcommons:
    description: NCBI Gene provides information for genes from a wide range of species.
      A record may include nomenclature, Reference Sequences (RefSeqs), maps, pathways,
      variations, phenotypes, and links to genome-, phenotype-, and locus-specific
      resources worldwide.
    example: '1'
    homepage: http://www.ncbi.nlm.nih.gov/gene
    keywords:
    - genome
    - gene
    - DNA
    name: NCBI Gene
    pattern: ^\d+$
    prefix: ncbigene
    pubmed_ids:
    - '15608257'
    synonyms:
    - entrez.gene
    - entrezgene/locuslink
    - geneid
    uri_format: http://www.ncbi.nlm.nih.gov/gene/$1
  providers:
  - code: marrvel
    description: Helps browse potential orthologs in model organisms for a given gene
    example: null
    first_party: null
    homepage: http://marrvel.org
    name: Model organism Aggregated Resources for Rare Variant ExpLoration
    publications: null
    status: null
    uri_format: http://marrvel.org/model/gene/$1
  - code: scholia
    description: Scholia is a service that creates visual scholarly profiles for topic,
      people, organizations, species, chemicals, etc using bibliographic and other
      information in Wikidata.
    example: null
    first_party: null
    homepage: https://scholia.toolforge.org/
    name: Scholia
    publications: null
    status: null
    uri_format: https://scholia.toolforge.org/ncbi-gene/$1
  publications:
  - doi: 10.1093/nar/gkq1237
    pmc: PMC3013746
    pubmed: '21115458'
    title: 'Entrez Gene: gene-centered information at NCBI'
    year: 2010
  - doi: 10.1093/nar/gki031
    pmc: PMC539985
    pubmed: '15608257'
    title: 'Entrez Gene: gene-centered information at NCBI'
    year: 2005
  - doi: 10.1093/nar/gki031
    pmc: null
    pubmed: null
    title: 'Entrez Gene: gene-centered information at NCBI.'
    year: null
  - doi: null
    pmc: null
    pubmed: '15608257'
    title: null
    year: null
  - doi: 10.1093/nar/gku1055
    pmc: null
    pubmed: '25355515'
    title: null
    year: null
  - doi: 10.1093/nar/gki031
    pmc: null
    pubmed: null
    title: 'Entrez Gene: gene-centered information at NCBI.'
    year: null
  - doi: null
    pmc: null
    pubmed: '15608257'
    title: null
    year: null
  - doi: 10.1093/nar/gku1055
    pmc: null
    pubmed: '25355515'
    title: null
    year: null
  - doi: 10.1093/nar/gki031
    pmc: null
    pubmed: null
    title: 'Entrez Gene: gene-centered information at NCBI.'
    year: null
  - doi: null
    pmc: null
    pubmed: '15608257'
    title: null
    year: null
  - doi: 10.1093/nar/gku1055
    pmc: null
    pubmed: '25355515'
    title: null
    year: null
  re3data:
    description: The Gene database provides detailed information for known and predicted
      genes defined by nucleotide sequence or map position. Gene supplies gene-specific
      connections in the nexus of map, sequence, expression, structure, function,
      citation, and homology data. Unique identifiers are assigned to genes with defining
      sequences, genes with known map positions, and genes inferred from phenotypic
      information. These gene identifiers are used throughout NCBI's databases and
      tracked through updates of annotation. Gene includes genomes represented by
      NCBI Reference Sequences (or RefSeqs) and is integrated for indexing and query
      and retrieval from NCBI's Entrez and E-Utilities systems.
    doi: 10.17616/R3603S
    homepage: https://www.ncbi.nlm.nih.gov/gene?db=gene
    name: NCBI Gene
    prefix: r3d100010650
    synonyms:
    - Entrez Gene
    - Gene
    xrefs:
      nif: 0000-02801
      omics: '01651'
  references:
  - https://github.com/biopragmatics/bioregistry/issues/983
  synonyms:
  - EGID
  - EntrezGene
  - GeneID
  - NCBIGene
  - NCBI_GeneID
  - entrez
  - entrez gene/locuslink
  - nihgeneid
  togoid:
    catalog: nbdc00073
    description: The gene database provides information on gene sequence, structure,
      location, and function for annotated genes from the NCBI database. Users can
      search by accession ID or keyword, compare and identify sequences using BLAST,
      or submit references into function (RIFs) based on experimental results. Bulk
      download and an update mailing list are available.
    examples:
    - '63962027'
    - '1046'
    - '63961921'
    - '102606930'
    - '100472895'
    - '407025'
    - '84148'
    - '88'
    - '31157'
    - '100463227'
    keywords:
    - Gene
    name: NCBI Gene
    pattern: ^(?\d+)$
    prefix: Ncbigene
    uri_format: http://identifiers.org/ncbigene/$1
  uniprot:
    abbreviation: GeneID
    category: Genome annotation databases
    homepage: https://www.ncbi.nlm.nih.gov/gene
    name: Database of genes from NCBI RefSeq genomes
    prefix: DB-0118
    publications:
    - doi: 10.1093/nar/gku1055
      pubmed: '25355515'
    uri_format: https://www.ncbi.nlm.nih.gov/gene/$1
  wikidata:
    description: identifier for a gene per the NCBI Entrez database
    example:
    - '1017'
    - '1207170'
    miriam: ncbigene
    name: Entrez Gene ID
    pattern: ^[1-9]\d{0,8}$
    prefix: P351
    uri_format: https://www.ncbi.nlm.nih.gov/gene/$1
    uri_format_rdf: http://purl.uniprot.org/geneid/$1
ncbigi:
  biocontext:
    prefix: NCBIGI
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: A GI number (for GenInfo Identifier, sometimes written in lower case,
    _gi_) is a simple series of digits that are assigned consecutively to each sequence
    record processed by NCBI. The GI number bears no resemblance to the Version number
    of the sequence record. Each time a sequence record is changed, it is assigned
    a new GI number.
  edam:
    description: A series of digits that are assigned consecutively to each sequence
      record processed by NCBI. The GI number bears no resemblance to the Accession
      number of the sequence record.
    name: GI number
    obsolete: false
    prefix: '2314'
  example: '568815597'
  go:
    homepage: http://www.ncbi.nlm.nih.gov/
    name: NCBI databases
    prefix: NCBI_gi
    uri_format: http://www.ncbi.nlm.nih.gov/entrez/viewer.fcgi?val=$1
  has_canonical: genbank
  homepage: https://www.ncbi.nlm.nih.gov/genbank/sequenceids/
  mappings:
    biocontext: NCBIGI
    edam: '2314'
    go: NCBI_gi
    ncbi: GI
  name: GenInfo Identifier
  ncbi:
    example: '1234567890'
    name: GenInfo identifier, used as a unique sequence identifier for nucleotide
      and proteins
    prefix: GI
  owners:
  - name: National Center for Biotechnology Information
    partnered: false
    ror: 02meqm098
    wikidata: null
  pattern: ^\d+$
  prefix: ncbigi
  references:
  - https://www.ncbi.nlm.nih.gov/Sitemap/sequenceIDs.html
  - https://www.ncbi.nlm.nih.gov/Class/MLACourse/Modules/Format/exercises/qa_accession_vs_gi.html
  synonyms:
  - NCBI_gi
  - ncbi.gi
ncbiortholog:
  comment: We do not currently have the source code for our ortholog resource available
    publicly, although we are looking at how to split it off and make it available
    in the next year. We are now in the process of adding this tag to the INSDC list
    for use in annotations, so I'd like to mirror that tag in bioregistry.
  contact:
    email: murphyte@ncbi.nlm.nih.gov
    github: murphyte
    name: Terence D. Murphy
    orcid: 0000-0001-9311-9745
  contributor:
    email: murphyte@ncbi.nlm.nih.gov
    github: murphyte
    name: Terence D. Murphy
    orcid: 0000-0001-9311-9745
  description: Database of one-to-one ortholog information provided by the NCBI as
    a subset of their Gene resource. Used for users to access ortholog information
    for over 1000 species of vertebrates and arthropods.
  example: '2'
  github_request_issue: 1181
  homepage: https://www.ncbi.nlm.nih.gov/gene/
  license: US gov't public domain
  name: NCBI Orthologs
  pattern: ^\d+$
  prefix: ncbiortholog
  reviewer:
    email: b.gyori@northeastern.edu
    github: bgyori
    name: Benjamin M. Gyori
    orcid: 0000-0001-9439-5346
  uri_format: https://www.ncbi.nlm.nih.gov/gene/$1/ortholog
ncbiprotein:
  biocontext:
    prefix: NCBIProtein
    uri_format: http://www.ncbi.nlm.nih.gov/protein/$1
  go:
    homepage: https://www.ncbi.nlm.nih.gov/protein
    name: NCBI Protein
    prefix: NCBI_NP
  integbio:
    description: NCBI Protein is a collection of amino acid sequences from several
      sources, including translations from annotated coding regions in GenBank, RefSeq
      and TPA, as well as records from SwissProt, PIR, PRF, and PDB. A record includes
      the amino acid sequence, organism information, literature, links to other NCBI
      databases such as BioProject, BioSample, etc.
    fairsharing: FAIRsharing.rtndct
    homepage: https://www.ncbi.nlm.nih.gov/protein
    information_keywords:
    - Sequence
    - Repository
    maintainer: NCBI (National Center for Biotechnology Information)
    name: NCBI Protein
    prefix: nbdc00636
    status: Active
    target_keywords:
    - Protein
  logo: https://www.ncbi.nlm.nih.gov/corehtml/logo256.gif
  mappings:
    biocontext: NCBIProtein
    go: NCBI_NP
    integbio: nbdc00636
    miriam: ncbiprotein
    n2t: ncbiprotein
    prefixcommons: ncbi.protein
    re3data: r3d100010776
  miriam:
    deprecated: false
    description: The Protein database is a collection of sequences from several sources,
      including translations from annotated coding regions in GenBank, RefSeq and
      TPA, as well as records from SwissProt, PIR, PRF, and PDB.
    homepage: https://www.ncbi.nlm.nih.gov/protein
    id: '00000344'
    name: NCBI Protein
    namespaceEmbeddedInLui: false
    pattern: ^\w+_?\d+(.\d+)?$
    prefix: ncbiprotein
    sampleId: CAA71118.1
    uri_format: https://www.ncbi.nlm.nih.gov/protein/$1
  n2t:
    description: The Protein database is a collection of sequences from several sources,
      including translations from annotated coding regions in GenBank, RefSeq and
      TPA, as well as records from SwissProt, PIR, PRF, and PDB.
    example: CAA71118.1
    homepage: https://www.ncbi.nlm.nih.gov/protein
    name: NCBI Protein at NCBI
    namespaceEmbeddedInLui: false
    pattern: ^(\w+\d+(\.\d+)?)|(NP_\d+)$
    prefix: ncbiprotein
    uri_format: https://www.ncbi.nlm.nih.gov/protein/$1
  owners:
  - name: National Center for Biotechnology Information
    partnered: false
    ror: 02meqm098
    wikidata: null
  preferred_prefix: NCBIProtein
  prefix: ncbiprotein
  prefixcommons:
    description: The Entrez Protein search and retrieval system contains protein entries
      that have been compiled from a variety of sources, including SwissProt, PIR,
      PRF, PDB, and translations from annotated coding regions in GenBank and RefSeq.
    example: CAA71118.1
    homepage: http://www.ncbi.nlm.nih.gov/protein
    keywords:
    - protein
    name: NCBI Protein
    pattern: ^\w+\d+(\.\d+)?$
    prefix: ncbi.protein
    synonyms:
    - protein
    - ncbi-proteinid
    uri_format: http://www.ncbi.nlm.nih.gov/protein/$1
  re3data:
    description: The Protein database is a collection of sequences from several sources,
      including translations from annotated coding regions in GenBank, RefSeq and
      TPA, as well as records from SwissProt, PIR, PRF, and PDB. Protein sequences
      are the fundamental determinants of biological structure and function.
    doi: 10.17616/R3X039
    homepage: https://www.ncbi.nlm.nih.gov/protein
    license: Copyrights
    name: NCBI Protein
    prefix: r3d100010776
    xrefs:
      nif: 0000-03178
ncbitaxon:
  aberowl:
    description: An ontology representation of the NCBI organismal taxonomy
    download_owl: http://aber-owl.net/media/ontologies/NCBITAXON/16/ncbitaxon.owl
    homepage: https://github.com/obophenotype/ncbitaxon
    name: NCBI organismal classification
    prefix: NCBITAXON
  agroportal:
    contact:
      email: info@ncbi.nlm.nih.gov
      name: NCBI information
    description: The NCBI Taxonomy Database is a curated classification and nomenclature
      for all of the organisms in the public sequence databases. This currently represents
      about 10% of the described species of life on the planet.
    example_uri: http://purl.bioontology.org/ontology/NCBITAXON/201174
    homepage: https://www.ncbi.nlm.nih.gov/
    name: National Center for Biotechnology Information (NCBI) Organismal Classification
    prefix: NCBITAXON
    repository: https://github.com/obophenotype/ncbitaxon
    version: 2023ab
  bartoc:
    description: 'The NCBI Taxonomy database is a curated set of names and classifications
      for all of the organisms that are represented in GenBank. When new sequences
      are submitted to GenBank, the submission is checked for new organism names,
      which are then classified and added to the Taxonomy database. As of April 2003,
      there were 176,890 total taxa represented.


      There are two main tools for viewing the information in the Taxonomy database:
      the Taxonomy Browser, and Taxonomy Entrez. Both systems allow searching of the
      Taxonomy database for names, and both link to the relevant sequence data. However,
      the Taxonomy Browser provides a hierarchical view of the classification (the
      best display for most casual users interested in exploring our classification),
      whereas Entrez Taxonomy provides a uniform indexing, search, and retrieval engine
      with a common mechanism for linking between the Taxonomy and other relevant
      Entrez databases.


      Organismal taxonomy is a powerful organizing principle in the study of biological
      systems. Inheritance, homology by common descent, and the conservation of sequence
      and structure in the determination of function are all central ideas in biology
      that are directly related to the evolutionary history of any group of organisms.
      Because of this, taxonomy plays an important cross-linking role in many of the
      NCBI tools and databases.


      The NCBITaxon ontology is an automatic translation of the NCBI taxonomy (a taxonomic
      classification of living organisms and associated artifacts) database into obo/owl.'
    homepage: http://www.ncbi.nlm.nih.gov/taxonomy
    name: National Center for Biotechnology Information Taxonomy
    prefix: '509'
  biocontext:
    prefix: TAXONOMY
  bioportal:
    contact:
      email: info@ncbi.nlm.nih.gov
      name: NCBI information
    description: The NCBI Taxonomy Database is a curated classification and nomenclature
      for all of the organisms in the public sequence databases.
    homepage: http://www.ncbi.nlm.nih.gov/taxonomy
    name: National Center for Biotechnology Information (NCBI) Organismal Classification
    prefix: NCBITAXON
    version: NCBI2024_04_02
  cellosaurus:
    category: Taxonomy
    homepage: https://www.ncbi.nlm.nih.gov/taxonomy
    name: NCBI taxonomy database
    prefix: NCBI_TaxID
    uri_format: https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&id=$1&lvl=3
  contact:
    email: schoch2@ncbi.nlm.nih.gov
    github: null
    name: Conrad L Schoch
    orcid: 0000-0003-1839-5322
  domain: taxonomy
  download_obo: http://purl.obolibrary.org/obo/ncbitaxon.obo.gz
  edam:
    description: A stable unique identifier for each taxon (for a species, a family,
      an order, or any other group in the NCBI taxonomy database.
    name: NCBI taxonomy
    obsolete: false
    prefix: '1179'
  example: '2170610'
  example_extras:
  - subclass
  fairsharing:
    abbreviation: NCBITaxon
    contact:
      email: frederic.bastian@unil.ch
      name: Frederic Bastian
      orcid: 0000-0002-9415-5104
    description: 'The National Center for Biotechnology Information Organismal Classification
      ontology (NCBITaxon) is an automatic semantic translation of the NCBI taxonomy
      database into obo/owl. '
    domains:
    - Taxonomic classification
    homepage: https://github.com/obophenotype/ncbitaxon
    name: NCBI Organismal Classification
    prefix: FAIRsharing.fj07xj
    publications:
    - doi: 10.5281/zenodo.8065005
      title: 'obophenotype/ncbitaxon: 2023-06-20 Release (v2023-06-20)'
      year: 2023
    repository: https://github.com/obophenotype/ncbitaxon/issues
    subjects:
    - Life Science
    - Knowledge and Information Systems
    - Taxonomy
    - Phylogenetics
    - Evolutionary Biology
    - Omics
    - Proteomics
    - Genomics
  go:
    homepage: http://www.ncbi.nlm.nih.gov/Taxonomy/taxonomyhome.html/
    name: NCBI Taxonomy
    prefix: NCBITaxon
    synonyms:
    - taxon
    - ncbi_taxid
    uri_format: http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=$1
  hl7:
    description: NCBI Taxonomy. National Center for Biotechnology Information, National
      Library of Medicine, Bethesda, MD, 2001. http://www.ncbi.nlm.nih.gov/Taxonomy/
    name: Taxonomy from NCBI
    preferred_prefix: NCBI
    prefix: 2.16.840.1.113883.6.205
    status: Pending
  lov:
    description: EUdaphobase Taxonomy Ontology for the European Soil-Biology Data
      Warehouse for Soil Protection
    homepage: https://w3id.org/EUTaxO
    keywords:
    - Biology
    modified: '2022-09-29'
    name: EUTaxO - EUdaphobase Taxonomy Ontology
    prefix: tax
    uri_prefix: https://w3id.org/EUTaxO#$1
  mappings:
    aberowl: NCBITAXON
    agroportal: NCBITAXON
    bartoc: '509'
    biocontext: TAXONOMY
    bioportal: NCBITAXON
    cellosaurus: NCBI_TaxID
    edam: '1179'
    fairsharing: FAIRsharing.fj07xj
    go: NCBITaxon
    hl7: 2.16.840.1.113883.6.205
    lov: tax
    miriam: taxonomy
    n2t: taxonomy
    ncbi: taxon
    obofoundry: ncbitaxon
    ols: ncbitaxon
    ontobee: NCBITaxon
    prefixcommons: taxonomy
    re3data: r3d100010415
    togoid: Taxonomy
    wikidata: P685
    wikidata.entity: Q81661717
  miriam:
    deprecated: false
    description: The taxonomy contains the relationships between all living forms
      for which nucleic acid or protein sequence have been determined.
    homepage: https://www.ncbi.nlm.nih.gov/Taxonomy/
    id: '00000006'
    name: Taxonomy
    namespaceEmbeddedInLui: false
    pattern: ^\d+$
    prefix: taxonomy
    providers:
    - code: ebi
      description: European Nucleotide Archive (ENA)
      homepage: https://www.ebi.ac.uk/ena/
      name: European Nucleotide Archive (ENA)
      uri_format: https://www.ebi.ac.uk/ena/data/view/Taxon:$1
    - code: ''
      description: Bio2RDF
      homepage: https://bio2rdf.org/
      name: Bio2RDF
      uri_format: https://bio2rdf.org/taxonomy:$1
    - code: ''
      description: Taxonomy through UniProt PURL
      homepage: https://www.uniprot.org/taxonomy/
      name: Taxonomy through UniProt PURL
      uri_format: https://purl.uniprot.org/taxonomy/$1
    sampleId: '9606'
    uri_format: https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&id=$1
  n2t:
    description: The taxonomy contains the relationships between all living forms
      for which nucleic acid or protein sequence have been determined.
    example: '9606'
    homepage: https://www.ncbi.nlm.nih.gov/Taxonomy/
    name: NCBI Taxonomy
    namespaceEmbeddedInLui: false
    pattern: ^\d+$
    prefix: taxonomy
    uri_format: https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&id=$1
  name: NCBI Taxonomy
  ncbi:
    example: '4932'
    homepage: https://www.ncbi.nlm.nih.gov/taxonomy
    name: NCBI's taxonomic identifier
    prefix: taxon
  obofoundry:
    appears_in:
    - agro
    - chiro
    - cl
    - clo
    - ecto
    - envo
    - foodon
    - gallont
    - genepio
    - go
    - hso
    - mco
    - ons
    - pcl
    - pco
    - uberon
    - vbo
    contact: frederic.bastian@unil.ch
    contact.github: fbastian
    contact.label: Frederic Bastian
    contact.orcid: 0000-0002-9415-5104
    deprecated: false
    description: An ontology representation of the NCBI organismal taxonomy
    domain: organisms
    download.json: http://purl.obolibrary.org/obo/ncbitaxon.json
    download.obo: http://purl.obolibrary.org/obo/ncbitaxon.obo
    download.owl: http://purl.obolibrary.org/obo/ncbitaxon.owl
    homepage: https://github.com/obophenotype/ncbitaxon
    license: CC0 1.0
    license.url: https://creativecommons.org/publicdomain/zero/1.0/
    name: NCBI organismal classification
    preferredPrefix: NCBITaxon
    prefix: ncbitaxon
    repository: https://github.com/obophenotype/ncbitaxon
  ols:
    description: An ontology representation of the NCBI organismal taxonomy
    download_owl: http://purl.obolibrary.org/obo/ncbitaxon.owl
    homepage: https://github.com/obophenotype/ncbitaxon
    name: NCBI organismal classification
    prefix: ncbitaxon
    tracker: https://github.com/obophenotype/ncbitaxon/issues
    uri_format: http://purl.obolibrary.org/obo/NCBITaxon_$1
    version: '2025-12-03'
    version.iri: http://purl.obolibrary.org/obo/ncbitaxon/2025-12-03/ncbitaxon.owl
  ontobee:
    library: Library
    name: NCBI organismal classification
    prefix: NCBITaxon
  owners:
  - name: National Center for Biotechnology Information
    partnered: false
    ror: 02meqm098
    wikidata: null
  pattern: ^(\d+)|([a-zA-Z_]+)$
  prefix: ncbitaxon
  prefixcommons:
    alt_uri_formats:
    - http://purl.org/obo/owl/NCBITaxon#$1
    - http://purl.org/obo/owl/TAXON#$1
    - http://bioportal.bioontology.org/ontologies/1132?p=terms&conceptid=obo:NCBITaxon_#$1
    bioportal: '1132'
    description: The NCBI taxonomy database contains the names of all organisms that
      are represented in the genetic databases with at least one nucleotide or protein
      sequence.
    example: '9606'
    homepage: http://www.ncbi.nlm.nih.gov/taxonomy
    keywords:
    - DNA
    - protein
    - structure
    - classification
    license: http://www.nlm.nih.gov/copyright.html
    name: NCBI Taxonomy
    pattern: ^\d+$
    prefix: taxonomy
    synonyms:
    - taxid
    - taxon
    - ncbitaxon
    - ncbitaxonomy
    - newt
    - taxman
    - ncbi_taxid
    - ncbi_taxon_id
    uri_format: http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=$1
  providers:
  - code: scholia
    description: Scholia is a service that creates visual scholarly profiles for topic,
      people, organizations, species, chemicals, etc using bibliographic and other
      information in Wikidata.
    example: null
    first_party: null
    homepage: https://scholia.toolforge.org/
    name: Scholia
    publications: null
    status: null
    uri_format: https://scholia.toolforge.org/ncbi-taxon/$1
  - code: bioportal.purl
    description: BioPortal assigns their own PURLs to entities in NCBI taxonomy database.
    example: null
    first_party: null
    homepage: https://purl.bioontology.org/ontology/NCBITAXON
    name: BioPortal
    publications: null
    status: null
    uri_format: http://purl.bioontology.org/ontology/NCBITAXON/$1
  publications:
  - doi: 10.1093/database/baaa062
    pmc: PMC7408187
    pubmed: '32761142'
    title: 'NCBI Taxonomy: a comprehensive update on curation, resources and tools'
    year: 2020
  - doi: 10.1093/nar/gkx1094
    pmc: PMC5753231
    pubmed: '29140468'
    title: GenBank
    year: 2018
  - doi: 10.1093/nar/gkr1178
    pmc: PMC3245000
    pubmed: '22139910'
    title: The NCBI Taxonomy database
    year: 2011
  - doi: 10.5281/zenodo.8065005
    pmc: null
    pubmed: null
    title: 'obophenotype/ncbitaxon: 2023-06-20 Release (v2023-06-20)'
    year: 2023
  - doi: 10.5281/zenodo.8065005
    pmc: null
    pubmed: null
    title: 'obophenotype/ncbitaxon: 2023-06-20 Release (v2023-06-20)'
    year: 2023
  - doi: 10.5281/zenodo.8065005
    pmc: null
    pubmed: null
    title: 'obophenotype/ncbitaxon: 2023-06-20 Release (v2023-06-20)'
    year: 2023
  re3data:
    description: The NCBI Taxonomy database is a curated set of names and classifications
      for all of the organisms that are represented in GenBank. The EMBL and DDBJ
      databases, as well as GenBank, now use the NCBI Taxonomy as the standard classification
      for nucleotide sequences. Taxonomy Contains the names and phylogenetic lineages
      of more than 160,000 organisms that have molecular data in the NCBI databases.
      New taxa are added to the Taxonomy database as data are deposited for them.
      When new sequences are submitted to GenBank, the submission is checked for new
      organism names, which are then classified and added to the Taxonomy database.
    doi: 10.17616/R3531R
    homepage: https://www.ncbi.nlm.nih.gov/taxonomy
    name: NCBI Taxonomy
    prefix: r3d100010415
    synonyms:
    - Entrez Taxonomy
    xrefs:
      nif: 0000-03179
  synonyms:
  - NCBI Taxonomy
  - NCBITaxon
  - NCBITaxonomyID
  - NCBI_Taxon_ID
  - NCBI_taxid
  - TAX
  - TaxonomyID
  - ncbiTaxUID
  - taxid
  - taxon
  - taxonomy
  - uniprot.taxonomy
  togoid:
    catalog: nbdc00700
    description: Taxonomy is a database of systematic classifications of organisms
      repesented in public sequencing databases. The database contains phylogenetic
      relatonships and nomenclature for an estimated 10% of all living species. Tools
      include a browser, genetic codes, and a common evolutionary tree. Taxonomic
      classificatinos can be downloaded via FTP.
    examples:
    - '1171376'
    - '484906'
    - '1214242'
    - '1124991'
    - '1037911'
    - '1266844'
    - '243277'
    - '696747'
    - '263820'
    - '713604'
    keywords:
    - Organism
    name: Taxonomy
    pattern: ^(?\d+)$
    prefix: Taxonomy
    uri_format: http://identifiers.org/taxonomy/$1
  uri_format: http://purl.obolibrary.org/obo/NCBITaxon_$1
  wikidata:
    description: identifier for a taxon in the Taxonomy Database by the National Center
      for Biotechnology Information
    example:
    - '9606'
    - '9986'
    homepage: http://www.ncbi.nlm.nih.gov/taxonomy
    name: NCBI taxonomy ID
    pattern: ^[1-9][0-9]{0,6}$
    prefix: P685
    uri_format: https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&id=$1
    uri_format_rdf: http://purl.uniprot.org/taxonomy/$1
nci.drug:
  mappings:
    wikidata: P11623
  prefix: nci.drug
  wikidata:
    description: identifier of an entry in the NCI Drug Dictionary
    example:
    - beta-carotene
    - edatrexate
    - hydroxychloroquine
    - l-carnitine-l-tartrate
    homepage: https://www.cancer.gov/publications/dictionaries/cancer-drug
    name: NCI Drug Dictionary ID
    prefix: P11623
    uri_format: https://www.cancer.gov/publications/dictionaries/cancer-drug/def/$1
ncim:
  biocontext:
    prefix: NCIM
  mappings:
    biocontext: NCIM
    miriam: ncim
    n2t: ncim
  miriam:
    deprecated: false
    description: NCI Metathesaurus (NCIm) is a wide-ranging biomedical terminology
      database that covers most terminologies used by NCI for clinical care, translational
      and basic research, and public information and administrative activities. It
      integrates terms and definitions from different terminologies, including NCI
      Thesaurus, however the representation is not identical.
    homepage: http://ncim.nci.nih.gov/
    id: '00000353'
    name: NCIm
    namespaceEmbeddedInLui: false
    pattern: ^C\d+$
    prefix: ncim
    sampleId: C0026339
    uri_format: http://ncim.nci.nih.gov/ncimbrowser/ConceptReport.jsp?dictionary=NCI%20MetaThesaurus&code=$1
  n2t:
    description: NCI Metathesaurus (NCIm) is a wide-ranging biomedical terminology
      database that covers most terminologies used by NCI for clinical care, translational
      and basic research, and public information and administrative activities. It
      integrates terms and definitions from different terminologies, including NCI
      Thesaurus, however the representation is not identical.
    example: C0026339
    homepage: http://ncim.nci.nih.gov/
    name: NCIm at National Cancer Institue
    namespaceEmbeddedInLui: false
    pattern: ^C\d+$
    prefix: ncim
    uri_format: http://ncim.nci.nih.gov/ncimbrowser/ConceptReport.jsp?dictionary=NCI%20MetaThesaurus&code=$1
  name: NCI Metathesaurus
  owners:
  - name: National Cancer Institute
    partnered: false
    ror: 040gcmg81
    wikidata: null
  prefix: ncim
ncit:
  aberowl:
    description: NCI Thesaurus (NCIt)is a reference terminology that includes broad
      coverage of the cancer domain, including cancer related diseases, findings and
      abnormalities. The NCIt OBO Edition aims to increase integration of the NCIt
      with OBO Library ontologies. NCIt OBO Edition releases should be considered
      experimental.
    download_owl: http://aber-owl.net/media/ontologies/NCIT/79/ncit.owl
    homepage: https://github.com/ncit-obo-org/ncit-obo-edition
    name: NCI Thesaurus OBO Edition
    prefix: NCIT
  biocontext:
    prefix: NCIT
  bioportal:
    contact:
      email: ncithesaurus@mail.nih.gov
      name: NCI Thesaurus Mailbox
    description: Vocabulary for clinical care, translational and basic research, and
      public information and administrative activities.
    homepage: https://ncithesaurus.nci.nih.gov/ncitbrowser/
    name: National Cancer Institute Thesaurus
    prefix: NCIT
    version: 24.01e
  cellosaurus:
    category: Medical resources
    homepage: https://evsexplore.semantics.cancer.gov/evsexplore/welcome
    name: NCI thesaurus
    prefix: NCIt
    uri_format: https://evsexplore.semantics.cancer.gov/evsexplore/concept/ncit/$1
  download_obo: http://purl.obolibrary.org/obo/ncit.obo
  example: C138986
  example_extras:
  - R123
  - A14
  - P320
  fairsharing:
    abbreviation: NCIt
    description: 'NCI Thesaurus (NCIt) provides reference terminology for many NCI
      and other systems. It covers vocabulary for clinical care, translational and
      basic research, and public information and administrative activities. NCIt features:
      stable, unique codes for biomedical concepts; preferred terms, synonyms, research
      codes, external source codes, and other information; over 100,000 textual definitions;
      links to NCI Metathesaurus and other information sources; and over 400,000 cross-links
      between concepts, providing formal logic-based definition of many concepts.
      NCIt is a widely recognized standard for biomedical coding and reference, used
      by a broad variety of public and private partners both nationally and internationally
      including the Clinical Data Interchange Standards Consortium Terminology (CDISC),
      the U.S. Food and Drug Administration (FDA), the Federal Medication Terminologies
      (FMT), and the National Council for Prescription Drug Programs (NCPDP).'
    domains:
    - cancer
    - disease
    homepage: https://ncit.nci.nih.gov
    license: CC-BY-4.0
    name: NCI Thesaurus
    prefix: FAIRsharing.4cvwxa
    publications:
    - doi: 10.3233/978-1-60750-949-3-33
      pubmed: '15360769'
      title: 'NCI Thesaurus: using science-based terminology to integrate cancer research
        results'
      year: 2004
    repository: https://github.com/NCI-Thesaurus/thesaurus-obo-edition
    subjects:
    - Translational Medicine
    - Preclinical Studies
    - Biomedical Science
  hl7:
    description: 'NCI Thesaurus, 2004. Bethesda, MD: National Cancer Institute, National
      Institutes of Health, July 2004.This OID entry has been rejected upon review,
      as the object has already been registered by the NCI (owners).'
    name: NCI Thesaurus
    preferred_prefix: NCI
    prefix: 2.16.840.1.113883.6.206
    status: Rejected
  integbio:
    alt_name: NCI Thesaurus
    description: 'NCI Thesaurus (NCIt) provides reference terminology for many NCI
      and other systems. It covers vocabulary for clinical care, translational and
      basic research, and public information and administrative activities. NCIt features:
      stable, unique codes for biomedical concepts; preferred terms, synonyms, research
      codes, external source codes, and other information; over 100,000 textual definitions;
      links to NCI Metathesaurus and other information sources; and over 400,000 cross-links
      between concepts, providing formal logic-based definition of many concepts.
      NCIt is a widely recognized standard for biomedical coding and reference, used
      by a broad variety of public and private partners both nationally and internationally
      including the Clinical Data Interchange Standards Consortium Terminology (CDISC),
      the U.S. Food and Drug Administration (FDA), the Federal Medication Terminologies
      (FMT), and the National Council for Prescription Drug Programs (NCPDP).'
    homepage: https://ncit.nci.nih.gov
    information_keywords:
    - Ontology/Terminology/Nomenclature
    maintainer: National Cancer Institute at Frederick
    name: NCIt
    prefix: nbdc02651
    status: Active
    target_keywords:
    - Health/Disease
  logo: https://evsexplore.semantics.cancer.gov/evsexplore/assets/images/NCItTile.png
  mappings:
    aberowl: NCIT
    biocontext: NCIT
    bioportal: NCIT
    cellosaurus: NCIt
    fairsharing: FAIRsharing.4cvwxa
    hl7: 2.16.840.1.113883.6.206
    integbio: nbdc02651
    miriam: ncit
    n2t: ncit
    obofoundry: ncit
    ols: ncit
    ontobee: NCIT
    prefixcommons: ncit
    tib: ncit
    wikidata: P1748
    wikidata.entity: Q113012671
  miriam:
    deprecated: false
    description: NCI Thesaurus (NCIt) provides reference terminology covering vocabulary
      for clinical care, translational and basic research, and public information
      and administrative activities, providing a stable and unique identification
      code.
    homepage: https://www.ebi.ac.uk/ols4/ontologies/ncit
    id: 00000139
    name: NCIt
    namespaceEmbeddedInLui: false
    pattern: ^C\d+$
    prefix: ncit
    providers:
    - code: ''
      description: NCIt at National Cancer Institute
      homepage: http://ncit.nci.nih.gov/
      name: NCIt at National Cancer Institute
      uri_format: http://ncit.nci.nih.gov/ncitbrowser/ConceptReport.jsp?dictionary=NCI%20Thesaurus&code=$1
    sampleId: C80519
    uri_format: https://www.ebi.ac.uk/ols4/ontologies/ncit/terms?short_form=NCIT_$1
  n2t:
    description: NCI Thesaurus (NCIt) provides reference terminology covering vocabulary
      for clinical care, translational and basic research, and public information
      and administrative activities, providing a stable and unique identification
      code.
    example: C80519
    homepage: http://ncit.nci.nih.gov/
    name: NCIt at National Cancer Institute
    namespaceEmbeddedInLui: false
    pattern: ^C\d+$
    prefix: ncit
    uri_format: http://ncit.nci.nih.gov/ncitbrowser/ConceptReport.jsp?dictionary=NCI%20Thesaurus&code=$1
  name: NCI Thesaurus
  obofoundry:
    appears_in:
    - ecto
    - mco
    - ontoavida
    - scdo
    deprecated: false
    description: NCI Thesaurus (NCIt)is a reference terminology that includes broad
      coverage of the cancer domain, including cancer related diseases, findings and
      abnormalities. The NCIt OBO Edition aims to increase integration of the NCIt
      with OBO Library ontologies. NCIt OBO Edition releases should be considered
      experimental.
    domain: health
    download.obo: http://purl.obolibrary.org/obo/ncit.obo
    download.owl: http://purl.obolibrary.org/obo/ncit.owl
    homepage: https://github.com/ncit-obo-org/ncit-obo-edition
    license: CC BY 4.0
    license.url: https://creativecommons.org/licenses/by/4.0/
    name: NCI Thesaurus OBO Edition
    preferredPrefix: NCIT
    prefix: ncit
    repository: https://github.com/ncit-obo-org/ncit-obo-edition
  ols:
    description: NCI Thesaurus (NCIt)is a reference terminology that includes broad
      coverage of the cancer domain, including cancer related diseases, findings and
      abnormalities. The NCIt OBO Edition aims to increase integration of the NCIt
      with OBO Library ontologies. NCIt OBO Edition releases should be considered
      experimental.
    download_owl: http://purl.obolibrary.org/obo/ncit.owl
    homepage: https://github.com/ncit-obo-org/ncit-obo-edition
    name: NCI Thesaurus OBO Edition
    prefix: ncit
    tracker: https://github.com/ncit-obo-org/ncit-obo-edition/issues
    version: '2025-08-06'
    version.iri: http://purl.obolibrary.org/obo/ncit/releases/2025-08-06/ncit.owl
  ontobee:
    library: Library
    name: NCI Thesaurus OBO Edition
    prefix: NCIT
  owners:
  - name: National Cancer Institute
    partnered: false
    ror: 040gcmg81
    wikidata: null
  pattern: ^[CRPA]\d+$
  prefix: ncit
  prefixcommons:
    bioportal: '1032'
    description: A vocabulary for clinical care, translational and basic research,
      and public information and administrative activities.
    example: C80519
    homepage: https://cabig.nci.nih.gov/community/concepts/EVS/
    keywords:
    - thesaurus
    name: NCI Thesaurus
    pattern: ^C\d+$
    prefix: ncit
    pubmed_ids:
    - '19789731'
    rdf_uri_format: http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#$1
    synonyms:
    - ncithesaurus
    - nci
    - nci2009_04d
    - nci_thesaurus_code
    uri_format: http://ncit.nci.nih.gov/ncitbrowser/ConceptReport.jsp?dictionary=NCI%20Thesaurus&code=$1
  providers:
  - code: evs
    description: Links to a no-longer existing OWL file
    example: null
    first_party: null
    homepage: https://ncit.nci.nih.gov/ncitbrowser/
    name: Legacy NCBI OWL
    publications: null
    status: null
    uri_format: http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#$1
  publications:
  - doi: 10.3233/ao-2008-0051
    pmc: PMC2753293
    pubmed: '19789731'
    title: 'Representing the NCI Thesaurus in OWL DL: Modeling tools help modeling
      languages'
    year: 2008
  - doi: 10.3233/978-1-60750-949-3-33
    pmc: null
    pubmed: '15360769'
    title: 'NCI Thesaurus: using science-based terminology to integrate cancer research
      results'
    year: 2004
  - doi: 10.3233/978-1-60750-949-3-33
    pmc: null
    pubmed: '15360769'
    title: 'NCI Thesaurus: using science-based terminology to integrate cancer research
      results'
    year: 2004
  - doi: null
    pmc: null
    pubmed: '19789731'
    title: null
    year: null
  - doi: 10.3233/978-1-60750-949-3-33
    pmc: null
    pubmed: '15360769'
    title: 'NCI Thesaurus: using science-based terminology to integrate cancer research
      results'
    year: 2004
  - doi: null
    pmc: null
    pubmed: '19789731'
    title: null
    year: null
  synonyms:
  - NCI
  - NCI2004_11_17
  - NCIT
  - NCIT_Thesaurus
  - NCIThesaurus
  - NCITm
  - NCITt
  - NCI_Thesaurus
  - NCIt
  - NCit
  - ncithesaurus
  tib:
    description: NCI Thesaurus (NCIt)is a reference terminology that includes broad
      coverage of the cancer domain, including cancer related diseases, findings and
      abnormalities. The NCIt OBO Edition aims to increase integration of the NCIt
      with OBO Library ontologies. NCIt OBO Edition releases should be considered
      experimental.
    download_owl: http://purl.obolibrary.org/obo/ncit.owl
    homepage: https://github.com/NCI-Thesaurus/thesaurus-obo-edition
    keywords:
    - NFDI4CHEM
    - DataPLANT
    - life sciences, biology
    name: NCI Thesaurus OBO Edition
    prefix: ncit
    tracker: https://github.com/NCI-Thesaurus/thesaurus-obo-edition/issues
    version.iri: http://purl.obolibrary.org/obo/ncit/releases/2025-08-06/ncit.owl
  uri_format: http://purl.obolibrary.org/obo/NCIT_$1
  wikidata:
    description: identifier in the United States National Cancer Institute Thesaurus,
      vocabulary for clinical care, translational and basic research, etc
    example:
    - C120871
    - C12431
    - C75016
    homepage: http://ncit.nci.nih.gov/ncitbrowser/ConceptReport.jsp?dictionary=NCI_Thesaurus&version=14.10d&code=C75016
    name: NCI Thesaurus ID
    pattern: ^C\d{3,7}$
    prefix: P1748
    uri_format: https://evsexplore.semantics.cancer.gov/evsexplore/concept/ncit/$1
    uri_format_rdf: http://purl.obolibrary.org/obo/NCIT_$1
ncro:
  aberowl:
    description: An ontology for non-coding RNA, both of biological origin, and engineered.
    download_owl: http://aber-owl.net/media/ontologies/NCRO/13/ncro.owl
    homepage: http://omnisearch.soc.southalabama.edu/OntologyFile.aspx
    name: Non-Coding RNA Ontology
    prefix: NCRO
  biocontext:
    prefix: NCRO
  bioportal:
    contact:
      email: huang@southalabama.edu
      name: Jingshan Huang
    description: The NCRO is a reference ontology in the non-coding RNA (ncRNA) field,
      aiming to provide a common set of terms and relations that will facilitate the
      curation, analysis, exchange, sharing, and management of ncRNA structural, functional,
      and sequence data.
    name: Non-coding RNA Ontology
    prefix: NCRO
    version: Working version 06102015
  download_obo: https://raw.githubusercontent.com/OmniSearch/ncro/master/src/ontology/ncro.obo
  download_owl: http://purl.obolibrary.org/obo/ncro.owl
  example: 0002927
  fairsharing:
    abbreviation: NCRO
    description: The NCRO is a reference ontology in the non-coding RNA (ncRNA) field,
      aiming to provide a common set of terms and relations that will facilitate the
      curation, analysis, exchange, sharing, and management of ncRNA structural, functional,
      and sequence data.
    domains:
    - ncRNA
    homepage: http://bioportal.bioontology.org/ontologies/NCRO
    name: Non-coding RNA Ontology
    prefix: FAIRsharing.vppyga
    publications:
    - doi: 10.1186/s13326-016-0066-0
      title: 'The Non-Coding RNA Ontology (NCRO): a comprehensive resource for the
        unification of non-coding RNA biology'
      year: 2016
    subjects:
    - Genomics
  mappings:
    aberowl: NCRO
    biocontext: NCRO
    bioportal: NCRO
    fairsharing: FAIRsharing.vppyga
    obofoundry: ncro
    ols: ncro
    ontobee: NCRO
    wikidata.entity: Q55118485
  obofoundry:
    contact: huang@southalabama.edu
    contact.github: Huang-OMIT
    contact.label: Jingshan Huang
    contact.orcid: 0000-0003-2408-2883
    deprecated: false
    description: An ontology for non-coding RNA, both of biological origin, and engineered.
    domain: investigations
    homepage: http://omnisearch.soc.southalabama.edu/w/index.php/Ontology
    license: CC BY 4.0
    license.url: https://creativecommons.org/licenses/by/4.0/
    name: Non-Coding RNA Ontology
    preferredPrefix: NCRO
    prefix: ncro
    repository: https://github.com/OmniSearch/ncro
  ols:
    description: An ontology for non-coding RNA, both of biological origin, and engineered.
    download_owl: http://purl.obolibrary.org/obo/ncro.owl
    homepage: http://omnisearch.soc.southalabama.edu/w/index.php/Ontology
    name: Non-Coding RNA Ontology
    prefix: ncro
    tracker: https://github.com/OmniSearch/ncro/issues
    version.iri: http://purl.obolibrary.org/obo/ncro/2015-12-10/ncro-combined.owl
  ontobee:
    library: Library
    name: Non-Coding RNA Ontology
    prefix: NCRO
  pattern: ^\d{7}$
  prefix: ncro
  publications:
  - doi: 10.1186/s13326-016-0066-0
    pmc: PMC4857245
    pubmed: '27152146'
    title: 'The Non-Coding RNA Ontology (NCRO): a comprehensive resource for the unification
      of non-coding RNA biology'
    year: 2016
  - doi: 10.1186/s13326-016-0066-0
    pmc: null
    pubmed: null
    title: 'The Non-Coding RNA Ontology (NCRO): a comprehensive resource for the unification
      of non-coding RNA biology'
    year: 2016
  uri_format: http://purl.obolibrary.org/obo/NCRO_$1
ndc:
  biocontext:
    prefix: NDC
  hl7:
    description: National Drug Codes System (which includes both the National Drug
      Codes (NDC) and the National Health Related Item Codes (NHRIC)).
    homepage: http://www.fda.gov/ForIndustry/DataStandards/default.htm
    name: National Drug Codes System
    organization: FDA Data Standards Council
    preferred_prefix: ndc
    prefix: 2.16.840.1.113883.6.69
    status: Complete
  mappings:
    biocontext: NDC
    hl7: 2.16.840.1.113883.6.69
    miriam: ndc
    n2t: ndc
    wikidata: P3640
    wikidata.entity: Q6972354
  miriam:
    deprecated: false
    description: The National Drug Code (NDC) is a unique, three-segment number used
      by the Food and Drug Administration (FDA) to identify drug products for commercial
      use. This is required by the Drug Listing Act of 1972. The FDA publishes and
      updates the listed NDC numbers daily.
    homepage: http://www.accessdata.fda.gov/scripts/cder/ndc/
    id: '00000431'
    name: National Drug Code
    namespaceEmbeddedInLui: false
    pattern: ^\d+\-\d+\-\d+$
    prefix: ndc
    providers:
    - code: ''
      description: Bio2RDF
      homepage: http://bio2rdf.org
      name: Bio2RDF
      uri_format: http://bio2rdf.org/ndc:$1
    sampleId: 0002-1975-61
    uri_format: http://www.hipaaspace.com/Medical_Billing/Coding/National.Drug.Codes/$1
  n2t:
    description: The National Drug Code (NDC) is a unique, three-segment number used
      by the Food and Drug Administration (FDA) to identify drug products for commercial
      use. This is required by the Drug Listing Act of 1972. The FDA publishes and
      updates the listed NDC numbers daily.
    example: 0002-1975-61
    homepage: http://www.accessdata.fda.gov/scripts/cder/ndc/
    name: National Drug Code at Food and Drug Administration
    namespaceEmbeddedInLui: false
    pattern: ^\d+\-\d+\-\d+
    prefix: ndc
    uri_format: http://www.hipaaspace.com/Medical_Billing/Coding/National.Drug.Codes/$1
  prefix: ndc
  wikidata:
    database: Q6972354
    description: pharmaceutical code issued by the Food and Drug Administration for
      every drug product (formulation) on the U.S. market. Includes a labeler code,
      product code and package code, unique for every drug product.
    example:
    - 0009-0417
    - 0037-6824
    - 50242-090
    homepage: https://www.nlm.nih.gov/research/umls/rxnorm/docs/rxnormfiles.html
    name: National Drug Code
    prefix: P3640
    uri_format: https://ndclist.com/ndc/$1
nddf:
  aberowl:
    description: National Drug Data File Plus Source Vocabulary
    name: National Drug Data File
    prefix: NDDF
    version: 2016AB
  biolink:
    is_identifiers: false
    is_obo: false
    prefix: NDDF
    uri_format: http://purl.bioontology.org/ontology/NDDF/$1
  bioportal:
    contact:
      email: cs@firstdatabank.com
      name: First DataBank Customer Support
    description: FDB MedKnowledge, formerly National Drug Data File (NDDF) Plus Source
      Vocabulary <p>FDB MedKnowledge encompasses medications approved by the U.S.
      Food and Drug Administration, and information on commonly-used over-the-counter
      and alternative therapy agents such as herbals, nutraceuticals and dietary supplements.</p>
    homepage: http://www.fdbhealth.com/fdb-medknowledge/
    name: National Drug Data File
    prefix: NDDF
    version: NDDF_2024_08_14
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: FDB MedKnowledge encompasses medications approved by the U.S. Food
    and Drug Administration, and information on commonly-used over-the-counter and
    alternative therapy agents such as herbals, nutraceuticals and dietary supplements.
  example: 002678
  fairsharing:
    abbreviation: NDDF
    description: The National Drug Data File vocabulary supports clinical research
      and patient care. Please note that we have been unable to confirm the current
      status of NDDF and its relationship with FDB MedKnowledge. Until that time,
      the FAIRsharing team has marked this resource as having an Uncertain status.
      Please get in touch if you have any information.
    domains:
    - drug
    - chemical entity
    homepage: http://bioportal.bioontology.org/ontologies/1424
    name: National Drug Data File
    prefix: FAIRsharing.8qcbs0
    subjects:
    - Medicinal Chemistry
    - Biomedical Science
  hl7:
    description: 'National Drug Data File Plus Source Vocabulary 2004. San Bruno,
      CA: First DataBank, March 11, 2004.This entry was generated to support the Sources
      in the UMLS.  Additional metadata is still missing.'
    name: National Drug Data File
    preferred_prefix: nddf
    prefix: 2.16.840.1.113883.6.208
    status: Complete
  homepage: https://www.nlm.nih.gov/research/umls/sourcereleasedocs/current/NDDF
  license: https://uts.nlm.nih.gov/uts/assets/LicenseAgreement.pdf
  mappings:
    aberowl: NDDF
    biolink: NDDF
    bioportal: NDDF
    fairsharing: FAIRsharing.8qcbs0
    hl7: 2.16.840.1.113883.6.208
  name: National Drug Data File
  pattern: ^\d{6}$
  prefix: nddf
  uri_format: http://purl.bioontology.org/ontology/NDDF/$1
ndex:
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: The Network Data Exchange (NDEx) is an open-source framework where
    scientists and organizations can store, share, manipulate, and publish biological
    network knowledge.
  example: aa78a43f-9c4d-11eb-9e72-0ac135e8bacf
  fairsharing:
    abbreviation: NDEx
    contact:
      email: rpillich@ucsd.edu
      name: Rudolf T. Pillich
      orcid: 0000-0001-8682-0568
    description: NDEx is an online commons where scientists can upload, share, and
      publicly distribute biological networks and pathway models. The NDEx Project
      maintains a web-accessible public server, a documentation website, provides
      seamless connectivity to Cytoscape as well as programmatic access using a variety
      of languages including Python and Java and R. NDEx users can easily create accounts
      or sign in using their Google credentials thanks to the supported open authentication
      (OAUTH2) method and mint DOIs for their networks to use in publications or include
      in other resources for long term access.
    homepage: https://www.ndexbio.org
    license: https://www.home.ndexbio.org/disclaimer-license
    name: The Network Data Exchange
    prefix: FAIRsharing.8nq9t6
    publications:
    - doi: 10.1007/978-1-4939-6783-4_13
      pubmed_id: 28150243
      title: 'NDEx: A Community Resource for Sharing and Publishing of Biological
        Networks.'
    - doi: 10.1016/j.cels.2015.10.001
      pubmed_id: 26594663
      title: NDEx, the Network Data Exchange.
    - doi: 10.1158/0008-5472.CAN-17-0606
      pubmed_id: 29092941
      title: 'NDEx 2.0: A Clearinghouse for Research on Cancer Pathways.'
    - doi: 10.1002/cpz1.258
      pubmed_id: null
      title: 'NDEx: Accessing Network Models and Streamlining Network Biology Workflows'
    repository: https://github.com/ndexbio
    subjects:
    - Life Science
    - Microbiology
    - Epidemiology
    twitter: NDExProject
  homepage: https://www.ndexbio.org
  mappings:
    fairsharing: FAIRsharing.8nq9t6
    re3data: r3d100012690
  name: Network Data Exchange
  prefix: ndex
  publications:
  - doi: 10.1002/cpz1.258
    pmc: PMC8544027
    pubmed: '34570431'
    title: 'NDEx: Accessing Network Models and Streamlining Network Biology Workflows'
    year: 2021
  - doi: 10.1158/0008-5472.can-17-0606
    pmc: PMC5679399
    pubmed: '29092941'
    title: 'NDEx 2.0: A Clearinghouse for Research on Cancer Pathways'
    year: 2017
  - doi: 10.1007/978-1-4939-6783-4_13
    pmc: null
    pubmed: '28150243'
    title: 'NDEx: A Community Resource for Sharing and Publishing of Biological Networks'
    year: 2017
  - doi: 10.1016/j.cels.2015.10.001
    pmc: PMC4649937
    pubmed: '26594663'
    title: NDEx, the Network Data Exchange
    year: 2015
  re3data:
    description: 'The NDEx Project provides an open-source framework where scientists
      and organizations can share, store, manipulate, and publish biological network
      knowledge.

      The NDEx Project maintains a free, public website; alternatively, users can
      also decide to run their own copies of the NDEx Server software in cases where
      the stored networks must be kept in a highly secure environment (such as for
      HIPAA compliance) or where high application load is incompatible with a shared
      public resource.'
    doi: 10.17616/R31NJMAA
    homepage: https://home.ndexbio.org/index/
    license: BSD
    name: Network Data Exchange
    prefix: r3d100012690
    synonyms:
    - NDEx
  uri_format: https://www.ndexbio.org/viewer/networks/$1
ndfrt:
  aberowl:
    description: National Drug File - Reference Terminology Public Inferred Edition,
      2008_03_11
    homepage: http://www.va.gov
    name: National Drug File - Reference Terminology
    prefix: NDFRT
    version: 2016AB
  bioportal:
    contact:
      email: michael.lincoln@va.gov
      name: Michael J. Lincoln MD
    description: National Drug File - Reference Terminology Public Inferred Edition,
      2008_03_11
    homepage: http://www.va.gov
    name: National Drug File - Reference Terminology
    prefix: NDFRT
    publications:
    - http://www.va.gov
    version: NDFRT_2018_02_05_18_03_05
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: 'NDF-RT combines the NDF hierarchical drug classification with a multi-category
    reference model. The categories are: Cellular or Molecular Interactions [MoA];
    Chemical Ingredients [Chemical/Ingredient]; Clinical Kinetics [PK]; Diseases,
    Manifestations or Physiologic States [Disease/Finding]Dose Forms [Dose Form];
    Pharmaceutical Preparations; Physiological Effects [PE]; Therapeutic Categories
    [TC]; and VA Drug Interactions [VA Drug Interaction].'
  example: N0000001662
  fairsharing:
    abbreviation: NDFRT
    description: The National Drug File Reference Terminology contains a novel reference
      hierarchy to describe physiologic effects (PE) of drugs.
    domains:
    - Drug name
    - chemical entity
    homepage: http://bioportal.bioontology.org/ontologies/NDFRT
    name: National Drug File
    prefix: FAIRsharing.901nkj
    publications:
    - pubmed: '14728237'
      title: Adequacy of representation of the National Drug File Reference Terminology
        Physiologic Effects reference hierarchy for commonly prescribed medications
      year: 2004
    subjects:
    - Physiology
    - Biomedical Science
    - Health Science
    - Medicine
  hl7:
    description: 'National Drug File - Reference Terminology, 2004_01. Washington,
      DC: U.S. Department of Veterans Affairs, Veterans Health Administration, January
      2004.'
    name: National Drug File - Reference Terminology
    preferred_prefix: NDFRT
    prefix: 2.16.840.1.113883.6.209
    status: Pending
  homepage: https://www.nlm.nih.gov/research/umls/sourcereleasedocs/current/NDFRT
  mappings:
    aberowl: NDFRT
    bioportal: NDFRT
    fairsharing: FAIRsharing.901nkj
    hl7: 2.16.840.1.113883.6.209
    ontobee: NDF-RT
    prefixcommons: ndfrt
    wikidata: P2115
  name: National Drug File - Reference Terminology
  ontobee:
    library: Not Specified/No
    name: National Drug File Reference Terminology
    prefix: NDF-RT
  prefix: ndfrt
  prefixcommons:
    bioportal: '1352'
    description: National Drug File - Reference Terminology Public Inferred Edition,
      2008_03_11
    example: N0000175600
    homepage: http://www.va.gov
    name: National Drug File
    pattern: ^N\d+$
    prefix: ndfrt
    rdf_uri_format: http://purl.bioontology.org/ontology/NDFRT/$1
  publications:
  - doi: null
    pmc: PMC1480331
    pubmed: '14728237'
    title: Adequacy of representation of the National Drug File Reference Terminology
      Physiologic Effects reference hierarchy for commonly prescribed medications
    year: 2003
  - doi: null
    pmc: null
    pubmed: '14728237'
    title: Adequacy of representation of the National Drug File Reference Terminology
      Physiologic Effects reference hierarchy for commonly prescribed medications
    year: 2004
  - doi: null
    pmc: null
    pubmed: '14728237'
    title: Adequacy of representation of the National Drug File Reference Terminology
      Physiologic Effects reference hierarchy for commonly prescribed medications
    year: 2004
  - doi: null
    pmc: null
    pubmed: '14728237'
    title: Adequacy of representation of the National Drug File Reference Terminology
      Physiologic Effects reference hierarchy for commonly prescribed medications
    year: 2004
  - doi: null
    pmc: null
    pubmed: '14728237'
    title: Adequacy of representation of the National Drug File Reference Terminology
      Physiologic Effects reference hierarchy for commonly prescribed medications
    year: 2004
  synonyms:
  - NUI
  - ndf-rt
  uri_format: https://ncit.nci.nih.gov/ncitbrowser/ConceptReport.jsp?dictionary=NDFRT&code=$1
  wikidata:
    description: identifier for the National Drug File Reference Terminology
    example:
    - N0000146291
    - N0000147795
    - N0000183250
    homepage: https://rxnav.nlm.nih.gov/
    name: NDF-RT ID
    pattern: ^N[0-9]{10}$
    prefix: P2115
    uri_format: https://bioportal.bioontology.org/ontologies/NDFRT?p=classes&conceptid=$1
    uri_format_rdf: http://purl.bioontology.org/ontology/NDFRT/$1
nembase:
  comment: This resource doesn't exist on the web anymore
  deprecated: true
  mappings:
    prefixcommons: nembase
  prefix: nembase
  prefixcommons:
    description: NEMBASE is a comprehensive Nematode Transcriptome Database. NEMBASE4
      includes robust protein predictions (NemPep4), and protein families for 63 nematode
      species, over 600,000 ESTs and over 250,000 proteins.
    example: NBC00001
    homepage: http://www.nematodes.org
    keywords:
    - RNA
    - protein
    - DNA
    name: Nematode & Neglected Genomics
    pattern: ^NBC\d+$
    prefix: nembase
    uri_format: http://www.nematodes.org/nembase4/cluster.php?cluster=$1
  reviewer:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
nemo:
  mappings:
    miriam: nemo
  miriam:
    deprecated: false
    description: This namespace is about Neuroscience Multi-Omic data, specially focused
      on that data generated from the BRAIN Initiative and related brain research
      projects.
    homepage: https://www.nemoarchive.org
    id: '00000744'
    name: Neuroscience Multi-Omic BRAIN Initiative Data
    namespaceEmbeddedInLui: false
    pattern: ^[a-z]{3}-[a-km-z0-9]{7}$
    prefix: nemo
    sampleId: smp-m3w9hbe
    uri_format: https://assets.nemoarchive.org/$1
  prefix: nemo
nemo.competence:
  contact:
    email: null
    github: jpalmeida
    name: João Paulo A. Almeida
    orcid: null
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: A small ontology expressing skills and competencies.
  download_rdf: https://github.com/jpalmeida/competence-ontology/raw/refs/heads/main/competence.ttl
  example: CognitiveCompetence
  github_request_issue: 1704
  homepage: https://github.com/jpalmeida/competence-ontology
  keywords:
  - competence
  - ontology
  - skills
  license: CC-BY-4.0
  name: Competence Ontology
  prefix: nemo.competence
  publications:
  - doi: 10.1109/edoc52215.2021.00018
    pmc: null
    pubmed: null
    title: Towards Ontology-based Competence Modeling in Enterprise Architecture
    year: 2021
  rdf_uri_format: http://purl.org/nemo/competence#$1
  repository: https://github.com/jpalmeida/competence-ontology
  uri_format: http://purl.org/nemo/competence#$1
nemo2:
  aberowl:
    description: 'Neural ElectroMagnetic Ontology (NEMO) describes classes of event-related
      brain potentials (ERP) and their properties, including spatial, temporal, and
      functional (cognitive/behavioral) attributes, and data-level attributes (acquisition
      and analysis parameters). Working (unstable), Release (stable), and Old (archival)
      versions of NEMO can be found on sourceforge: http://sourceforge.net/projects/nemoontologies/.'
    download_owl: http://aber-owl.net/media/ontologies/NEMO/24/nemo.owl
    homepage: http://nemo.nic.uoregon.edu
    name: Neural ElectroMagnetic Ontology
    prefix: NEMO
    version: v3.10
  bioportal:
    contact:
      email: gfrishkoff@gsu.edu
      name: Gwen Frishkoff
    description: 'Neural ElectroMagnetic Ontology (NEMO) describes classes of event-related
      brain potentials (ERP) and their properties, including spatial, temporal, and
      functional (cognitive/behavioral) attributes, and data-level attributes (acquisition
      and analysis parameters). Working (unstable), Release (stable), and Old (archival)
      versions of NEMO can be found on sourceforge: http://sourceforge.net/projects/nemoontologies/.'
    homepage: http://nemo.nic.uoregon.edu
    name: Neural ElectroMagnetic Ontology
    prefix: NEMO
    publications:
    - http://nemo.nic.uoregon.edu/wiki/Publications
    version: v3.10
  contact:
    email: gfrishkoff@gsu.edu
    github: null
    name: Gwen Frishkoff
    orcid: 0000-0003-0612-0970
  example: 0000196
  fairsharing:
    abbreviation: NEMO
    description: Neural ElectroMagnetic Ontology (NEMO) describes classes of event-related
      brain potentials (ERP) and their properties, including spatial, temporal, and
      functional (cognitive/behavioral) attributes, and data-level attributes (acquisition
      and analysis parameters). FAIRsharing curators have been unable to contact the
      project developers, and as such this record has been marked as Uncertain. Please
      contact us if you have any information on this resource.
    domains:
    - Imaging
    - neuron
    - cognition
    - electroencephalography
    - brain
    homepage: http://aimlab.cs.uoregon.edu/NEMO/web/index.html
    name: Neural ElectroMagnetic Ontologies
    prefix: FAIRsharing.n66krd
    publications:
    - doi: 10.4056/sigs.2025347
      pubmed: '22180824'
      title: 'Minimal Information for Neural Electromagnetic Ontologies (MINEMO):
        A standards-compliant method for analysis and integration of event-related
        potentials (ERP) data'
      year: 2011
    - doi: 10.1038/npre.2009.3458.1
      title: 'Development of Neural Electromagnetic Ontologies (NEMO): Ontology-based
        Tools for Representation and Integration of Event-related Brain Potentials'
      year: 2009
    subjects:
    - Life Science
    - Neurobiology
    - Cognitive Neuroscience
  mappings:
    aberowl: NEMO
    bioportal: NEMO
    fairsharing: FAIRsharing.n66krd
  prefix: nemo2
  publications:
  - doi: 10.4056/sigs.2025347
    pmc: PMC3235514
    pubmed: '22180824'
    title: 'Minimal Information for Neural Electromagnetic Ontologies (MINEMO): A
      standards-compliant method for analysis and integration of event-related potentials
      (ERP) data'
    year: 2011
  - doi: 10.1038/npre.2009.3458.1
    pmc: null
    pubmed: null
    title: 'Development of Neural Electromagnetic Ontologies (NEMO): Ontology-based
      Tools for Representation and Integration of Event-related Brain Potentials'
    year: 2009
  uri_format: http://purl.bioontology.org/NEMO/ontology/NEMO.owl#NEMO_$1
nepomuk.nao:
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: The annotation ontology provides vocabulary that enables users to attach
    custom descriptions, identifiers, tags and ratings to resources on their desktop.
    Via other properties, the user is also able to make generic relationships between
    related resources explicit. Some relationships between resources are too general
    to be included at the domain ontology level. Instead, these properties are also
    defined in the annotation ontology. Given the high-level status of this ontology,
    these propreties can be used to link any related resources on the user's desktop,
    as well as provide custom human-readable textual annotations. (from homepage)
  example: created
  homepage: http://www.semanticdesktop.org/ontologies/nao
  license: https://www.semanticdesktop.org/ontologies/2007/11/01/pimo/LICENSE.txt
  name: NEPOMUK Annotation Ontology Specification
  prefix: nepomuk.nao
  rdf_uri_format: http://www.semanticdesktop.org/ontologies/2007/08/15/nao#$1
  uri_format: http://www.semanticdesktop.org/ontologies/2007/08/15/nao#$1
nepomuk.nco:
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: NEPOMUK Contact Ontology describes contact information, common in many
    places on the desktop. It evolved from the VCARD specification (RFC 2426) and
    has been inspired by the Vcard Ontology by Renato Ianella. The scope of NCO is
    much broader though. This document gives an overview of the classes, properties
    and intended use cases of the NCO ontology. (from homepage)
  example: fullname
  homepage: http://www.semanticdesktop.org/ontologies/2007/03/22/nco
  license: https://www.semanticdesktop.org/ontologies/2007/11/01/pimo/LICENSE.txt
  name: NEPOMUK Contact Ontology
  prefix: nepomuk.nco
  rdf_uri_format: http://www.semanticdesktop.org/ontologies/2007/03/22/nco#$1
  uri_format: http://www.semanticdesktop.org/ontologies/2007/03/22/nco#$1
nepomuk.pimo:
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: The PIMO Ontology can be used to express Personal Information Models
    of individuals. It is based on RDF and NRL, the NEPOMUK Representational Language
    and other Semantic Web ontologies. This document describes the principle elements
    of the language and how to use them. (from homepage)
  example: Note
  homepage: http://www.semanticdesktop.org/ontologies/pimo
  license: https://www.semanticdesktop.org/ontologies/2007/11/01/pimo/LICENSE.txt
  name: Personal Information Model
  prefix: nepomuk.pimo
  rdf_uri_format: http://www.semanticdesktop.org/ontologies/2007/11/01/pimo#$1
  uri_format: http://www.semanticdesktop.org/ontologies/2007/11/01/pimo#$1
neurolex:
  biocontext:
    prefix: NEUROLEX
  contact:
    email: tgbugs@gmail.com
    github: tgbugs
    name: Tom Gillespie
    orcid: 0000-0002-7509-4801
  example: '4'
  homepage: https://github.com/SciCrunch/NIF-Ontology
  license: CC BY-4.0
  mappings:
    biocontext: NEUROLEX
    miriam: neurolex
    n2t: neurolex
    prefixcommons: neurolex
  miriam:
    deprecated: false
    description: The NeuroLex project is a dynamic lexicon of terms used in neuroscience.  It
      is supported by the Neuroscience Information Framework project and incorporates
      information from the NIF standardised ontology (NIFSTD), and its predecessor,
      the Biomedical Informatics Research Network Lexicon (BIRNLex).
    homepage: https://scicrunch.org/scicrunch/interlex/dashboard
    id: '00000126'
    name: NeuroLex
    namespaceEmbeddedInLui: false
    pattern: ^([Bb]irnlex_|Sao|nlx_|GO_|CogPO|HDO|nifext_)\d+$
    prefix: neurolex
    sampleId: Birnlex_721
    uri_format: https://scicrunch.org/scicrunch/interlex/search?q=$1
  n2t:
    description: The NeuroLex project is a dynamic lexicon of terms used in neuroscience.  It
      is supported by the Neuroscience Information Framework project and incorporates
      information from the NIF standardised ontology (NIFSTD), and its predecessor,
      the Biomedical Informatics Research Network Lexicon (BIRNLex).
    example: Birnlex_721
    homepage: http://www.neurolex.org/wiki/Main_Page
    name: NeuroLex Neuroscience Lexicon
    namespaceEmbeddedInLui: false
    pattern: ^([Bb]irnlex_|Sao|nlx_|GO_|CogPO|HDO|nifext_)\d+$
    prefix: neurolex
    uri_format: http://www.neurolex.org/wiki/$1
  name: 'NIF Standard Ontology: Neurolex'
  part_of_database: nif
  pattern: ^\d+$
  prefix: neurolex
  prefixcommons:
    description: The NeuroLex project is a dynamic lexicon of terms used in neuroscience.  It
      is supported by the Neuroscience Information Framework project and incorporates
      information from the NIF standardised ontology (NIFSTD), and its predecessor,
      the Biomedical Informatics Research Network Lexicon (BIRNLex).
    example: Birnlex_721
    homepage: http://www.neurolex.org/wiki/Main_Page
    keywords:
    - classification
    - neuroscience
    - ontology
    name: NeuroLex
    pattern: ^([Bb]irnlex_|Sao|nlx_|GO_|CogPO|HDO)\d+$
    prefix: neurolex
    pubmed_ids:
    - '18975148'
    uri_format: http://www.neurolex.org/wiki/$1
  publications:
  - doi: 10.1007/s12021-008-9032-z
    pmc: PMC2743139
    pubmed: '18975148'
    title: 'The NIFSTD and BIRNLex vocabularies: building comprehensive ontologies
      for neuroscience'
    year: 2008
  - doi: null
    pmc: null
    pubmed: '18975148'
    title: null
    year: null
  repository: https://github.com/SciCrunch/NIF-Ontology
  synonyms:
  - NLX
  - nlx
  twitter: SciCrunch
  uri_format: http://uri.neuinfo.org/nif/nifstd/nlx_$1
neuromorpho:
  biocontext:
    prefix: NEUROMORPHO
  contact:
    email: Ascoli@gmu.edu
    github: null
    name: Giorgio Ascoli
    orcid: 0000-0002-0964-676X
  edam:
    description: A unique identifier of a neuron from the NeuroMorpho database.
    name: NeuroMorpho
    obsolete: false
    prefix: '2657'
  mappings:
    biocontext: NEUROMORPHO
    edam: '2657'
    miriam: neuromorpho
    n2t: neuromorpho
    prefixcommons: neuromorpho
  miriam:
    deprecated: false
    description: NeuroMorpho.Org is a centrally curated inventory of  digitally reconstructed
      neurons.
    homepage: http://neuromorpho.org/index.jsp
    id: 00000095
    name: NeuroMorpho
    namespaceEmbeddedInLui: false
    pattern: ^\w+$
    prefix: neuromorpho
    sampleId: Rosa2
    uri_format: http://neuromorpho.org/neuron_info.jsp?neuron_name=$1
  n2t:
    description: NeuroMorpho.Org is a centrally curated inventory of  digitally reconstructed
      neurons.
    example: Rosa2
    homepage: http://neuromorpho.org/index.jsp
    name: NeuroMorpho
    namespaceEmbeddedInLui: false
    pattern: ^\w+$
    prefix: neuromorpho
    uri_format: http://neuromorpho.org/neuron_info.jsp?neuron_name=$1
  prefix: neuromorpho
  prefixcommons:
    description: NeuroMorpho.Org is a centrally curated inventory of digitally reconstructed
      neurons.
    example: Rosa2
    homepage: http://neuromorpho.org/neuroMorpho/index.jsp
    keywords:
    - anatomy
    - structure
    license: CC-BY-3.0
    name: NeuroMorpho
    pattern: ^\w+$
    prefix: neuromorpho
    pubmed_ids:
    - '16552417'
    uri_format: http://neuromorpho.org/neuroMorpho/neuron_info.jsp?neuron_name=$1
  publications:
  - doi: 10.1038/nrn1885
    pmc: null
    pubmed: '16552417'
    title: 'Mobilizing the base of neuroscience data: the case of neuronal morphologies'
    year: 2006
neuronames:
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: BrainInfo is designed to help you identify structures in the brain.
    If you provide the name of a structure, BrainInfo will show it and tell you about
    it.
  example: '268'
  homepage: http://braininfo.rprc.washington.edu/
  mappings:
    wikidata: P4394
    wikidata.entity: Q1773567
  name: NeuroNames
  pattern: ^\d+$
  prefix: neuronames
  providers:
  - code: neuronames.alt1
    description: Alternate URI inside neuronames, appearning in birnlex
    example: null
    first_party: null
    homepage: http://braininfo.rprc.washington.edu
    name: Neuronames Alternate 1
    publications: null
    status: null
    uri_format: http://braininfo.rprc.washington.edu/Scripts/hiercentraldirectory.aspx?ID=$1
  references:
  - https://en.wikipedia.org/wiki/NeuroNames
  synonyms:
  - neuroname
  uri_format: http://braininfo.rprc.washington.edu/centraldirectory.aspx?ID=$1
  wikidata:
    database: Q1773567
    description: numeric identifier of a brain structure in the BrainInfo (NeuroNames)
      database in plain mode
    example:
    - '21'
    - '22'
    - '300'
    name: NeuroNames ID (plain mode)
    prefix: P4394
    uri_format: http://braininfo.rprc.washington.edu/centraldirectory.aspx?ID=$1
neurondb:
  biocontext:
    prefix: NEURONDB
  edam:
    description: A unique identifier of a neuron from the NeuronDB database.
    name: NeuronDB
    obsolete: false
    prefix: '2656'
  fairsharing:
    abbreviation: NeuronDB
    description: 'NeuronDB provides a dynamically searchable database of three types
      of neuronal properties: voltage gated conductances, neurotransmitter receptors,
      and neurotransmitter substances. It contains tools that provide for integration
      of these properties in a given type of neuron and compartment, and for comparison
      of properties across different types of neurons and compartments.'
    homepage: https://senselab.med.yale.edu/NeuronDB
    name: NeuronDB
    prefix: FAIRsharing.45a10e
    publications: []
    subjects:
    - Cellular Neuroscience
    - Neurophysiology
    - Neurobiology
    - Computational Neuroscience
    - Molecular Neuroscience
    - Comparative Neurobiology
  mappings:
    biocontext: NEURONDB
    edam: '2656'
    fairsharing: FAIRsharing.45a10e
    miriam: neurondb
    n2t: neurondb
    prefixcommons: neurondb
  miriam:
    deprecated: true
    description: 'NeuronDB provides a dynamically searchable database of three types
      of neuronal properties: voltage gated conductances, neurotransmitter receptors,
      and neurotransmitter substances. It contains tools that provide for integration
      of these properties in a given type of neuron and compartment, and for comparison
      of properties across different types of neurons and compartments.'
    homepage: http://senselab.med.yale.edu/NeuronDB/
    id: 00000094
    name: NeuronDB
    namespaceEmbeddedInLui: false
    pattern: ^\d+$
    prefix: neurondb
    sampleId: '265'
    uri_format: http://senselab.med.yale.edu/NeuronDB/NeuronProp.aspx?id=$1
  n2t:
    description: 'NeuronDB provides a dynamically searchable database of three types
      of neuronal properties: voltage gated conductances, neurotransmitter receptors,
      and neurotransmitter substances. It contains tools that provide for integration
      of these properties in a given type of neuron and compartment, and for comparison
      of properties across different types of neurons and compartments.'
    example: '265'
    homepage: http://senselab.med.yale.edu/NeuronDB/
    name: NeuronDB at SenseLab
    namespaceEmbeddedInLui: false
    pattern: ^\d+$
    prefix: neurondb
    uri_format: http://senselab.med.yale.edu/NeuronDB/NeuronProp.aspx?id=$1
  prefix: neurondb
  prefixcommons:
    description: 'NeuronDB provides a dynamically searchable database of three types
      of neuronal properties: voltage gated conductances, neurotransmitter receptors,
      and neurotransmitter substances. It contains tools that provide for integration
      of these properties in a given type of neuron and compartment, and for comparison
      of properties across different types of neurons and compartments.'
    example: '265'
    homepage: http://senselab.med.yale.edu/NeuronDB/
    keywords:
    - anatomy
    - structure
    license: CC-BY-3.0
    name: NeuronDB
    pattern: ^\d+$
    prefix: neurondb
    uri_format: http://senselab.med.yale.edu/NeuronDB/NeuronProp.aspx?id=$1
neurovault.collection:
  biocontext:
    prefix: NEUROVAULT.COLLECTION
  mappings:
    biocontext: NEUROVAULT.COLLECTION
    miriam: neurovault.collection
    n2t: neurovault.collection
  miriam:
    deprecated: false
    description: Neurovault is an online repository for statistical maps, parcellations
      and atlases of the brain. This collection references sets (collections) of images.
    homepage: http://neurovault.org
    id: '00000635'
    name: NeuroVault Collection
    namespaceEmbeddedInLui: false
    pattern: ^[1-9][0-9]*$
    prefix: neurovault.collection
    sampleId: '3304'
    uri_format: https://neurovault.org/collections/$1
  n2t:
    description: Neurovault is an online repository for statistical maps, parcellations
      and atlases of the brain. This collection references sets (collections) of images.
    example: '3304'
    homepage: http://neurovault.org
    name: NeuroVault Collection
    namespaceEmbeddedInLui: false
    pattern: ^[1-9][0-9]*$
    prefix: neurovault.collection
    uri_format: https://neurovault.org/collections/$1
  prefix: neurovault.collection
neurovault.image:
  biocontext:
    prefix: NEUROVAULT.IMAGE
  mappings:
    biocontext: NEUROVAULT.IMAGE
    miriam: neurovault.image
    n2t: neurovault.image
  miriam:
    deprecated: false
    description: Neurovault is an online repository for statistical maps, parcellations
      and atlases of the brain. This collection references individual images.
    homepage: http://neurovault.org
    id: 00000638
    name: NeuroVault Image
    namespaceEmbeddedInLui: false
    pattern: ^[1-9][0-9]*$
    prefix: neurovault.image
    sampleId: '58788'
    uri_format: https://neurovault.org/images/$1
  n2t:
    description: Neurovault is an online repository for statistical maps, parcellations
      and atlases of the brain. This collection references individual images.
    example: '58788'
    homepage: http://neurovault.org
    name: NeuroVault
    namespaceEmbeddedInLui: false
    pattern: ^[1-9][0-9]*$
    prefix: neurovault.image
    uri_format: https://neurovault.org/images/$1
  prefix: neurovault.image
nextdb:
  biocontext:
    prefix: NEXTDB
  fairsharing:
    abbreviation: NextDB
    description: The Kohara lab has been constructing an expression pattern map of
      the 100Mb genome of the nematode Caenorhabditis elegans through EST analysis
      and systematic whole mount in situ hybridization. NEXTDB is the database to
      integrate all information from the expression pattern project.
    homepage: http://nematode.lab.nig.ac.jp/
    license: http://opendatacommons.org/licenses/pddl/1.0
    name: Nematode Expression Pattern DataBase
    prefix: FAIRsharing.xz5m1a
    publications: []
    subjects:
    - Life Science
  integbio:
    alt_name: The Nematode Expression Pattern DataBase
    description: NEXTDB is a database of nematode expression data. The database contains
      EST information as well as images from in situ hybridization. Maps of genetic
      entities, images of hybridizations, sequences, and homology search are available,
      as is a list of RNAi phenotypes.
    fairsharing: biodbcore-000466
    homepage: http://nematode.nig.ac.jp
    information_keywords:
    - Expression
    - Image/Movie
    maintainer: National Institute of Genetics
    name: NEXTDB
    prefix: nbdc00594
    pubmeds:
    - '11231151'
    status: Active
    target_keywords:
    - cDNA/EST
    - Organism
  mappings:
    biocontext: NEXTDB
    fairsharing: FAIRsharing.xz5m1a
    integbio: nbdc00594
    miriam: nextdb
    n2t: nextdb
    ncbi: NextDB
    prefixcommons: nextdb
  miriam:
    deprecated: false
    description: NextDb is a database that provides information on the expression
      pattern map of the 100Mb genome of the nematode Caenorhabditis elegans. This
      was done through EST analysis and systematic whole mount in situ hybridization.
      Information available includes 5' and 3' ESTs, and in-situ hybridization images
      of 11,237 cDNA clones.
    homepage: http://nematode.lab.nig.ac.jp/
    id: 00000289
    name: NEXTDB
    namespaceEmbeddedInLui: false
    pattern: ^[A-Za-z0-9]+$
    prefix: nextdb
    sampleId: 6b1
    uri_format: http://nematode.lab.nig.ac.jp/db2/ShowCloneInfo.php?clone=$1
  n2t:
    description: NextDb is a database that provides information on the expression
      pattern map of the 100Mb genome of the nematode Caenorhabditis elegans. This
      was done through EST analysis and systematic whole mount in situ hybridization.
      Information available includes 5' and 3' ESTs, and in-situ hybridization images
      of 11,237 cDNA clones.
    example: 6b1
    homepage: http://nematode.lab.nig.ac.jp/
    name: NEXTDB at Shizuoka
    namespaceEmbeddedInLui: false
    pattern: ^[A-Za-z0-9]+$
    prefix: nextdb
    uri_format: http://nematode.lab.nig.ac.jp/db2/ShowCloneInfo.php?clone=$1
  ncbi:
    example: CELK01662
    homepage: http://nematode.lab.nig.ac.jp/
    name: Nematode Expression Pattern DataBase
    prefix: NextDB
  prefix: nextdb
  prefixcommons:
    description: The Kohara lab has been constructing an expression pattern map of
      the 100Mb genome of the nematode Caenorhabditis elegans through EST analysis
      and systematic whole mount in situ hybridization. NEXTDB is the database to
      integrate all information from the expression pattern project.
    example: C24A3
    homepage: http://nematode.lab.nig.ac.jp/
    keywords:
    - gene expression
    - genome
    - DNA
    name: Nematode Expression Pattern DataBase
    pattern: ^[A-Z]\d+$
    prefix: nextdb
    uri_format: http://nematode.lab.nig.ac.jp/cgi-bin/dbest/SrchByCosmid.sh?csmd=$1
nextprot:
  biocontext:
    prefix: NEXTPROT
  fairsharing:
    abbreviation: neXtProt
    contact:
      email: monique.zahn@sib.swiss
      name: Monique Zahn
      orcid: 0000-0001-7961-6091
    description: neXtProt is a comprehensive human-centric discovery platform, offering
      its users a seamless integration of and navigation through protein-related data.
    homepage: https://www.nextprot.org
    license: https://www.nextprot.org/legal-disclaimer
    name: neXtProt
    prefix: FAIRsharing.62evqh
    publications:
    - doi: 10.1093/nar/gkr1179
      pubmed_id: 22139911
      title: 'neXtProt: a knowledge platform for human proteins.'
    - doi: 10.1093/nar/gku1178.
      pubmed_id: 25593349
      title: 'The neXtProt knowledgebase on human proteins: current status.'
    - doi: 10.1093/nar/gkw1062.
      pubmed_id: 27899619
      title: 'The neXtProt knowledgebase on human proteins: 2017 update.'
    - doi: 10.1021/pr300830v.
      pubmed_id: 23205526
      title: 'neXtProt: organizing protein knowledge in the context of human proteome
        projects.'
    - doi: 10.1093/nar/gkz995
      pubmed_id: 31724716
      title: 'The neXtProt knowledgebase in 2020: data, tools and usability improvements.'
    subjects:
    - Proteomics
    - Life Science
  integbio:
    description: neXtProt is a comprehensive human-centric discovery platform, offering
      its users a seamless integration of and navigation through protein-related data.
    fairsharing: FAIRsharing.62evqh
    homepage: https://www.nextprot.org
    information_keywords:
    - Sequence
    - Expression
    maintainer: CALIPHO (Computer and Laboratory Investigation of Proteins of Human
      Origin Group, Swiss Institute of Bioinformatics)||SIB (Swiss Institute of Bioinformatics)
    name: neXtProt
    prefix: nbdc02107
    pubmeds:
    - '22139911'
    - '25593349'
    - '23205526'
    - '27899619'
    status: Closed
    target_keywords:
    - Genetic variation
    - Protein
    - Cell/Organelle
    - Genome/Gene
    - Health/Disease
  mappings:
    biocontext: NEXTPROT
    fairsharing: FAIRsharing.62evqh
    integbio: nbdc02107
    miriam: nextprot
    n2t: nextprot
    uniprot: DB-0161
    wikidata.entity: Q6983890
  miriam:
    deprecated: false
    description: neXtProt is a resource on human proteins, and includes information
      such as proteins’ function, subcellular location, expression, interactions and
      role in diseases.
    homepage: https://www.nextprot.org/
    id: '00000236'
    name: nextProt
    namespaceEmbeddedInLui: false
    pattern: ^NX_\w+$
    prefix: nextprot
    sampleId: NX_O00165
    uri_format: https://www.nextprot.org/db/entry/$1
  n2t:
    description: neXtProt is a resource on human proteins, and includes information
      such as proteins&#x2019; function, subcellular location, expression, interactions
      and role in diseases.
    example: NX_O00165
    homepage: https://www.nextprot.org/
    name: nextProt at Swiss Institute of Bioinformatics
    namespaceEmbeddedInLui: false
    pattern: ^NX_\w+
    prefix: nextprot
    uri_format: https://www.nextprot.org/db/entry/$1
  part_of_database: nextprot
  prefix: nextprot
  publications:
  - doi: 10.1093/nar/gkz995
    pmc: PMC7145669
    pubmed: '31724716'
    title: 'The neXtProt knowledgebase in 2020: data, tools and usability improvements'
    year: 2020
  - doi: 10.1093/nar/gkw1062
    pmc: PMC5210547
    pubmed: '27899619'
    title: 'The neXtProt knowledgebase on human proteins: 2017 update'
    year: 2016
  - doi: 10.1093/nar/gku1178
    pmc: PMC4383972
    pubmed: '25593349'
    title: 'The neXtProt knowledgebase on human proteins: current status'
    year: 2015
  - doi: 10.1021/pr300830v
    pmc: null
    pubmed: '23205526'
    title: 'neXtProt: organizing protein knowledge in the context of human proteome
      projects'
    year: 2012
  - doi: 10.1093/nar/gkr1179
    pmc: PMC3245017
    pubmed: '22139911'
    title: 'neXtProt: a knowledge platform for human proteins'
    year: 2011
  synonyms:
  - NXP
  twitter: neXtProt_news
  uniprot:
    abbreviation: neXtProt
    category: Organism-specific databases
    homepage: https://www.nextprot.org/
    name: neXtProt; the human protein knowledge platform
    prefix: DB-0161
    publications:
    - doi: 10.1093/nar/gkz995
      pubmed: '31724716'
    uri_format: https://www.nextprot.org/entry/$1
  wikidata:
    database: Q6983890
nextprot.family:
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: "NeXtProt is a comprehensive human-centric discovery platform, offering\
    \ its users a seamless integration of and navigation through protein-related data.\
    \ \n(Developed by the SIB Swiss Institute of Bioinformatics)"
  example: '01406'
  homepage: https://www.nextprot.org/
  name: neXtProt family
  part_of_database: nextprot
  pattern: ^\d+$
  prefix: nextprot.family
  synonyms:
  - NXPFA
  twitter: neXtProt_news
  uri_format: https://www.nextprot.org/term/FA-$1
nexus:
  example: version
  mappings:
    tib: nexus
  prefix: nexus
  tib:
    description: 'NeXusOntology: Machine-readable ontology of the NeXus definitions'
    download_owl: https://raw.githubusercontent.com/nexusformat/NeXusOntology/refs/heads/main/ontology/NeXusOntology.owl
    homepage: https://github.com/nexusformat/NeXusOntology
    keywords:
    - TIB
    - FAIRmat
    - physics
    name: NeXusOntology
    prefix: nexus
    tracker: https://github.com/nexusformat/NeXusOntology/issues
    uri_format: http://purl.org/nexusformat/definitions/NeXusOntology#$1
nfdi.core:
  contact:
    email: joerg.waitelonis@fiz-karlsruhe.de
    github: joergwa
    name: Jörg Waitelonis
    orcid: 0000-0001-7192-7143
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: A mid-level ontology for representing metadata related to NFDI resources,
    including individuals, organizations, projects, data portals, and more
  download_owl: https://github.com/ISE-FIZKarlsruhe/nfdicore/raw/refs/heads/main/nfdicore.owl
  download_rdf: https://github.com/ISE-FIZKarlsruhe/nfdicore/raw/refs/heads/main/nfdicore.ttl
  example: '0000106'
  github_request_issue: 1448
  homepage: https://ise-fizkarlsruhe.github.io/nfdicore/
  license: CC0-1.0
  name: NFDI Core Ontology
  pattern: ^\d+$
  prefix: nfdi.core
  repository: https://github.com/ISE-FIZKarlsruhe/nfdicore
  uri_format: https://nfdi.fiz-karlsruhe.de/ontology/NFDI_$1
nfdi.kgi:
  contact:
    email: lozana.rossenova@tib.eu
    github: lozanaross
    name: Lozana Rossenova
    orcid: 0000-0002-5190-1867
  contact_group_email: kgi4nfdi@lists.nfdi.de
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: Assigns identifiers to knowledge graphs (KGs) that are used and/or
    maintained within any NFDI consortium.
  example: KGR1
  github_request_issue: 1665
  homepage: https://kgi.services.base4nfdi.de
  keywords:
  - knowledge graph
  license: CC-BY-SA-4.0
  name: NFDI Knowledge Graph Registry
  pattern: ^KGR\d+$
  prefix: nfdi.kgi
  repository: https://github.com/KGI4NFDI/kgi4nfdi_registry_data
  uri_format: http://kgi.services.base4nfdi.de/entity/$1
nfdi4chem.ontocape:
  comment: This ontology ecosystem is near unusable
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  deprecated: true
  description: OntoCAPE is a large-scale ontology for the domain of Computer Aided
    Process Engineering (CAPE). Represented in a formal, machine-interpretable ontology
    language, OntoCAPE captures consensual knowledge of the process engineering domain
    in a generic way such that it can be reused and shared by groups of people and
    across software systems. On the basis of OntoCAPE, novel software support for
    various engineering activities can be developed; possible applications include
    the systematic management and retrieval of simulation models and design documents,
    electronic procurement of plant equipment, mathematical modeling, as well as the
    integration of design data from distributed sources.
  homepage: https://www.avt.rwth-aachen.de/cms/AVT/Forschung/Software/~ipts/OntoCape/
  license: GPL-2.0
  name: Ontology for computer aided process engineering
  prefix: nfdi4chem.ontocape
nfdi4chem.osmo:
  bartoc:
    abbreviation: OSMO
    description: OSMO is an ontologization and extension of MODA, a workflow metadata
      standard that constitutes a mandatory requirement within a number of European
      calls and projects in the context of materials modelling. OSMO was developed
      within the Horizon 2020 project VIMMP (Virtual Materials Marketplace) and is
      part of a larger effort in ontology engineering driven by the European Materials
      Modelling Council, with the European Materials and Modelling Ontology (EMMO)
      as its core.
    homepage: https://doi.org/10.5281/zenodo.5237774
    license: http://rightsstatements.org/vocab/InC/1.0
    name: Ontology for simulation, modelling, and optimization
    prefix: '20710'
  comment: locked behind a private GitLab instance
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  deprecated: true
  description: OSMO is an ontologization and extension of MODA, a workflow metadata
    standard that constitutes a mandatory requirement within a number of European
    calls and projects in the context of materials modelling. OSMO was developed within
    the Horizon 2020 project VIMMP (Virtual Materials Marketplace) and is part of
    a larger effort in ontology engineering driven by the European Materials Modelling
    Council, with the European Materials and Modelling Ontology (EMMO) as its core.
    (from https://nfdi4cat.org/services/ontologie-sammlung/)
  example: application_case
  homepage: https://zenodo.org/record/5237774#.YXq72hxCRGo
  mappings:
    bartoc: '20710'
    tib: osmo
  name: Ontology for simulation, modelling, and optimization
  prefix: nfdi4chem.osmo
  tib:
    description: OSMO is an Ontology for Simulation, Modelling, and Optimization
    download_rdf: https://gitlab.com/vimmp-semantics/vimmp-ontologies/-/raw/alignment-with-emmo-2022/osmo/osmo.ttl
    keywords:
    - NFDI4CAT
    - material science
    - computer science
    name: Ontology for simulation, modelling, and optimization
    prefix: osmo
    uri_format: https://purl.org/vimmp/osmo#$1
    version.iri: https://purl.org/vimmp/osmo
nfdi4culture.cto:
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: The NFDI4Culture Ontology (CTO) is a domain-specific ontology module
    developed within the Task Area 5 of the NFDI4Culture initiative. (from homepage)
  download_owl: https://github.com/ISE-FIZKarlsruhe/nfdi4culture/raw/refs/heads/main/cto.owl
  example: '0001003'
  homepage: https://nfdi4culture.de/ontology/
  license: CC0-1.0
  mappings:
    tib: cto
  name: NFDI4Culture Ontology
  pattern: ^\d{7}$
  prefix: nfdi4culture.cto
  repository: https://github.com/ISE-FIZKarlsruhe/nfdi4culture
  tib:
    description: 'The NFDI4Culture Ontology (CTO) models cultural heritage research
      resources with the goal of enabling a research data index. CTO is a domain-specific
      module built on top of the mid-level NFDIcore Ontology v.3 (https://ise-fizkarlsruhe.github.io/nfdicore/)
      and is aligned with the Basic Formal Ontology (BFO) 2020. It describes and interlinks
      the diverse entities that exist within the communitys research (meta)data, including
      connections between persons, organizations, places and events, media objects,
      legal statements, external vocabulary references, musical incipits, and more.
      Further infomration can be found at in the detailed documentation: https://nfdi.fiz-karlsruhe.de/4culture/'
    download_rdf: https://raw.githubusercontent.com/ISE-FIZKarlsruhe/nfdi4culture/refs/heads/main/cto-full.ttl
    homepage: https://nfdi.fiz-karlsruhe.de/4culture/
    keywords:
    - NFDI4CULTURE
    - architecture
    - other subjects
    name: NFDI4Culture Ontology
    prefix: cto
    tracker: https://github.com/ISE-FIZKarlsruhe/nfdi4culture/issues
    uri_format: https://nfdi4culture.de/ontology/CTO_$1
    version.iri: https://nfdi4culture.de/ontology/3.0.0
  uri_format: https://nfdi4culture.de/ontology/CTO_$1
nfdi4culture.id:
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: The NFDI4Culture portal offers all content as Linked Open Data over
    this RESTful API. The API implements the Hydra-Specification of the W3C Hydra
    Community Group. The semantic description of this API can be retrieved by clients
    via the Hydra documentation file (JSON). Each metadata record offered via this
    API can also be retrieved in one of following machine-readable LOD serializations.
    The API is the basis for the Culture Research Information Graph, which together
    with the Culture Research Data Graph forms the [Culture Knowledge Graph](https://nfdi4culture.de/services/details/culture-knowledge-graph.html)
    (for more details see [this presentation](https://doi.org/10.5281/zenodo.7748740))
    (from homepage).
  example: E4330
  github_request_issue: 1627
  homepage: https://nfdi4culture.de/id
  keywords:
  - digital humanities
  - generic
  - organization
  name: NFDI4Culture Metadata API
  prefix: nfdi4culture.id
  rdf_uri_format: https://nfdi4culture.de/id/$1
  uri_format: https://nfdi4culture.de/id/$1
nfdi4dso:
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: The NFDI4DS ontology (nfdi4dso) is an ontology describing various resources
    all resources (datasets, data providers, persons, projects and other entities)
    within the domain of NFDI4DataScience. nfdi4dso is a module that builds upon the
    NFDIcore Ontology (https://ise-fizkarlsruhe.github.io/nfdicore/2.0.0/) and maintains
    alignment with the Basic Formal Ontology (BFO). [from homepage]
  download_rdf: https://ise-fizkarlsruhe.github.io/NFDI4DS-Ontology/ontology.ttl
  example: City
  homepage: https://nfdi.fiz-karlsruhe.de/nfdi4dso/
  name: NFDI4DS Ontology
  prefix: nfdi4dso
  rdf_uri_format: https://nfdi.fiz-karlsruhe.de/nfdi4dso/$1
  uri_format: https://nfdi.fiz-karlsruhe.de/nfdi4dso/$1
nfportal.tool:
  contact:
    email: robert.j.allaway@gmail.com
    github: allaway
    name: Robert Allaway
    orcid: 0000-0003-3573-3565
  contributor:
    email: ji.kang@northeastern.edu
    github: kanghosaeyo
    name: Kangho Ji
    orcid: 0009-0009-3402-8013
  description: Identifiers represent experimental tools and resources for neurofibromatosis
    (NF) research in the NF Data Portal Tools catalog.
  example: 02dacc42-ea46-48fb-a4df-7a875d801086
  github_request_issue: 1724
  homepage: https://nf.synapse.org
  keywords:
  - experimental tools
  - neurofibromatosis
  - research resources
  name: Neurofibromatosis Data Portal Tools
  pattern: ^[0-9a-f]{8}-[0-9a-f]{4}-[0-9a-f]{4}-[0-9a-f]{4}-[0-9a-f]{12}$
  prefix: nfportal.tool
  publications:
  - doi: 10.1038/s41597-019-0317-x
    pmc: PMC6910996
    pubmed: '31836719'
    title: Engaging a community to enable disease-centric data sharing with the NF
      Data Portal
    year: 2019
  reviewer:
    email: b.gyori@northeastern.edu
    github: bgyori
    name: Benjamin M. Gyori
    orcid: 0000-0001-9439-5346
  uri_format: https://nf.synapse.org/Explore/Tools/DetailsPage?resourceId=$1
ngbo:
  aberowl:
    description: 'The Next Generation Biobanking Ontology (NGBO) is an open application
      ontology representing contextual data about omics digital assets in biobank.
      The ontology focuses on capturing the information about three main activities:
      wet bench analysis used to generate omics data, bioinformatics analysis used
      to analyze and interpret data, and data management.'
    download_owl: http://aber-owl.net/media/ontologies/NGBO/3/ngbo.owl
    homepage: https://github.com/Dalalghamdi/NGBO
    name: Next Generation Biobanking Ontology
    prefix: NGBO
  bioportal:
    contact:
      email: dal.alghamdi92@gmail.com
      name: Dalia Alghamdi
    description: 'The Next Generation Biobanking Ontology (NGBO) is an open application
      ontology representing contextual data about omics digital assets in biobank.
      The ontology focuses on capturing the information about three main activities:
      wet bench analysis used to generate omics data, bioinformatics analysis used
      to analyze and interpret data, and data management.'
    homepage: https://github.com/Dalalghamdi/NGBO
    name: Next Generation Biobanking Ontology
    prefix: NGBO
    version: '2024-08-27'
  example: '6000122'
  mappings:
    aberowl: NGBO
    bioportal: NGBO
    obofoundry: ngbo
    ols: ngbo
    ontobee: NGBO
  obofoundry:
    contact: dal.alghamdi92@gmail.com
    contact.github: dalalghamdi
    contact.label: Dalia Alghamdi
    contact.orcid: 0000-0002-2801-0767
    deprecated: false
    description: 'The Next Generation Biobanking Ontology (NGBO) is an open application
      ontology representing contextual data about omics digital assets in biobank.
      The ontology focuses on capturing the information about three main activities:
      wet bench analysis used to generate omics data, bioinformatics analysis used
      to analyze and interpret data, and data management.'
    domain: investigations
    download.owl: http://purl.obolibrary.org/obo/ngbo.owl
    homepage: https://github.com/Dalalghamdi/NGBO
    license: CC BY 4.0
    license.url: https://creativecommons.org/licenses/by/4.0/
    name: Next Generation Biobanking Ontology
    preferredPrefix: NGBO
    prefix: ngbo
    repository: https://github.com/Dalalghamdi/NGBO
  ols:
    description: 'Next Generation Biobanking Ontology (NGBO) is an open application
      ontology representing contextual data about omics digital assets in biobank.
      The ontology focuses on capturing the information about three main activities:
      wet bench analysis used to generate omics data, bioinformatics analysis used
      to analyze and interpret data, and data management.'
    download_owl: http://purl.obolibrary.org/obo/ngbo.owl
    homepage: https://github.com/Dalalghamdi/NGBO
    name: Next generation biobanking ontology(NGBO).
    prefix: ngbo
    tracker: https://github.com/Dalalghamdi/NGBO/issues
    version: '2024-08-27'
    version.iri: http://purl.obolibrary.org/obo/ngbo/2024-08-27/ngbo.owl
  ontobee:
    library: Library
    name: Next Generation Biobanking Ontology
    prefix: NGBO
  pattern: ^\d{7}$
  prefix: ngbo
  uri_format: http://purl.obolibrary.org/obo/NGBO_$1
ngl:
  biocontext:
    prefix: NGL
  mappings:
    biocontext: NGL
    miriam: ngl
    n2t: ngl
  miriam:
    deprecated: false
    description: NASA's GeneLab gathers spaceflight genomic data, RNA and protein
      expression, and metabolic profiles, interfaces with existing databases for expanded
      research, will offer tools to conduct data analysis, and is in the process of
      creating a place online where scientists, researchers, teachers and students
      can connect with their peers, share their results, and communicate with NASA.
    homepage: https://genelab-data.ndc.nasa.gov/genelab/
    id: 00000618
    name: NASA GeneLab
    namespaceEmbeddedInLui: false
    pattern: ^GLDS-\d+$
    prefix: ngl
    sampleId: GLDS-141
    uri_format: https://genelab-data.ndc.nasa.gov/genelab/accession/$1
  n2t:
    description: NASA's GeneLab gathers spaceflight genomic data, RNA and protein
      expression, and metabolic profiles, interfaces with existing databases for expanded
      research, will offer tools to conduct data analysis, and is in the process of
      creating a place online where scientists, researchers, teachers and students
      can connect with their peers, share their results, and communicate with NASA.
    example: GLDS-141
    homepage: https://genelab-data.ndc.nasa.gov/genelab/
    name: NASA GeneLab
    namespaceEmbeddedInLui: false
    pattern: ^GLDS-\d+$
    prefix: ngl
    uri_format: https://genelab-data.ndc.nasa.gov/genelab/accession/$1
  prefix: ngl
nhcdr:
  cellosaurus:
    category: Cell line collections (Providers)
    homepage: https://stemcells.nindsgenetics.org
    name: NINDS Human Cell and Data Repository
    prefix: NHCDR
    uri_format: https://stemcells.nindsgenetics.org?line=$1
  example: ND50028
  mappings:
    cellosaurus: NHCDR
  prefix: nhcdr
niaest:
  biocontext:
    prefix: NIAEST
  fairsharing:
    abbreviation: niaEST
    contact:
      email: dawood@helix.nih.gov
      name: Dawood B. Dudekula
      orcid: 0000-0002-4054-1827
    description: A catalog of mouse genes expressed in early embryos, embryonic and
      adult stem cells was assembled. The cDNA libraries are freely distributed to
      the research community, providing a standard platform for expression studies
      using microarrays.
    homepage: http://lgsun.grc.nia.nih.gov/cDNA/cDNA.html
    name: NIA Mouse cDNA Project
    prefix: FAIRsharing.xwqg9h
    publications:
    - doi: 10.1016/j.crvi.2003.09.008
      pubmed_id: 14744099
      title: The NIA cDNA project in mouse stem cells and early embryos.
    subjects:
    - Life Science
  mappings:
    biocontext: NIAEST
    fairsharing: FAIRsharing.xwqg9h
    miriam: niaest
    n2t: niaest
    ncbi: niaEST
    prefixcommons: niaest
  miriam:
    deprecated: true
    description: A catalog of mouse genes expressed in early embryos, embryonic and
      adult stem cells, including 250000 ESTs, was assembled by the NIA (National
      Institute on Aging) assembled.This collection represents the name and sequence
      from individual cDNA clones.
    homepage: http://lgsun.grc.nia.nih.gov/cDNA/
    id: '00000305'
    name: NIAEST
    namespaceEmbeddedInLui: false
    pattern: ^\w\d{4}\w\d{2}(\-[35])?$
    prefix: niaest
    sampleId: J0705A10
    uri_format: http://lgsun.grc.nia.nih.gov/cgi-bin/pro3?sname1=$1
  n2t:
    description: A catalog of mouse genes expressed in early embryos, embryonic and
      adult stem cells, including 250000 ESTs, was assembled by the NIA (National
      Institute on Aging) assembled.This collection represents the name and sequence
      from individual cDNA clones.
    example: J0705A10
    homepage: http://lgsun.grc.nia.nih.gov/cDNA/
    name: NIAEST at National Institute on Aging
    namespaceEmbeddedInLui: false
    pattern: ^\w\d{4}\w\d{2}(\-[35])?$
    prefix: niaest
    uri_format: http://lgsun.grc.nia.nih.gov/cgi-bin/pro3?sname1=$1
  ncbi:
    example: L0304H12-3
    homepage: http://esbank.nia.nih.gov/
    name: NIA Mouse cDNA Project
    prefix: niaEST
  prefix: niaest
  prefixcommons:
    description: A searchable mouse cDNA library.
    example: J0705A10-3
    homepage: http://lgsun.grc.nia.nih.gov/cDNA/cDNA.html
    keywords:
    - DNA
    name: NIA Mouse cDNA Project
    pattern: ^[A-Z,0-9]+$
    prefix: niaest
    uri_format: http://lgsun.grc.nia.nih.gov/cgi-bin/pro3?sname1=$1
  publications:
  - doi: 10.1016/j.crvi.2003.09.008
    pmc: null
    pubmed: '14744099'
    title: The NIA cDNA project in mouse stem cells and early embryos
    year: 2003
niaid.chemdb:
  homepage: http://chemdb.niaid.nih.gov
  mappings:
    wikidata: P2065
  prefix: niaid.chemdb
  wikidata:
    description: ID in NIAID ChemDB
    example:
    - 059486
    - 070944
    - '112081'
    name: NIAID ChemDB ID
    prefix: P2065
    uri_format: http://chemdb.niaid.nih.gov/CompoundDetails.aspx?AIDSNO=$1
nif.cell:
  aberowl:
    description: Cell types from NIFSTD
    download_owl: http://aber-owl.net/media/ontologies/NIFCELL/15/nifcell.owl
    homepage: http://neuinfo.org/
    name: Neuroscience Information Framework (NIF) Cell Ontology
    prefix: NIFCELL
    version: v.1.10 - July 17, 2013
  biocontext:
    prefix: NIF_CELL
  bioportal:
    contact:
      email: smtifahim@gmail.com
      name: Fahim Imam
    description: Cell types from NIFSTD
    homepage: http://neuinfo.org/
    name: Neuroscience Information Framework (NIF) Cell Ontology
    prefix: NIFCELL
    version: v.1.10 - July 17, 2013
  contact:
    email: smtifahim@gmail.com
    github: null
    name: Fahim Imam
    orcid: 0000-0003-4752-543X
  mappings:
    aberowl: NIFCELL
    biocontext: NIF_CELL
    bioportal: NIFCELL
    obofoundry: nif_cell
  obofoundry:
    contact: smtifahim@gmail.com
    contact.label: Fahim Imam
    contact.orcid: 0000-0003-4752-543X
    deprecated: true
    description: Neuronal cell types
    domain: anatomy and development
    homepage: http://neuinfo.org/
    name: NIF Cell
    prefix: nif_cell
  part_of_database: nif
  prefix: nif.cell
nif.dysfunction:
  biocontext:
    prefix: NIF_DYSFUNCTION
  contact:
    email: smtifahim@gmail.com
    github: null
    name: Fahim Imam
    orcid: 0000-0003-4752-543X
  mappings:
    biocontext: NIF_DYSFUNCTION
    obofoundry: nif_dysfunction
  obofoundry:
    contact: smtifahim@gmail.com
    contact.label: Fahim Imam
    contact.orcid: 0000-0003-4752-543X
    deprecated: true
    domain: health
    homepage: http://neuinfo.org/
    name: NIF Dysfunction
    prefix: nif_dysfunction
  part_of_database: nif
  prefix: nif.dysfunction
nif.ext:
  contact:
    email: tgbugs@gmail.com
    github: tgbugs
    name: Tom Gillespie
    orcid: 0000-0002-7509-4801
  contributor:
    email: tgbugs@gmail.com
    github: tgbugs
    name: Tom Gillespie
    orcid: 0000-0002-7509-4801
  description: NIFEXT covers IRIs that were "external" identifiers that were brought
    into the ontology at some point in time. This was done before most of the current
    standard ontology and identifier management practices had been developed.
  example: '7123'
  homepage: https://github.com/SciCrunch/NIF-Ontology
  license: CC BY-4.0
  name: 'NIF Standard Ontology: External'
  part_of_database: nif
  pattern: ^\d+$
  prefix: nif.ext
  repository: https://github.com/SciCrunch/NIF-Ontology
  reviewer:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  synonyms:
  - NIFEXT
  twitter: SciCrunch
  uri_format: http://uri.neuinfo.org/nif/nifstd/nifext_$1
nif.grossanatomy:
  biocontext:
    prefix: NIF_GROSSANATOMY
  contact:
    email: smtifahim@gmail.com
    github: null
    name: Fahim Imam
    orcid: 0000-0003-4752-543X
  mappings:
    biocontext: NIF_GROSSANATOMY
    obofoundry: nif_grossanatomy
  obofoundry:
    contact: smtifahim@gmail.com
    contact.label: Fahim Imam
    contact.orcid: 0000-0003-4752-543X
    deprecated: true
    domain: anatomy and development
    homepage: http://neuinfo.org/
    name: NIF Gross Anatomy
    prefix: nif_grossanatomy
  part_of_database: nif
  prefix: nif.grossanatomy
nif.std:
  aberowl:
    description: NIF Standard ontology (NIFSTD) is a core component of Neuroscience
      Information Framework (NIF) project (http://neuinfo.org), a semantically enhanced
      portal for accessing and integrating neuroscience data, tools and information.
      NIFSTD includes a set of modular ontologies that provide a comprehensive collection
      of terminologies to describe neuroscience data and resources.
    download_owl: http://aber-owl.net/media/ontologies/NIFSTD/23/nifstd.owl
    homepage: http://ontology.neuinfo.org
    name: Neuroscience Information Framework (NIF) Standard Ontology
    prefix: NIFSTD
    version: 3.0 - October 16, 2017
  bioportal:
    contact:
      email: tgbugs@gmail.com
      name: Tom Gillespie
    description: NIF Standard ontology (NIFSTD) is a core component of Neuroscience
      Information Framework (NIF) project (http://neuinfo.org), a semantically enhanced
      portal for accessing and integrating neuroscience data, tools and information.
      NIFSTD includes a set of modular ontologies that provide a comprehensive collection
      of terminologies to describe neuroscience data and resources.
    homepage: http://ontology.neuinfo.org
    name: Neuroscience Information Framework (NIF) Standard Ontology
    prefix: NIFSTD
    publications:
    - http://neuinfo.org/about/publications.shtm
    version: 3.1 - January 15, 2018
  contact:
    email: tgbugs@gmail.com
    github: tgbugs
    name: Tom Gillespie
    orcid: 0000-0002-7509-4801
  contributor:
    email: tgbugs@gmail.com
    github: tgbugs
    name: Tom Gillespie
    orcid: 0000-0002-7509-4801
  description: NIFSTD is a base namespace (like obo:) which houses many other prefixes.
    Sometimes NIFSTD prefixed identifiers appear undifferentiated, but usually if
    it shows up it means that another prefix definition is missing when serializing.
  example: BAMSC981
  fairsharing:
    abbreviation: NIFSTD
    contact:
      email: tgbugs@gmail.com
      name: Tom Gillespie
      orcid: 0000-0002-7509-4801
    description: NIF Standard ontology (NIFSTD) is a core component of Neuroscience
      Information Framework (NIF) project (http://neuinfo.org), a semantically enhanced
      portal for accessing and integrating neuroscience data, tools and information.
      NIFSTD includes a set of modular ontologies that provide a comprehensive collection
      of terminologies to describe neuroscience data and resources.
    domains:
    - disease
    - brain
    homepage: https://github.com/SciCrunch/NIF-Ontology
    license: CC-BY-4.0
    name: Neuroscience Information Framework Standard Ontology
    prefix: FAIRsharing.vgw1m6
    publications:
    - doi: 10.1007/s12021-008-9032-z
      pubmed: '18975148'
      title: 'The NIFSTD and BIRNLex vocabularies: building comprehensive ontologies
        for neuroscience'
      year: 2008
    subjects:
    - Neuroscience
  homepage: https://github.com/SciCrunch/NIF-Ontology
  license: CC BY-4.0
  mappings:
    aberowl: NIFSTD
    bioportal: NIFSTD
    fairsharing: FAIRsharing.vgw1m6
  name: NIF Standard Ontology
  part_of_database: nif
  pattern: ^BAMSC\d+$
  prefix: nif.std
  publications:
  - doi: 10.1007/s12021-008-9032-z
    pmc: PMC2743139
    pubmed: '18975148'
    title: 'The NIFSTD and BIRNLex vocabularies: building comprehensive ontologies
      for neuroscience'
    year: 2008
  - doi: 10.1007/s12021-008-9032-z
    pmc: null
    pubmed: '18975148'
    title: 'The NIFSTD and BIRNLex vocabularies: building comprehensive ontologies
      for neuroscience'
    year: 2008
  repository: https://github.com/SciCrunch/NIF-Ontology
  reviewer:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  synonyms:
  - NIFSTD
  twitter: SciCrunch
  uri_format: http://uri.neuinfo.org/nif/nifstd/$1
nihhesc:
  cellosaurus:
    category: Cell line databases/resources
    homepage: https://grants.nih.gov/stem_cells/registry/current.htm
    name: NIH Human Embryonic Stem Cell Registry
    prefix: NIHhESC
    uri_format: https://grants.nih.gov/stem_cells/registry/current.htm?ID=$1
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: The NIH registration number should be used on all NIH competing applications
    and annual progress reports to identify the stem cell line proposed for use. Identify
    the specific line(s) from the Registry using the NIH Registration Number (e.g.,
    0001), in the specified location in the application (from homepage)
  example: NIHhESC-10-0083
  homepage: https://grants.nih.gov/stem_cells/registry/current.htm
  mappings:
    cellosaurus: NIHhESC
  name: NIH Human Embryonic Stem Cell Registry
  prefix: nihhesc
  uri_format: https://grants.nih.gov/stem_cells/registry/current.htm?ID=$1
nihreporter.project:
  contact:
    email: report@mail.nih.gov
    github: null
    name: NIH Reporter Helpdesk
    orcid: null
  contact_group_email: report@mail.nih.gov
  contributor:
    email: benjamin_gyori@hms.harvard.edu
    github: bgyori
    name: Benjamin M. Gyori
    orcid: 0000-0001-9439-5346
  description: RePORTER is an electronic tool that allows users to search a repository
    of both intramural and extramural NIH-funded research projects and access publications
    and patents resulting from NIH funding.
  domain: project
  example: '10343835'
  github_request_issue: 400
  homepage: https://reporter.nih.gov/
  keywords:
  - bibliometrics
  - project
  logo: https://files.nccih.nih.gov/nccih-nih-reporter-twitter-card-01.jpg
  name: NIH RePORTER
  pattern: ^\d+$
  prefix: nihreporter.project
  reviewer:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  uri_format: https://reporter.nih.gov/project-details/$1
nist:
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: The NIST Chemistry WebBook provides users with easy access to chemical
    and physical property data for chemical species through the internet. The data
    provided in the site are from collections maintained by the NIST Standard Reference
    Data Program and outside contributors. Data in the WebBook system are organized
    by chemical species.
  homepage: https://webbook.nist.gov/chemistry/
  name: NIST Chemistry WebBook
  no_own_terms: true
  prefix: nist
  synonyms:
  - NIST
  - NIST Chemistry WebBook
nist.codata:
  mappings:
    wikidata: P1645
  part_of_database: nist
  prefix: nist.codata
  wikidata:
    description: identifier for a physical constant
    example:
    - c
    - h
    homepage: http://physics.nist.gov/cuu/Constants/index.html
    name: NIST/CODATA ID
    prefix: P1645
    uri_format: https://physics.nist.gov/cgi-bin/cuu/Value?$1
nkos:
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: 'NKOS is devoted to the discussion of the functional and data model
    for enabling knowledge organization systems/services (KOS), such as classification
    systems, thesauri, gazetteers, and ontologies, as networked interactive information
    services to support the description and retrieval of diverse information resources
    through the Internet.


    Knowledge Organization Systems/Services (KOS) model the underlying semantic structure
    of a domain. Embodied as Web-based services, they can facilitate resource discovery
    and retrieval. They act as semantic road maps and make possible a common orientation
    by indexers and future users (whether human or machine). -- Douglas Tudhope, Traugott
    Koch (2004).'
  download_rdf: https://nkos.dublincore.org/nkos.rdf
  example: alignedWith
  homepage: http://w3id.org/nkos
  name: Networked Knowledge Organization Systems/Services/Structures
  prefix: nkos
  uri_format: http://w3id.org/nkos/$1
nlcd:
  appears_in:
  - envo
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: A vocabulary for describing the usage of land cover (e.g., pasture,
    wetlands, barren, forest, water) extended from the original 16 land cover classes
    proposed by the [Anderson Level II classification system](https://doi.org/10.3133/pp964)
    in 1976
  example: '12'
  homepage: https://www.mrlc.gov/data/type/land-cover
  keywords:
  - environment
  - forestry
  name: United States Geological Survey - National Land Cover Database
  pattern: ^\d+$
  prefix: nlcd
  references:
  - https://www.mrlc.gov/data/legends/national-land-cover-database-class-legend-and-description
  - https://www.usgs.gov/centers/eros/science/national-land-cover-database
nlfff:
  mappings:
    miriam: nlfff
  miriam:
    deprecated: false
    description: Nonlinear Force-Free Field Three-Dimensional Magnetic Fields Data
      of Solar Active Regions Database
    homepage: https://nlfff.dataset.deepsolar.space/en/
    id: 00000988
    name: NLFFF Database
    namespaceEmbeddedInLui: false
    pattern: ^[0-9]+$
    prefix: nlfff
    sampleId: '345201101230312003'
    uri_format: http://database.deepsolar.space:18080/dbs/nlfff/$1
  prefix: nlfff
nlm:
  bartoc:
    abbreviation: NLM
    description: The NLM Classification covers the field of medicine and related sciences.
      The scheme is a system of classification intended to be used for the shelf arrangement
      of all library materials, regardless of format. Designed as a broad classification,
      it is suitable for both large and small library collections and may be adapted
      to handle specialized collections of any size. The NLM Classification is a system
      of mixed notation patterned after the Library of Congress (LC) Classification
      where alphabetical letters which denote broad subject categories are further
      subdivided by numbers. The NLM Classification utilizes schedules QS-QZ and W-WZ,
      permanently excluded from the LC Classification Schedules and is intended to
      be used with the LC schedules which supplement the NLM Classification for subjects
      bordering on medicine and for general reference materials. The LC schedules
      for Human Anatomy (QM), Microbiology (QR), and Medicine (R) are not used at
      all by the National Library of Medicine since they overlap the NLM Classification.
      The headings for the individual schedules are given in brief form (e.g., WE
      - Musculoskeletal System; WG - Cardiovascular System) and together they provide
      an outline of the subjects that constitute the NLM Classification. These headings
      are interpreted broadly and include the physiological system, the specialty
      or specialties connected with them, the regions of the body chiefly concerned
      and subordinate related fields. The Classification is hierarchical, and within
      each schedule, division by organ usually has priority. Each main schedule, as
      well as some sections within a schedule, begins with a group of form numbers
      ranging generally from 1-49 which are used to classify materials by publication
      type, e.g., dictionaries, atlases, laboratory manuals, etc. The main schedules
      QS-QZ, W-WY, and WZ (excluding WZ 220-270) are used to classify works published
      after 1913; the 19th century schedule is used for works published 1801-1913;
      and WZ 220-270 is used to provide century groupings for works published before
      1801 and Americana. Geographic subdivision is provided for certain subjects
      in the NLM schedules by the application of Table G notations.
    homepage: http://www.nlm.nih.gov/class/
    name: National Library of Medicine Classification
    pattern: ^[A-Z]+ [0-9]+(.[0-9](.[A-Z0-9]+)?)?$
    prefix: '528'
    wikidata_database: Q986957
  biolink:
    is_identifiers: false
    is_obo: false
    prefix: NLMID
    uri_format: https://www.ncbi.nlm.nih.gov/nlmcatalog/?term=$1
  contact:
    email: custserv@nlm.nih.gov
    github: null
    name: NLM Customer Service
    orcid: null
  contact_group_email: custserv@nlm.nih.gov
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: The NLM Catalog provides access to NLM bibliographic data for journals,
    books, audiovisuals, computer software, electronic resources and other materials.
    Links to the library's holdings in LocatorPlus, NLM's online public access catalog,
    are also provided. [from homepage]
  domain: publication
  example: '101775319'
  homepage: https://www.ncbi.nlm.nih.gov/nlmcatalog
  keywords:
  - journal
  license: public domain
  logo: https://upload.wikimedia.org/wikipedia/commons/5/52/Logo_of_U.S._National_Library_of_Medicine.png
  mappings:
    bartoc: '528'
    biolink: NLMID
    wikidata.entity: Q986957
  name: National Library of Medicine Catalog
  pattern: ^\d+$
  prefix: nlm
  uri_format: https://www.ncbi.nlm.nih.gov/nlmcatalog/$1
nlm.publisher:
  appears_in:
  - nlm
  contact:
    email: custserv@nlm.nih.gov
    github: null
    name: NLM Customer Service
    orcid: null
  contact_group_email: custserv@nlm.nih.gov
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: Publisher short codes appearin in the NLM Catalog.
  domain: organization
  example: wiley
  github_request_issue: 1318
  homepage: https://ftp.ncbi.nlm.nih.gov/pubmed/xmlprovidernames.txt
  keywords:
  - bibliometrics
  - publisher
  license: public domain
  logo: https://upload.wikimedia.org/wikipedia/commons/5/52/Logo_of_U.S._National_Library_of_Medicine.png
  name: NLM Publisher Codes
  prefix: nlm.publisher
nlx.anat:
  contact:
    email: tgbugs@gmail.com
    github: tgbugs
    name: Tom Gillespie
    orcid: 0000-0002-7509-4801
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: NLXANAT covers anatomy terms. Almost all terms are also in Uberon.
  example: 090201
  homepage: https://scicrunch.org/scicrunch/interlex/dashboard
  keywords:
  - anatomy
  name: NeuroLex Anatomy
  part_of_database: nif
  pattern: ^\d+$
  prefix: nlx.anat
  reviewer:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  twitter: SciCrunch
  uri_format: http://uri.neuinfo.org/nif/nifstd/nlx_anat_$1
nlx.br:
  contact:
    email: tgbugs@gmail.com
    github: tgbugs
    name: Tom Gillespie
    orcid: 0000-0002-7509-4801
  contributor:
    email: tgbugs@gmail.com
    github: tgbugs
    name: Tom Gillespie
    orcid: 0000-0002-7509-4801
  description: NLXBR covers brain regions from the PHT00 macaque parcellation, Paxinos,
    Huang, and Tog The Rhesus Monkey Brain In Stereotaxic Coordinates (1999).
  example: '145'
  homepage: https://github.com/SciCrunch/NIF-Ontology
  keywords:
  - anatomy
  - brain regions
  - neuroscience
  license: CC BY-4.0
  name: 'NIF Standard Ontology: Brain Regions'
  part_of_database: nif
  pattern: ^\d+$
  prefix: nlx.br
  repository: https://github.com/SciCrunch/NIF-Ontology
  reviewer:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  synonyms:
  - NLXBR
  twitter: SciCrunch
  uri_format: http://uri.neuinfo.org/nif/nifstd/nlx_br_$1
nlx.cell:
  contact:
    email: tgbugs@gmail.com
    github: tgbugs
    name: Tom Gillespie
    orcid: 0000-0002-7509-4801
  contributor:
    email: tgbugs@gmail.com
    github: tgbugs
    name: Tom Gillespie
    orcid: 0000-0002-7509-4801
  description: NLXCELL conatins cell types with a focus on neuron types.
  example: 091005
  homepage: https://github.com/SciCrunch/NIF-Ontology
  keywords:
  - cell lines
  - cell types
  - cells
  - neuroscience
  license: CC BY-4.0
  name: 'NIF Standard Ontology: Cell Types'
  part_of_database: nif
  pattern: ^\d+$
  prefix: nlx.cell
  repository: https://github.com/SciCrunch/NIF-Ontology
  reviewer:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  synonyms:
  - NLXCELL
  twitter: SciCrunch
  uri_format: http://uri.neuinfo.org/nif/nifstd/nlx_cell_$1
nlx.chem:
  contact:
    email: tgbugs@gmail.com
    github: tgbugs
    name: Tom Gillespie
    orcid: 0000-0002-7509-4801
  contributor:
    email: tgbugs@gmail.com
    github: tgbugs
    name: Tom Gillespie
    orcid: 0000-0002-7509-4801
  description: NLXCHEM covers chemicals. Most classes are also in ChEBI.
  example: 090801
  homepage: https://github.com/SciCrunch/NIF-Ontology
  keywords:
  - chemistry
  license: CC BY-4.0
  name: 'NIF Standard Ontology: Chemical'
  part_of_database: nif
  pattern: ^\d+$
  prefix: nlx.chem
  repository: https://github.com/SciCrunch/NIF-Ontology
  reviewer:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  synonyms:
  - NLXCHEM
  twitter: SciCrunch
  uri_format: http://uri.neuinfo.org/nif/nifstd/nlx_chem_$1
nlx.dys:
  appears_in:
  - mondo
  contact:
    email: tgbugs@gmail.com
    github: tgbugs
    name: Tom Gillespie
    orcid: 0000-0002-7509-4801
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: NLXDYS covers dysfunction, diseases, and disorders. Most classes are
    also in Disease Ontology (DOID), Monarch Disease Ontology (MONDO), Human Phenotype
    Ontology (HPO), etc.
  example: '20090602'
  homepage: https://scicrunch.org/scicrunch/interlex/dashboard
  keywords:
  - disease
  - disorders
  - phenotypes
  name: NeuroLex Dysfunction
  part_of_database: nif
  pattern: ^\d+$
  prefix: nlx.dys
  reviewer:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  twitter: SciCrunch
  uri_format: http://uri.neuinfo.org/nif/nifstd/nlx_dys_$1
nlx.func:
  contact:
    email: tgbugs@gmail.com
    github: tgbugs
    name: Tom Gillespie
    orcid: 0000-0002-7509-4801
  contributor:
    email: tgbugs@gmail.com
    github: tgbugs
    name: Tom Gillespie
    orcid: 0000-0002-7509-4801
  description: NLXFUNC covers terms for cognitive function.
  example: '90801'
  homepage: https://github.com/SciCrunch/NIF-Ontology
  keywords:
  - neuroscience
  license: CC BY-4.0
  name: 'NIF Standard Ontology: Cognitive Function'
  part_of_database: nif
  pattern: ^\d+$
  prefix: nlx.func
  repository: https://github.com/SciCrunch/NIF-Ontology
  reviewer:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  synonyms:
  - NLXFUNC
  twitter: SciCrunch
  uri_format: http://uri.neuinfo.org/nif/nifstd/nlx_func_$1
nlx.inv:
  contact:
    email: tgbugs@gmail.com
    github: tgbugs
    name: Tom Gillespie
    orcid: 0000-0002-7509-4801
  contributor:
    email: tgbugs@gmail.com
    github: tgbugs
    name: Tom Gillespie
    orcid: 0000-0002-7509-4801
  description: NLXINV includes funding agencies and some terms related to documenting
    scientific investigations data acquisition and analysis.
  example: '90901'
  homepage: https://github.com/SciCrunch/NIF-Ontology
  keywords:
  - data analysis
  - funding agencies
  license: CC BY-4.0
  name: 'NIF Standard Ontology: Investigations'
  part_of_database: nif
  pattern: ^\d+$
  prefix: nlx.inv
  repository: https://github.com/SciCrunch/NIF-Ontology
  reviewer:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  synonyms:
  - NLXINV
  twitter: SciCrunch
  uri_format: http://uri.neuinfo.org/nif/nifstd/nlx_inv_$1
nlx.mol:
  contact:
    email: tgbugs@gmail.com
    github: tgbugs
    name: Tom Gillespie
    orcid: 0000-0002-7509-4801
  contributor:
    email: tgbugs@gmail.com
    github: tgbugs
    name: Tom Gillespie
    orcid: 0000-0002-7509-4801
  description: NLXMOL covers molecules, proteins, and molecular roles, similar to
    entities in the Protein Ontology, UniProt, and ChEBI, with a focus on those of
    particular relevance in the nervous system.
  example: '90806'
  homepage: https://github.com/SciCrunch/NIF-Ontology
  keywords:
  - biology
  - chemistry
  - neuroscience
  - proteins
  license: CC BY-4.0
  name: 'NIF Standard Ontology: Molecules'
  part_of_database: nif
  pattern: ^\d+$
  prefix: nlx.mol
  repository: https://github.com/SciCrunch/NIF-Ontology
  reviewer:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  synonyms:
  - NLXMOL
  twitter: SciCrunch
  uri_format: http://uri.neuinfo.org/nif/nifstd/nlx_mol_$1
nlx.oen:
  contact:
    email: tgbugs@gmail.com
    github: tgbugs
    name: Tom Gillespie
    orcid: 0000-0002-7509-4801
  contributor:
    email: tgbugs@gmail.com
    github: tgbugs
    name: Tom Gillespie
    orcid: 0000-0002-7509-4801
  description: NLXOEN prefixed identifiers are from the version of the Ontology for
    Experimental Neurophysiology (OEN; https://github.com/G-Node/OEN) that were originally
    deposited in Neurolex (for examples, see https://scicrunch.org/scicrunch/interlex/search?q=NLXOEN
    results).
  example: '0001000'
  homepage: https://github.com/SciCrunch/NIF-Ontology
  keywords:
  - neuroscience
  license: CC BY-4.0
  name: 'NIF Standard Ontology: OEN Terms in Neurolex'
  part_of_database: nif
  pattern: ^\d+$
  prefix: nlx.oen
  repository: https://github.com/SciCrunch/NIF-Ontology
  reviewer:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  synonyms:
  - NLXOEN
  twitter: SciCrunch
  uri_format: http://uri.neuinfo.org/nif/nifstd/oen_$1
nlx.org:
  contact:
    email: tgbugs@gmail.com
    github: tgbugs
    name: Tom Gillespie
    orcid: 0000-0002-7509-4801
  contributor:
    email: tgbugs@gmail.com
    github: tgbugs
    name: Tom Gillespie
    orcid: 0000-0002-7509-4801
  description: NLXORG covers organisms.
  example: 090701
  homepage: https://github.com/SciCrunch/NIF-Ontology
  keywords:
  - taxonomy
  license: CC BY-4.0
  name: 'NIF Standard Ontology: Organisms'
  part_of_database: nif
  pattern: ^\d+$
  prefix: nlx.org
  repository: https://github.com/SciCrunch/NIF-Ontology
  reviewer:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  synonyms:
  - NLXORG
  twitter: SciCrunch
  uri_format: http://uri.neuinfo.org/nif/nifstd/nlx_organ_$1
nlx.qual:
  contact:
    email: tgbugs@gmail.com
    github: tgbugs
    name: Tom Gillespie
    orcid: 0000-0002-7509-4801
  contributor:
    email: tgbugs@gmail.com
    github: tgbugs
    name: Tom Gillespie
    orcid: 0000-0002-7509-4801
  description: NLXQUAL covers qualities and dispositions similar to the Phenotype
    And Trait Ontology (PATO).
  example: '100810'
  homepage: https://github.com/SciCrunch/NIF-Ontology
  keywords:
  - dispositions
  - qualities
  license: CC BY-4.0
  name: 'NIF Standard Ontology: Qualities'
  part_of_database: nif
  pattern: ^\d+$
  prefix: nlx.qual
  repository: https://github.com/SciCrunch/NIF-Ontology
  reviewer:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  synonyms:
  - NLXQUAL
  twitter: SciCrunch
  uri_format: http://uri.neuinfo.org/nif/nifstd/nlx_qual_$1
nlx.res:
  contact:
    email: tgbugs@gmail.com
    github: tgbugs
    name: Tom Gillespie
    orcid: 0000-0002-7509-4801
  contributor:
    email: tgbugs@gmail.com
    github: tgbugs
    name: Tom Gillespie
    orcid: 0000-0002-7509-4801
  description: NLXRES covers digital resources. Most classes are high level types
    covering everything from databases and sourcecode to source code licenses and
    instrument supplier websites
  example: 090924
  homepage: https://github.com/SciCrunch/NIF-Ontology
  keywords:
  - software and information systems
  license: CC BY-4.0
  name: 'NIF Standard Ontology: Digital Resources'
  part_of_database: nif
  pattern: ^\d+$
  prefix: nlx.res
  repository: https://github.com/SciCrunch/NIF-Ontology
  reviewer:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  synonyms:
  - NLXRES
  twitter: SciCrunch
  uri_format: http://uri.neuinfo.org/nif/nifstd/nlx_res_$1
nlx.sub:
  contact:
    email: tgbugs@gmail.com
    github: tgbugs
    name: Tom Gillespie
    orcid: 0000-0002-7509-4801
  contributor:
    email: tgbugs@gmail.com
    github: tgbugs
    name: Tom Gillespie
    orcid: 0000-0002-7509-4801
  description: NLXSUB covers subcellular entities similar to the cellular component
    branch of the Gene Ontology (GO).
  example: 090803
  go:
    homepage: http://www.neurolex.org/wiki
    name: Neuroscience Information Framework standard ontology, subcellular hierarchy
    prefix: NIF_Subcellular
    uri_format: http://www.neurolex.org/wiki/$1
  homepage: https://github.com/SciCrunch/NIF-Ontology
  keywords:
  - cellular components
  license: CC BY-4.0
  mappings:
    go: NIF_Subcellular
  name: 'NIF Standard Ontology: Subcellular Entities'
  part_of: neurolex
  part_of_database: nif
  pattern: ^\d+$
  prefix: nlx.sub
  repository: https://github.com/SciCrunch/NIF-Ontology
  reviewer:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  synonyms:
  - NLXSUB
  - nif_subcellular
  twitter: SciCrunch
  uri_format: http://uri.neuinfo.org/nif/nifstd/nlx_subcell_$1
nmdc:
  contact:
    email: donny@polyneme.xyz
    github: dwinston
    name: Donny Winston
    orcid: 0000-0002-8424-0604
  contributor:
    email: donny@polyneme.xyz
    github: dwinston
    name: Donny Winston
    orcid: 0000-0002-8424-0604
  contributor_extras:
  - email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: An initiative to empower the research community to harness microbiome
    data exploration and discovery through a collaborative integrative data science
    ecosystem.
  example: y3ax-8bq3-60
  github_request_issue: 130
  homepage: https://microbiomedata.org/
  keywords:
  - microbiome
  mappings:
    miriam: nmdc
    wikidata.entity: Q107698738
  miriam:
    deprecated: false
    description: The National Microbiome Data Collaborative (NMDC) is an initiative
      to empower the research community to harness microbiome data exploration and
      discovery through a collaborative integrative data science ecosystem.
    homepage: http://www.lbl.gov/
    id: 00000837
    name: National Microbiome Data Collaborative
    namespaceEmbeddedInLui: false
    pattern: ^[A-Za-z0-9._~\-\:]+$
    prefix: nmdc
    sampleId: 6m4e-1vbv-03
    uri_format: https://w3id.org/nmdc/$1
  name: National Microbiome Data Collaborative
  pattern: ^.{2,}$
  prefix: nmdc
  providers:
  - code: web
    description: Direct link
    example: null
    first_party: null
    homepage: https://drs.microbiomedata.org
    name: NMDC Web Page
    publications: null
    status: null
    uri_format: https://drs.microbiomedata.org/objects/$1
  rdf_uri_format: https://w3id.org/nmdc/$1
  references:
  - https://github.com/biopragmatics/bioregistry/pull/982
  reviewer:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  uri_format: https://w3id.org/nmdc/$1
  wikidata:
    database: Q107698738
nmpdr:
  comment: This resource doesn't exist on the web anymore
  deprecated: true
  mappings:
    ncbi: NMPDR
    prefixcommons: nmpdr
  ncbi:
    example: fig|306254.1.peg.183
    homepage: http://www.nmpdr.org
    name: National Microbial Pathogen Data Resource
    prefix: NMPDR
  prefix: nmpdr
  prefixcommons:
    description: The NMPDR provided curated annotations in an environment for comparative
      analysis of genomes and biological subsystems, with an emphasis on the food-borne
      pathogens Campylobacter, Listeria, Staphylococcus, Streptococcus, and Vibrio;
      as well as the STD pathogens Chlamydiaceae, Haemophilus, Mycoplasma, Neisseria,
      Treponema, and Ureaplasma.
    example: fig|360108.3.peg.195
    homepage: http://www.nmpdr.org
    keywords:
    - genome
    name: National Microbial Pathogen Data Resource
    pattern: ^[A-Z,0-9]+$
    prefix: nmpdr
    uri_format: http://www.nmpdr.org/FIG/wiki/rest.cgi/NmpdrPlugin/SeedViewer?page=Annotation;feature=$1
  reviewer:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
nmr:
  aberowl:
    description: This is the new msi-sanctioned nmr CV, created within the COSMOS
      EU project, to support the nmrML data standard for nuclear magnetic resonance
      data in metabolomics with meaningful raw data descriptors.
    download_owl: http://aber-owl.net/media/ontologies/NMR/12/nmr.owl
    homepage: http://nmrml.org/cv/
    name: NMR-Controlled Vocabulary
    prefix: NMR
    version: 1.1.0
  biocontext:
    prefix: NMR
  bioportal:
    contact:
      email: dschober@ipb-halle.de
      name: Daniel Schober
    description: This is the new msi-sanctioned nmr CV, created within the COSMOS
      EU project, to support the nmrML data standard for nuclear magnetic resonance
      data in metabolomics with meaningful raw data descriptors.
    homepage: http://nmrml.org/cv/
    name: NMR-Controlled Vocabulary
    prefix: NMR
    version: 1.1.0
  contact:
    email: schober@imbi.uni-freiburg.de
    github: DSchober
    name: Daniel Schober
    orcid: 0000-0001-8014-6648
  download_owl: https://nmrml.org/cv/stable/nmrCV.owl
  mappings:
    aberowl: NMR
    biocontext: NMR
    bioportal: NMR
    miriam: nmr
    n2t: nmr
    obofoundry: nmr
    ols: nmrcv
    prefixcommons: nmr
    tib: nmrcv
    wikidata.entity: Q114677901
  miriam:
    deprecated: false
    description: nmrCV is a controlled vocabulary to deliver standardized descriptors
      for the open mark-up language for NMR raw and spectrum data, sanctioned by the
      metabolomics standards initiative msi.
    homepage: https://www.ebi.ac.uk/ols4/ontologies/nmrcv
    id: 00000639
    name: Nuclear Magnetic Resonance Controlled Vocabulary
    namespaceEmbeddedInLui: true
    pattern: ^NMR:\d+$
    prefix: nmr
    sampleId: '1000003'
    uri_format: https://www.ebi.ac.uk/ols4/ontologies/nmrcv/terms?curie=NMR:$1
  n2t:
    description: nmrCV is a controlled vocabulary to deliver standardized descriptors
      for the open mark-up language for NMR raw and spectrum data, sanctioned by the
      metabolomics standards initiative msi.
    example: '1000003'
    homepage: https://www.ebi.ac.uk/ols/ontologies/nmrcv
    name: NMR through OLS
    namespaceEmbeddedInLui: true
    pattern: ^NMR:\d+$
    prefix: nmr
    uri_format: https://www.ebi.ac.uk/ols/ontologies/nmrcv/terms?short_form=NMR:$1
  obofoundry:
    contact: schober@imbi.uni-freiburg.de
    contact.label: Schober Daniel
    deprecated: true
    description: Descriptors relevant to the experimental conditions of the Nuclear
      Magnetic Resonance (NMR) component in a metabolomics investigation.
    domain: investigations
    download.owl: http://purl.obolibrary.org/obo/nmr.owl
    homepage: http://msi-ontology.sourceforge.net/
    name: NMR-instrument specific component of metabolomics investigations
    prefix: nmr
  ols:
    description: 'This artefact is an MSI-approved controlled vocabulary primarily
      developed under COSMOS EU and PhenoMeNal EU governance. The nmrCV is supporting
      the nmrML XML format with standardized terms. nmrML is a vendor agnostic open
      access NMR raw data standard. Its primaly role is analogous to the mzCV for
      the PSI-approved mzML XML format. It uses BFO2.0 as its Top level. This CV was
      derived from two predecessors (The NMR CV from the David Wishart Group, developed
      by Joseph Cruz) and the MSI nmr CV developed by Daniel Schober at the EBI.  This
      simple taxonomy of terms (no DL semantics used) serves the nuclear magnetic
      resonance markup language (nmrML) with meaningful descriptors to amend the nmrML
      xml file with CV terms. Metabolomics scientists are encouraged to use this CV
      to annotrate their raw and experimental context data, i.e. within nmrML. The
      approach to have an exchange syntax mixed of an xsd and CV stems from the PSI
      mzML effort. The reason to branch out from an xsd into a CV is, that in areas
      where the terminology is likely to change faster than the nmrML xsd could be
      updated and aligned, an externally and decentrallised maintained CV can accompensate
      for such dynamics in a more flexible way. A second reason for this set-up is
      that semantic validity of CV terms used in an nmrML XML instance (allowed CV
      terms, position/relation to each other, cardinality) can be validated by rule-based
      proprietary validators:  By means of cardinality specifications and XPath expressions
      defined in an XML mapping file (an instances of the CvMappingRules.xsd ), one
      can define what ontology terms are allowed in a specific location of the data
      model.'
    download_owl: http://nmrml.org/cv/stable/nmrCV.owl
    homepage: http://nmrml.org/cv/
    name: nuclear magnetic resonance CV
    prefix: nmrcv
    uri_format: http://nmrML.org/nmrCV#NMR$1
    version: 1.1.0
    version.iri: http://nmrml.org/cv/v1.1.0/nmrCV.owl
  pattern: ^\d+$
  prefix: nmr
  prefixcommons:
    bioportal: '1033'
    description: Descriptors relevant to the experimental conditions of the Nuclear
      Magnetic Resonance (NMR) component in a metabolomics investigation.
    example: NMR_400113
    homepage: http://msi-ontology.sourceforge.net/
    keywords:
    - owl
    - nmr
    name: NMR-instrument specific component of metabolomics investigations
    pattern: ^NMR_\d+$
    prefix: nmr
    rdf_uri_format: http://msi-ontology.sourceforge.net/ontology/NMR.owl#$1
    synonyms:
    - msi.nmr
  repository: https://github.com/nmrML/nmrCV
  synonyms:
  - nmrcv
  tib:
    description: 'This artefact is an MSI-approved controlled vocabulary primarily
      developed under COSMOS EU and PhenoMeNal EU governance. The nmrCV is supporting
      the nmrML XML format with standardized terms. nmrML is a vendor agnostic open
      access NMR raw data standard. Its primaly role is analogous to the mzCV for
      the PSI-approved mzML XML format. It uses BFO2.0 as its Top level. This CV was
      derived from two predecessors (The NMR CV from the David Wishart Group, developed
      by Joseph Cruz) and the MSI nmr CV developed by Daniel Schober at the EBI.  This
      simple taxonomy of terms (no DL semantics used) serves the nuclear magnetic
      resonance markup language (nmrML) with meaningful descriptors to amend the nmrML
      xml file with CV terms. Metabolomics scientists are encouraged to use this CV
      to annotrate their raw and experimental context data, i.e. within nmrML. The
      approach to have an exchange syntax mixed of an xsd and CV stems from the PSI
      mzML effort. The reason to branch out from an xsd into a CV is, that in areas
      where the terminology is likely to change faster than the nmrML xsd could be
      updated and aligned, an externally and decentrallised maintained CV can accompensate
      for such dynamics in a more flexible way. A second reason for this set-up is
      that semantic validity of CV terms used in an nmrML XML instance (allowed CV
      terms, position/relation to each other, cardinality) can be validated by rule-based
      proprietary validators: By means of cardinality specifications and XPath expressions
      defined in an XML mapping file (an instances of the CvMappingRules.xsd ), one
      can define what ontology terms are allowed in a specific location of the data
      model.'
    download_owl: http://nmrml.org/cv/v1.1.0/nmrCV.owl
    homepage: http://nmrml.org/cv/
    keywords:
    - NFDI4CHEM
    - chemistry
    - chemical and environmental engineering
    name: nuclear magnetic resonance CV
    prefix: nmrcv
    tracker: https://github.com/nmrML/nmrML/issues
    uri_format: http://nmrML.org/nmrCV#$1
    version.iri: http://nmrml.org/cv/v1.1.0/nmrCV.owl
nmrshiftdb2:
  contributor_extras:
  - email: b.gyori@northeastern.edu
    github: bgyori
    name: Benjamin M. Gyori
    orcid: 0000-0001-9439-5346
  fairsharing:
    abbreviation: nmrshiftdb2
    contact:
      email: stefan.kuhn@dmu.ac.uk
      name: Stefan Kuhn
      orcid: 0000-0002-5990-4157
    description: nmrshiftdb2 is an NMR database for organic structures and their nuclear
      magnetic resonance (NMR) spectra. It allows for spectrum prediction (13C, 1H
      and other nuclei) as well as for searching spectra, structures and other properties.
      It also features peer-reviewed submission of datasets by its users. The nmrshiftdb2
      software is open source, the data is published under an open content license.
    homepage: https://nmrshiftdb.nmr.uni-koeln.de/
    name: nmrshiftdb2
    prefix: FAIRsharing.nYaZ1N
    publications:
    - doi: 10.1021/ci0341363
      pubmed_id: 14632418
      title: NMRShiftDB-constructing a free chemical information system with open-source
        components.
    - doi: 10.1002/mrc.4263
      pubmed_id: 25998807
      title: 'Facilitating quality control for spectra assignments of small organic
        molecules: nmrshiftdb2--a free in-house NMR database with integrated LIMS
        for academic service laboratories.'
    - doi: 10.1016/j.phytochem.2004.08.027
      pubmed_id: 15464159
      title: NMRShiftDB -- compound identification and structure elucidation support
        through a free community-built web database.
    subjects:
    - Analytical Chemistry
  mappings:
    fairsharing: FAIRsharing.nYaZ1N
    miriam: nmrshiftdb2
    re3data: r3d100010316
    wikidata: P9405
  miriam:
    deprecated: false
    description: NMR database for organic structures and their nuclear magnetic resonance
      (nmr) spectra. It allows for spectrum prediction (13C, 1H and other nuclei)
      as well as for searching spectra, structures and other properties.
    homepage: https://nmrshiftdb.nmr.uni-koeln.de
    id: 00000748
    name: NMR Shift Database
    namespaceEmbeddedInLui: false
    pattern: ^[0-9]+$
    prefix: nmrshiftdb2
    sampleId: '234'
    uri_format: https://nmrshiftdb.nmr.uni-koeln.de/molecule/$1
  name: NMRShiftDB structure
  prefix: nmrshiftdb2
  publications:
  - doi: 10.1002/mrc.4263
    pmc: null
    pubmed: '25998807'
    title: 'Facilitating quality control for spectra assignments of small organic
      molecules: nmrshiftdb2--a free in-house NMR database with integrated LIMS for
      academic service laboratories'
    year: 2015
  - doi: 10.1016/j.phytochem.2004.08.027
    pmc: null
    pubmed: '15464159'
    title: NMRShiftDB -- compound identification and structure elucidation support
      through a free community-built web database
    year: 2004
  - doi: 10.1021/ci0341363
    pmc: null
    pubmed: '14632418'
    title: NMRShiftDB-constructing a free chemical information system with open-source
      components
    year: 2003
  - doi: 10.1021/ci0341363
    pmc: null
    pubmed: null
    title: NMRShiftDB-constructing a free chemical information system with open-source
      components.
    year: null
  - doi: 10.1002/mrc.4263
    pmc: null
    pubmed: null
    title: 'Facilitating quality control for spectra assignments of small organic
      molecules: nmrshiftdb2--a free in-house NMR database with integrated LIMS for
      academic service laboratories.'
    year: null
  - doi: 10.1016/j.phytochem.2004.08.027
    pmc: null
    pubmed: null
    title: NMRShiftDB -- compound identification and structure elucidation support
      through a free community-built web database.
    year: null
  - doi: 10.1021/ci0341363
    pmc: null
    pubmed: null
    title: NMRShiftDB-constructing a free chemical information system with open-source
      components.
    year: null
  - doi: 10.1002/mrc.4263
    pmc: null
    pubmed: null
    title: 'Facilitating quality control for spectra assignments of small organic
      molecules: nmrshiftdb2--a free in-house NMR database with integrated LIMS for
      academic service laboratories.'
    year: null
  - doi: 10.1016/j.phytochem.2004.08.027
    pmc: null
    pubmed: null
    title: NMRShiftDB -- compound identification and structure elucidation support
      through a free community-built web database.
    year: null
  - doi: 10.1021/ci0341363
    pmc: null
    pubmed: null
    title: NMRShiftDB-constructing a free chemical information system with open-source
      components.
    year: null
  - doi: 10.1002/mrc.4263
    pmc: null
    pubmed: null
    title: 'Facilitating quality control for spectra assignments of small organic
      molecules: nmrshiftdb2--a free in-house NMR database with integrated LIMS for
      academic service laboratories.'
    year: null
  - doi: 10.1016/j.phytochem.2004.08.027
    pmc: null
    pubmed: null
    title: NMRShiftDB -- compound identification and structure elucidation support
      through a free community-built web database.
    year: null
  re3data:
    description: nmrshiftdb is a NMR database (web database) for organic structures
      and their nuclear magnetic resonance (nmr) spectra. It allows for spectrum prediction
      (13C, 1H and other nuclei) as well as for searching spectra, structures and
      other properties. Last not least, it features peer-reviewed submission of datasets
      by its users. The nmrshiftdb2 software is open source, the data is published
      under an open content license. Please consult the documentation for more detailed
      information. nmrshiftdb2 is the continuation of the NMRShiftDB project with
      additional data and bugfixes and changes in the software.
    doi: 10.17616/R3MK6H
    homepage: https://nmrshiftdb.nmr.uni-koeln.de/
    license: other
    name: NMRshiftDB
    prefix: r3d100010316
    xrefs:
      omics: '18926'
  synonyms:
  - NMRShiftDB
  wikidata:
    description: structure identifiers in the NMRShiftDB
    example:
    - '20143612'
    - '20188613'
    - '20213347'
    homepage: https://nmrshiftdb.nmr.uni-koeln.de/
    name: NMRShiftDB structure ID
    pattern: ^\d+$
    prefix: P9405
    uri_format: https://nmrshiftdb.nmr.uni-koeln.de/molecule/$1
nmrxiv.compound:
  contact:
    email: null
    github: vcnainala
    name: Chandu Nainala
    orcid: 0000-0002-2564-3243
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: compounds appearing in nmrXiv that have associated spectra.
  domain: chemical
  example: '188'
  github_request_issue: 1708
  homepage: https://nmrxiv.org/compounds
  keywords:
  - chemical
  - compound
  name: nmrXiv compound
  part_of_database: nmrxiv
  prefix: nmrxiv.compound
  uri_format: https://nmrxiv.org/spectra?compound=$1
nmrxiv.project:
  contact:
    email: null
    github: vcnainala
    name: Chandu Nainala
    orcid: 0000-0002-2564-3243
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: A project in the nmrXiv
  domain: project
  example: P136
  github_request_issue: 1708
  homepage: https://nmrxiv.org/projects
  keywords:
  - datasets
  - project
  name: nmrXiv project
  part_of_database: nmrxiv
  pattern: ^P\d+$
  prefix: nmrxiv.project
  uri_format: https://nmrxiv.org/project/$1
nmrxiv.sample:
  contact:
    email: null
    github: vcnainala
    name: Chandu Nainala
    orcid: 0000-0002-2564-3243
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: spectra (samples) in the nmrXiv database
  domain: experiment
  example: S1295
  github_request_issue: 1708
  homepage: https://nmrxiv.org/spectra
  keywords:
  - nmr
  - sample
  - spectra
  - spectrum
  name: nmrXiv sample
  part_of_database: nmrxiv
  pattern: ^S\d+$
  prefix: nmrxiv.sample
  uri_format: https://nmrxiv.org/sample/$1
noaa.cameo:
  description: CAMEO Chemicals is a database of hazardous chemical datasheets that
    emergency responders and planners can use to get response recommendations and
    predict hazards—such as explosions or toxic fumes.
  mappings:
    wikidata: P11931
    wikidata.entity: Q125807660
  part_of_database: noaa
  prefix: noaa.cameo
  wikidata:
    database: Q125807660
    description: chemical in the database supplied by National Oceanic and Atmospheric
      Administration
    example:
    - '19757'
    - '667'
    - '8754'
    homepage: https://cameochemicals.noaa.gov
    name: CAMEO Chemicals ID
    pattern: ^\d*$
    prefix: P11931
    uri_format: https://cameochemicals.noaa.gov/chemical/$1
noaa.species:
  contributor:
    email: meghan.balk@gmail.com
    github: megbalk
    name: Meghan Balk
    orcid: 0000-0003-2699-3066
  description: Identifier for a species on the noaa fisheries website
  example: long-finned-pilot-whale
  github_request_issue: 456
  homepage: https://www.fisheries.noaa.gov/species-directory
  mappings:
    wikidata: P6049
  name: NOAA Fisheries Species Directory
  part_of_database: noaa
  pattern: ^[a-z]+(\-[a-z]+)*$
  prefix: noaa.species
  reviewer:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  synonyms:
  - noaa
  uri_format: https://www.fisheries.noaa.gov/species/$1
  wikidata:
    description: identifier for a species on the NOAA Fisheries website
    example:
    - alaska-snow-crab
    - blue-mussel
    - long-finned-pilot-whale
    homepage: https://www.fisheries.noaa.gov/species-directory
    name: NOAA Fisheries Species Directory ID
    pattern: ^[a-z]+(\-[a-z]+)*$
    prefix: P6049
    uri_format: https://www.fisheries.noaa.gov/species/$1
nomen:
  aberowl:
    description: NOMEN is a nomenclatural ontology for biological names (not concepts).
      It encodes the goverened rules of nomenclature.
    download_owl: http://aber-owl.net/media/ontologies/NOMEN/11/nomen.owl
    homepage: https://github.com/SpeciesFileGroup/nomen
    name: NOMEN - A nomenclatural ontology for biological names
    prefix: NOMEN
  bioportal:
    contact:
      email: diapriid@gmail.com
      name: Matt Yoder
    description: NOMEN is a nomenclatural ontology for biological names (not concepts).
      It encodes the goverened rules of nomenclature.
    homepage: https://github.com/SpeciesFileGroup/nomen
    name: NOMEN - A nomenclatural ontology for biological names
    prefix: NOMEN
  example: 0000295
  mappings:
    aberowl: NOMEN
    bioportal: NOMEN
    obofoundry: nomen
    ols: nomen
    ontobee: NOMEN
    wikidata.entity: Q81661723
  name: A nomenclatural ontology for biological names
  obofoundry:
    contact: diapriid@gmail.com
    contact.github: mjy
    contact.label: Matt Yoder
    contact.orcid: 0000-0002-5640-5491
    deprecated: false
    description: NOMEN is a nomenclatural ontology for biological names (not concepts).  It
      encodes the goverened rules of nomenclature.
    domain: information
    download.owl: http://purl.obolibrary.org/obo/nomen.owl
    homepage: https://github.com/SpeciesFileGroup/nomen
    license: CC0 1.0
    license.url: https://creativecommons.org/publicdomain/zero/1.0/
    name: NOMEN - A nomenclatural ontology for biological names
    preferredPrefix: NOMEN
    prefix: nomen
    repository: https://github.com/SpeciesFileGroup/nomen
  ols:
    description: NOMEN is a nomenclatural ontology for biological names (not concepts).  It
      encodes the goverened rules of nomenclature.
    download_owl: http://purl.obolibrary.org/obo/nomen.owl
    homepage: https://github.com/SpeciesFileGroup/nomen
    name: NOMEN - A nomenclatural ontology for biological names
    prefix: nomen
    tracker: https://github.com/SpeciesFileGroup/nomen/issues
  ontobee:
    library: Library
    name: NOMEN - A nomenclatural ontology for biological names
    prefix: NOMEN
  pattern: ^\d{7}$
  prefix: nomen
  uri_format: http://purl.obolibrary.org/obo/NOMEN_$1
noncodev3:
  biocontext:
    prefix: NONCODEV3
  contact:
    email: biozy@ict.ac.cn
    github: null
    name: Yi Zhao
    orcid: 0000-0001-6049-8347
  mappings:
    biocontext: NONCODEV3
    miriam: noncodev3
    n2t: noncodev3
    prefixcommons: noncode
  miriam:
    deprecated: true
    description: NONCODE is a database of expression and functional lncRNA (long noncoding
      RNA) data obtained from microarray studies. LncRNAs have been shown to play
      key roles in various biological processes such as imprinting control, circuitry
      controlling pluripotency and differentiation, immune responses and chromosome
      dynamics. The collection references NONCODE version 3. This was replaced in
      2013 by version 4.
    homepage: http://www.noncode.org/
    id: 00000248
    name: NONCODE v3
    namespaceEmbeddedInLui: false
    pattern: ^\d+$
    prefix: noncodev3
    sampleId: '377550'
    uri_format: http://www.noncode.org/NONCODERv3/ncrna.php?ncid=$1
  n2t:
    description: NONCODE is a database of expression and functional lncRNA (long noncoding
      RNA) data obtained from microarray studies. LncRNAs have been shown to play
      key roles in various biological processes such as imprinting control, circuitry
      controlling pluripotency and differentiation, immune responses and chromosome
      dynamics. The collection references NONCODE version 3. This was replaced in
      2013 by version 4.
    example: '377550'
    homepage: http://www.noncode.org/
    name: NONCODE at Chinese Academy of Sciences
    namespaceEmbeddedInLui: false
    pattern: ^\d+$
    prefix: noncodev3
    uri_format: http://www.noncode.org/NONCODERv3/ncrna.php?ncid=$1
  prefix: noncodev3
  prefixcommons:
    description: NONCODE is a database of expression and functional lncRNA (long noncoding
      RNA) data obtained from microarray studies. LncRNAs have been shown to play
      key roles in various biological processes such as imprinting control, circuitry
      controlling pluripotency and differentiation, immune responses and chromosome
      dynamics.
    example: '377550'
    homepage: http://www.noncode.org/
    keywords:
    - expression
    - nucleotide
    name: NONCODE
    pattern: ^\d+$
    prefix: noncode
    pubmed_ids:
    - '22135294'
    uri_format: http://www.noncode.org/NONCODERv3/ncrna.php?ncid=$1
  publications:
  - doi: 10.1093/nar/gkr1175
    pmc: PMC3245065
    pubmed: '22135294'
    title: 'NONCODE v3.0: integrative annotation of long noncoding RNAs'
    year: 2011
  - doi: null
    pmc: null
    pubmed: '22135294'
    title: null
    year: null
noncodev4.gene:
  biocontext:
    prefix: NONCODEV4.GENE
  mappings:
    biocontext: NONCODEV4.GENE
    miriam: noncodev4.gene
    n2t: noncodev4.gene
  miriam:
    deprecated: true
    description: NONCODE is a database of expression and functional lncRNA (long noncoding
      RNA) data obtained from microarray studies. LncRNAs have been shown to play
      key roles in various biological processes such as imprinting control, circuitry
      controlling pluripotency and differentiation, immune responses and chromosome
      dynamics. The collection references NONCODE version 4 and relates to gene regions.
    homepage: http://www.bioinfo.org/NONCODEv4/
    id: 00000480
    name: NONCODE v4 Gene
    namespaceEmbeddedInLui: false
    pattern: ^NONHSAG\d{5}$
    prefix: noncodev4.gene
    sampleId: NONHSAG00001
    uri_format: http://www.bioinfo.org/NONCODEv4/show_gene.php?id=$1
  n2t:
    description: NONCODE is a database of expression and functional lncRNA (long noncoding
      RNA) data obtained from microarray studies. LncRNAs have been shown to play
      key roles in various biological processes such as imprinting control, circuitry
      controlling pluripotency and differentiation, immune responses and chromosome
      dynamics. The collection references NONCODE version 4 and relates to gene regions.
    example: NONHSAG00001
    homepage: http://www.bioinfo.org/NONCODEv4/
    name: NONCODE v4 Gene at Chinese Academy of Sciences
    namespaceEmbeddedInLui: false
    pattern: ^NONHSAG\d{5}$
    prefix: noncodev4.gene
    uri_format: http://www.bioinfo.org/NONCODEv4/show_gene.php?id=$1
  prefix: noncodev4.gene
noncodev4.rna:
  biocontext:
    prefix: NONCODEV4.RNA
  mappings:
    biocontext: NONCODEV4.RNA
    miriam: noncodev4.rna
    n2t: noncodev4.rna
  miriam:
    deprecated: true
    description: NONCODE is a database of expression and functional lncRNA (long noncoding
      RNA) data obtained from microarray studies. LncRNAs have been shown to play
      key roles in various biological processes such as imprinting control, circuitry
      controlling pluripotency and differentiation, immune responses and chromosome
      dynamics. The collection references NONCODE version 4 and relates to individual
      transcripts.
    homepage: http://www.bioinfo.org/NONCODEv4/
    id: 00000481
    name: NONCODE v4 Transcript
    namespaceEmbeddedInLui: false
    pattern: ^NONHSAT\d{6}$
    prefix: noncodev4.rna
    sampleId: NONHSAT000001
    uri_format: http://www.bioinfo.org/NONCODEv4/show_rna.php?id=$1
  n2t:
    description: NONCODE is a database of expression and functional lncRNA (long noncoding
      RNA) data obtained from microarray studies. LncRNAs have been shown to play
      key roles in various biological processes such as imprinting control, circuitry
      controlling pluripotency and differentiation, immune responses and chromosome
      dynamics. The collection references NONCODE version 4 and relates to individual
      transcripts.
    example: NONHSAT000001
    homepage: http://www.bioinfo.org/NONCODEv4/
    name: NONCODE v4 Transcript at Chinese Academy of Sciences
    namespaceEmbeddedInLui: false
    pattern: ^NONHSAT\d{6}$
    prefix: noncodev4.rna
    uri_format: http://www.bioinfo.org/NONCODEv4/show_rna.php?id=$1
  prefix: noncodev4.rna
nord:
  appears_in:
  - mondo
  contact:
    email: sean@skm.digital
    github: skm16
    name: Sean Roberts
    orcid: null
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: A website containing information about rare diseases, powered by Wordpress.
  example: '1693'
  github_request_issue: 1375
  homepage: https://rarediseases.org
  name: National Organization for Rare Disorders
  pattern: ^\d+$
  prefix: nord
  references:
  - https://github.com/monarch-initiative/mondo/issues/8588
  uri_format: https://rarediseases.org/?p=$1
norine:
  biocontext:
    prefix: NORINE
  contact:
    email: maude.pupin@univ-lille.fr
    github: null
    name: Maude Pupin
    orcid: 0000-0003-3197-0715
  fairsharing:
    abbreviation: NORINE
    description: Norine is a platform that includes a database of nonribosomal peptides
      together with tools for their analysis.
    homepage: http://norine.univ-lille.fr/norine/
    license: CC BY-NC-SA 4.0
    name: Non-Ribosomal Peptides Database
    prefix: FAIRsharing.gf8yhy
    publications:
    - doi: 10.1093/nar/gkm792
      pubmed_id: 17913739
      title: 'NORINE: a database of nonribosomal peptides.'
    - doi: 10.1093/nar/gkz1000
      pubmed_id: null
      title: 'Norine: update of the nonribosomal peptide resource'
    subjects:
    - Life Science
  mappings:
    biocontext: NORINE
    fairsharing: FAIRsharing.gf8yhy
    miriam: norine
    n2t: norine
    prefixcommons: norine
  miriam:
    deprecated: false
    description: Norine is a database dedicated to nonribosomal peptides (NRPs). In
      bacteria and fungi, in addition to the traditional ribosomal proteic biosynthesis,
      an alternative ribosome-independent pathway called NRP synthesis allows peptide
      production. The molecules synthesized by NRPS contain a high proportion of nonproteogenic
      amino acids whose primary structure is not always linear, often being more complex
      and containing cycles and branchings.
    homepage: https://bioinfo.cristal.univ-lille.fr/norine/
    id: 00000498
    name: NORINE
    namespaceEmbeddedInLui: false
    pattern: ^NOR\d+$
    prefix: norine
    sampleId: NOR00681
    uri_format: https://bioinfo.cristal.univ-lille.fr/norine/result.jsp?ID=$1
  n2t:
    description: Norine is a database dedicated to nonribosomal peptides (NRPs). In
      bacteria and fungi, in addition to the traditional ribosomal proteic biosynthesis,
      an alternative ribosome-independent pathway called NRP synthesis allows peptide
      production. The molecules synthesized by NRPS contain a high proportion of nonproteogenic
      amino acids whose primary structure is not always linear, often being more complex
      and containing cycles and branchings.
    example: NOR00681
    homepage: http://bioinfo.lifl.fr/norine/
    name: NORINE at Computer Science Laboratory of Lille
    namespaceEmbeddedInLui: false
    pattern: ^NOR\d+$
    prefix: norine
    uri_format: http://bioinfo.lifl.fr/norine/result.jsp?ID=$1
  name: Nonribosomal Peptides Database
  prefix: norine
  prefixcommons:
    description: Norine is a platform that includes a database of nonribosomal peptides
      together with tools for their analysis. Norine currently contains more than
      1000 peptides.
    example: NOR00681
    homepage: http://bioinfo.lifl.fr/norine/
    keywords:
    - protein
    name: Non-Ribosomal Peptides Database
    pattern: ^NOR\d+$
    prefix: norine
    uri_format: http://bioinfo.lifl.fr/norine/result.jsp?ID=$1
  publications:
  - doi: 10.1093/nar/gkz1000
    pmc: PMC7145658
    pubmed: '31691799'
    title: 'Norine: update of the nonribosomal peptide resource'
    year: 2020
  - doi: 10.1093/nar/gkm792
    pmc: PMC2238963
    pubmed: '17913739'
    title: 'NORINE: a database of nonribosomal peptides'
    year: 2007
novus:
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: A vendor of antibodies and other biologics
  example: nb100-56351
  homepage: https://www.novusbio.com
  name: Novus Biologicals
  prefix: novus
  uri_format: https://www.novusbio.com/products/$1
npass:
  comment: This resource does not have an explicit license. The [lotus database](https://github.com/lotusnprod/lotus-processor/blob/main/docs/licenses/npass.md)
    inferred that the CC-BY-NC license from the paper might be good enough for applying
    to the data itself.
  contact:
    email: chenyuzong@sz.tsinghua.edu.cn
    github: null
    name: Yu Zong Chen
    orcid: 0000-0002-5473-8022
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: Database for integrating species source of natural products & connecting
    natural products to biological targets via  experimental-derived quantitative
    activity data.
  domain: chemical
  example: NPC139585
  homepage: http://bidd.group/NPASS/
  keywords:
  - chemical
  - compound
  - natural product
  - small molecule
  license: CC-BY-NC
  logo: https://bidd.group/NPASS/images/logo.png
  name: Natural Product Activity and Species Source Database
  pattern: ^NPC\d+$
  prefix: npass
  publications:
  - doi: 10.1093/nar/gkac1069
    pmc: PMC9825494
    pubmed: '36624664'
    title: 'NPASS database update 2023: quantitative natural product activity and
      species source database for biomedical research'
    year: 2023
  - doi: 10.1093/nar/gkx1026
    pmc: PMC5753227
    pubmed: '29106619'
    title: 'NPASS: natural product activity and species source database for natural
      product research, discovery and tool development'
    year: 2018
  uri_format: https://bidd.group/NPASS/compound.php?compoundID=$1
npatlas:
  contact:
    email: rliningt@sfu.ca
    github: null
    name: Roger Linington
    orcid: 0000-0003-1818-4971
  contributor:
    email: m.naguthana@hotmail.com
    github: nagutm
    name: Mufaddal Naguthanawala
    orcid: 0009-0009-5240-7463
  description: Identifiers for microbially derived natural products that contains
    compound structures, producing organism taxonomy, biosynthetic and chemical properties.
  example: NPA000001
  github_request_issue: 1295
  homepage: https://www.npatlas.org
  name: The Natural Products Atlas
  pattern: ^NPA\d{6}$
  prefix: npatlas
  publications:
  - doi: 10.1093/nar/gkae1093
    pmc: null
    pubmed: '39588755'
    title: 'The Natural Products Atlas 3.0: extending the database of microbially
      derived natural products'
    year: 2024
  - doi: 10.1093/nar/gkab941
    pmc: PMC8728154
    pubmed: '34718710'
    title: 'The Natural Products Atlas 2.0: a database of microbially-derived natural
      products'
    year: 2021
  - doi: 10.1021/acscentsci.9b00806
    pmc: PMC6891855
    pubmed: '31807684'
    title: 'The Natural Products Atlas: An Open Access Knowledge Base for Microbial
      Natural Products Discovery'
    year: 2019
  reviewer:
    email: b.gyori@northeastern.edu
    github: bgyori
    name: Benjamin M. Gyori
    orcid: 0000-0001-9439-5346
  uri_format: https://www.npatlas.org/explore/compounds/$1
npm:
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: A repository of software packages written in Javascript, TypeScript,
    and related.
  example: '@biopragmatics/curies'
  example_extras:
  - ansi-pad
  homepage: https://www.npmjs.com
  name: Node Package Manager
  prefix: npm
  uri_format: https://www.npmjs.com/package/$1
npo:
  aberowl:
    description: An ontology that represents the basic knowledge of physical, chemical
      and functional characteristics of nanotechnology as used in cancer diagnosis
      and therapy.
    download_owl: http://aber-owl.net/media/ontologies/NPO/31/npo.owl
    homepage: http://www.nano-ontology.org
    name: NanoParticle Ontology
    prefix: NPO
    version: 2011-12-08 (yyyy-mm-dd)
  bioportal:
    contact:
      email: nathan.baker@pnl.gov
      name: Nathan Baker
    description: An ontology that represents the basic knowledge of physical, chemical
      and functional characteristics of nanotechnology as used in cancer diagnosis
      and therapy.
    homepage: http://www.nano-ontology.org
    name: NanoParticle Ontology
    prefix: NPO
    publications:
    - http://www.nano-ontology.org
    version: 2011-12-08 (yyyy-mm-dd)
  contact:
    email: nathan.baker@pnnl.gov
    github: sobolevnrm
    name: Nathan Baker
    orcid: 0000-0002-5892-6506
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: An ontology that represents the basic knowledge of physical, chemical
    and functional characteristics of nanotechnology as used in cancer diagnosis and
    therapy.
  example: '1731'
  fairsharing:
    abbreviation: NPO
    contact:
      email: nathan.baker@pnl.gov
      name: Nathan Baker
      orcid: 0000-0002-5892-6506
    description: An ontology that represents the basic knowledge of physical, chemical
      and functional characteristics of nanotechnology as used in cancer diagnosis
      and therapy.
    domains:
    - molecular entity
    - nanoparticle
    - structure
    homepage: http://www.nano-ontology.org
    name: NanoParticle Ontology
    prefix: FAIRsharing.vy0p71
    publications:
    - doi: 10.1016/j.jbi.2010.03.001
      pubmed: '20211274'
      title: NanoParticle Ontology for cancer nanotechnology research
      year: 2010
    subjects:
    - Life Science
  homepage: https://bioportal.bioontology.org/ontologies/NPO
  mappings:
    aberowl: NPO
    bioportal: NPO
    fairsharing: FAIRsharing.vy0p71
  name: NanoParticle Ontology
  pattern: ^\d+$
  prefix: npo
  publications:
  - doi: 10.1016/j.jbi.2010.03.001
    pmc: PMC3042056
    pubmed: '20211274'
    title: NanoParticle Ontology for cancer nanotechnology research
    year: 2010
  repository: https://github.com/sobolevnrm/npo
  uri_format: http://purl.bioontology.org/ontology/npo#NPO_$1
nrfc:
  cellosaurus:
    category: Cell line collections (Providers)
    homepage: https://mail.nbfgr.res.in/nrfc/
    name: National Repository of Fish Cell Line
    prefix: NRFC
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: The NRFC was established at ICAR-National Bureau of Fish Genetic Resources,
    Lucknow in the form of a research project entitled ‘Establishment of a National
    Repository at NBFGR, Lucknow for conservation and characterization of fish cell
    lines’ during 09 November, 2010 to 08 November, 2014 with the financial support
    from Department of Biotechnology, Govt. of India, New Delhi. NRFC aims to receive,
    authenticate, store and supply the fish cell lines to the researchers and academicians
    for Research & Development works and to serve as a National Referral Centre for
    fish cell lines in the country. NRFC also aims to provide need-based support for
    training and education to stakeholders. (from homepage)
  example: NRFC051
  homepage: https://mail.nbfgr.res.in/nrfc/index.php
  mappings:
    cellosaurus: NRFC
  name: National Repository of Fish Cell Lines
  pattern: ^NRFC\d+$
  prefix: nrfc
nsc:
  cheminf:
    description: Identifier used by the Cancer Chemotherapy National Service Center.
    name: National Service Center number
    obsolete: false
    prefix: '000565'
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  example: '27223'
  homepage: https://wiki.nci.nih.gov/display/NCIDTPdata/Chemical+Data
  mappings:
    cheminf: '000565'
  name: USA National Service Center Number
  pattern: ^\d+$
  prefix: nsc
  references:
  - https://pubchem.ncbi.nlm.nih.gov/source/DTP/NCI
  uri_format: https://dtp.cancer.gov/dtpstandard/servlet/ChemData?searchtype=NSC&searchlist=$1
nsf.award:
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: Information about research projects that NSF has funded since 1989
    can be found by searching the Award Abstracts database. The information includes
    abstracts that describe the research, and names of principal investigators and
    their institutions. The database includes both completed and in-process research.
  example: '1458400'
  homepage: https://www.nsf.gov/awards/about.jsp
  name: National Science Foundation Award
  pattern: ^\d+$
  prefix: nsf.award
  uri_format: https://www.nsf.gov/awardsearch/showAward?AWD_ID=$1
nsrrc:
  description: Provides access to critically needed swine models of human health and
    disease as well as a central resource for reagents, creation of new genetically
    modified swine, and information and training related to use of swine models in
    biomedical research. [from RRID]
  example: '0005'
  mappings:
    rrid: NSRRC
  pattern: ^\d+$
  prefix: nsrrc
  rrid:
    homepage: http://www.nsrrc.missouri.edu/
    keywords:
    - biomaterial manufacture
    - breeding
    - consulting
    - cryopreservation
    - fetal fibroblast
    - fetus
    - fibroblast
    - genetically modified pig
    - genetics
    - genome
    - genotyping
    - health monitoring
    - live animal
    - phenotyping
    - pig
    - reproduction
    - tissue
    name: National Swine Resource and Research Center
    prefix: NSRRC
    scr: 006855
  uri_format: https://nsrrc.missouri.edu/nsrrc$1info/
nucc.characteristic:
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: The Provider Characteristics code set is for use with health care provider
    information for enrollment and credentialing transactions and their corresponding
    responses. It is intended to provide codified responses to questions presented
    to a health care provider applying to or registering with an entity and to report
    the outcome of such application or registration. It may also be used for responses
    to inquiries regarding provider participation or registration in a program or
    plan.
  example: 2A
  example_extras:
  - '11'
  - '10'
  homepage: https://nucc.org/index.php/code-sets-mainmenu-41/provider-characteristics-mainmenu-39
  name: National Uniform Claim Committee Characteristic
  pattern: ^\d(\d|\w)$
  prefix: nucc.characteristic
nucc.taxonomy:
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: "The Health Care Provider Taxonomy code set is an external, nonmedical\
    \ data code set designed for use in an electronic environment, specifically within\
    \ the ASC X12N Health Care transactions. This includes the transactions mandated\
    \ under HIPAA.\n\nThe taxonomy code is a unique alphanumeric code, ten characters\
    \ in length. The code set is structured into three distinct \"Levels\" including\
    \ Provider Grouping, Classification, and Area of Specialization.\n\n - **Level\
    \ I, Provider Grouping** A major grouping of service(s) or occupation(s) of health\
    \ care providers. For example: Allopathic & Osteopathic Physicians, Dental Providers,\
    \ Hospitals, etc.\n - **Level II, Classification** A more specific service or\
    \ occupation related to the Provider Grouping. For example, the Classification\
    \ for Allopathic & Osteopathic Physicians is based upon the General Specialty\
    \ Certificates as issued by the appropriate national boards. The following boards\
    \ will however, have their general certificates appear as Level III areas of specialization\
    \ strictly due to display limitations of the code set for Boards that have multiple\
    \ general certificates: Medical Genetics, Preventive Medicine, Psychiatry & Neurology,\
    \ Radiology, Surgery, Otolaryngology, Pathology.\n - **Level III, Area of Specialization**\
    \ A more specialized area of the Classification in which a provider chooses to\
    \ practice or make services available. For example, the Area of Specialization\
    \ for provider grouping Allopathic & Osteopathic Physicians is based upon the\
    \ Subspecialty Certificates as issued by the appropriate national boards."
  example: 207LH0002X
  homepage: https://taxonomy.nucc.org
  name: National Uniform Claim Committee Taxonomy
  pattern: ^\d{3}\w(\w|\d_)\d{4}X$
  prefix: nucc.taxonomy
  references:
  - https://www.nucc.org/images/stories/CSV/nucc_taxonomy_221.csv
  - https://www.nucc.org
nucleardb:
  biocontext:
    prefix: NUCLEARBD
  comment: Note that the typo from MIRIAM has spread to several other sources
  contact:
    email: vriend@cmbi.ru.nl
    github: null
    name: Gert Vriend
    orcid: 0000-0002-1067-7053
  integbio:
    alt_name: information system for Nuclear Receptors
    description: NucleaRDB is a database of nuclear hormone receptors. The database
      contains gene and protein sequence, mutation, and ligand binding information.
      Users can search or browse receptors by family or structure. BLAST search and
      an alignment builidng tool are also available.
    fairsharing: biodbcore-000077
    homepage: http://www.receptors.org/nucleardb/
    information_keywords:
    - Sequence
    maintainer: University of California, San Francisco, Centre for Molecular and
      Biomolecular Informatics
    name: NucleaRDB
    prefix: nbdc00599
    pubmeds:
    - '11125133'
    status: Active
    target_keywords:
    - Protein
  mappings:
    biocontext: NUCLEARBD
    integbio: nbdc00599
    miriam: nuclearbd
    n2t: nuclearbd
    prefixcommons: nucleardb
  miriam:
    deprecated: false
    description: NucleaRDB is an information system that stores heterogenous data
      on Nuclear Hormone Receptors (NHRs). It contains data on sequences, ligand binding
      constants and mutations for NHRs.
    homepage: http://www.receptors.org/nucleardb/
    id: '00000356'
    name: NucleaRDB
    namespaceEmbeddedInLui: false
    pattern: ^\w+\_\w+$
    prefix: nuclearbd
    sampleId: prgr_human
    uri_format: http://www.receptors.org/nucleardb/proteins/$1
  n2t:
    description: NucleaRDB is an information system that stores heterogenous data
      on Nuclear Hormone Receptors (NHRs). It contains data on sequences, ligand binding
      constants and mutations for NHRs.
    example: prgr_human
    homepage: http://www.receptors.org/nucleardb/
    name: NucleaRDB at Radboud University Nijmegen Medical Centre
    namespaceEmbeddedInLui: false
    pattern: ^\w+\_\w+$
    prefix: nuclearbd
    uri_format: http://www.receptors.org/nucleardb/proteins/$1
  prefix: nucleardb
  prefixcommons:
    description: The NucleaRDB is a part of a project devoted to build Molecular Class-Specific
      Information Systems (MCSIS) to provide, disseminate and harvest heterogeneous
      data. The NucleaRDB was built using the software developed for the GPCRDB.
    example: prgr_human
    homepage: http://www.receptors.org/NR/
    keywords:
    - classification
    name: 'NucleaRDB: An Information System for Nuclear Receptors'
    pattern: ^\w+\_\w+$
    prefix: nucleardb
    pubmed_ids:
    - '22064856'
    uri_format: http://www.receptors.org/NR/seq/DR/$1.html
  publications:
  - doi: 10.1093/nar/gkr960
    pmc: PMC3245090
    pubmed: '22064856'
    title: 'NucleaRDB: information system for nuclear receptors'
    year: 2011
  - doi: null
    pmc: null
    pubmed: '22064856'
    title: null
    year: null
  synonyms:
  - nuclearbd
nucleotide:
  has_canonical: insdc
  integbio:
    description: Nucleotide is a database of nucleic acid sequences. The database
      contains sequence entities from a variety of sources covering hundreds of organisms.
      The major resources GenBank and RefSeq repositories are both available through
      Nucleotide. Users can submit nucleotide sequences and data is available for
      download.
    homepage: http://www.ncbi.nlm.nih.gov/nuccore
    information_keywords:
    - Sequence
    - Repository
    maintainer: NCBI (National Center for Biotechnology Information)
    name: Nucleotide
    prefix: nbdc00600
    status: Active
    target_keywords:
    - Genome/Gene
    - cDNA/EST
    - Genetic variation
  mappings:
    integbio: nbdc00600
    miriam: nucleotide
  miriam:
    deprecated: false
    description: The Nucleotide database is a collection of sequences from several
      sources, including GenBank, RefSeq, TPA and PDB. Genome, gene and transcript
      sequence data provide the foundation for biomedical research and discovery.
    homepage: https://www.ncbi.nlm.nih.gov/
    id: 00000882
    name: Nucleotide
    namespaceEmbeddedInLui: false
    pattern: ^[a-zA-Z0-9_\.]+$
    prefix: nucleotide
    sampleId: '880798137'
    uri_format: https://www.ncbi.nlm.nih.gov/nuccore/$1
  prefix: nucleotide
nvs:
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: SKOS concept collections held in the NERC Vocabulary Server. A concept
    collection is useful where a group of concepts shares something in common, and
    it is convenient to group them under a common label. In the NVS, concept collections
    are synonymous with controlled vocabularies or code lists. Each collection is
    associated with its governance body. An external website link is displayed when
    applicable.
  example: P06
  homepage: https://vocab.nerc.ac.uk/collection/
  name: NERC Vocabulary Server
  prefix: nvs
  uri_format: https://vocab.nerc.ac.uk/collection/$1
nxr:
  description: National stock center for X. laevis and X. tropicalis and training
    center for advanced technologies (e.g. husbandry, cell biology, imaging, genetics,
    transgenesis, genomics). [from RRID]
  example: '0024'
  mappings:
    rrid: NXR
  pattern: ^\d+$
  prefix: nxr
  rrid:
    homepage: http://www.mbl.edu/xenopus/
    keywords:
    - Xenopus
    - laevis
    - tropicalis
    name: National Xenopus Resource
    prefix: NXR
    scr: '013731'
  uri_format: https://scicrunch.org/resolver/RRID:NXR_$1
nztcs:
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  contributor_extras:
  - email: sumirp77@gmail.com
    github: SumirHPandit
    name: Sumir Pandit
    orcid: 0000-0002-1216-4761
  keywords:
  - taxon
  - taxonomy
  license: CC-BY-4.0
  mappings:
    wikidata: P9889
  name: New Zealand Threat Classification System
  prefix: nztcs
  references:
  - https://github.com/biopragmatics/bioregistry/pull/1083
  wikidata:
    description: identifier for species classified under the New Zealand Threat Classification
      System
    example:
    - '11061'
    - '11974'
    - '13104'
    - '26916'
    - '3004'
    homepage: https://nztcs.org.nz/
    name: NZTCS ID
    pattern: ^[1-9]\d{2,6}$
    prefix: P9889
    uri_format: https://nztcs.org.nz/nztcs-species/$1
oa:
  aberowl:
    description: The Web Annotation Data Model specification describes a structured
      model and format to enable annotations to be shared and reused across different
      hardware and software platforms. Annotations are typically used to convey information
      about a resource or associations between resources. Simple examples include
      a comment or tag on a single web page or image, or a blog post about a news
      article.
    download_owl: http://aber-owl.net/media/ontologies/OA/4/oa.owl
    homepage: https://www.w3.org/TR/annotation-model/
    name: Web Annotation Ontology
    prefix: OA
    version: '2016-11-12T21:28:11Z'
  biocontext:
    prefix: oa
    uri_format: http://www.w3.org/ns/oa#$1
  bioportal:
    description: The Web Annotation Data Model specification describes a structured
      model and format to enable annotations to be shared and reused across different
      hardware and software platforms. Annotations are typically used to convey information
      about a resource or associations between resources. Simple examples include
      a comment or tag on a single web page or image, or a blog post about a news
      article.
    homepage: https://www.w3.org/TR/annotation-model/
    name: Web Annotation Ontology
    prefix: OA
    version: '2016-11-12T21:28:11Z'
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: The W3C Web Annotation Working Group is chartered to develop a set
    of specifications for an interoperable, sharable, distributed Web Annotation architecture.
  example: sourceDateStart
  homepage: http://www.w3.org/ns/oa
  lov:
    description: The Open Annotation Core Data Model specifies an interoperable framework
      for creating associations between related resources, annotations, using a methodology
      that conforms to the Architecture of the World Wide Web.  This ontology is a
      non-normative OWL formalization of the textual OA specification at http://www.openannotation.org/spec/core/20130208/index.html
    homepage: http://www.w3.org/ns/oa#
    keywords:
    - Quality
    modified: '2016-11-12'
    name: Open Annotation Data Model
    prefix: oa
    uri_prefix: http://www.w3.org/ns/oa#$1
  mappings:
    aberowl: OA
    biocontext: oa
    bioportal: OA
    lov: oa
    zazuko: oa
  name: Web Annotation Ontology
  preferred_prefix: oa
  prefix: oa
  uri_format: http://www.w3.org/ns/oa#$1
  zazuko:
    prefix: oa
    uri_format: http://www.w3.org/ns/oa#$1
oae:
  aberowl:
    description: A biomedical ontology in the domain of adverse events
    download_owl: http://aber-owl.net/media/ontologies/OAE/178/oae.owl
    homepage: https://github.com/OAE-ontology/OAE/
    name: Ontology of Adverse Events
    prefix: OAE
  biocontext:
    prefix: OAE
  bioportal:
    contact:
      email: yongqunh@med.umich.edu
      name: Yongqun "Oliver" He
    description: The Ontology of Adverse Events (OAE) is a community-based biomedical
      ontology in the domain of adverse events. OAE is developed to standardize adverse
      event annotation, integrate various adverse event data, and support computer-assisted
      reasoning. Its development follows the OBO Foundry principles.
    homepage: http://www.oae-ontology.org/
    name: Ontology of Adverse Events
    prefix: OAE
    publications:
    - http://www.ncbi.nlm.nih.gov/pubmed/25093068
    version: 1.2.47
  example: 0002959
  fairsharing:
    abbreviation: OAE
    contact:
      email: yongqunh@med.umich.edu
      name: Yongqun "Oliver" He
      orcid: 0000-0001-9189-9661
    description: The Ontology of Adverse Events (OAE) is a community-driven ontology
      that is developed to standardize and integrate data on biomedical adverse events
      (e.g., vaccine and drug adverse events) and support computer-assisted reasoning.
      As a result of a medical intervention, events may occur which lie outside the
      intended consequences of the intervention. Some of these events are adverse
      events, in the sense that they are pathological bodily processes. For many such
      adverse events it is unclear whether they are causal consequences of the medical
      intervention which preceded them, since adverse events may also occur due to
      other reasons (for example a natural viral infection). OAE was created to represent
      the whole process from initial medical intervention to subsequent outcomes.
    domains:
    - drug
    - Adverse Reaction
    - vaccine
    homepage: https://github.com/oae-ontology
    license: CC-BY-3.0
    name: Ontology of Adverse Events
    prefix: FAIRsharing.tw4q8x
    publications:
    - doi: 10.1186/2041-1480-5-29
      pubmed: '25093068'
      title: 'OAE: The Ontology of Adverse Events'
      year: 2014
    - doi: 10.1371/journal.pone.0049941
      title: Ontology-Based Combinatorial Comparative Analysis of Adverse Events Associated
        with Killed and Live Influenza Vaccines
      year: 2012
    repository: https://github.com/OAE-ontology/OAE/issues
    subjects:
    - Biomedical Science
  mappings:
    aberowl: OAE
    biocontext: OAE
    bioportal: OAE
    fairsharing: FAIRsharing.tw4q8x
    obofoundry: oae
    ols: oae
    ontobee: OAE
    wikidata.entity: Q81661725
  obofoundry:
    contact: yongqunh@med.umich.edu
    contact.github: yongqunh
    contact.label: Yongqunh He
    contact.orcid: 0000-0001-9189-9661
    deprecated: false
    description: A biomedical ontology in the domain of adverse events
    domain: health
    download.owl: http://purl.obolibrary.org/obo/oae.owl
    homepage: https://github.com/OAE-ontology/OAE/
    license: CC BY 3.0
    license.url: http://creativecommons.org/licenses/by/3.0/
    name: Ontology of Adverse Events
    preferredPrefix: OAE
    prefix: oae
    repository: https://github.com/OAE-ontology/OAE
  ols:
    description: The Ontology of Adverse Eventsy (OAE) is a biomedical ontology in
      the domain of adverse events. OAE aims to standardize adverse event annotation,
      integrate various adverse event data, and support computer-assisted reasoning.  OAE
      is a community-based ontology. Its development follows the OBO Foundry principles.
      Vaccine adverse events have been used as an initial testing use case. OAE also
      studies adverse events associated with the administration of drug and nutritional
      products, the operation of surgeries, and the usage of medical devices, etc.
    download_owl: http://purl.obolibrary.org/obo/oae.owl
    homepage: https://github.com/OAE-ontology/OAE/
    name: 'OAE: Ontology of Adverse Events'
    prefix: oae
    tracker: https://github.com/OAE-ontology/OAE/issues
    version: 1.2.47
  ontobee:
    library: Library
    name: Ontology of Adverse Events
    prefix: OAE
  pattern: ^\d{7}$
  prefix: oae
  publications:
  - doi: 10.1186/2041-1480-5-29
    pmc: PMC4120740
    pubmed: '25093068'
    title: 'OAE: The Ontology of Adverse Events'
    year: 2014
  - doi: 10.1186/2041-1480-5-29
    pmc: null
    pubmed: '25093068'
    title: 'OAE: The Ontology of Adverse Events'
    year: 2014
  - doi: 10.1371/journal.pone.0049941
    pmc: null
    pubmed: null
    title: Ontology-Based Combinatorial Comparative Analysis of Adverse Events Associated
      with Killed and Live Influenza Vaccines
    year: 2012
  uri_format: http://purl.obolibrary.org/obo/OAE_$1
oarcs:
  aberowl:
    description: OArCS is an ontology describing the Arthropod ciruclatory system.
    download_owl: http://aber-owl.net/media/ontologies/OARCS/3/oarcs.owl
    homepage: https://github.com/aszool/oarcs
    name: Ontology of Arthropod Circulatory Systems
    prefix: OARCS
  biocontext:
    prefix: OARCS
  bioportal:
    contact:
      email: mjyoder@illinois.edu
      name: Matt Yoder
    description: OArCS is an ontology describing the Arthropod ciruclatory system.
    homepage: https://github.com/aszool/oarcs
    name: Ontology of Arthropod Circulatory Systems
    prefix: OARCS
    version: '2019-04-18'
  example: 0000029
  fairsharing:
    abbreviation: OArCS
    description: OArCS is a structural model for the description of anatomical features
      (morphemes) using ontologies. Its domain is the Arthropod ciruclatory system.
      This ontology has not been updated recently, and therefore has been marked as
      uncertain. Please get in touch with us if you have any information.
    homepage: https://github.com/aszool/oarcs
    name: Ontology of Arthropod Circulatory Systems
    prefix: FAIRsharing.yqn857
    publications:
    - doi: 10.1093/sysbio/syw108
      title: The first organ-based free ontology for arthropods (Ontology of Arthropod
        Circulatory Systems - OArCS) and its integration into a novel formalization
        scheme for morphological descriptions
      year: 2017
    subjects:
    - Anatomy
    - Angiology
  mappings:
    aberowl: OARCS
    biocontext: OARCS
    bioportal: OARCS
    fairsharing: FAIRsharing.yqn857
    obofoundry: oarcs
    ols: oarcs
    ontobee: OARCS
    wikidata.entity: Q81661727
  obofoundry:
    contact: mjyoder@illinois.edu
    contact.github: mjy
    contact.label: Matt Yoder
    contact.orcid: 0000-0002-5640-5491
    deprecated: false
    description: OArCS is an ontology describing the Arthropod ciruclatory system.
    domain: anatomy and development
    download.owl: http://purl.obolibrary.org/obo/oarcs.owl
    homepage: https://github.com/aszool/oarcs
    license: CC BY 3.0
    license.url: http://creativecommons.org/licenses/by/3.0/
    name: Ontology of Arthropod Circulatory Systems
    preferredPrefix: OARCS
    prefix: oarcs
    repository: https://github.com/aszool/oarcs
  ols:
    description: OArCS is an ontology describing the Arthropod ciruclatory system.
    download_owl: http://purl.obolibrary.org/obo/oarcs.owl
    homepage: https://github.com/aszool/oarcs
    name: Ontology of Arthropod Circulatory Systems
    prefix: oarcs
    tracker: https://github.com/aszool/oarcs/issues
    version: '2019-04-18'
    version.iri: http://purl.obolibrary.org/obo/hao/2019-04-18/hao.owl
  ontobee:
    library: Library
    name: Ontology of Arthropod Circulatory Systems
    prefix: OARCS
  pattern: ^\d{7}$
  prefix: oarcs
  publications:
  - doi: 10.1093/sysbio/syw108
    pmc: null
    pubmed: '28123116'
    title: The First Organ-Based Ontology for Arthropods (Ontology of Arthropod Circulatory
      Systems - OArCS) and its Integration into a Novel Formalization Scheme for Morphological
      Descriptions
    year: 2017
  - doi: 10.1093/sysbio/syw108
    pmc: null
    pubmed: null
    title: The first organ-based free ontology for arthropods (Ontology of Arthropod
      Circulatory Systems - OArCS) and its integration into a novel formalization
      scheme for morphological descriptions
    year: 2017
  uri_format: http://purl.obolibrary.org/obo/OARCS_$1
oba:
  aberowl:
    description: A collection of biological attributes (traits) covering all kingdoms
      of life.
    download_owl: http://aber-owl.net/media/ontologies/OBA/28/oba.owl
    homepage: https://github.com/obophenotype/bio-attribute-ontology
    name: Ontology of Biological Attributes
    prefix: OBA
  agroportal:
    contact:
      email: cjmungall@lbl.gov
      name: Chris Mungall
    description: The Ontology of Biological Attributes (OBA) is a formalised, species-independent
      collection of interoperable phenotypic trait categories that is intended to
      fulfil a data integration role. OBA is a standardised representational framework
      for observable attributes that are characteristics of biological entities, organisms,
      or parts of organisms. It is collection of biological attributes (traits) covering
      all kingdoms of life. Interoperable with VT (vertebrate trait ontology) and
      TO (plant trait ontology). Extends PATO., A collection of biological attributes
      (traits) covering all kingdoms of life. Interoperable with VT (vertebrate trait
      ontology) and TO (plant trait ontology). Extends PATO.
    example_uri: http://purl.obolibrary.org/obo/OBA_0000005
    homepage: https://github.com/obophenotype/bio-attribute-ontology
    license: CC0-1.0
    name: Ontology of Biological Attributes
    prefix: OBA
    publications:
    - https://doi.org/10.1007/s00335-023-09992-1
    repository: https://github.com/obophenotype/bio-attribute-ontology
    version: '2025-10-29'
  biocontext:
    prefix: OBA
  bioportal:
    contact:
      email: cjmungall@lbl.gov
      name: Chris Mungall
    description: A collection of biological attributes (traits) covering all kingdoms
      of life. Interoperable with VT (vertebrate trait ontology) and TO (plant trait
      ontology). Extends PATO.
    homepage: https://github.com/obophenotype/bio-attribute-ontology
    license: CC0-1.0
    name: Ontology of Biological Attributes
    prefix: OBA
    version: '2025-10-29'
  download_json: http://purl.obolibrary.org/obo/oba.json
  example: '0000001'
  example_extras:
  - VT0003769
  fairsharing:
    abbreviation: OBA
    description: 'The Ontology of Biological Attributes (OBA) is a formalised, species-independent
      collection of interoperable phenotypic trait categories that is intended to
      fulfil a data integration role. OBA is a standardised representational framework
      for observable attributes that are characteristics of biological entities, organisms,
      or parts of organisms. '
    homepage: https://github.com/obophenotype/bio-attribute-ontology
    license: CC0-1.0
    name: Ontology of Biological Attributes
    prefix: FAIRsharing.mp0rwf
    subjects:
    - Biology
  mappings:
    aberowl: OBA
    agroportal: OBA
    biocontext: OBA
    bioportal: OBA
    fairsharing: FAIRsharing.mp0rwf
    obofoundry: oba
    ols: oba
    ontobee: OBA
    wikidata.entity: Q81661730
  obofoundry:
    appears_in:
    - fovt
    contact: cjmungall@lbl.gov
    contact.github: cmungall
    contact.label: Chris Mungall
    contact.orcid: 0000-0002-6601-2165
    deprecated: false
    description: A collection of biological attributes (traits) covering all kingdoms
      of life.
    domain: phenotype
    download.obo: http://purl.obolibrary.org/obo/oba.obo
    download.owl: http://purl.obolibrary.org/obo/oba.owl
    homepage: https://github.com/obophenotype/bio-attribute-ontology
    license: CC0 1.0
    license.url: http://creativecommons.org/publicdomain/zero/1.0/
    name: Ontology of Biological Attributes
    preferredPrefix: OBA
    prefix: oba
    publications:
    - id: https://doi.org/10.1007/s00335-023-09992-1
      title: The Ontology of Biological Attributes (OBA) - computational traits for
        the life sciences
    repository: https://github.com/obophenotype/bio-attribute-ontology
  ols:
    description: A collection of biological attributes (traits) covering all kingdoms
      of life. Interoperable with VT (vertebrate trait ontology) and TO (plant trait
      ontology). Extends PATO.
    download_owl: http://purl.obolibrary.org/obo/oba.owl
    homepage: https://github.com/obophenotype/bio-attribute-ontology
    name: Ontology of Biological Attributes (OBA)
    prefix: oba
    tracker: https://github.com/obophenotype/bio-attribute-ontology/issues
    version: '2025-10-29'
    version.iri: http://purl.obolibrary.org/obo/oba/releases/2025-10-29/oba.owl
  ontobee:
    library: Library
    name: Ontology of Biological Attributes
    prefix: OBA
  pattern: ^(VT)?\d{7}$
  prefix: oba
  publications:
  - doi: 10.1101/2023.01.26.525742
    pmc: PMC9900877
    pubmed: '36747660'
    title: The Ontology of Biological Attributes (OBA) - Computational Traits for
      the Life Sciences
    year: 2023
  - doi: 10.1007/s00335-023-09992-1
    pmc: null
    pubmed: '37076585'
    title: The Ontology of Biological Attributes (OBA)-computational traits for the
      life sciences
    year: 2023
  - doi: 10.1007/s00335-023-09992-1
    pmc: null
    pubmed: null
    title: The Ontology of Biological Attributes (OBA) - computational traits for
      the life sciences
    year: null
  uri_format: http://purl.obolibrary.org/obo/OBA_$1
oban:
  biocontext:
    prefix: OBAN
    uri_format: http://purl.org/oban/$1
  biolink:
    is_identifiers: false
    is_obo: false
    prefix: OBAN
    uri_format: http://purl.org/oban/$1
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: It is an ontology model used to describe associations between biomedical
    entities in triple format based on W3C specification. OBAN is a generic association
    representation model that loosely couples a subject and object (e.g. disease and
    its associated phenotypes supported by the source of evidence for that association)
    via a construction of class OBAN:association. [from GitHub]
  download_owl: https://raw.githubusercontent.com/EBISPOT/OBAN/master/ontology/oban_core.owl
  download_rdf: https://raw.githubusercontent.com/EBISPOT/OBAN/master/ontology/oban_core.ttl
  example: provenance
  homepage: https://github.com/EBISPOT/OBAN
  mappings:
    biocontext: OBAN
    biolink: OBAN
  name: Open Biomedical Annotations
  pattern: ^\w+$
  prefix: oban
  repository: https://github.com/EBISPOT/OBAN
  uri_format: http://purl.org/oban/$1
obci:
  contact:
    email: dan5@georgetown.edu
    github: nataled
    name: Darren A. Natale
    orcid: 0000-0001-5809-9523
  contributor:
    email: dan5@georgetown.edu
    github: nataled
    name: Darren A. Natale
    orcid: 0000-0001-5809-9523
  description: The Ontology for Biomarkers of Clinical Interest (OBCI) formally defines
    biomarkers for diseases, phenotypes, and effects.
  download_owl: https://proteininformationresource.org/staff/nataled/OBCI/obci.owl
  example: '000000001'
  github_request_issue: 1174
  homepage: https://github.com/clinical-biomarkers/OBCI
  name: Ontology for Biomarkers of Clinical Interest
  pattern: ^\d+$
  prefix: obci
  reviewer:
    email: b.gyori@northeastern.edu
    github: bgyori
    name: Benjamin M. Gyori
    orcid: 0000-0001-9439-5346
  uri_format: http://purl.obolibrary.org/obo/OBCI_$1
obcs:
  aberowl:
    description: A biomedical ontology in the domain of biological and clinical statistics.
    download_owl: http://aber-owl.net/media/ontologies/OBCS/16/obcs.owl
    homepage: https://github.com/obcs/obcs
    name: Ontology of Biological and Clinical Statistics
    prefix: OBCS
  biocontext:
    prefix: OBCS
  bioportal:
    contact:
      email: jiezheng@upenn.edu
      name: Jie Zheng
    description: The Ontology of Biological and Clinical Statistics (OBCS) is a biomedical
      ontology in the domain of biological and clinical statistics. OBCS is primarily
      targeted for statistical representation in the fields in biological, biomedical,
      and clinical domains. OBCS uses the Basic Formal Ontology (BFO) as the upper
      level ontology. OBCS imports all biostatistics related terms in the Ontology
      for Biomedical Investigations (OBI) including all logical axioms.
    homepage: https://github.com/obcs/obcs
    name: Ontology of Biological and Clinical Statistics
    prefix: OBCS
    publications:
    - https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5024438/
    version: '2023-12-08'
  example: '0000121'
  fairsharing:
    abbreviation: OBCS
    description: The Ontology of Biological and Clinical Statistics (OBCS) is a biomedical
      ontology in the domain of biological and clinical statistics. OBCS is primarily
      targeted for statistical representation in the fields in biological, biomedical,
      and clinical domains. OBCS uses the Basic Formal Ontology (BFO) as the upper
      level ontology. OBCS imports all biostatistics related terms in the Ontology
      for Biomedical Investigations (OBI) including all logical axioms.
    domains:
    - vaccine
    homepage: https://github.com/obcs/obcs
    license: CC-BY-3.0
    name: Ontology of Biological and Clinical Statistics
    prefix: FAIRsharing.5p12xh
    publications:
    - doi: 10.1186/s13326-016-0100-2
      pubmed: '27627881'
      title: The Ontology of Biological and Clinical Statistics (OBCS) for standardized
        and reproducible statistical analysis
      year: 2016
    repository: https://github.com/obcs/obcs/issues
    subjects:
    - Biomedical Science
    - Biology
    - Medical Informatics
    - Statistics
    - Medicine
  mappings:
    aberowl: OBCS
    biocontext: OBCS
    bioportal: OBCS
    fairsharing: FAIRsharing.5p12xh
    miriam: obcs
    obofoundry: obcs
    ols: obcs
    ontobee: OBCS
    wikidata.entity: Q55118544
  miriam:
    deprecated: false
    description: OBCS stands for the Ontology of Biological and Clinical Statistics.
      OBCS is an ontology in the domain of biological and clinical statistics. It
      is aligned with the Basic Formal Ontology (BFO) and the Ontology for Biomedical
      Investigations (OBI)
    homepage: https://www.ebi.ac.uk/ols4/ontologies/obcs
    id: '00001053'
    name: ' Ontology of Biological and Clinical Statistics'
    namespaceEmbeddedInLui: true
    pattern: ^OBCS:\d+$
    prefix: obcs
    sampleId: 0000086
    uri_format: https://www.ebi.ac.uk/ols4/ontologies/obcs/classes?obo_id=OBCS:$1
  obofoundry:
    contact: jiezhen@med.umich.edu
    contact.github: zhengj2007
    contact.label: Jie Zheng
    contact.orcid: 0000-0002-2999-0103
    deprecated: false
    description: A biomedical ontology in the domain of biological and clinical statistics.
    domain: information technology
    download.owl: http://purl.obolibrary.org/obo/obcs.owl
    homepage: https://github.com/obcs/obcs
    license: CC BY 4.0
    license.url: http://creativecommons.org/licenses/by/4.0/
    name: Ontology of Biological and Clinical Statistics
    preferredPrefix: OBCS
    prefix: obcs
    repository: https://github.com/obcs/obcs
  ols:
    description: OBCS stands for the Ontology of Biological and Clinical Statistics.
      OBCS is an ontology in the domain of biological and clinical statistics. It
      is aligned with the Basic Formal Ontology (BFO) and the Ontology for Biomedical
      Investigations (OBI). OBCS imports all possible biostatistics terms in OBI and
      includes many additional biostatistics terms, some of which were proposed and
      discussed in the OBI face-to-face workshop in Ann Arbor in 2012.
    download_owl: http://purl.obolibrary.org/obo/obcs.owl
    homepage: https://github.com/obcs/obcs
    name: 'OBCS: Ontology of Biological and Clinical Statistics'
    prefix: obcs
    tracker: https://github.com/obcs/obcs/issues
    version: '2023-12-08'
    version.iri: http://purl.obolibrary.org/obo/obcs/2023-12-08/obcs.owl
  ontobee:
    library: Library
    name: Ontology of Biological and Clinical Statistics
    prefix: OBCS
  pattern: ^\d{7}$
  prefix: obcs
  publications:
  - doi: 10.1186/s13326-016-0100-2
    pmc: PMC5024438
    pubmed: '27627881'
    title: The Ontology of Biological and Clinical Statistics (OBCS) for standardized
      and reproducible statistical analysis
    year: 2016
  uri_format: http://purl.obolibrary.org/obo/OBCS_$1
obi:
  aberowl:
    description: An integrated ontology for the description of life-science and clinical
      investigations
    download_owl: http://aber-owl.net/media/ontologies/OBI/62/obi.owl
    homepage: http://obi-ontology.org
    name: Ontology for Biomedical Investigations
    prefix: OBI
  banana: OBI
  banana_peel: _
  biocontext:
    prefix: OBI
  bioportal:
    contact:
      email: bpeters@liai.org
      name: Bjoern Peters
    description: 'OBI is an ontology of investigations, the protocols and instrumentation
      used, the material used, the data generated and the types of analysis performed
      on it. <br><br> To import,<br> Latest version: <a href="http://purl.obolibrary.org/obo/obi.owl">http://purl.obolibrary.org/obo/obi.owl</a><br>
      <br> Latest release notes at <a href="http://purl.obolibrary.org/obo/obi/release-notes.html">http://purl.obolibrary.org/obo/obi/release-notes.html</a><br>
      <br> Note: BFO 2.0 pre-Graz release (not official release version) was used
      in this release., An ontology for representing biomedical investigations, including
      study designs, the collection and preparation of the targets of investigation,
      assays, instrumentation and reagents used, as well as the data generated and
      the types of analysis performed on the data to reach conclusions, and their
      documentation.'
    homepage: http://purl.obolibrary.org/obo/obi
    license: CC-BY-4.0
    name: Ontology for Biomedical Investigations
    prefix: OBI
    publications:
    - http://purl.obolibrary.org/obo/obi/Technical_Reports
    version: '2025-10-14'
  download_obo: https://github.com/obi-ontology/obi/raw/master/views/obi.obo
  example: 0400109
  fairsharing:
    abbreviation: OBI
    contact:
      email: bpeters@lji.org
      name: Bjoern Peters
      orcid: 0000-0002-8457-6693
    description: The Ontology for Biomedical Investigations (OBI) is an ontology that
      provides terms with precisely defined meanings to describe all aspects of how
      investigations in the biological and medical domains are conducted. OBI fosters
      clear communication about scientific investigations by defining more than 2500
      terms for assays, devices, objectives, and more.
    domains:
    - reagent
    - assay
    - device
    - data transformation
    - study design
    homepage: http://obi-ontology.org/
    license: CC-BY-3.0
    name: Ontology for Biomedical Investigations
    prefix: FAIRsharing.284e1z
    publications:
    - doi: 10.1186/2041-1480-4-s1-s6
      pubmed: '23734660'
      title: 'Query enhancement through the practical application of ontology: the
        IEDB and OBI'
      year: 2013
    - doi: 10.4056/sigs.1994602
      pubmed: '22180825'
      title: Minimum Information about a Genotyping Experiment (MIGEN)
      year: 2011
    - doi: 10.1093/database/bau132
      pubmed: '25632945'
      title: 'Modeling a microbial community and biodiversity assay with OBO Foundry
        ontologies: the interoperability gains of a modular approach'
      year: 2015
    - doi: 10.1371/journal.pone.0154556
      pubmed: '27128319'
      title: The Ontology for Biomedical Investigations
      year: 2016
    - doi: 10.1186/2041-1480-1-s1-s7
      pubmed: '20626927'
      title: Modeling biomedical experimental processes with OBI
      year: 2010
    repository: https://github.com/obi-ontology/obi
    subjects:
    - Life Science
    - Functional Genomics
    - Biomedical Science
  go:
    homepage: http://obi-ontology.org/
    name: Ontology for Biomedical Investigations
    prefix: OBI
  mappings:
    aberowl: OBI
    biocontext: OBI
    bioportal: OBI
    fairsharing: FAIRsharing.284e1z
    go: OBI
    miriam: obi
    n2t: obi
    obofoundry: obi
    ols: obi
    ontobee: OBI
    prefixcommons: obi
    tib: obi
    wikidata.entity: Q7095051
  miriam:
    deprecated: false
    description: The Ontology for Biomedical Investigations (OBI) project is developing
      an integrated ontology for the description of biological and clinical investigations.
      The ontology will represent the design of an investigation, the protocols and
      instrumentation used, the material used, the data generated and the type analysis
      performed on it. Currently OBI is being built under the Basic Formal Ontology
      (BFO).
    homepage: http://www.ontobee.org/
    id: '00000127'
    name: Ontology for Biomedical Investigations
    namespaceEmbeddedInLui: false
    pattern: ^OBI_\d{7}$
    prefix: obi
    sampleId: OBI_0000070
    uri_format: http://purl.obolibrary.org/obo/$1
  n2t:
    description: The Ontology for Biomedical Investigations (OBI) project is developing
      an integrated ontology for the description of biological and clinical investigations.
      The ontology will represent the design of an investigation, the protocols and
      instrumentation used, the material used, the data generated and the type analysis
      performed on it. Currently OBI is being built under the Basic Formal Ontology
      (BFO).
    example: OBI_0000070
    homepage: http://www.ontobee.org/
    name: OBI through Ontobee
    namespaceEmbeddedInLui: false
    pattern: (^OBI:\d{7}$)|(^OBI_\d{7}$)
    prefix: obi
    uri_format: http://purl.obolibrary.org/obo/$1
  namespace_in_lui: true
  obofoundry:
    appears_in:
    - agro
    - foodon
    - gallont
    - hso
    - labo
    - maxo
    - mco
    - one
    - ons
    - proco
    - rbo
    - scdo
    contact: bpeters@lji.org
    contact.github: bpeters42
    contact.label: Bjoern Peters
    contact.orcid: 0000-0002-8457-6693
    deprecated: false
    description: An integrated ontology for the description of life-science and clinical
      investigations
    domain: investigations
    download.obo: http://purl.obolibrary.org/obo/obi.obo
    download.owl: http://purl.obolibrary.org/obo/obi.owl
    homepage: http://obi-ontology.org
    license: CC BY 4.0
    license.url: https://creativecommons.org/licenses/by/4.0/
    logo: https://svn.code.sf.net/p/obi/code/trunk/web/htdocs/images/obi-lotext.png
    name: Ontology for Biomedical Investigations
    preferredPrefix: OBI
    prefix: obi
    publications:
    - id: https://www.ncbi.nlm.nih.gov/pubmed/27128319
      title: The Ontology for Biomedical Investigations
    repository: https://github.com/obi-ontology/obi
  ols:
    description: An ontology for representing biomedical investigations, including
      study designs, the collection and preparation of the targets of investigation,
      assays, instrumentation and reagents used, as well as the data generated and
      the types of analysis performed on the data to reach conclusions, and their
      documentation.
    download_owl: http://purl.obolibrary.org/obo/obi.owl
    homepage: http://obi-ontology.org
    name: Ontology for Biomedical Investigations
    prefix: obi
    tracker: http://purl.obolibrary.org/obo/obi/tracker
    version: '2025-10-14'
    version.iri: http://purl.obolibrary.org/obo/obi/2025-10-14/obi.owl
  ontobee:
    library: Foundry
    name: Ontology for Biomedical Investigations
    prefix: OBI
  pattern: ^\d{7}$
  prefix: obi
  prefixcommons:
    alt_uri_formats:
    - http://purl.org/obo/owl/OBI#$1
    bioportal: '1123'
    description: The Ontology for Biomedical Investigations (OBI) an ontology of investigations,
      the protocols and instrumentation used, the material used, the data generated
      and the types of analysis performed on it.
    example: OBI_0000011
    homepage: http://purl.obolibrary.org/obo/obi
    keywords:
    - ontology
    license: CC-BY-3.0
    name: Ontology for Biomedical Investigations
    pattern: ^OBI_\d{7}$
    prefix: obi
    synonyms:
    - obo.obi
  publications:
  - doi: 10.1371/journal.pone.0154556
    pmc: PMC4851331
    pubmed: '27128319'
    title: The Ontology for Biomedical Investigations
    year: 2016
  - doi: 10.1093/database/bau132
    pmc: PMC4309925
    pubmed: '25632945'
    title: 'Modeling a microbial community and biodiversity assay with OBO Foundry
      ontologies: the interoperability gains of a modular approach'
    year: 2015
  - doi: 10.1186/2041-1480-4-s1-s6
    pmc: PMC3633001
    pubmed: '23734660'
    title: 'Query enhancement through the practical application of ontology: the IEDB
      and OBI'
    year: 2013
  - doi: 10.4056/sigs.1994602
    pmc: PMC3235517
    pubmed: '22180825'
    title: Minimum Information about a Genotyping Experiment (MIGEN)
    year: 2011
  - doi: 10.1186/2041-1480-1-s1-s7
    pmc: PMC2903726
    pubmed: '20626927'
    title: Modeling biomedical experimental processes with OBI
    year: 2010
  - doi: null
    pmc: null
    pubmed: '27128319'
    title: The Ontology for Biomedical Investigations
    year: null
  - doi: 10.1186/2041-1480-4-s1-s6
    pmc: null
    pubmed: '23734660'
    title: 'Query enhancement through the practical application of ontology: the IEDB
      and OBI'
    year: 2013
  - doi: 10.4056/sigs.1994602
    pmc: null
    pubmed: '22180825'
    title: Minimum Information about a Genotyping Experiment (MIGEN)
    year: 2011
  - doi: 10.1093/database/bau132
    pmc: null
    pubmed: '25632945'
    title: 'Modeling a microbial community and biodiversity assay with OBO Foundry
      ontologies: the interoperability gains of a modular approach'
    year: 2015
  - doi: 10.1371/journal.pone.0154556
    pmc: null
    pubmed: '27128319'
    title: The Ontology for Biomedical Investigations
    year: 2016
  - doi: 10.1186/2041-1480-1-s1-s7
    pmc: null
    pubmed: '20626927'
    title: Modeling biomedical experimental processes with OBI
    year: 2010
  - doi: null
    pmc: null
    pubmed: '27128319'
    title: The Ontology for Biomedical Investigations
    year: null
  - doi: 10.1186/2041-1480-4-s1-s6
    pmc: null
    pubmed: '23734660'
    title: 'Query enhancement through the practical application of ontology: the IEDB
      and OBI'
    year: 2013
  - doi: 10.4056/sigs.1994602
    pmc: null
    pubmed: '22180825'
    title: Minimum Information about a Genotyping Experiment (MIGEN)
    year: 2011
  - doi: 10.1093/database/bau132
    pmc: null
    pubmed: '25632945'
    title: 'Modeling a microbial community and biodiversity assay with OBO Foundry
      ontologies: the interoperability gains of a modular approach'
    year: 2015
  - doi: 10.1371/journal.pone.0154556
    pmc: null
    pubmed: '27128319'
    title: The Ontology for Biomedical Investigations
    year: 2016
  - doi: 10.1186/2041-1480-1-s1-s7
    pmc: null
    pubmed: '20626927'
    title: Modeling biomedical experimental processes with OBI
    year: 2010
  - doi: null
    pmc: null
    pubmed: '27128319'
    title: The Ontology for Biomedical Investigations
    year: null
  - doi: 10.1186/2041-1480-4-s1-s6
    pmc: null
    pubmed: '23734660'
    title: 'Query enhancement through the practical application of ontology: the IEDB
      and OBI'
    year: 2013
  - doi: 10.4056/sigs.1994602
    pmc: null
    pubmed: '22180825'
    title: Minimum Information about a Genotyping Experiment (MIGEN)
    year: 2011
  - doi: 10.1093/database/bau132
    pmc: null
    pubmed: '25632945'
    title: 'Modeling a microbial community and biodiversity assay with OBO Foundry
      ontologies: the interoperability gains of a modular approach'
    year: 2015
  - doi: 10.1371/journal.pone.0154556
    pmc: null
    pubmed: '27128319'
    title: The Ontology for Biomedical Investigations
    year: 2016
  - doi: 10.1186/2041-1480-1-s1-s7
    pmc: null
    pubmed: '20626927'
    title: Modeling biomedical experimental processes with OBI
    year: 2010
  - doi: null
    pmc: null
    pubmed: '27128319'
    title: The Ontology for Biomedical Investigations
    year: null
  - doi: 10.1186/2041-1480-4-s1-s6
    pmc: null
    pubmed: '23734660'
    title: 'Query enhancement through the practical application of ontology: the IEDB
      and OBI'
    year: 2013
  - doi: 10.4056/sigs.1994602
    pmc: null
    pubmed: '22180825'
    title: Minimum Information about a Genotyping Experiment (MIGEN)
    year: 2011
  - doi: 10.1093/database/bau132
    pmc: null
    pubmed: '25632945'
    title: 'Modeling a microbial community and biodiversity assay with OBO Foundry
      ontologies: the interoperability gains of a modular approach'
    year: 2015
  - doi: 10.1371/journal.pone.0154556
    pmc: null
    pubmed: '27128319'
    title: The Ontology for Biomedical Investigations
    year: 2016
  - doi: 10.1186/2041-1480-1-s1-s7
    pmc: null
    pubmed: '20626927'
    title: Modeling biomedical experimental processes with OBI
    year: 2010
  - doi: null
    pmc: null
    pubmed: '27128319'
    title: The Ontology for Biomedical Investigations
    year: null
  - doi: 10.1186/2041-1480-4-s1-s6
    pmc: null
    pubmed: '23734660'
    title: 'Query enhancement through the practical application of ontology: the IEDB
      and OBI'
    year: 2013
  - doi: 10.4056/sigs.1994602
    pmc: null
    pubmed: '22180825'
    title: Minimum Information about a Genotyping Experiment (MIGEN)
    year: 2011
  - doi: 10.1093/database/bau132
    pmc: null
    pubmed: '25632945'
    title: 'Modeling a microbial community and biodiversity assay with OBO Foundry
      ontologies: the interoperability gains of a modular approach'
    year: 2015
  - doi: 10.1371/journal.pone.0154556
    pmc: null
    pubmed: '27128319'
    title: The Ontology for Biomedical Investigations
    year: 2016
  - doi: 10.1186/2041-1480-1-s1-s7
    pmc: null
    pubmed: '20626927'
    title: Modeling biomedical experimental processes with OBI
    year: 2010
  tib:
    description: An ontology for representing biomedical investigations, including
      study designs, the collection and preparation of the targets of investigation,
      assays, instrumentation and reagents used, as well as the data generated and
      the types of analysis performed on the data to reach conclusions, and their
      documentation.
    download_owl: http://purl.obolibrary.org/obo/obi.owl
    homepage: http://obi-ontology.org
    keywords:
    - NFDI4CHEM
    - DataPLANT
    - NFDI4CAT
    - life sciences, biology
    name: Ontology for Biomedical Investigations
    prefix: obi
    tracker: http://purl.obolibrary.org/obo/obi/tracker
    version.iri: http://purl.obolibrary.org/obo/obi/2025-10-14/obi.owl
  uri_format: http://purl.obolibrary.org/obo/OBI_$1
obib:
  aberowl:
    description: An ontology built for annotation and modeling of biobank repository
      and biobanking administration
    download_owl: http://aber-owl.net/media/ontologies/OBIB/15/obib.owl
    homepage: https://github.com/biobanking/biobanking
    name: Ontology for Biobanking
    prefix: OBIB
  biocontext:
    prefix: OBIB
  bioportal:
    contact:
      email: jiezhen@umich.edu
      name: Jie Zheng
    description: The ontology for Biobanking (OBIB) is an ontology built for annotation
      and modeling of biobank repository and biobanking administration. It is developed
      based on subset of Ontology for Biomedical Investigations (OBI) using Basic
      Formal Ontology (BFO) as top ontology and following OBO Foundry principles.
      The first version of the ontology is merged of two existing biobank related
      ontologies, OMIABIS and biobank ontology.
    homepage: https://github.com/biobanking/biobanking/wiki
    name: Ontology for Biobanking
    prefix: OBIB
    version: '2023-04-05'
  example: 0000389
  fairsharing:
    abbreviation: OBIB
    description: The ontology for Biobanking (OBIB) is an ontology built for annotation
      and modeling of biobank repository and biobanking administration. It is developed
      based on subset of Ontology for Biomedical Investigations (OBI) using Basic
      Formal Ontology (BFO) as top ontology and following OBO Foundry principles.
      The first version of the ontology is merged of two existing biobank related
      ontologies, OMIABIS and biobank ontology.
    domains:
    - Biobank
    homepage: https://github.com/biobanking/biobanking/wiki
    license: CC-BY-4.0
    name: Ontology for Biobanking
    prefix: FAIRsharing.bxc508
    publications:
    - doi: 10.1186/s13326-016-0068-y
      title: OBIB-a novel ontology for biobanking
      year: 2016
    subjects:
    - Health Science
  mappings:
    aberowl: OBIB
    biocontext: OBIB
    bioportal: OBIB
    fairsharing: FAIRsharing.bxc508
    obofoundry: obib
    ols: obib
    ontobee: OBIB
    wikidata.entity: Q55118499
  obofoundry:
    contact: jmwhorton@uams.edu
    contact.github: jmwhorton
    contact.label: Justin Whorton
    contact.orcid: 0009-0003-4268-6207
    deprecated: false
    description: An ontology built for annotation and modeling of biobank repository
      and biobanking administration
    domain: investigations
    download.owl: http://purl.obolibrary.org/obo/obib.owl
    homepage: https://github.com/biobanking/biobanking
    license: CC BY 4.0
    license.url: http://creativecommons.org/licenses/by/4.0/
    name: Ontology for Biobanking
    preferredPrefix: OBIB
    prefix: obib
    repository: https://github.com/biobanking/biobanking
  ols:
    description: The Ontology for Biobanking (OBIB) is an ontology for the annotation
      and modeling of the activities, contents, and administration of a biobank. Biobanks
      are facilities that store specimens, such as bodily fluids and tissues, typically
      along with specimen annotation and clinical data. OBIB is based on a subset
      of the Ontology for Biomedical Investigation (OBI), has the Basic Formal Ontology
      (BFO) as its upper ontology, and is developed following OBO Foundry principles.
      The first version of OBIB resulted from the merging of two existing biobank-related
      ontologies, OMIABIS and biobank ontology.
    download_owl: http://purl.obolibrary.org/obo/obib.owl
    homepage: https://github.com/biobanking/biobanking
    name: Ontology for BIoBanking (OBIB)
    prefix: obib
    tracker: https://github.com/biobanking/biobanking/issues
    version: '2023-04-05'
    version.iri: http://purl.obolibrary.org/obo/obib/2023-04-05/obib.owl
  ontobee:
    library: Library
    name: Ontology for Biobanking
    prefix: OBIB
  pattern: ^\d{7}$
  prefix: obib
  publications:
  - doi: 10.1186/s13326-016-0068-y
    pmc: PMC4855778
    pubmed: '27148435'
    title: OBIB-a novel ontology for biobanking
    year: 2016
  uri_format: http://purl.obolibrary.org/obo/OBIB_$1
obo:
  biocontext:
    prefix: OBO
  contact:
    email: nicolas.matentzoglu@gmail.com
    github: matentzn
    name: Nicolas Matentzoglu
    orcid: 0000-0002-7356-1779
  description: The OBO namespace is the top-level namespace used by Open Biological
    and Biomedical Ontology (OBO) Foundry ontologies.
  example: uberon
  example_extras:
  - go
  - uberon.owl
  fairsharing:
    abbreviation: OBO
    description: The Open Biological and Biomedical Ontology (OBO) Foundry is a collective
      of ontology developers that are committed to collaboration and adherence to
      shared principles. The mission of the OBO Foundry is to develop a family of
      interoperable ontologies that are both logically well-formed and scientifically
      accurate. To achieve this, OBO Foundry participants voluntarily adhere to and
      contribute to the development of an evolving set of principles including open
      use, collaborative development, non-overlapping and strictly-scoped content,
      and common syntax and relations, based on ontology models that work well, such
      as the Gene Ontology (GO). The OBO Foundry is overseen by an Operations Committee
      with Editorial, Technical and Outreach working groups.
    homepage: http://www.obofoundry.org/
    name: OBO Foundry
    prefix: FAIRsharing.847069
    publications:
    - doi: 10.1038/nbt1346
      pubmed_id: 17989687
      title: 'The OBO Foundry: coordinated evolution of ontologies to support biomedical
        data integration.'
    repository: https://github.com/OBOFoundry/OBOFoundry.github.io
    subjects:
    - Ontology and Terminology
    twitter: OBOFoundry
  homepage: http://www.obofoundry.org/
  integbio:
    alt_name: Open Biomedical Ontologies
    description: The OBO Foundry provides a catalog of ontologies used in medicine
      or life sciences. Users can find details of each ontology in the list. Each
      ontology and the list are downloadable as owl file, and as YAML, JSON-LD and
      RDF/Turtle, respectively.
    homepage: http://www.obofoundry.org/
    information_keywords:
    - Ontology/Terminology/Nomenclature
    maintainer: BBOP （Berkeley Bioinformatics Open-source Project）
    name: OBO
    prefix: nbdc00305
    pubmeds:
    - '16564748'
    - '17321117'
    - '16549013'
    - '16964349'
    - '16442850'
    - '16964349'
    - '16435295'
    - '16360342'
    status: Active
  lov:
    description: The Ontology for Biomedical Investigations (OBI) is build in a collaborative,
      international effort and will serve as a resource for annotating biomedical
      investigations, including the study design, protocols and instrumentation used,
      the data generated and the types of analysis performed on the data. This ontology
      arose from the Functional Genomics Investigation Ontology (FuGO) and will contain
      both terms that are common to all biomedical investigations, including functional
      genomics investigations and those that are more domain specific.
    homepage: http://purl.obolibrary.org/obo/obi.owl
    keywords:
    - Biology
    - Health
    modified: '2019-08-06'
    name: Ontology for Biomedical Investigation
    prefix: obo
    uri_prefix: http://purl.obolibrary.org/obo/$1
  mappings:
    biocontext: OBO
    fairsharing: FAIRsharing.847069
    integbio: nbdc00305
    lov: obo
  name: Open Biological and Biomedical Ontologies
  preferred_prefix: obo
  prefix: obo
  publications:
  - doi: 10.1038/nbt1346
    pmc: PMC2814061
    pubmed: '17989687'
    title: 'The OBO Foundry: coordinated evolution of ontologies to support biomedical
      data integration'
    year: 2007
  rdf_uri_format: http://purl.obolibrary.org/obo/$1
  references:
  - https://github.com/biopragmatics/bioregistry/pull/913
  - https://github.com/biopragmatics/bioregistry/issues/910
  uri_format: http://purl.obolibrary.org/obo/$1
oboe:
  aberowl:
    description: 'The Extensible Observation Ontology (OBOE) is a formal ontology
      for capturing the semantics of scientific observation and measurement. The ontology
      supports researchers to add detailed semantic annotations to scientific data,
      thereby clarifying the inherent meaning of scientific observations. The main
      concepts in OBOE include: - Observation: an event in which one or more measurements
      are taken - Measurement: the measured value of a property for a specific object
      or phenomenon (e.g., 3.2) - Entity: an object or phenomenon on which measurements
      are made (e.g., Quercus rubrum) - Characteristic: the property being measured
      (e.g., VolumetricDensity) - Standard: units and controlled vocabularies for
      interpreting measured values (e.g., g/cm^3) - Protocol: the procedures followed
      to obtain measurements (e.g., DensityProtocol2014) OBOE can characterize the
      context of an observation (e.g., space and time), as well as dependencies such
      as nested experimental observations. It includes an extensive set of unit definitions
      (e.g., grams of carbon per liter of seawater), and can facilitate automatic
      unit conversions (e.g., pounds to kilograms). OBOE can be easily extended to
      create Entities and Characteristics for specific research domains, making it
      both broadly applicable and highly customizable. OBOE is being used to improve
      data interpretation, facilitate reuse, and create precise and effective systems
      for data search and discovery.'
    download_owl: http://aber-owl.net/media/ontologies/OBOE/4/oboe.owl
    homepage: https://github.com/NCEAS/oboe
    name: The Extensible Observation Ontology
    prefix: OBOE
    version: Version 1.2
  agroportal:
    contact:
      email: joshua.madin@mq.edu.au
      name: Joshua Madin
    description: The Extensible Observation Ontology (OBOE) is a formal ontology for
      capturing the semantics of scientific observation and measurement. The ontology
      supports researchers to add detailed semantic annotations to scientific data,
      thereby clarifying the inherent meaning of scientific observations.
    example_uri: http://ecoinformatics.org/oboe/oboe.1.2/oboe-characteristics.owl#SpectralRadiance
    homepage: https://github.com/NCEAS/oboe/
    license: CC-BY-3.0
    name: The Extensible Observation Ontology
    prefix: OBOE
    publications:
    - https://doi.org/10.1016/j.ecoinf.2007.05.004
    repository: https://github.com/NCEAS/oboe
    version: Version 1.2
  bioportal:
    contact:
      email: mecum@nceas.ucsb.edu
      name: Bryce Mecum
    description: 'The Extensible Observation Ontology (OBOE) is a formal ontology
      for capturing the semantics of scientific observation and measurement. The ontology
      supports researchers to add detailed semantic annotations to scientific data,
      thereby clarifying the inherent meaning of scientific observations. The main
      concepts in OBOE include: - Observation: an event in which one or more measurements
      are taken - Measurement: the measured value of a property for a specific object
      or phenomenon (e.g., 3.2) - Entity: an object or phenomenon on which measurements
      are made (e.g., Quercus rubrum) - Characteristic: the property being measured
      (e.g., VolumetricDensity) - Standard: units and controlled vocabularies for
      interpreting measured values (e.g., g/cm^3) - Protocol: the procedures followed
      to obtain measurements (e.g., DensityProtocol2014) OBOE can characterize the
      context of an observation (e.g., space and time), as well as dependencies such
      as nested experimental observations. It includes an extensive set of unit definitions
      (e.g., grams of carbon per liter of seawater), and can facilitate automatic
      unit conversions (e.g., pounds to kilograms). OBOE can be easily extended to
      create Entities and Characteristics for specific research domains, making it
      both broadly applicable and highly customizable. OBOE is being used to improve
      data interpretation, facilitate reuse, and create precise and effective systems
      for data search and discovery.'
    homepage: https://github.com/NCEAS/oboe
    name: The Extensible Observation Ontology
    prefix: OBOE
    publications:
    - http://www.example.com
    version: Version 1.2
  contact:
    email: brycemecum@gmail.com
    github: amoeba
    name: Bryce Mecum
    orcid: 0000-0002-0381-3766
  contributor:
    email: philip.stroemert@tib.eu
    github: StroemPhi
    name: Philip Strömert
    orcid: 0000-0002-1595-3213
  description: The Extensible Observation Ontology (OBOE) is a formal ontology for
    capturing the semantics of scientific observation and measurement. The ontology
    supports researchers to add detailed semantic annotations to scientific data,
    thereby clarifying the inherent meaning of scientific observations.
  download_owl: https://raw.githubusercontent.com/NCEAS/oboe/refs/heads/master/oboe.owl
  ecoportal:
    contact:
      email: joshua.madin@mq.edu.au
      name: Joshua Madin
    description: The Extensible Observation Ontology (OBOE) is a formal ontology for
      capturing the semantics of scientific observation and measurement. The ontology
      supports researchers to add detailed semantic annotations to scientific data,
      thereby clarifying the inherent meaning of scientific observations.
    example_uri: http://ecoinformatics.org/oboe/oboe.1.2/oboe-characteristics.owl#SpectralRadiance
    homepage: https://github.com/NCEAS/oboe/
    license: CC-BY-3.0
    name: The Extensible Observation Ontology
    prefix: OBOE
    publications:
    - https://doi.org/10.1016/j.ecoinf.2007.05.004
    repository: https://github.com/NCEAS/oboe
    version: Version 1.2
  example: Characteristic
  fairsharing:
    abbreviation: OBOE
    contact:
      email: mecum@nceas.ucsb.edu
      name: Bryce Mecum
      orcid: 0000-0002-0381-3766
    description: OBOE is a suite of OWL-DL ontologies for modeling and representing
      scientific observations. The OBOE model is designed as a generic data model
      with a number of constructs for defining observational data. Key features of
      OBOE include its ability to represent a wide range of measurement types, a mechanism
      for specifying measurement context, and the ability to associate the type of
      entity (e.g., sample, organism, etc.) being measured. OBOE is being used and
      developed within the Semtools project for describing a wide variety of ecological
      data stored within the Knowledge Network for Biodiversity (KNB) as well as extensions
      for ontology-based data annotation and discovery within the MetaCat software
      infrastructure.
    homepage: https://github.com/NCEAS/oboe/
    license: CC-BY-3.0
    name: 'OBOE: The Extensible Observation Ontology'
    prefix: FAIRsharing.5970hq
    repository: https://github.com/NCEAS/oboe/issues
    subjects:
    - Environmental Science
    - Biodiversity
    - Ecology
    user_defined_tags:
    - Observations
  github_request_issue: 1276
  homepage: https://github.com/NCEAS/oboe
  license: CC-BY-3.0
  mappings:
    aberowl: OBOE
    agroportal: OBOE
    bioportal: OBOE
    ecoportal: OBOE
    fairsharing: FAIRsharing.5970hq
    tib: oboe-core
  name: The Extensible Observation Ontology
  prefix: oboe
  publications:
  - doi: 10.1016/j.ecoinf.2007.05.004
    pmc: PMC8612252
    pubmed: '34817235'
    title: An ontology for describing and synthesizing ecological observation data
    year: 2007
  repository: https://github.com/NCEAS/oboe
  reviewer:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  tib:
    description: This ontology provides the core OBOE modeling constructs.
    download_owl: http://ecoinformatics.org/oboe/oboe.1.2/oboe-core.owl
    homepage: https://github.com/NCEAS/oboe
    keywords:
    - FAIR Data Spaces
    - NFDI4CHEM
    - ESS
    name: oboe-core
    prefix: oboe-core
    uri_format: http://ecoinformatics.org/oboe/oboe.1.2/oboe-core.owl#$1
  uri_format: http://ecoinformatics.org/oboe/oboe.1.2/oboe-core.owl#$1
oboe.standard:
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: Units in OBOE
  example: Acre
  github_request_issue: 1643
  homepage: https://github.com/NCEAS/oboe
  keywords:
  - ontology
  - unit
  - units
  name: OBOE Standard
  prefix: oboe.standard
  uri_format: http://ecoinformatics.org/oboe/oboe.1.2/oboe-standards.owl$1
oboinowl:
  biocontext:
    prefix: oboInOwl
    uri_format: http://www.geneontology.org/formats/oboInOwl#$1
  biolink:
    is_identifiers: false
    is_obo: false
    prefix: oboformat
    uri_format: http://www.geneontology.org/formats/oboInOwl#$1
  contact:
    email: cjmungall@lbl.gov
    github: cmungall
    name: Chris Mungall
    orcid: 0000-0002-6601-2165
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: This meta-ontology is self-describing. OBO metamodel properties are
    described using OBO metamodel properties
  download_obo: http://www.geneontology.org/formats/oboInOwl.obo
  download_owl: http://www.geneontology.org/formats/oboInOwl.owl
  example: hasDbXref
  example_extras:
  - hasExactSynonym
  - hasBroadSynonym
  - hasNarrowSynonym
  - auto_generated_by
  fairsharing:
    abbreviation: OBO Format
    description: The first part of this specification describes the syntax and structure
      of OBO Format using BNF. This states how strings of characters in OBOF Files
      are parsed into abstract OBO documents, and describes constraints on the structure
      of these documents. The second part of this specification describes the semantics
      of an OBO document via a mapping to OWL2-DL and community metadata vocabularies.
    homepage: http://oboformat.org
    name: OBO Format Syntax and Semantics
    prefix: FAIRsharing.aa0eat
    publications: []
    subjects:
    - Life Science
  homepage: https://github.com/geneontology/go-ontology/tree/master/contrib
  mappings:
    biocontext: oboInOwl
    biolink: oboformat
    fairsharing: FAIRsharing.aa0eat
    ols: oio
  name: OBO in OWL
  ols:
    prefix: oio
    uri_format: http://www.geneontology.org/formats/oboInOwl#$1
  pattern: ^[\w-]+$
  preferred_prefix: oboInOwl
  prefix: oboinowl
  references:
  - https://github.com/biopragmatics/bioregistry/pull/973
  - https://github.com/geneontology/go-site/issues/2157
  repository: https://github.com/geneontology/go-ontology
  synonyms:
  - oboformat
  - oio
  uri_format: http://www.geneontology.org/formats/oboInOwl#$1
obv:
  bartoc:
    abbreviation: OBV
    description: The OBV classes are used in the Austrian Library Network (OBV) as
      broad classification.
    name: OBV classes
    pattern: ^[0-9][0-9]$
    prefix: '20430'
  mappings:
    bartoc: '20430'
    miriam: obv
  miriam:
    deprecated: false
    description: The Austrian Library Network (OBV) is the largest network of scientific
      and administrative libraries in Austria with 70 participants, representing more
      than 90 individual institutions - including the Austrian National Library, university
      libraries, the colleges of education, individual ministries, numerous technical
      colleges and other important collections.
    homepage: https://www.obvsg.at/
    id: '00001000'
    name: Austrian Library Network
    namespaceEmbeddedInLui: false
    pattern: ^AC[0-9]{8}$
    prefix: obv
    sampleId: AC00963334
    uri_format: https://permalink.obvsg.at/$1
  prefix: obv
occ:
  mappings:
    miriam: occ
    n2t: occ
  miriam:
    deprecated: false
    description: The OpenCitations Corpus is open repository of scholarly citation
      data made available under a Creative Commons public domain dedication (CC0),
      which provides accurate bibliographic references harvested from the scholarly
      literature that others may freely build upon, enhance and reuse for any purpose,
      without restriction under copyright or database law.
    homepage: https://w3id.org/oc/corpus
    id: 00000693
    name: OpenCitations Corpus
    namespaceEmbeddedInLui: false
    pattern: ^[a-z][a-z]/[0-9]+$
    prefix: occ
    sampleId: br/1
    uri_format: https://w3id.org/oc/corpus/$1
  n2t:
    description: The OpenCitations Corpus is open repository of scholarly citation
      data made available under a Creative Commons public domain dedication (CC0),
      which provides accurate bibliographic references harvested from the scholarly
      literature that others may freely build upon, enhance and reuse for any purpose,
      without restriction under copyright or database law.
    example: br/1
    homepage: https://w3id.org/oc/corpus
    name: OpenCitations Corpus
    namespaceEmbeddedInLui: false
    pattern: ^[a-z][a-z]/[0-9]+$
    prefix: occ
    uri_format: https://w3id.org/oc/corpus/$1
  prefix: occ
occo:
  aberowl:
    description: An ontology representing occupations. It is designed to facilitate
      harmonization of existing occupation standards, such as the US Bureau of Labor
      Statistics Standard Occupational Classification (US SOC), the International
      Standard Classification of Occupations (ISCO), the UK National Statistics Standard
      Occupational Classification (UK SOC), and the European Skills, Competences,
      Qualifications and Occupations (ESCO) of the European Union.
    download_owl: http://aber-owl.net/media/ontologies/OCCO/9/occo.owl
    homepage: https://github.com/Occupation-Ontology/OccO
    name: Occupation Ontology
    prefix: OCCO
  bioportal:
    contact:
      email: yongqunh@med.umich.edu
      name: Yongqun (Oliver) He
    description: This Occupaton Ontology (OccO) is an ontology in the domain of human
      occupations. Current OccO version is developed based on the US Bureau of Labor
      Statistics Standard Occupation Classification (SOC) and the related O*Net System.
      The OccO development follows the principles of the Open Biological and Biomedical
      (OBO) Foundry.
    homepage: https://hegroup.org/
    name: Occupation Ontology
    prefix: OCCO
    version: '2023-08-20'
  example: '00000001'
  mappings:
    aberowl: OCCO
    bioportal: OCCO
    obofoundry: occo
    ols: occo
    ontobee: OCCO
  obofoundry:
    contact: zhengj2007@gmail.com
    contact.github: zhengj2007
    contact.label: Jie Zheng
    contact.orcid: 0000-0002-2999-0103
    deprecated: false
    description: An ontology representing occupations. It is designed to facilitate
      harmonization of existing occupation standards, such as the US Bureau of Labor
      Statistics Standard Occupational Classification (US SOC), the International
      Standard Classification of Occupations (ISCO), the UK National Statistics Standard
      Occupational Classification (UK SOC), and the European Skills, Competences,
      Qualifications and Occupations (ESCO) of the European Union.
    domain: information
    download.owl: http://purl.obolibrary.org/obo/occo.owl
    homepage: https://github.com/Occupation-Ontology/OccO
    license: CC BY 4.0
    license.url: https://creativecommons.org/licenses/by/4.0/
    name: Occupation Ontology
    preferredPrefix: OCCO
    prefix: occo
    repository: https://github.com/Occupation-Ontology/OccO
  ols:
    description: This Occupaton Ontology (OccO) is an ontology in the domain of human
      occupaitons. Current OccO version is developed based on the US Bureau of Labor
      Statistics Standard Occupation Classification (SOC) and the related O*Net System.
      The OccO development follows the principles of the Open Biological and Biomedical
      (OBO) Foundry.
    download_owl: http://purl.obolibrary.org/obo/occo.owl
    homepage: https://github.com/Occupation-Ontology/OccO
    name: Occupation Ontology (OccO)
    prefix: occo
    tracker: https://github.com/Occupation-Ontology/OccO/issues
    version: '2025-10-06'
    version.iri: http://purl.obolibrary.org/obo/occo/releases/2025-10-06/occo.owl
  ontobee:
    library: Library
    name: Occupation Ontology
    prefix: OCCO
  pattern: ^\d+$
  prefix: occo
ocdo:
  contact:
    email: a.azocar.guzman@fz-juelich.de
    github: aazocar
    name: Abril Azocar Guzman
    orcid: 0000-0001-7564-7990
  contributor:
    email: philip.stroemert@tib.eu
    github: StroemPhi
    name: Philip Strömert
    orcid: 0000-0002-1595-3213
  description: The Crystallographic Defect Core Ontology (CDCO) defines the common
    terminology shared across all types of crystallographic defects, providing a unified
    framework for data integration in materials science.
  download_owl: https://github.com/OCDO/cdco/raw/refs/heads/main/cdco.owl
  example: hasDefectComplex
  github_request_issue: 1742
  homepage: https://github.com/OCDO/cdco
  license: CC-BY-4.0
  logo: https://raw.githubusercontent.com/OCDO/.github/refs/heads/main/profile/ocdo_logo.png
  name: Crystallographic Defect Core Ontology
  prefix: ocdo
  repository: https://github.com/OCDO/cdco
  reviewer:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  uri_format: http://purls.helmholtz-metadaten.de/cdos/cdco/$1
oci:
  biocontext:
    prefix: OCI
  mappings:
    biocontext: OCI
    miriam: oci
    n2t: oci
  miriam:
    deprecated: false
    description: 'Each OCI (Open Citation Identifier) has a simple structure: oci:<identifier>-<identifier>,
      where “oci:” is the identifier prefix, and is used to identify a citation as
      a first-class data entity - see https://doi.org/10.6084/m9.figshare.7127816.v2
      for additional information. In each OCI, the first <identifier> is the identifier
      for the citing bibliographic resource, while the second <identifier> is the
      identifier for the cited bibliographic resource.'
    homepage: http://opencitations.net
    id: '00000660'
    name: OCI
    namespaceEmbeddedInLui: false
    pattern: ^0[1-9]+0[0-9]+-0[1-9]+0[0-9]+$
    prefix: oci
    sampleId: 01027931310-01022252312
    uri_format: https://opencitations.net/index/ci/$1
  n2t:
    description: 'Each OCI (Open Citation Identifier) has a simple structure: oci:number-number,
      where &#x201C;oci:&#x201D; is the identifier prefix, and is used to identify
      a citation as a first-class data entitiy - see https://opencitations.wordpress.com/2018/02/19/citations-as-first-class-data-entities-introduction/
      for additional information.  OCIs for citations stored within the OpenCitations
      Corpus are constructed by combining the OpenCitations Corpus local identifiers
      for the citing and cited bibliographic resources, separating them with a dash.
      For example, oci:2544384-7295288 is a valid OCI for the citation between two
      papers stored within the OpenCitations Corpus.  OCIs can also be created for
      bibliographic resources described in an external bibliographic database, if
      they are similarly identified there by identifiers having a unique numerical
      part. For example, the OCI for the citation that exists between Wikidata resources
      Q27931310 and Q22252312 is oci:01027931310&#x2013;01022252312.  OCIs can also
      be created for bibliographic resources described in external bibliographic database
      such as Crossref or DataCite where they are identified by alphanumeric Digital
      Object Identifiers (DOIs), rather than purely numerical strings.'
    example: 1-18
    homepage: http://opencitations.net
    name: OpenCitations
    namespaceEmbeddedInLui: false
    pattern: ^[0-9]+-[0-9]+$
    prefix: oci
    uri_format: https://w3id.org/oc/oci/$1
  name: Open Citation Identifier
  prefix: oci
ocid:
  banana: ocid
  mappings:
    miriam: ocid
  miriam:
    deprecated: false
    description: '''ocid'' stands for "Ontology Concept Identifiers" and are 12 digit
      long integers covering IDs in topical ontologies from anatomy up to toxicology.'
    homepage: https://ontochem.com/
    id: 00000738
    name: Ontology Concept Identifiers
    namespaceEmbeddedInLui: true
    pattern: ^ocid:[0-9]{12}$
    prefix: ocid
    sampleId: '190000021540'
    uri_format: https://ocid.ontochem.com/prefname?ocid=$1
  pattern: ^[0-9]{12}$
  prefix: ocid
oclc:
  biocontext:
    prefix: OCLC
  mappings:
    biocontext: OCLC
    miriam: oclc
    n2t: oclc
  miriam:
    deprecated: false
    description: The global library cooperative OCLC maintains WorldCat. WorldCat
      is the world's largest network of library content and services. WorldCat libraries
      are dedicated to providing access to their resources on the Web, where most
      people start their search for information.
    homepage: https://www.oclc.org/en/about.html
    id: 00000669
    name: Online Computer Library Center (OCLC) WorldCat
    namespaceEmbeddedInLui: false
    pattern: ^[0-9]+$
    prefix: oclc
    sampleId: '634515043'
    uri_format: https://www.worldcat.org/oclc/$1
  n2t:
    description: The global library cooperative OCLC maintains WorldCat. WorldCat
      is the world's largest network of library content and services. WorldCat libraries
      are dedicated to providing access to their resources on the Web, where most
      people start their search for information.
    example: '634515043'
    homepage: https://www.oclc.org/en/about.html
    name: Online Computer Library Center (OCLC) WorldCat
    namespaceEmbeddedInLui: false
    pattern: ^[0-9]+$
    prefix: oclc
    uri_format: https://www.worldcat.org/oclc/$1
  name: Online Computer Library Center WorldCat
  prefix: oclc
odam:
  mappings:
    miriam: odam
  miriam:
    deprecated: false
    description: Experimental data table management software to make research data
      accessible and available for reuse with minimal effort on the part of the data
      provider. Designed to manage experimental data tables in an easy way for users,
      ODAM provides a model for structuring both data and metadata that facilitates
      data handling and analysis. It also encourages data dissemination according
      to FAIR principles by making the data interoperable and reusable by both humans
      and machines, allowing the dataset to be explored and then extracted in whole
      or in part as needed.
    homepage: https://metabolome.cgfb.u-bordeaux.fr/
    id: '00000722'
    name: Open Data for Access and Mining
    namespaceEmbeddedInLui: false
    pattern: ^[A-Za-z0-9]+$
    prefix: odam
    sampleId: frim1
    uri_format: http://pmb-bordeaux.fr/getdata/json/$1/datapackage?links=1
  prefix: odam
odamexplorer:
  mappings:
    miriam: odam.explorer
  miriam:
    deprecated: false
    description: 'ODAM (Open Data for Access and Mining) is an Experimental data table
      management software (EDTMS) to make research data accessible and available for
      reuse with minimal effort on the part of the data provider. Designed to manage
      experimental data tables in an easy way for users, ODAM provides a model for
      structuring both data and metadata that facilitates data handling and analysis.
      It also encourages data dissemination according to FAIR principles by making
      the data interoperable and reusable by both humans and machines.


      ODAM allows datasets to be explored and then extracted in whole or in part as
      needed.


      For more information/explanation, see ODAM User''s Guide : https://inrae.github.io/ODAM/'
    homepage: https://eng-bfp.bordeaux-aquitaine.hub.inrae.fr/
    id: '00001076'
    name: ODAM Data explorer
    namespaceEmbeddedInLui: false
    pattern: ^[A-Za-z][A-Za-z0-9]+$
    prefix: odam.explorer
    sampleId: frim1
    uri_format: https://pmb-bordeaux.fr/dataexplorer/?ds=$1
  prefix: odamexplorer
odc.sci:
  fairsharing:
    abbreviation: ODC-SCI
    contact:
      email: jgrethe@ucsd.edu
      name: Jeffrey Grethe
      orcid: 0000-0001-5212-7052
    description: The Open Data Commons for Spinal Cord Injury is a cloud-based community-driven
      repository to store, share, and publish spinal cord injury research data. There
      are several challenges for scientific reproducibility and bench-to-bedside translation.
      For example, only research and data that are published actually get disseminated,
      a phenomenon known as publication bias. Published research reflects to only
      a small fraction of all data collected, and data that do not lead to publication
      are largely ignored, hidden away in filing cabinets and hard drives. This results
      in an abundance of inaccessible scientific data known as “dark data”. Even when
      research is disseminated, it is usually in the form of summary reports of aggregated
      data (e.g. averages across individual subjects) such as scientific articles.
      The fact that the individual subject-level data are inaccessible further contributes
      to dark data. The spinal cord injury (SCI) community created the ODC-SCI to
      mitigate dark data in SCI research. The ODC-SCI also aims to increase transparency
      with individual-level data, enhance collaboration, facilitate advanced analytics,
      and conform to increasing mandates by funders and publishers to make data accessible.
      Members of the ODC-SCI have access to a private digital lab space managed by
      the PI or multi-PIs for dataset storage and sharing. The PIs can share their
      labs’ datasets with the registered members of the ODC-SCI community and make
      their datasets public and citable. The ODC-SCI implements stewardship principles
      that scientific data be made FAIR (Findable, Accessible, Interoperable and Reusable)
      and has been widely adopted by the international SCI research community.
    homepage: https://odc-sci.org
    license: CC-BY-4.0
    name: Open Data Commons for Spinal Cord Injury
    prefix: FAIRsharing.M6Ruz3
    publications:
    - doi: 10.1038/ncomms9581
      pubmed_id: 26466022
      title: Topological data analysis for discovery in preclinical spinal cord injury
        and traumatic brain injury.
    - doi: 10.1007/s12975-011-0121-1
      pubmed_id: 22207883
      title: 'Syndromics: a bioinformatics approach for neurotrauma research.'
    - doi: 10.1089/neu.2014.3399
      pubmed_id: 25077610
      title: Development of a database for translational spinal cord injury research.
    - doi: 10.1371/journal.pone.0059712
      pubmed_id: 23544088
      title: Derivation of multivariate syndromic outcome metrics for consistent testing
        across multiple models of cervical spinal cord injury in rats.
    - doi: 10.1089/neu.2019.6674
      pubmed_id: 31608767
      title: 'FAIR SCI Ahead: The Evolution of the Open Data Commons for Pre-Clinical
        Spinal Cord Injury Research.'
    - doi: S0014-4886(17)30137-1
      pubmed_id: 28576567
      title: Developing a data sharing community for spinal cord injury research.
    - doi: 10.1038/nn.3838
      pubmed_id: 25349910
      title: 'Big data from small data: data-sharing in the ''long tail'' of neuroscience.'
    subjects:
    - Neurobiology
    - Neurology
    - Biomedical Science
    - Neuroscience
  mappings:
    fairsharing: FAIRsharing.M6Ruz3
    miriam: odc.sci
    re3data: r3d100014071
  miriam:
    deprecated: false
    description: The Open Data Commons for Spinal Cord Injury is a cloud-based community-driven
      repository to store, share, and publish spinal cord injury research data.
    homepage: https://odc-sci.org
    id: 00000804
    name: Open Data Commons for Spinal Cord Injury
    namespaceEmbeddedInLui: false
    pattern: ^[0-9]*$
    prefix: odc.sci
    sampleId: '602'
    uri_format: https://odc-sci.org/data/$1
  prefix: odc.sci
  publications:
  - doi: 10.1089/neu.2019.6674
    pmc: PMC7071068
    pubmed: '31608767'
    title: 'FAIR SCI Ahead: The Evolution of the Open Data Commons for Pre-Clinical
      Spinal Cord Injury Research'
    year: 2019
  - doi: 10.1016/j.expneurol.2017.05.012
    pmc: PMC6448396
    pubmed: '28576567'
    title: Developing a data sharing community for spinal cord injury research
    year: 2017
  - doi: 10.1038/ncomms9581
    pmc: PMC4634208
    pubmed: '26466022'
    title: Topological data analysis for discovery in preclinical spinal cord injury
      and traumatic brain injury
    year: 2015
  - doi: 10.1038/nn.3838
    pmc: PMC4728080
    pubmed: '25349910'
    title: 'Big data from small data: data-sharing in the ''long tail'' of neuroscience'
    year: 2014
  - doi: 10.1089/neu.2014.3399
    pmc: PMC4186058
    pubmed: '25077610'
    title: Development of a database for translational spinal cord injury research
    year: 2014
  - doi: 10.1371/journal.pone.0059712
    pmc: PMC3609747
    pubmed: '23544088'
    title: Derivation of multivariate syndromic outcome metrics for consistent testing
      across multiple models of cervical spinal cord injury in rats
    year: 2013
  - doi: 10.1007/s12975-011-0121-1
    pmc: PMC3236294
    pubmed: '22207883'
    title: 'Syndromics: a bioinformatics approach for neurotrauma research'
    year: 2011
  re3data:
    description: A community platform to Share Data, Publish Data with a DOI, and
      get Citations. Advancing Spinal Cord Injury research through sharing of data
      from basic and clinical research.
    doi: 10.17616/R31NJNCN
    homepage: https://odc-sci.org/
    name: Open Data Commons for Spinal Cord Injury
    prefix: r3d100014071
    synonyms:
    - ODC-SCI
odc.tbi:
  mappings:
    miriam: odc.tbi
  miriam:
    deprecated: false
    description: The Open Data Commons for Traumatic Brain Injury is a cloud-based
      community-driven repository to store, share, and publish traumatic brain injury
      research data.
    homepage: https://odc-tbi.org
    id: 00000816
    name: Open Data Commons for Traumatic Brain Injury
    namespaceEmbeddedInLui: false
    pattern: ^[0-9]*$
    prefix: odc.tbi
    sampleId: '408'
    uri_format: https://odc-tbi.org/data/$1
  prefix: odc.tbi
odor:
  biocontext:
    prefix: ODOR
  mappings:
    biocontext: ODOR
    miriam: odor
    n2t: odor
  miriam:
    deprecated: false
    description: OdorDB stores information related to odorous compounds, specifically
      identifying those that have been shown to interact with olfactory receptors
    homepage: https://ordb.biotech.ttu.edu/OdorDB
    id: '00000500'
    name: Odor Molecules DataBase
    namespaceEmbeddedInLui: false
    pattern: ^\d+$
    prefix: odor
    sampleId: '74'
    uri_format: https://ordb.biotech.ttu.edu/OdorDB/Data/$1
  n2t:
    description: OdorDB stores information related to odorous compounds, specifically
      identifying those that have been shown to interact with olfactory receptors
    example: '74'
    homepage: http://senselab.med.yale.edu/OdorDB
    name: Odor Molecules DataBase at Yale University School of Medicine
    namespaceEmbeddedInLui: false
    pattern: ^\d+$
    prefix: odor
    uri_format: http://senselab.med.yale.edu/OdorDB/Data/$1/?db=5
  prefix: odor
odrl:
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: The ODRL Vocabulary and Expression defines a set of concepts and terms
    (the vocabulary) and encoding mechanism (the expression) for permissions and obligations
    statements describing digital content usage based on the ODRL Information Model.
  download_rdf: https://www.w3.org/ns/odrl/2/ODRL22.rdf
  example: assetConcepts
  homepage: http://www.w3.org/ns/odrl/2
  lov:
    description: The Open Digital Rights Language (ODRL) provides flexible and interoperable
      mechanisms to support transparent and innovative use of digital content in publishing,
      distribution, and consumption of of digital media across all sectors and communities.
      The ODRL Policy model is broad enough to support traditional rights expressions
      for commercial transaction, open access expressions for publicly distributed
      content, and privacy expressions for social media.
    homepage: https://www.w3.org/TR/odrl-vocab/
    keywords:
    - Metadata
    modified: '2017-09-16'
    name: The Open Digital Rights Language (ODRL) Ontology
    prefix: odrl
    uri_prefix: http://www.w3.org/ns/odrl/2/$1
  mappings:
    lov: odrl
  name: Open Digital Rights Language Ontology
  prefix: odrl
  uri_format: http://www.w3.org/ns/odrl/2/$1
oecd.template:
  comment: The identifiers have two numbers separated by a dot. The first one corresponds
    to the template number which can be found on the homepage. The second number referes
    to the row within the corresponding spreadsheet.
  contributor:
    email: null
    github: bgyori
    name: Benjamin M. Gyori
    orcid: 0000-0001-9439-5346
  description: The Organisation for Economic Co-operation and Development (OECD) Harmonised
    Templates (OHTs) are standard data formats for reporting information used for
    the risk assessment of chemicals, mainly studies done on chemicals to determine
    their properties or effects on human health and the environment, but also for
    storing data on use and exposure.
  example: '74.186'
  github_request_issue: 997
  homepage: https://www.oecd.org/ehs/templates/
  name: OECD Harmonised Templates
  pattern: ^\d+\.\d+$
  prefix: oecd.template
  references:
  - https://github.com/biopragmatics/bioregistry/issues/991
  reviewer:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
oefos:
  example: '509015'
  mappings:
    tib: oefos
  name: Austrian Fields of Science and Technology Classification
  prefix: oefos
  tib:
    description: 'The Austrian Fields of Science and Technology Classification (ÖFOS
      2012) is the Austrian version of the revised international Fields of Science
      and Technology Classification of the OECD (FOS) published in the Frascati Manual
      2015 as Fields of Research and Development (FORD). These fields are adjusted
      to national needs, whose application for international comparisons is binding,
      particularly within the European Statistical System. The six major Fields of
      Science: Natural Sciences; Technical Sciences; Human Medicine, Health Sciences;
      Agricultural Sciences, Veterinary Medicine; Social Sciences and Humanities remained
      unchanged in comparison to ÖFOS 2002. In order to ensure international comparability,
      the previous 2-digit levels from 2002, which are no longer applicable, were
      replaced by new 3-digit levels (groups) according to the international FOS respectively
      FORD. These 3-digit levels were provided with further sub-groups (4-digits)
      taking into account the comments of the international classification. It is
      therefore feasible that the new Austrian Fields of Science adapt to national
      peculiarities of the Austrian research activities. The research area with the
      corresponding 6-digits in alphabetical order serves as a description of the
      fields of activities and research projects and/or for the coverage of the main
      scientific activities of a statistical unit in the research and development
      surveys. (Current revision status: August 2017)'
    download_rdf: https://vocabs-downloads.acdh.oeaw.ac.at/vocabs-main/GeneralConcepts/OeFOS/oefos_disciplines.ttl
    homepage: https://vocabs.dariah.eu/oefos/en/
    keywords:
    - Educational Resources
    - educational science
    name: The Austrian Fields of Science and Technology Classification (ÖFOS 2012)
    prefix: oefos
    uri_format: https://vocabs.acdh.oeaw.ac.at/oefosdisciplines/$1
oeh.educationlevel:
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: A list of values for class levels. Created in the context of the OpenEduHub
  download_rdf: https://github.com/openeduhub/oeh-metadata-vocabs/raw/refs/heads/master/educationalLevel.ttl
  example: '1'
  github_request_issue: 1626
  homepage: https://github.com/openeduhub/oeh-metadata-vocabs
  keywords:
  - education level
  - open educational resources
  name: OpenEduHub Education Level
  prefix: oeh.educationlevel
  rdf_uri_format: http://w3id.org/openeduhub/vocabs/educationalLevel/$1
  repository: https://github.com/openeduhub/oeh-metadata-vocabs
  uri_format: http://w3id.org/openeduhub/vocabs/educationalLevel/$1
oeo:
  bartoc:
    abbreviation: OEO
    description: The Open Energy Ontology (OEO) is a domain ontology of the energy
      system analysis context. It is developed as part of the Open Energy Family.
      The OEO is published on GitHub under an open source license. The language used
      is the Manchester OWL Syntax, which was chosen because it is user-friendly for
      editing and viewing differences of edited files. The OEO is constantly being
      extended. The first version of the OEO has been released on June 11th 2020.
      A Steering Committee (OEO-SC) was created to accompany the development, increase
      awareness of the ontology and include it in current projects.
    homepage: https://openenergyplatform.org/ontology/
    license: CC0-1.0
    name: Open Energy Ontology
    prefix: '20826'
  contact:
    email: mirjam.stappel@uni-osnabrueck.de
    github: stap-m
    name: Mirjam Stappel
    orcid: 0000-0003-3722-5564
  contact_group_email: oeo-info@lists.rl-institut.de
  contributor:
    email: mirjam.stappel@uni-osnabrueck.de
    github: stap-m
    name: Mirjam Stappel
    orcid: 0000-0003-3722-5564
  description: OEO is a domain reference ontology for energy system modeling.
  download_owl: https://openenergyplatform.org/ontology/oeo/dev/oeo-full.owl
  example: '00030015'
  fairsharing:
    abbreviation: OEO
    contact:
      email: ludwig.huelk@rl-institut.de
      name: Ludwig Hülk
      orcid: 0000-0003-4655-2321
    description: The Open Energy Ontology (OEO) is a domain ontology within the field
      of energy system modelling. The goal of OEO is to ease cooperation and exchange
      of information across the energy systems analysis domain. It is designed to
      map the complexity of this research area and to collect, connect and structure
      the ambiguous terminology of those adjacent domains the energy systems analysis
      domain needs information from.
    homepage: https://openenergyplatform.org/ontology/
    license: CC0-1.0
    logo: https://api.fairsharing.org/rails/active_storage/blobs/redirect/eyJfcmFpbHMiOnsibWVzc2FnZSI6IkJBaHBBallIIiwiZXhwIjpudWxsLCJwdXIiOiJibG9iX2lkIn19--7d85634a28722b48af9b2ccf2398db652d0b9753/OpenEnergyFamily_Logo_OpenEnergyOntology_OEO.png?disposition=inline
    name: Open Energy Ontology
    prefix: FAIRsharing.b91873
    publications:
    - doi: 10.1016/j.egyai.2021.100074
      title: 'Introducing the Open Energy Ontology: Enhancing data interpretation
        and interfacing in energy systems analysis'
      year: 2021
    repository: https://github.com/OpenEnergyPlatform/ontology
    subjects:
    - Energy Engineering
  github_request_issue: 1757
  homepage: https://openenergyplatform.org/ontology/
  keywords:
  - energy
  license: CC0-1.0
  mappings:
    bartoc: '20826'
    fairsharing: FAIRsharing.b91873
    tib: oeo
  name: Open Energy Ontology
  pattern: ^\d+$
  preferred_prefix: OEO
  prefix: oeo
  publications:
  - doi: 10.1016/j.egyai.2021.100074
    pmc: null
    pubmed: null
    title: 'Introducing the Open Energy Ontology: Enhancing data interpretation and
      interfacing in energy systems analysis'
    year: 2021
  rdf_uri_format: https://openenergyplatform.org/ontology/oeo/OEO_$1
  repository: https://github.com/OpenEnergyPlatform/ontology
  reviewer:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  tib:
    description: 'The Open Energy Ontology is an ontology for all aspects of the energy
      modelling domain.


      It is developed in four main modules: ''oeo-model'', a module for all entities
      related to models and modelling; ''oeo-physical'', a module for all entities
      related to the world of energy and energy generation; ''oeo-social'', a module
      for all relevant social and economic aspects of the energy domain; ''oeo-shared'',
      a module to cover entities and relations needed in all of the modules above
      to prevent them getting implemented multiple times.

      A supplementary module is the oeo-physical-axioms module, which contains general
      class axioms.'
    download_owl: https://openenergy-platform.org/ontology/oeo/releases/oeo-full.owl
    homepage: https://openenergy-platform.org/ontology/
    keywords:
    - NFDI4ING
    - NFDI4Energy
    - mechanical engineering, energy technology
    - engineering
    name: Repository for the Open Energy Ontology (OEO)
    prefix: oeo
    tracker: https://github.com/OpenEnergyPlatform/ontology/issues
    uri_format: http://openenergy-platform.org/ontology/oeo/OEO_$1
    version.iri: https://openenergyplatform.org/ontology/oeo/releases/2.9.0/oeo.owl
  uri_format: https://openenergyplatform.org/ontology/oeo/OEO_$1
oerschema:
  contact:
    email: null
    github: michael-collins
    name: Michael Collins
    orcid: null
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: A RDF vocabulary for OER content on the web.
  domain: data model
  example: InstructionalPattern
  github_request_issue: 1661
  homepage: https://oerschema.org
  keywords:
  - curricula
  - curriculum
  - education
  - oer
  - oers
  - open educational resources
  license: MIT
  name: OER Schema
  prefix: oerschema
  repository: https://github.com/open-curriculum/oerschema
  uri_format: https://oerschema.org/$1
og:
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: A vocabulary for embedding provenance metadata into webpages via RDFa
  example: title
  github_request_issue: 1632
  homepage: https://ogp.me
  keywords:
  - data schema
  - linked open data
  - semantic web
  lov:
    description: The Open Graph protocol enables any web page to become a rich object
      in a social graph. For instance, this is used on Facebook to enable any web
      page to have the same functionality as a Facebook Page.
    homepage: http://ogp.me/
    keywords:
    - API
    modified: '2013-02-16'
    name: Open Graph Protocol Vocabulary
    prefix: og
    uri_prefix: http://ogp.me/ns#$1
  mappings:
    lov: og
    zazuko: og
  name: Open Graph protocol
  prefix: og
  rdf_uri_format: https://ogp.me/ns#$1
  uri_format: https://ogp.me/ns#$1
  zazuko:
    prefix: og
    uri_format: http://ogp.me/ns#$1
ogc.sf:
  description: An RDF/OWL vocabulary for defining SimpleFeature geometry types
  download_rdf: https://opengeospatial.github.io/ogc-geosparql/geosparql11/sf_geometries.ttl
  example: Triangle
  homepage: https://opengeospatial.github.io/ogc-geosparql/geosparql11/sf_geometries.html
  mappings:
    zazuko: sf
  name: Open Geospatial Consortium Simple Features Vocabulary
  prefix: ogc.sf
  uri_format: http://www.opengis.net/ont/sf#$1
  zazuko:
    prefix: sf
    uri_format: http://www.opengis.net/ont/sf#$1
ogg:
  aberowl:
    description: A formal ontology of genes and genomes of biological organisms.
    download_owl: http://aber-owl.net/media/ontologies/OGG/4/ogg.owl
    homepage: https://bitbucket.org/hegroup/ogg
    name: The Ontology of Genes and Genomes
    prefix: OGG
  biocontext:
    prefix: OGG
  bioportal:
    contact:
      email: yongqunh@med.umich.edu
      name: Oliver He
    description: OGG is a biological ontology in the area of genes and genomes. OGG
      uses the Basic Formal Ontology (BFO) as its upper level ontology. This OGG document
      contains the genes and genomes of a list of selected organisms, including human,
      two viruses (HIV and influenza virus), and bacteria (B. melitensis strain 16M,
      E. coli strain K-12 substrain MG1655, M. tuberculosis strain H37Rv, and P. aeruginosa
      strain PAO1). More OGG information for other organisms (e.g., mouse, zebrafish,
      fruit fly, yeast, etc.) may be found in other OGG subsets.
    homepage: https://bitbucket.org/hegroup/ogg
    name: Ontology of Genes and Genomes
    prefix: OGG
    version: 'Vision Release: 1.0.59'
  example: '3000887619'
  fairsharing:
    abbreviation: OGG
    contact:
      email: yongqunh@med.umich.edu
      name: Yongqun He
      orcid: 0000-0001-9189-9661
    description: OGG is a biological ontology in the area of genes and genomes. OGG
      uses the Basic Formal Ontology (BFO) as its upper level ontology. This OGG document
      contains the genes and genomes of a list of selected organisms. Each gene in
      OGG has over 10 annotation items, includes gene-associated Gene Ontology (GO)
      and PubMed article information. OGG has represented genes in human, two viruses,
      and four bacteria. Additionally, 7 OGG subsets are developed to represent genes
      and genomes of 7 model systems including mouse, fruit fly, zebrafish, yeast,
      A. thaliana, C. elegans, and P. falciparum.
    domains:
    - Gene name
    - gene
    - genome
    homepage: https://bitbucket.org/hegroup/ogg
    license: CC-BY-3.0
    name: Ontology of Genes and Genomes
    prefix: FAIRsharing.zmx7nn
    subjects:
    - Life Science
    - Biology
  mappings:
    aberowl: OGG
    biocontext: OGG
    bioportal: OGG
    fairsharing: FAIRsharing.zmx7nn
    obofoundry: ogg
    ols: ogg
    ontobee: OGG
    wikidata.entity: Q81661736
  obofoundry:
    contact: yongqunh@med.umich.edu
    contact.github: yongqunh
    contact.label: Yongqun Oliver He
    contact.orcid: 0000-0001-9189-9661
    deprecated: false
    description: A formal ontology of genes and genomes of biological organisms.
    domain: biological systems
    download.owl: http://purl.obolibrary.org/obo/ogg.owl
    homepage: https://bitbucket.org/hegroup/ogg
    license: CC BY 3.0
    license.url: http://creativecommons.org/licenses/by/3.0/
    name: The Ontology of Genes and Genomes
    preferredPrefix: OGG
    prefix: ogg
    repository: https://bitbucket.org/hegroup/ogg
  ols:
    description: OGG is a biological ontology in the area of genes and genomes. OGG
      uses the Basic Formal Ontology (BFO) as its upper level ontology. This OGG document
      contains the genes and genomes of a list of selected organisms, including human,
      two viruses (HIV and influenza virus), and bacteria (B. melitensis strain 16M,
      E. coli strain K-12 substrain MG1655, M. tuberculosis strain H37Rv, and P. aeruginosa
      strain PAO1). More OGG information for other organisms (e.g., mouse, zebrafish,
      fruit fly, yeast, etc.) may be found in other OGG subsets.
    download_owl: http://purl.obolibrary.org/obo/ogg.owl
    homepage: https://bitbucket.org/hegroup/ogg
    name: 'OGG: Ontology of Genes and Genomes'
    prefix: ogg
    tracker: https://bitbucket.org/hegroup/ogg/issues/
    version: 1.0.59
  ontobee:
    library: Library
    name: The Ontology of Genes and Genomes
    prefix: OGG
  pattern: ^\d+$
  prefix: ogg
  uri_format: http://purl.obolibrary.org/obo/OGG_$1
ogi:
  aberowl:
    description: Using BFO as its framwork, OGI formalized the genomic element by
      defining an upper class 'genetic interval'. The definition of 'genetic interval'
      is "the spatial continuous physical entity which contains ordered genomic sets(DNA,
      RNA, Allele, Marker,etc.) between and including two points (Nucleic_Acid_Base_Residue)
      on a chromosome or RNA molecule which must have a liner primary sequence sturcture.
    download_owl: http://aber-owl.net/media/ontologies/OGI/18/ogi.owl
    homepage: https://code.google.com/p/ontology-for-genetic-interval/
    name: Ontology for genetic interval
    prefix: OGI
    version: '2.0'
  biocontext:
    prefix: OGI
  bioportal:
    contact:
      email: linikujp@gmail.com
      name: Yu Lin
    description: Using BFO as its framwork, OGI formalized the genomic element by
      defining an upper class 'genetic interval'. The definition of 'genetic interval'
      is "the spatial continuous physical entity which contains ordered genomic sets(DNA,
      RNA, Allele, Marker,etc.) between and including two points (Nucleic_Acid_Base_Residue)
      on a chromosome or RNA molecule which must have a liner primary sequence sturcture.
    homepage: https://code.google.com/p/ontology-for-genetic-interval/
    name: Ontology for Genetic Interval
    prefix: OGI
    version: '2.0'
  deprecated: true
  example: 0000019
  homepage: https://code.google.com/archive/p/ontology-for-genetic-interval/
  mappings:
    aberowl: OGI
    biocontext: OGI
    bioportal: OGI
    obofoundry: ogi
    ols: ogi
    ontobee: OGI
    wikidata.entity: Q55118520
  obofoundry:
    contact: linikujp@gmail.com
    contact.github: linikujp
    contact.label: Asiyah Yu Lin
    contact.orcid: 0000-0002-5379-5359
    deprecated: true
    description: An ontology that formalizes the genomic element by defining an upper
      class genetic interval
    domain: chemistry and biochemistry
    download.owl: http://purl.obolibrary.org/obo/ogi.owl
    homepage: https://code.google.com/p/ontology-for-genetic-interval/
    name: Ontology for genetic interval
    prefix: ogi
  ols:
    description: "OGI formalized the genomic element by defining an upper class 'genetic\
      \ interval'.\n\nThe definition of 'genetic interval' is \"the spatial continuous\
      \ physical entity which contains ordered genomic sets(DNA, RNA, Allele, Marker,etc.)\
      \ between and including two points (Nucleic Acid Base Residue) on a chromosome\
      \ or RNA molecule which must have a liner primary sequence sturcture.\" \n\n\
      Related paper:\n\n1. Yu Lin, Norihiro Sakamoto (2009) “Genome, Gene, Interval\
      \ and Ontology” Interdisciplinary Ontology Vol.2 - Proceedings of the Second\
      \ Interdisciplinary Meeting, Tokyo, Feb. 28th- Mar. 1st, 2009. Page(s):25-34\
      \ (http://cdb-riken.academia.edu/LinYu/Papers/142399/Genome_Gene_Interval_and_Ontology)\n\
      Yu Lin, Hiroshi Tarui, Peter Simons (2009) “From Ontology for Genetic Interval(OGI)\
      \ to Sequence Assembly – Ontology apply to next generation sequencing” Proceeding\
      \ of the Semantic Web Applications and Tools for Life Science Workshop, Amsterdam,\
      \ Nov.20th, 2009. (http://ceur-ws.org/Vol-559/Poster2.pdf)\nYu Lin, Peter Simons\
      \ (2010) “DNA sequence from below: A Nominalist Approach” Interdisciplinary\
      \ Ontology Vol.3 - Proceedings of the Second Interdisciplinary Meeting, Tokyo,\
      \ Feb. 28th- Mar. 1st, 2010. (http://philpapers.org/rec/LINDSF)\n\n\n"
    download: http://purl.obolibrary.org/obo/ogi.owl
    homepage: https://code.google.com/p/ontology-for-genetic-interval/
    name: Ontology for genetic interval
    prefix: ogi
    version: '2.0'
  ontobee:
    library: Library
    name: Ontology for genetic interval
    prefix: OGI
  pattern: ^\d{7}$
  prefix: ogi
  synonyms:
  - OGI.owl
ogms:
  aberowl:
    description: An ontology for representing treatment of disease and diagnosis and
      on carcinomas and other pathological entities
    download_owl: http://aber-owl.net/media/ontologies/OGMS/20/ogms.owl
    homepage: https://github.com/OGMS/ogms
    name: Ontology for General Medical Science
    prefix: OGMS
  bartoc:
    description: 'BFO grows out of a philosophical orientation which overlaps with
      that of DOLCE and SUMO. Unlike these, however, it is narrowly focused on the
      task of providing a genuine upper ontology which can be used in support of domain
      ontologies developed for scientific research, as for example in biomedicine
      within the framework of the OBO Foundry. Thus BFO does not contain physical,
      chemical, biological or other terms which would properly fall within the special
      sciences domains.


      The BFO project was initiated in 2002. The theory behind BFO was developed initially
      by Barry Smith and Pierre Grenon and presented in a series of publications listed
      here. Since then important contributions to BFO have been made by many people,
      including: Werner Ceusters, Chris Mungall, Fabian Neuhaus, Holger Stenzhorn,
      Alan Ruttenberg, Mathias Brochausen, Bjoern Peters, Kerry Trentelman, and by
      more than hundred other members of the BFO Discussion Group. Its development
      has been carried out under the auspices of the project Forms of Life sponsored
      by the Volkswagen Foundation.'
    homepage: http://www.ifomis.org/bfo/
    prefix: '216'
    wikidata_database: Q4866972
  biocontext:
    prefix: OGMS
  bioportal:
    contact:
      email: rscheuermann@jcvi.org
      name: Richard Scheuermann
    description: The Ontology for General Medical Science (OGMS) is based on the papers
      Toward an Ontological Treatment of Disease and Diagnosis and On Carcinomas and
      Other Pathological Entities. The ontology attempts to address some of the issues
      raised at the Workshop on Ontology of Diseases (Dallas, TX) and the Signs, Symptoms,
      and Findings Workshop(Milan, Italy). OGMS was formerly called the clinical phenotype
      ontology. Terms from OGMS hang from the Basic Formal Ontology. See http://ontology.buffalo.edu/medo/Disease_and_Diagnosis.pdf
    homepage: https://github.com/OGMS/ogms
    name: Ontology for General Medical Science
    prefix: OGMS
    publications:
    - http://ontology.buffalo.edu/medo/Disease_and_Diagnosis.pdf
    version: '2021-08-19'
  download_obo: http://purl.obolibrary.org/obo/ogms.obo
  example: '0000031'
  fairsharing:
    abbreviation: OGMS
    contact:
      email: rscheuermann@jcvi.org
      name: Richard Scheuermann
      orcid: 0000-0003-1355-892X
    description: 'The Ontology for General Medical Science (OGMS) is an ontology of
      entities involved in a clinical encounter. OGMS includes very general terms
      that are used across medical disciplines, including: ''disease'', ''disorder'',
      ''disease course'', ''diagnosis'', ''patient'', and ''healthcare provider''.
      The scope of OGMS is restricted to humans, but many terms can be applied to
      a variety of organisms. OGMS provides a formal theory of disease that can be
      further elaborated by specific disease ontologies.'
    domains:
    - cancer
    - disease phenotype
    - disease
    - diagnosis
    homepage: https://github.com/OGMS/ogms
    name: Ontology for General Medical Science
    prefix: FAIRsharing.rvz0m9
    publications:
    - doi: 10.1186/2041-1480-4-42
      pubmed: '24314207'
      title: The neurological disease ontology
      year: 2013
    repository: https://github.com/OGMS/ogms/issues
    subjects:
    - Biomedical Science
    - Medicine
  mappings:
    aberowl: OGMS
    bartoc: '216'
    biocontext: OGMS
    bioportal: OGMS
    fairsharing: FAIRsharing.rvz0m9
    obofoundry: ogms
    ols: ogms
    ontobee: OGMS
    wikidata.entity: Q55118512
  obofoundry:
    appears_in:
    - labo
    - scdo
    contact: baeverma@jcvi.org
    contact.github: BAevermann
    contact.label: Brian Aevermann
    contact.orcid: 0000-0003-1346-1327
    deprecated: false
    description: An ontology for representing treatment of disease and diagnosis and
      on carcinomas and other pathological entities
    domain: health
    download.owl: http://purl.obolibrary.org/obo/ogms.owl
    homepage: https://github.com/OGMS/ogms
    license: CC BY 4.0
    license.url: http://creativecommons.org/licenses/by/4.0/
    logo: https://avatars2.githubusercontent.com/u/12973154?s=200&v=4
    name: Ontology for General Medical Science
    preferredPrefix: OGMS
    prefix: ogms
    publications:
    - id: https://www.ncbi.nlm.nih.gov/pubmed/21347182
      preferred: true
      title: Toward an ontological treatment of disease and diagnosis
    - id: https://www.ncbi.nlm.nih.gov/pubmed/25991121
      title: Biomarkers in the Ontology for General Medical Science
    repository: https://github.com/OGMS/ogms
  ols:
    description: 'The Ontology for General Medical Science (OGMS) is an ontology of
      entities involved in a clinical encounter. OGMS includes very general terms
      that are used across medical disciplines, including: ''disease'', ''disorder'',
      ''disease course'', ''diagnosis'', ''patient'', and ''healthcare provider''.
      OGMS uses the Basic Formal Ontology (BFO) as an upper-level ontology. The scope
      of OGMS is restricted to humans, but many terms can be applied to a variety
      of organisms. OGMS provides a formal theory of disease that can be further elaborated
      by specific disease ontologies. This theory is implemented using OWL-DL and
      OBO Relation Ontology relations and is available in OWL and OBO formats.


      OGMS is based on the papers Toward an Ontological Treatment of Disease and Diagnosis
      and On Carcinomas and Other Pathological Entities. The ontology attempts to
      address some of the issues raised at the Workshop on Ontology of Diseases (Dallas,
      TX) and the Signs, Symptoms, and Findings Workshop(Milan, Italy). OGMS was formerly
      called the clinical phenotype ontology. Terms from OGMS hang from the Basic
      Formal Ontology.'
    download_owl: http://purl.obolibrary.org/obo/ogms.owl
    homepage: https://github.com/OGMS/ogms
    name: Ontology for General Medical Science
    prefix: ogms
    tracker: https://github.com/OGMS/ogms/issues
    version: '2021-08-19'
    version.iri: http://purl.obolibrary.org/obo/ogms/2021-08-19/ogms.owl
  ontobee:
    library: Library
    name: Ontology for General Medical Science
    prefix: OGMS
  pattern: ^\d{7}$
  prefix: ogms
  providers:
  - code: omre
    description: null
    example: null
    first_party: null
    homepage: null
    name: null
    publications: null
    status: null
    uri_format: http://purl.obolibrary.org/obo/ogms/OMRE_$1
  publications:
  - doi: null
    pmc: null
    pubmed: '25991121'
    title: Biomarkers in the ontology for general medical science
    year: 2015
  - doi: 10.1186/2041-1480-4-42
    pmc: PMC4028878
    pubmed: '24314207'
    title: The neurological disease ontology
    year: 2013
  - doi: null
    pmc: PMC3041577
    pubmed: '21347182'
    title: Toward an ontological treatment of disease and diagnosis
    year: 2009
  - doi: null
    pmc: null
    pubmed: '21347182'
    title: Toward an ontological treatment of disease and diagnosis
    year: null
  - doi: null
    pmc: null
    pubmed: '25991121'
    title: Biomarkers in the Ontology for General Medical Science
    year: null
  - doi: 10.1186/2041-1480-4-42
    pmc: null
    pubmed: '24314207'
    title: The neurological disease ontology
    year: 2013
  - doi: null
    pmc: null
    pubmed: '21347182'
    title: Toward an ontological treatment of disease and diagnosis
    year: null
  - doi: null
    pmc: null
    pubmed: '25991121'
    title: Biomarkers in the Ontology for General Medical Science
    year: null
  - doi: 10.1186/2041-1480-4-42
    pmc: null
    pubmed: '24314207'
    title: The neurological disease ontology
    year: 2013
  synonyms:
  - ogms/OMRE
  uri_format: http://purl.obolibrary.org/obo/OGMS_$1
  wikidata:
    database: Q4866972
ogsf:
  aberowl:
    description: An application ontology to represent genetic susceptibility to a
      specific disease, adverse event, or a pathological process.
    download_owl: http://aber-owl.net/media/ontologies/OGSF/11/ogsf.owl
    homepage: none
    name: Ontology of Genetic Susceptibility Factor
    prefix: OGSF
  biocontext:
    prefix: OGSF
  bioportal:
    contact:
      email: linikujp@gmail.com
      name: Asiyah Yu Lin
    description: Ontology for Genetic Susceptibility Factor (OGSF) is an application
      ontology to model/represent the notion of genetic susceptibility to a specific
      disease or an adverse event or a pathological biological process. It is developed
      using BFO2.0's framwork. The ontology is under the domain of genetic epidemiology.
    homepage: https://code.google.com/p/ogsf/
    name: Ontology for Genetic Susceptibility Factor
    prefix: OGSF
    version: '2.0'
  example: '0000025'
  fairsharing:
    abbreviation: OGSF
    contact:
      email: linikujp@gmail.com
      name: Asiyah Yu Lin
      orcid: 0000-0003-2620-0345
    description: 'Ontology for Genetic Susceptibility Factor (OGSF) is an application
      ontology to model/represent the notion of genetic susceptibility to a specific
      disease or an adverse event or a pathological biological process. It is developed
      using BFO 2.0''s framework. The ontology is under the domain of genetic epidemiology.
      OGSF is built from a combination of three ontologies: the Ontology of Geographical
      Region (OGR), the Ontology of Glucose Metabolism (OGMD), and the Ontology of
      Genetic Disease Investigations (OGDI). '
    domains:
    - Adverse Reaction
    - disease
    - genetic disorder
    homepage: https://github.com/linikujp/OGSF
    name: Ontology for Genetic Susceptibility Factor
    prefix: FAIRsharing.egv2cz
    publications:
    - doi: 10.1186/2041-1480-5-19
      pubmed: '24963371'
      title: The ontology of genetic susceptibility factors (OGSF) and its application
        in modeling genetic susceptibility to vaccine adverse events
      year: 2014
    - pubmed: '20847592'
      title: Ontology driven modeling for the knowledge of genetic susceptibility
        to disease
      year: 2009
    subjects:
    - Biomedical Science
    - Epidemiology
    - Genetics
  mappings:
    aberowl: OGSF
    biocontext: OGSF
    bioportal: OGSF
    fairsharing: FAIRsharing.egv2cz
    obofoundry: ogsf
    ols: ogsf
    ontobee: OGSF
    wikidata.entity: Q113012672
  obofoundry:
    contact: linikujp@gmail.com
    contact.github: linikujp
    contact.label: Asiyah Yu Lin
    contact.orcid: 0000-0002-5379-5359
    deprecated: true
    description: An application ontology to represent genetic susceptibility to a
      specific disease, adverse event, or a pathological process.
    domain: investigations
    download.owl: http://purl.obolibrary.org/obo/ogsf.owl
    homepage: https://github.com/linikujp/OGSF
    license: CC BY 3.0
    license.url: https://creativecommons.org/licenses/by/3.0/
    name: Ontology of Genetic Susceptibility Factor
    preferredPrefix: OGSF
    prefix: ogsf
    repository: https://github.com/linikujp/OGSF
  ols:
    description: An application ontology to represent genetic susceptibility to a
      specific disease, adverse event, or a pathological process.
    download_owl: http://purl.obolibrary.org/obo/ogsf.owl
    homepage: https://github.com/linikujp/OGSF
    name: Ontology of Genetic Susceptibility Factor
    prefix: ogsf
    tracker: https://github.com/linikujp/OGSF/issues
    version: '2.0'
  ontobee:
    library: Library
    name: Ontology of Genetic Susceptibility Factor
    prefix: OGSF
  pattern: ^\d{7}$
  prefix: ogsf
  publications:
  - doi: 10.1186/2041-1480-5-19
    pmc: PMC4068904
    pubmed: '24963371'
    title: The ontology of genetic susceptibility factors (OGSF) and its application
      in modeling genetic susceptibility to vaccine adverse events
    year: 2014
  - doi: null
    pmc: null
    pubmed: '20847592'
    title: Ontology driven modeling for the knowledge of genetic susceptibility to
      disease
    year: 2009
  uri_format: http://purl.obolibrary.org/obo/OGSF_$1
ohd:
  aberowl:
    description: The Oral Health and Disease Ontology is used for representing the
      diagnosis and treatment of dental maladies.
    download_owl: http://aber-owl.net/media/ontologies/OHD/9/ohd.owl
    homepage: https://purl.obolibrary.org/obo/ohd/home
    name: Oral Health and Disease Ontology
    prefix: OHD
  biocontext:
    prefix: OHD
  bioportal:
    contact:
      email: wdduncan@gmail.com
      name: Bill Duncan
    description: The Oral Health and Disease Ontology (OHD) is an OBO Foundry ontology
      used for representing oral-health maladies, their diagnosis, and treatment.
      It is has been used to represent the content of dental practice health records
      and is intended to be further developed for use in translation medicine. It
      demonstrates a principled split between billing codes as information entities
      and what the codes are about, such as dental procedures, materials, and patients.
    homepage: https://github.com/oral-health-and-disease-ontologies/ohd-ontology
    license: CC-BY-4.0
    name: The Oral Health and Disease Ontology
    prefix: OHD
    version: '2025-06-28'
  example: '0000006'
  fairsharing:
    abbreviation: OHD
    description: The Oral Health and Disease Ontology is intended as a BFO and OBO
      Foundry compliant ontology for the oral health domain. It is currently used
      to represent the content of dental practice health records and is intended to
      be further developed for use in translation medicine. It demonstrates a principled
      split between billing codes as information entities and what the codes are about,
      such as dental procedures, materials, and patients. OHD is structured using
      BFO uses terms from OGMS, OBI, IAO and FMA. In addition it uses terms from CARO,
      OMRSE, NCBITaxon, and a subset of terms from the Current Dental Terminology
      (CDT) OHD is in early development and subject to change without notice.
    homepage: https://github.com/oral-health-and-disease-ontologies/ohd-ontology
    name: The Oral Health and Disease Ontology
    prefix: FAIRsharing.bg7bb6
    subjects:
    - Dentistry
    - Oral Surgery
    - Medicine
  mappings:
    aberowl: OHD
    biocontext: OHD
    bioportal: OHD
    fairsharing: FAIRsharing.bg7bb6
    obofoundry: ohd
    ols: ohd
    ontobee: OHD
    wikidata.entity: Q55118561
  obofoundry:
    contact: wdduncan@gmail.com
    contact.github: wdduncan
    contact.label: Bill Duncan
    contact.orcid: 0000-0001-9625-1899
    deprecated: false
    description: The Oral Health and Disease Ontology is used for representing the
      diagnosis and treatment of dental maladies.
    domain: health
    download.owl: http://purl.obolibrary.org/obo/ohd.owl
    homepage: https://purl.obolibrary.org/obo/ohd/home
    license: CC BY 4.0
    license.url: http://creativecommons.org/licenses/by/4.0/
    name: Oral Health and Disease Ontology
    preferredPrefix: OHD
    prefix: ohd
    publications:
    - id: https://www.ncbi.nlm.nih.gov/pubmed/32819435
      title: Structuring, reuse and analysis of electronic dental data using the Oral
        Health and Disease Ontology
    repository: https://github.com/oral-health-and-disease-ontologies/ohd-ontology
  ols:
    description: The Oral Health and Disease Ontology is used for representing the
      diagnosis and treatment of dental maladies.
    download_owl: http://purl.obolibrary.org/obo/ohd.owl
    homepage: https://purl.obolibrary.org/obo/ohd/home
    name: Oral Health and Disease Ontology
    prefix: ohd
    tracker: https://github.com/oral-health-and-disease-ontologies/ohd-ontology/issues
    version: '2025-06-28'
    version.iri: http://purl.obolibrary.org/obo/ohd/releases/2025-06-28/ohd.owl
  ontobee:
    library: Library
    name: Oral Health and Disease Ontology
    prefix: OHD
  pattern: ^\d{7}$
  prefix: ohd
  publications:
  - doi: 10.1186/s13326-020-00222-0
    pmc: PMC7439527
    pubmed: '32819435'
    title: Structuring, reuse and analysis of electronic dental data using the Oral
      Health and Disease Ontology
    year: 2020
  - doi: null
    pmc: null
    pubmed: '32819435'
    title: Structuring, reuse and analysis of electronic dental data using the Oral
      Health and Disease Ontology
    year: null
  uri_format: http://purl.obolibrary.org/obo/OHD_$1
ohmi:
  aberowl:
    description: The Ontology of Host-Microbiome Interactions aims to ontologically
      represent and standardize various entities and relations related to microbiomes,
      microbiome host organisms (e.g., human and mouse), and the interactions between
      the hosts and microbiomes at different conditions.
    download_owl: http://aber-owl.net/media/ontologies/OHMI/16/ohmi.owl
    homepage: https://github.com/ohmi-ontology/ohmi
    name: Ontology of Host-Microbiome Interactions
    prefix: OHMI
  biocontext:
    prefix: OHMI
  bioportal:
    contact:
      email: yongqunh@med.umich.edu
      name: Oliver He
    description: OHMI is a biomedical ontology that represents the entities and relations
      in the domain of host-microbiome interactions.
    homepage: https://github.com/ohmi-ontology/ohmi
    name: Ontology of Host-Microbe Interactions
    prefix: OHMI
    version: '2019-09-17'
  example: '0000460'
  fairsharing:
    abbreviation: OHMI
    description: OHMI is aimed to ontologically represent various entities and relations
      related to microbiomes, microbiome host organisms (e.g., human and mouse), and
      the interactions between the hosts and microbiomes at different conditions.
    domains:
    - host
    - microbiome
    homepage: https://github.com/ohmi-ontology/ohmi
    license: CC-BY-4.0
    name: Ontology of Host-Microbe Interactions
    prefix: FAIRsharing.cz9cnp
    publications:
    - doi: 10.1186/s13326-019-0217-1
      title: 'OHMI: the ontology of host-microbiome interactions'
      year: 2019
    repository: https://github.com/OHMI-ontology/OHMI/issues
    subjects:
    - Life Science
  mappings:
    aberowl: OHMI
    biocontext: OHMI
    bioportal: OHMI
    fairsharing: FAIRsharing.cz9cnp
    obofoundry: ohmi
    ols: ohmi
    ontobee: OHMI
    wikidata.entity: Q113012673
  obofoundry:
    contact: yongqunh@med.umich.edu
    contact.github: yongqunh
    contact.label: Yongqun Oliver He
    contact.orcid: 0000-0001-9189-9661
    deprecated: false
    description: The Ontology of Host-Microbiome Interactions aims to ontologically
      represent and standardize various entities and relations related to microbiomes,
      microbiome host organisms (e.g., human and mouse), and the interactions between
      the hosts and microbiomes at different conditions.
    domain: organisms
    download.owl: http://purl.obolibrary.org/obo/ohmi.owl
    homepage: https://github.com/ohmi-ontology/ohmi
    license: CC BY 4.0
    license.url: http://creativecommons.org/licenses/by/4.0/
    name: Ontology of Host-Microbiome Interactions
    preferredPrefix: OHMI
    prefix: ohmi
    repository: https://github.com/ohmi-ontology/ohmi
  ols:
    description: OHMI is a biomedical ontology that represents the entities and relations
      in the domain of host-microbiome interactions.
    download_owl: http://purl.obolibrary.org/obo/ohmi.owl
    homepage: https://github.com/ohmi-ontology/ohmi
    name: 'OHMI: Ontology of Host-Microbiome Interactions'
    prefix: ohmi
    tracker: https://github.com/ohmi-ontology/ohmi/issues
    version: '2019-09-17'
    version.iri: http://purl.obolibrary.org/obo/ohmi/2019-09-17/ohmi.owl
  ontobee:
    library: Library
    name: Ontology of Host-Microbiome Interactions
    prefix: OHMI
  pattern: ^\d{7}$
  prefix: ohmi
  uri_format: http://purl.obolibrary.org/obo/OHMI_$1
ohpi:
  aberowl:
    description: OHPI is a community-driven ontology of host-pathogen interactions
      (OHPI) and represents the virulence factors (VFs) and how the mutants of VFs
      in the Victors database become less virulence inside a host organism or host
      cells. It is developed to represent manually curated HPI knowledge available
      in the PHIDIAS resource.
    download_owl: http://aber-owl.net/media/ontologies/OHPI/12/ohpi.owl
    homepage: https://github.com/OHPI/ohpi
    name: Ontology of Host Pathogen Interactions
    prefix: OHPI
  bioportal:
    contact:
      email: edong@umich.edu
      name: Edison Ong
    description: The Ontology of Host-Pathogen Interactions (OHPI) is a biomedical
      ontology of the host-pathogen interactions. Its development follows the OBO
      Foundry Principles.
    homepage: https://github.com/OHPI/ohpi/
    name: Ontology of Host-Pathogen Interactions
    prefix: OHPI
    publications:
    - https://www.ncbi.nlm.nih.gov/pubmed/30365026
    version: 1.0.26
  example: '9001411'
  fairsharing:
    abbreviation: OHPI
    contact:
      email: edong@umich.edu
      name: Edison Ong
      orcid: 0000-0002-5159-414X
    description: OHPI is a community-driven ontology of host-pathogen interactions
      (OHPI) and represents the virulence factors (VFs) and how the mutants of VFs
      in the Victors database become less virulence inside a host organism or host
      cells. It is also developed to represent manually curated HPI knowledge available
      in the PHIDIAS resource.
    domains:
    - host
    - infection process
    - pathogen
    homepage: https://github.com/OHPI/ohpi
    license: CC-BY-4.0
    name: Ontology of Host-Pathogen Interactions
    prefix: FAIRsharing.vxpUJ6
    publications:
    - doi: 10.1093/nar/gky999
      pubmed: '30365026'
      title: 'Victors: a web-based knowledge base of virulence factors in human and
        animal pathogens'
      year: 2018
    repository: https://github.com/OHPI/ohpi/issues
    subjects:
    - Biomedical Science
    - Bioinformatics
  mappings:
    aberowl: OHPI
    bioportal: OHPI
    fairsharing: FAIRsharing.vxpUJ6
    obofoundry: ohpi
    ols: ohpi
    ontobee: OHPI
    wikidata.entity: Q113012674
  obofoundry:
    contact: edong@umich.edu
    contact.github: e4ong1031
    contact.label: Edison Ong
    contact.orcid: 0000-0002-5159-414X
    deprecated: false
    description: OHPI is a community-driven ontology of host-pathogen interactions
      (OHPI) and represents the virulence factors (VFs) and how the mutants of VFs
      in the Victors database become less virulence inside a host organism or host
      cells. It is developed to represent manually curated HPI knowledge available
      in the PHIDIAS resource.
    domain: biological systems
    download.owl: http://purl.obolibrary.org/obo/ohpi.owl
    homepage: https://github.com/OHPI/ohpi
    license: CC BY 4.0
    license.url: http://creativecommons.org/licenses/by/4.0/
    name: Ontology of Host Pathogen Interactions
    preferredPrefix: OHPI
    prefix: ohpi
    publications:
    - id: https://www.ncbi.nlm.nih.gov/pubmed/30365026
      title: 'Victors: a web-based knowledge base of virulence factors in human and
        animal pathogens'
    repository: https://github.com/OHPI/ohpi
  ols:
    description: OHPI is a biomedical ontology in the area of host-pathogen interactions.
      OHPI is developed by following the OBO Foundry Principles (e.g., openness and
      collaboration).
    download_owl: http://purl.obolibrary.org/obo/ohpi.owl
    homepage: https://github.com/OHPI/ohpi
    name: 'OHPI: Ontology of Host-Pathogen Interactions'
    prefix: ohpi
    tracker: https://github.com/OHPI/ohpi/issues
    version: '2019-09-30'
    version.iri: http://purl.obolibrary.org/obo/ohpi/releases/2019-09-30
  ontobee:
    library: Library
    name: Ontology of Host Pathogen Interactions
    prefix: OHPI
  pattern: ^\d+$
  prefix: ohpi
  publications:
  - doi: 10.1093/nar/gky999
    pmc: PMC6324020
    pubmed: '30365026'
    title: 'Victors: a web-based knowledge base of virulence factors in human and
      animal pathogens'
    year: 2019
  uri_format: http://purl.obolibrary.org/obo/OHPI_$1
oid:
  contact:
    email: info@daniel-marschall.de
    github: danielmarschall
    name: Daniel Marschall
    orcid: 0009-0001-5055-9262
  contributor_extras:
  - email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  - email: info@daniel-marschall.de
    github: danielmarschall
    name: Daniel Marschall
    orcid: 0009-0001-5055-9262
  example_extras:
  - '2'
  - '2.16'
  - 2.16.840.1
  - 2.16.840.1.113883
  - 2.16.840.1.113883.6
  - 2.16.840.1.113883.6.88
  homepage: https://oid-base.com
  mappings:
    miriam: oid
    n2t: oid
  miriam:
    deprecated: false
    description: OIDs provide a persistent identification of objects based on a hierarchical
      structure of Registration Authorities (RA), where each parent has an object
      identifier and allocates object identifiers to child nodes.
    homepage: https://oid-base.com
    id: '00000673'
    name: OID Repository
    namespaceEmbeddedInLui: false
    pattern: ^[\d.]+$
    prefix: oid
    sampleId: 2.16.840
    uri_format: https://oid-base.com/cgi-bin/display?a=display&oid=$1
  n2t:
    description: OIDs provide a persistent identification of objects based on a hierarchical
      structure of Registration Authorities (RA), where each parent has an object
      identifier and allocates object identifiers to child nodes.
    example: 2.16.840
    homepage: http://www.oid-info.com/introduction.htm
    name: OID Repository
    namespaceEmbeddedInLui: false
    pattern: ^[\d.]+$
    prefix: oid
    uri_format: http://www.oid-info.com/cgi-bin/display?oid=$1&submit=Display&action=display
  name: ISO Object Identifier
  prefix: oid
  providers:
  - code: orange
    description: Mirror of OID site from Orange
    example: null
    first_party: null
    homepage: https://oid-rep.orange-labs.fr
    name: Mirror of OID site from Orange
    publications: null
    status:
      contributor: 0000-0003-4423-4370
      date: '2025-07-02'
      notes: null
      value: gone
    uri_format: https://oid-rep.orange-labs.fr/get/$1
  - code: oid_www
    description: OID w/ WWW
    example: null
    first_party: null
    homepage: http://www.oid-info.com
    name: OID w/ WWW
    publications: null
    status:
      contributor: 0000-0003-4423-4370
      date: '2025-07-02'
      notes: null
      value: gone
    uri_format: http://www.oid-info.com/get/$1
  references:
  - https://en.wikipedia.org/wiki/Object_identifier
  uri_format: https://oid-base.com/get/$1
oidc:
  description: The OpenID Connect vocabulary used by the Solid-OIDC authentication
    specification
  download_rdf: http://www.w3.org/ns/solid/oidc
  example: client_name
  homepage: https://solidproject.org/TR/oidc
  mappings:
    zazuko: oidc
  name: Solid OpenID Connect vocabulary
  prefix: oidc
  zazuko:
    prefix: oidc
    uri_format: http://www.w3.org/ns/solid/oidc#$1
okn.sd:
  example: CatalogIdentifier
  mappings:
    tib: sd
  prefix: okn.sd
  tib:
    description: An ontology for describing software components, including their metadata
      (attribution, licensing, usage instructions, how to get support) and their inputs,
      outputs and variables. The ontology extends schema.org and codemeta vocabularies
      and is based on OntoSoft, which proposed a vocabulary for describing software
      by asking scientists questions.
    download_rdf: https://knowledgecaptureanddiscovery.github.io/SoftwareDescriptionOntology/release/1.9.0/ontology.ttl
    homepage: https://knowledgecaptureanddiscovery.github.io/SoftwareDescriptionOntology/release/1.9.0/index-en.html
    keywords:
    - NFDI4ING
    - computer science
    name: The Software Description Ontology
    prefix: sd
    tracker: https://github.com/KnowledgeCaptureAndDiscovery/SoftwareDescriptionOntology/issues
    uri_format: https://w3id.org/okn/o/sd#$1
    version.iri: https://w3id.org/okn/o/sd/1.9.0
olatdv:
  aberowl:
    description: Life cycle stages for Medaka
    download_owl: http://aber-owl.net/media/ontologies/OLATDV/9/olatdv.owl
    homepage: https://github.com/obophenotype/developmental-stage-ontologies/wiki/OlatDv
    name: Medaka Developmental Stages
    prefix: OLATDV
  biocontext:
    prefix: OLATDV
  bioportal:
    contact:
      email: cjmungall@lbl.gov
      name: Chris Mungall
    description: Life cycle stages for Medaka. OlatDv is based on the original medaka
      stage ontology MFO by Thorsten Henrich. Currently it includes only pre-adult
      stages.
    homepage: https://github.com/obophenotype/developmental-stage-ontologies/wiki/OlatDv
    name: Medaka Developmental Stages
    prefix: OLATDV
  example: '0000210'
  fairsharing:
    abbreviation: OlatDv
    contact:
      email: frederic.bastian@unil.ch
      name: Frédéric Bastian
      orcid: 0000-0002-9415-5104
    description: Life cycle stages for Medaka. OlatDv is based on the original medaka
      stage ontology MFO by Thorsten Henrich. Currently it includes only pre-adult
      stages. While this resource remains available and we therefore retain its Ready
      status, note that the OBO Foundry has marked it as Inactive (https://obofoundry.org/ontology/olatdv.html).
    domains:
    - life cycle stage
    homepage: https://github.com/obophenotype/developmental-stage-ontologies/wiki/OlatDv
    license: CC-BY-3.0
    name: Medaka Stage Ontology
    prefix: FAIRsharing.c86z66
    repository: https://github.com/obophenotype/developmental-stage-ontologies/issues
    subjects:
    - Life Science
    - Aquaculture
    - Developmental Biology
  mappings:
    aberowl: OLATDV
    biocontext: OLATDV
    bioportal: OLATDV
    fairsharing: FAIRsharing.c86z66
    obofoundry: olatdv
    ols: olatdv
    ontobee: OlatDv
    wikidata.entity: Q81661748
  obofoundry:
    contact: frederic.bastian@unil.ch
    contact.github: fbastian
    contact.label: Frédéric Bastian
    contact.orcid: 0000-0002-9415-5104
    deprecated: true
    description: Life cycle stages for Medaka
    domain: anatomy and development
    download.obo: http://purl.obolibrary.org/obo/olatdv.obo
    download.owl: http://purl.obolibrary.org/obo/olatdv.owl
    homepage: https://github.com/obophenotype/developmental-stage-ontologies/wiki/OlatDv
    license: CC BY 3.0
    license.url: http://creativecommons.org/licenses/by/3.0/
    name: Medaka Developmental Stages
    preferredPrefix: OlatDv
    prefix: olatdv
    repository: https://github.com/obophenotype/developmental-stage-ontologies
  ols:
    description: Life cycle stages for Medaka
    download_owl: http://purl.obolibrary.org/obo/olatdv.owl
    homepage: https://github.com/obophenotype/developmental-stage-ontologies/wiki/OlatDv
    name: Medaka Developmental Stages
    prefix: olatdv
    tracker: https://github.com/obophenotype/developmental-stage-ontologies/issues
  ontobee:
    library: Library
    name: Medaka Developmental Stages
    prefix: OlatDv
  pattern: ^\d{7}$
  prefix: olatdv
  uri_format: http://purl.obolibrary.org/obo/OlatDv_$1
om:
  aberowl:
    description: 'The Ontology of units of Measure (OM) 2.0 models concepts and relations
      important to scientific research. It has a strong focus on units, quantities,
      measurements, and dimensions. OM is modelled in OWL 2 - Web Ontology Language.
      The OM ontology provides classes, instances, and properties that represent the
      different concepts used for defining and using measures and units. It includes,
      for instance, common units such as the SI units metre and kilogram, but also
      units from other systems of units such as the mile or nautical mile. For many
      application areas it includes more specific units and quantities, such as the
      unit of the Hubble constant or the quantity vaselife. The following application
      areas are supported by OM: Geometry; Mechanics; Thermodynamics; Electromagnetism;
      Fluid mechanics; Chemical physics; Photometry; Radiometry and Radiobiology;
      Nuclear physics; Astronomy and Astrophysics; Cosmology; Earth science; Meteorology;
      Material science; Microbiology; Economics; Information technology and Typography.'
    download_owl: http://aber-owl.net/media/ontologies/OM/33/om.owl
    homepage: https://github.com/HajoRijgersberg/OM
    name: Ontology of units of Measure
    prefix: OM
    version: 2.0.59
  agroportal:
    contact:
      email: hajo.rijgersberg@wur.nl
      name: Hajo Rijgersberg
    description: The Ontology of units of Measure (OM) 2.0 models concepts and relations
      important to scientific research. It has a strong focus on units, quantities,
      measurements, and dimensions., 測定単位のオントロジー (Ontology of units of Measure; OM)
      は，科学技術にとって重要な概念及び関係をモデル化する。OMは，単位・量・測定・次元に特に焦点を当てている。, measures, De Ontologie
      van Maateenheden (OM) 2.0 modelleert concepten en relaties die belangrijk zijn
      voor wetenschappelijk onderzoek. Het heeft een sterkre focus op eenheden, grootheden,
      maten, en dimensies., De Ontologie van Maateenheden (OM) 2.0 modelleert concepten
      en relaties die belangrijk zijn voor wetenschappelijk onderzoek. Het heeft een
      sterke focus op eenheden
    example_uri: http://www.wurvoc.org/vocabularies/om-1.8/Molar_energy
    homepage: http://www.ontology-of-units-of-measure.org/
    license: CC-BY-4.0
    name: Ontology of units of Measure
    prefix: OM
    repository: https://github.com/HajoRijgersberg/OM
    version: 2.0.59
  bioportal:
    contact:
      email: hajo.rijgersberg@wur.nl
      name: Hajo Rijgersberg
    description: 'The Ontology of units of Measure (OM) 2.0 models concepts and relations
      important to scientific research. It has a strong focus on units, quantities,
      measurements, and dimensions. OM is modelled in OWL 2 - Web Ontology Language.
      The OM ontology provides classes, instances, and properties that represent the
      different concepts used for defining and using measures and units. It includes,
      for instance, common units such as the SI units metre and kilogram, but also
      units from other systems of units such as the mile or nautical mile. For many
      application areas it includes more specific units and quantities, such as the
      unit of the Hubble constant or the quantity vaselife. The following application
      areas are supported by OM: Geometry; Mechanics; Thermodynamics; Electromagnetism;
      Fluid mechanics; Chemical physics; Photometry; Radiometry and Radiobiology;
      Nuclear physics; Astronomy and Astrophysics; Cosmology; Earth science; Meteorology;
      Material science; Microbiology; Economics; Information technology and Typography.'
    homepage: https://github.com/HajoRijgersberg/OM
    name: Ontology of units of Measure
    prefix: OM
    publications:
    - https://github.com/HajoRijgersberg/OM/blob/master/README.md#papers-on-om
    version: 2.0.59
  example: Dimension
  keywords:
  - ontology
  - unit
  - units
  mappings:
    aberowl: OM
    agroportal: OM
    bioportal: OM
    ols: om
    ontobee: OM
    tib: om
  name: Ontology of units of Measure
  ols:
    contact: hajo.rijgersberg@wur.nl
    description: The Ontology of units of Measure (OM) 2.0 models concepts and relations
      important to scientific research. It has a strong focus on units, quantities,
      measures, and dimensions.
    download_rdf: https://raw.githubusercontent.com/HajoRijgersberg/OM/master/om-2.0.rdf
    homepage: https://github.com/HajoRijgersberg/OM
    name: Ontology of units of Measure (OM)
    prefix: om
    uri_format: http://www.ontology-of-units-of-measure.org/resource/om-2/$1
    version: 2.0.59
  ontobee:
    library: Not Specified/No
    name: Ontology of units of Measure
    prefix: OM
  prefix: om
  repository: https://github.com/HajoRijgersberg/OM
  tib:
    description: The Ontology of units of Measure (OM) 2.0 models concepts and relations
      important to scientific research. It has a strong focus on units, quantities,
      measures, and dimensions.
    download_rdf: https://raw.githubusercontent.com/HajoRijgersberg/OM/master/om-2.0.rdf
    keywords:
    - NFDI4ING
    - NFDI4CHEM
    - ESS
    - NFDI4CAT
    - physics
    - life sciences, biology
    - earth sciences
    name: Ontology of units of Measure (OM)
    prefix: om
    tracker: https://github.com/HajoRijgersberg/OM/issues
    uri_format: http://www.ontology-of-units-of-measure.org/resource/om-2/$1
  uri_format: http://www.ontology-of-units-of-measure.org/resource/om-2/$1
oma.grp:
  biocontext:
    prefix: OMA.GRP
  mappings:
    biocontext: OMA.GRP
    miriam: oma.grp
    n2t: oma.grp
  miriam:
    deprecated: false
    description: OMA (Orthologous MAtrix) is a database that identifies orthologs
      among publicly available, complete genome sequences. It identifies orthologous
      relationships which can be accessed either group-wise, where all group members
      are orthologous to all other group members, or on a sequence-centric basis,
      where for a given protein all its orthologs in all other species are displayed.
      This collection references groupings of orthologs.
    homepage: https://omabrowser.org/cgi-bin/gateway.pl
    id: '00000343'
    name: OMA Group
    namespaceEmbeddedInLui: false
    pattern: ^[A-Z]+$
    prefix: oma.grp
    sampleId: LCSCCPN
    uri_format: https://omabrowser.org/cgi-bin/gateway.pl?f=DisplayGroup&p1=$1
  n2t:
    description: OMA (Orthologous MAtrix) is a database that identifies orthologs
      among publicly available, complete genome sequences. It identifies orthologous
      relationships which can be accessed either group-wise, where all group members
      are orthologous to all other group members, or on a sequence-centric basis,
      where for a given protein all its orthologs in all other species are displayed.
      This collection references groupings of orthologs.
    example: LCSCCPN
    homepage: https://omabrowser.org/cgi-bin/gateway.pl
    name: OMA Group through OMA browser at ETH Zurich
    namespaceEmbeddedInLui: false
    pattern: ^[A-Z]+$
    prefix: oma.grp
    uri_format: https://omabrowser.org/cgi-bin/gateway.pl?f=DisplayGroup&p1=$1
  prefix: oma.grp
oma.hog:
  banana: HOG
  example: 0459895
  mappings:
    miriam: oma.hog
  miriam:
    deprecated: false
    description: 'Hierarchical orthologous groups predicted by OMA (Orthologous MAtrix)
      database. Hierarchical orthologous groups are sets of genes that have started
      diverging from a single common ancestor gene at a certain taxonomic level of
      reference. '
    homepage: https://omabrowser.org
    id: 00000785
    name: OMA HOGs
    namespaceEmbeddedInLui: false
    pattern: ^HOG:[0-9A-Z._]+$
    prefix: oma.hog
    sampleId: HOG:E0666575
    uri_format: https://omabrowser.org/oma/hog/$1/
  pattern: ^[0-9]{7}(\.[0-9a-z.]+)?(_[0-9]+)?$
  prefix: oma.hog
  uri_format: https://omabrowser.org/oma/hog/HOG:$1
oma.protein:
  biocontext:
    prefix: OMA.PROTEIN
  mappings:
    biocontext: OMA.PROTEIN
    miriam: oma.protein
    n2t: oma.protein
    togoid: OmaProtein
  miriam:
    deprecated: false
    description: OMA (Orthologous MAtrix) is a database that identifies orthologs
      among publicly available, complete genome sequences. It identifies orthologous
      relationships which can be accessed either group-wise, where all group members
      are orthologous to all other group members, or on a sequence-centric basis,
      where for a given protein all its orthologs in all other species are displayed.
      This collection references individual protein records.
    homepage: https://omabrowser.org/oma/home/
    id: '00000342'
    name: OMA Protein
    namespaceEmbeddedInLui: false
    pattern: ^[A-Z0-9]{5}\d+$
    prefix: oma.protein
    sampleId: HUMAN16963
    uri_format: https://omabrowser.org/oma/vps/$1
  n2t:
    description: OMA (Orthologous MAtrix) is a database that identifies orthologs
      among publicly available, complete genome sequences. It identifies orthologous
      relationships which can be accessed either group-wise, where all group members
      are orthologous to all other group members, or on a sequence-centric basis,
      where for a given protein all its orthologs in all other species are displayed.
      This collection references individual protein records.
    example: HUMAN16963
    homepage: https://omabrowser.org/cgi-bin/gateway.pl
    name: OMA Protein through OMA browser at ETH Zurich
    namespaceEmbeddedInLui: false
    pattern: ^[A-Z0-9]{5}\d+$
    prefix: oma.protein
    uri_format: https://omabrowser.org/cgi-bin/gateway.pl?f=DisplayEntry&p1=$1
  prefix: oma.protein
  togoid:
    catalog: nbdc02221
    examples:
    - ACIB400217
    - ACIB400465
    - HUMAN00333
    - HUMAN01170
    - HUMAN00470
    - HUMAN03367
    - ACIB400486
    - HUMAN01061
    - HUMAN02190
    - HUMAN02112
    keywords:
    - Protein
    name: OMA protein
    pattern: ^(?[A-Z]{3}[A-Z0-9]{2}[0-9]{5,6})$
    prefix: OmaProtein
    uri_format: http://identifiers.org/oma.protein/$1
omia:
  biocontext:
    prefix: OMIA
  contact:
    email: imke.tammen@sydney.edu.au
    github: ImkeTammen
    name: Imke Tammen
    orcid: 0000-0002-5520-6597
  contributor_extras:
  - email: imke.tammen@sydney.edu.au
    github: ImkeTammen
    name: Imke Tammen
    orcid: 0000-0002-5520-6597
  description: Online Mendelian Inheritance in Animals (OMIA) is a catalogue/compendium
    of inherited disorders, other (single-locus) traits, and associated genes and
    variants in more than 500 vertebrate animal species (other than human, mouse,
    rats, zebrafish and western clawed frog, which have their own resources). The
    'omia' prefix is used for phenes, either across species (omia:001000) or in a
    specific species (omia:001000-9615)
  example: '001000'
  example_extras:
  - 001000-9615
  homepage: https://omia.org
  integbio:
    alt_name: Online Mendelian Inheritance in Animals
    description: OMIA is a database of inherited disorders, other (single-locus) traits,
      and genes in animals which is not include human, mouse and rat because of presence
      of their own resources. The records contain basical textual information, references,
      and links to OMIM, PubMed, and gene. The content on the site is manually curated.
    fairsharing: biodbcore-000579
    homepage: https://omia.org/home/
    information_keywords:
    - Bibliography/Documents
    maintainer: University of Sydney
    name: OMIA
    prefix: nbdc00153
    pubmeds:
    - '12520001'
    - '33156546'
    status: Active
    target_keywords:
    - Genome/Gene
    - Health/Disease
  keywords:
  - disorders
  - model organism database
  - traits
  mappings:
    biocontext: OMIA
    integbio: nbdc00153
    miriam: omia
    n2t: omia
    prefixcommons: omia
  miriam:
    deprecated: false
    description: Online Mendelian Inheritance in Animals is a a database of genes,
      inherited disorders and traits in animal species (other than human and mouse).
    homepage: https://www.omia.org/home/
    id: '00000142'
    name: OMIA
    namespaceEmbeddedInLui: false
    pattern: ^\d+$
    prefix: omia
    sampleId: '1000'
    uri_format: https://www.omia.org/OMIA$1
  n2t:
    description: Online Mendelian Inheritance in Animals is a a database of genes,
      inherited disorders and traits in animal species (other than human and mouse).
    example: '1000'
    homepage: http://omia.angis.org.au/
    name: OMIA at University of Sydney
    namespaceEmbeddedInLui: false
    pattern: ^\d+$
    prefix: omia
    uri_format: http://omia.angis.org.au/$1/
  name: Online Mendelian Inheritance in Animals
  part_of_database: omia
  pattern: ^\d{6}(-\d+)?$
  prefix: omia
  prefixcommons:
    description: Online Mendelian Inheritance in Animals is a a database of genes,
      inherited disorders and traits in animal species (other than human and mouse).
    example: '1000'
    homepage: http://omia.angis.org.au/
    keywords:
    - gene
    - classification
    name: Online Mendelian Inheritance in Animals
    pattern: ^\d+$
    prefix: omia
    uri_format: http://omia.angis.org.au/retrieve.shtml?pid=$1
  publications:
  - doi: 10.1007/s00335-024-10059-y
    pmc: null
    pubmed: '39143381'
    title: 'Online Mendelian Inheritance in Animals (OMIA): a genetic resource for
      vertebrate animals'
    year: 2024
  synonyms:
  - OMIA
  uri_format: https://omia.org/phene/omia:$1
omia.variant:
  biocontext:
    prefix: OMIA
  contact:
    email: imke.tammen@sydney.edu.au
    github: ImkeTammen
    name: Imke Tammen
    orcid: 0000-0002-5520-6597
  contributor_extras:
  - email: imke.tammen@sydney.edu.au
    github: ImkeTammen
    name: Imke Tammen
    orcid: 0000-0002-5520-6597
  description: Online Mendelian Inheritance in Animals (OMIA) is a catalogue/compendium
    of inherited disorders, other (single-locus) traits, and associated genes and
    variants in more than 500 vertebrate animal species (other than human, mouse,
    rats, zebrafish and western clawed frog, which have their own resources). The
    'omia.variant' prefix is used for genetic variants associated with phenes listed
    in OMIA
  example: '1710'
  example_extras:
  - '620'
  homepage: https://omia.org
  integbio:
    alt_name: Online Mendelian Inheritance in Animals
    description: OMIA is a database of inherited disorders, other (single-locus) traits,
      and genes in animals which is not include human, mouse and rat because of presence
      of their own resources. The records contain basical textual information, references,
      and links to OMIM, PubMed, and gene. The content on the site is manually curated.
    fairsharing: biodbcore-000579
    homepage: https://www.omia.org/home/
    information_keywords:
    - Bibliography/Documents
    maintainer: University of Sydney
    name: OMIA
    prefix: nbdc00153
    pubmeds:
    - '12520001'
    - '33156546'
    status: Active
    target_keywords:
    - Genome/Gene
    - Health/Disease
  keywords:
  - disorders
  - model organism database
  - traits
  mappings:
    biocontext: OMIA
    integbio: nbdc00153
  name: OMIA variants
  part_of_database: omia
  pattern: ^\d+$
  prefix: omia.variant
  publications:
  - doi: 10.1007/s00335-024-10059-y
    pmc: null
    pubmed: '39143381'
    title: 'Online Mendelian Inheritance in Animals (OMIA): a genetic resource for
      vertebrate animals'
    year: 2024
  reviewer:
    email: b.gyori@northeastern.edu
    github: bgyori
    name: Benjamin M. Gyori
    orcid: 0000-0001-9439-5346
  uri_format: https://omia.org/variant/omia.variant:$1
omiabis:
  aberowl:
    description: An ontological version of MIABIS (Minimum Information About BIobank
      data Sharing)
    download_owl: http://aber-owl.net/media/ontologies/OMIABIS/2/omiabis.owl
    homepage: https://github.com/OMIABIS/omiabis-dev
    name: Ontologized MIABIS
    prefix: OMIABIS
  biocontext:
    prefix: OMIABIS
  bioportal:
    name: Ontologized MIABIS
    prefix: OMIABIS
  example: 0001079
  mappings:
    aberowl: OMIABIS
    biocontext: OMIABIS
    bioportal: OMIABIS
    obofoundry: omiabis
    ols: omiabis
    ontobee: OMIABIS
  obofoundry:
    appears_in:
    - labo
    contact: mbrochhausen@gmail.com
    contact.label: Mathias Brochhausen
    contact.orcid: 0000-0003-1834-3856
    deprecated: true
    description: An ontological version of MIABIS (Minimum Information About BIobank
      data Sharing)
    domain: health
    download.owl: http://purl.obolibrary.org/obo/omiabis.owl
    homepage: https://github.com/OMIABIS/omiabis-dev
    license: CC BY 3.0
    license.url: http://creativecommons.org/licenses/by/3.0/
    name: Ontologized MIABIS
    prefix: omiabis
    repository: https://github.com/OMIABIS/omiabis-dev
  ols:
    description: An ontological version of MIABIS (Minimum Information About BIobank
      data Sharing)
    homepage: https://github.com/OMIABIS/omiabis-dev
    name: Ontologized MIABIS
    prefix: omiabis
    tracker: https://github.com/OMIABIS/omiabis-dev/issues
    version: '2014-05-28'
  ontobee:
    library: Library
    name: Ontologized MIABIS
    prefix: OMIABIS
  pattern: ^\d{7}$
  prefix: omiabis
omid:
  mappings:
    miriam: omid
  miriam:
    deprecated: false
    description: Every entity in OpenCitations Meta (https://opencitations.net/meta)
      is assigned persistent internal identifier called OpenCitations Meta Identifier
      (OMID). The OMID has structure [[entity_type_abbreviation]]/[[supplier_prefix]][[sequential_number]].
      For example, the first journal article ever processed has OMID br/0601 (the
      full URI is https://w3id.org/oc/meta/br/0601), where br is the abbreviation
      of bibliographic resource, and 060 corresponds to the supplier prefix, helpful
      in recognising at a glance the index it belongs to (i.e., OpenCitations Meta).
      Finally, 1 indicates that this is the index's first bibliographic resource ever
      minted.
    homepage: http://opencitations.net/
    id: '00001004'
    name: OpenCitations Meta Identifier
    namespaceEmbeddedInLui: false
    pattern: ^[a-z][a-z]/06[1-9]*0[1-9][0-9]*$
    prefix: omid
    sampleId: br/0601
    uri_format: https://w3id.org/oc/meta/$1
  prefix: omid
omim:
  aberowl:
    description: Online Mendelian Inheritance in Man, OMIM (TM). McKusick-Nathans
      Institute for Genetic Medicine, Johns Hopkins University (Baltimore, MD) and
      National Center for Biotechnology Information, National Library of Medicine
    homepage: http://www.ncbi.nlm.nih.gov/omim/
    name: Online Mendelian Inheritance in Man
    prefix: OMIM
    version: 2016AB
  biocontext:
    prefix: OMIM
  bioportal:
    contact:
      email: custserv@nlm.nih.gov
      name: NLM Customer Service
    description: Online Mendelian Inheritance in Man, OMIM (TM). McKusick-Nathans
      Institute for Genetic Medicine, Johns Hopkins University (Baltimore, MD) and
      National Center for Biotechnology Information, National Library of Medicine
    homepage: http://www.ncbi.nlm.nih.gov/omim/
    name: Online Mendelian Inheritance in Man
    prefix: OMIM
    publications:
    - http://www.ncbi.nlm.nih.gov/omim/
    version: OMIM2024_08_09
  contact:
    email: ahamosh@jhmi.edu
    github: ahamosh
    name: Ada Hamosh
    orcid: 0000-0002-1780-5230
  contact_page: https://www.omim.org/contact
  edam:
    description: Identifier of an entry from the OMIM database.
    name: OMIM
    obsolete: false
    prefix: '1153'
  fairsharing:
    abbreviation: OMIM Ontology
    description: OMIM is a comprehensive, authoritative compendium of human genes
      and genetic phenotypes as well as the relationship between them, that is freely
      available and updated daily. The OMIM ontology contains terms used within the
      OMIM database.
    domains:
    - phenotype
    - disease
    - disease course
    - genetic disorder
    - genotype
    homepage: http://omim.org/
    name: Online Mendelian Inheritance in Man Ontology
    prefix: FAIRsharing.b084yh
    publications:
    - doi: 10.1093/nar/gku1205
      pubmed: '25428349'
      title: 'OMIM.org: Online Mendelian Inheritance in Man (OMIM(R)), an online catalog
        of human genes and genetic disorders'
      year: 2014
    subjects:
    - Biomedical Science
  go:
    homepage: https://omim.org/
    name: Mendelian Inheritance in Man
    prefix: OMIM
    synonyms:
    - MIM
    uri_format: https://omim.org/entry/$1
  hl7:
    description: 'Online Mendelian Inheritance in Man (OMIM). Baltimore (MD): Johns
      Hopkins University, Center for Biotechnology Information, 1994.'
    name: Online Mendelian Inheritance in Man 1993
    preferred_prefix: MIM
    prefix: 2.16.840.1.113883.6.174
    status: Pending
  integbio:
    alt_name: Online Mendelian Inheritance in Man
    description: OMIM is a database of human disease and genetic information and the
      online representation of Mendelian Inheritance in Man, a project initiated in
      the 1960s. The database summarizes heritable traits and provides information
      on both the trait and experimentally determined genetic causes. The database
      is manually curated by experts and can be searched by OMIM ID, gene, disease,
      or phenotype.
    fairsharing: biodbcore-000761
    homepage: http://www.ncbi.nlm.nih.gov/omim
    information_keywords:
    - Bibliography/Documents
    maintainer: NCBI (National Center for Biotechnology Information)
    name: OMIM
    prefix: nbdc00154
    pubmeds:
    - '18842627'
    status: Active
    target_keywords:
    - Genome/Gene
    - Genetic variation
    - Health/Disease
  license: https://www.omim.org/help/agreement
  logo: https://omim.org/static/omim/icons/OMIM_davinciman.001.png
  mappings:
    aberowl: OMIM
    biocontext: OMIM
    bioportal: OMIM
    edam: '1153'
    fairsharing: FAIRsharing.b084yh
    go: OMIM
    hl7: 2.16.840.1.113883.6.174
    integbio: nbdc00154
    miriam: mim
    n2t: mim
    ncbi: MIM
    prefixcommons: omim
    uniprot: DB-0062
    wikidata: P492
    wikidata.entity: Q7187
  miriam:
    deprecated: false
    description: Online Mendelian Inheritance in Man is a catalog of human genes and
      genetic disorders.
    homepage: https://omim.org/
    id: '00000016'
    name: OMIM
    namespaceEmbeddedInLui: false
    pattern: ^[*#+%^]?\d{6}$
    prefix: mim
    providers:
    - code: ''
      description: OMIM mirror at John Hopkins
      homepage: http://mirror.omim.org/
      name: OMIM mirror at John Hopkins
      uri_format: http://mirror.omim.org/entry/$1
    sampleId: '603903'
    uri_format: https://omim.org/entry/$1
  n2t:
    description: Online Mendelian Inheritance in Man is a catalog of human genes and
      genetic disorders.
    example: '603903'
    homepage: https://omim.org/
    name: OMIM at John Hopkins
    namespaceEmbeddedInLui: false
    pattern: ^[*#+%^]?\d{6}$
    prefix: mim
    uri_format: https://omim.org/entry/$1
  name: Online Mendelian Inheritance in Man
  ncbi:
    example: '123456'
    homepage: https://www.ncbi.nlm.nih.gov/omim
    name: Mendelian Inheritance in Man numbers
    prefix: MIM
  part_of_database: omim
  pattern: ^\d+$
  prefix: omim
  prefixcommons:
    alt_uri_formats:
    - http://europe.omim.org/entry/#$1
    - http://us-east.omim.org/entry/#$1
    - http://omim.org/entry/#$1
    description: OMIM is a comprehensive, authoritative, and timely compendium of
      human genes and genetic phenotypes. The full-text, referenced overviews in OMIM
      contain information on all known mendelian disorders and over 12,000 genes.
      OMIM focuses on the relationship between phenotype and genotype.
    example: '603903'
    homepage: http://www.ncbi.nlm.nih.gov/omim/
    keywords:
    - gene
    - gene expression
    license: http://www.nlm.nih.gov/copyright.html
    name: Online Mendelian Inheritance in Man
    pattern: ^[*#+%^]?\d{6}$
    prefix: omim
    pubmed_ids:
    - '15608251'
    synonyms:
    - mim
    uri_format: http://www.ncbi.nlm.nih.gov/omim/$1
  providers:
  - code: legacy
    description: This is the actual endpoint for OMIM entries
    example: null
    first_party: null
    homepage: https://www.omim.org
    name: OMIM
    publications: null
    status: null
    uri_format: https://www.omim.org/entry/$1
  - code: miriam_legacy
    description: Legacy URLs for identifiers.org
    example: null
    first_party: null
    homepage: http://identifiers.org
    name: MIRIAM Legacy
    publications: null
    status: null
    uri_format: http://identifiers.org/omim/$1
  - code: ncbi.omim
    description: An NCBI endpoint for OMIM entries
    example: null
    first_party: null
    homepage: http://www.ncbi.nlm.nih.gov/omim
    name: NCBI
    publications: null
    status: null
    uri_format: http://www.ncbi.nlm.nih.gov/omim/$1
  - code: purl
    description: An extra purl that was registred, but probably won't be used.
    example: null
    first_party: null
    homepage: https://www.omim.org
    name: OMIM PURL (not in use)
    publications: null
    status: null
    uri_format: https://purl.org/mim/MIM:$1
  - code: purl2
    description: An extra purl that was registred, but probably won't be used.
    example: null
    first_party: null
    homepage: https://www.omim.org
    name: OMIM PURL (not in use)
    publications: null
    status: null
    uri_format: https://omim.org/OMIM:$1
  publications:
  - doi: 10.1093/nar/gku1205
    pmc: PMC4383985
    pubmed: '25428349'
    title: 'OMIM.org: Online Mendelian Inheritance in Man (OMIM®), an online catalog
      of human genes and genetic disorders'
    year: 2014
  - doi: 10.1093/nar/gki033
    pmc: PMC539987
    pubmed: '15608251'
    title: Online Mendelian Inheritance in Man (OMIM), a knowledgebase of human genes
      and genetic disorders
    year: 2005
  - doi: 10.1093/nar/gku1205
    pmc: null
    pubmed: '25428349'
    title: 'OMIM.org: Online Mendelian Inheritance in Man (OMIM(R)), an online catalog
      of human genes and genetic disorders'
    year: 2014
  - doi: null
    pmc: null
    pubmed: '15608251'
    title: null
    year: null
  - doi: 10.1093/nar/gky1151
    pmc: null
    pubmed: '30445645'
    title: null
    year: null
  references:
  - https://github.com/biopragmatics/bioregistry/issues/497
  synonyms:
  - OMIM
  - mim
  uniprot:
    abbreviation: MIM
    category: Organism-specific databases
    homepage: https://www.omim.org/
    name: Online Mendelian Inheritance in Man (OMIM)
    prefix: DB-0062
    publications:
    - doi: 10.1093/nar/gky1151
      pubmed: '30445645'
    uri_format: https://www.omim.org/entry/$1
  uri_format: https://omim.org/MIM:$1
  wikidata:
    database: Q7187
    description: Online "Mendelian Inheritance in Man" catalogue codes for diseases,
      genes, or phenotypes
    example:
    - '143100'
    - '614371'
    name: OMIM ID
    pattern: ^\d{6}$
    prefix: P492
    uri_format: https://omim.org/OMIM:$1
omim.ps:
  banana: PS
  biolink:
    is_identifiers: false
    is_obo: false
    prefix: OMIM.PS
    uri_format: https://www.omim.org/phenotypicSeries/$1
  contact:
    email: ahamosh@jhmi.edu
    github: ahamosh
    name: Ada Hamosh
    orcid: 0000-0002-1780-5230
  contact_page: https://www.omim.org/contact
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  contributor_extras:
  - email: smoxon@lbl.gov
    github: sierra-moxon
    name: Sierra Moxon
    orcid: 0000-0002-8719-7760
  description: A Phenotypic Series is a tabular view of genetic heterogeneity of similar
    phenotypes across the genome.
  domain: disease
  example: '214100'
  homepage: https://www.omim.org/phenotypicSeriesTitles/all
  keywords:
  - disease
  - phenotype
  license: https://www.omim.org/help/agreement
  logo: https://www.omim.org/static/omim/icons/OMIM_davinciman.001.png
  mappings:
    biolink: OMIM.PS
  name: OMIM Phenotypic Series
  part_of_database: omim
  pattern: ^\d+$
  prefix: omim.ps
  providers:
  - code: legacy
    description: This is the actual endpoint for OMIM phenotypic series entries
    example: null
    first_party: null
    homepage: https://www.omim.org
    name: OMIM
    publications: null
    status: null
    uri_format: https://omim.org/phenotypicSeries/PS$1
  synonyms:
  - MIMPS
  - OMIMPS
  - PS
  - mim.ps
  uri_format: https://omim.org/MIM:PS$1
omit:
  aberowl:
    description: Ontology to establish data exchange standards and common data elements
      in the microRNA (miR) domain
    download_owl: http://aber-owl.net/media/ontologies/OMIT/41/omit.owl
    homepage: http://omit.cis.usouthal.edu/
    name: Ontology for MIRNA Target
    prefix: OMIT
  biocontext:
    prefix: OMIT
  bioportal:
    contact:
      email: huang@southalabama.edu
      name: Jingshan Huang
    description: The purpose of the OMIT ontology is to establish data exchange standards
      and common data elements in the microRNA (miR) domain. Biologists (cell biologists
      in particular) and bioinformaticians can make use of OMIT to leverage emerging
      semantic technologies in knowledge acquisition and discovery for more effective
      identification of important roles performed by miRs in humans' various diseases
      and biological processes (usually through miRs' respective target genes). OMIT
      has reused and extended a set of well-established concepts from existing bio-ontologies,
      e.g., Gene Ontology, Sequence Ontology, Protein Ontology, NCBI Organism Taxonomy,
      Human Disease Ontology, Foundational Model of Anatomy, and so forth.
    homepage: http://omnisearch.soc.southalabama.edu/
    name: Ontology for MicroRNA Target
    prefix: OMIT
    version: OBO 4.0-12122013-2338
  download_obo: https://raw.githubusercontent.com/OmniSearch/omit/master/src/ontology/omit.obo
  example: 0000069
  fairsharing:
    abbreviation: OMIT
    description: The purpose of the OMIT ontology is to establish data exchange standards
      and common data elements in the microRNA (miR) domain. Biologists (cell biologists
      in particular) and bioinformaticians can make use of OMIT to leverage emerging
      semantic technologies in knowledge acquisition and discovery for more effective
      identification of important roles performed by miRs in humans' various diseases
      and biological processes (usually through miRs' respective target genes). Please
      note that, although the ontology is available at the stated GitHub repository,
      it has not been updated in a number of years and you may wish to carefully review
      the ontology before use.
    domains:
    - Annotation
    - Prediction and recognition
    - Gene prediction
    - molecular entity
    - cell
    - regulation of gene expression
    - molecular interaction
    - protein
    - miRNA
    - gene
    homepage: https://github.com/OmniSearch/omit
    license: CC-BY-3.0
    name: Ontology for MicroRNA Target
    prefix: FAIRsharing.mf91p5
    publications:
    - doi: 10.1371/journal.pone.0100855
      pubmed: '25025130'
      title: 'OMIT: dynamic, semi-automated ontology development for the microRNA
        domain'
      year: 2014
    - doi: 10.1007/s11095-011-0573-8
      pubmed: '21879385'
      title: 'OMIT: a domain-specific knowledge base for microRNA target prediction'
      year: 2011
    - doi: 10.1186/s13326-016-0064-2
      pubmed: '27175225'
      title: 'OmniSearch: a semantic search system based on the Ontology for MIcroRNA
        Target (OMIT) for microRNA-target gene interaction data'
      year: 2016
    repository: https://github.com/OmniSearch/omit
    subjects:
    - Life Science
    - Biology
  mappings:
    aberowl: OMIT
    biocontext: OMIT
    bioportal: OMIT
    fairsharing: FAIRsharing.mf91p5
    miriam: omit
    n2t: omit
    obofoundry: omit
    ols: omit
    ontobee: OMIT
    wikidata.entity: Q81661752
  miriam:
    deprecated: false
    description: The purpose of the OMIT ontology is to establish data exchange standards
      and common data elements in the microRNA (miR) domain. Biologists (cell biologists
      in particular) and bioinformaticians can make use of OMIT to leverage emerging
      semantic technologies in knowledge acquisition and discovery for more effective
      identification of important roles performed by miRs in humans' various diseases
      and biological processes (usually through miRs' respective target genes).
    homepage: https://www.ebi.ac.uk/ols4/ontologies/omit/
    id: '00000605'
    name: OMIT
    namespaceEmbeddedInLui: false
    pattern: ^\d{7}$
    prefix: omit
    sampleId: '0005506'
    uri_format: https://www.ebi.ac.uk/ols4/ontologies/omit/terms?short_form=OMIT_$1
  n2t:
    description: The purpose of the OMIT ontology is to establish data exchange standards
      and common data elements in the microRNA (miR) domain. Biologists (cell biologists
      in particular) and bioinformaticians can make use of OMIT to leverage emerging
      semantic technologies in knowledge acquisition and discovery for more effective
      identification of important roles performed by miRs in humans' various diseases
      and biological processes (usually through miRs' respective target genes).
    example: '0005506'
    homepage: https://www.ebi.ac.uk/ols/ontologies/omit/
    name: Ontology for miRNA Target (OMIT) through OLS
    namespaceEmbeddedInLui: false
    pattern: ^\d{7}$
    prefix: omit
    uri_format: https://www.ebi.ac.uk/ols/ontologies/omit/terms?short_form=OMIT_$1
  name: Ontology for MicroRNA Target
  obofoundry:
    appears_in:
    - mco
    contact: huang@southalabama.edu
    contact.github: Huang-OMIT
    contact.label: Jingshan Huang
    contact.orcid: 0000-0003-2408-2883
    deprecated: false
    description: Ontology to establish data exchange standards and common data elements
      in the microRNA (miR) domain
    domain: chemistry and biochemistry
    download.owl: http://purl.obolibrary.org/obo/omit.owl
    homepage: http://omit.cis.usouthal.edu/
    license: CC BY 3.0
    license.url: https://creativecommons.org/licenses/by/3.0/
    name: Ontology for MIRNA Target
    preferredPrefix: OMIT
    prefix: omit
    repository: https://github.com/OmniSearch/omit
  ols:
    description: Ontology to establish data exchange standards and common data elements
      in the microRNA (miR) domain
    download_owl: http://purl.obolibrary.org/obo/omit.owl
    homepage: http://omit.cis.usouthal.edu/
    name: Ontology for MIRNA Target
    prefix: omit
    tracker: https://github.com/OmniSearch/omit/issues
    version: dev
    version.iri: http://purl.obolibrary.org/obo/omit/dev/omit.owl
  ontobee:
    library: Library
    name: Ontology for MIRNA Target
    prefix: OMIT
  prefix: omit
  publications:
  - doi: 10.1186/s13326-016-0064-2
    pmc: PMC4863347
    pubmed: '27175225'
    title: 'OmniSearch: a semantic search system based on the Ontology for MIcroRNA
      Target (OMIT) for microRNA-target gene interaction data'
    year: 2016
  - doi: 10.1371/journal.pone.0100855
    pmc: PMC4099014
    pubmed: '25025130'
    title: 'OMIT: dynamic, semi-automated ontology development for the microRNA domain'
    year: 2014
  - doi: 10.1007/s11095-011-0573-8
    pmc: null
    pubmed: '21879385'
    title: 'OMIT: a domain-specific knowledge base for microRNA target prediction'
    year: 2011
  synonyms:
  - OMIT
  uri_format: http://purl.obolibrary.org/obo/OMIT_$1
  wikidata:
    database: Q55118529
omo:
  aberowl:
    description: An ontology specifies terms that are used to annotate ontology terms
      for all OBO ontologies. The ontology was developed as part of Information Artifact
      Ontology (IAO).
    download_owl: http://aber-owl.net/media/ontologies/OMO/12/omo.owl
    homepage: https://github.com/information-artifact-ontology/ontology-metadata
    name: OBO Metadata Ontology
    prefix: OMO
  bioportal:
    contact:
      email: cjmungall@lbl.gov
      name: Chris Mungall
    description: The OBO Metadata Ontology (OMO) specifies terms that are used to
      annotate ontology terms for all OBO ontologies. The ontology was developed as
      part of Information Artifact Ontology (IAO) before.
    homepage: https://github.com/information-artifact-ontology/ontology-metadata
    name: OBO Metadata Ontology
    prefix: OMO
  example: '0003003'
  mappings:
    aberowl: OMO
    bioportal: OMO
    obofoundry: omo
    ols: omo
    ontobee: OMO
    wikidata.entity: Q113012675
  obofoundry:
    appears_in:
    - cl
    - pcl
    - uberon
    contact: cjmungall@lbl.gov
    contact.github: cmungall
    contact.label: Chris Mungall
    contact.orcid: 0000-0002-6601-2165
    deprecated: false
    description: An ontology specifies terms that are used to annotate ontology terms
      for all OBO ontologies. The ontology was developed as part of Information Artifact
      Ontology (IAO).
    domain: information
    download.owl: http://purl.obolibrary.org/obo/omo.owl
    homepage: https://github.com/information-artifact-ontology/ontology-metadata
    license: CC0 1.0
    license.url: https://creativecommons.org/publicdomain/zero/1.0/
    name: OBO Metadata Ontology
    preferredPrefix: OMO
    prefix: omo
    repository: https://github.com/information-artifact-ontology/ontology-metadata
  ols:
    description: An ontology specifies terms that are used to annotate ontology terms
      for all OBO ontologies. The ontology was developed as part of Information Artifact
      Ontology (IAO).
    download_owl: http://purl.obolibrary.org/obo/omo.owl
    homepage: https://github.com/information-artifact-ontology/ontology-metadata
    name: OBO Metadata Ontology
    prefix: omo
    tracker: https://github.com/information-artifact-ontology/ontology-metadata/issues
    version: '2025-06-18'
    version.iri: http://purl.obolibrary.org/obo/omo/releases/2025-06-18/omo.owl
  ontobee:
    library: Library
    name: OBO Metadata Ontology
    prefix: OMO
  pattern: ^\d{7}$
  prefix: omo
  uri_format: http://purl.obolibrary.org/obo/OMO_$1
omon:
  contributor:
    email: oga.t@northeastern.edu
    github: tomo-oga
    name: Tomohiro Oga
    orcid: 0009-0001-6787-3995
  description: The new national clinical trials registry of the Netherlands
  example: '53367'
  github_request_issue: 1157
  homepage: https://onderzoekmetmensen.nl/en
  logo: https://onderzoekmetmensen.nl/themes/custom/trialregister/logo.svg
  name: Overview of Medical Research in the Netherlands
  pattern: ^\d{5}$
  prefix: omon
  reviewer:
    email: b.gyori@northeastern.edu
    github: bgyori
    name: Benjamin M. Gyori
    orcid: 0000-0001-9439-5346
  uri_format: https://onderzoekmetmensen.nl/en/trial/$1
omop:
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  contributor_extras:
  - email: nicolas.matentzoglu@gmail.com
    github: matentzn
    name: Nicolas Matentzoglu
    orcid: 0000-0002-7356-1779
  description: The OMOP Common Data Model allows for the systematic analysis of disparate
    observational databases. The concept behind this approach is to transform data
    contained within those databases into a common format (data model) as well as
    a common representation (terminologies, vocabularies, coding schemes), and then
    perform systematic analyses using a library of standard analytic routines that
    have been written based on the common format.
  example: '1'
  homepage: https://www.ohdsi.org/data-standardization/the-common-data-model/
  name: Observational Medical Outcomes Partnership
  pattern: ^\d+$
  prefix: omop
  providers:
  - code: ohdsi.api
    description: Programmatic access to OMOP terms
    example: null
    first_party: null
    homepage: http://api.ohdsi.org
    name: OHDSI API
    publications: null
    status: null
    uri_format: http://api.ohdsi.org/WebAPI/vocabulary/concept/$1
  - code: ohdsi.data
    description: ' https://faircookbook.elixir-europe.org/content/recipes/applied-examples/ehden-ohdsi.html
      suggests https://data.ohdsi.org/concept/ as another uri expansion but it does
      not resolve.'
    example: null
    first_party: null
    homepage: https://data.ohdsi.org/concept
    name: OHDSI Data Endpoint
    publications: null
    status: null
    uri_format: https://data.ohdsi.org/concept/$1
  references:
  - https://github.com/callahantiff/OMOP2OBO
  - https://github.com/biopragmatics/bioregistry/issues/599
  - https://github.com/biopragmatics/bioregistry/pull/600
  synonyms:
  - OMOP
  uri_format: https://athena.ohdsi.org/search-terms/terms/$1
omp:
  aberowl:
    description: An ontology of phenotypes covering microbes
    download_owl: http://aber-owl.net/media/ontologies/OMP/59/omp.owl
    homepage: http://microbialphenotypes.org
    name: Ontology of Microbial Phenotypes
    prefix: OMP
  biocontext:
    prefix: OMP
  bioportal:
    contact:
      email: d-siegele@tamu.edu
      name: Deborah A. Siegele
    description: 'OMP is a formal ontology of phenotypes observed in all microbes:
      bacteria, archaea, protists, fungi, and viruses. OMP is being developed to be
      compatible with other microbial phenotype ontologies, such as the Fission Yeast
      Phenotype Ontology (FYPO) and the Ascomycete Phenotype Ontology (APO), and aims
      to standardize the capture of phenotypic information to allow improved cross-species
      data mining and analysis.'
    homepage: http://microbialphenotypes.org
    name: Ontology of Microbial Phenotypes
    prefix: OMP
    publications:
    - https://bmcmicrobiol.biomedcentral.com/articles/10.1186/s12866-014-0294-3
    version: releases/2019-06-07
  example: '0005067'
  fairsharing:
    abbreviation: OMP
    contact:
      email: jimhu@tamu.edu
      name: James C. Hu
      orcid: 0000-0001-9016-2684
    description: The Ontology of Microbial Phenotypes (OMP) is a community ontology
      for annotating microbial phenotypes, including bacteria, archaea, protists,
      fungi, and viruses. It has been created to help with standardized capture of
      essential phenotypic information. OMP is designed to be compatible with other
      microbial phenotype ontologies, such as the Fission Yeast Phenotype Ontology
      (FYPO) and the Ascomycete Phenotype Ontology (APO), and aims to standardize
      the capture of phenotypic information to allow improved cross-species data mining
      and analysis.
    domains:
    - Data analysis
    - phenotype
    - microbe-host interaction phenotype
    homepage: https://github.com/microbialphenotypes/OMP-ontology
    license: CC-BY-3.0
    name: Ontology of Microbial Phenotypes
    prefix: FAIRsharing.cc3f2x
    publications:
    - doi: 10.1186/s12866-014-0294-3
      pubmed: '25433798'
      title: An ontology for microbial phenotypes
      year: 2014
    - doi: 10.1186/s13326-019-0205-5
      title: Phenotype annotation with the ontology of microbial phenotypes (OMP)
      year: 2019
    repository: https://github.com/microbialphenotypes/OMP-ontology/issues
    subjects:
    - Phenomics
    - Chemical Biology
    - Omics
    - Microbial Ecology
    - Microbiology
  mappings:
    aberowl: OMP
    biocontext: OMP
    bioportal: OMP
    fairsharing: FAIRsharing.cc3f2x
    obofoundry: omp
    ols: omp
    ontobee: OMP
    tib: omp
    wikidata.entity: Q81661753
  obofoundry:
    appears_in:
    - mco
    contact: jimhu@tamu.edu
    contact.github: jimhu-tamu
    contact.label: James C. Hu
    contact.orcid: 0000-0001-9016-2684
    deprecated: false
    description: An ontology of phenotypes covering microbes
    domain: phenotype
    download.obo: http://purl.obolibrary.org/obo/omp.obo
    download.owl: http://purl.obolibrary.org/obo/omp.owl
    homepage: http://microbialphenotypes.org
    license: CC BY 3.0
    license.url: http://creativecommons.org/licenses/by/3.0/
    name: Ontology of Microbial Phenotypes
    preferredPrefix: OMP
    prefix: omp
    publications:
    - id: https://doi.org/10.1186/s12866-014-0294-3
      title: An ontology for microbial phenotypes
    repository: https://github.com/microbialphenotypes/OMP-ontology
  ols:
    description: An ontology of phenotypes covering microbes
    download_owl: http://purl.obolibrary.org/obo/omp.owl
    homepage: http://microbialphenotypes.org
    name: Ontology of Microbial Phenotypes
    prefix: omp
    tracker: https://github.com/microbialphenotypes/OMP-ontology/issues
    version: '2024-03-25'
    version.iri: http://purl.obolibrary.org/obo/omp/releases/2024-03-25/omp.owl
  ontobee:
    library: Library
    name: Ontology of Microbial Phenotypes
    prefix: OMP
  pattern: ^\d{7}$
  prefix: omp
  publications:
  - doi: 10.1186/s12866-014-0294-3
    pmc: PMC4287307
    pubmed: '25433798'
    title: An ontology for microbial phenotypes
    year: 2014
  tib:
    description: OMP is a community ontology for annotating microbial phenotypes.
    download_owl: http://purl.obolibrary.org/obo/omp.owl
    homepage: https://github.com/microbialphenotypes/
    keywords:
    - DataPLANT
    - life sciences, biology
    name: Ontology of Microbial Phenotypes
    prefix: omp
    tracker: https://github.com/microbialphenotypes/OMP-ontology/issues
    version.iri: http://purl.obolibrary.org/obo/omp/releases/2024-03-25/omp.owl
  uri_format: http://purl.obolibrary.org/obo/OMP_$1
  wikidata:
    database: Q81661753
omrse:
  aberowl:
    description: The Ontology for Modeling and Representation of Social Entities (OMRSE)
      is an OBO Foundry ontology that represents the various entities that arise from
      human social interactions, such as social acts, social roles, social groups,
      and organizations.
    download_owl: http://aber-owl.net/media/ontologies/OMRSE/63/omrse.owl
    homepage: https://github.com/mcwdsi/OMRSE/wiki/OMRSE-Overview
    name: Ontology for Modeling and Representation of Social Entities
    prefix: OMRSE
  biocontext:
    prefix: OMRSE
  bioportal:
    contact:
      email: hoganwr@gmail.com
      name: Bill Hogan
    description: The Ontology for Modeling and Representation of Social Entities (OMRSE)
      is an OBO Foundry ontology that represents the various entities that arise from
      human social interactions, such as social acts, social roles, social groups,
      and organizations.
    homepage: https://github.com/mcwdsi/OMRSE
    license: CC-BY-4.0
    name: Ontology for Modeling and Representation of Social Entities
    prefix: OMRSE
    publications:
    - https://github.com/mcwdsi/OMRSE#list-of-publications
    version: '2025-08-13'
  download_json: http://purl.obolibrary.org/obo/omrse.json
  download_obo: https://github.com/ufbmi/OMRSE/raw/master/omrse-full.obo
  example: '00000022'
  fairsharing:
    abbreviation: OMRSE
    contact:
      email: hoganwr@gmail.com
      name: William Hogan
      orcid: 0000-0002-9881-1017
    description: The Ontology for Modeling and Representation of Social Entities (OMRSE)
      is an OBO Foundry ontology that represents the various entities that arise from
      human social interactions, such as social acts, social roles, social groups,
      and organizations. For more information on the social entities represented in
      OMRSE, please visit our wiki page or list of publications. OMRSE is designed
      to be a mid-level ontology that bridges the gap between BFO, which it reuses
      for its top-level hierarchy, and more specific domain or application ontologies.
      For this reason, we are always open to working with ontology developers who
      want to build interoperability between their projects and OMRSE.
    domains:
    - Patient Care
    - Hospital
    homepage: https://github.com/mcwdsi/OMRSE
    license: CC-BY-4.0
    name: Ontology for Modeling and Representation of Social Entities
    prefix: FAIRsharing.z0p37e
    publications:
    - doi: 10.1186/s13326-016-0087-8
      pubmed: '27406187'
      title: 'The ontology of medically related social entities: recent developments'
      year: 2016
    repository: https://github.com/mcwdsi/OMRSE/issues
    subjects:
    - Biomedical Science
    - Demographics
    - Social Science
    - Health Science
  mappings:
    aberowl: OMRSE
    biocontext: OMRSE
    bioportal: OMRSE
    fairsharing: FAIRsharing.z0p37e
    obofoundry: omrse
    ols: omrse
    ontobee: OMRSE
    wikidata.entity: Q55118551
  obofoundry:
    appears_in:
    - labo
    contact: hoganwr@gmail.com
    contact.github: hoganwr
    contact.label: Bill Hogan
    contact.orcid: 0000-0002-9881-1017
    deprecated: false
    description: The Ontology for Modeling and Representation of Social Entities (OMRSE)
      is an OBO Foundry ontology that represents the various entities that arise from
      human social interactions, such as social acts, social roles, social groups,
      and organizations.
    domain: health
    download.owl: http://purl.obolibrary.org/obo/omrse.owl
    homepage: https://github.com/mcwdsi/OMRSE/wiki/OMRSE-Overview
    license: CC BY 4.0
    license.url: https://creativecommons.org/licenses/by/4.0/
    name: Ontology for Modeling and Representation of Social Entities
    preferredPrefix: OMRSE
    prefix: omrse
    publications:
    - id: https://www.ncbi.nlm.nih.gov/pubmed/27406187
      title: 'The ontology of medically related social entities: recent developments'
    repository: https://github.com/mcwdsi/OMRSE
  ols:
    description: The Ontology for Modeling and Representation of Social Entities (OMRSE)
      is an OBO Foundry ontology that represents the various entities that arise from
      human social interactions, such as social acts, social roles, social groups,
      and organizations.
    download_owl: http://purl.obolibrary.org/obo/omrse.owl
    homepage: https://github.com/mcwdsi/OMRSE/wiki/OMRSE-Overview
    name: Ontology for Modeling and Representation of Social Entities
    prefix: omrse
    tracker: https://github.com/mcwdsi/OMRSE/issues
    version: '2025-08-13'
    version.iri: http://purl.obolibrary.org/obo/omrse/releases/2025-08-13/omrse.owl
  ontobee:
    library: Library
    name: Ontology for Modeling and Representation of Social Entities
    prefix: OMRSE
  pattern: ^\d{8}$
  prefix: omrse
  publications:
  - doi: 10.1186/s13326-016-0087-8
    pmc: PMC4942889
    pubmed: '27406187'
    title: 'The ontology of medically related social entities: recent developments'
    year: 2016
  uri_format: http://purl.obolibrary.org/obo/OMRSE_$1
omx.dataset:
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: OncoMX is a knowledgebase for exploring cancer biomarkers in the context
    of related cancer and healthy data. This resource is for datasets within OncoMX.
  example: 000059
  homepage: https://data.oncomx.org
  name: OncoMX Dataset
  pattern: ^\d+$
  prefix: omx.dataset
  uri_format: https://data.oncomx.org/OMX_$1
oncotree:
  appears_in:
  - efo
  contact:
    email: SchultzN@mskcc.org
    github: null
    name: Nikolaus Schultz
    orcid: 0000-0002-0131-4904
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: OncoTree is a dynamic and flexible community-driven cancer classification
    platform encompassing rare and common cancers that provides clinically relevant
    and appropriately granular cancer classification for clinical decision support
    systems and oncology research.
  example: BLL
  homepage: http://oncotree.mskcc.org
  keywords:
  - cancer
  - clinical decision support systems
  - oncology
  name: OncoTree
  prefix: oncotree
  publications:
  - doi: 10.1200/cci.20.00108
    pmc: PMC8240791
    pubmed: '33625877'
    title: 'OncoTree: A Cancer Classification System for Precision Oncology'
    year: 2021
  uri_format: http://oncotree.mskcc.org/api/tumorTypes/search/code/$1
one:
  aberowl:
    description: An ontology to standardize research output of nutritional epidemiologic
      studies.
    download_owl: http://aber-owl.net/media/ontologies/ONE/9/one.owl
    homepage: https://github.com/cyang0128/Nutritional-epidemiologic-ontologies
    name: Ontology for Nutritional Epidemiology
    prefix: ONE
  bioportal:
    contact:
      email: Chen.Yang@UGent.be
      name: Chen Yang
    description: Nutritional epidemiology is a specific research area. The generic
      ontologies for food science, nutrition science or medical science failed to
      cover the specific characteristics of nutritional epidemiologic studies. As
      a result, we developed the ontology for nutritional epidemiology (ONE) in order
      to describe nutritional epidemiologic studies accurately.
    homepage: https://github.com/cyang0128/Nutritional-epidemiological-ontologies
    name: Ontology for Nutritional Epidemiology
    prefix: ONE
    publications:
    - https://www.mdpi.com/2072-6643/11/6/1300
    version: V2.2
  example: '0001021'
  fairsharing:
    abbreviation: ONE
    contact:
      email: carl.lachat@ugent.be
      name: Carl Lachat
      orcid: 0000-0002-1389-8855
    description: The ontology for nutritional epidemiology (ONE) describes nutritional
      epidemiologic studies, and was created to improve on how generic ontologies
      for food science, nutrition science or medical science covered the specific
      characteristics of nutritional epidemiologic studies.
    homepage: https://github.com/cyang0128/Nutritional-epidemiologic-ontologies
    license: CC-BY-4.0
    name: Ontology for Nutritional epidemiology
    prefix: FAIRsharing.USxx0K
    publications:
    - pubmed: '31181762'
      title: 'An Ontology to Standardize Research Output of Nutritional Epidemiology:
        From Paper-Based Standards to Linked Content'
      year: 2019
    repository: https://github.com/cyang0128/Nutritional-Epidemiologic-ontologies
    subjects:
    - Metabolomics
    - Nutritional Science
    - Epidemiology
  mappings:
    aberowl: ONE
    bioportal: ONE
    fairsharing: FAIRsharing.USxx0K
    obofoundry: one
    ols: one
    ontobee: ONE
    wikidata.entity: Q113014430
  obofoundry:
    contact: chenyangnutrition@gmail.com
    contact.github: cyang0128
    contact.label: Chen Yang
    contact.orcid: 0000-0001-9202-5309
    depends_on:
    - foodon
    - obi
    - ons
    deprecated: false
    description: An ontology to standardize research output of nutritional epidemiologic
      studies.
    domain: diet, metabolomics, and nutrition
    download.owl: http://purl.obolibrary.org/obo/one.owl
    homepage: https://github.com/cyang0128/Nutritional-epidemiologic-ontologies
    license: CC BY 4.0
    license.url: https://creativecommons.org/licenses/by/4.0/
    name: Ontology for Nutritional Epidemiology
    preferredPrefix: ONE
    prefix: one
    repository: https://github.com/cyang0128/Nutritional-epidemiologic-ontologies
  ols:
    description: An ontology to standardize research output of nutritional epidemiologic
      studies.
    download_owl: http://purl.obolibrary.org/obo/one.owl
    homepage: https://github.com/cyang0128/Nutritional-epidemiologic-ontologies
    name: Ontology for Nutritional Epidemiology
    prefix: one
    tracker: https://github.com/cyang0128/Nutritional-epidemiologic-ontologies/issues
  ontobee:
    library: Library
    name: Ontology for Nutritional Epidemiology
    prefix: ONE
  pattern: ^\d{7}$
  prefix: one
  publications:
  - doi: 10.3390/nu11061300
    pmc: PMC6628051
    pubmed: '31181762'
    title: 'An Ontology to Standardize Research Output of Nutritional Epidemiology:
      From Paper-Based Standards to Linked Content'
    year: 2019
  - doi: null
    pmc: null
    pubmed: '31181762'
    title: 'An Ontology to Standardize Research Output of Nutritional Epidemiology:
      From Paper-Based Standards to Linked Content'
    year: 2019
  - doi: null
    pmc: null
    pubmed: '31181762'
    title: 'An Ontology to Standardize Research Output of Nutritional Epidemiology:
      From Paper-Based Standards to Linked Content'
    year: 2019
  uri_format: http://purl.obolibrary.org/obo/ONE_$1
ons:
  aberowl:
    description: An ontology for description of concepts in the nutritional studies
      domain.
    download_owl: http://aber-owl.net/media/ontologies/ONS/28/ons.owl
    homepage: https://github.com/enpadasi/Ontology-for-Nutritional-Studies
    name: Ontology for Nutritional Studies
    prefix: ONS
  agroportal:
    contact:
      email: francesco.vitali.bio@gmail.com
      name: Francesco Vitali
    description: ONS was developed under the ENPADASI European project, to assist
      the standardized description of (human) nutritional studies. As such, it includes
      and covers classes and relations that are commonly encountered while conducting,
      storing, harmonizing, integrating, describing and querying for nutritional studies.
      ONS main objective and long-term goal, is to represent a comprehensive resource
      for the description of concepts in the broader human nutrition domain, representing
      a solid and extensible formal ontology framework, where integration of new information
      can be easily achieved by the addition of extra modules.
    example_uri: http://purl.obolibrary.org/obo/ONS_0000083
    name: Ontology for Nutritional Studies
    prefix: ONS
    version: Relese version 1.0
  bioportal:
    contact:
      email: francesco.vitali@ibba.cnr.it
      name: Francesco Vitali
    description: Ontology For Nutritional Studies (ONS) is the first systematic effort
      to provide a formal ontology framework for the description of nutritional studies.
    homepage: https://github.com/enpadasi/Ontology-for-Nutritional-Studies
    name: Ontology for Nutritional Studies
    prefix: ONS
    publications:
    - https://doi.org/10.1186/s12263-018-0601-y
    version: '2024-07-03'
  example: '0000060'
  fairsharing:
    abbreviation: ONS
    description: Ontology For Nutritional Studies (ONS) has been developed as part
      of the ENPADASI European project (http://www.enpadasi.eu/) with the aim to define
      a common language and building ontologies for nutritional studies. It is the
      first systematic effort to provide a formal ontology framework for the description
      of nutritional studies. ONS provides an extensible formal ontology framework
      for nutritional studies, where integration of new information can be easily
      achieved by the addition of extra modules (i.e. Nutrigenomics, Metabolomics,
      Nutrikinetics, Quality appraisal, etc.). Nutritional researchers who might not
      necessarily be familiar with ontologies and concept standardization, can find
      in ONS a single knowledge entry point for a unified and standardized terminology
      for their studies.
    homepage: https://enpadasi.github.io/Ontology-for-Nutritional-Studies/
    license: CC-BY-4.0
    name: Ontology for Nutritional Studies
    prefix: FAIRsharing.rfec93
    repository: https://github.com/enpadasi/Ontology-for-Nutritional-Studies/issues
    subjects:
    - Nutritional Science
    - Biomedical Science
  mappings:
    aberowl: ONS
    agroportal: ONS
    bioportal: ONS
    fairsharing: FAIRsharing.rfec93
    obofoundry: ons
    ols: ons
    ontobee: ONS
    wikidata.entity: Q113014431
  obofoundry:
    appears_in:
    - one
    contact: francesco.vitali@ibba.cnr.it
    contact.github: FrancescoVit
    contact.label: Francesco Vitali
    contact.orcid: 0000-0001-9125-4337
    depends_on:
    - bfo
    - chebi
    - envo
    - foodon
    - ncbitaxon
    - obi
    - ro
    - uberon
    deprecated: false
    description: An ontology for description of concepts in the nutritional studies
      domain.
    domain: diet, metabolomics, and nutrition
    download.owl: http://purl.obolibrary.org/obo/ons.owl
    homepage: https://github.com/enpadasi/Ontology-for-Nutritional-Studies
    license: CC BY 4.0
    license.url: https://creativecommons.org/licenses/by/4.0/
    name: Ontology for Nutritional Studies
    preferredPrefix: ONS
    prefix: ons
    publications:
    - id: https://www.ncbi.nlm.nih.gov/pubmed/29736190
      title: 'ONS: an ontology for a standardized description of interventions and
        observational studies in nutrition'
    repository: https://github.com/enpadasi/Ontology-for-Nutritional-Studies
  ols:
    description: An ontology for description of concepts in the nutritional studies
      domain.
    download_owl: http://purl.obolibrary.org/obo/ons.owl
    homepage: https://github.com/enpadasi/Ontology-for-Nutritional-Studies
    name: Ontology for Nutritional Studies
    prefix: ons
    tracker: https://github.com/enpadasi/Ontology-for-Nutritional-Studies/issues
    version: '2024-07-03'
    version.iri: https://raw.githubusercontent.com/enpadasi/Ontology-for-Nutritional-Studies/releases/download/v2024-07-03/ons.owl
  ontobee:
    library: Library
    name: Ontology for Nutritional Studies
    prefix: ONS
  pattern: ^\d{7}$
  prefix: ons
  publications:
  - doi: 10.1186/s12263-018-0601-y
    pmc: PMC5928560
    pubmed: '29736190'
    title: 'ONS: an ontology for a standardized description of interventions and observational
      studies in nutrition'
    year: 2018
  - doi: null
    pmc: null
    pubmed: '29736190'
    title: 'ONS: an ontology for a standardized description of interventions and observational
      studies in nutrition'
    year: null
  uri_format: http://purl.obolibrary.org/obo/ONS_$1
ontie:
  contact:
    email: bpeters@lji.org
    github: bpeters42
    name: Bjoern Peters
    orcid: 0000-0002-8457-6693
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: The Ontology of Immune Epitopes (ONTIE) is an effort to represent terms
    in the immunology domain in a formal ontology with the specific goal of representing
    experiments that identify and characterize immune epitopes.
  download_owl: https://raw.githubusercontent.com/IEDB/ONTIE/master/ontie.owl
  example: '0000001'
  fairsharing:
    abbreviation: ONTIE
    description: The Ontology of Immune Epitopes (ONTIE) is an effort to represent
      terms in the immunology domain in a formal ontology with the specific goal of
      representing experiments that identify and characterize immune epitopes. ONTIE
      has been developed as a subset of OBI (Ontology of Biomedical Investigations)
      and includes terms relating to experiments involving immune epitopes. This file
      contains the minimal amount of upper ontology terms and axioms from BFO (Basic
      Formal Ontology), IAO (Information Artifact Ontology) and OBI, in order to view
      and reason upon ONTIE. It is currently at version 0.1 beta. ONTIE covers terms
      regarding immune responses, adaptive immune receptors, immune epitope assays,
      MHC molecules, and infectious diseases. ONTIE is (at this development stage)
      a virtual ontology, drawing together terms from multiple reference ontologies.
      We are actively working on adding more terms to ONTIE either through term requests
      or through active contribution to external ontologies.
    domains:
    - infection process
    - Major Histocompatibility Complex
    homepage: http://ontology.iedb.org
    name: Ontology of Immune Epitopes
    prefix: FAIRsharing.kx2md1
    subjects:
    - Life Science
    - Immunology
  homepage: https://ontology.iedb.org/
  mappings:
    fairsharing: FAIRsharing.kx2md1
  name: Ontology for Immune Epitopes
  pattern: ^\d{7}$
  prefix: ontie
  repository: https://github.com/IEDB/ONTIE
  uri_format: https://ontology.iedb.org/ontology/ONTIE_$1
ontoavida:
  aberowl:
    description: OntoAvida develops an integrated vocabulary for the description of
      the most widely-used computational approach for studying evolution using digital
      organisms (i.e., self-replicating computer programs that evolve within a user-defined
      computational environment).
    download_owl: http://aber-owl.net/media/ontologies/ONTOAVIDA/3/ontoavida.owl
    homepage: https://gitlab.com/fortunalab/ontoavida
    name: 'OntoAvida: ontology for Avida digital evolution platform'
    prefix: ONTOAVIDA
  bioportal:
    contact:
      email: fortuna@ebd.csic.es
      name: Miguel A. Fortuna
    description: OntoAvida develops an integrated vocabulary for the description of
      the most widely-used computational approach for studying evolution using digital
      organisms (i.e., self-replicating computer programs that evolve within a user-defined
      computational environment).
    homepage: https://gitlab.com/fortunalab/ontoavida
    name: 'OntoAvida: ontology for Avida digital evolution platform'
    prefix: ONTOAVIDA
  example: '00000001'
  mappings:
    aberowl: ONTOAVIDA
    bioportal: ONTOAVIDA
    obofoundry: ontoavida
    ols: ontoavida
    ontobee: ONTOAVIDA
    wikidata.entity: Q113014432
  name: Ontology for Avida digital evolution platform
  obofoundry:
    contact: fortuna@ebd.csic.es
    contact.github: miguelfortuna
    contact.label: Miguel A. Fortuna
    contact.orcid: 0000-0002-8374-1941
    depends_on:
    - fbcv
    - gsso
    - ncit
    - ro
    - stato
    deprecated: false
    description: OntoAvida develops an integrated vocabulary for the description of
      the most widely-used computational approach for studying evolution using digital
      organisms (i.e., self-replicating computer programs that evolve within a user-defined
      computational environment).
    domain: simulation
    download.obo: http://purl.obolibrary.org/obo/ontoavida.obo
    download.owl: http://purl.obolibrary.org/obo/ontoavida.owl
    homepage: https://gitlab.com/fortunalab/ontoavida
    license: CC BY 4.0
    license.url: https://creativecommons.org/licenses/by/4.0/
    name: 'OntoAvida: ontology for Avida digital evolution platform'
    preferredPrefix: ONTOAVIDA
    prefix: ontoavida
    publications:
    - id: https://doi.org/10.1038/s41597-023-02514-3
      title: Ontology for the Avida digital evolution platform
    repository: https://gitlab.com/fortunalab/ontoavida
  ols:
    description: 'The Ontology for Avida (OntoAvida) project aims to develop an integrated
      vocabulary for the description of the most widely used computational approach
      for performing experimental evolution using digital organisms (i.e., self-replicating
      computer programs that evolve within a user-defined computational environment).


      The lack of a clearly defined vocabulary makes biologists feel reluctant to
      embrace the field of digital evolution. This unique ontology has the potential
      to change this picture overnight.


      OntoAvida was initially developed by https://fortunalab.org, the computational
      biology lab at the Doñana Biological Station (a research institute of the Spanish
      National Research Council based at Seville, Spain). Contributors to OntoAvida
      are expected to include members of the Digital Evolution Laboratory (https://devolab.org/)
      at Michigan State University (USA).


      More information can be found at https://obofoundry.org/ontology/ontoavida.html'
    download_owl: http://purl.obolibrary.org/obo/ontoavida.owl
    homepage: https://gitlab.com/fortunalab/ontoavida
    name: 'OntoAvida: ontology for Avida digital evolution platform.'
    prefix: ontoavida
    tracker: https://gitlab.com/fortunalab/ontoavida/-/issues
    version: '2022-03-15'
    version.iri: http://purl.obolibrary.org/obo/ontoavida/releases/2022-03-15/ontoavida.owl
  ontobee:
    library: Library
    name: 'OntoAvida: ontology for Avida digital evolution platform'
    prefix: ONTOAVIDA
  pattern: ^\d{8}$
  prefix: ontoavida
  uri_format: http://purl.obolibrary.org/obo/ONTOAVIDA_$1
ontodm:
  appears_in:
  - efo
  bioportal:
    contact:
      email: pance.panov@ijs.si
      name: Pance Panov
    description: OntoDM is a generic ontology for the domain of data mining. The ontology
      includes the information processing processes that occur in the domain of data
      mining, participants in the processes and their specifications. OntoDM is highly
      transferable and extendable due to its adherence to accepted standards, and
      compliance with existing ontology resources. The generality in scope allows
      wide number of applications of the ontology, such as semantic annotation of
      data mining scenarios, ontology based support for QSARs, etc.
    homepage: http://www.ontodm.com
    name: Ontology of Core Data Mining Entities
    prefix: ONTODM-CORE
    publications:
    - http://link.springer.com/article/10.1007/s10618-014-0363-0#
    version: '2.0'
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: OntoDM-core defines the most essential data mining entities in a three-layered
    ontological structure comprising of a specification, an implementation and an
    application layer. It provides a representational framework for the description
    of mining structured data, and in addition provides taxonomies of datasets, data
    mining tasks, generalizations, data mining algorithms and constraints, based on
    the type of data. OntoDM-core is designed to support a wide range of applications/use
    cases, such as semantic annotation of data mining algorithms, datasets and results;
    annotation of QSAR studies in the context of drug discovery investigations; and
    disambiguation of terms in text mining. (from abstract)
  download_owl: https://raw.githubusercontent.com/panovp/ontodm-core/master/OntoDM.owl
  example: '000072'
  homepage: http://www.ontodm.com/
  mappings:
    bioportal: ONTODM-CORE
  name: Ontology of Core Data Mining Entities
  pattern: ^\d+$
  prefix: ontodm
  providers:
  - code: legacy
    description: legacy URIs
    example: null
    first_party: null
    homepage: http://kt.ijs.si/panovp
    name: Legacy URIs
    publications: null
    status: null
    uri_format: http://kt.ijs.si/panovp/OntoDM#OntoDM_$1
  - code: legacy2
    description: legacy URIs
    example: null
    first_party: null
    homepage: http://kt.ijs.si/panovp
    name: Legacy URIs
    publications: null
    status: null
    uri_format: http://kt.ijs.si/panovp/OntoDM#OntoDM-KDD_$1
  publications:
  - doi: 10.1007/s10618-014-0363-0
    pmc: null
    pubmed: null
    title: Ontology of core data mining entities
    year: 2014
  repository: https://github.com/panovp/ontodm-core
  uri_format: http://www.ontodm.com/OntoDM-core/OntoDM_$1
ontoneo:
  aberowl:
    description: The Obstetric and Neonatal Ontology is a structured controlled vocabulary
      to provide a representation of the data from electronic health records (EHRs)
      involved in the care of the pregnant woman, and of her baby.
    download_owl: http://aber-owl.net/media/ontologies/ONTONEO/12/ontoneo.owl
    homepage: ontoneo.com
    name: Obstetric and Neonatal Ontology
    prefix: ONTONEO
  biocontext:
    prefix: ONTONEO
  bioportal:
    contact:
      email: fernanda.farinelli@gmail.com
      name: Fernanda Farinelli
    description: The Obstetric and Neonatal Ontology is a structured controlled vocabulary
      to provide a representation of the data from electronic health records (EHRs)
      involved in the care of the pregnant woman, and of her baby.
    homepage: https://ontoneo.com/
    name: Obstetric and Neonatal Ontology
    prefix: ONTONEO
    publications:
    - https://github.com/ontoneo-project/Ontoneo
    version: '2025-03-14'
  example: 00000098
  fairsharing:
    abbreviation: ONTONEO
    description: The Obstetric and Neonatal Ontology is a structured controlled vocabulary
      to provide a representation of the data from electronic health records (EHRs)
      involved in the care of the pregnant woman, and of her baby.
    domains:
    - Electronic Health Record
    homepage: https://ontoneo.com/
    name: Obstetric and Neonatal Ontology
    prefix: FAIRsharing.5a4y1y
    publications:
    - doi: 10.1002/asi.23900
      title: 'Ontologies for the representation of electronic medical records: The
        obstetric and neonatal ontology'
      year: 2017
    subjects:
    - Obstetrics
  homepage: http://ontoneo.com
  mappings:
    aberowl: ONTONEO
    biocontext: ONTONEO
    bioportal: ONTONEO
    fairsharing: FAIRsharing.5a4y1y
    obofoundry: ontoneo
    ols: ontoneo
    ontobee: ONTONEO
    wikidata.entity: Q113014434
  obofoundry:
    contact: fernanda.farinelli@gmail.com
    contact.github: FernandaFarinelli
    contact.label: Fernanda Farinelli
    contact.orcid: 0000-0003-2338-8872
    deprecated: false
    description: The Obstetric and Neonatal Ontology is a structured controlled vocabulary
      to provide a representation of the data from electronic health records (EHRs)
      involved in the care of the pregnant woman, and of her baby.
    domain: health
    download.owl: http://purl.obolibrary.org/obo/ontoneo.owl
    homepage: https://ontoneo.com/
    license: CC BY 4.0
    license.url: https://creativecommons.org/licenses/by/4.0/
    name: Obstetric and Neonatal Ontology
    preferredPrefix: ONTONEO
    prefix: ontoneo
    publications:
    - id: https://doi.org/10.5281/zenodo.17429771
      title: 'OntONeo: The Obstetric and Neonatal Ontology'
    - id: https://doi.org/10.5281/zenodo.17508651
      title: Formal Ontologies in Knowledge Organization within the Obstetric and
        Neonatal Domain
    repository: https://github.com/ontoneo-project/Ontoneo
  ols:
    description: The Obstetric and Neonatal Ontology is a structured controlled vocabulary
      to provide a representation of the data from electronic health records (EHRs)
      involved in the care of the pregnant woman, and of her baby.
    download_owl: http://purl.obolibrary.org/obo/ontoneo.owl
    homepage: https://ontoneo.com/
    name: Obstetric and Neonatal Ontology
    prefix: ontoneo
    tracker: https://github.com/ontoneo-project/Ontoneo/issues
    version: '2025-03-14'
    version.iri: http://purl.obolibrary.org/obo/ontoneo/releases/2025-03-14/ontoneo.owl
  ontobee:
    library: Library
    name: Obstetric and Neonatal Ontology
    prefix: ONTONEO
  pattern: ^\d{8}$
  prefix: ontoneo
  publications:
  - doi: 10.1002/asi.23900
    pmc: null
    pubmed: null
    title: 'Ontologies for the representation of electronic medical records: The obstetric
      and neonatal ontology'
    year: 2017
  - doi: 10.5281/zenodo.17429771
    pmc: null
    pubmed: null
    title: 'OntONeo: The Obstetric and Neonatal Ontology'
    year: null
  - doi: 10.5281/zenodo.17508651
    pmc: null
    pubmed: null
    title: Formal Ontologies in Knowledge Organization within the Obstetric and Neonatal
      Domain
    year: null
  - doi: 10.1002/asi.23900
    pmc: null
    pubmed: null
    title: 'Ontologies for the representation of electronic medical records: The obstetric
      and neonatal ontology'
    year: 2017
  uri_format: http://purl.obolibrary.org/obo/ONTONEO_$1
ontorxn:
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: OntoRXN is an ontology for the description of reaction networks as
    undirected graphs characterized by energies.
  download_owl: https://gitlab.com/dgarayr/ontorxn/-/raw/prod/OntoRXN.owl
  example: hasCalculation
  github_request_issue: 1311
  homepage: https://gitlab.com/dgarayr/ontorxn
  license: CC-BY-4.0
  mappings:
    tib: ontorxn
  name: OntoRXN
  prefix: ontorxn
  publications:
  - doi: 10.1186/s13321-022-00610-x
    pmc: PMC9153116
    pubmed: '35637523'
    title: 'Chemical reaction network knowledge graphs: the OntoRXN ontology'
    year: 2022
  tib:
    description: OntoRXN is an ontology for the description of reaction networks as
      undirected graphs characterized by energies.
    download_owl: https://gitlab.com/dgarayr/ontorxn/-/raw/prod/OntoRXN.owl
    homepage: https://www.iochem-bd.org
    keywords:
    - NFDI4CHEM
    - chemistry
    name: OntoRXN
    prefix: ontorxn
    tracker: https://gitlab.com/dgarayr/ontorxn/-/issues
    version.iri: http://www.semanticweb.com/OntoRxn/0.2.5
oostt:
  aberowl:
    description: An ontology built for representating the organizational components
      of trauma centers and trauma systems.
    download_owl: http://aber-owl.net/media/ontologies/OOSTT/16/oostt.owl
    homepage: https://github.com/OOSTT/OOSTT
    name: Ontology of Organizational Structures of Trauma centers and Trauma systems
    prefix: OOSTT
  biocontext:
    prefix: OOSTT
  bioportal:
    contact:
      email: MBrochhausen@uams.edu
      name: Mathias Brochhausen
    description: The Ontology of Organizational Structures of Trauma centers and Trauma
      systems (OOSTT) is a representation of the components of trauma centers and
      trauma systems coded in Web Ontology Language (OWL2). It is developed collaboratively
      by domain and ontology experts in the NIH-funded CAFE (Comparative Assessment
      Framework for Environments of trauma care) project (1R01GM111324-01A1). It will
      be used as the ontology backbone of a graphical user interface comparing graphical
      representations of organizational structures.
    homepage: https://github.com/OOSTT/OOSTT
    name: Ontology of Organizational Structures of Trauma centers and Trauma systems
    prefix: OOSTT
    version: release version - 2025-01-24
  example: 00000099
  fairsharing:
    abbreviation: OOSTT
    description: The Ontology of Organizational Structures of Trauma centers and Trauma
      systems (OOSTT) is a representation of the components of trauma centers and
      trauma systems coded in Web Ontology Language (OWL2). It is developed collaboratively
      by domain and ontology experts in the NIH-funded CAFE (Comparative Assessment
      Framework for Environments of trauma care) project (1R01GM111324-01A1). It will
      be used as the ontology backbone of a graphical user interface comparing graphical
      representations of organizational structures.
    homepage: https://github.com/OOSTT/OOSTT
    license: CC-BY-4.0
    name: Ontology of Organizational Structures of Trauma centers and Trauma systems
    prefix: FAIRsharing.b4sa0w
    repository: https://github.com/OOSTT/OOSTT/
    subjects:
    - Traumatology
  mappings:
    aberowl: OOSTT
    biocontext: OOSTT
    bioportal: OOSTT
    fairsharing: FAIRsharing.b4sa0w
    obofoundry: oostt
    ols: oostt
    ontobee: OOSTT
    wikidata.entity: Q81661760
  obofoundry:
    contact: mbrochhausen@gmail.com
    contact.github: mbrochhausen
    contact.label: Mathias Brochhausen
    contact.orcid: 0000-0003-1834-3856
    deprecated: false
    description: An ontology built for representating the organizational components
      of trauma centers and trauma systems.
    domain: health
    download.owl: http://purl.obolibrary.org/obo/oostt.owl
    homepage: https://github.com/OOSTT/OOSTT
    license: CC BY 4.0
    license.url: http://creativecommons.org/licenses/by/4.0/
    name: Ontology of Organizational Structures of Trauma centers and Trauma systems
    preferredPrefix: OOSTT
    prefix: oostt
    repository: https://github.com/OOSTT/OOSTT
  ols:
    description: The Ontology of Organizational Structures of Trauma centers and Trauma
      systems (OOSTT) is a representation of the components of trauma centers and
      trauma systems coded in Web Ontology Language (OWL2).
    download_owl: http://purl.obolibrary.org/obo/oostt.owl
    homepage: https://github.com/OOSTT/OOSTT
    name: Ontology of Organizational Structures of Trauma centers and Trauma Systems
    prefix: oostt
    tracker: https://github.com/OOSTT/OOSTT/issues
    version: '2025-08-28'
    version.iri: http://purl.obolibrary.org/obo/oostt/release/2025-08-28/oostt.owl
  ontobee:
    library: Library
    name: Ontology of Organizational Structures of Trauma centers and Trauma systems
    prefix: OOSTT
  pattern: ^\d{8}$
  prefix: oostt
  uri_format: http://purl.obolibrary.org/obo/OOSTT_$1
opb:
  aberowl:
    description: The OPB is a reference ontology of classical physics and thermodynamics
      as applied to the dynamics of biological systems. It is designed to encompass
      the multiple structural scales (multiscale atoms to organisms) and multiple
      physical domains (multidomain fluid dynamics, chemical kinetics, particle diffusion,
      etc.) that are encountered in the study and analysis of biological organisms.
    download_owl: http://aber-owl.net/media/ontologies/OPB/13/opb.owl
    homepage: https://sites.google.com/site/semanticsofbiologicalprocesses/projects/the-ontology-of-physics-for-biology-opb
    name: Ontology of Physics for Biology
    prefix: OPB
    version: '1.05'
  banana: OPB
  banana_peel: _
  biocontext:
    prefix: OPB
  bioportal:
    contact:
      email: dcook@u.washington.edu
      name: Daniel L. Cook
    description: The OPB is a reference ontology of classical physics and thermodynamics
      as applied to the dynamics of biological systems. It is designed to encompass
      the multiple structural scales (atoms to organisms) and multiple physical domains
      (fluid dynamics, chemical kinetics, particle diffusion, etc.) that are encountered
      in the study and analysis of biological organisms.
    homepage: https://sites.google.com/site/semanticsofbiologicalprocesses/projects/the-ontology-of-physics-for-biology-opb
    name: Ontology of Physics for Biology
    prefix: OPB
    publications:
    - http://dx.plos.org/10.1371/journal.pone.0028708
    version: '1.2'
  contact:
    email: maxneal@gmail.com
    github: null
    name: Maxwell L. Neal
    orcid: 0000-0002-2390-6572
  contributor_extras:
  - email: benjamin_gyori@hms.harvard.edu
    github: bgyori
    name: Benjamin M. Gyori
    orcid: 0000-0001-9439-5346
  example: '00573'
  fairsharing:
    abbreviation: OPB
    description: The Ontology of Physics for Biology is a reference of classical physics
      as applied to the dynamics of biological systems. This resource provides a reference
      ontology of physical properties (e.g., pressure, chemical concentration) and
      principles (e.g., Ohm’s law, Ficke’s law) by which the physical meaning of biosimulation
      models may be annotated.
    domains:
    - Concentration
    homepage: https://sites.google.com/site/semanticsofbiologicalprocesses/projects/the-ontology-of-physics-for-biology-opb
    name: Ontology of Physics for Biology
    prefix: FAIRsharing.qcceez
    publications:
    - doi: 10.1371/journal.pone.0028708
      pubmed: '22216106'
      title: 'Physical properties of biological entities: an introduction to the ontology
        of physics for biology'
      year: 2012
    - doi: 10.1186/2041-1480-4-41
      pubmed: '24295137'
      title: 'Ontology of physics for biology: representing physical dependencies
        as a basis for biological processes'
      year: 2013
    subjects:
    - Life Science
    - Physics
  mappings:
    aberowl: OPB
    biocontext: OPB
    bioportal: OPB
    fairsharing: FAIRsharing.qcceez
    miriam: opb
    n2t: opb
    prefixcommons: opb
  miriam:
    deprecated: false
    description: The OPB is a reference ontology of classical physics as applied to
      the dynamics of biological systems. It is designed to encompass the multiple
      structural scales (multiscale atoms to organisms) and multiple physical domains
      (multidomain fluid dynamics, chemical kinetics, particle diffusion, etc.) that
      are encountered in the study and analysis of biological organisms.
    homepage: http://bioportal.bioontology.org/ontologies/OPB
    id: 00000129
    name: Ontology of Physics for Biology
    namespaceEmbeddedInLui: false
    pattern: ^OPB_\d+$
    prefix: opb
    sampleId: OPB_00573
    uri_format: http://purl.bioontology.org/ontology/OPB?conceptid=http%3A%2F%2Fbhi.washington.edu%2FOPB%23$1
  n2t:
    description: The OPB is a reference ontology of classical physics as applied to
      the dynamics of biological systems. It is designed to encompass the multiple
      structural scales (multiscale atoms to organisms) and multiple physical domains
      (multidomain fluid dynamics, chemical kinetics, particle diffusion, etc.) that
      are encountered in the study and analysis of biological organisms.
    example: OPB_00573
    homepage: http://bioportal.bioontology.org/ontologies/OPB
    name: Ontology of Physics for Biology through Bioportal
    namespaceEmbeddedInLui: false
    pattern: ^OPB_\d+$
    prefix: opb
    uri_format: http://purl.bioontology.org/ontology/OPB?conceptid=http%3A%2F%2Fbhi.washington.edu%2FOPB%23$1
  pattern: ^\d+$
  prefix: opb
  prefixcommons:
    bioportal: '1141'
    description: The OPB is a reference ontology of classical physics as applied to
      the dynamics of biological systems. It is designed to encompass the multiple
      structural scales (multiscale atoms to organisms) and multiple physical domains
      (multidomain fluid dynamics, chemical kinetics, particle diffusion, etc.) that
      are encountered in the study and analysis of biological organisms.
    example: OPB_00573
    homepage: https://sites.google.com/site/semanticsofbiologicalprocesses/projects/the-ontology-of-physics-for-biology-opb
    keywords:
    - ontology
    - structure
    name: Ontology of Physics for Biology
    pattern: ^OPB_\d+$
    prefix: opb
    rdf_uri_format: http://bhi.washington.edu/OPB#$1
    synonyms:
    - opb.properties
  publications:
  - doi: 10.1186/2041-1480-4-41
    pmc: PMC3904761
    pubmed: '24295137'
    title: 'Ontology of physics for biology: representing physical dependencies as
      a basis for biological processes'
    year: 2013
  - doi: 10.1371/journal.pone.0028708
    pmc: PMC3246444
    pubmed: '22216106'
    title: 'Physical properties of biological entities: an introduction to the ontology
      of physics for biology'
    year: 2011
  - doi: 10.1371/journal.pone.0028708
    pmc: null
    pubmed: '22216106'
    title: 'Physical properties of biological entities: an introduction to the ontology
      of physics for biology'
    year: 2012
  - doi: 10.1186/2041-1480-4-41
    pmc: null
    pubmed: '24295137'
    title: 'Ontology of physics for biology: representing physical dependencies as
      a basis for biological processes'
    year: 2013
  uri_format: https://bioportal.bioontology.org/ontologies/OPB/?p=classes&conceptid=http%3A%2F%2Fbhi.washington.edu%2FOPB%23OPB_$1
openadr:
  example: BidEnergySetpointSignal
  mappings:
    tib: openadr
  prefix: openadr
  tib:
    description: This ontology describes the openADR protocol based on the documentation
      provided by the openADR Profile B
    download_owl: https://raw.githubusercontent.com/albaizq/OpenADRontology/master/ontology/openADRontology.owl
    homepage: https://albaizq.github.io/OpenADRontology/OnToology/ontology/openADRontology.owl/documentation/index-en.html
    keywords:
    - NFDI4Energy
    - engineering
    name: OpenADR ontology
    prefix: openadr
    tracker: https://github.com/albaizq/OpenADRontology/issues
    uri_format: https://w3id.org/def/openadr#$1
openalex:
  contact:
    email: hpiwowar@gmail.com
    github: hpiwowar
    name: Heather Piwowar
    orcid: 0000-0003-1613-5981
  contributor:
    email: null
    github: dhimmel
    name: Daniel Himmelstein
    orcid: 0000-0002-3012-7446
  description: OpenAlex is a fully open catalog of the global research system that
    describes scholarly entities and how those entities are connected to each other.
  example: W2741809807
  github_request_issue: 280
  homepage: https://openalex.org/
  keywords:
  - knowledge graph
  - wikidata
  name: OpenAlex
  pattern: ^[WAICV]\d{2,}$
  prefix: openalex
  reviewer:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  uri_format: https://openalex.org/$1
openeduhub.context:
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: educational levels
  download_jskos: https://vocabs.openeduhub.de/w3id.org/openeduhub/vocabs/educationalContext/index.json
  example: sekundarstufe_2
  homepage: http://w3id.org/openeduhub/vocabs/educationalContext/
  keywords:
  - education level
  - open educational resources
  name: Educational Context
  prefix: openeduhub.context
  rdf_uri_format: http://w3id.org/openeduhub/vocabs/educationalContext/$1
  uri_format: http://w3id.org/openeduhub/vocabs/educationalContext/$1
openwemi:
  contact:
    email: kcoyle@kcoyle.net
    github: kcoyle
    name: Karen Coyle
    orcid: 0000-0002-1085-7089
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: openWEMI is a minimally constrained vocabulary for describing created
    resources using the concepts of Work, Expression, Manifestation, Item.
  example: Endeavor
  homepage: https://dcmi.github.io/openwemi/
  license: CC0-1.0
  name: openWEMI Vocabulary
  pattern: ^\w+$
  prefix: openwemi
  references:
  - https://journal.code4lib.org/articles/16491
  - http://archive.ifla.org/VII/s13/frbr/frbr_2008.pdf
  repository: https://github.com/dcmi/openwemi
  uri_format: https://dcmi.github.io/openwemi/ns#$1
opl:
  aberowl:
    description: A reference ontology for parasite life cycle stages.
    download_owl: http://aber-owl.net/media/ontologies/OPL/12/opl.owl
    homepage: https://github.com/OPL-ontology/OPL
    name: Ontology for Parasite LifeCycle
    prefix: OPL
  biocontext:
    prefix: OPL
  bioportal:
    contact:
      email: preets79@gmail.com
      name: Priti Parikh
    description: The Ontology for Parasite LifeCycle (OPL) models the life cycle stage
      details of various parasites, including Trypanosoma sp., Leishmania major, and
      Plasmodium sp., etc. In addition to life cycle stages, the ontology also models
      necessary contextual details, such as host information, vector information,
      and anatomical location. OPL is based on the Basic Formal Ontology (BFO) and
      follows the rules set by the OBO Foundry consortium.
    homepage: http://knoesis.wright.edu/trykipedia/parasitelifecycle
    name: Ontology for Parasite LifeCycle
    prefix: OPL
    publications:
    - http://knoesis.wright.edu/trykipedia/parasitelifecycle
    version: '2023-08-28'
  example: 0000319
  fairsharing:
    abbreviation: OPL
    contact:
      email: zhengj2007@gmail.com
      name: Jie Zheng
      orcid: 0000-0002-2999-0103
    description: The Ontology for Parasite Lifecycle (OPL) models the life cycle stage
      details of various parasites, including Trypanosoma sp., Leishmania major, and
      Plasmodium sp., etc. In addition to life cycle stages, the ontology also models
      necessary contextual details, such as host information, vector information,
      and anatomical location. OPL is based on the Basic Formal Ontology (BFO) and
      follows the rules set by the OBO Foundry consortium.
    domains:
    - host
    - life cycle
    - life cycle stage
    homepage: https://github.com/OPL-ontology/OPL
    license: CC-BY-4.0
    name: Ontology for Parasite LifeCycle
    prefix: FAIRsharing.ez2nhb
    publications:
    - doi: 10.1186/2041-1480-3-5
      pubmed: '22621763'
      title: 'The Ontology for Parasite Lifecycle (OPL): towards a consistent vocabulary
        of lifecycle stages in parasitic organisms'
      year: 2012
    repository: https://github.com/OPL-ontology/OPL
    subjects:
    - Life Science
    - Anatomy
    - Developmental Biology
  mappings:
    aberowl: OPL
    biocontext: OPL
    bioportal: OPL
    fairsharing: FAIRsharing.ez2nhb
    miriam: opl
    obofoundry: opl
    ols: opl
    ontobee: OPL
  miriam:
    deprecated: false
    description: The Ontology for Parasite Lifecycle (OPL) models the life cycle stage
      details of various parasites, including Trypanosoma sp., Leishmania major, and
      Plasmodium sp., etc.
    homepage: https://www.ebi.ac.uk/ols4/ontologies/opl
    id: '00001047'
    name: Ontology for Parasite Lifecycle
    namespaceEmbeddedInLui: true
    pattern: ^OPL:\d+$
    prefix: opl
    sampleId: '0000134'
    uri_format: https://www.ebi.ac.uk/ols4/ontologies/opl/classes?obo_id=OPL:$1
  obofoundry:
    contact: zhengj2007@gmail.com
    contact.github: zhengj2007
    contact.label: Jie Zheng
    contact.orcid: 0000-0002-2999-0103
    deprecated: false
    description: A reference ontology for parasite life cycle stages.
    domain: organisms
    download.owl: http://purl.obolibrary.org/obo/opl.owl
    homepage: https://github.com/OPL-ontology/OPL
    license: CC BY 4.0
    license.url: https://creativecommons.org/licenses/by/4.0/
    name: Ontology for Parasite LifeCycle
    preferredPrefix: OPL
    prefix: opl
    repository: https://github.com/OPL-ontology/OPL
  ols:
    description: The Ontology for Parasite Lifecycle (OPL) models the life cycle stage
      details of various parasites, including Trypanosoma sp., Leishmania major, and
      Plasmodium sp., etc. In addition to life cycle stages, the ontology also models
      necessary contextual details, such as host information, vector information,
      and anatomical location. OPL is based on the Basic Formal Ontology (BFO) and
      follows the rules set by the OBO Foundry consortium.
    download_owl: http://purl.obolibrary.org/obo/opl.owl
    homepage: https://github.com/OPL-ontology/OPL
    name: Ontology for Parasite Lifecycle
    prefix: opl
    tracker: https://github.com/OPL-ontology/OPL/issues
    version: '2023-08-28'
    version.iri: http://purl.obolibrary.org/obo/opl/2023-08-28/opl.owl
  ontobee:
    library: Library
    name: Ontology for Parasite LifeCycle
    prefix: OPL
  pattern: ^\d{7}$
  prefix: opl
  publications:
  - doi: 10.1186/2041-1480-3-5
    pmc: PMC3488002
    pubmed: '22621763'
    title: 'The Ontology for Parasite Lifecycle (OPL): towards a consistent vocabulary
      of lifecycle stages in parasitic organisms'
    year: 2012
  - doi: 10.1186/2041-1480-3-5
    pmc: null
    pubmed: '22621763'
    title: 'The Ontology for Parasite Lifecycle (OPL): towards a consistent vocabulary
      of lifecycle stages in parasitic organisms'
    year: 2012
  uri_format: http://purl.obolibrary.org/obo/OPL_$1
opm:
  biocontext:
    prefix: OPM
  fairsharing:
    abbreviation: OPM
    description: 'The Open Provenance Model (OPM) is a model of provenance that is
      designed to meet the following requirements: (1) To allow provenance information
      to be exchanged between systems, by means of a compatibility layer based on
      a shared provenance model. (2) To allow developers to build and share tools
      that operate on such a provenance model. (3) To define provenance in a precise,
      technology-agnostic manner. (4) To support a digital representation of provenance
      for any ''thing'', whether produced by computer systems or not. (5) To allow
      multiple levels of description to coexist. (6) To define a core set of rules
      that identify the valid inferences that can be made on provenance representation.'
    homepage: https://doi.org/10.1016/j.future.2010.07.005
    name: Open Provenance Model
    prefix: FAIRsharing.7c683b
    publications: []
    subjects:
    - Data Management
    - Computer Science
  mappings:
    biocontext: OPM
    fairsharing: FAIRsharing.7c683b
    miriam: opm
    n2t: opm
  miriam:
    deprecated: false
    description: The Orientations of Proteins in Membranes (OPM) database provides
      spatial positions of membrane-bound peptides and proteins of known three-dimensional
      structure in the lipid bilayer, together with their structural classification,
      topology and intracellular localization.
    homepage: http://opm.phar.umich.edu/
    id: '00000333'
    name: OPM
    namespaceEmbeddedInLui: false
    pattern: ^[0-9][A-Za-z0-9]{3}$
    prefix: opm
    sampleId: 1h68
    uri_format: http://opm.phar.umich.edu/protein.php?pdbid=$1
  n2t:
    description: The Orientations of Proteins in Membranes (OPM) database provides
      spatial positions of membrane-bound peptides and proteins of known three-dimensional
      structure in the lipid bilayer, together with their structural classification,
      topology and intracellular localization.
    example: 1h68
    homepage: http://opm.phar.umich.edu/
    name: OPM at University of Michigan
    namespaceEmbeddedInLui: false
    pattern: ^[0-9][A-Za-z0-9]{3}$
    prefix: opm
    uri_format: http://opm.phar.umich.edu/protein.php?pdbid=$1
  name: Orientations of Proteins in Membranes Database
  prefix: opm
opmi:
  aberowl:
    description: The Ontology of Precision Medicine and Investigation (OPMI) aims
      to ontologically represent and standardize various entities and relations associated
      with precision medicine and related investigations at different conditions.
    download_owl: http://aber-owl.net/media/ontologies/OPMI/29/opmi.owl
    homepage: https://github.com/OPMI/opmi
    name: Ontology of Precision Medicine and Investigation
    prefix: OPMI
  bioportal:
    contact:
      email: yongqunh@med.umich.edu
      name: Oliver He
    description: The Ontology of Precision Medicine and Investigation (OPMI) is an
      application ontology to support precision medicine and its related investigations.
      OPMI is community-driven and developed by following the OBO Foundry ontology
      development principles. OPMI reuses, aligns, and integrates related terms from
      existing OBO ontologies.
    homepage: https://github.com/OPMI/opmi
    name: Ontology of Precision Medicine and Investigation
    prefix: OPMI
    version: 'Vision Release: 1.0.166'
  example: '0000101'
  fairsharing:
    abbreviation: OPMI
    contact:
      email: yongqunh@umich.edu
      name: Yongqun He
      orcid: 0000-0001-9189-9661
    description: 'The Ontology of Precision Medicine and Investigation (OPMI) ontology
      is an application ontology to support precision medicine and related investigations.
      It is community-driven and developed by following the OBO Foundry ontology development
      principles. OPMI reuses, aligns, and integrates related terms from existing
      ontologies in the OBO ontology library. OPMI aims to represent and standardize
      the entities associated with precision medicine, including all the data/metadata
      types, investigation processes, and analysis in various aspects of clinical,
      pathological, and molecular studies to be conducted in KPMP. The Kidney Tissue
      Atlas Ontology (KTAO) is a more kidney-specific complementary addition to OMPI
      precision medicine-related terms that can be used in parallel. '
    domains:
    - disease
    homepage: https://github.com/OPMI/opmi
    license: CC-BY-4.0
    name: Ontology of Precision Medicine and Investigation
    prefix: FAIRsharing.d2d84f
    subjects:
    - Omics
    - Clinical Studies
  mappings:
    aberowl: OPMI
    bioportal: OPMI
    fairsharing: FAIRsharing.d2d84f
    obofoundry: opmi
    ols: opmi
    ontobee: OPMI
    wikidata.entity: Q81661763
  obofoundry:
    appears_in:
    - labo
    - scdo
    contact: yongqunh@med.umich.edu
    contact.github: yongqunh
    contact.label: Yongqun Oliver He
    contact.orcid: 0000-0001-9189-9661
    deprecated: false
    description: The Ontology of Precision Medicine and Investigation (OPMI) aims
      to ontologically represent and standardize various entities and relations associated
      with precision medicine and related investigations at different conditions.
    domain: investigations
    download.owl: http://purl.obolibrary.org/obo/opmi.owl
    homepage: https://github.com/OPMI/opmi
    license: CC BY 4.0
    license.url: http://creativecommons.org/licenses/by/4.0/
    name: Ontology of Precision Medicine and Investigation
    preferredPrefix: OPMI
    prefix: opmi
    repository: https://github.com/OPMI/opmi
  ols:
    description: OPMI is a biomedical ontology in the area of precision medicine and
      its related investigations. It is community-driven and developed by following
      the OBO Foundry ontology development principles.
    download_owl: http://purl.obolibrary.org/obo/opmi.owl
    homepage: https://github.com/OPMI/opmi
    name: 'OPMI: Ontology of Precision Medicine and Investigation'
    prefix: opmi
    tracker: https://github.com/OPMI/opmi/issues
    version: 1.0.166
  ontobee:
    library: Library
    name: Ontology of Precision Medicine and Investigation
    prefix: OPMI
  pattern: ^\d{7}$
  prefix: opmi
  uri_format: http://purl.obolibrary.org/obo/OPMI_$1
oprlm:
  contact:
    email: wonpil@lehigh.edu
    github: null
    name: Wonpil Im
    orcid: 0000-0001-5642-6041
  contributor:
    email: palayoor.n@northeastern.edu
    github: nalikapalayoor
    name: Nalika Palayoor
    orcid: 0009-0008-8406-631X
  description: Orientations of Proteins in Realistic Lipid Membranes (OPRLM) is a
    database for visualizing proteins in realistic lipid membranes. It includes the
    classification of proteins into types, superfamilies, and families, and also provides
    information on intracellular localizations of the proteins. Identifiers represent
    proteins.
  example: '6782'
  github_request_issue: 1558
  homepage: https://oprlm.org
  name: Orientation of Proteins in Realistic Lipid Membranes
  pattern: ^\d*$
  prefix: oprlm
  publications:
  - doi: 10.1016/j.jmb.2025.168966
    pmc: null
    pubmed: '40133776'
    title: 'OPRLM: A Web Tool and a Database for Positioning and Simulations of Proteins
      in Realistic Lipid Membranes'
    year: 2025
  reviewer:
    email: b.gyori@northeastern.edu
    github: bgyori
    name: Benjamin M. Gyori
    orcid: 0000-0001-9439-5346
  uri_format: https://oprlm.org/proteins/$1
orangebook:
  comment: The web pages on the digital edition can be constructed with some programmatic
    logic, but not directly
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: The first number is the chapter then the remainder are subsections.
  example: 10.2.1.1.3
  github_request_issue: 1311
  homepage: https://media.iupac.org/publications/analytical_compendium/
  name: IUPAC Compendium of Analytical Nomenclature (Orange Book)
  prefix: orangebook
  references:
  - https://iupac.org/what-we-do/books/orangebook/
orcid:
  bartoc:
    description: ORCID provides a persistent digital identifier that distinguishes
      you from every other researcher and, through integration in key research workflows
      such as manuscript and grant submission, supports automated linkages between
      you and your professional activities ensuring that your work is recognized.
    homepage: http://orcid.org/
    license: CC0-1.0
    name: ORCID
    prefix: '2021'
    wikidata_database: Q51044
  biocontext:
    prefix: ORCID
  biolink:
    is_identifiers: false
    is_obo: false
    prefix: ORCID
    uri_format: https://orcid.org/$1
  contact:
    email: w.simpson@orcid.org
    github: wjrsimpson
    name: Will Simpson
    orcid: 0000-0003-4654-1403
  example: 0000-0003-4423-4370
  fairsharing:
    abbreviation: ORCID
    description: ORCID is an open, non-profit, community-driven effort to create and
      maintain a registry of unique researcher identifiers and a transparent method
      of linking research activities and outputs to these identifiers. The ORCID Registry
      is a repository of unique researcher identifiers which allows researchers to
      manage a record of their research activities. In addition, there are APIs that
      support system-to-system communication and authentication. ORCID makes its code
      available under an open source license, and will post an annual public data
      file under a CC0 waiver for free download.
    homepage: http://orcid.org/
    license: http://orcid.org/node/43
    name: Open Researcher and Contributor ID Registry
    prefix: FAIRsharing.nx58jg
    publications:
    - doi: 10.23640/07243.16687207.v1
      pubmed_id: null
      title: 'From Vision to Value: ORCID''s 2022–2025 Strategic Plan'
    - doi: 10.23640/07243.12009255.v3
      pubmed_id: null
      title: ORCID's 2025 Vision
    repository: https://github.com/ORCID
    subjects:
    - Subject Agnostic
    twitter: ORCID_Org
  go:
    description: ORCID (Open Researcher and Contributor ID) is an open, non-profit,
      community-based effort to create and maintain a registry of unique identifiers
      for individual researchers.
    homepage: https://orcid.org/
    name: Open Researcher and Contributor
    prefix: orcid
    uri_format: https://orcid.org/$1
  keywords:
  - person
  mappings:
    bartoc: '2021'
    biocontext: ORCID
    biolink: ORCID
    fairsharing: FAIRsharing.nx58jg
    go: orcid
    miriam: orcid
    n2t: orcid
    wikidata: P496
    wikidata.entity: Q51044
  mastodon: ORCID_Org@scicomm.xyz
  miriam:
    deprecated: false
    description: ORCID (Open Researcher and Contributor ID) is an open, non-profit,
      community-based effort to create and maintain a registry of unique identifiers
      for individual researchers. ORCID records hold non-sensitive information such
      as name, email, organization name, and research activities.
    homepage: https://orcid.org
    id: 00000382
    name: ORCID
    namespaceEmbeddedInLui: false
    pattern: ^\d{4}-\d{4}-\d{4}-\d{3}(\d|X)$
    prefix: orcid
    sampleId: 0000-0002-5355-2576
    uri_format: https://orcid.org/$1
  n2t:
    description: ORCID (Open Researcher and Contributor ID) is an open, non-profit,
      community-based effort to create and maintain a registry of unique identifiers
      for individual researchers. ORCID records hold non-sensitive information such
      as name, email, organization name, and research activities.
    example: 0000-0002-5355-2576
    homepage: https://orcid.org
    name: ORCID at Bethesda
    namespaceEmbeddedInLui: false
    pattern: ^\d{4}-\d{4}-\d{4}-\d{3}(\d|X)$
    prefix: orcid
    uri_format: https://orcid.org/$1
  name: Open Researcher and Contributor
  prefix: orcid
  providers:
  - code: scholia
    description: Scholia is a service that creates visual scholarly profiles for topic,
      people, organizations, species, chemicals, etc using bibliographic and other
      information in Wikidata.
    example: null
    first_party: null
    homepage: https://scholia.toolforge.org/
    name: Scholia
    publications: null
    status: null
    uri_format: https://scholia.toolforge.org/orcid/$1
  publications:
  - doi: 10.23640/07243.16687207.v1
    pmc: null
    pubmed: null
    title: 'From Vision to Value: ORCID''s 2022–2025 Strategic Plan'
    year: 2021
  - doi: 10.23640/07243.12009255.v3
    pmc: null
    pubmed: null
    title: ORCID's 2025 Vision
    year: 2020
  - doi: 10.23640/07243.16687207.v1
    pmc: null
    pubmed: null
    title: 'From Vision to Value: ORCID''s 2022–2025 Strategic Plan'
    year: null
  - doi: 10.23640/07243.12009255.v3
    pmc: null
    pubmed: null
    title: ORCID's 2025 Vision
    year: null
  - doi: 10.23640/07243.16687207.v1
    pmc: null
    pubmed: null
    title: 'From Vision to Value: ORCID''s 2022–2025 Strategic Plan'
    year: null
  - doi: 10.23640/07243.12009255.v3
    pmc: null
    pubmed: null
    title: ORCID's 2025 Vision
    year: null
  synonyms:
  - ORCID
  - ORCiD
  wikidata:
    database: Q51044
    description: identifier for a person
    example:
    - 0000-0001-8994-2210
    - 0000-0002-1003-5675
    - 0000-0002-1825-0097
    homepage: https://orcid.org/
    miriam: orcid
    name: ORCID iD
    pattern: ^\d{4}-\d{4}-\d{4}-\d{3}[\dX]$
    prefix: P496
    uri_format: https://orcid.org/$1
    uri_format_rdf: https://orcid.org/$1
ordb:
  biocontext:
    prefix: ORDB
  fairsharing:
    abbreviation: ORDB
    description: ORDB began as a database of vertebrate OR genes and proteins and
      continues to support sequencing and analysis of these receptors by providing
      a comprehensive archive with search tools for this expanding family.
    homepage: http://senselab.med.yale.edu/OrDB/
    license: https://senselab.med.yale.edu/OrDB
    name: Olfactory Receptor Database
    prefix: FAIRsharing.6375zh
    publications:
    - doi: 10.1093/nar/30.1.354
      pubmed_id: 11752336
      title: 'Olfactory Receptor Database: a metadata-driven automated population
        from sources of gene and protein sequences.'
    - doi: 10.1093/database/baw132
      pubmed_id: 27694208
      title: ORDB, HORDE, ODORactor and other on-line knowledge resources of olfactory
        receptor-odorant interactions.
    - doi: 10.1093/nar/28.1.341
      pubmed_id: 10592268
      title: 'Olfactory receptor database: a sensory chemoreceptor resource.'
    subjects:
    - Life Science
  mappings:
    biocontext: ORDB
    fairsharing: FAIRsharing.6375zh
    miriam: ordb
    n2t: ordb
    pathguide: '65'
    prefixcommons: ordb
  miriam:
    deprecated: false
    description: The Olfactory Receptor Database (ORDB) is a repository of genomics
      and proteomics information of olfactory receptors (ORs). It includes a broad
      range of chemosensory genes and proteins, that includes in addition to ORs the
      taste papilla receptors (TPRs), vomeronasal organ receptors (VNRs), insect olfactory
      receptors (IORs), Caenorhabditis elegans chemosensory receptors (CeCRs), fungal
      pheromone receptors (FPRs).
    homepage: http://senselab.med.yale.edu/OrDB/
    id: 00000499
    name: Olfactory Receptor Database
    namespaceEmbeddedInLui: false
    pattern: ^\d+$
    prefix: ordb
    sampleId: '8497'
    uri_format: https://ordb.biotech.ttu.edu/ORDB/Data/$1
  n2t:
    description: The Olfactory Receptor Database (ORDB) is a repository of genomics
      and proteomics information of olfactory receptors (ORs). It includes a broad
      range of chemosensory genes and proteins, that includes in addition to ORs the
      taste papilla receptors (TPRs), vomeronasal organ receptors (VNRs), insect olfactory
      receptors (IORs), Caenorhabditis elegans chemosensory receptors (CeCRs), fungal
      pheromone receptors (FPRs).
    example: '8497'
    homepage: http://senselab.med.yale.edu/OrDB/
    name: Olfactory Receptor Database at Yale University School of Medicine
    namespaceEmbeddedInLui: false
    pattern: ^\d+$
    prefix: ordb
    uri_format: http://senselab.med.yale.edu/ORDB/Data/$1
  pathguide:
    abbreviation: ORDB
    homepage: http://senselab.med.yale.edu/OrDB/
    name: Olfactory Receptor Database
    prefix: '65'
  prefix: ordb
  prefixcommons:
    description: ORDB began as a database of vertebrate OR genes and proteins and
      continues to support sequencing and analysis of these receptors by providing
      a comprehensive archive with search tools for this expanding family.
    example: '14673'
    homepage: http://senselab.med.yale.edu/senselab/ordb/
    keywords:
    - gene
    - protein
    name: Olfactory Receptor Database
    pattern: ^\d+$
    prefix: ordb
    synonyms:
    - ord
    uri_format: http://senselab.med.yale.edu/ordb/eavdata.asp?o=$1
  publications:
  - doi: 10.1093/database/baw132
    pmc: PMC5045865
    pubmed: '27694208'
    title: ORDB, HORDE, ODORactor and other on-line knowledge resources of olfactory
      receptor-odorant interactions
    year: 2016
  - doi: 10.1093/nar/30.1.354
    pmc: PMC99065
    pubmed: '11752336'
    title: 'Olfactory Receptor Database: a metadata-driven automated population from
      sources of gene and protein sequences'
    year: 2002
  - doi: 10.1093/nar/28.1.341
    pmc: PMC102443
    pubmed: '10592268'
    title: 'Olfactory receptor database: a sensory chemoreceptor resource'
    year: 2000
org:
  example: ChangeEvent
  lov:
    description: Vocabulary for describing organizational structures, specializable
      to a broad variety of types of organization.
    homepage: http://www.w3.org/TR/vocab-org/
    keywords:
    - W3C Rec
    modified: '2014-04-12'
    name: Core organization ontology
    prefix: org
    uri_prefix: http://www.w3.org/ns/org#$1
  mappings:
    lov: org
    tib: org
    zazuko: org
  prefix: org
  tib:
    contact: public-gld-comments@w3.org
    description: Vocabulary for describing organizational structures, specializable
      to a broad variety of types of organization.
    download_rdf: http://www.w3.org/ns/org.rdf
    homepage: https://www.w3.org/TR/vocab-org/
    keywords:
    - Digital Planning and Construction
    - FID BAUdigital
    - social sciences
    - economics
    name: Core organization ontology
    prefix: org
    uri_format: http://www.w3.org/ns/org#$1
  zazuko:
    prefix: org
    uri_format: http://www.w3.org/ns/org#$1
oridb.sacch:
  biocontext:
    prefix: ORIDB.SACCH
  mappings:
    biocontext: ORIDB.SACCH
    miriam: oridb.sacch
    n2t: oridb.sacch
  miriam:
    deprecated: false
    description: OriDB is a database of collated genome-wide mapping studies of confirmed
      and predicted replication origin sites in Saccharomyces cerevisiae and the fission
      yeast Schizosaccharomyces pombe. This collection references Saccharomyces cerevisiae.
    homepage: http://cerevisiae.oridb.org/index.php
    id: 00000369
    name: OriDB Saccharomyces
    namespaceEmbeddedInLui: false
    pattern: ^\d+$
    prefix: oridb.sacch
    sampleId: '1'
    uri_format: http://cerevisiae.oridb.org/details.php?id=$1
  n2t:
    description: OriDB is a database of collated genome-wide mapping studies of confirmed
      and predicted replication origin sites in Saccharomyces cerevisiae and the fission
      yeast Schizosaccharomyces pombe. This collection references Saccharomyces cerevisiae.
    example: '1'
    homepage: http://cerevisiae.oridb.org/index.php
    name: OriDB Saccharomyces at University of Nottingham
    namespaceEmbeddedInLui: false
    pattern: ^\d+$
    prefix: oridb.sacch
    uri_format: http://cerevisiae.oridb.org/details.php?id=$1
  prefix: oridb.sacch
oridb.schizo:
  biocontext:
    prefix: ORIDB.SCHIZO
  mappings:
    biocontext: ORIDB.SCHIZO
    miriam: oridb.schizo
    n2t: oridb.schizo
  miriam:
    deprecated: false
    description: OriDB is a database of collated genome-wide mapping studies of confirmed
      and predicted replication origin sites in Saccharomyces cerevisiae and the fission
      yeast Schizosaccharomyces pombe. This collection references Schizosaccharomyces
      pombe.
    homepage: http://pombe.oridb.org/index.php
    id: 00000368
    name: OriDB Schizosaccharomyces
    namespaceEmbeddedInLui: false
    pattern: ^\d+$
    prefix: oridb.schizo
    sampleId: '1'
    uri_format: http://pombe.oridb.org/details.php?id=$1
  n2t:
    description: OriDB is a database of collated genome-wide mapping studies of confirmed
      and predicted replication origin sites in Saccharomyces cerevisiae and the fission
      yeast Schizosaccharomyces pombe. This collection references Schizosaccharomyces
      pombe.
    example: '1'
    homepage: http://pombe.oridb.org/index.php
    name: OriDB Schizosaccharomyces at University of Nottingham
    namespaceEmbeddedInLui: false
    pattern: ^\d+$
    prefix: oridb.schizo
    uri_format: http://pombe.oridb.org/details.php?id=$1
  prefix: oridb.schizo
ornaseq:
  aberowl:
    description: An application ontology designed to annotate next-generation sequencing
      experiments performed on RNA.
    download_owl: http://aber-owl.net/media/ontologies/ORNASEQ/2/ornaseq.owl
    homepage: http://kim.bio.upenn.edu/software/ornaseq.shtml
    name: Ontology of RNA Sequencing
    prefix: ORNASEQ
  bioportal:
    contact:
      email: safisher@upenn.edu
      name: Stephen Fisher
    description: This is an application ontology used to annotate next-generation
      sequencing experiments performed on RNA (RNAseq). It uses terms from BFO, CHEBI,
      CL, GENEPIO, GO, IAO, NCBITaxon, NCIT, OBI, OBIws, OGMS, OMIABIS, SO, TAXRANK,
      and UBERON as well as EFO.
    homepage: http://kim.bio.upenn.edu/software/ornaseq.shtml
    name: Ontology of RNA Sequencing
    prefix: ORNASEQ
  download_obo: http://purl.obolibrary.org/obo/ornaseq.obo
  example: '0000010'
  fairsharing:
    abbreviation: ORNASEQ
    description: The Ontology for RNA Sequencing (ORNASEQ) is an application ontology
      based largely on the Ontology for Biomedical Investigations (OBI), using the
      principles of OBO Foundry. This ontology is designed to annotate single-cell
      next-generation sequencing experiments performed on RNA.
    domains:
    - RNA-seq assay
    homepage: https://kim.bio.upenn.edu/software/ornaseq.shtml
    license: CC-BY-4.0
    name: Ontology of RNA Sequencing
    prefix: FAIRsharing.e6f303
    repository: https://github.com/safisher/ornaseq
    subjects:
    - Transcriptomics
    user_defined_tags:
    - single cell
    - single cell rna-seq
  mappings:
    aberowl: ORNASEQ
    bioportal: ORNASEQ
    fairsharing: FAIRsharing.e6f303
    obofoundry: ornaseq
    ols: ornaseq
    ontobee: ORNASEQ
    wikidata.entity: Q81661765
  obofoundry:
    contact: safisher@upenn.edu
    contact.github: safisher
    contact.label: Stephen Fisher
    contact.orcid: 0000-0001-8034-7685
    deprecated: false
    description: An application ontology designed to annotate next-generation sequencing
      experiments performed on RNA.
    domain: investigations
    download.owl: http://purl.obolibrary.org/obo/ornaseq.owl
    homepage: http://kim.bio.upenn.edu/software/ornaseq.shtml
    license: CC BY 4.0
    license.url: http://creativecommons.org/licenses/by/4.0/
    name: Ontology of RNA Sequencing
    preferredPrefix: ORNASEQ
    prefix: ornaseq
    repository: https://github.com/safisher/ornaseq
  ols:
    description: An application ontology designed to annotate next-generation sequencing
      experiments performed on RNA.
    download_owl: http://purl.obolibrary.org/obo/ornaseq.owl
    homepage: http://kim.bio.upenn.edu/software/ornaseq.shtml
    name: Ontology for RNA sequencing (ORNASEQ)
    prefix: ornaseq
    tracker: https://github.com/safisher/ornaseq/issues
    version: '2019-07-08'
    version.iri: http://purl.obolibrary.org/obo/ornaseq/2019-07-08/ornaseq.owl
  ontobee:
    library: Library
    name: Ontology of RNA Sequencing
    prefix: ORNASEQ
  pattern: ^\d{7}$
  prefix: ornaseq
  uri_format: http://purl.obolibrary.org/obo/ORNASEQ_$1
orpha:
  biocontext:
    prefix: Orphanet
    uri_format: http://www.orpha.net/ORDO/Orphanet_$1
  biolink:
    is_identifiers: false
    is_obo: false
    prefix: orphanet
    uri_format: http://www.orpha.net/ORDO/Orphanet_$1
  contact:
    email: marc.hanauer@inserm.fr
    github: Orphanet
    name: Marc Hanauer
    orcid: 0000-0002-6758-2506
  contributor_extras:
  - email: nicolas.matentzoglu@gmail.com
    github: matentzn
    name: Nicolas Matentzoglu
    orcid: 0000-0002-7356-1779
  download_owl: http://www.orphadata.org/data/ORDO/ordo_orphanet.owl
  fairsharing:
    abbreviation: Orphanet
    description: Orphanet is the reference resource for information on rare diseases
      and orphan drugs for all publics. Its aim is to contribute to the improvement
      of the diagnosis, care and treatment of patients with rare diseases. Orphanet
      maintains the Orphanet nomenclature, essential for interoperability, and the
      Orphanet Rare Disease Ontology (ORDO).
    homepage: http://www.orpha.net/consor/cgi-bin/index.php?lng=EN
    license: CC-BY-4.0
    name: Orphanet
    prefix: FAIRsharing.6bd5k6
    publications:
    - doi: null
      pubmed_id: 19058507
      title: '[Orphanet and the Dutch Steering Committee Orphan Drugs. A European
        and Dutch databank of information on rare diseases].'
    subjects:
    - Life Science
    - Ontology and Terminology
    twitter: orphanet
  homepage: https://www.orpha.net
  integbio:
    description: Orphanet is a portal site for rare diseases and orphan drugs. It
      provides inventory of rare diseases and classification, inventory of orphan
      drugs, clinical trials, etc.
    fairsharing: biodbcore-000497
    homepage: http://www.orpha.net/consor/cgi-bin/Disease_Search_List.php?lng=EN
    information_keywords:
    - Bibliography/Documents
    maintainer: Orphanet
    name: Orphanet
    prefix: nbdc01422
    pubmeds:
    - '12655825'
    status: Active
    target_keywords:
    - Health/Disease
  license: CC-BY-4.0
  logo: https://www.orpha.net/build/images/logo-orphanet.png
  mappings:
    biocontext: Orphanet
    biolink: orphanet
    fairsharing: FAIRsharing.6bd5k6
    integbio: nbdc01422
    miriam: orphanet
    n2t: orphanet
    prefixcommons: orphanet
    uniprot: DB-0068
    wikidata: P1550
    wikidata.entity: Q929833
  miriam:
    deprecated: false
    description: Orphanet is a reference portal for information on rare diseases and
      orphan drugs. It’s aim is to help improve the diagnosis, care and treatment
      of patients with rare diseases.
    homepage: http://www.orpha.net/consor/
    id: '00000220'
    name: Orphanet
    namespaceEmbeddedInLui: false
    pattern: ^\d+$
    prefix: orphanet
    providers:
    - code: ''
      description: Bio2RDF
      homepage: http://bio2rdf.org/
      name: Bio2RDF
      uri_format: http://bio2rdf.org/orphanet:$1
    sampleId: '85163'
    uri_format: http://www.orpha.net/consor/cgi-bin/OC_Exp.php?Lng=EN&Expert=$1
  n2t:
    description: Orphanet is a reference portal for information on rare diseases and
      orphan drugs. It&#x2019;s aim is to help improve the diagnosis, care and treatment
      of patients with rare diseases.
    example: '85163'
    homepage: http://www.orpha.net/consor/
    name: Orphanet at Inserm
    namespaceEmbeddedInLui: false
    pattern: ^\d+$
    prefix: orphanet
    uri_format: http://www.orpha.net/consor/cgi-bin/OC_Exp.php?Lng=EN&Expert=$1
  name: Orphanet
  pattern: ^C?\d+$
  preferred_prefix: ORPHA
  prefix: orpha
  prefixcommons:
    description: Orphanet is a database of information on rare diseases and orphan
      drugs for all publics. Its aim is to contribute to the improvement of the diagnosis,
      care and treatment of patients with rare diseases.
    example: '85163'
    homepage: http://www.orpha.net/consor/cgi-bin/home.php?Lng=GB
    keywords:
    - disease
    - drug
    - human
    license: CC BY-ND 3.0
    name: Orphanet; a database dedicated to information on rare diseases and orphan
      drugs
    pattern: ^\d+$
    prefix: orphanet
    pubmed_ids:
    - '19058507'
    uri_format: http://www.orpha.net/consor/cgi-bin/OC_Exp.php?lng=EN&Expert=$1
  publications:
  - doi: null
    pmc: null
    pubmed: '19058507'
    title: '[Orphanet and the Dutch Steering Committee Orphan Drugs. A European and
      Dutch databank of information on rare diseases]'
    year: 2008
  synonyms:
  - Orphanet
  - orphanet
  uniprot:
    abbreviation: Orphanet
    category: Organism-specific databases
    homepage: https://www.orpha.net
    name: Orphanet; a database dedicated to information on rare diseases and orphan
      drugs
    prefix: DB-0068
    uri_format: https://www.orpha.net/en/disease/detail/$1
  uri_format: http://www.orpha.net/ORDO/Orphanet_$1
  wikidata:
    database: Q929833
    description: identifier in the Orpha.net database (without ORPHA prefix)
    example:
    - '723'
    - '82038'
    homepage: https://www.orpha.net
    name: Orphanet ID
    pattern: ^[1-9]\d{0,5}$
    prefix: P1550
    uri_format: https://www.orpha.net/en/disease/detail/$1
orphanet.ordo:
  aberowl:
    download_owl: http://aber-owl.net/media/ontologies/ordo/1/ordo.owl
    homepage: https://www.ebi.ac.uk/ols/ontologies/ordo
    name: Orphanet Rare Disease Ontology
    prefix: ordo
    version: '2.7'
  banana: Orphanet
  banana_peel: _
  bartoc:
    abbreviation: ORDO
    description: The Orphanet Rare Disease ontology (ORDO) is jointly developed by
      Orphanet and the EBI to provide a structured vocabulary for rare diseases capturing
      relationships between diseases, genes and other relevant features which will
      form a useful resource for the computational analysis of rare diseases. It derived
      from the Orphanet database (www.orpha.net ) , a multilingual database dedicated
      to rare diseases populated from literature and validated by international experts.
      It integrates a nosology (classification of rare diseases), relationships (gene-disease
      relations, epiemological data) and connections with other terminologies (MeSH,
      UMLS, MedDRA),databases (OMIM, UniProtKB, HGNC, ensembl, Reactome, IUPHAR, Geantlas)
      or classifications (ICD10).
    homepage: https://www.orphadata.com/ordo/
    license: CC-BY-4.0
    name: Orphanet Rare Disease Ontology
    prefix: '20698'
  biocontext:
    prefix: ORPHANET.ORDO
  biolink:
    is_identifiers: false
    is_obo: false
    prefix: ORPHA
    uri_format: http://www.orpha.net/ORDO/Orphanet_$1
  bioportal:
    contact:
      email: ordo.orphanet@inserm.fr
      name: Ana Rath
    description: The Orphanet Rare Disease ontology (ORDO) is jointly developed by
      Orphanet and the EBI to provide a structured vocabulary for rare diseases capturing
      relationships between diseases, genes and other relevant features which will
      form a useful resource for the computational analysis of rare diseases. It derived
      from the Orphanet database (www.orpha.net <http://www.orpha.net>) , a multilingual
      database dedicated to rare diseases populated from literature and validated
      by international experts. It integrates a nosology (classification of rare diseases),
      relationships (gene-disease relations, epiemological data) and connections with
      other terminologies (MeSH, SNOMED CT, UMLS, MedDRA),databases (OMIM, UniProtKB,
      HGNC, ensembl, Reactome, IUPHAR, Geantlas) or classifications (ICD10). The ontology
      will be maintained by Orphanet and further populated with new data. Orphanet
      classifications can be browsed in the OLS view. The Orphanet Rare Disease Ontology
      is updated twice a year and follows the OBO guidelines on deprecation of terms.
      It constitutes the official ontology of rare diseases produced and maintained
      by Orphanet (INSERM, US14).
    homepage: https://sciences.orphadata.com/ordo/
    license: CC-BY-4.0
    name: Orphanet Rare Disease Ontology
    prefix: ORDO
    version: '4.7'
  cellosaurus:
    category: Medical resources
    homepage: https://www.orphadata.com/ontologies/
    name: Orphanet Rare Disease Ontology
    prefix: ORDO
    uri_format: https://www.ebi.ac.uk/ols4/ontologies/ordo/classes/http%253A%252F%252Fwww.orpha.net%252FORDO%252F$1
  contact:
    email: marc.hanauer@inserm.fr
    github: Orphanet
    name: Marc Hanauer
    orcid: 0000-0002-6758-2506
  download_owl: http://www.orphadata.org/data/ORDO/ordo_orphanet.owl
  example: C023
  example_extras:
  - '478'
  fairsharing:
    abbreviation: ORDO
    contact:
      email: ordo.orphanet@inserm.fr
      name: Ana Rath
      orcid: 0000-0003-4308-6337
    description: Orphanet Rare Diseases Ontology (ORDO) provide a structured vocabulary
      for rare diseases capturing relationships between diseases, genes and other
      relevant features which will form a useful resource for the computational analysis
      of rare diseases.
    domains:
    - Rare Disorder
    - phenotype
    - disease
    - diagnosis
    - gene
    homepage: https://www.orphadata.com/ordo/
    license: CC-BY-4.0
    name: Orphanet Rare Diseases Ontology
    prefix: FAIRsharing.pbbnwa
    publications:
    - pubmed: '22874158'
      title: 'Rare diseases knowledge management: the contribution of proximity measurements
        in OntoOrpha and OMIM'
      year: 2012
    subjects:
    - Biomedical Science
    - Health Science
  has_canonical: orpha
  homepage: https://www.orpha.net
  license: CC-BY-4.0
  mappings:
    aberowl: ordo
    bartoc: '20698'
    biocontext: ORPHANET.ORDO
    biolink: ORPHA
    bioportal: ORDO
    cellosaurus: ORDO
    fairsharing: FAIRsharing.pbbnwa
    miriam: orphanet.ordo
    n2t: orphanet.ordo
    ols: ordo
  miriam:
    deprecated: false
    description: "The Orphanet Rare Disease ontology (ORDO) is a structured vocabulary\
      \ for rare diseases, capturing relationships between diseases, genes and other\
      \ relevant features which will form a useful resource for the computational\
      \ analysis of rare diseases.\r\nIt integrates a nosology (classification of\
      \ rare diseases), relationships (gene-disease relations, epiemological data)\
      \ and connections with other terminologies (MeSH, UMLS, MedDRA), databases (OMIM,\
      \ UniProtKB, HGNC, ensembl, Reactome, IUPHAR, Geantlas) and classifications\
      \ (ICD10)."
    homepage: https://www.ebi.ac.uk/ols4/ontologies/ordo
    id: '00000532'
    name: Orphanet Rare Disease Ontology
    namespaceEmbeddedInLui: false
    pattern: ^Orphanet(_|:)C?\d+$
    prefix: orphanet.ordo
    sampleId: Orphanet_C022
    uri_format: https://www.ebi.ac.uk/ols4/ontologies/ordo/terms/http%253A%252F%252Fwww.orpha.net%252FORDO%252F$1
  n2t:
    description: The Orphanet Rare Disease ontology (ORDO) is a structured vocabulary
      for rare diseases, capturing relationships between diseases, genes and other
      relevant features which will form a useful resource for the computational analysis
      of rare diseases. It integrates a nosology (classification of rare diseases),
      relationships (gene-disease relations, epiemological data) and connections with
      other terminologies (MeSH, UMLS, MedDRA), databases (OMIM, UniProtKB, HGNC,
      ensembl, Reactome, IUPHAR, Geantlas) and classifications (ICD10).
    example: Orphanet_C023
    homepage: https://www.ebi.ac.uk/ols/ontologies/ordo
    name: ORDO via OLS
    namespaceEmbeddedInLui: false
    pattern: ^Orphanet(_|:)C?\d+$
    prefix: orphanet.ordo
    uri_format: https://www.ebi.ac.uk/ols/ontologies/ordo/terms?short_form=$1
  ols:
    description: The Orphanet Rare Disease ontology (ORDO) is jointly developed by
      Orphanet and the EBI to provide a structured vocabulary for rare diseases capturing
      relationships between diseases, genes and other relevant features which will
      form a useful resource for the computational analysis of rare diseases. It derived
      from the Orphanet database (www.orpha.net ) , a multilingual database dedicated
      to rare diseases populated from literature and validated by international experts.
      It integrates a nosology (classification of rare diseases), relationships (gene-disease
      relations, epiemological data) and connections with other terminologies (MeSH,
      UMLS, MedDRA),databases (OMIM, UniProtKB, HGNC, ensembl, Reactome, IUPHAR, Geantlas)
      or classifications (ICD10).
    download_owl: http://www.orphadata.org/data/ORDO/ordo_orphanet.owl
    name: Orphanet Rare Disease Ontology
    prefix: ordo
    uri_format: http://www.orpha.net/ORDO/Orphanet_$1
    version: '4.7'
    version.iri: https://www.orphadata.com/data/ontologies/ordo/last_version/ORDO_en_4.7.owl
  pattern: ^C?\d+$
  prefix: orphanet.ordo
  providers:
  - code: legacy
    description: This link is no longer live
    example: null
    first_party: null
    homepage: https://www.orpha.net
    name: Legacy Orphanet Expert
    publications: null
    status: null
    uri_format: https://www.orpha.net/consor/cgi-bin/OC_Exp.php?Lng=en&Expert=$1
  publications:
  - doi: null
    pmc: null
    pubmed: '22874158'
    title: 'Rare diseases knowledge management: the contribution of proximity measurements
      in OntoOrpha and OMIM'
    year: 2012
  - doi: null
    pmc: null
    pubmed: '22874158'
    title: 'Rare diseases knowledge management: the contribution of proximity measurements
      in OntoOrpha and OMIM'
    year: 2012
  - doi: null
    pmc: null
    pubmed: '22874158'
    title: 'Rare diseases knowledge management: the contribution of proximity measurements
      in OntoOrpha and OMIM'
    year: 2012
  synonyms:
  - ordo
  uri_format: http://www.orpha.net/ORDO/Orphanet_$1
orth:
  aberowl:
    description: Orthology Ontology
    download_owl: http://aber-owl.net/media/ontologies/ORTH/4/orth.owl
    homepage: https://github.com/qfo/OrthologyOntology
    name: Orthology Ontology
    prefix: ORTH
    version: '2015-11-27'
  bioportal:
    contact:
      email: jfernand@um.es
      name: Jesualdo Tomás Fernández-Breis
    description: Orthology Ontology
    homepage: https://github.com/qfo/OrthologyOntology
    name: Orthology Ontology
    prefix: ORTH
    publications:
    - http://www.jbiomedsem.com/content/7/1/34
    version: '2.0'
  contact:
    email: jfernand@um.es
    github: jesualdotomasfernandezbreis
    name: Jesualdo Tomás Fernández-Breis
    orcid: 0000-0002-7558-2880
  download_owl: https://github.com/qfo/OrthologyOntology/raw/master/orthOntology_RC_v2_A.owl
  example: HomologyRelation
  fairsharing:
    abbreviation: ORTH
    description: ORTH ontology is designed to describe sequence homology data such
      as gene region, gene and protein-centric orthology, paralogy, and xenology information.
      Depending on the database, the homology information is structured in different
      ways. ORTH ontology accommodates these disparate data structures in a single
      terminology.
    domains:
    - protein
    - region
    - gene
    - homologous
    - orthologous
    - paralogous
    homepage: https://github.com/qfo/OrthologyOntology
    license: CC-BY-4.0
    name: Orthology Ontology
    prefix: FAIRsharing.4877h0
    publications:
    - doi: 10.1186/s13326-016-0077-x
      title: 'The Orthology Ontology: development and applications'
      year: 2016
    subjects:
    - Comparative Genomics
  homepage: https://github.com/qfo/OrthologyOntology
  mappings:
    aberowl: ORTH
    bioportal: ORTH
    fairsharing: FAIRsharing.4877h0
    ols: orth
  ols:
    description: 'The need of a common ontology for describing orthology information
      in biological research communities has led to the creation of the Orthology
      Ontology (ORTH). ORTH ontology is designed to describe sequence homology data
      available in multiple orthology databases on the Web (e.g.: OMA, OrthoDB, HieranoiDB,
      and etc.). By sequence homology data, we mostly mean gene region, gene and protein
      centric orthology, paralogy, and xenology information. Depending on the database,
      the homology information is structured in different ways. ORTH ontology accommodates
      these disparate data structures namely Hierarchical Orthologous Group (HOG),
      cluster of homologous sequences and homologous-pairwise relations between sequences.
      In addition to the specific ORTH terms, this specification includes terms of
      the imported ontologies (e.g. Semanticscience Integrated Ontology, SIO) which
      are pertinents to represent the information from various orthology databases
      in a homogeneous way.'
    homepage: http://purl.org/net/orth
    name: Orthology Ontology
    prefix: orth
    uri_format: http://purl.org/net/orth#$1
    version: '2.0'
    version.iri: http://purl.org/net/orth/2.0
  prefix: orth
  publications:
  - doi: 10.1186/s13326-016-0077-x
    pmc: PMC4893294
    pubmed: '27259657'
    title: 'The Orthology Ontology: development and applications'
    year: 2016
  repository: https://github.com/qfo/OrthologyOntology
  uri_format: http://purl.org/net/orth#$1
orthodb:
  biocontext:
    prefix: ORTHODB
  contact:
    email: evgeny.zdobnov@unige.ch
    github: null
    name: Evgeny M Zdobnov
    orcid: 0000-0002-5178-1498
  fairsharing:
    abbreviation: OrthoDB
    description: OrthoDB presents a catalog of eukaryotic orthologous protein-coding
      genes. Orthology refers to the last common ancestor of the species under consideration,
      and thus OrthoDB explicitly delineates orthologs at each radiation along the
      species phylogeny.
    homepage: http://www.orthodb.org/v9/
    license: CC-BY-4.0
    name: Database of Orthologous Groups
    prefix: FAIRsharing.x989d5
    publications:
    - doi: 10.1093/nar/gku1220
      pubmed_id: 25428351
      title: 'OrthoDB v8: update of the hierarchical catalog of orthologs and the
        underlying free software.'
    - doi: 10.1093/nar/gkq930
      pubmed_id: 20972218
      title: 'OrthoDB: the hierarchical catalog of eukaryotic orthologs in 2011.'
    subjects:
    - Life Science
  homepage: https://www.orthodb.org
  mappings:
    biocontext: ORTHODB
    fairsharing: FAIRsharing.x989d5
    miriam: orthodb
    n2t: orthodb
    prefixcommons: orthodb
    uniprot: DB-0143
  miriam:
    deprecated: false
    description: OrthoDB presents a catalog of eukaryotic orthologous protein-coding
      genes across vertebrates, arthropods, and fungi. Orthology refers to the last
      common ancestor of the species under consideration, and thus OrthoDB explicitly
      delineates orthologs at each radiation along the species phylogeny. The database
      of orthologs presents available protein descriptors, together with Gene Ontology
      and InterPro attributes, which serve to provide general descriptive annotations
      of the orthologous groups
    homepage: http://cegg.unige.ch/orthodb4
    id: '00000221'
    name: OrthoDB
    namespaceEmbeddedInLui: false
    pattern: ^\w+$
    prefix: orthodb
    sampleId: Q9P0K8
    uri_format: http://cegg.unige.ch/orthodb/results?searchtext=$1
  n2t:
    description: OrthoDB presents a catalog of eukaryotic orthologous protein-coding
      genes across vertebrates, arthropods, and fungi. Orthology refers to the last
      common ancestor of the species under consideration, and thus OrthoDB explicitly
      delineates orthologs at each radiation along the species phylogeny. The database
      of orthologs presents available protein descriptors, together with Gene Ontology
      and InterPro attributes, which serve to provide general descriptive annotations
      of the orthologous groups
    example: Q9P0K8
    homepage: http://cegg.unige.ch/orthodb4
    name: OrthoDB at Swiss Institute of Bioinformatics
    namespaceEmbeddedInLui: false
    pattern: ^\w+$
    prefix: orthodb
    uri_format: http://cegg.unige.ch/orthodb/results?searchtext=$1
  prefix: orthodb
  prefixcommons:
    description: OrthoDB presents a catalog of eukaryotic orthologous protein-coding
      genes. Orthology refers to the last common ancestor of the species under consideration,
      and thus OrthoDB explicitly delineates orthologs at each radiation along the
      species phylogeny.
    example: EOG9VMFMQ
    homepage: http://cegg.unige.ch/orthodb/browse
    keywords:
    - eukaryotic
    - protein
    - DNA
    name: Database of Orthologous Groups
    pattern: ^EOG[A-Z,0-9]+$
    prefix: orthodb
    pubmed_ids:
    - '20972218'
    uri_format: http://cegg.unige.ch/orthodb3/results?searchtext=$1
  provides: uniprot
  publications:
  - doi: 10.1093/nar/gky1053
    pmc: PMC6323947
    pubmed: '30395283'
    title: 'OrthoDB v10: sampling the diversity of animal, plant, fungal, protist,
      bacterial and viral genomes for evolutionary and functional annotations of orthologs'
    year: 2019
  - doi: 10.1093/nar/gku1220
    pmc: PMC4383991
    pubmed: '25428351'
    title: 'OrthoDB v8: update of the hierarchical catalog of orthologs and the underlying
      free software'
    year: 2014
  - doi: 10.1093/nar/gkq930
    pmc: PMC3013786
    pubmed: '20972218'
    title: 'OrthoDB: the hierarchical catalog of eukaryotic orthologs in 2011'
    year: 2010
  - doi: 10.1093/nar/gku1220
    pmc: null
    pubmed: null
    title: 'OrthoDB v8: update of the hierarchical catalog of orthologs and the underlying
      free software.'
    year: null
  - doi: 10.1093/nar/gkq930
    pmc: null
    pubmed: null
    title: 'OrthoDB: the hierarchical catalog of eukaryotic orthologs in 2011.'
    year: null
  - doi: null
    pmc: null
    pubmed: '20972218'
    title: null
    year: null
  - doi: 10.1093/nar/gkae987
    pmc: null
    pubmed: '39535043'
    title: null
    year: null
  uniprot:
    abbreviation: OrthoDB
    category: Phylogenomic databases
    homepage: https://www.orthodb.org
    name: Database of Orthologous Groups
    prefix: DB-0143
    publications:
    - doi: 10.1093/nar/gkae987
      pubmed: '39535043'
    uri_format: https://www.orthodb.org/?gene=$1
oryzabase.gene:
  biocontext:
    prefix: ORYZABASE.GENE
  mappings:
    biocontext: ORYZABASE.GENE
    miriam: oryzabase.gene
    n2t: oryzabase.gene
  miriam:
    deprecated: false
    description: Oryzabase provides a view of rice (Oryza sativa) as a model monocot
      plant by integrating biological data with molecular genomic information. It
      contains information about rice development and anatomy, rice mutants, and genetic
      resources, especially for wild varieties of rice. Developmental and anatomical
      descriptions include in situ gene expression data serving as stage and tissue
      markers. This collection references gene information.
    homepage: http://www.shigen.nig.ac.jp/rice/oryzabaseV4/
    id: 00000482
    name: Oryzabase Gene
    namespaceEmbeddedInLui: false
    pattern: ^\d+$
    prefix: oryzabase.gene
    sampleId: '117'
    uri_format: http://www.shigen.nig.ac.jp/rice/oryzabaseV4/gene/detail/$1
  n2t:
    description: Oryzabase provides a view of rice (Oryza sativa) as a model monocot
      plant by integrating biological data with molecular genomic information. It
      contains information about rice development and anatomy, rice mutants, and genetic
      resources, especially for wild varieties of rice. Developmental and anatomical
      descriptions include in situ gene expression data serving as stage and tissue
      markers. This collection references gene information.
    example: '117'
    homepage: http://www.shigen.nig.ac.jp/rice/oryzabaseV4/
    name: Oryzabase v4 Gene at National Institute of Genetics (Japan)
    namespaceEmbeddedInLui: false
    pattern: ^\d+$
    prefix: oryzabase.gene
    uri_format: http://www.shigen.nig.ac.jp/rice/oryzabaseV4/gene/detail/$1
  prefix: oryzabase.gene
oryzabase.mutant:
  biocontext:
    prefix: ORYZABASE.MUTANT
  mappings:
    biocontext: ORYZABASE.MUTANT
    miriam: oryzabase.mutant
    n2t: oryzabase.mutant
  miriam:
    deprecated: false
    description: Oryzabase provides a view of rice (Oryza sativa) as a model monocot
      plant by integrating biological data with molecular genomic information. It
      contains information about rice development and anatomy, rice mutants, and genetic
      resources, especially for wild varieties of rice. Developmental and anatomical
      descriptions include in situ gene expression data serving as stage and tissue
      markers. This collection references mutant strain information.
    homepage: http://www.shigen.nig.ac.jp/rice/oryzabaseV4/
    id: 00000483
    name: Oryzabase Mutant
    namespaceEmbeddedInLui: false
    pattern: ^\d+$
    prefix: oryzabase.mutant
    sampleId: '21393'
    uri_format: http://www.shigen.nig.ac.jp/rice/oryzabaseV4/strain/inducedMutationLine/detail/$1
  n2t:
    description: Oryzabase provides a view of rice (Oryza sativa) as a model monocot
      plant by integrating biological data with molecular genomic information. It
      contains information about rice development and anatomy, rice mutants, and genetic
      resources, especially for wild varieties of rice. Developmental and anatomical
      descriptions include in situ gene expression data serving as stage and tissue
      markers. This collection references mutant strain information.
    example: '21393'
    homepage: http://www.shigen.nig.ac.jp/rice/oryzabaseV4/
    name: Oryzabase v4 Mutant at National Institute of Genetics (Japan)
    namespaceEmbeddedInLui: false
    pattern: ^\d+$
    prefix: oryzabase.mutant
    uri_format: http://www.shigen.nig.ac.jp/rice/oryzabaseV4/strain/inducedMutationLine/detail/$1
  prefix: oryzabase.mutant
oryzabase.reference:
  mappings:
    miriam: oryzabase.reference
    n2t: oryzabase.reference
  miriam:
    deprecated: false
    description: The Oryzabase is a comprehensive rice science database established
      in 2000 by rice researcher's committee in Japan.
    homepage: http://www.shigen.nig.ac.jp/rice/oryzabaseV4/
    id: 00000689
    name: Oryzabase
    namespaceEmbeddedInLui: false
    pattern: ^\d+$
    prefix: oryzabase.reference
    sampleId: '42840'
    uri_format: https://shigen.nig.ac.jp/rice/oryzabase/reference/detail/$1
  n2t:
    description: The Oryzabase is a comprehensive rice science database established
      in 2000 by rice researcher's committee in Japan.
    example: '42840'
    homepage: http://www.shigen.nig.ac.jp/rice/oryzabaseV4/
    name: Oryzabase
    namespaceEmbeddedInLui: false
    pattern: ^\d+$
    prefix: oryzabase.reference
    uri_format: https://shigen.nig.ac.jp/rice/oryzabase/reference/detail/$1
  name: Oryzabase Reference
  prefix: oryzabase.reference
oryzabase.stage:
  biocontext:
    prefix: ORYZABASE.STAGE
  mappings:
    biocontext: ORYZABASE.STAGE
    miriam: oryzabase.stage
    n2t: oryzabase.stage
  miriam:
    deprecated: false
    description: Oryzabase provides a view of rice (Oryza sativa) as a model monocot
      plant by integrating biological data with molecular genomic information. It
      contains information about rice development and anatomy, rice mutants, and genetic
      resources, especially for wild varieties of rice. Developmental and anatomical
      descriptions include in situ gene expression data serving as stage and tissue
      markers. This collection references development stage information.
    homepage: http://www.shigen.nig.ac.jp/rice/oryzabaseV4/
    id: 00000485
    name: Oryzabase Stage
    namespaceEmbeddedInLui: false
    pattern: ^\d+$
    prefix: oryzabase.stage
    sampleId: '34'
    uri_format: http://www.shigen.nig.ac.jp/rice/oryzabaseV4/devstageineachorgan/detail/$1
  n2t:
    description: Oryzabase provides a view of rice (Oryza sativa) as a model monocot
      plant by integrating biological data with molecular genomic information. It
      contains information about rice development and anatomy, rice mutants, and genetic
      resources, especially for wild varieties of rice. Developmental and anatomical
      descriptions include in situ gene expression data serving as stage and tissue
      markers. This collection references development stage information.
    example: '34'
    homepage: http://www.shigen.nig.ac.jp/rice/oryzabaseV4/
    name: Oryzabase v4 Stage at National Institute of Genetics (Japan)
    namespaceEmbeddedInLui: false
    pattern: ^\d+$
    prefix: oryzabase.stage
    uri_format: http://www.shigen.nig.ac.jp/rice/oryzabaseV4/devstageineachorgan/detail/$1
  prefix: oryzabase.stage
oryzabase.strain:
  biocontext:
    prefix: ORYZABASE.STRAIN
  mappings:
    biocontext: ORYZABASE.STRAIN
    miriam: oryzabase.strain
    n2t: oryzabase.strain
  miriam:
    deprecated: false
    description: Oryzabase provides a view of rice (Oryza sativa) as a model monocot
      plant by integrating biological data with molecular genomic information. It
      contains information about rice development and anatomy, rice mutants, and genetic
      resources, especially for wild varieties of rice. Developmental and anatomical
      descriptions include in situ gene expression data serving as stage and tissue
      markers. This collection references wild strain information.
    homepage: http://www.shigen.nig.ac.jp/rice/oryzabaseV4/
    id: 00000484
    name: Oryzabase Strain
    namespaceEmbeddedInLui: false
    pattern: ^\d+$
    prefix: oryzabase.strain
    sampleId: '1'
    uri_format: http://www.shigen.nig.ac.jp/rice/oryzabaseV4/strain/wildCore/detail/$1
  n2t:
    description: Oryzabase provides a view of rice (Oryza sativa) as a model monocot
      plant by integrating biological data with molecular genomic information. It
      contains information about rice development and anatomy, rice mutants, and genetic
      resources, especially for wild varieties of rice. Developmental and anatomical
      descriptions include in situ gene expression data serving as stage and tissue
      markers. This collection references wild strain information.
    example: '1'
    homepage: http://www.shigen.nig.ac.jp/rice/oryzabaseV4/
    name: Oryzabase v4 Strain at National Institute of Genetics (Japan)
    namespaceEmbeddedInLui: false
    pattern: ^\d+$
    prefix: oryzabase.strain
    uri_format: http://www.shigen.nig.ac.jp/rice/oryzabaseV4/strain/wildCore/detail/$1
  prefix: oryzabase.strain
osf:
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  homepage: https://osf.io
  keywords:
  - author
  - paper
  - person
  - researcher
  - work
  mappings:
    wikidata: P7238
  prefix: osf
  references:
  - https://github.com/biopragmatics/bioregistry/pull/1171
  wikidata:
    description: ID in osf.io
    example:
    - 2u4tf
    - e9tg8
    - wx9bf
    name: Open Science Framework ID
    pattern: ^[a-z0-9]{5}$
    prefix: P7238
    uri_format: https://osf.io/$1
oslc:
  contact:
    email: jamsden@us.ibm.com
    github: null
    name: Jim Amsden
    orcid: null
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: Core Vocabulary defines the OSLC Core RDF vocabulary terms and resources,
    that have broad applicability across various domains.
  example: Property
  homepage: http://open-services.net/ns/core
  lov:
    description: The Open Services for Lifecycle Collaboration (OSLC) initiative is
      creating a family of web services specifications for products, services and
      other tools that support all phases of the software and product lifecycle. This
      OSLC Core Specification sets out the common features that every OSLC Service
      can be expected to support
    homepage: http://open-services.net/bin/view/Main/OslcCoreSpecification
    keywords:
    - PLM
    modified: '2014-05-23'
    name: OSLC Core Vocabulary
    prefix: oslc
    uri_prefix: http://open-services.net/ns/core#$1
  mappings:
    lov: oslc
  name: OASIS Open Services for Lifecycle Collaboration Core Vocabulary
  preferred_prefix: oslc
  prefix: oslc
  uri_format: http://open-services.net/ns/core#$1
osti.article:
  comment: Corresponding GitHub linked to software registrations is located at https://github.com/doecode.
    All related contact information can be found here https://www.osti.gov/contact
  contributor:
    email: Lindsey.Anderson@pnnl.gov
    github: lnanderson
    name: Lindsey N. Anderson
    orcid: 0000-0002-8741-7823
  description: 'The U.S. Department of Energy (DOE) Office of Scientific and Technical
    Information (OSTI) is the main metadata archive for permanent storage of registered
    [DOE DOI products](https://www.osti.gov/pids/doi-services/doe-data-id-service)
    (datasets, code, articles, patents, multimedia, etc.). When a DOI is minted a
    unique OSTI identifier for each record [{osti_id}](https://www.osti.gov/api/v1/docs#endpoints-singlerecord)
    is provided as the suffix in the DOI schema ([{site-specific-prefix}/{user-supplied-doi-infix}/{osti_id}](https://www.osti.gov/pids/doi-services))
    and can be alternatively used as the main product identifier endpoint when [searching
    OSTI.GOV](https://www.osti.gov/search-tools) registry archive (see example below).
    OSTI.GOV is the primary registry and search tool for all Department of Energy
    (DOE) funded science, technology, and engineering research and development (R&D)
    results and the organizational hub for information about the DOE Office of Scientific
    and Technical Information (OSTI. **Data Product Type Example:** - https://www.osti.gov/biblio/1668761
    - https://www.osti.gov/search/semantic:1668761 - https://www.osti.gov/dataexplorer/biblio/dataset/1668761
    - https://www.osti.gov/api/v1/records/1668761 - https://doi.org/10.11578/1668761
    **Other Core Product Registry Examples:** - Journal Articles: https://www.osti.gov/pages/biblio
    - Datasets: https://www.osti.gov/dataexplorer/biblio/dataset/ - Software: https://www.osti.gov/doecode/biblio/
    - Patents: https://www.osti.gov/doepatents/biblio/ - Multimedia: https://www.osti.gov/sciencecinema/biblio/'
  example: '1668761'
  github_request_issue: 1050
  homepage: https://www.osti.gov/
  keywords:
  - article
  - articles
  - publication
  - publications
  license: https://www.osti.gov/disclaim
  mappings:
    wikidata: P3894
  name: Office of Scientific and Technical Information (OSTI)
  pattern: ^\d+$
  prefix: osti.article
  references:
  - https://www.energy.gov/doe-public-access-plan
  reviewer:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  uri_format: https://www.osti.gov/biblio/$1
  wikidata:
    description: identifier of a scientific article at Office of Scientific and Technical
      Information
    example:
    - '1121958'
    - '1271300'
    - '6071133'
    name: OSTI article ID
    pattern: ^\d+$
    prefix: P3894
    uri_format: https://www.osti.gov/biblio/$1
otl:
  biocontext:
    prefix: OTL
  contact:
    email: guiderdoni@cirad.fr
    github: null
    name: Emmanuel Guiderdoni
    orcid: 0000-0003-2760-2864
  fairsharing:
    abbreviation: OTL
    description: Oryza Tag Line consists in a searchable database developed under
      the Oracle management system integrating phenotypic data resulting from the
      evaluation of the Genoplante rice insertion line library.
    homepage: http://oryzatagline.cirad.fr/
    name: Oryza Tag Line
    prefix: FAIRsharing.61c2x6
    publications:
    - doi: '17947330'
      pubmed_id: 17947330
      title: Oryza Tag Line, a phenotypic mutant database for the Genoplante rice
        insertion line library.
    subjects:
    - Life Science
  mappings:
    biocontext: OTL
    fairsharing: FAIRsharing.61c2x6
    miriam: otl
    n2t: otl
    prefixcommons: otl
  miriam:
    deprecated: false
    description: Oryza Tag Line is a database that was developed to collect information
      generated from the characterization of rice (Oryza sativa L cv. Nipponbare)
      insertion lines resulting in potential gene disruptions. It collates morpho-physiological
      alterations observed during field evaluation, with each insertion line documented
      through a generic passport data including production records, seed stocks and
      FST information.
    homepage: http://oryzatagline.cirad.fr/
    id: 00000486
    name: Oryza Tag Line
    namespaceEmbeddedInLui: false
    pattern: ^A[A-Z]+\d+$
    prefix: otl
    sampleId: AADB12
    uri_format: http://oryzatagline.cirad.fr/cgi-bin/general_mutant.pl?line=$1
  n2t:
    description: Oryza Tag Line is a database that was developed to collect information
      generated from the characterization of rice (Oryza sativa L cv. Nipponbare)
      insertion lines resulting in potential gene disruptions. It collates morpho-physiological
      alterations observed during field evaluation, with each insertion line documented
      through a generic passport data including production records, seed stocks and
      FST information.
    example: AADB12
    homepage: http://oryzatagline.cirad.fr/
    name: Oryza Tag Line at CIRAD-INRA-SUPAGRO-UMI
    namespaceEmbeddedInLui: false
    pattern: ^A[A-Z]+\d+$
    prefix: otl
    uri_format: http://oryzatagline.cirad.fr/cgi-bin/general_mutant.pl?line=$1
  prefix: otl
  prefixcommons:
    description: Oryza Tag Line consists in a searchable database developed under
      the Oracle management system integrating phenotypic data resulting from the
      evaluation of the Génoplante rice insertion line library.
    example: AGFC04
    homepage: http://urgi.versailles.inra.fr/OryzaTagLine/
    keywords:
    - DNA
    name: 'Oryza Tag Line: An integrated database for the functional analysis of the
      rice genome'
    pattern: ^A[A-Z]+\d+$
    prefix: otl
    uri_format: http://urgi.versailles.inra.fr/OryzaTagLine/cgi-bin/general_mutant.pl?line=$1
  publications:
  - doi: 10.1093/nar/gkm762
    pmc: PMC2238859
    pubmed: '17947330'
    title: Oryza Tag Line, a phenotypic mutant database for the Genoplante rice insertion
      line library
    year: 2007
  - doi: '17947330'
    pmc: null
    pubmed: null
    title: Oryza Tag Line, a phenotypic mutant database for the Genoplante rice insertion
      line library.
    year: null
otol:
  contributor:
    email: meghan.balk@gmail.com
    github: megbalk
    name: Meghan Balk
    orcid: 0000-0003-2699-3066
  description: Identifier for an entity in open tree of life
  example: '3905431'
  github_request_issue: 470
  homepage: https://tree.opentreeoflife.org
  mappings:
    wikidata: P9157
    wikidata.entity: Q22661281
  name: Open Tree of Life
  pattern: ^[1-9]\d*$
  prefix: otol
  reviewer:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  uri_format: https://tree.opentreeoflife.org/taxonomy/browse?id=$1
  wikidata:
    database: Q22661281
    description: identifier for an entity in Open Tree of Life, a comprehensive, dynamic
      and digitally-available tree of life by synthesizing published phylogenetic
      trees along with taxonomic data
    example:
    - '259588'
    - '309263'
    - '3905431'
    homepage: https://tree.opentreeoflife.org/opentree
    name: Open Tree of Life ID
    pattern: ^[1-9]\d*$
    prefix: P9157
    uri_format: https://tree.opentreeoflife.org/taxonomy/browse?id=$1
ovae:
  aberowl:
    description: A biomedical ontology in the domain of vaccine adverse events.
    download_owl: http://aber-owl.net/media/ontologies/OVAE/11/ovae.owl
    homepage: http://www.violinet.org/ovae/
    name: Ontology of Vaccine Adverse Events
    prefix: OVAE
  biocontext:
    prefix: OVAE
  bioportal:
    contact:
      email: yongqunh@med.umich.edu
      name: Oliver He
    description: The Ontology of Vaccine Adverse Events (OVAE) is a biomedical ontology
      in the area of vaccine adverse events. OVAE is an extension of the Ontology
      of Adverse Events (OAE) and the Vaccine Ontology (VO). OVAE is aimed to represent
      and analyze various vaccine-specific adverse events.
    homepage: http://www.violinet.org/ovae
    name: Ontology of Vaccine Adverse Events
    prefix: OVAE
    version: 'Vision Release: 1.0.34'
  example: 0000609
  fairsharing:
    abbreviation: OVAE
    contact:
      email: yongqunh@med.umich.edu
      name: Yongqunh He
      orcid: 0000-0001-9189-9661
    description: The Ontology of Vaccine Adverse Events (OVAE) is a biomedical ontology
      in the area of vaccine adverse events. While they are extremely useful in decreasing
      infection prevalence in human populations, vaccines may also induce some unintended
      adverse events. As vaccine usage increases, the risk of adverse events proportionally
      increases. To protect public health, it is necessary to represent, study, and
      analyze various vaccine adverse events (VAES). Two existing ontologies are closely
      related to the VAE studies. The Ontology of Adverse Events (OAE) is a community-based
      biomedical ontology in the area of adverse events. The Vaccine Ontology (VO)
      represents various vaccines, vaccine components, and vaccinations. Both OAE
      and VO are OBO Foundry candidate ontologies and are developed by following the
      OBO Foundry principles.    To better represent various VAEs and support vaccine
      safety study, we developed the Ontology of Vaccine Adverse Events (OVAE) as
      an extension of the biomedical ontologies OAE and VO.
    domains:
    - Adverse Reaction
    - vaccine
    homepage: https://github.com/OVAE-Ontology/ovae
    license: Apache 2.0 License
    name: Ontology of Vaccine Adverse Events
    prefix: FAIRsharing.w4x6n4
    publications:
    - doi: 10.1186/2041-1480-4-40
      pubmed: '24279920'
      title: The Ontology of Vaccine Adverse Events (OVAE) and its usage in representing
        and analyzing adverse events associated with US-licensed human vaccines
      year: 2013
    subjects:
    - Biomedical Science
  mappings:
    aberowl: OVAE
    biocontext: OVAE
    bioportal: OVAE
    fairsharing: FAIRsharing.w4x6n4
    obofoundry: ovae
    ols: ovae
    ontobee: OVAE
    wikidata.entity: Q55118555
  obofoundry:
    contact: yongqunh@med.umich.edu
    contact.github: yongqunh
    contact.label: Yongqunh He
    contact.orcid: 0000-0001-9189-9661
    deprecated: false
    description: A biomedical ontology in the domain of vaccine adverse events.
    domain: health
    download.owl: http://purl.obolibrary.org/obo/ovae.owl
    homepage: http://www.violinet.org/ovae/
    license: CC BY 3.0
    license.url: http://creativecommons.org/licenses/by/3.0/
    name: Ontology of Vaccine Adverse Events
    preferredPrefix: OVAE
    prefix: ovae
    repository: https://github.com/OVAE-Ontology/ovae
  ols:
    description: OVAE is a biomedical ontology in the area of vaccine adverse events.
      OVAE is an extension of the community-based Ontology of Adverse Events (OAE).
    download_owl: http://purl.obolibrary.org/obo/ovae.owl
    homepage: http://www.violinet.org/ovae/
    name: 'OVAE: Ontology of Vaccine Adverse Events'
    prefix: ovae
    tracker: https://github.com/OVAE-Ontology/ovae/issues
    version: 1.0.34
  ontobee:
    library: Library
    name: Ontology of Vaccine Adverse Events
    prefix: OVAE
  pattern: ^\d{7}$
  prefix: ovae
  publications:
  - doi: 10.1186/2041-1480-4-40
    pmc: PMC4177204
    pubmed: '24279920'
    title: The Ontology of Vaccine Adverse Events (OVAE) and its usage in representing
      and analyzing adverse events associated with US-licensed human vaccines
    year: 2013
  uri_format: http://purl.obolibrary.org/obo/OVAE_$1
owl:
  biocontext:
    prefix: owl
    uri_format: http://www.w3.org/2002/07/owl#$1
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: Overview of the Web Ontology Language (OWL) which provides an introduction
    to OWL by informally describing the features of each of the sublanguages.
  download_owl: https://triplydb.com/w3c/owl/download.trig.gz
  example: Ontology
  fairsharing:
    abbreviation: OWL
    contact:
      email: rmrich5@gmail.com
      name: Rafael Richards
      orcid: 0000-0001-5699-0515
    description: The Web Ontology Language (OWL) is a family of knowledge representation
      languages or ontology languages for authoring ontologies or knowledge bases.
      The languages are characterized by formal semantics and RDF/XML-based serializations
      for the Semantic Web. OWL is endorsed by the World Wide Web Consortium (W3C)
      and has attracted academic, medical and commercial interest. The OWL 2 Web Ontology
      Language, informally OWL 2, is an ontology language for the Semantic Web with
      formally defined meaning. OWL 2 ontologies provide classes, properties, individuals,
      and data values and are stored as Semantic Web documents. OWL 2 ontologies can
      be used along with information written in RDF, and OWL 2 ontologies themselves
      are primarily exchanged as RDF documents.
    homepage: http://www.w3.org/TR/owl-overview/
    name: Web Ontology Language
    prefix: FAIRsharing.atygwy
    publications: []
    subjects:
    - Informatics
    - Computer Science
    - Subject Agnostic
    - Ontology and Terminology
  homepage: https://www.w3.org/TR/owl-features/
  integbio:
    description: 'OWL Version 31.1 is a database comprised of the results of a comparative
      study of 4 sources of sequence information.

      These sources are SWISS-PROT, PIR, GenBank and NRL-3D.

      Redundancies of sequences have been avoided at all cost, even by eliminating
      sequences that display trivial differences from other sequences that are already
      present.

      OWL is therefore a comparatively small repository, simplifying the process of
      similarity checks.

      This version of the repository contains 279,796 entries and 89,624,288 residues.

      The database can be searched by means of entering an accession number, a database
      code, a sequence or by making use of the provided keyword search option.'
    homepage: http://www.bioinf.manchester.ac.uk/dbbrowser/OWL/index.php
    information_keywords:
    - Sequence
    maintainer: University of Manchester Bioinformatics Education and Research
    name: OWL
    prefix: nbdc00307
    status: Active
    target_keywords:
    - Protein
  lov:
    description: This ontology partially describes the built-in classes and   properties
      that together form the basis of the RDF/XML syntax of OWL 2.
    homepage: http://www.w3.org/TR/owl2-rdf-based-semantics/
    keywords:
    - W3C Rec
    modified: '2009-11-15'
    name: The OWL 2 Schema vocabulary
    prefix: owl
    uri_prefix: http://www.w3.org/2002/07/owl#$1
  mappings:
    biocontext: owl
    fairsharing: FAIRsharing.atygwy
    integbio: nbdc00307
    lov: owl
    ols: owl
    zazuko: owl
  name: Web Ontology Language
  ols:
    name: The OWL 2 Schema vocabulary (OWL 2)
    prefix: owl
    uri_format: http://www.w3.org/2002/07/owl#$1
    version: '$Date: 2009/11/15 10:54:12 $'
    version.iri: http://www.w3.org/2002/07/owl
  preferred_prefix: owl
  prefix: owl
  uri_format: http://www.w3.org/2002/07/owl#$1
  zazuko:
    prefix: owl
    uri_format: http://www.w3.org/2002/07/owl#$1
owlstar:
  biolink:
    is_identifiers: false
    is_obo: false
    prefix: os
    uri_format: https://github.com/cmungall/owlstar/blob/master/owlstar.ttl$1
  contact:
    email: cjmungall@lbl.gov
    github: cmungall
    name: Chris Mungall
    orcid: 0000-0002-6601-2165
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: This proposed vocabulary allows edges in Property Graphs (e.g Neo4j,
    RDF*) to be augmented with edge properties that specify ontological semantics,
    including (but not limited) to OWL-DL interpretations. [from GitHub]
  download_rdf: https://github.com/linkml/owlstar/raw/master/owlstar.ttl
  example: AllSomeInterpretation
  homepage: https://linkml.io/owlstar/
  license: CC0-1.0
  mappings:
    biolink: os
  name: Ontological Interpretations for Web Property Graphs
  pattern: ^\w+$
  prefix: owlstar
  repository: https://github.com/linkml/owlstar
  uri_format: http://w3id.org/owlstar/$1
p3db.protein:
  biocontext:
    prefix: P3DB.PROTEIN
  mappings:
    biocontext: P3DB.PROTEIN
    miriam: p3db.protein
    n2t: p3db.protein
    prefixcommons: p3db
  miriam:
    deprecated: false
    description: Plant Protein Phosphorylation DataBase (P3DB) is a database that
      provides information on experimentally determined phosphorylation sites in the
      proteins of various plant species. This collection references plant proteins
      that contain phosphorylation sites.
    homepage: http://www.p3db.org/
    id: '00000501'
    name: P3DB Protein
    namespaceEmbeddedInLui: false
    pattern: ^\d+$
    prefix: p3db.protein
    sampleId: '70'
    uri_format: http://www.p3db.org/protein.php?id=$1&amp;ref=0
  n2t:
    description: Plant Protein Phosphorylation DataBase (P3DB) is a database that
      provides information on experimentally determined phosphorylation sites in the
      proteins of various plant species. This collection references plant proteins
      that contain phosphorylation sites.
    example: '70'
    homepage: http://www.p3db.org/
    name: P3DB Protein at University of Missouri
    namespaceEmbeddedInLui: false
    pattern: ^\d+$
    prefix: p3db.protein
    uri_format: http://www.p3db.org/protein.php?id=$1&amp;ref=0
  prefix: p3db.protein
  prefixcommons:
    description: P3DB was established with an overall objective to provide a resource
      of protein phosphorylation data from multiple plants. P3DB uses MySQL database
      to store phosphorylation data.
    example: '6401'
    homepage: http://www.p3db.org
    keywords:
    - protein
    - small molecule
    name: Plant Protein Phosphorylation Database
    pattern: ^\d+$
    prefix: p3db
    uri_format: http://digbio.missouri.edu/p3db/data/protein.php?id=$1
p3db.site:
  biocontext:
    prefix: P3DB.SITE
  mappings:
    biocontext: P3DB.SITE
    miriam: p3db.site
    n2t: p3db.site
  miriam:
    deprecated: false
    description: Plant Protein Phosphorylation DataBase (P3DB) is a database that
      provides information on experimentally determined phosphorylation sites in the
      proteins of various plant species. This collection references phosphorylation
      sites in proteins.
    homepage: http://www.p3db.org/
    id: '00000502'
    name: P3DB Site
    namespaceEmbeddedInLui: false
    pattern: ^\d+$
    prefix: p3db.site
    sampleId: '65'
    uri_format: http://www.p3db.org/phosphosite.php?id=$1&ref=0
  n2t:
    description: Plant Protein Phosphorylation DataBase (P3DB) is a database that
      provides information on experimentally determined phosphorylation sites in the
      proteins of various plant species. This collection references phosphorylation
      sites in proteins.
    example: '65'
    homepage: http://www.p3db.org/
    name: P3DB Site at University of Missouri
    namespaceEmbeddedInLui: false
    pattern: ^\d+$
    prefix: p3db.site
    uri_format: http://www.p3db.org/phosphosite.php?id=$1&ref=0
  prefix: p3db.site
packagist:
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: A repository of software packages written in PHP.
  example: florianv/swap
  homepage: https://packagist.org
  name: Packagist
  prefix: packagist
  uri_format: https://packagist.org/packages/$1
pactr:
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: The Pan African Clinical Trials Registry (PACTR) is a regional register
    of clinical trials conducted in Africa. The registry is an African initiative
    serving the needs of Africans. It provides an open-access platform where clinical
    trials can be registered free of charge. The PACTR aims to increase clinical trial
    registration in Africa by developing awareness of the need to register trials
    and supporting trialists during registration. (from homepage)
  example: PACTR202304525632216
  homepage: https://pactr.samrc.ac.za/
  logo: https://pactr.samrc.ac.za/images/Banner_Split.jpg
  name: Pan African Clinical Trials Registry
  pattern: ^PACTR\d+$
  prefix: pactr
  references:
  - https://pactr.samrc.ac.za/TrialDisplay.aspx?TrialID=25488
paleodb:
  biocontext:
    prefix: PALEODB
  mappings:
    biocontext: PALEODB
    miriam: paleodb
    n2t: paleodb
    prefixcommons: paleodb
  miriam:
    deprecated: false
    description: The Paleobiology Database seeks to provide researchers and the public
      with information about the entire fossil record. It stores global, collection-based
      occurrence and taxonomic data for marine and terrestrial animals and plants
      of any geological age, as well as web-based software for statistical analysis
      of the data.
    homepage: http://paleodb.org/
    id: 00000197
    name: PaleoDB
    namespaceEmbeddedInLui: false
    pattern: ^\d+$
    prefix: paleodb
    sampleId: '83088'
    uri_format: http://fossilworks.org/?a=taxonInfo&taxon_no=$1
  n2t:
    description: The Paleobiology Database seeks to provide researchers and the public
      with information about the entire fossil record. It stores global, collection-based
      occurrence and taxonomic data for marine and terrestrial animals and plants
      of any geological age, as well as web-based software for statistical analysis
      of the data.
    example: '83088'
    homepage: http://paleodb.org/
    name: PaleoDB at Macquarie University
    namespaceEmbeddedInLui: false
    pattern: ^\d+$
    prefix: paleodb
    uri_format: http://fossilworks.org/?a=taxonInfo&taxon_no=$1
  name: Paleobiology Database
  prefix: paleodb
  prefixcommons:
    description: The Paleobiology Database seeks to provide researchers and the public
      with information about the entire fossil record. It stores global, collection-based
      occurrence and taxonomic data for marine and terrestrial animals and plants
      of any geological age, as well as web-based software for statistical analysis
      of the data.
    example: '83088'
    keywords:
    - taxonomy
    name: Paleobiology Database
    pattern: ^\d+$
    prefix: paleodb
    uri_format: http://paleodb.geology.wisc.edu/cgi-bin/bridge.pl?a=basicTaxonInfo&taxon_no=$1
pandit:
  integbio:
    alt_name: Protein and Associated Nucleotide Domains with Inferred Trees
    description: PANDIT is a database of protein domain conservation and relationship
      information. The database contains phylogenic trees of proteins indicating the
      degree of similarity between domains of evolutionarily related proteins represented
      in the Pfam database. Raw data for all phylogenies can be downloaded.
    homepage: http://www.ebi.ac.uk/research/goldman/software/pandit
    information_keywords:
    - Sequence
    - Classification
    maintainer: EMBL-EBI (European Bioinformatics Institute)
    name: PANDIT
    prefix: nbdc00607
    pubmeds:
    - '16381879'
    status: Active
    target_keywords:
    - Protein
  mappings:
    integbio: nbdc00607
    prefixcommons: pandit
    re3data: r3d100011232
  prefix: pandit
  prefixcommons:
    description: PANDIT is a collection of multiple sequence alignments and phylogenetic
      trees covering many common protein domains.
    example: PF00004
    homepage: http://www.ebi.ac.uk/goldman-srv/pandit
    keywords:
    - DNA
    - protein
    - structure
    name: Protein and Associated NucleotideDomains with Inferred Trees
    pattern: ^PF\d+$
    prefix: pandit
    uri_format: http://www.ebi.ac.uk/goldman-srv/pandit/pandit.cgi?action=browse&fam=$1
  provides: pfam
  re3data:
    description: <<<!!!<<< Efforts to obtain renewed funding after 2008 were unfortunately
      not successful.  PANDIT has therefore been frozen since November 2008, and its
      data are not updated since September 2005 when version 17.0 was released (corresponding
      to Pfam 17.0).  The existing data and website remain available from these pages,
      and should remain stable and, we hope, useful. >>>!!!>>> PANDIT is a collection
      of multiple sequence alignments and phylogenetic trees. It contains corresponding
      amino acid and nucleotide sequence alignments, with trees inferred from each
      alignment. PANDIT is based on the Pfam database (Protein families database of
      alignments and HMMs), and includes the seed amino acid alignments of most families
      in the Pfam-A database. DNA sequences for as many members of each family as
      possible are extracted from the EMBL Nucleotide Sequence Database and aligned
      according to the amino acid alignment. PANDIT also contains a further copy of
      the amino acid alignments, restricted to the sequences for which DNA sequences
      were found.
    doi: 10.17616/R3X63C
    homepage: https://www.ebi.ac.uk/research/goldman/software/pandit
    license: other
    name: PANDIT
    prefix: r3d100011232
    synonyms:
    - Protein and Associated Nucleotide Domains with Inferred Trees
    xrefs:
      nif: 0000-03241
  reviewer:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
panet:
  aberowl:
    description: The PaNET ontology provides a taxonomy and thesaurus of photon and
      neutron (PaN) experimental techniques, based mainly on accelerator-based light
      sources and neutron facilities. The primary use of the ontology is to enhance
      the FAIRness of PaN data catalogues services. The ontology defines specific
      techniques in terms of more general technique classes and provides synonyms
      and references.
    download_owl: http://aber-owl.net/media/ontologies/PANET/27/panet.owl
    name: PaN Experimental technique
    prefix: PANET
    version: 1.3.0
  bioportal:
    contact:
      email: mriyayi@hotmail.com
      name: Daniel Iyayi
    description: The PaNET ontology provides a taxonomy and thesaurus of photon and
      neutron (PaN) experimental techniques, based mainly on accelerator-based light
      sources and neutron facilities. The primary use of the ontology is to enhance
      the FAIRness of PaN data catalogues services. The ontology defines specific
      techniques in terms of more general technique classes and provides synonyms
      and references.
    license: CC-BY-4.0
    name: PaN Experimental technique
    prefix: PANET
    publications:
    - https://doi.org/10.5281/zenodo.4806026
    version: 1.3.0
  example: '00001'
  fairsharing:
    abbreviation: PaNET
    description: The ExPaNDS Photon and Neutron Experimental Techniques (PaNET) ontology
      provides a taxonomy and thesaurus of photon and neutron (PaN) experimental techniques.
      Based mainly on accelerator-based light sources and neutron facilities, the
      primary use of the ontology is to enhance the FAIRness of PaN data catalogues
      services. The ontology defines specific techniques in terms of more general
      technique classes and provides synonyms and references.
    domains:
    - Experimental measurement
    - Imaging
    - X-ray diffraction
    homepage: https://github.com/ExPaNDS-eu/ExPaNDS-experimental-techniques-ontology
    license: CC-BY-4.0
    name: ExPaNDS Photon and Neutron Experimental Techniques Ontology
    prefix: FAIRsharing.a08d34
    publications:
    - doi: 10.5281/zenodo.4806026
      title: ExPaNDS ontologies v1.0
      year: 2021
    subjects:
    - Physics
    user_defined_tags:
    - Neutron Science
    - photon science
  mappings:
    aberowl: PANET
    bioportal: PANET
    fairsharing: FAIRsharing.a08d34
    tib: panet
  prefix: panet
  tib:
    description: The PaNET ontology provides a taxonomy and thesaurus of photon and
      neutron (PaN) experimental techniques, based mainly on accelerator-based light
      sources and neutron facilities. The primary use of the ontology is to enhance
      the FAIRness of PaN data catalogues services. The ontology defines specific
      techniques in terms of more general technique classes and provides synonyms
      and references.
    download_owl: http://purl.org/pan-science/PaNET/PaNET.owl
    homepage: https://expands-eu.github.io/ExPaNDS-experimental-techniques-ontology/index-en.html
    keywords:
    - NFDI4ING
    - physics
    name: The Photon and Neutron Experimental Techniques Ontology
    prefix: panet
    uri_format: http://purl.org/pan-science/PaNET/PaNET$1
  uri_format: http://purl.org/pan-science/PaNET/PaNET$1
panorama:
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: Panorama is a freely-available, open-source repository server application
    for targeted mass spectrometry assays that integrates into a Skyline mass spec
    workflow. It makes links to the Proteomics Exchange when possible.
  example: FxnI151FMs
  fairsharing:
    abbreviation: Panorama Public
    contact:
      email: brendanx@uw.edu
      name: Brendan MacLean
      orcid: 0000-0002-9575-0255
    description: Panorama Public is a data repository for sharing and disseminating
      results from analyzing mass spectrometry data with the Skyline software. Skyline
      supports targeted analysis of proteomics or metabolomics data from a variety
      of mass spectrometry data acquisition techniques. As a member of the ProteomeXchange
      Consortium, Panorama Public can assign ProteomeXchange accessions to submitted
      proteomics datasets.
    homepage: https://panoramaweb.org
    license: https://www.washington.edu/online/terms
    name: Panorama Public
    prefix: FAIRsharing.uBpQ1q
    publications:
    - doi: 10.1074/mcp.RA117.000543
      pubmed_id: 29487113
      title: 'Panorama Public: A Public Repository for Quantitative Data Sets Processed
        in Skyline.'
    - doi: 10.1021/pr5006636
      pubmed_id: 25102069
      title: 'Panorama: a targeted proteomics knowledge base.'
    subjects:
    - Proteomics
    - Life Science
    - Metabolomics
  homepage: https://panoramaweb.org
  mappings:
    fairsharing: FAIRsharing.uBpQ1q
  name: Panorama Public
  prefix: panorama
  publications:
  - doi: 10.1074/mcp.ra117.000543
    pmc: PMC5986241
    pubmed: '29487113'
    title: 'Panorama Public: A Public Repository for Quantitative Data Sets Processed
      in Skyline'
    year: 2018
  - doi: 10.1021/pr5006636
    pmc: PMC4156235
    pubmed: '25102069'
    title: 'Panorama: a targeted proteomics knowledge base'
    year: 2014
  uri_format: https://panoramaweb.org/$1.url
panther.family:
  biocontext:
    prefix: PANTHER.FAMILY
  biolink:
    is_identifiers: false
    is_obo: false
    prefix: PANTHER.FAMILY
    uri_format: http://www.pantherdb.org/panther/family.do?clsAccession=$1
  contact:
    email: pdthomas@usc.edu
    github: null
    name: Paul D Thomas
    orcid: 0000-0002-9074-3507
  go:
    homepage: https://www.pantherdb.org/
    name: Protein ANalysis THrough Evolutionary Relationships Classification System
    prefix: PANTHER
    uri_format: https://www.pantherdb.org/panther/lookupId.jsp?id=$1
  mappings:
    biocontext: PANTHER.FAMILY
    biolink: PANTHER.FAMILY
    go: PANTHER
    miriam: panther.family
    n2t: panther.family
    prefixcommons: panther
    uniprot: DB-0069
  miriam:
    deprecated: false
    description: The PANTHER (Protein ANalysis THrough Evolutionary Relationships)
      Classification System is a resource that classifies genes by their functions,
      using published scientific experimental evidence and evolutionary relationships
      to predict function even in the absence of direct experimental evidence. This
      collection references groups of genes that have been organised as families.
    homepage: http://www.pantherdb.org/
    id: '00000060'
    name: PANTHER Family
    namespaceEmbeddedInLui: false
    pattern: ^PTHR\d{5}(\:SF\d{1,3})?$
    prefix: panther.family
    sampleId: PTHR12345
    uri_format: http://www.pantherdb.org/panther/family.do?clsAccession=$1
  n2t:
    description: The PANTHER (Protein ANalysis THrough Evolutionary Relationships)
      Classification System is a resource that classifies genes by their functions,
      using published scientific experimental evidence and evolutionary relationships
      to predict function even in the absence of direct experimental evidence. This
      collection references groups of genes that have been organised as families.
    example: PTHR12345
    homepage: http://www.pantherdb.org/
    name: PANTHER Family at USC (Los Angeles)
    namespaceEmbeddedInLui: false
    pattern: ^PTHR\d{5}(\:SF\d{1,3})?$
    prefix: panther.family
    uri_format: http://www.pantherdb.org/panther/family.do?clsAccession=$1
  name: PANTHER Family
  part_of_database: panther
  prefix: panther.family
  prefixcommons:
    description: The PANTHER (Protein ANalysis THrough Evolutionary Relationships)
      Classification System is a unique resource that classifies genes by their functions,
      using published scientific experimental evidence and evolutionary relationships
      to predict function even in the absence of direct experimental evidence.
    example: PTHR12345
    homepage: http://www.pantherdb.org
    keywords:
    - protein
    - classification
    - gene
    - pathway
    - ontology
    license: http://www.pantherdb.org/tou.jsp
    name: 'Protein ANalysis THrough Evolutionary Relationships: Classification of
      Genes and Proteins'
    pattern: ^PTHR\d{5}(\:SF{1,3})?$
    prefix: panther
    pubmed_ids:
    - '12952881'
    uri_format: http://www.pantherdb.org/panther/family.do?clsAccession=$1
  publications:
  - doi: 10.1093/nar/gky1038
    pmc: PMC6323939
    pubmed: '30407594'
    title: 'PANTHER version 14: more genomes, a new PANTHER GO-slim and improvements
      in enrichment analysis tools'
    year: 2019
  - doi: 10.1101/gr.772403
    pmc: PMC403709
    pubmed: '12952881'
    title: 'PANTHER: a library of protein families and subfamilies indexed by function'
    year: 2003
  uniprot:
    abbreviation: PANTHER
    category: Family and domain databases
    homepage: https://www.pantherdb.org/
    name: The PANTHER Classification System
    prefix: DB-0069
    publications:
    - doi: 10.1093/nar/gkaa1106
      pubmed: '33290554'
    uri_format: https://www.pantherdb.org/panther/family.do?clsAccession=$1
panther.node:
  biocontext:
    prefix: PANTHER.NODE
  mappings:
    biocontext: PANTHER.NODE
    miriam: panther.node
    n2t: panther.node
  miriam:
    deprecated: false
    description: The PANTHER (Protein ANalysis THrough Evolutionary Relationships)
      Classification System is a resource that classifies genes by their functions,
      using published scientific experimental evidence and evolutionary relationships
      to predict function even in the absence of direct experimental evidence. PANTHER
      tree is a key element of the PANTHER System to represent ‘all’ of the evolutionary
      events in the gene family. PANTHER nodes represent the evolutionary events,
      either speciation or duplication, within the tree. PANTHER is maintaining stable
      identifier for these nodes.
    homepage: http://pantree.org/
    id: '00000374'
    name: PANTHER Node
    namespaceEmbeddedInLui: false
    pattern: ^PTN\d{9}$
    prefix: panther.node
    sampleId: PTN000000026
    uri_format: http://www.pantree.org/node/annotationNode.jsp?id=$1
  n2t:
    description: The PANTHER (Protein ANalysis THrough Evolutionary Relationships)
      Classification System is a resource that classifies genes by their functions,
      using published scientific experimental evidence and evolutionary relationships
      to predict function even in the absence of direct experimental evidence. PANTHER
      tree is a key element of the PANTHER System to represent &#x2018;all&#x2019;
      of the evolutionary events in the gene family. PANTHER nodes represent the evolutionary
      events, either speciation or duplication, within the tree. PANTHER is maintaining
      stable identifier for these nodes.
    example: PTN000000026
    homepage: http://pantree.org/
    name: PANTHER Node at USC (Los Angeles)
    namespaceEmbeddedInLui: false
    pattern: ^PTN\d{9}$
    prefix: panther.node
    uri_format: http://www.pantree.org/node/annotationNode.jsp?id=$1
  part_of_database: panther
  prefix: panther.node
panther.pathway:
  biocontext:
    prefix: PANTHER.PATHWAY
  edam:
    description: Identifier of a biological pathway from the Panther Pathways database.
    name: Pathway ID (Panther)
    obsolete: false
    prefix: '1161'
  mappings:
    biocontext: PANTHER.PATHWAY
    edam: '1161'
    miriam: panther.pathway
    n2t: panther.pathway
  miriam:
    deprecated: false
    description: The PANTHER (Protein ANalysis THrough Evolutionary Relationships)
      Classification System is a resource that classifies genes by their functions,
      using published scientific experimental evidence and evolutionary relationships
      to predict function even in the absence of direct experimental evidence. The
      PANTHER Pathway collection references pathway information, primarily for signaling
      pathways, each with subfamilies and protein sequences mapped to individual pathway
      components.
    homepage: http://www.pantherdb.org/
    id: '00000363'
    name: PANTHER Pathway
    namespaceEmbeddedInLui: false
    pattern: ^P\d{5}$
    prefix: panther.pathway
    sampleId: P00024
    uri_format: http://www.pantherdb.org/pathway/pathwayDiagram.jsp?catAccession=$1
  n2t:
    description: The PANTHER (Protein ANalysis THrough Evolutionary Relationships)
      Classification System is a resource that classifies genes by their functions,
      using published scientific experimental evidence and evolutionary relationships
      to predict function even in the absence of direct experimental evidence. The
      PANTHER Pathway collection references pathway information, primarily for signaling
      pathways, each with subfamilies and protein sequences mapped to individual pathway
      components.
    example: P00024
    homepage: http://www.pantherdb.org/
    name: PANTHER Pathway at USC (Los Angeles)
    namespaceEmbeddedInLui: false
    pattern: ^P\d{5}$
    prefix: panther.pathway
    uri_format: http://www.pantherdb.org/pathway/pathwayDiagram.jsp?catAccession=$1
  part_of_database: panther
  prefix: panther.pathway
panther.pthcmp:
  biocontext:
    prefix: PANTHER.PTHCMP
  mappings:
    biocontext: PANTHER.PTHCMP
    miriam: panther.pthcmp
    n2t: panther.pthcmp
  miriam:
    deprecated: false
    description: "The PANTHER (Protein ANalysis THrough Evolutionary Relationships)\
      \ Classification System is a resource that classifies genes by their functions,\
      \ using published scientific experimental evidence and evolutionary relationships\
      \ to predict function even in the absence of direct experimental evidence. The\
      \ PANTHER Pathway Component collection references specific classes of molecules\
      \ that play the same mechanistic role within a pathway, across species. Pathway\r\
      \ncomponents may be proteins, genes/DNA, RNA, or simple molecules. Where the\
      \ identified component is a protein, DNA, or transcribed RNA, it is associated\
      \ with protein sequences in the PANTHER protein family trees through manual\
      \ curation."
    homepage: http://www.pantherdb.org/
    id: '00000422'
    name: PANTHER Pathway Component
    namespaceEmbeddedInLui: false
    pattern: ^[GPUCS]\d{5}$
    prefix: panther.pthcmp
    sampleId: P00266
    uri_format: http://www.pantherdb.org/pathway/pathCatDetail.do?clsAccession=$1
  n2t:
    description: The PANTHER (Protein ANalysis THrough Evolutionary Relationships)
      Classification System is a resource that classifies genes by their functions,
      using published scientific experimental evidence and evolutionary relationships
      to predict function even in the absence of direct experimental evidence. The
      PANTHER Pathway Component collection references specific classes of molecules
      that play the same mechanistic role within a pathway, across species. Pathway
      components may be proteins, genes/DNA, RNA, or simple molecules. Where the identified
      component is a protein, DNA, or transcribed RNA, it is associated with protein
      sequences in the PANTHER protein family trees through manual curation.
    example: P00266
    homepage: http://www.pantherdb.org/
    name: PANTHER Pathway Component at USC (Los Angeles)
    namespaceEmbeddedInLui: false
    pattern: ^G|P|U|C|S\d{5}$
    prefix: panther.pthcmp
    uri_format: http://www.pantherdb.org/pathway/pathCatDetail.do?clsAccession=$1
  part_of_database: panther
  pattern: ^(G|P|U|C|S)\d{5}$
  prefix: panther.pthcmp
pao:
  biocontext:
    prefix: PAO
  mappings:
    biocontext: PAO
    obofoundry: pao
    wikidata.entity: Q114677904
  obofoundry:
    contact: jaiswalp@science.oregonstate.edu
    contact.github: jaiswalp
    contact.label: Pankaj Jaiswal
    contact.orcid: 0000-0002-1005-8383
    deprecated: true
    domain: anatomy and development
    homepage: http://www.plantontology.org
    name: Plant Anatomy Ontology
    prefix: pao
  prefix: pao
pass2:
  biocontext:
    prefix: PASS2
  deprecated: true
  homepage: http://caps.ncbs.res.in/pass2
  integbio:
    description: PASS2 contains alignments of structural motifs of protein superfamilies.
      PASS2 is an automatic version of the original superfamily alignment database,
      CAMPASS (CAMbridge database of Protein Alignments organised as Structural Superfamilies).
      PASS2 contains alignments of protein structures at the superfamily level and
      is in direct correspondence with SCOPe 2.04 release.
    fairsharing: FAIRsharing.htzwqf
    homepage: http://caps.ncbs.res.in/pass2/
    information_keywords:
    - Sequence
    - 3D structure
    maintainer: Department of Biochemistry, University of Cambridge||NCBS (National
      Center for Biological Sciences)||Department of Crystallography, Birkbeck College,
      University of London
    name: PASS2
    prefix: nbdc02108
    pubmeds:
    - '2181150'
    - '10089493'
    - '9730927'
    - '11752316'
    - '15059245'
    - '9753697'
    status: Active
    target_keywords:
    - Protein
  mappings:
    biocontext: PASS2
    integbio: nbdc02108
    miriam: pass2
    n2t: pass2
    prefixcommons: pass2
  miriam:
    deprecated: false
    description: The PASS2 database provides alignments of proteins related at the
      superfamily level and are characterized by low sequence identity.
    homepage: https://caps.ncbs.res.in/pass2.8
    id: 00000468
    name: PASS2
    namespaceEmbeddedInLui: false
    pattern: ^\d+$
    prefix: pass2
    sampleId: '46977'
    uri_format: https://caps.ncbs.res.in/pass2.8/?q=superfamily/$1
  n2t:
    description: The PASS2 database provides alignments of proteins related at the
      superfamily level and are characterized by low sequence identity.
    example: '46977'
    homepage: http://caps.ncbs.res.in/pass2/
    name: PASS2 at National centre for Biological Sciences (India)
    namespaceEmbeddedInLui: false
    pattern: ^\d+$
    prefix: pass2
    uri_format: http://caps.ncbs.res.in/cgi-bin/pass2//show_sf.py?sf_id=$1
  name: Protein Alignment organised as Structural Superfamily
  prefix: pass2
  prefixcommons:
    description: PASS2 is an automatic version of the original superfamily alignment
      database, CAMPASS. The current version contains 628 multi member superfamilies
      and 566 structure based sequence annotated single member superfamilies. Sequence
      members for the superfamilies in different genomes have been listed and aligned.
    example: '47391'
    homepage: http://www.ncbs.res.in/~faculty/mini/campass/pass2.html
    keywords:
    - structure
    - DNA
    - genome
    - classification
    name: Protein Alignments organised as Structural Superfamilies
    pattern: ^\d+$
    prefix: pass2
    uri_format: http://caps.ncbs.res.in/cgi-bin/mini/databases/campass/pass/pass.cgi?code=$1
pathbank:
  contact:
    email: david.wishart@ualberta.ca
    github: DavidWishartLab
    name: David S. Wishart
    orcid: 0000-0002-3207-2434
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: PathBank is an interactive, visual database containing more than 100
    000 machine-readable pathways found in model organisms such as humans, mice, E.
    coli, yeast, and Arabidopsis thaliana.
  domain: pathway
  example: SMP0000219
  fairsharing:
    abbreviation: PathBank
    description: PathBank is an interactive, visual database containing more than
      100 000 machine-readable pathways found in model organisms such as humans, mice,
      E. coli, yeast, and Arabidopsis thaliana. The majority of these pathways are
      not found in any other pathway database. PathBank is designed specifically to
      support pathway elucidation and pathway discovery in metabolomics, transcriptomics,
      proteomics, and systems biology. All PathBank pathways include information on
      the relevant organelles, subcellular compartments, protein complex cofactors,
      protein complex locations, metabolite locations, chemical structures, and protein
      complex quaternary structures. The database is easily browsed and supports full
      text, sequence, and chemical structure searching.
    homepage: http://pathbank.org/
    license: ODBL
    name: PathBank
    prefix: FAIRsharing.3xwMon
    publications: []
    subjects:
    - Endocrinology
    - Molecular biology
    - Animal Genetics
    - Cheminformatics
    - Bioinformatics
    - Genetics
    - Proteomics
    - Drug Metabolism
    - Human Genetics
    - Molecular Microbiology
    - Metabolomics
    - Transcriptomics
    - Cell Biology
    - Database Management
    - Microbiology
    - Biology
    - Systems Biology
    - Medical Informatics
    - Plant Genetics
  homepage: https://pathbank.org
  license: ODbL-1.0
  logo: https://pathbank.org/assets/pathbank_banner-2f8ec31838b9f453482e0748c0da1b7ebbb77b0f2b1a6e60ff1222ca0984db07.png
  mappings:
    fairsharing: FAIRsharing.3xwMon
    togoid: Pathbank
  name: PathBank
  pattern: ^(SMP|PW)\d+$
  prefix: pathbank
  togoid:
    examples:
    - SMP0000055
    - SMP0000057
    - SMP0000029
    - SMP0000044
    - SMP0000048
    - SMP0000046
    - SMP0000059
    - SMP0000067
    - SMP0000007
    - SMP0000004
    keywords:
    - Pathway
    name: Pathbank
    pattern: ^(?SMP\d+)$
    prefix: Pathbank
    uri_format: http://pathbank.org/view/$1
  uri_format: https://pathbank.org/view/$1
pathguide:
  contact:
    email: gary.bader@utoronto.ca
    github: gbader
    name: Gary Bader
    orcid: 0000-0003-0185-8861
  integbio:
    alt_name: Pathway resource list
    description: Pathguide is a database of biological pathways. The database contains
      information on hundreds of pathways including metabolic and signaling pathways
      as well as protein-protein and gene regulatory networks. The website collects
      information from several other web resources and formats. Users can search by
      organism, availability, and data standard, and links are provided to the constituent
      databases.
    homepage: http://www.pathguide.org/
    information_keywords:
    - Interaction/Pathway
    maintainer: Memorial Sloan-Kettering Cancer Center, the University of Toronto
    name: Pathguide
    prefix: nbdc00608
    pubmeds:
    - '16381921'
    status: Active
    target_keywords:
    - Genome/Gene
    - Protein
    - Metabolite
  mappings:
    integbio: nbdc00608
    prefixcommons: pathguide
  name: Pathguide
  pattern: ^\d+$
  prefix: pathguide
  prefixcommons:
    description: Pathguide contains information about 325 biological related resources
      and molecular interaction related resources.
    example: '49'
    homepage: http://pathguide.org
    keywords:
    - pathway
    - interaction
    - small molecule
    - protein
    - gene
    name: 'Pathguide: The Pathway Resource List'
    pattern: ^\d+$
    prefix: pathguide
    uri_format: http://www.pathguide.org/fullrecord.php?organisms=all&availability=all&standards=all&order=alphabetic&DBID=$1
  reviewer:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
pathoplant:
  mappings:
    pathguide: '333'
    prefixcommons: pathoplant
  pathguide:
    abbreviation: PathoPlant
    homepage: http://www.pathoplant.de/
    name: PathoPlant
    prefix: '333'
  prefix: pathoplant
  prefixcommons:
    description: PathoPlant® is a database on plant-pathogen interactions and components
      of signal transduction pathways related to plant pathogenesis. PathoPlant® also
      harbors gene expression data from Arabidopsis thaliana microarray experiments
      to enable searching for specific genes regulated upon pathogen infection or
      elicitor treatment.
    example: MO000027
    homepage: http://www.pathoplant.de
    keywords:
    - interaction
    - pathway
    - small molecule
    - gene expression
    - protein
    name: PathoPlant®
    pattern: ^MO\d+$
    prefix: pathoplant
    uri_format: http://www.pathoplant.de/detail.php?accNo=$1
  reviewer:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
pathwaycommons:
  biocontext:
    prefix: PATHWAYCOMMONS
  contact:
    email: chris@sanderlab.org
    github: sanderlab
    name: Chris Sander
    orcid: 0000-0001-6059-6270
  mappings:
    biocontext: PATHWAYCOMMONS
    miriam: pathwaycommons
    n2t: pathwaycommons
    prefixcommons: pathwaycommons
    re3data: r3d100012731
    uniprot: DB-0253
  miriam:
    deprecated: false
    description: Pathway Commons is a convenient point of access to biological pathway
      information collected from public pathway databases, which you can browse or
      search. It is a collection of publicly available pathways from multiple organisms
      that provides researchers with convenient access to a comprehensive collection
      of pathways from multiple sources represented in a common language.
    homepage: http://www.pathwaycommons.org/pc/
    id: '00000073'
    name: Pathway Commons
    namespaceEmbeddedInLui: false
    pattern: ^\d+$
    prefix: pathwaycommons
    sampleId: '485991'
    uri_format: http://www.pathwaycommons.org/pc/record2.do?id=$1
  n2t:
    description: Pathway Commons is a convenient point of access to biological pathway
      information collected from public pathway databases, which you can browse or
      search. It is a collection of publicly available pathways from multiple organisms
      that provides researchers with convenient access to a comprehensive collection
      of pathways from multiple sources represented in a common language.
    example: '485991'
    homepage: http://www.pathwaycommons.org/pc/
    name: Pathway Commons
    namespaceEmbeddedInLui: false
    pattern: ^\d+$
    prefix: pathwaycommons
    uri_format: http://www.pathwaycommons.org/pc/record2.do?id=$1
  prefix: pathwaycommons
  prefixcommons:
    description: Pathway Commons is a convenient point of access to biological pathway
      information collected from public pathway databases
    example: '485991'
    homepage: http://www.pathwaycommons.org/pc/
    keywords:
    - pathway
    license: http://www.pathwaycommons.org/pc/about.do
    name: Pathway Commons
    pattern: ^\d+$
    prefix: pathwaycommons
    synonyms:
    - cpath
    uri_format: http://www.pathwaycommons.org/pc/record2.do?id=$1
  publications:
  - doi: 10.1093/nar/gkq1039
    pmc: PMC3013659
    pubmed: '21071392'
    title: Pathway Commons, a web resource for biological pathway data
    year: 2010
  - doi: 10.1093/nar/gkz946/5606621
    pmc: null
    pubmed: '31647099'
    title: null
    year: null
  re3data:
    description: Pathway Commons is a convenient point of access to biological pathway
      information collected from public pathway databases. Information is sourced
      from public pathway databases and is readily searched, visualized, and downloaded.
      The data is freely available under the license terms of each contributing database.
    doi: 10.17616/R3080J
    homepage: https://www.pathwaycommons.org/
    name: Pathway Commons
    prefix: r3d100012731
    xrefs:
      nif: 0000-20884
      omics: '02761'
  uniprot:
    abbreviation: PathwayCommons
    category: Enzyme and pathway databases
    homepage: https://www.pathwaycommons.org
    name: Pathway Commons web resource for biological pathway data
    prefix: DB-0253
    publications:
    - doi: 10.1093/nar/gkz946/5606621
      pubmed: '31647099'
    uri_format: https://apps.pathwaycommons.org/search?q=$1
pato:
  aberowl:
    description: An ontology of phenotypic qualities (properties, attributes or characteristics)
    download_owl: http://aber-owl.net/media/ontologies/PATO/200/pato.owl
    homepage: https://github.com/pato-ontology/pato/
    name: Phenotype And Trait Ontology
    prefix: PATO
  agroportal:
    contact:
      email: g.gkoutos@gmail.com
      name: George Gkoutos
    description: An ontology of phenotypic qualities (properties, attributes or characteristics).
      This ontology can be used in conjunction with other ontologies such as GO or
      anatomical ontologies to refer to phenotypes. Examples of qualities are red,
      ectopic, high temperature, fused, small, edematous and arrested., attributes
      or characteristics).
    example_uri: http://purl.obolibrary.org/obo/PATO_0001464
    homepage: https://github.com/pato-ontology
    license: CC-BY-3.0
    name: Phenotype And Trait Ontology
    prefix: PATO
    publications:
    - https://doi.org/10.1093/bib/bbx035
    - https://doi.org/10.1186/gb-2004-6-1-r8
    repository: https://github.com/pato-ontology/pato/
    version: '2025-05-14'
  biocontext:
    prefix: PATO
  bioportal:
    contact:
      email: g.gkoutos@gmail.com
      name: George Gkoutos
    description: Phenotypic qualities (properties). This ontology can be used in conjunction
      with other ontologies such as GO or anatomical ontologies to refer to phenotypes.
      Examples of qualities are red, ectopic, high temperature, fused, small, edematous
      and arrested.
    homepage: https://github.com/pato-ontology/pato/
    name: Phenotypic Quality Ontology
    prefix: PATO
    version: '2025-05-14'
  fairsharing:
    abbreviation: PATO
    contact:
      email: g.gkoutos@gmail.com
      name: George Gkoutos
      orcid: 0000-0002-2061-091X
    description: PATO is an ontology of phenotypic qualities, intended for use in
      a number of applications, primarily phenotype annotation. This ontology can
      be used in conjunction with other ontologies such as GO or anatomical ontologies
      to refer to phenotypes.
    domains:
    - phenotype
    homepage: https://github.com/pato-ontology/pato/
    license: CC-BY-3.0
    name: Phenotypic QualiTy Ontology
    prefix: FAIRsharing.ezwdhz
    publications:
    - doi: 10.1186/gb-2004-6-1-r8
      pubmed: '15642100'
      title: Using ontologies to describe mouse phenotypes
      year: 2005
    - doi: 10.1186/gb-2010-11-1-r2
      pubmed: '20064205'
      title: Integrating phenotype ontologies across multiple species
      year: 2010
    repository: https://github.com/pato-ontology/pato/blob/master/CHANGES.md
    subjects:
    - Biodiversity
    - Biology
  go:
    homepage: http://www.obofoundry.org/ontology/pato.html
    name: Phenotypic quality ontology
    prefix: PATO
  mappings:
    aberowl: PATO
    agroportal: PATO
    biocontext: PATO
    bioportal: PATO
    fairsharing: FAIRsharing.ezwdhz
    go: PATO
    miriam: pato
    n2t: pato
    obofoundry: pato
    ols: pato
    ontobee: PATO
    prefixcommons: pato
    tib: pato
    wikidata.entity: Q81661522
  miriam:
    deprecated: false
    description: PATO is an ontology of phenotypic qualities, intended for use in
      a number of applications, primarily defining composite phenotypes and phenotype  annotation.
    homepage: http://bioportal.bioontology.org/ontologies/PATO
    id: '00000112'
    name: PATO
    namespaceEmbeddedInLui: true
    pattern: ^PATO:\d{7}$
    prefix: pato
    sampleId: 0001998
    uri_format: http://purl.bioontology.org/ontology/PATO/PATO:$1
  n2t:
    description: PATO is an ontology of phenotypic qualities, intended for use in
      a number of applications, primarily defining composite phenotypes and phenotype  annotation.
    example: 0001998
    homepage: http://bioportal.bioontology.org/ontologies/PATO
    name: PATO through BioPortal
    namespaceEmbeddedInLui: true
    pattern: ^PATO:\d{7}$
    prefix: pato
    uri_format: http://purl.bioontology.org/ontology/PATO/PATO:$1
  obofoundry:
    appears_in:
    - agro
    - aism
    - cdno
    - cl
    - colao
    - ecocore
    - ecto
    - fovt
    - gallont
    - lepao
    - mco
    - ms
    - pcl
    - pco
    - phipo
    - planp
    - proco
    - rbo
    - uberon
    - xpo
    - zp
    contact: g.gkoutos@gmail.com
    contact.github: gkoutos
    contact.label: George Gkoutos
    contact.orcid: 0000-0002-2061-091X
    deprecated: false
    description: An ontology of phenotypic qualities (properties, attributes or characteristics)
    domain: phenotype
    download.json: http://purl.obolibrary.org/obo/pato.json
    download.obo: http://purl.obolibrary.org/obo/pato.obo
    download.owl: http://purl.obolibrary.org/obo/pato.owl
    homepage: https://github.com/pato-ontology/pato/
    license: CC BY 3.0
    license.url: http://creativecommons.org/licenses/by/3.0/
    name: Phenotype And Trait Ontology
    preferredPrefix: PATO
    prefix: pato
    publications:
    - id: https://www.ncbi.nlm.nih.gov/pubmed/28387809
      title: 'The anatomy of phenotype ontologies: principles, properties and applications'
    - id: https://www.ncbi.nlm.nih.gov/pubmed/15642100
      title: Using ontologies to describe mouse phenotypes
    repository: https://github.com/pato-ontology/pato
  ols:
    description: An ontology of phenotypic qualities (properties, attributes or characteristics).
    download_owl: http://purl.obolibrary.org/obo/pato.owl
    homepage: https://github.com/pato-ontology/pato/
    name: PATO - the Phenotype And Trait Ontology
    prefix: pato
    tracker: https://github.com/pato-ontology/pato/issues
    version: '2025-05-14'
    version.iri: http://purl.obolibrary.org/obo/pato/releases/2025-05-14/pato.owl
  ontobee:
    library: Foundry
    name: Phenotype And Trait Ontology
    prefix: PATO
  pattern: ^\d{7}$
  prefix: pato
  prefixcommons:
    alt_uri_formats:
    - http://purl.org/obo/owl/PATO#$1
    bioportal: '1107'
    description: PATO is an ontology of phenotypic qualities, intended for use in
      a number of applications, primarily defining composite phenotypes and phenotype
      annotation.
    example: PATO:0001998
    homepage: http://obofoundry.org/wiki/index.php/PATO:Main_Page
    keywords:
    - obo
    - ontology
    - quality
    - phenotype
    license: http://www.ebi.ac.uk/Information/termsofuse.html
    name: PATO
    pattern: ^PATO:\d{7}$
    prefix: pato
    synonyms:
    - obo.pato
  providers:
  - code: purl
    description: Legacy PURLs found in OAE
    example: null
    first_party: null
    homepage: http://purl.org/obo/owl/
    name: Legacy PURL
    publications: null
    status: null
    uri_format: http://purl.org/obo/owl/PATO#PATO_$1
  publications:
  - doi: 10.1093/bib/bbx035
    pmc: PMC6169674
    pubmed: '28387809'
    title: 'The anatomy of phenotype ontologies: principles, properties and applications'
    year: 2018
  - doi: 10.1186/gb-2010-11-1-r2
    pmc: PMC2847714
    pubmed: '20064205'
    title: Integrating phenotype ontologies across multiple species
    year: 2010
  - doi: 10.1186/gb-2004-6-1-r8
    pmc: PMC549069
    pubmed: '15642100'
    title: Using ontologies to describe mouse phenotypes
    year: 2004
  - doi: null
    pmc: null
    pubmed: '28387809'
    title: 'The anatomy of phenotype ontologies: principles, properties and applications'
    year: null
  - doi: null
    pmc: null
    pubmed: '15642100'
    title: Using ontologies to describe mouse phenotypes
    year: null
  - doi: 10.1186/gb-2004-6-1-r8
    pmc: null
    pubmed: '15642100'
    title: Using ontologies to describe mouse phenotypes
    year: 2005
  - doi: 10.1186/gb-2010-11-1-r2
    pmc: null
    pubmed: '20064205'
    title: Integrating phenotype ontologies across multiple species
    year: 2010
  - doi: null
    pmc: null
    pubmed: '28387809'
    title: 'The anatomy of phenotype ontologies: principles, properties and applications'
    year: null
  - doi: null
    pmc: null
    pubmed: '15642100'
    title: Using ontologies to describe mouse phenotypes
    year: null
  - doi: 10.1186/gb-2004-6-1-r8
    pmc: null
    pubmed: '15642100'
    title: Using ontologies to describe mouse phenotypes
    year: 2005
  - doi: 10.1186/gb-2010-11-1-r2
    pmc: null
    pubmed: '20064205'
    title: Integrating phenotype ontologies across multiple species
    year: 2010
  tib:
    description: An ontology of phenotypic qualities (properties, attributes or characteristics).
    download_owl: http://purl.obolibrary.org/obo/pato.owl
    homepage: https://github.com/pato-ontology/pato/
    keywords:
    - NFDI4CHEM
    - ESS
    - DataPLANT
    - life sciences, biology
    - earth sciences
    name: PATO - the Phenotype And Trait Ontology
    prefix: pato
    tracker: https://github.com/pato-ontology/pato/issues
    version.iri: http://purl.obolibrary.org/obo/pato/releases/2025-05-14/pato.owl
  uri_format: http://purl.obolibrary.org/obo/PATO_$1
pav:
  aberowl:
    description: PAV is a lightweight ontology for tracking Provenance, Authoring
      and Versioning. PAV specializes the W3C provenance ontology PROV-O in order
      to describe authorship, curation and digital creation of online resources. This
      ontology describes the defined PAV properties and their usage. Note that PAV
      does not define any explicit classes or domain/ranges, as every property is
      meant to be used directly on the described online resource.
    download_owl: http://aber-owl.net/media/ontologies/PAV/3/pav.owl
    homepage: https://github.com/pav-ontology/pav/
    name: PAV Provenance, Authoring and Versioning
    prefix: PAV
    version: 2.3.1
  biocontext:
    prefix: pav
    uri_format: http://purl.org/pav/$1
  biolink:
    is_identifiers: false
    is_obo: false
    prefix: pav
    uri_format: http://purl.org/pav/$1
  bioportal:
    contact:
      email: stian@soiland-reyes.com
      name: Stian Soiland-Reyes
    description: PAV is a lightweight ontology for tracking Provenance, Authoring
      and Versioning. PAV specializes the W3C provenance ontology PROV-O in order
      to describe authorship, curation and digital creation of online resources. This
      ontology describes the defined PAV properties and their usage. Note that PAV
      does not define any explicit classes or domain/ranges, as every property is
      meant to be used directly on the described online resource.
    homepage: https://github.com/pav-ontology/pav/
    name: PAV Provenance, Authoring and Versioning
    prefix: PAV
    publications:
    - https://github.com/pav-ontology/pav/wiki/Publications
    version: 2.3.1
  contributor:
    email: nicolas.matentzoglu@gmail.com
    github: matentzn
    name: Nicolas Matentzoglu
    orcid: 0000-0002-7356-1779
  contributor_extras:
  - email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: PAV is a lightweight ontology for tracking provenance, authorship,
    and versioning. It specializes the W3C provenance ontology PROV-O in order to
    describe authorship, curation and digital creation of online resources.
  example: authoredBy
  fairsharing:
    abbreviation: PAV
    contact:
      email: stian@soiland-reyes.com
      name: Stian Soiland-Reyes
      orcid: 0000-0001-9842-9718
    description: PAV is a lightweight ontology for tracking Provenance, Authoring
      and Versioning. PAV specializes the W3C provenance ontology PROV-O in order
      to describe authorship, curation and digital creation of online resources. This
      ontology describes the defined PAV properties and their usage. Note that PAV
      does not define any explicit classes or domain/ranges, as every property is
      meant to be used directly on the described online resource.
    domains:
    - Resource metadata
    homepage: https://github.com/pav-ontology/pav/
    license: Apache 2.0 License
    name: Provenance, Authoring and Versioning Ontology
    prefix: FAIRsharing.nbfwwv
    publications:
    - doi: 10.1186/2041-1480-4-37
      pubmed: '24267948'
      title: 'PAV ontology: provenance, authoring and versioning'
      year: 2013
    repository: http://pav-ontology.github.io/pav/
    subjects:
    - Data Management
    - Subject Agnostic
  github_request_issue: 186
  homepage: https://pav-ontology.github.io/pav/
  lov:
    description: PAV is a lightweight ontology for tracking Provenance, Authoring
      and Versioning. PAV specializes the W3C provenance ontology PROV-O in order
      to describe authorship, curation and digital creation of online resources.
    homepage: http://pav-ontology.github.io/pav/
    keywords:
    - Quality
    modified: '2014-08-28'
    name: Provenance, Authoring and Versioning
    prefix: pav
    uri_prefix: http://purl.org/pav/$1
  mappings:
    aberowl: PAV
    biocontext: pav
    biolink: pav
    bioportal: PAV
    fairsharing: FAIRsharing.nbfwwv
    lov: pav
  name: Provenance, Authoring, and Versioning Vocabulary
  pattern: ^[a-z][a-zA-Z]+$
  preferred_prefix: pav
  prefix: pav
  publications:
  - doi: 10.1186/2041-1480-4-37
    pmc: PMC4177195
    pubmed: '24267948'
    title: 'PAV ontology: provenance, authoring and versioning'
    year: 2013
  - doi: 10.1186/2041-1480-4-37
    pmc: null
    pubmed: '24267948'
    title: 'PAV ontology: provenance, authoring and versioning'
    year: 2013
  reviewer:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  uri_format: http://purl.org/pav/$1
paxdb.organism:
  biocontext:
    prefix: PAXDB.ORGANISM
  mappings:
    biocontext: PAXDB.ORGANISM
    miriam: paxdb.organism
    n2t: paxdb.organism
  miriam:
    deprecated: false
    description: PaxDb is a resource dedicated to integrating information on absolute
      protein abundance levels across different organisms. Publicly available experimental
      data are mapped onto a common namespace and, in the case of tandem mass spectrometry
      data, re-processed using a standardized spectral counting pipeline. Data sets
      are scored and ranked to assess consistency against externally provided protein-network
      information. PaxDb provides whole-organism data as well as tissue-resolved data,
      for numerous proteins. This collection references protein abundance information
      by species.
    homepage: http://pax-db.org/
    id: 00000488
    name: PaxDb Organism
    namespaceEmbeddedInLui: false
    pattern: ^\d+$
    prefix: paxdb.organism
    sampleId: '9606'
    uri_format: http://pax-db.org/#!species/$1
  n2t:
    description: PaxDb is a resource dedicated to integrating information on absolute
      protein abundance levels across different organisms. Publicly available experimental
      data are mapped onto a common namespace and, in the case of tandem mass spectrometry
      data, re-processed using a standardized spectral counting pipeline. Data sets
      are scored and ranked to assess consistency against externally provided protein-network
      information. PaxDb provides whole-organism data as well as tissue-resolved data,
      for numerous proteins. This collection references protein abundance information
      by species.
    example: '9606'
    homepage: http://pax-db.org/
    name: PaxDb v3 at University of Zurich
    namespaceEmbeddedInLui: false
    pattern: ^\d+$
    prefix: paxdb.organism
    uri_format: http://pax-db.org/#!species/$1
  prefix: paxdb.organism
paxdb.protein:
  biocontext:
    prefix: PAXDB.PROTEIN
  mappings:
    biocontext: PAXDB.PROTEIN
    miriam: paxdb.protein
    n2t: paxdb.protein
  miriam:
    deprecated: false
    description: PaxDb is a resource dedicated to integrating information on absolute
      protein abundance levels across different organisms. Publicly available experimental
      data are mapped onto a common namespace and, in the case of tandem mass spectrometry
      data, re-processed using a standardized spectral counting pipeline. Data sets
      are scored and ranked to assess consistency against externally provided protein-network
      information. PaxDb provides whole-organism data as well as tissue-resolved data,
      for numerous proteins. This collection references individual protein abundance
      levels.
    homepage: http://pax-db.org/
    id: 00000489
    name: PaxDb Protein
    namespaceEmbeddedInLui: false
    pattern: ^\d+$
    prefix: paxdb.protein
    sampleId: '977869'
    uri_format: http://pax-db.org/#!protein/$1
  n2t:
    description: PaxDb is a resource dedicated to integrating information on absolute
      protein abundance levels across different organisms. Publicly available experimental
      data are mapped onto a common namespace and, in the case of tandem mass spectrometry
      data, re-processed using a standardized spectral counting pipeline. Data sets
      are scored and ranked to assess consistency against externally provided protein-network
      information. PaxDb provides whole-organism data as well as tissue-resolved data,
      for numerous proteins. This collection references individual protein abundance
      levels.
    example: '977869'
    homepage: http://pax-db.org/
    name: PaxDb v3 at University of Zurich
    namespaceEmbeddedInLui: false
    pattern: ^\d+$
    prefix: paxdb.protein
    uri_format: http://pax-db.org/#!protein/$1
  prefix: paxdb.protein
pazar:
  biocontext:
    prefix: PAZAR
  fairsharing:
    abbreviation: PAZAR
    contact:
      email: wyeth@cmmt.ubc.ca
      name: Wyeth W. Wasserman
      orcid: 0000-0001-6098-6412
    description: PAZAR is a software framework for the construction and maintenance
      of regulatory sequence data annotations; a framework which allows multiple boutique
      databases to function independently within a larger system (or information mall).
      The goal of PAZAR is to be the public repository for regulatory data.
    homepage: http://www.pazar.info/
    name: PAZAR
    prefix: FAIRsharing.33yggg
    publications:
    - doi: 10.1093/nar/gkn783
      pubmed_id: 18971253
      title: The PAZAR database of gene regulatory information coupled to the ORCA
        toolkit for the study of regulatory sequences.
    - doi: 10.1186/gb-2007-8-10-r207
      pubmed_id: 17916232
      title: 'PAZAR: a framework for collection and dissemination of cis-regulatory
        sequence annotation.'
    subjects:
    - Life Science
  integbio:
    alt_name: A Public Database of Transcription Factor and Regulatory Sequence Annotation
    description: PAZAR is a database of regulatory sequence information, including
      information about transcription factors. The database contains information collected
      from dozens of published studies of gene regulatory information. Users can search
      by transcription factor, target gene, or regulatory sequence of interest as
      well as browse by gene or study.
    fairsharing: biodbcore-000499
    homepage: http://www.pazar.info
    information_keywords:
    - Sequence
    maintainer: Centre for Molecular Medicine and Therapeutic
    name: PAZAR
    prefix: nbdc00611
    pubmeds:
    - '17916232'
    - '18971253'
    target_keywords:
    - Genome/Gene
    - Protein
  mappings:
    biocontext: PAZAR
    fairsharing: FAIRsharing.33yggg
    integbio: nbdc00611
    miriam: pazar
    n2t: pazar
    pathguide: '521'
    prefixcommons: pazar
  miriam:
    deprecated: true
    description: The PAZAR database unites independently created and maintained data
      collections of transcription factor and regulatory sequence annotation. It provides
      information on the sequence and target of individual transcription factors.
    homepage: http://www.pazar.info/
    id: '00000306'
    name: Pazar Transcription Factor
    namespaceEmbeddedInLui: false
    pattern: ^TF\w+$
    prefix: pazar
    sampleId: TF0001053
    uri_format: http://www.pazar.info/cgi-bin/tf_search.cgi?geneID=$1
  n2t:
    description: The PAZAR database unites independently created and maintained data
      collections of transcription factor and regulatory sequence annotation. It provides
      information on the sequence and target of individual transcription factors.
    example: TF0001053
    homepage: http://www.pazar.info/
    name: Pazar Transcription Factor at University of British Columbia
    namespaceEmbeddedInLui: false
    pattern: ^TF\w+$
    prefix: pazar
    uri_format: http://www.pazar.info/cgi-bin/tf_search.cgi?geneID=$1
  pathguide:
    abbreviation: PAZAR
    homepage: http://www.pazar.info/
    name: A Public Database of Transcription Factor and Regulatory Sequence Annotation
    prefix: '521'
  prefix: pazar
  prefixcommons:
    description: PAZAR is a software framework for the construction and maintenance
      of regulatory sequence data annotations; a framework which allows multiple boutique
      databases to function independently within a larger system (or information mall).
      The goal of PAZAR is to be the public repository for regulatory data.
    example: TF0000448
    homepage: http://www.pazar.info/
    keywords:
    - regulation
    - DNA
    - RNA
    name: PAZAR
    pattern: ^TF\d+$
    prefix: pazar
    uri_format: http://www.pazar.info/cgi-bin/tf_search.cgi?searchtab=tfs&ID_list=PAZAR_TF&geneID=$1
  publications:
  - doi: 10.1093/nar/gkn783
    pmc: PMC2686574
    pubmed: '18971253'
    title: The PAZAR database of gene regulatory information coupled to the ORCA toolkit
      for the study of regulatory sequences
    year: 2008
  - doi: 10.1186/gb-2007-8-10-r207
    pmc: PMC2246282
    pubmed: '17916232'
    title: 'PAZAR: a framework for collection and dissemination of cis-regulatory
      sequence annotation'
    year: 2007
  - doi: 10.1093/nar/gkn783
    pmc: null
    pubmed: null
    title: The PAZAR database of gene regulatory information coupled to the ORCA toolkit
      for the study of regulatory sequences.
    year: null
  - doi: 10.1186/gb-2007-8-10-r207
    pmc: null
    pubmed: null
    title: 'PAZAR: a framework for collection and dissemination of cis-regulatory
      sequence annotation.'
    year: null
pba:
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: A controlled vocabulary to support the study of transcription in the
    primate brain
  download_obo: https://raw.githubusercontent.com/obophenotype/uberon/master/source-ontologies/allen-pba.obo
  example: '128011350'
  homepage: https://www.blueprintnhpatlas.org/
  name: Primate Brain Atlas
  pattern: ^\d+$
  preferred_prefix: PBA
  prefix: pba
  repository: https://github.com/brain-bican/primate_brain_atlas_ontology
  uri_format: https://biopragmatics.github.io/providers/pba/$1
pcl:
  aberowl:
    description: Cell types that are provisionally defined by experimental techniques
      such as single cell or single nucleus transcriptomics rather than a straightforward
      & coherent set of properties.
    download_owl: http://aber-owl.net/media/ontologies/PCL/28/pcl.owl
    homepage: https://github.com/obophenotype/provisional_cell_ontology
    name: Provisional Cell Ontology
    prefix: PCL
  bioportal:
    contact:
      email: davidos@ebi.ac.uk
      name: David Osumi-Sutherland
    description: Cell types that are provisionally defined by experimental techniques
      such as single cell or single nucleus transcriptomics rather than a straightforward
      & coherent set of properties., Cell types that are provisionally defined by
      experimental techniques such as single cell transcriptomics rather than a straightforward
      & coherent set of properties.
    homepage: https://github.com/obophenotype/provisional_cell_ontology
    license: CC-BY-4.0
    name: Provisional Cell Ontology
    prefix: PCL
    publications:
    - https://doi.org/10.1101/2021.10.10.463703
    version: '2025-07-07'
  example: '0011124'
  fairsharing:
    abbreviation: PCL
    contact:
      email: davidos@ebi.ac.uk
      name: David Osumi-Sutherland
      orcid: 0000-0002-7073-9172
    description: PCL is an ontology created to record claims of potential new cell
      types derived from single cell data analysis, where there is no additional evidence
      that supports the addition of corresponding classically defined cell type to
      the Cell Ontology (CL). PCL hence provides a place for terms that might not
      be ready for CL.
    domains:
    - Annotation
    - cell
    - sequencing assay
    homepage: https://github.com/obophenotype/provisional_cell_ontology
    license: CC-BY-4.0
    name: Provisional Cell Ontology
    prefix: FAIRsharing.bfcfd0
    publications:
    - doi: 10.1101/2021.10.10.463703
      title: 'Brain Data Standards Ontology: A data-driven ontology of transcriptomically
        defined cell types in the primary motor cortex'
      year: 2021
    - doi: 10.1038/s41597-022-01886-2
      title: Brain Data Standards - A method for building data-driven cell-type ontologies
      year: 2023
    repository: https://github.com/obophenotype/provisional_cell_ontology/issues
    subjects:
    - Life Science
    - Anatomy
    - Phenomics
    - Transcriptomics
    - Omics
    - Cell Biology
    user_defined_tags:
    - single-cell multimodal omics
  mappings:
    aberowl: PCL
    bioportal: PCL
    fairsharing: FAIRsharing.bfcfd0
    obofoundry: pcl
    ols: pcl
    ontobee: PCL
    wikidata.entity: Q113014435
  obofoundry:
    contact: davidos@ebi.ac.uk
    contact.github: dosumis
    contact.label: David Osumi-Sutherland
    contact.orcid: 0000-0002-7073-9172
    depends_on:
    - bfo
    - chebi
    - cl
    - go
    - nbo
    - ncbitaxon
    - omo
    - pato
    - pr
    - ro
    - so
    - uberon
    deprecated: false
    description: Cell types that are provisionally defined by experimental techniques
      such as single cell or single nucleus transcriptomics rather than a straightforward
      & coherent set of properties.
    domain: phenotype
    download.json: http://purl.obolibrary.org/obo/pcl.json
    download.obo: http://purl.obolibrary.org/obo/pcl.obo
    download.owl: http://purl.obolibrary.org/obo/pcl.owl
    homepage: https://github.com/obophenotype/provisional_cell_ontology
    license: CC BY 4.0
    license.url: http://creativecommons.org/licenses/by/4.0/
    name: Provisional Cell Ontology
    preferredPrefix: PCL
    prefix: pcl
    repository: https://github.com/obophenotype/provisional_cell_ontology
  ols:
    description: Cell types that are provisionally defined by experimental techniques
      such as single cell transcriptomics rather than a straightforward & coherent
      set of properties.
    download_owl: http://purl.obolibrary.org/obo/pcl.owl
    homepage: https://github.com/obophenotype/provisional_cell_ontology
    name: Provisional Cell Ontology
    prefix: pcl
    tracker: https://github.com/obophenotype/provisional_cell_ontology/issues
    version: '2025-07-07'
    version.iri: http://purl.obolibrary.org/obo/pcl/releases/2025-07-07/pcl.owl
  ontobee:
    library: Library
    name: Provisional Cell Ontology
    prefix: PCL
  pattern: ^\d{7}$
  prefix: pcl
  publications:
  - doi: 10.1101/2021.10.10.463703
    pmc: null
    pubmed: null
    title: Brain Data Standards - A method for building data-driven cell-type ontologies
    year: 2021
  - doi: 10.1101/2021.10.10.463703
    pmc: null
    pubmed: null
    title: 'Brain Data Standards Ontology: A data-driven ontology of transcriptomically
      defined cell types in the primary motor cortex'
    year: 2021
  - doi: 10.1038/s41597-022-01886-2
    pmc: null
    pubmed: null
    title: Brain Data Standards - A method for building data-driven cell-type ontologies
    year: 2023
  uri_format: http://purl.obolibrary.org/obo/PCL_$1
pco:
  aberowl:
    description: An ontology about groups of interacting organisms such as populations
      and communities
    download_owl: http://aber-owl.net/media/ontologies/PCO/18/pco.owl
    homepage: https://github.com/PopulationAndCommunityOntology/pco
    name: Population and Community Ontology
    prefix: PCO
  agroportal:
    contact:
      email: rwalls2008@gmail.com
      name: Ramona Walls
    description: The Population and Community Ontology (PCO) describes material entities,
      qualities, and processes related to collections of interacting organisms such
      as populations and communities. It is taxon neutral, and can be used for any
      species, including humans. The classes in the PCO are useful for describing
      evolutionary processes, organismal interactions, and ecological experiments.
      Practical applications of the PCO include community health care, plant pathology,
      behavioral studies, sociology, and ecology.
    example_uri: http://purl.obolibrary.org/obo/PCO_0000061
    homepage: https://github.com/PopulationAndCommunityOntology/pco
    license: CC0-1.0
    name: Population and Community Ontology
    prefix: PCO
    repository: https://github.com/PopulationAndCommunityOntology/pco
    version: '2021-05-03'
  biocontext:
    prefix: PCO
  bioportal:
    contact:
      email: rlwalls2008@gmail.com
      name: Ramona Walls
    description: The Population and Community Ontology (PCO) models material entities,
      qualities, and processes related to collections of interacting organisms such
      as populations and communities. It is taxon neutral, and can be used for any
      species, including humans. The classes in the PCO are useful for describing
      evolutionary processes, organismal interactions, and ecological experiments.
      Practical applications of the PCO include community health care, plant pathology,
      behavioral studies, sociology, and ecology. The PCO is complient with the Basic
      Formal Ontology (BFO) and is designed to be compatible with other OBO Foundry
      ontologies.
    homepage: https://github.com/PopulationAndCommunityOntology/pco
    name: Population and Community Ontology
    prefix: PCO
    version: '2013-10-03'
  download_obo: http://purl.obolibrary.org/obo/pco.obo
  ecoportal:
    contact:
      email: rlwalls2008@gmail.com
      name: Ramona Walls
    description: The Population and Community Ontology (PCO) describes material entities,
      qualities, and processes related to collections of interacting organisms such
      as populations and communities. It is taxon neutral, and can be used for any
      species, including humans. The classes in the PCO are useful for describing
      evolutionary processes, organismal interactions, and ecological experiments.
      Practical applications of the PCO include community health care, plant pathology,
      behavioral studies, sociology, and ecology.
    example_uri: http://purl.obolibrary.org/obo/PCO_0000061
    homepage: https://github.com/PopulationAndCommunityOntology/pco
    license: CC0-1.0
    name: Population and Community Ontology
    prefix: PCO
    publications:
    - https://doi.org/10.1371/journal.pone.0089606
    repository: https://github.com/PopulationAndCommunityOntology/pco
    version: '2021-05-03'
  example: '0000021'
  fairsharing:
    abbreviation: PCO
    contact:
      email: rlwalls2008@gmail.com
      name: Ramona Walls
      orcid: 0000-0001-8815-0078
    description: Population and Community Ontology (PCO) is an ontology standard for
      describing the collective and interacting species of any taxa such as humans
      or plants. PCO has useful application in community health care, plant pathology,
      behavioral studies, sociology, and ecology. The PCO is compliant with the Basic
      Formal Ontology (BFO) and is designed to be compatible with other OBO Foundry
      ontologies.
    domains:
    - Evolution
    homepage: https://github.com/PopulationAndCommunityOntology/pco
    license: CC0-1.0
    name: Population and Community Ontology
    prefix: FAIRsharing.vq28qp
    publications:
    - doi: 10.1371/journal.pone.0089606
      pubmed: '24595056'
      title: 'Semantics in support of biodiversity knowledge discovery: an introduction
        to the biological collections ontology and related ontologies'
      year: 2014
    repository: https://github.com/PopulationAndCommunityOntology/pco/issues
    subjects:
    - Biodiversity
    - Population Genetics
    - Ecology
    - Social and Behavioural Science
    - Community Care
  mappings:
    aberowl: PCO
    agroportal: PCO
    biocontext: PCO
    bioportal: PCO
    ecoportal: PCO
    fairsharing: FAIRsharing.vq28qp
    obofoundry: pco
    ols: pco
    ontobee: PCO
    tib: pco
    wikidata.entity: Q55118575
  obofoundry:
    appears_in:
    - ecocore
    - envo
    contact: rlwalls2008@gmail.com
    contact.github: ramonawalls
    contact.label: Ramona Walls
    contact.orcid: 0000-0001-8815-0078
    depends_on:
    - bfo
    - caro
    - envo
    - go
    - iao
    - ncbitaxon
    - pato
    - ro
    deprecated: false
    description: An ontology about groups of interacting organisms such as populations
      and communities
    domain: environment
    download.owl: http://purl.obolibrary.org/obo/pco.owl
    homepage: https://github.com/PopulationAndCommunityOntology/pco
    license: CC0 1.0
    license.url: http://creativecommons.org/publicdomain/zero/1.0/
    name: Population and Community Ontology
    preferredPrefix: PCO
    prefix: pco
    repository: https://github.com/PopulationAndCommunityOntology/pco
  ols:
    description: The Population and Community Ontology (PCO) describes material entities,
      qualities, and processes related to collections of interacting organisms such
      as populations and communities. It is taxon neutral, and can be used for any
      species, including humans. The classes in the PCO are useful for describing
      evolutionary processes, organismal interactions, and ecological experiments.
      Practical applications of the PCO include community health care, plant pathology,
      behavioral studies, sociology, and ecology.
    download_owl: http://purl.obolibrary.org/obo/pco.owl
    homepage: https://github.com/PopulationAndCommunityOntology/pco
    name: Population and Community Ontology
    prefix: pco
    tracker: https://github.com/PopulationAndCommunityOntology/pco/issues
    version: '2021-05-03'
    version.iri: http://purl.obolibrary.org/obo/pco/releases/2021-05-03/pco.owl
  ontobee:
    library: Library
    name: Population and Community Ontology
    prefix: PCO
  pattern: ^\d{7}$
  prefix: pco
  tib:
    description: The Population and Community Ontology (PCO) describes material entities,
      qualities, and processes related to collections of interacting organisms such
      as populations and communities. It is taxon neutral, and can be used for any
      species, including humans. The classes in the PCO are useful for describing
      evolutionary processes, organismal interactions, and ecological experiments.
      Practical applications of the PCO include community health care, plant pathology,
      behavioral studies, sociology, and ecology.
    download_owl: http://purl.obolibrary.org/obo/pco.owl
    homepage: https://github.com/PopulationAndCommunityOntology/pco/
    keywords:
    - DataPLANT
    - life sciences, biology
    - social sciences
    name: Population and Community Ontology
    prefix: pco
    tracker: https://github.com/PopulationAndCommunityOntology/pco/issues/
    version.iri: http://purl.obolibrary.org/obo/pco/releases/2021-05-03/pco.owl
  uri_format: http://purl.obolibrary.org/obo/PCO_$1
pd_st:
  biocontext:
    prefix: PD_ST
  mappings:
    biocontext: PD_ST
    obofoundry: pd_st
  obofoundry:
    contact: henrich@embl.de
    contact.github: ThorstenHen
    contact.label: Thorsten Henrich
    contact.orcid: 0000-0002-1548-3290
    deprecated: true
    domain: anatomy and development
    homepage: http://4dx.embl.de/platy
    name: Platynereis stage ontology
    prefix: pd_st
  prefix: pd_st
pdb:
  biocontext:
    prefix: PDB
    uri_format: http://www.ebi.ac.uk/pdbsum/$1
  edam:
    description: An identifier of an entry from the PDB database.
    name: PDB
    obsolete: false
    prefix: '1127'
  fairsharing:
    abbreviation: PDBj
    contact:
      email: harukin@protein.osaka-u.ac.jp
      name: Haruki Nakamura
      orcid: 0000-0001-6690-5863
    description: PDBj (Protein Data Bank Japan) maintains the single global PDB/BMRB/EMDB
      archives of macromolecular structures and provide integrated tools, under the
      Joint Usage and Research activities of the Institute for Protein Research. Supports
      browsing in multiple languages such as Japanese, Chinese, and Korean; SeSAW
      identifies functionally or evolutionarily conserved motifs by locating and annotating
      sequence and structural similarities, tools for bioinformaticians, and more.
    homepage: http://www.pdbj.org/
    license: CC0-1.0
    name: Protein Data Bank Japan
    prefix: FAIRsharing.rs2815
    publications:
    - doi: 10.1002/pro.3273
      pubmed_id: 28815765
      title: New tools and functions in data-out activities at Protein Data Bank Japan
        (PDBj).
    - doi: 10.1093/nar/gkr811
      pubmed_id: 21976737
      title: 'Protein Data Bank Japan (PDBj): maintaining a structural data archive
        and resource description framework format.'
    - doi: null
      pubmed_id: 12099029
      title: '[Development of PDBj: Advanced database for protein structures].'
    - doi: 10.1093/database/baq021
      pubmed_id: 20798081
      title: 'PDBj Mine: design and implementation of relational database interface
        for Protein Data Bank Japan.'
    - doi: 10.1007/s10822-011-9460-y
      pubmed_id: 21796434
      title: 'Protein Data Bank Japan (PDBj): an interview with Haruki Nakamura of
        Osaka University by Wendy A. Warr.'
    - doi: 10.1093/nar/gkw962
      pubmed_id: 27789697
      title: 'Protein Data Bank Japan (PDBj): updated user interfaces, resource description
        framework, analysis tools for large structures.'
    - doi: 10.1002/pro.4211
      pubmed_id: null
      title: 'Protein Data Bank Japan: Celebrating our 20th anniversary during a global
        pandemic as the Asian hub of three dimensional macromolecular structural data'
    subjects:
    - Bioinformatics
    - Structural Biology
    - Proteomics
    - Virology
    - Epidemiology
    twitter: PDBj_en
  go:
    homepage: https://www.rcsb.org/pdb/
    name: Protein Data Bank
    prefix: PDB
    uri_format: https://www.rcsb.org/structure/$1
  integbio:
    alt_name: Protein Data Bank Europe
    description: PDBe is a database of protein structures. The database is the European
      resource for the Protein Databank and contains molecular structure coordinates
      and visualizations of thousands of proteins. Users can search for entries, browse
      by several curated categories, submit structures, and download coordinate data.
    fairsharing: biodbcore-000322
    homepage: http://www.ebi.ac.uk/pdbe/
    information_keywords:
    - Image/Movie
    - 3D structure
    - Repository
    maintainer: EMBL-EBI (European Bioinformatics Institute)
    name: PDBe
    prefix: nbdc00613
    pubmeds:
    - '22110033'
    status: Active
    target_keywords:
    - DNA
    - RNA
    - Protein
  logo: https://cdn.rcsb.org/wwpdb/img/core/wwpdb-logo.png
  mappings:
    biocontext: PDB
    edam: '1127'
    fairsharing: FAIRsharing.rs2815
    go: PDB
    integbio: nbdc00613
    miriam: pdb
    n2t: pdb
    ncbi: PDB
    pathguide: '398'
    prefixcommons: pdbj
    re3data: r3d100010910
    togoid: Pdb
    uniprot: DB-0172
    wikidata: P638
  miriam:
    deprecated: false
    description: The Protein Data Bank is the single worldwide archive of structural
      data of biological macromolecules.
    homepage: https://www.wwpdb.org/
    id: '00000020'
    name: Protein Data Bank
    namespaceEmbeddedInLui: false
    pattern: ^[0-9][A-Za-z0-9]{3}$
    prefix: pdb
    providers:
    - code: ebi
      description: Protein Databank through PDBsum
      homepage: https://www.ebi.ac.uk/pdbsum/
      name: Protein Databank through PDBsum
      uri_format: https://www.ebi.ac.uk/pdbsum/$1
    - code: rcsb
      description: RCSB PDB
      homepage: https://www.rcsb.org/
      name: RCSB PDB
      uri_format: https://www.rcsb.org/structure/$1
    - code: pdbj
      description: Protein Data Bank Japan (PDBj)
      homepage: http://www.pdbj.org/
      name: Protein Data Bank Japan (PDBj)
      uri_format: https://pdbj.org/mine/summary/$1
    - code: pdbe
      description: Protein Databank in Europe (PDBe)
      homepage: http://www.pdbe.org/
      name: Protein Databank in Europe (PDBe)
      uri_format: https://www.ebi.ac.uk/pdbe/entry/pdb/$1
    - code: ''
      description: Proteopedia
      homepage: http://www.proteopedia.org/
      name: Proteopedia
      uri_format: http://proteopedia.org/wiki/index.php/$1
    sampleId: 2gc4
    uri_format: https://www.wwpdb.org/pdb?id=pdb_0000$1
  n2t:
    description: The Protein Data Bank is the single worldwide archive of structural
      data of biological macromolecules.
    example: 2gc4
    homepage: https://www.pdb.org/
    name: RCSB PDB
    namespaceEmbeddedInLui: false
    pattern: ^[0-9][A-Za-z0-9]{3}$
    prefix: pdb
    uri_format: https://www.rcsb.org/pdb/explore/explore.do?structureId=$1
  name: PDB Structure
  ncbi:
    example: 12GS
    homepage: http://www.rcsb.org/pdb/
    name: Biological macromolecule three dimensional structure database
    prefix: PDB
  pathguide:
    abbreviation: RCSB PDB
    homepage: http://www.rcsb.org/pdb/home/home.do
    name: The Research Collaboratory for Structural Bioinformatics Protein Data Bank
    prefix: '398'
  prefix: pdb
  prefixcommons:
    description: The Protein Data Bank is the single worldwide archive of structural
      data of biological macromolecules.
    example: 2OM1
    homepage: http://www.pdbj.org/
    keywords:
    - protein
    - structure
    name: Protein Data Bank Japan
    pattern: ^\d+[A-Z]+$
    prefix: pdbj
    uri_format: http://service.pdbj.org/mine/Detail?PDBID=$1&PAGEID=Summary
  providers:
  - code: sabdab
    description: SAbDab is a database containing all the antibody structures available
      in the PDB. Each structure is annotated with a number of properties including
      experimental details, antibody nomenclature (e.g. heavy-light pairings), curated
      affinity data and sequence annotations.
    example: 9ii2
    first_party: null
    homepage: https://opig.stats.ox.ac.uk/webapps/sabdab-sabpred/sabdab
    name: The Structural Antibody Database
    publications:
    - doi: 10.1093/nar/gkt1043
      pmc: PMC3965125
      pubmed: '24214988'
      title: 'SAbDab: the structural antibody database'
      year: 2013
    status: null
    uri_format: https://opig.stats.ox.ac.uk/webapps/sabdab-sabpred/sabdab/structureviewer/?pdb=$1
  - code: furna
    description: FURNA (Functions of RNAs) is a database of ligand-RNA interactions
      and Gene Ontology annotations for RNAs in the Protein Data Bank (PDB).
    example: 157d
    first_party: null
    homepage: https://seq2fun.dcmb.med.umich.edu/furna/
    name: furna
    publications:
    - doi: 10.1371/journal.pbio.3002476
      pmc: PMC11309384
      pubmed: '39074139'
      title: 'FURNA: A database for functional annotations of RNA structures'
      year: 2024
    status: null
    uri_format: https://seq2fun.dcmb.med.umich.edu/furna/pdb.cgi?pdbid=$1
  - code: dionysus
    description: DIONYSUS is a database of protein-carbohydrate interfaces, offering
      annotated data and tools for exploring interaction patterns and annotating proteins.
    example: null
    first_party: null
    homepage: www.dsimb.inserm.fr/DIONYSUS
    name: DIONYSUS
    publications:
    - doi: 10.1093/nar/gkae890
      pmc: null
      pubmed: '39436020'
      title: 'DIONYSUS: a database of protein-carbohydrate interfaces'
      year: 2024
    status: null
    uri_format: https://www.dsimb.inserm.fr/DIONYSUS/structure/$1
  - code: rnaprodb
    description: RNAproDB assists research in structural analysis of RNA-protein complexes
      by providing information about the nucleic acid structure as well as interacting
      proteins.
    example: null
    first_party: null
    homepage: https://rnaprodb.usc.edu
    name: RNA Protein Database
    publications:
    - doi: 10.1016/j.jmb.2025.169012
      pmc: null
      pubmed: '40126909'
      title: 'RNAproDB: A Webserver and Interactive Database for Analyzing Protein-RNA
        Interactions'
      year: 2025
    status: null
    uri_format: https://rnaprodb.usc.edu/$1
  - code: proteinsplus
    description: Database of protein-ligand interactions.
    example: null
    first_party: null
    homepage: https://proteins.plus/
    name: ProteinsPlus
    publications:
    - doi: 10.1093/nar/gkaf377
      pmc: null
      pubmed: '40326518'
      title: 'ProteinsPlus: a publicly available resource for protein structure mining'
      year: 2025
    status: null
    uri_format: https://proteins.plus/$1
  publications:
  - doi: 10.1002/pro.4211
    pmc: PMC8740847
    pubmed: '34664328'
    title: 'Protein Data Bank Japan: Celebrating our 20th anniversary during a global
      pandemic as the Asian hub of three dimensional macromolecular structural data'
    year: 2021
  - doi: 10.1002/pro.3273
    pmc: PMC5734392
    pubmed: '28815765'
    title: New tools and functions in data-out activities at Protein Data Bank Japan
      (PDBj)
    year: 2017
  - doi: 10.1093/nar/gkw962
    pmc: PMC5210648
    pubmed: '27789697'
    title: 'Protein Data Bank Japan (PDBj): updated user interfaces, resource description
      framework, analysis tools for large structures'
    year: 2016
  - doi: 10.1007/s10822-011-9460-y
    pmc: null
    pubmed: '21796434'
    title: 'Protein Data Bank Japan (PDBj): an interview with Haruki Nakamura of Osaka
      University by Wendy A. Warr'
    year: 2011
  - doi: 10.1093/nar/gkr811
    pmc: PMC3245181
    pubmed: '21976737'
    title: 'Protein Data Bank Japan (PDBj): maintaining a structural data archive
      and resource description framework format'
    year: 2011
  - doi: 10.1093/database/baq021
    pmc: PMC2997606
    pubmed: '20798081'
    title: 'PDBj Mine: design and implementation of relational database interface
      for Protein Data Bank Japan'
    year: 2010
  - doi: null
    pmc: null
    pubmed: '12099029'
    title: '[Development of PDBj: Advanced database for protein structures]'
    year: 2002
  - doi: 10.1002/pro.3273
    pmc: null
    pubmed: null
    title: New tools and functions in data-out activities at Protein Data Bank Japan
      (PDBj).
    year: null
  - doi: 10.1093/nar/gkr811
    pmc: null
    pubmed: null
    title: 'Protein Data Bank Japan (PDBj): maintaining a structural data archive
      and resource description framework format.'
    year: null
  - doi: 10.1093/database/baq021
    pmc: null
    pubmed: null
    title: 'PDBj Mine: design and implementation of relational database interface
      for Protein Data Bank Japan.'
    year: null
  - doi: 10.1007/s10822-011-9460-y
    pmc: null
    pubmed: null
    title: 'Protein Data Bank Japan (PDBj): an interview with Haruki Nakamura of Osaka
      University by Wendy A. Warr.'
    year: null
  - doi: 10.1093/nar/gkw962
    pmc: null
    pubmed: null
    title: 'Protein Data Bank Japan (PDBj): updated user interfaces, resource description
      framework, analysis tools for large structures.'
    year: null
  - doi: 10.1002/pro.4211
    pmc: null
    pubmed: null
    title: 'Protein Data Bank Japan: Celebrating our 20th anniversary during a global
      pandemic as the Asian hub of three dimensional macromolecular structural data'
    year: null
  - doi: 10.1002/pro.4211
    pmc: null
    pubmed: '34664328'
    title: null
    year: null
  - doi: 10.1093/nar/gkt1043
    pmc: PMC3965125
    pubmed: '24214988'
    title: 'SAbDab: the structural antibody database'
    year: 2013
  - doi: 10.1371/journal.pbio.3002476
    pmc: PMC11309384
    pubmed: '39074139'
    title: 'FURNA: A database for functional annotations of RNA structures'
    year: 2024
  - doi: 10.1093/nar/gkae890
    pmc: null
    pubmed: '39436020'
    title: 'DIONYSUS: a database of protein-carbohydrate interfaces'
    year: 2024
  - doi: 10.1016/j.jmb.2025.169012
    pmc: null
    pubmed: '40126909'
    title: 'RNAproDB: A Webserver and Interactive Database for Analyzing Protein-RNA
      Interactions'
    year: 2025
  - doi: 10.1093/nar/gkaf377
    pmc: null
    pubmed: '40326518'
    title: 'ProteinsPlus: a publicly available resource for protein structure mining'
    year: 2025
  - doi: 10.1002/pro.3273
    pmc: null
    pubmed: null
    title: New tools and functions in data-out activities at Protein Data Bank Japan
      (PDBj).
    year: null
  - doi: 10.1093/nar/gkr811
    pmc: null
    pubmed: null
    title: 'Protein Data Bank Japan (PDBj): maintaining a structural data archive
      and resource description framework format.'
    year: null
  - doi: 10.1093/database/baq021
    pmc: null
    pubmed: null
    title: 'PDBj Mine: design and implementation of relational database interface
      for Protein Data Bank Japan.'
    year: null
  - doi: 10.1007/s10822-011-9460-y
    pmc: null
    pubmed: null
    title: 'Protein Data Bank Japan (PDBj): an interview with Haruki Nakamura of Osaka
      University by Wendy A. Warr.'
    year: null
  - doi: 10.1093/nar/gkw962
    pmc: null
    pubmed: null
    title: 'Protein Data Bank Japan (PDBj): updated user interfaces, resource description
      framework, analysis tools for large structures.'
    year: null
  - doi: 10.1002/pro.4211
    pmc: null
    pubmed: null
    title: 'Protein Data Bank Japan: Celebrating our 20th anniversary during a global
      pandemic as the Asian hub of three dimensional macromolecular structural data'
    year: null
  - doi: 10.1002/pro.4211
    pmc: null
    pubmed: '34664328'
    title: null
    year: null
  - doi: 10.1093/nar/gkt1043
    pmc: PMC3965125
    pubmed: '24214988'
    title: 'SAbDab: the structural antibody database'
    year: 2013
  - doi: 10.1371/journal.pbio.3002476
    pmc: PMC11309384
    pubmed: '39074139'
    title: 'FURNA: A database for functional annotations of RNA structures'
    year: 2024
  - doi: 10.1093/nar/gkae890
    pmc: null
    pubmed: '39436020'
    title: 'DIONYSUS: a database of protein-carbohydrate interfaces'
    year: 2024
  - doi: 10.1016/j.jmb.2025.169012
    pmc: null
    pubmed: '40126909'
    title: 'RNAproDB: A Webserver and Interactive Database for Analyzing Protein-RNA
      Interactions'
    year: 2025
  - doi: 10.1093/nar/gkaf377
    pmc: null
    pubmed: '40326518'
    title: 'ProteinsPlus: a publicly available resource for protein structure mining'
    year: 2025
  re3data:
    description: PDBj (Protein Data Bank Japan) provides a centralized PDB archive
      of macromolecular structures, integrated tools for data retrieval, visualization,
      and functional characterization. PDBj is supported by JST-NBDC and Osaka University.
    doi: 10.17616/R3RP75
    homepage: https://pdbj.org/
    license: CC
    name: PDBj
    prefix: r3d100010910
    synonyms:
    - Protein Data Bank Japan
  synonyms:
  - RCSB_PDB
  - pdbe
  - pdbj
  - wwpdb
  togoid:
    catalog: nbdc00156
    description: This is an international public repository for three-dimensional
      structures and structure coordinates (conformations) of proteins and nucleic
      acids, and the central database for biological structural data. Data obtained
      through X-ray crystallography and NMR experiments are stored in PDB. In addition
      to three-dimensional information of proteins, users can find amino acid sequences,
      protein-related information on GO, and other compounds bound to the protein.
    examples:
    - 3PFQ
    - 2OUY
    - 6EBX
    - 5GHP
    - 6ETH
    - 1Y28
    - 6FB2
    - 5JO3
    - 2JQZ
    - 5L5P
    keywords:
    - Structure
    name: PDB
    pattern: ^(?[0-9][A-Za-z0-9]{3})$
    prefix: Pdb
    uri_format: http://rdf.wwpdb.org/pdb/$1
  uniprot:
    abbreviation: PDBj
    category: 3D structure databases
    homepage: https://pdbj.org/
    name: Protein Data Bank Japan
    prefix: DB-0172
    publications:
    - doi: 10.1002/pro.4211
      pubmed: '34664328'
    uri_format: https://pdbj.org/mine/summary/$1
  wikidata:
    description: identifier for 3D structural data as per the PDB (Protein Data Bank)
      database
    example:
    - 1XU7
    - 4P38
    - 4ZHD
    homepage: https://www.rcsb.org/
    miriam: pdb
    name: PDB structure ID
    pattern: ^[0-9][0-9A-Za-z]{3}$
    prefix: P638
    uri_format: https://www.rcsb.org/structure/$1
    uri_format_rdf: https://rdf.wwpdb.org/pdb/$1
pdb-ccd:
  biocontext:
    prefix: PDB-CCD
  comment: might be same as pdb.ligand, not sure though
  contact:
    email: berman@rcsb.rutgers.edu
    github: null
    name: Helen Berman
    orcid: 0000-0002-3337-0660
  contributor_extras:
  - email: bmeldal@ebi.ac.uk
    github: bmeldal-eg
    name: Birgit Meldal
    orcid: 0000-0003-4062-6158
  example_extras:
  - A
  - PI
  has_canonical: pdb.ligand
  mappings:
    biocontext: PDB-CCD
    miriam: pdb-ccd
    n2t: pdb-ccd
    prefixcommons: ccd
    togoid: PdbCcd
  miriam:
    deprecated: false
    description: The Chemical Component Dictionary is as an external reference file
      describing all residue and small molecule components found in Protein Data Bank
      entries. It contains detailed chemical descriptions for standard and modified
      amino acids/nucleotides, small molecule ligands, and solvent molecules. Each
      chemical definition includes descriptions of chemical properties such as stereochemical
      assignments, aromatic bond assignments, idealized coordinates, chemical descriptors
      (SMILES & InChI), and systematic chemical names.
    homepage: https://www.ebi.ac.uk/pdbe-srv/pdbechem/
    id: '00000113'
    name: Chemical Component Dictionary
    namespaceEmbeddedInLui: false
    pattern: ^\w{1,3}$
    prefix: pdb-ccd
    sampleId: AB0
    uri_format: https://www.ebi.ac.uk/pdbe-srv/pdbechem/chemicalCompound/show/$1
  n2t:
    description: The Chemical Component Dictionary is as an external reference file
      describing all residue and small molecule components found in Protein Data Bank
      entries. It contains detailed chemical descriptions for standard and modified
      amino acids/nucleotides, small molecule ligands, and solvent molecules. Each
      chemical definition includes descriptions of chemical properties such as stereochemical
      assignments, aromatic bond assignments, idealized coordinates, chemical descriptors
      (SMILES & InChI), and systematic chemical names.
    example: AB0
    homepage: https://www.ebi.ac.uk/pdbe-srv/pdbechem/
    name: Protein Data Bank Chemical Component Dictionary at EBI
    namespaceEmbeddedInLui: false
    pattern: ^\w{3}$
    prefix: pdb-ccd
    uri_format: https://www.ebi.ac.uk/pdbe-srv/pdbechem/chemicalCompound/show/$1
  pattern: ^\w{1,3}$
  prefix: pdb-ccd
  prefixcommons:
    description: The Chemical Component Dictionary is as an external reference file
      describing all residue and small molecule components found in Protein Data Bank
      entries. It contains detailed chemical descriptions for standard and modified
      amino acids/nucleotides, small molecule ligands, and solvent molecules. Each
      chemical definition includes descriptions of chemical properties such as stereochemical
      assignments, aromatic bond assignments, idealized coordinates, chemical descriptors
      (SMILES & InChI), and systematic chemical names.
    example: AB0
    homepage: http://www.ebi.ac.uk/msd-srv/msdchem/cgi-bin/cgi.pl?APPLICATION=1
    keywords:
    - chemical
    - classification
    license: http://www.ebi.ac.uk/Information/termsofuse.html
    name: Chemical Component Dictionary
    pattern: ^\w{3}$
    prefix: ccd
    pubmed_ids:
    - '14634627'
    synonyms:
    - het
    - pdb.het
    - pdb.ccd
    uri_format: http://www.ebi.ac.uk/msd-srv/msdchem/cgi-bin/cgi.pl?FUNCTION=record&ENTITY=CHEM_COMP&PRIMARYKEY=$1&APPLICATION=1
  publications:
  - doi: 10.1038/nsb1203-980
    pmc: null
    pubmed: '14634627'
    title: Announcing the worldwide Protein Data Bank
    year: 2003
  - doi: null
    pmc: null
    pubmed: '14634627'
    title: null
    year: null
  synonyms:
  - PDBeChem
  - pdbechem
  togoid:
    catalog: nbdc01766
    examples:
    - D5Y
    - P2B
    - A6L
    - M35
    - A6M
    - S1P
    - D5Z
    - M36
    - P2C
    - P2D
    keywords:
    - Compound
    name: PDB CCD
    pattern: ^(?\w{1,3})$
    prefix: PdbCcd
    uri_format: http://identifiers.org/pdb-ccd/$1
  uri_format: https://www.ebi.ac.uk/pdbe-srv/pdbechem/chemicalCompound/show/$1
pdb.ligand:
  biocontext:
    prefix: PDB.LIGAND
  mappings:
    biocontext: PDB.LIGAND
    miriam: pdb.ligand
    n2t: pdb.ligand
    pathguide: '169'
    prefixcommons: pdbligand
    wikidata: P3636
  miriam:
    deprecated: false
    description: The Protein Data Bank is the single worldwide archive of structural
      data of biological macromolecules. This collection references ligands.
    homepage: http://www.rcsb.org
    id: 00000490
    name: Protein Data Bank Ligand
    namespaceEmbeddedInLui: false
    pattern: ^[A-Za-z0-9]+$
    prefix: pdb.ligand
    providers:
    - code: ''
      description: PDB Ligand at Protein Databank in Europe (PDBe)
      homepage: https://www.pdbe.org/
      name: PDB Ligand at Protein Databank in Europe (PDBe)
      uri_format: https://www.ebi.ac.uk/pdbe-srv/pdbechem/chemicalCompound/show/$1
    sampleId: TRQ
    uri_format: http://www.rcsb.org/ligand/$1
  n2t:
    description: The Protein Data Bank is the single worldwide archive of structural
      data of biological macromolecules. This collection references ligands.
    example: TRQ
    homepage: http://www.pdb.org/
    name: PDB Ligand at RCSB
    namespaceEmbeddedInLui: false
    pattern: ^[A-Za-z0-9]+$
    prefix: pdb.ligand
    uri_format: http://www.rcsb.org/pdb/ligand/ligandsummary.do?hetId=$1
  name: PDB ligand
  part_of_database: pdb
  pathguide:
    abbreviation: PDB-Ligand
    homepage: http://www.idrtech.com/PDB-Ligand/
    name: PDB-Ligand
    prefix: '169'
  prefix: pdb.ligand
  prefixcommons:
    description: PDB-Ligand is a three dimensional structure database of small molecular
      ligands that are bound to larger biolomocules deposited in the Protein Data
      Bank (PDB).
    example: 1iij
    homepage: http://www.idrtech.com/PDB-Ligand/
    keywords:
    - small molecule
    - protein
    - interaction
    - structure
    name: PDB-Ligand
    pattern: ^[A-Z,0-9]+$
    prefix: pdbligand
  synonyms:
  - PDB_CHEM_ID
  wikidata:
    description: identifier for small molecules and ligands in the Protein Data Bank
      (PDB)
    example:
    - '010'
    - '032'
    - '601'
    homepage: http://www.wwpdb.org/
    miriam: pdb.ligand
    name: PDB ligand ID
    pattern: ^[A-Z0-9]{1,3}|PRD_[0-9]+$
    prefix: P3636
    uri_format: https://www.rcsb.org/ligand/$1
pdbsum:
  fairsharing:
    abbreviation: PDBsum
    contact:
      email: roman@ebi.ac.uk
      name: Roman Laskowski
      orcid: 0000-0001-5528-0087
    description: PDBsum provides an overview of every macromolecular structure deposited
      in the Protein Data Bank (PDB), giving schematic diagrams of the molecules in
      each structure and of the interactions between them.
    homepage: http://www.ebi.ac.uk/pdbsum
    license: http://opendatacommons.org/licenses/pddl/1.0
    name: PDBsum; at-a-glance overview of macromolecular structures
    prefix: FAIRsharing.7vjq5t
    publications:
    - doi: 10.1093/nar/gkt940
      pubmed_id: 24153109
      title: PDBsum additions.
    - doi: 10.1002/pro.3289
      pubmed_id: 28875543
      title: 'PDBsum: Structural summaries of PDB entries.'
    - doi: 10.1093/nar/gkn860
      pubmed_id: 18996896
      title: PDBsum new things.
    subjects:
    - Structural Biology
  integbio:
    description: 'PDBsum is a database that contains the annotated 3-dimensional structures
      of all the proteins in the Protein Data Bank (PDB).

      The diagrams indicate the protein chains, ligands, DNA and the metal ions present
      in the protein structures and also how these molecules interact with each other.

      This database contains 92,037 ProteinDataBase entries.

      PDB code, text and sequence search options are available.

      Data files can also be downloaded from the site.'
    fairsharing: biodbcore-000323
    homepage: http://www.ebi.ac.uk/thornton-srv/databases/pdbsum/
    information_keywords:
    - Image/Movie
    - 3D structure
    maintainer: EMBL-EBI (European Bioinformatics Institute)
    name: PDBsum
    prefix: nbdc00308
    pubmeds:
    - '18996896'
    - '15608193'
    - '11125097'
    - '9433130'
    - '17384425'
    status: Active
    target_keywords:
    - Protein
  mappings:
    fairsharing: FAIRsharing.7vjq5t
    integbio: nbdc00308
    pathguide: '461'
    prefixcommons: pdbsum
    uniprot: DB-0119
  pathguide:
    abbreviation: PDBsum
    homepage: http://www.ebi.ac.uk/thornton-srv/databases/cgi-bin/pdbsum/GetPage.pl?pdbcode=index.html
    name: 'PDBsum: pictorial database of 3D structures in the Protein Data Bank'
    prefix: '461'
  prefix: pdbsum
  prefixcommons:
    description: PDBsum provides an at-a-glance overview of every macromolecular structure
      deposited in the Protein Data Bank (PDB), giving schematic diagrams of the molecules
      in each structure and of the interactions between them.
    example: 1kfv
    homepage: http://www.ebi.ac.uk/pdbsum
    keywords:
    - protein
    - structure
    - interaction
    license: http://www.ebi.ac.uk/Information/termsofuse.html
    name: PDBsum; at-a-glance overview of macromolecular structures
    pattern: ^[A-Z,0-9]+$
    prefix: pdbsum
    uri_format: http://www.ebi.ac.uk/pdbsum/$1
  provides: pdb
  publications:
  - doi: 10.1002/pro.3289
    pmc: PMC5734310
    pubmed: '28875543'
    title: 'PDBsum: Structural summaries of PDB entries'
    year: 2017
  - doi: 10.1093/nar/gkt940
    pmc: PMC3965036
    pubmed: '24153109'
    title: PDBsum additions
    year: 2013
  - doi: 10.1093/nar/gkn860
    pmc: PMC2686501
    pubmed: '18996896'
    title: PDBsum new things
    year: 2008
  reviewer:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  uniprot:
    abbreviation: PDBsum
    category: 3D structure databases
    homepage: https://www.ebi.ac.uk/pdbsum/
    name: PDBsum; at-a-glance overview of macromolecular structures
    prefix: DB-0119
    publications:
    - doi: 10.1002/pro.3289
      pubmed: '28875543'
    uri_format: https://www.ebi.ac.uk/pdbsum/$1
pdc.study:
  contributor:
    email: benjamin_gyori@hms.harvard.edu
    github: bgyori
    name: Benjamin M. Gyori
    orcid: 0000-0001-9439-5346
  description: The National Cancer Institute's Proteomic Data Commons (PDC) makes
    cancer-related proteomic datasets easily accessible to the public.
  example: PDC000351
  github_request_issue: 430
  homepage: https://pdc.cancer.gov/pdc
  name: Proteomic Data Commons
  pattern: ^PDC\d+$
  prefix: pdc.study
  reviewer:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  uri_format: https://pdc.cancer.gov/pdc/study/$1
pdro:
  aberowl:
    description: An ontology to describe entities related to prescription of drugs
    download_owl: http://aber-owl.net/media/ontologies/PDRO/8/pdro.owl
    homepage: https://github.com/OpenLHS/PDRO
    name: The Prescription of Drugs Ontology
    prefix: PDRO
  biocontext:
    prefix: PDRO
  bioportal:
    contact:
      email: ryeyan.taseen@gmail.com
      name: Ryeyan Taseen
    description: PDRO is a realist ontology that aims to represent the domain of drug
      prescriptions. Such an ontology is currently missing in the OBOFoundry and is
      highly relevant to the domains of existing ontologies like DRON, OMRSE and OAE.
      PDRO’s central focus is the structure of a drug prescription, which is represented
      as a mereology of informational entities. Our current use cases are (1) refining
      this structure (e.g., adding closure axioms, cardinality, datatype bindings,
      etc) for prospectively standardizing local electronic prescriptions and (2)
      annotating prescription data of differing EHRs for detecting inappropriate prescriptions
      using a central semantic framework. Future ontological work will include aligning
      PDRO more closely with the Document Acts Ontology.
    homepage: https://github.com/OpenLHS/PDRO
    name: The Prescription of Drugs Ontology
    prefix: PDRO
  example: 0010039
  fairsharing:
    abbreviation: PDRO
    description: PDRO is a realist ontology that aims to represent the domain of drug
      prescriptions. Such an ontology is currently missing in the OBOFoundry and is
      highly relevant to the domains of existing ontologies like DRON, OMRSE and OAE.
      PDRO’s central focus is the structure of a drug prescription, which is represented
      as a mereology of informational entities. Our current use cases are (1) refining
      this structure (e.g., adding closure axioms, cardinality, datatype bindings,
      etc) for prospectively standardizing local electronic prescriptions and (2)
      annotating prescription data of differing EHRs for detecting inappropriate prescriptions
      using a central semantic framework. Future ontological work will include aligning
      PDRO more closely with the Document Acts Ontology.
    domains:
    - drug
    homepage: https://github.com/OpenLHS/PDRO
    license: CC-BY-4.0
    name: The Prescription of Drugs Ontology
    prefix: FAIRsharing.9te3ev
    subjects:
    - Primary Health Care
  mappings:
    aberowl: PDRO
    biocontext: PDRO
    bioportal: PDRO
    fairsharing: FAIRsharing.9te3ev
    obofoundry: pdro
    ols: pdro
    ontobee: PDRO
    wikidata.entity: Q81661774
  obofoundry:
    contact: paul.fabry@usherbrooke.ca
    contact.github: pfabry
    contact.label: Paul Fabry
    contact.orcid: 0000-0002-3336-2476
    deprecated: false
    description: An ontology to describe entities related to prescription of drugs
    domain: information
    download.owl: http://purl.obolibrary.org/obo/pdro.owl
    homepage: https://github.com/OpenLHS/PDRO
    license: CC BY 4.0
    license.url: https://creativecommons.org/licenses/by/4.0/
    name: The Prescription of Drugs Ontology
    preferredPrefix: PDRO
    prefix: pdro
    publications:
    - id: https://www.ncbi.nlm.nih.gov/pubmed/34831777
      title: 'The Prescription of Drug Ontology 2.0 (PDRO): More Than the Sum of Its
        Parts'
    repository: https://github.com/OpenLHS/PDRO
  ols:
    description: An ontology to describe entities related to prescription of drugs
    download_owl: http://purl.obolibrary.org/obo/pdro.owl
    homepage: https://github.com/OpenLHS/PDRO
    name: The Prescription of Drugs Ontology
    prefix: pdro
    tracker: https://github.com/OpenLHS/PDRO/issues
    version: '2021-06-08'
    version.iri: http://purl.obolibrary.org/obo/pdro/2021-06-08/pdro.owl
  ontobee:
    library: Library
    name: The Prescription of Drugs Ontology
    prefix: PDRO
  pattern: ^\d{7}$
  prefix: pdro
  providers:
  - code: pdro.legacy
    description: An incorrect encoding of OBO purls
    example: null
    first_party: null
    homepage: http://purl.obolibrary.org/obo/pdro
    name: PDRO Hash
    publications: null
    status: null
    uri_format: http://purl.obolibrary.org/obo/PDRO/PDRO.owl#PDRO_$1
  publications:
  - doi: 10.3390/ijerph182212025
    pmc: PMC8619589
    pubmed: '34831777'
    title: 'The Prescription of Drug Ontology 2.0 (PDRO): More Than the Sum of Its
      Parts'
    year: 2021
  uri_format: http://purl.obolibrary.org/obo/PDRO_$1
pdumdv:
  aberowl:
    description: Life cycle stages for Platynereis dumerilii
    download_owl: http://aber-owl.net/media/ontologies/PDUMDV/10/pdumdv.owl
    homepage: https://github.com/obophenotype/developmental-stage-ontologies/wiki/PdumDv
    name: Platynereis Developmental Stages
    prefix: PDUMDV
  biocontext:
    prefix: PDUMDV
  bioportal:
    contact:
      email: cjmungall@lbl.gov
      name: Chris Mungall
    description: Life cycle stages for Platynereis dumerilii.
    homepage: https://github.com/obophenotype/developmental-stage-ontologies
    name: Platynereis Developmental Stages
    prefix: PDUMDV
  example: '0001410'
  fairsharing:
    abbreviation: PDUMDV
    description: Life cycle stages for Platynereis dumerilii. The status of this resource
      is "in development", confirmed via developer remarks within the GitHub project
      stating that the ontology is not ready.
    domains:
    - life cycle stage
    homepage: https://github.com/obophenotype/developmental-stage-ontologies/tree/master/src/pdumdv
    name: Platynereis Developmental Stages
    prefix: FAIRsharing.493qns
    repository: https://github.com/obophenotype/developmental-stage-ontologies/wiki
    subjects:
    - Life Science
    - Developmental Biology
  mappings:
    aberowl: PDUMDV
    biocontext: PDUMDV
    bioportal: PDUMDV
    fairsharing: FAIRsharing.493qns
    obofoundry: pdumdv
    ols: pdumdv
    ontobee: PdumDv
    wikidata.entity: Q81661775
  obofoundry:
    contact: frederic.bastian@unil.ch
    contact.github: fbastian
    contact.label: Frédéric Bastian
    contact.orcid: 0000-0002-9415-5104
    deprecated: true
    description: Life cycle stages for Platynereis dumerilii
    domain: anatomy and development
    download.obo: http://purl.obolibrary.org/obo/pdumdv.obo
    download.owl: http://purl.obolibrary.org/obo/pdumdv.owl
    homepage: https://github.com/obophenotype/developmental-stage-ontologies/wiki/PdumDv
    license: CC BY 3.0
    license.url: http://creativecommons.org/licenses/by/3.0/
    name: Platynereis Developmental Stages
    preferredPrefix: PdumDv
    prefix: pdumdv
    repository: https://github.com/obophenotype/developmental-stage-ontologies
  ols:
    description: Life cycle stages for Platynereis dumerilii
    download_owl: http://purl.obolibrary.org/obo/pdumdv.owl
    homepage: https://github.com/obophenotype/developmental-stage-ontologies/wiki/PdumDv
    name: Platynereis Developmental Stages
    prefix: pdumdv
    tracker: https://github.com/obophenotype/developmental-stage-ontologies/issues
  ontobee:
    library: Library
    name: Platynereis Developmental Stages
    prefix: PdumDv
  pattern: ^\d{7}$
  prefix: pdumdv
  synonyms:
  - PdumDv
  uri_format: http://purl.obolibrary.org/obo/PdumDv_$1
peco:
  aberowl:
    description: A structured, controlled vocabulary which describes the treatments,
      growing conditions, and/or study types used in plant biology experiments.
    download_owl: http://aber-owl.net/media/ontologies/PECO/32/peco.owl
    homepage: http://planteome.org/
    name: Plant Experimental Conditions Ontology
    prefix: PECO
  agroportal:
    contact:
      email: cooperl@oregonstate.edu
      name: Laurel Cooper
    description: A structured, controlled vocabulary which describes the treatments,
      growing conditions, and/or study types used in plant biology experiments.
    example_uri: http://purl.obolibrary.org/obo/PECO_0007359
    homepage: https://planteome.org/
    license: CC-BY-4.0
    name: Plant Experimental Conditions Ontology
    prefix: PECO
    publications:
    - https://planteome.org/references
    - https://doi.org/10.3732/ajb.1200222
    repository: https://github.com/Planteome/plant-experimental-conditions-ontology
    version: December 2025
  biocontext:
    prefix: PECO
  bioportal:
    contact:
      email: jaiswalp@science.oregonstate.edu
      name: Pankaj Jaiswal
    description: The Plant Experimental Conditions Ontology describes the treatments,
      growing conditions, and/or study types used in plant biology experiments. The
      subjects of the studies may also include in vitro plant structures (PO:0000004).
      A plant treatment is the most specific,and may be a component of a plant growing
      condition, and the plant study type. The broadest classes are the plant study
      types where the terms can be used to identify the growth study facility. Each
      growth facility such as field study, growth chamber, green house etc is a environment
      on its own and it may also involve instances of biotic and abiotic treatments
      and different growing conditions.
    homepage: http://browser.planteome.org/amigo/term/EO:0007359
    name: Plant Experimental Conditions Ontology
    prefix: PECO
    publications:
    - http://planteome.org/pub
    version: releases/2023-11-10
  download_obo: https://raw.githubusercontent.com/Planteome/plant-experimental-conditions-ontology/master/peco.obo
  example: '0007114'
  fairsharing:
    abbreviation: PECO
    description: PECO is a structured, controlled vocabulary for the representation
      of plant experimental conditions. It describes the treatments, growing conditions,
      and/or study types used in various types of plant biology experiments.
    domains:
    - Experimental measurement
    - study design
    - experimentally determined
    homepage: https://github.com/Planteome/plant-experimental-conditions-ontology
    license: CC-BY-4.0
    name: Plant Experimental Condition Ontology
    prefix: FAIRsharing.6yNXYK
    publications:
    - doi: 10.1093/nar/gkx1152
      pubmed: '29186578'
      title: 'The Planteome database: an integrated resource for reference ontologies,
        plant genomics and phenomics'
      year: 2017
    repository: https://github.com/Planteome/plant-experimental-conditions-ontology/issues
    subjects:
    - Botany
    user_defined_tags:
    - Experimental condition
  mappings:
    aberowl: PECO
    agroportal: PECO
    biocontext: PECO
    bioportal: PECO
    fairsharing: FAIRsharing.6yNXYK
    obofoundry: peco
    ols: peco
    ontobee: PECO
    tib: peco
    wikidata.entity: Q81661777
  obofoundry:
    appears_in:
    - agro
    - mco
    contact: jaiswalp@science.oregonstate.edu
    contact.github: jaiswalp
    contact.label: Pankaj Jaiswal
    contact.orcid: 0000-0002-1005-8383
    deprecated: false
    description: A structured, controlled vocabulary which describes the treatments,
      growing conditions, and/or study types used in plant biology experiments.
    domain: investigations
    download.obo: http://purl.obolibrary.org/obo/peco.obo
    download.owl: http://purl.obolibrary.org/obo/peco.owl
    homepage: http://planteome.org/
    license: CC BY 4.0
    license.url: https://creativecommons.org/licenses/by/4.0/
    logo: http://planteome.org/sites/default/files/garland_logo.PNG
    name: Plant Experimental Conditions Ontology
    preferredPrefix: PECO
    prefix: peco
    publications:
    - id: https://www.ncbi.nlm.nih.gov/pubmed/29186578
      title: 'The Planteome database: an integrated resource for reference ontologies,
        plant genomics and phenomics.'
    repository: https://github.com/Planteome/plant-experimental-conditions-ontology
  ols:
    description: A structured, controlled vocabulary which describes the treatments,
      growing conditions, and/or study types used in plant biology experiments.
    download_owl: http://purl.obolibrary.org/obo/peco.owl
    homepage: http://planteome.org/
    name: Plant Experimental Conditions Ontology
    prefix: peco
    tracker: https://github.com/Planteome/plant-experimental-conditions-ontology/issues
    version: '2025-12-02'
    version.iri: http://purl.obolibrary.org/obo/peco/releases/2025-12-02/peco.owl
  ontobee:
    library: Library
    name: Plant Experimental Conditions Ontology
    prefix: PECO
  pattern: ^\d{7}$
  preferred_prefix: PECO
  prefix: peco
  publications:
  - doi: 10.1093/nar/gkx1152
    pmc: PMC5753347
    pubmed: '29186578'
    title: 'The Planteome database: an integrated resource for reference ontologies,
      plant genomics and phenomics'
    year: 2018
  - doi: null
    pmc: null
    pubmed: '29186578'
    title: 'The Planteome database: an integrated resource for reference ontologies,
      plant genomics and phenomics'
    year: null
  - doi: 10.1093/nar/gkx1152
    pmc: null
    pubmed: '29186578'
    title: 'The Planteome database: an integrated resource for reference ontologies,
      plant genomics and phenomics'
    year: 2017
  - doi: null
    pmc: null
    pubmed: '29186578'
    title: 'The Planteome database: an integrated resource for reference ontologies,
      plant genomics and phenomics'
    year: null
  - doi: 10.1093/nar/gkx1152
    pmc: null
    pubmed: '29186578'
    title: 'The Planteome database: an integrated resource for reference ontologies,
      plant genomics and phenomics'
    year: 2017
  - doi: null
    pmc: null
    pubmed: '29186578'
    title: 'The Planteome database: an integrated resource for reference ontologies,
      plant genomics and phenomics'
    year: null
  - doi: 10.1093/nar/gkx1152
    pmc: null
    pubmed: '29186578'
    title: 'The Planteome database: an integrated resource for reference ontologies,
      plant genomics and phenomics'
    year: 2017
  - doi: null
    pmc: null
    pubmed: '29186578'
    title: 'The Planteome database: an integrated resource for reference ontologies,
      plant genomics and phenomics'
    year: null
  - doi: 10.1093/nar/gkx1152
    pmc: null
    pubmed: '29186578'
    title: 'The Planteome database: an integrated resource for reference ontologies,
      plant genomics and phenomics'
    year: 2017
  rdf_uri_format: http://purl.obolibrary.org/obo/PECO_$1
  tib:
    contact: jaiswalp@oregonstate.edu
    description: A structured, controlled vocabulary which describes the treatments,
      growing conditions, and/or study types used in plant biology experiments.
    download_owl: http://purl.obolibrary.org/obo/peco.owl
    homepage: http://planteome.org/
    keywords:
    - DataPLANT
    - life sciences, biology
    name: Plant Environmental Conditions Ontology
    prefix: peco
    tracker: https://github.com/Planteome/plant-experimental-conditions-ontology/issues/
    version.iri: http://purl.obolibrary.org/obo/peco/releases/2025-10-30/peco.owl
  uri_format: https://browser.planteome.org/amigo/term/PECO:$1
ped:
  contact:
    email: zhangzhang@big.ac.cn
    github: null
    name: Zhang Zhang
    orcid: 0000-0001-6603-5060
  fairsharing:
    abbreviation: PED
    description: The Plant Editosome Database (PED) is a curated database of plant
      RNA editing factors (editosomes). The data has been drawn from publications
      and organelle genome annotations. PED incorporates RNA editing factors and associated
      data across a number of plant species.
    homepage: https://bigd.big.ac.cn/ped
    license: https://creativecommons.org/licenses/by/3.0/cn
    name: Plant Editosome Database
    prefix: FAIRsharing.4ef690
    publications:
    - doi: 10.1093/nar/gky1026
      pubmed_id: 30364952
      title: 'Plant editosome database: a curated database of RNA editosome in plants.'
    subjects:
    - Botany
    - Plant Genetics
  integbio:
    alt_name: Plant Editosome Database
    description: PED is a curated database of RNA editosome in plants, which is focused
      on the curation, integration and standardization of plant RNA editing factors
      (editosome) and the related data. It provides detailed relevant information,
      including factor name, protein family, subclass, structure, species, associated
      plant phenotype(s), edited gene(s), organelle and PMID(s). Each entry also contains
      more details covering treatment, trait, phenotype, editing frequency, etc.
    homepage: https://bigd.big.ac.cn/ped/home
    information_keywords:
    - Sequence
    - Interaction/Pathway
    maintainer: National Genomics Data Center, Beijing Institute of Genomics, Chinese
      Academy of Sciences
    name: PED
    prefix: nbdc02490
    pubmeds:
    - '30364952'
    - '30365034'
    status: Active
    target_keywords:
    - Genome/Gene
    - RNA
    - Cell/Organelle
  mappings:
    fairsharing: FAIRsharing.4ef690
    integbio: nbdc02490
    miriam: ped
  miriam:
    deprecated: false
    description: The Protein Ensemble Database is an open access database for the
      deposition of structural ensembles, including intrinsically disordered proteins.
    homepage: https://proteinensemble.org/
    id: '00000777'
    name: Protein Ensemble Database
    namespaceEmbeddedInLui: false
    pattern: ^PED\d{5}$
    prefix: ped
    sampleId: PED00037
    uri_format: https://proteinensemble.org/$1
  prefix: ped
  publications:
  - doi: 10.1093/nar/gky1026
    pmc: PMC6324055
    pubmed: '30364952'
    title: 'Plant editosome database: a curated database of RNA editosome in plants'
    year: 2019
  - doi: 10.1093/nar/gky1026
    pmc: null
    pubmed: null
    title: 'Plant editosome database: a curated database of RNA editosome in plants.'
    year: null
ped.ensemble:
  mappings:
    miriam: ped.ensemble
  miriam:
    deprecated: false
    description: The Protein Ensemble Database is an open access database for the
      deposition of structural ensembles, including intrinsically disordered proteins.
    homepage: https://proteinensemble.org/
    id: 00000795
    name: Protein Ensemble Database ensemble
    namespaceEmbeddedInLui: false
    pattern: ^PED\d{5}e\d{3}$
    prefix: ped.ensemble
    sampleId: PED00017e001
    uri_format: https://proteinensemble.org/$1
  part_of: ped
  prefix: ped.ensemble
peff:
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  deprecated: true
  download_obo: https://github.com/HUPO-PSI/PEFF/raw/master/CV/psi-peff-OBSOLETE-DO_NOT_USE.obo
  example: '0001011'
  homepage: https://www.psidev.info/peff
  name: PSI Extended File Format
  pattern: ^\d{7}$
  prefix: peff
  uri_format: https://biopragmatics.github.io/providers/peff/$1
pennsieve:
  mappings:
    miriam: ps
  miriam:
    deprecated: false
    description: 'Pennsieve is a publicly accessible Scientific Data Management and
      publication platform. The platform supports data curation, sharing and publishing
      complex scientific datasets with a focus on integration between graph-based
      metadata and file-archival. The platform provides a "peer"-reviewed publication
      mechanism and public datasets are available through its Discover Web Application
      and APIs. '
    homepage: https://discover.pennsieve.io
    id: 00000951
    name: Pennsieve
    namespaceEmbeddedInLui: false
    pattern: ^N:package:[a-z0-9]{8}-[a-z0-9]{4}-[a-z0-9]{4}-[a-z0-9]{4}-[a-z0-9]{12}$
    prefix: ps
    sampleId: N:package:e3243db3-7986-488e-9a10-c7a0bfdcfe8a
    uri_format: https://discover.pennsieve.io/package/$1
  prefix: pennsieve
pepbank:
  comment: This resource doesn't exist on the web anymore
  deprecated: true
  mappings:
    pathguide: '235'
    prefixcommons: pepbank
  pathguide:
    abbreviation: PepBank
    homepage: http://pepbank.mgh.harvard.edu/
    name: PepBank Peptide Database
    prefix: '235'
  prefix: pepbank
  prefixcommons:
    description: PepBank is a database of peptides based on sequence text mining and
      public peptide data sources. Only peptides that are 20 amino acids or shorter
      are stored. Only peptides with available sequences are stored.
    example: '21877'
    homepage: http://pepbank.mgh.harvard.edu/
    keywords:
    - protein
    - structure
    name: PepBank Peptide Database
    pattern: ^\d+$
    prefix: pepbank
    uri_format: http://pepbank.mgh.harvard.edu/interactions/details/$1
  reviewer:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
pephub:
  contact:
    email: nsheffield@virginia.edu
    github: nsheff
    name: Nathan Sheffield
    orcid: 0000-0001-5643-4068
  contributor:
    email: m.naguthana@hotmail.com
    github: nagutm
    name: Mufaddal Naguthanawala
    orcid: 0009-0009-5240-7463
  description: PEPhub is a database, web interface, and API for sharing, retrieving,
    and validating sample metadata. PEPhub uses Portable Encapsulated Projects (PEP)
    biological metadata standard to store, edit, and access PEPs in one place.
  example: geo
  example_extras:
  - geo/gse185244
  - bedbase/gse198944
  - databio/encode_batch_1
  github_request_issue: 1194
  homepage: https://pephub.databio.org/
  name: PEPhub
  pattern: ^[A-Za-z0-9_\-]+(/[A-Za-z0-9_\-]+)?$
  prefix: pephub
  publications:
  - doi: 10.1093/gigascience/giae033
    pmc: PMC11238423
    pubmed: '38991851'
    title: 'PEPhub: a database, web interface, and API for editing, sharing, and validating
      biological sample metadata'
    year: 2024
  reviewer:
    email: b.gyori@northeastern.edu
    github: bgyori
    name: Benjamin M. Gyori
    orcid: 0000-0001-9439-5346
  uri_format: https://pephub.databio.org/$1
peptideatlas.dataset:
  mappings:
    miriam: peptideatlas.dataset
    n2t: peptideatlas.dataset
  miriam:
    deprecated: false
    description: Experiment details about PeptideAtlas entries. Each PASS entry provides
      direct access to the data files submitted to PeptideAtlas.
    homepage: https://db.systemsbiology.net/sbeams/cgi/PeptideAtlas/PASS_Summary
    id: 00000690
    name: PeptideAtlas Dataset
    namespaceEmbeddedInLui: false
    pattern: ^PASS\d{5}$
    prefix: peptideatlas.dataset
    sampleId: PASS01237
    uri_format: http://www.peptideatlas.org/PASS/$1
  n2t:
    description: Experiment details about PeptideAtlas entries. Each PASS entry provides
      direct access to the data files submitted to PeptideAtlas.
    example: PASS01237
    homepage: https://db.systemsbiology.net/sbeams/cgi/PeptideAtlas/PASS_Summary
    name: PeptideAtlas Dataset
    namespaceEmbeddedInLui: false
    pattern: ^PASS\d{5}$
    prefix: peptideatlas.dataset
    uri_format: http://www.peptideatlas.org/PASS/$1
  part_of_database: peptideatlas
  prefix: peptideatlas.dataset
peptideatlas.peptide:
  biocontext:
    prefix: PEPTIDEATLAS
  contact:
    email: edeutsch@systemsbiology.org
    github: edeutsch
    name: Eric W. Deutsch
    orcid: 0000-0001-8732-0928
  edam:
    description: Identifier of a peptide from the PeptideAtlas peptide databases.
    name: PeptideAtlas
    obsolete: false
    prefix: '2626'
  fairsharing:
    abbreviation: PeptideAtlas
    contact:
      email: edeutsch@systemsbiology.org
      name: Eric W. Deutsch
      orcid: 0000-0001-8732-0928
    description: The PeptideAtlas Project provides a publicly-accessible database
      of peptides identified in tandem mass spectrometry proteomics studies and software
      tools. Mass spectrometer output files are collected for human, mouse, yeast,
      and several other organisms, and sequence and spectral library searches are
      applied. Analyses are performed to produce a probability of correct identification
      for all results in a uniform manner, together with false discovery rates at
      the whole-atlas level.
    homepage: http://www.peptideatlas.org
    name: PeptideAtlas
    prefix: FAIRsharing.dvyrsz
    publications:
    - doi: 10.1038/embor.2008.56.
      pubmed_id: 18451766
      title: 'PeptideAtlas: a resource for target selection for emerging targeted
        proteomics workflows.'
    - doi: 10.1093/nar/gkj040
      pubmed_id: 16381952
      title: The PeptideAtlas project
    subjects:
    - Proteomics
  integbio:
    description: The PeptideAtlas Project provides a publicly-accessible database
      of peptides identified in tandem mass spectrometry proteomics studies and software
      tools. Mass spectrometer output files are collected for human, mouse, yeast,
      and several other organisms, and sequence and spectral library searches are
      applied. Analyses are performed to produce a probability of correct identification
      for all results in a uniform manner, together with false discovery rates at
      the whole-atlas level.
    fairsharing: FAIRsharing.dvyrsz
    homepage: http://www.peptideatlas.org
    information_keywords:
    - Sequence
    maintainer: ISB (Institute for Systems Biology)||Seattle Proteome Center
    name: PeptideAtlas
    prefix: nbdc01812
    pubmeds:
    - '18451766'
    - '16381952'
    status: Active
    target_keywords:
    - Protein
  mappings:
    biocontext: PEPTIDEATLAS
    edam: '2626'
    fairsharing: FAIRsharing.dvyrsz
    integbio: nbdc01812
    miriam: peptideatlas
    n2t: peptideatlas
    prefixcommons: peptideatlas
    re3data: r3d100010889
    uniprot: DB-0071
  miriam:
    deprecated: false
    description: The PeptideAtlas Project provides a publicly accessible database
      of peptides identified in tandem mass spectrometry proteomics studies and software
      tools.
    homepage: http://www.peptideatlas.org/
    id: '00000053'
    name: PeptideAtlas
    namespaceEmbeddedInLui: false
    pattern: ^PAp[0-9]{8}$
    prefix: peptideatlas
    sampleId: PAp00000009
    uri_format: https://db.systemsbiology.net/sbeams/cgi/PeptideAtlas/Summarize_Peptide?query=QUERY&searchForThis=$1
  n2t:
    description: The PeptideAtlas Project provides a publicly accessible database
      of peptides identified in tandem mass spectrometry proteomics studies and software
      tools.
    example: PAp00000009
    homepage: http://www.peptideatlas.org/
    name: PeptideAtlas at ISB
    namespaceEmbeddedInLui: false
    pattern: ^PAp[0-9]{8}$
    prefix: peptideatlas
    uri_format: https://db.systemsbiology.net/sbeams/cgi/PeptideAtlas/Summarize_Peptide?query=QUERY&searchForThis=$1
  name: PeptideAtlas Peptide
  prefix: peptideatlas.peptide
  prefixcommons:
    description: The PeptideAtlas Project provides a publicly accessible database
      of peptides identified in tandem mass spectrometry proteomics studies and software
      tools.
    example: PAp00000009
    homepage: http://www.peptideatlas.org
    keywords:
    - mass spectrometry
    - protein
    - structure
    license: http://www.peptideatlas.org/publications.php
    name: PeptideAtlas
    pattern: ^PAp[0-9]{8}$
    prefix: peptideatlas
    pubmed_ids:
    - '18451766'
    uri_format: https://db.systemsbiology.net/sbeams/cgi/PeptideAtlas/GetProtein?atlas_build_id=242&protein_name=$1&action=QUERY
  publications:
  - doi: 10.1038/embor.2008.56
    pmc: PMC2373374
    pubmed: '18451766'
    title: 'PeptideAtlas: a resource for target selection for emerging targeted proteomics
      workflows'
    year: 2008
  - doi: 10.1093/nar/gkj040
    pmc: PMC1347403
    pubmed: '16381952'
    title: The PeptideAtlas project
    year: 2006
  re3data:
    description: The PeptideAtlas validates expressed proteins to provide eukaryotic
      genome data.  Peptide Atlas provides data to advance biological discoveries
      in humans.  The PeptideAtlas accepts proteomic data from high-throughput processes
      and encourages data submission.
    doi: 10.17616/R3BK61
    homepage: http://www.peptideatlas.org/
    name: PeptideAtlas
    prefix: r3d100010889
    xrefs:
      nif: 0000-03266
      omics: '02454'
  synonyms:
  - peptideatlas
  uniprot:
    abbreviation: PeptideAtlas
    category: Proteomic databases
    homepage: https://peptideatlas.org
    name: PeptideAtlas
    prefix: DB-0071
    publications:
    - doi: 10.1093/nar/gkj040
      pubmed: '16381952'
    uri_format: https://db.systemsbiology.net/sbeams/cgi/PeptideAtlas/Search?action=GO&search_key=$1
perkinelmer:
  cellosaurus:
    category: Cell line collections (Providers)
    homepage: https://www.perkinelmer.com/
    name: PerkinElmer cell line collection
    prefix: PerkinElmer
    uri_format: https://www.perkinelmer.com/searchresult?searchName=$1
  example: SCC111
  mappings:
    cellosaurus: PerkinElmer
  prefix: perkinelmer
peroxibase:
  biocontext:
    prefix: PEROXIBASE
  contact:
    email: dunand@lrsv.ups-tlse.fr
    github: null
    name: Christophe Dunand
    orcid: 0000-0003-1637-4042
  fairsharing:
    abbreviation: PeroxiBase
    description: Peroxibase provides access to peroxidase sequences from all kingdoms
      of life, and provides a series of bioinformatics tools and facilities suitable
      for analysing these sequences.
    homepage: http://peroxibase.toulouse.inra.fr/
    name: PeroxiBase
    prefix: FAIRsharing.z1czxj
    publications:
    - doi: 10.1093/nar/gks1083
      pubmed_id: 23180785
      title: 'PeroxiBase: a database for large-scale evolutionary analysis of peroxidases.'
    - doi: 10.1093/jxb/ern317
      pubmed_id: 19112168
      title: 'PeroxiBase: a powerful tool to collect and analyse peroxidase sequences
        from Viridiplantae.'
    subjects:
    - Life Science
  integbio:
    description: Peroxibase provides access to peroxidase sequences from all kingdoms
      of life, and provides a series of bioinformatics tools and facilities suitable
      for analysing these sequences.
    fairsharing: FAIRsharing.z1czxj
    homepage: http://peroxibase.toulouse.inra.fr/
    information_keywords:
    - Sequence
    - Classification
    name: PeroxiBase
    prefix: nbdc01869
    pubmeds:
    - '19112168'
    - '23180785'
    status: Inactive
    target_keywords:
    - Protein
  mappings:
    biocontext: PEROXIBASE
    fairsharing: FAIRsharing.z1czxj
    integbio: nbdc01869
    miriam: peroxibase
    n2t: peroxibase
    prefixcommons: peroxibase
    uniprot: DB-0072
  miriam:
    deprecated: false
    description: Peroxibase provides access to peroxidase sequences from all kingdoms
      of life, and provides a series of bioinformatics tools and facilities suitable
      for analysing these sequences.
    homepage: https://peroxibase.toulouse.inra.fr/
    id: '00000222'
    name: Peroxibase
    namespaceEmbeddedInLui: false
    pattern: ^\d+$
    prefix: peroxibase
    sampleId: '5282'
    uri_format: https://redoxibase.toulouse.inrae.fr/display_perox/view_perox/$1
  n2t:
    description: Peroxibase provides access to peroxidase sequences from all kingdoms
      of life, and provides a series of bioinformatics tools and facilities suitable
      for analysing these sequences.
    example: '5282'
    homepage: http://peroxibase.toulouse.inra.fr/
    name: Peroxibase at University of Geneva
    namespaceEmbeddedInLui: false
    pattern: ^\d+$
    prefix: peroxibase
    uri_format: http://peroxibase.toulouse.inra.fr/browse/process/view_perox.php?id=$1
  prefix: peroxibase
  prefixcommons:
    description: Peroxibase provides access to peroxidase sequences from all kingdoms
      of life, and provides a series of bioinformatics tools and facilities suitable
      for analysing these sequences.
    example: '5282'
    homepage: http://peroxibase.toulouse.inra.fr/
    keywords:
    - enzyme
    - protein
    - regulation
    name: PeroxiBase, a peroxidase database
    pattern: ^\d+$
    prefix: peroxibase
    pubmed_ids:
    - '19112168'
    uri_format: http://peroxibase.toulouse.inra.fr/listing.php?action=view&id=$1
  publications:
  - doi: 10.1093/nar/gks1083
    pmc: PMC3531118
    pubmed: '23180785'
    title: 'PeroxiBase: a database for large-scale evolutionary analysis of peroxidases'
    year: 2012
  - doi: 10.1093/jxb/ern317
    pmc: null
    pubmed: '19112168'
    title: 'PeroxiBase: a powerful tool to collect and analyse peroxidase sequences
      from Viridiplantae'
    year: 2008
  - doi: 10.1093/nar/gks1083
    pmc: null
    pubmed: null
    title: 'PeroxiBase: a database for large-scale evolutionary analysis of peroxidases.'
    year: null
  - doi: 10.1093/jxb/ern317
    pmc: null
    pubmed: null
    title: 'PeroxiBase: a powerful tool to collect and analyse peroxidase sequences
      from Viridiplantae.'
    year: null
  - doi: null
    pmc: null
    pubmed: '19112168'
    title: null
    year: null
  - doi: 10.1093/nar/gks1083
    pmc: null
    pubmed: '23180785'
    title: null
    year: null
  uniprot:
    abbreviation: PeroxiBase
    category: Protein family/group databases
    homepage: https://peroxibase.toulouse.inra.fr/
    name: PeroxiBase, a peroxidase database
    prefix: DB-0072
    publications:
    - doi: 10.1093/nar/gks1083
      pubmed: '23180785'
    uri_format: https://peroxibase.toulouse.inra.fr/display_perox/view_perox/$1
pesticideinfo:
  mappings:
    wikidata: P11949
  prefix: pesticideinfo
  wikidata:
    description: chemical in the database supplied by Pesticide Action Network North
      America
    example:
    - PRI10
    - PRI1700
    - PRI381
    homepage: https://www.pesticideinfo.org
    name: PesticideInfo chemical ID
    pattern: ^PRI\d*$
    prefix: P11949
    uri_format: https://www.pesticideinfo.org/chemical/$1
pesticides:
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: The Alan Wood’s Pesticides is a compendium of pesticides which contain
    nomenclature data sheets for more than 1700 different active ingredients.
  example: derivatives%2Fthiocyclam%20hydrochloride
  homepage: http://www.alanwood.net/pesticides
  name: Alan Wood's Pesticides
  prefix: pesticides
  uri_format: http://www.alanwood.net/pesticides/$1.html
pfam:
  biocontext:
    prefix: PFAM
  domain: protein family
  edam:
    description: Accession number of a Pfam entry.
    name: Pfam accession number
    obsolete: false
    prefix: '1138'
  example: PF11779
  fairsharing:
    abbreviation: Pfam
    contact:
      email: agb@ebi.ac.uk
      name: Alex Bateman
      orcid: 0000-0002-6982-4660
    description: The Pfam database is a large collection of protein families, each
      represented by multiple sequence alignments and hidden Markov models (HMMs).
      Pfam also generates higher-level groupings of related entries, known as clans.
      A clan is a collection of Pfam entries which are related by similarity of sequence,
      structure or profile-HMM.
    homepage: http://pfam.xfam.org/
    license: CC0-1.0
    name: Protein Families
    prefix: FAIRsharing.y3scf6
    publications:
    - doi: 10.1093/nar/gkr1065
      pubmed_id: 22127870
      title: The Pfam protein families database.
    - doi: 10.1093/nar/gkaa913
      pubmed_id: 33125078
      title: 'Pfam: The protein families database in 2021.'
    - doi: 10.1093/nar/gkp985
      pubmed_id: 19920124
      title: The Pfam protein families database.
    - doi: 10.1002/(sici)1097-0134(199707)28:3<405::aid-prot10>3.0.co;2-l
      pubmed_id: 9223186
      title: 'Pfam: a comprehensive database of protein domain families based on seed
        alignments.'
    - doi: 10.1093/nar/gkv1344
      pubmed_id: 26673716
      title: 'The Pfam protein families database: towards a more sustainable future.'
    - doi: 10.1093/nar/gkt1223
      pubmed_id: 24288371
      title: 'Pfam: the protein families database.'
    - doi: 10.1093/nar/gkm960
      pubmed_id: 18039703
      title: The Pfam protein families database.
    - doi: 10.1093/nar/gkj149
      pubmed_id: 16381856
      title: 'Pfam: clans, web tools and services.'
    - doi: 10.1093/nar/gky995
      pubmed_id: 30357350
      title: The Pfam protein families database in 2019.
    subjects:
    - Biology
    twitter: Xfam_EBI
  go:
    description: Pfam is a collection of protein families represented by sequence
      alignments and hidden Markov models (HMMs)
    homepage: https://www.ebi.ac.uk/interpro/entry/pfam
    name: Pfam database of protein families
    prefix: Pfam
  integbio:
    description: "Pfam Version 26.0 is a comprehensive database of protein families\
      \ containing multiple sequence alignments and HMMs.\nThis repository provides\
      \ data on 13,672 protein families.\nThe site can be searched with a known protein\
      \ sequence for matching families. \nOptions to search for a Pfam family, clan,\
      \ sequence or structure are available.\nA keyword search option is also provided."
    fairsharing: biodbcore-000081
    homepage: http://pfam.xfam.org
    information_keywords:
    - Sequence
    - Classification
    maintainer: EMBL-EBI (European Bioinformatics Institute)
    name: Pfam
    prefix: nbdc00163
    pubmeds:
    - '16381856'
    - '22127870'
    - '26673716'
    target_keywords:
    - Protein
  license: CC0-1.0
  logo: https://upload.wikimedia.org/wikipedia/commons/0/03/Pfam_logo.gif
  mappings:
    biocontext: PFAM
    edam: '1138'
    fairsharing: FAIRsharing.y3scf6
    go: Pfam
    integbio: nbdc00163
    miriam: pfam
    n2t: pfam
    ncbi: PFAM
    prefixcommons: pfam
    re3data: r3d100012850
    togoid: Pfam
    uniprot: DB-0073
    wikidata: P3519
  miriam:
    deprecated: false
    description: The Pfam database contains information about protein domains and
      families. For each entry a protein sequence alignment and a Hidden Markov Model
      is stored.
    homepage: https://www.ebi.ac.uk/interpro/
    id: 00000028
    name: Pfam
    namespaceEmbeddedInLui: false
    pattern: ^PF\d{5}$
    prefix: pfam
    sampleId: PF01234
    uri_format: https://www.ebi.ac.uk/interpro/entry/pfam/$1
  n2t:
    description: The Pfam database contains information about protein domains and
      families. For each entry a protein sequence alignment and a Hidden Markov Model
      is stored.
    example: PF01234
    homepage: https://pfam.xfam.org/
    name: Pfam at EMBL-EBI
    namespaceEmbeddedInLui: false
    pattern: ^PF\d{5}$
    prefix: pfam
    uri_format: https://pfam.xfam.org/family/$1
  name: Pfam protein family
  ncbi:
    example: PF00003
    homepage: http://pfam.xfam.org/
    name: Collection of protein families
    prefix: PFAM
  part_of_database: pfam
  prefix: pfam
  prefixcommons:
    alt_uri_formats:
    - http://pfam.sbc.su.se/family/#$1
    description: The Pfam database contains information about protein domains and
      families. For each entry a protein sequence alignment and a Hidden Markov Model
      is stored.
    example: PF01234
    homepage: http://pfam.sanger.ac.uk/
    keywords:
    - domain
    - protein
    license: CC0-1.0
    name: Sanger Pfam Mirror
    pattern: ^PF\d{5}$
    prefix: pfam
    pubmed_ids:
    - '9847196'
    - '14681378'
    - '11752314'
    - '10592242'
    - '9399864'
    - '9223186'
    rdf_uri_format: http://pfam.janelia.org/family/#$1
    uri_format: http://pfam.sanger.ac.uk/family?entry=$1
  providers:
  - code: xfam
    description: Pfam's familes in their old home in the xfam.org
    example: null
    first_party: null
    homepage: https://pfam.xfam.org
    name: Xfam
    publications: null
    status: null
    uri_format: https://pfam.xfam.org/family?acc=$1
  - code: sanger
    description: The Pfam database contains information about protein domains and
      families. For each entry a protein sequence alignment and a Hidden Markov Model
      is stored.
    example: null
    first_party: null
    homepage: http://pfam.sanger.ac.uk/
    name: Sanger Pfam Mirror
    publications: null
    status: null
    uri_format: http://pfam.sanger.ac.uk/family?entry=$1
  publications:
  - doi: 10.1093/nar/gkae997
    pmc: null
    pubmed: '39540428'
    title: 'The Pfam protein families database: embracing AI/ML'
    year: 2024
  - doi: 10.1093/nar/gkaa913
    pmc: PMC7779014
    pubmed: '33125078'
    title: 'Pfam: The protein families database in 2021'
    year: 2021
  - doi: 10.1093/nar/gky995
    pmc: PMC6324024
    pubmed: '30357350'
    title: The Pfam protein families database in 2019
    year: 2019
  - doi: 10.1093/nar/gkv1344
    pmc: PMC4702930
    pubmed: '26673716'
    title: 'The Pfam protein families database: towards a more sustainable future'
    year: 2015
  - doi: 10.1093/nar/gkt1223
    pmc: PMC3965110
    pubmed: '24288371'
    title: 'Pfam: the protein families database'
    year: 2013
  - doi: 10.1093/nar/gkr1065
    pmc: PMC3245129
    pubmed: '22127870'
    title: The Pfam protein families database
    year: 2011
  - doi: 10.1093/nar/gkp985
    pmc: PMC2808889
    pubmed: '19920124'
    title: The Pfam protein families database
    year: 2009
  - doi: 10.1093/nar/gkm960
    pmc: PMC2238907
    pubmed: '18039703'
    title: The Pfam protein families database
    year: 2007
  - doi: 10.1093/nar/gkj149
    pmc: PMC1347511
    pubmed: '16381856'
    title: 'Pfam: clans, web tools and services'
    year: 2006
  - doi: 10.1093/nar/gkh121
    pmc: PMC308855
    pubmed: '14681378'
    title: The Pfam protein families database
    year: 2004
  - doi: 10.1093/nar/30.1.276
    pmc: PMC99071
    pubmed: '11752314'
    title: The Pfam protein families database
    year: 2002
  - doi: 10.1093/nar/28.1.263
    pmc: PMC102420
    pubmed: '10592242'
    title: The Pfam protein families database
    year: 2000
  - doi: 10.1093/nar/27.1.260
    pmc: PMC148151
    pubmed: '9847196'
    title: 'Pfam 3.1: 1313 multiple alignments and profile HMMs match the majority
      of proteins'
    year: 1999
  - doi: 10.1093/nar/26.1.320
    pmc: PMC147209
    pubmed: '9399864'
    title: 'Pfam: multiple sequence alignments and HMM-profiles of protein domains'
    year: 1998
  - doi: 10.1002/(sici)1097-0134(199707)28:3<405::aid-prot10>3.0.co;2-l
    pmc: null
    pubmed: '9223186'
    title: 'Pfam: a comprehensive database of protein domain families based on seed
      alignments'
    year: 1997
  - doi: 10.1093/nar/gkr1065
    pmc: null
    pubmed: null
    title: The Pfam protein families database.
    year: null
  - doi: 10.1093/nar/gkaa913
    pmc: null
    pubmed: null
    title: 'Pfam: The protein families database in 2021.'
    year: null
  - doi: 10.1093/nar/gkp985
    pmc: null
    pubmed: null
    title: The Pfam protein families database.
    year: null
  - doi: 10.1002/(sici)1097-0134(199707)28:3<405::aid-prot10>3.0.co;2-l
    pmc: null
    pubmed: null
    title: 'Pfam: a comprehensive database of protein domain families based on seed
      alignments.'
    year: null
  - doi: 10.1093/nar/gkv1344
    pmc: null
    pubmed: null
    title: 'The Pfam protein families database: towards a more sustainable future.'
    year: null
  - doi: 10.1093/nar/gkt1223
    pmc: null
    pubmed: null
    title: 'Pfam: the protein families database.'
    year: null
  - doi: 10.1093/nar/gkm960
    pmc: null
    pubmed: null
    title: The Pfam protein families database.
    year: null
  - doi: 10.1093/nar/gkj149
    pmc: null
    pubmed: null
    title: 'Pfam: clans, web tools and services.'
    year: null
  - doi: 10.1093/nar/gky995
    pmc: null
    pubmed: null
    title: The Pfam protein families database in 2019.
    year: null
  - doi: null
    pmc: null
    pubmed: '9847196'
    title: null
    year: null
  - doi: null
    pmc: null
    pubmed: '14681378'
    title: null
    year: null
  - doi: null
    pmc: null
    pubmed: '11752314'
    title: null
    year: null
  - doi: null
    pmc: null
    pubmed: '10592242'
    title: null
    year: null
  - doi: null
    pmc: null
    pubmed: '9399864'
    title: null
    year: null
  - doi: null
    pmc: null
    pubmed: '9223186'
    title: null
    year: null
  - doi: 10.1093/nar/gkaa913
    pmc: null
    pubmed: '33125078'
    title: null
    year: null
  re3data:
    description: "<<<!!!<<<  Pfam data and new releases are available through InterPro\
      \ https://www.re3data.org/repository/r3d100010798 \nThe Pfam website now serves\
      \ as a static page with no data updates. All links below redirect to the closest\
      \ alternative page in the InterPro website.  >>>!!!>>>"
    doi: 10.17616/R3QV4F
    homepage: http://pfam.xfam.org/
    license: CC0
    name: Pfam Protein Families
    prefix: r3d100012850
    synonyms:
    - Pfam
    xrefs:
      omics: 01696
  references:
  - https://twitter.com/PfamDB/status/1555149527228813314
  synonyms:
  - PF
  togoid:
    catalog: nbdc00163
    description: Pfam Version 26.0 is a comprehensive database of protein families
      containing multiple sequence alignments and HMMs. This repository provides data
      on 13,672 protein families. The site can be searched with a known protein sequence
      for matching families.  Options to search for a Pfam family, clan, sequence
      or structure are available. A keyword search option is also provided.
    examples:
    - PF03719
    - PF03726
    - PF02809
    - PF00105
    - PF00250
    - PF00412
    - PF01412
    - PF00459
    - PF02532
    - PF01226
    keywords:
    - Domain
    name: Pfam
    pattern: ^(?PF\d{5})$
    prefix: Pfam
    uri_format: http://identifiers.org/pfam/$1
  uniprot:
    abbreviation: Pfam
    category: Family and domain databases
    homepage: https://www.ebi.ac.uk/interpro/
    name: Pfam protein domain database
    prefix: DB-0073
    publications:
    - doi: 10.1093/nar/gkaa913
      pubmed: '33125078'
    uri_format: https://www.ebi.ac.uk/interpro/entry/pfam/$1
  uri_format: https://www.ebi.ac.uk/interpro/entry/pfam/$1
  wikidata:
    description: identifier in the Pfam database of protein families
    example:
    - PF00372
    - PF00439
    - PF08441
    homepage: https://pfam.xfam.org/
    miriam: pfam
    name: Pfam ID
    pattern: ^(PF\d{5}|CL\d{4})$
    prefix: P3519
    uri_format: https://pfam.xfam.org/family?acc=$1
pfam.clan:
  contact:
    email: agb@ebi.ac.uk
    github: bateman-research
    name: Alex Bateman
    orcid: 0000-0002-6982-4660
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: Higher order grouping of Pfam families
  domain: protein family
  edam:
    description: Accession number of a Pfam clan.
    name: Pfam clan
    obsolete: false
    prefix: '2758'
  example: CL0192
  homepage: https://pfam.xfam.org
  keywords:
  - protein family
  license: CC0-1.0
  logo: https://upload.wikimedia.org/wikipedia/commons/0/03/Pfam_logo.gif
  mappings:
    edam: '2758'
  name: Pfam protein clan
  part_of_database: pfam
  pattern: ^CL\d+$
  prefix: pfam.clan
  providers:
  - code: xfam
    description: Pfam's clans in their old home in the xfam.org
    example: null
    first_party: null
    homepage: https://pfam.xfam.org
    name: Xfam
    publications: null
    status: null
    uri_format: https://pfam.xfam.org/clan/$1
  references:
  - https://twitter.com/PfamDB/status/1555149527228813314
  uri_format: https://www.ebi.ac.uk/interpro/set/pfam/$1
pfr:
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: Database that provides a central location for scientists to browse
    uniquely observed proteoforms and to contribute their own datasets.
  example: '1001'
  fairsharing:
    abbreviation: TDR
    description: The Texas Data Repository is a platform for publishing and managing
      datasets (and other data products) created by faculty, staff, and students at
      Texas higher education institutions. The repository is built in an open-source
      application called Dataverse, developed and used by Harvard University. The
      repository is hosted by the Texas Digital Library, a consortium of academic
      libraries in Texas with a proven history of providing shared technology services
      that support secure, reliable access to digital collections of research and
      scholarship. Researchers deposit data within the TDR to, for example, comply
      with funding requirements and ensure reliable, managed access for data.
    homepage: https://dataverse.tdl.org
    license: CC0-1.0
    name: Texas Data Repository
    prefix: FAIRsharing.wqsxtg
    publications: []
    subjects:
    - Data Management
    - Subject Agnostic
  homepage: http://repository.topdownproteomics.org/proteoforms
  mappings:
    fairsharing: FAIRsharing.wqsxtg
    re3data: r3d100012385
  name: Proteoform Atlas
  pattern: ^\d+$
  prefix: pfr
  re3data:
    description: 'The Texas Data Repository is a platform for publishing and archiving
      datasets (and other data products) created by faculty, staff, and students at
      Texas higher education institutions. The repository is built in an open-source
      application called Dataverse, developed and used by Harvard University.

      The repository is hosted by the Texas Digital Library, a consortium of academic
      libraries in Texas with a proven history of providing shared technology services
      that support secure, reliable access to digital collections of research and
      scholarship. For a list of TDL participating institutions, please visit:  https://www.tdl.org/members/.'
    doi: 10.17616/R31H21
    homepage: https://dataverse.tdl.org/
    name: Texas Data Repository
    prefix: r3d100012385
    synonyms:
    - TDR
  synonyms:
  - TDR
  uri_format: http://repository.topdownproteomics.org/proteoforms/$1
pgdso:
  biocontext:
    prefix: PGDSO
  mappings:
    biocontext: PGDSO
    obofoundry: pgdso
    wikidata.entity: Q114677907
  obofoundry:
    contact: po-discuss@plantontology.org
    contact.label: Plant Ontology Administrators
    deprecated: true
    domain: anatomy and development
    homepage: http://www.plantontology.org
    name: Plant Growth and Development Stage
    prefix: pgdso
  prefix: pgdso
pgs:
  mappings:
    miriam: pgs
  miriam:
    deprecated: false
    description: The Polygenic Score (PGS) Catalog is an open database of PGS and
      the relevant metadata required for accurate application and evaluation.
    homepage: http://pgscatalog.org
    id: '00000753'
    name: Polygenic Score Catalog
    namespaceEmbeddedInLui: false
    pattern: ^PGS[0-9]{6}$
    prefix: pgs
    sampleId: PGS000018
    uri_format: https://www.pgscatalog.org/pgs/$1/
  prefix: pgs
  uri_format: https://www.pgscatalog.org/pgs/$1
pgx:
  biocontext:
    prefix: PGX
  cellosaurus:
    category: Polymorphism and mutation databases
    homepage: https://progenetix.org/
    name: Cancer genome data @ progenetix.org
    prefix: Progenetix
    uri_format: https://progenetix.org/cellline/?id=cellosaurus:$1
  fairsharing:
    abbreviation: Progenetix
    contact:
      email: mbaudis@me.com
      name: Michael Baudis
      orcid: 0000-0002-9903-4248
    description: The Progenetix database provides an overview of copy number abnormalities
      in human cancer from Comparative Genomic Hybridization (CGH) experiments. Progenetix
      is the largest curated database for whole genome copy number profiles in cancer.
      The current dataset  contains more than 130'000 profiles from genomic CNV screening
      experiments. This data covers 700 diagnostic entities according to the NCIt
      Neoplasm Core  and the International Classification of Disease in Oncology (ICD-O
      3). Additionally, the website attempts to lists all publications referring to
      cancer genome profiling experiments.
    homepage: https://progenetix.org/
    license: CC-BY-4.0
    name: Progenetix
    prefix: FAIRsharing.65tdnz
    publications:
    - doi: 10.1371/journal.pone.0036944
      pubmed_id: 22629346
      title: 'arrayMap: a reference resource for genomic copy number imbalances in
        human malignancies.'
    - doi: 10.1186/1471-2407-7-226
      pubmed_id: 18088415
      title: 'Genomic imbalances in 5918 malignant epithelial tumors: an explorative
        meta-analysis of chromosomal CGH data'
    - doi: 10.2144/000112102
      pubmed_id: 16568815
      title: Online database and bioinformatics toolbox to support data mining in
        cancer cytogenetics.
    - doi: 10.1093/nar/gkt1108
      pubmed_id: 24225322
      title: 'Progenetix: 12 years of oncogenomic data curation.'
    - doi: 10.1093/nar/gku1123
      pubmed_id: 25428357
      title: 'arrayMap 2014: an updated cancer genome resource.'
    - doi: 10.1186/1471-2164-15-82
      pubmed_id: 24476156
      title: Chromothripsis-like patterns are recurring but heterogeneously distributed
        features in a survey of 22,347 cancer genome screens.
    - doi: 10.1093/bioinformatics/17.12.1228
      pubmed_id: 11751233
      title: 'Progenetix.net: an online repository for molecular cytogenetic aberration
        data.'
    subjects:
    - Genomics
    - Biomedical Science
    twitter: progenetix
  mappings:
    biocontext: PGX
    cellosaurus: Progenetix
    fairsharing: FAIRsharing.65tdnz
    miriam: pgx
    n2t: pgx
    re3data: r3d100012820
  miriam:
    deprecated: false
    description: The Progenetix database provides an overview of mutation data in
      cancer, with a focus on copy number abnormalities (CNV / CNA), for all types
      of human malignancies. The resource contains genome profiles of more than 130'000
      individual samples and represents about 700 cancer types, according to the NCIt
      "neoplasm" classification. Additionally to this genome profiles and associated
      metadata, the website present information about thousands of publications referring
      to cancer genome profiling experiments, and services for mapping cancer classifications
      and accessing supplementary data through its APIs.
    homepage: https://progenetix.org/
    id: '00000600'
    name: Progenetix
    namespaceEmbeddedInLui: false
    pattern: ^\w{3,15}[-_]\w[\w.-]{3,128}$
    prefix: pgx
    sampleId: pgxbs-kftva5zv
    uri_format: https://progenetix.org/services/ids/$1
  n2t:
    description: The Progenetix database provides an overview of copy number abnormalities
      in human cancer from currently 32317 array and chromosomal Comparative Genomic
      Hybridization (CGH) experiments, as well as Whole Genome or Whole Exome Sequencing
      (WGS, WES) studies. The cancer profile data in Progenetix was curated from 1026
      articles and represents 364 different cancer types, according to the International
      classification of Diseases in Oncology (ICD-O).
    example: icdom:8500_3
    homepage: http://progenetix.org/
    name: Progenetix
    namespaceEmbeddedInLui: false
    pattern: ^[\w\-:,]{3,64}$
    prefix: pgx
    uri_format: http://progenetix.org/pgx:$1
  prefix: pgx
  publications:
  - doi: 10.1093/nar/gku1123
    pmc: PMC4383937
    pubmed: '25428357'
    title: 'arrayMap 2014: an updated cancer genome resource'
    year: 2014
  - doi: 10.1186/1471-2164-15-82
    pmc: PMC3909908
    pubmed: '24476156'
    title: Chromothripsis-like patterns are recurring but heterogeneously distributed
      features in a survey of 22,347 cancer genome screens
    year: 2014
  - doi: 10.1093/nar/gkt1108
    pmc: PMC3965091
    pubmed: '24225322'
    title: 'Progenetix: 12 years of oncogenomic data curation'
    year: 2013
  - doi: 10.1371/journal.pone.0036944
    pmc: PMC3356349
    pubmed: '22629346'
    title: 'arrayMap: a reference resource for genomic copy number imbalances in human
      malignancies'
    year: 2012
  - doi: 10.1186/1471-2407-7-226
    pmc: PMC2225423
    pubmed: '18088415'
    title: 'Genomic imbalances in 5918 malignant epithelial tumors: an explorative
      meta-analysis of chromosomal CGH data'
    year: 2007
  - doi: 10.2144/000112102
    pmc: null
    pubmed: '16568815'
    title: Online database and bioinformatics toolbox to support data mining in cancer
      cytogenetics
    year: 2006
  - doi: 10.1093/bioinformatics/17.12.1228
    pmc: null
    pubmed: '11751233'
    title: 'Progenetix.net: an online repository for molecular cytogenetic aberration
      data'
    year: 2001
  - doi: 10.1371/journal.pone.0036944
    pmc: null
    pubmed: null
    title: 'arrayMap: a reference resource for genomic copy number imbalances in human
      malignancies.'
    year: null
  - doi: 10.1186/1471-2407-7-226
    pmc: null
    pubmed: null
    title: 'Genomic imbalances in 5918 malignant epithelial tumors: an explorative
      meta-analysis of chromosomal CGH data'
    year: null
  - doi: 10.2144/000112102
    pmc: null
    pubmed: null
    title: Online database and bioinformatics toolbox to support data mining in cancer
      cytogenetics.
    year: null
  - doi: 10.1093/nar/gkt1108
    pmc: null
    pubmed: null
    title: 'Progenetix: 12 years of oncogenomic data curation.'
    year: null
  - doi: 10.1093/nar/gku1123
    pmc: null
    pubmed: null
    title: 'arrayMap 2014: an updated cancer genome resource.'
    year: null
  - doi: 10.1186/1471-2164-15-82
    pmc: null
    pubmed: null
    title: Chromothripsis-like patterns are recurring but heterogeneously distributed
      features in a survey of 22,347 cancer genome screens.
    year: null
  - doi: 10.1093/bioinformatics/17.12.1228
    pmc: null
    pubmed: null
    title: 'Progenetix.net: an online repository for molecular cytogenetic aberration
      data.'
    year: null
  re3data:
    description: The Progenetix database provides an overview of copy number abnormalities
      in human cancer from currently 32548 array and chromosomal Comparative Genomic
      Hybridization (CGH) experiments, as well as Whole Genome or Whole Exome Sequencing
      (WGS, WES) studies. The cancer profile data in Progenetix was curated from 1031
      articles  and represents 366 different cancer types, according to the International
      classification of Diseases in Oncology (ICD-O).
    doi: 10.17616/R3KV46
    homepage: https://www.progenetix.org/
    name: Progenetix
    prefix: r3d100012820
    xrefs:
      omics: 02591
  synonyms:
  - Progenetix
phagedive:
  contact:
    email: johannes.wittmann@dsmz.de
    github: null
    name: Johannes Wittmann
    orcid: 0000-0002-7275-9927
  contributor:
    email: m.naguthana@hotmail.com
    github: nagutm
    name: Mufaddal Naguthanawala
    orcid: 0009-0009-5240-7463
  description: PhageDive is a database for bacteriophages and archaeal viruses. It
    provides information regarding taxonomy, host strain, phage morphology, life cycle,
    origin and genomic data.
  example: '3'
  github_request_issue: 1454
  homepage: https://phagedive.dsmz.de
  mappings:
    re3data: r3d100014540
  name: PhageDive
  pattern: ^\d+$
  prefix: phagedive
  publications:
  - doi: 10.1093/nar/gkae1220
    pmc: PMC11701545
    pubmed: '39373542'
    title: 'PhageDive: the comprehensive strain database of prokaryotic viral diversity'
    year: 2024
  re3data:
    description: PhageDive is a specific database for bacteriophages and archaeal
      viruses. Built on the BacDive model, it gathers and links all the experimental
      data and metadata of the viruses present in different culture collections. Its
      implementation aims to facilitate access to all viruses information for the
      scientific community. The database covers taxonomy, host strain, phage morphology,
      life cycle, origin and genomic data.
    doi: 10.17616/R31NJNPO
    homepage: https://phagedive.dsmz.de/
    license: CC
    name: PhageDive
    prefix: r3d100014540
  reviewer:
    email: b.gyori@northeastern.edu
    github: bgyori
    name: Benjamin M. Gyori
    orcid: 0000-0001-9439-5346
  uri_format: https://phagedive.dsmz.de/strain/$1
pharmacodb.cell:
  cellosaurus:
    category: Chemistry resources
    homepage: https://pharmacodb.ca/
    name: PharmacoDB integrative pharmacogenomic database
    prefix: PharmacoDB
    uri_format: https://pharmacodb.ca/cell_lines/$1
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: Web-application assembling the largest in vitro drug screens in a single
    database, and allowing users to easily query the union of studies released to
    date. Query by cell line.
  example: 22RV1_12_2019
  homepage: https://pharmacodb.ca/cell_lines
  mappings:
    cellosaurus: PharmacoDB
  name: PharmacoDB Cells
  prefix: pharmacodb.cell
  uri_format: https://pharmacodb.ca/cell_lines/$1
pharmacodb.dataset:
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: Web-application assembling the largest in vitro drug screens in a single
    database, and allowing users to easily query the union of studies released to
    date. Query by dataset.
  example: '1'
  homepage: https://pharmacodb.ca/datasets
  name: PharmacoDB Datasets
  pattern: ^\d+$
  prefix: pharmacodb.dataset
  uri_format: https://pharmacodb.ca/datasets/$1
pharmacodb.tissue:
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: Web-application assembling the largest in vitro drug screens in a single
    database, and allowing users to easily query the union of studies released to
    date. Query by tissue.
  example: '13'
  homepage: https://pharmacodb.ca/tissues
  name: PharmacoDB Tissues
  pattern: ^\d+$
  prefix: pharmacodb.tissue
  uri_format: https://pharmacodb.ca/tissues/$1
pharmgkb.disease:
  biocontext:
    prefix: PHARMGKB.DISEASE
  biolink:
    is_identifiers: false
    is_obo: false
    prefix: PHARMGKB.DISEASE
    uri_format: https://www.pharmgkb.org/disease/$1
  contact:
    email: teri.klein@stanford.edu
    github: TeriKlein
    name: Teri E Klein
    orcid: 0000-0001-5527-6475
  contact_group_email: feedback@clinpgx.org
  domain: disease
  edam:
    description: Identifier of a disease from the pharmacogenetics and pharmacogenomics
      knowledge base (PharmGKB).
    name: Disease ID (PharmGKB)
    obsolete: false
    prefix: '2651'
  license: CC-BY-SA-4.0
  logo: https://rxgenomix.com/wp-content/uploads/2019/10/pharmgKB.png
  mappings:
    biocontext: PHARMGKB.DISEASE
    biolink: PHARMGKB.DISEASE
    edam: '2651'
    miriam: pharmgkb.disease
    n2t: pharmgkb.disease
    prefixcommons: pharmgkb.disease
    wikidata: P7001
  miriam:
    deprecated: false
    description: The PharmGKB database is a central repository for genetic, genomic,
      molecular and cellular phenotype data and clinical information about people
      who have participated in pharmacogenomics research studies. The data includes,
      but is not limited to, clinical and basic pharmacokinetic and pharmacogenomic
      research in the cardiovascular, pulmonary, cancer, pathways, metabolic and transporter
      domains.
    homepage: http://www.pharmgkb.org/
    id: 00000090
    name: PharmGKB Disease
    namespaceEmbeddedInLui: false
    pattern: ^PA\d+$
    prefix: pharmgkb.disease
    sampleId: PA447218
    uri_format: http://www.pharmgkb.org/disease/$1
  n2t:
    description: The PharmGKB database is a central repository for genetic, genomic,
      molecular and cellular phenotype data and clinical information about people
      who have participated in pharmacogenomics research studies. The data includes,
      but is not limited to, clinical and basic pharmacokinetic and pharmacogenomic
      research in the cardiovascular, pulmonary, cancer, pathways, metabolic and transporter
      domains.
    example: PA447218
    homepage: http://www.pharmgkb.org/
    name: PharmGKB Disease at Stanford
    namespaceEmbeddedInLui: false
    pattern: ^PA\d+$
    prefix: pharmgkb.disease
    uri_format: http://www.pharmgkb.org/disease/$1
  prefix: pharmgkb.disease
  prefixcommons:
    description: The PharmGKB database is a central repository for genetic, genomic,
      molecular and cellular phenotype data and clinical information about people
      who have participated in pharmacogenomics research studies. The data includes,
      but is not limited to, clinical and basic pharmacokinetic and pharmacogenomic
      research in the cardiovascular, pulmonary, cancer, pathways, metabolic and transporter
      domains.
    example: PA447218
    keywords:
    - pharmacogenomics
    name: PharmGKB Disease
    pattern: ^PA\d+$
    prefix: pharmgkb.disease
    pubmed_ids:
    - '11908751'
    - '22103613'
    uri_format: http://www.pharmgkb.org/disease/$1
  publications:
  - doi: 10.2217/bmm.11.94
    pmc: PMC3339046
    pubmed: '22103613'
    title: 'From pharmacogenomic knowledge acquisition to clinical applications: the
      PharmGKB as a clinical pharmacogenomic biomarker resource'
    year: 2011
  - doi: 10.1038/sj.tpj.6500035
    pmc: null
    pubmed: '11908751'
    title: 'Integrating genotype and phenotype information: an overview of the PharmGKB
      project. Pharmacogenetics Research Network and Knowledge Base'
    year: 2001
  - doi: null
    pmc: null
    pubmed: '11908751'
    title: null
    year: null
  - doi: null
    pmc: null
    pubmed: '22103613'
    title: null
    year: null
  - doi: null
    pmc: null
    pubmed: '11908751'
    title: null
    year: null
  - doi: null
    pmc: null
    pubmed: '22103613'
    title: null
    year: null
  wikidata:
    prefix: P7001
pharmgkb.drug:
  biocontext:
    prefix: PHARMGKB.DRUG
  biolink:
    is_identifiers: false
    is_obo: false
    prefix: PHARMGKB.DRUG
    uri_format: https://www.pharmgkb.org/chemical/$1
  contact:
    email: teri.klein@stanford.edu
    github: TeriKlein
    name: Teri E Klein
    orcid: 0000-0001-5527-6475
  contact_group_email: feedback@clinpgx.org
  domain: chemical
  edam:
    description: Identifier of a drug from the pharmacogenetics and pharmacogenomics
      knowledge base (PharmGKB).
    name: Drug ID (PharmGKB)
    obsolete: false
    prefix: '2652'
  license: CC-BY-SA-4.0
  logo: https://rxgenomix.com/wp-content/uploads/2019/10/pharmgKB.png
  mappings:
    biocontext: PHARMGKB.DRUG
    biolink: PHARMGKB.DRUG
    edam: '2652'
    miriam: pharmgkb.drug
    n2t: pharmgkb.drug
    prefixcommons: pharmgkb.drug
    wikidata: P7001
  miriam:
    deprecated: false
    description: The PharmGKB database is a central repository for genetic, genomic,
      molecular and cellular phenotype data and clinical information about people
      who have participated in pharmacogenomics research studies. The data includes,
      but is not limited to, clinical and basic pharmacokinetic and pharmacogenomic
      research in the cardiovascular, pulmonary, cancer, pathways, metabolic and transporter
      domains.
    homepage: http://www.pharmgkb.org/
    id: 00000091
    name: PharmGKB Drug
    namespaceEmbeddedInLui: false
    pattern: ^PA\d+$
    prefix: pharmgkb.drug
    sampleId: PA448710
    uri_format: http://www.pharmgkb.org/drug/$1
  n2t:
    description: The PharmGKB database is a central repository for genetic, genomic,
      molecular and cellular phenotype data and clinical information about people
      who have participated in pharmacogenomics research studies. The data includes,
      but is not limited to, clinical and basic pharmacokinetic and pharmacogenomic
      research in the cardiovascular, pulmonary, cancer, pathways, metabolic and transporter
      domains.
    example: PA448710
    homepage: http://www.pharmgkb.org/
    name: PharmGKB Drug at Stanford
    namespaceEmbeddedInLui: false
    pattern: ^PA\d+$
    prefix: pharmgkb.drug
    uri_format: http://www.pharmgkb.org/drug/$1
  prefix: pharmgkb.drug
  prefixcommons:
    description: The PharmGKB database is a central repository for genetic, genomic,
      molecular and cellular phenotype data and clinical information about people
      who have participated in pharmacogenomics research studies. The data includes,
      but is not limited to, clinical and basic pharmacokinetic and pharmacogenomic
      research in the cardiovascular, pulmonary, cancer, pathways, metabolic and transporter
      domains.
    example: PA448710
    keywords:
    - drug
    - pharmacogenomics
    name: PharmGKB Drug
    pattern: ^PA\d+$
    prefix: pharmgkb.drug
    pubmed_ids:
    - '11908751'
    - '22103613'
    uri_format: http://www.pharmgkb.org/drug/$1
  publications:
  - doi: 10.2217/bmm.11.94
    pmc: PMC3339046
    pubmed: '22103613'
    title: 'From pharmacogenomic knowledge acquisition to clinical applications: the
      PharmGKB as a clinical pharmacogenomic biomarker resource'
    year: 2011
  - doi: 10.1038/sj.tpj.6500035
    pmc: null
    pubmed: '11908751'
    title: 'Integrating genotype and phenotype information: an overview of the PharmGKB
      project. Pharmacogenetics Research Network and Knowledge Base'
    year: 2001
  wikidata:
    prefix: P7001
pharmgkb.gene:
  biocontext:
    prefix: PHARMGKB.GENE
  biolink:
    is_identifiers: false
    is_obo: false
    prefix: PHARMGKB.GENE
    uri_format: https://www.pharmgkb.org/gene/$1
  bioportal:
    name: PharmGKB Ontology
    prefix: PHARMGKB
  contact:
    email: teri.klein@stanford.edu
    github: TeriKlein
    name: Teri E Klein
    orcid: 0000-0001-5527-6475
  contact_group_email: feedback@clinpgx.org
  domain: gene
  go:
    homepage: https://www.pharmgkb.org
    name: Pharmacogenetics and Pharmacogenomics Knowledge Base
    prefix: PharmGKB
    uri_format: https://www.pharmgkb.org/do/serve?objId=$1
  license: CC-BY-SA-4.0
  logo: https://rxgenomix.com/wp-content/uploads/2019/10/pharmgKB.png
  mappings:
    biocontext: PHARMGKB.GENE
    biolink: PHARMGKB.GENE
    bioportal: PHARMGKB
    go: PharmGKB
    miriam: pharmgkb.gene
    n2t: pharmgkb.gene
    prefixcommons: pharmgkb.gene
    uniprot: DB-0074
    wikidata: P7001
  miriam:
    deprecated: false
    description: The PharmGKB database is a central repository for genetic, genomic,
      molecular and cellular phenotype data and clinical information about people
      who have participated in pharmacogenomics research studies. The data includes,
      but is not limited to, clinical and basic pharmacokinetic and pharmacogenomic
      research in the cardiovascular, pulmonary, cancer, pathways, metabolic and transporter
      domains.
    homepage: http://www.pharmgkb.org/
    id: '00000245'
    name: PharmGKB Gene
    namespaceEmbeddedInLui: false
    pattern: ^PA\w+$
    prefix: pharmgkb.gene
    sampleId: PA131
    uri_format: http://www.pharmgkb.org/gene/$1
  n2t:
    description: The PharmGKB database is a central repository for genetic, genomic,
      molecular and cellular phenotype data and clinical information about people
      who have participated in pharmacogenomics research studies. The data includes,
      but is not limited to, clinical and basic pharmacokinetic and pharmacogenomic
      research in the cardiovascular, pulmonary, cancer, pathways, metabolic and transporter
      domains.
    example: PA131
    homepage: http://www.pharmgkb.org/
    name: PharmGKB Gene at Stanford
    namespaceEmbeddedInLui: false
    pattern: ^PA\w+$
    prefix: pharmgkb.gene
    uri_format: http://www.pharmgkb.org/gene/$1
  name: PharmGKB Gene
  prefix: pharmgkb.gene
  prefixcommons:
    description: The PharmGKB database is a central repository for genetic, genomic,
      molecular and cellular phenotype data and clinical information about people
      who have participated in pharmacogenomics research studies. The data includes,
      but is not limited to, clinical and basic pharmacokinetic and pharmacogenomic
      research in the cardiovascular, pulmonary, cancer, pathways, metabolic and transporter
      domains.
    example: PA131
    keywords:
    - gene
    - pharmacogenomics
    name: PharmGKB Gene
    pattern: ^PA\w+$
    prefix: pharmgkb.gene
    pubmed_ids:
    - '22103613'
    uri_format: http://www.pharmgkb.org/gene/$1
  publications:
  - doi: 10.2217/bmm.11.94
    pmc: PMC3339046
    pubmed: '22103613'
    title: 'From pharmacogenomic knowledge acquisition to clinical applications: the
      PharmGKB as a clinical pharmacogenomic biomarker resource'
    year: 2011
  - doi: 10.1385/1-59259-957-5:179
    pmc: null
    pubmed: '16100408'
    title: 'PharmGKB: the pharmacogenetics and pharmacogenomics knowledge base'
    year: 2005
  - doi: null
    pmc: null
    pubmed: '22103613'
    title: null
    year: null
  - doi: 10.1385/1-59259-957-5:179
    pmc: null
    pubmed: '16100408'
    title: null
    year: null
  uniprot:
    abbreviation: PharmGKB
    category: Organism-specific databases
    homepage: https://www.pharmgkb.org/
    name: The Pharmacogenetics and Pharmacogenomics Knowledge Base
    prefix: DB-0074
    publications:
    - doi: 10.1385/1-59259-957-5:179
      pubmed: '16100408'
    uri_format: https://www.pharmgkb.org/gene/$1
  wikidata:
    prefix: P7001
pharmgkb.pathways:
  biocontext:
    prefix: PHARMGKB.PATHWAYS
  biolink:
    is_identifiers: false
    is_obo: false
    prefix: PHARMGKB.PATHWAYS
    uri_format: https://www.pharmgkb.org/pathway/$1
  contact:
    email: teri.klein@stanford.edu
    github: TeriKlein
    name: Teri E Klein
    orcid: 0000-0001-5527-6475
  contact_group_email: feedback@clinpgx.org
  domain: pathway
  edam:
    description: Identifier of a pathway from the pharmacogenetics and pharmacogenomics
      knowledge base (PharmGKB).
    name: Pathway ID (PharmGKB)
    obsolete: false
    prefix: '2650'
  license: CC-BY-SA-4.0
  logo: https://rxgenomix.com/wp-content/uploads/2019/10/pharmgKB.png
  mappings:
    biocontext: PHARMGKB.PATHWAYS
    biolink: PHARMGKB.PATHWAYS
    edam: '2650'
    miriam: pharmgkb.pathways
    n2t: pharmgkb.pathways
    prefixcommons: pharmgkb.pathways
    wikidata: P7001
  miriam:
    deprecated: false
    description: "The PharmGKB database is a central repository for genetic, genomic,\
      \ molecular and cellular phenotype data and clinical information about people\
      \ who have participated in pharmacogenomics research studies. The data includes,\
      \ but is not limited to, clinical and basic pharmacokinetic and pharmacogenomic\
      \ research in the cardiovascular, pulmonary, cancer, pathways, metabolic and\
      \ transporter domains. \r\nPharmGKB Pathways are drug centric, gene based, interactive\
      \ pathways which focus on candidate genes and gene groups and associated genotype\
      \ and phenotype data of relevance for pharmacogenetic and pharmacogenomic studies."
    homepage: http://www.pharmgkb.org/
    id: 00000089
    name: PharmGKB Pathways
    namespaceEmbeddedInLui: false
    pattern: ^PA\d+$
    prefix: pharmgkb.pathways
    sampleId: PA146123006
    uri_format: http://www.pharmgkb.org/pathway/$1
  n2t:
    description: The PharmGKB database is a central repository for genetic, genomic,
      molecular and cellular phenotype data and clinical information about people
      who have participated in pharmacogenomics research studies. The data includes,
      but is not limited to, clinical and basic pharmacokinetic and pharmacogenomic
      research in the cardiovascular, pulmonary, cancer, pathways, metabolic and transporter
      domains.  PharmGKB Pathways are drug centric, gene based, interactive pathways
      which focus on candidate genes and gene groups and associated genotype and phenotype
      data of relevance for pharmacogenetic and pharmacogenomic studies.
    example: PA146123006
    homepage: http://www.pharmgkb.org/
    name: PharmGKB at Stanford
    namespaceEmbeddedInLui: false
    pattern: ^PA\d+$
    prefix: pharmgkb.pathways
    uri_format: http://www.pharmgkb.org/pathway/$1
  name: PharmGKB pathway
  prefix: pharmgkb.pathways
  prefixcommons:
    description: The PharmGKB database is a central repository for genetic, genomic,
      molecular and cellular phenotype data and clinical information about people
      who have participated in pharmacogenomics research studies. The data includes,
      but is not limited to, clinical and basic pharmacokinetic and pharmacogenomic
      research in the cardiovascular, pulmonary, cancer, pathways, metabolic and transporter
      domains.  PharmGKB Pathways are drug centric, gene based, interactive pathways
      which focus on candidate genes and gene groups and associated genotype and phenotype
      data of relevance for pharmacogenetic and pharmacogenomic studies.
    example: PA146123006
    keywords:
    - pathway
    - pharmacogenomics
    name: PharmGKB Pathways
    pattern: ^PA\d+$
    prefix: pharmgkb.pathways
    pubmed_ids:
    - '11908751'
    - '22103613'
    uri_format: http://www.pharmgkb.org/pathway/$1
  publications:
  - doi: 10.2217/bmm.11.94
    pmc: PMC3339046
    pubmed: '22103613'
    title: 'From pharmacogenomic knowledge acquisition to clinical applications: the
      PharmGKB as a clinical pharmacogenomic biomarker resource'
    year: 2011
  - doi: 10.1038/sj.tpj.6500035
    pmc: null
    pubmed: '11908751'
    title: 'Integrating genotype and phenotype information: an overview of the PharmGKB
      project. Pharmacogenetics Research Network and Knowledge Base'
    year: 2001
  wikidata:
    description: unique identifier for an entity in the PharmGKB knowledgebase
    example:
    - PA134955224
    - PA356
    - PA443560
    - PA451581
    - PA451906
    homepage: https://www.pharmgkb.org/
    name: PharmGKB ID
    pattern: ^PA[1-9]\d*$
    prefix: P7001
    uri_format: https://www.pharmgkb.org/accession/$1
pharmgkb.variant:
  biolink:
    is_identifiers: false
    is_obo: false
    prefix: PHARMGKB.VARIANT
    uri_format: https://www.pharmgkb.org/variant/$1
  contact:
    email: teri.klein@stanford.edu
    github: TeriKlein
    name: Teri E Klein
    orcid: 0000-0001-5527-6475
  contact_group_email: feedback@clinpgx.org
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: SNPs and other variants that can be mapped to dbSNP.
  domain: variant
  example: PA166156302
  github_request_issue: 1368
  homepage: https://www.pharmgkb.org
  keywords:
  - genetic variant
  - genetic variation
  - snp
  license: CC-BY-SA-4.0
  logo: https://rxgenomix.com/wp-content/uploads/2019/10/pharmgKB.png
  mappings:
    biolink: PHARMGKB.VARIANT
  name: PharmGKB Variant
  pattern: ^PA\d+$
  prefix: pharmgkb.variant
  uri_format: https://www.pharmgkb.org/variant/$1
pharmvar:
  contact:
    email: agaedigk@cmh.edu
    github: null
    name: Andrea Gaedigk
    orcid: 0000-0001-6968-1893
  mappings:
    prefixcommons: pharmvar
  name: Pharmacogene Variation Consortium
  prefix: pharmvar
  prefixcommons:
    description: The Pharmacogene Variation (PharmVar) Consortium is the new home
      for PGx gene nomenclature serving as a centralized ‘Next-Generation’ Pharmacogene
      Variation data repository.  The major focus of PharmVar is to catalogue allelic
      variation of genes impacting drug metabolism, disposition and response and provide
      a unifying designation system (nomenclature) for the global pharmacogenetic/genomic
      community. Efforts are synchronized between PharmVar, the Pharmacogenomic KnowledgeBase,
      and the Clinical Pharmacogenetic Implementation Consortium.
    example: CYP2A6
    homepage: https://www.pharmvar.org
    keywords:
    - variant
    - gene
    - pharmacogenomics
    name: PharmVar
    pattern: ^[A-z0-9]+$
    prefix: pharmvar
    pubmed_ids:
    - '29134625'
    synonyms:
    - pharmvar.gene
    uri_format: https://www.pharmvar.org/gene/$1
  provides: hgnc.symbol
  publications:
  - doi: 10.1002/cpt.910
    pmc: PMC5836850
    pubmed: '29134625'
    title: 'The Pharmacogene Variation (PharmVar) Consortium: Incorporation of the
      Human Cytochrome P450 (CYP) Allele Nomenclature Database'
    year: 2017
  reviewer:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
phenolexplorer:
  biocontext:
    prefix: PHENOLEXPLORER
  mappings:
    biocontext: PHENOLEXPLORER
    miriam: phenolexplorer
    n2t: phenolexplorer
    re3data: r3d100012197
  miriam:
    deprecated: false
    description: Phenol-Explorer is an electronic database on polyphenol content in
      foods. Polyphenols form a wide group of natural antioxidants present in a large
      number of foods and beverages. They contribute to food characteristics such
      as taste, colour or shelf-life. They also participate in the prevention of several
      major chronic diseases such as cardiovascular diseases, diabetes, cancers, neurodegenerative
      diseases or osteoporosis.
    homepage: http://www.phenol-explorer.eu/foods/
    id: 00000268
    name: Phenol-Explorer
    namespaceEmbeddedInLui: false
    pattern: ^\d+$
    prefix: phenolexplorer
    sampleId: '75'
    uri_format: http://phenol-explorer.eu/foods/$1
  n2t:
    description: Phenol-Explorer is an electronic database on polyphenol content in
      foods. Polyphenols form a wide group of natural antioxidants present in a large
      number of foods and beverages. They contribute to food characteristics such
      as taste, colour or shelf-life. They also participate in the prevention of several
      major chronic diseases such as cardiovascular diseases, diabetes, cancers, neurodegenerative
      diseases or osteoporosis.
    example: '75'
    homepage: http://www.phenol-explorer.eu/foods/
    name: Phenol-Explorer Database on Phenol content of foods
    namespaceEmbeddedInLui: false
    pattern: ^\d+$
    prefix: phenolexplorer
    uri_format: http://phenol-explorer.eu/foods/$1
  prefix: phenolexplorer
  re3data:
    description: Phenol-Explorer is the first comprehensive database on polyphenol
      content in foods
    doi: 10.17616/R33361
    homepage: http://phenol-explorer.eu/
    name: Phenol-Explorer
    prefix: r3d100012197
    synonyms:
    - Database on Polyphenol Content in Foods
    xrefs:
      nif: 0000-32996
phenx:
  aberowl:
    description: Standard measures related to complex diseases, phenotypic traits
      and environmental exposures
    download_owl: http://aber-owl.net/media/ontologies/PHENX/16/phenx.owl
    name: PhenX Phenotypic Terms
    prefix: PHENX
    version: '1.2'
  bioportal:
    contact:
      email: yingqin@rti.org
      name: PhenX Admin
    description: Standard measures related to complex diseases, phenotypic traits
      and environmental exposures
    name: PhenX Phenotypic Terms
    prefix: PHENX
    version: '1.2'
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: A web-based catalog of recommended measurement protocols selected by
    experts to include in studies with human participants.
  example: '130502'
  fairsharing:
    abbreviation: PhenX
    description: Standard measures related to complex diseases, phenotypic traits
      and environmental exposures.
    domains:
    - phenotype
    - disease
    - exposure
    homepage: https://www.phenx.org/
    name: PhenX Phenotypic Terms
    prefix: FAIRsharing.y5jcwa
    publications:
    - doi: 10.1097/mol.0b013e3283377395
      pubmed: '20154612'
      title: 'PhenX: a toolkit for interdisciplinary genetics research'
      year: 2010
    - doi: 10.1093/aje/kwr193
      pubmed: '21749974'
      title: 'The PhenX Toolkit: get the most from your measures'
      year: 2011
    - doi: 10.1038/gim.2016.199
      pubmed: '28079902'
      title: PhenX measures for phenotyping rare genetic conditions
      year: 2017
    subjects:
    - Environmental Science
    - Life Science
    - Biomedical Science
  github_request_issue: 503
  homepage: https://www.phenxtoolkit.org/
  integbio:
    description: The PhenX (consensus measures for Phenotypes and eXposures) Toolkit
      is a web-based catalog of recommended, standard measures of phenotypes and environmental
      exposures for use in biomedical research. The PhenX Toolkit offers well-established,
      broadly validated measures of phenotypes and exposures relevant to investigators
      in human genomics, epidemiology, and biomedical research. The measures in the
      Toolkit are selected by Working Groups of domain experts using a consensus process.
      The Toolkit provides detailed protocols, information about the measures, and
      tools to help investigators incorporate PhenX measures into their studies.
    fairsharing: FAIRsharing.2wa7v7
    homepage: https://www.phenxtoolkit.org
    information_keywords:
    - Phenotype
    - Method
    - Bibliography/Documents
    maintainer: Pat West
    name: PhenX Toolkit
    prefix: nbdc02244
    pubmeds:
    - '26132000'
    - '22954959'
    status: Active
    target_keywords:
    - Organism
    - Health/Disease
  mappings:
    aberowl: PHENX
    bioportal: PHENX
    fairsharing: FAIRsharing.y5jcwa
    integbio: nbdc02244
  name: PhenX Toolkit
  pattern: ^\d+$
  prefix: phenx
  publications:
  - doi: 10.1038/gim.2016.199
    pmc: PMC5507752
    pubmed: '28079902'
    title: PhenX measures for phenotyping rare genetic conditions
    year: 2017
  - doi: 10.1093/aje/kwr193
    pmc: PMC3141081
    pubmed: '21749974'
    title: 'The PhenX Toolkit: get the most from your measures'
    year: 2011
  - doi: 10.1097/mol.0b013e3283377395
    pmc: PMC8038872
    pubmed: '20154612'
    title: 'PhenX: a toolkit for interdisciplinary genetics research'
    year: 2010
  synonyms:
  - phenxtoolkit
  uri_format: https://www.phenxtoolkit.org/protocols/view/$1
phipo:
  aberowl:
    description: PHIPO is a formal ontology of species-neutral phenotypes observed
      in pathogen-host interactions.
    download_owl: http://aber-owl.net/media/ontologies/PHIPO/41/phipo.owl
    homepage: https://github.com/PHI-base/phipo
    name: Pathogen Host Interaction Phenotype Ontology
    prefix: PHIPO
  bioportal:
    contact:
      email: alayne.cuzick@rothamsted.ac.uk
      name: Alayne Cuzick
    description: PHIPO is a formal ontology of species-neutral phenotypes observed
      in pathogen-host interactions. PHIPO is being developed to support the comprehensive
      and detailed representation of phenotypes in PHI-base, the multi-species Pathogen-Host
      Interactions database available online at http://www.phi-base.org. PHIPO is
      pre-composed and logically defined., Ontology of species-neutral phenotypes
      observed in pathogen-host interactions.
    homepage: https://github.com/PHI-base/phipo
    license: CC-BY-3.0
    name: Pathogen Host Interaction Phenotype Ontology
    prefix: PHIPO
    version: '2025-10-29'
  example: '0000001'
  mappings:
    aberowl: PHIPO
    bioportal: PHIPO
    obofoundry: phipo
    ols: phipo
    ontobee: PHIPO
    wikidata.entity: Q81661779
  obofoundry:
    contact: alayne.cuzick@rothamsted.ac.uk
    contact.github: CuzickA
    contact.label: Alayne Cuzick
    contact.orcid: 0000-0001-8941-3984
    depends_on:
    - pato
    deprecated: false
    description: PHIPO is a formal ontology of species-neutral phenotypes observed
      in pathogen-host interactions.
    domain: phenotype
    download.obo: http://purl.obolibrary.org/obo/phipo.obo
    download.owl: http://purl.obolibrary.org/obo/phipo.owl
    homepage: https://github.com/PHI-base/phipo
    license: CC BY 3.0
    license.url: http://creativecommons.org/licenses/by/3.0/
    name: Pathogen Host Interaction Phenotype Ontology
    preferredPrefix: PHIPO
    prefix: phipo
    publications:
    - id: https://www.ncbi.nlm.nih.gov/pubmed/34788826
      title: 'PHI-base in 2022: a multi-species phenotype database for Pathogen-Host
        Interactions'
    repository: https://github.com/PHI-base/phipo
  ols:
    description: Ontology of species-neutral phenotypes observed in pathogen-host
      interactions.
    download_owl: http://purl.obolibrary.org/obo/phipo.owl
    homepage: https://github.com/PHI-base/phipo
    name: Pathogen Host Interactions Phenotype Ontology
    prefix: phipo
    tracker: https://github.com/PHI-base/phipo/issues
    version: '2025-10-29'
    version.iri: http://purl.obolibrary.org/obo/phipo/releases/2025-10-29/phipo.owl
  ontobee:
    library: Library
    name: Pathogen Host Interaction Phenotype Ontology
    prefix: PHIPO
  pattern: ^\d{7}$
  prefix: phipo
  publications:
  - doi: 10.1093/nar/gkab1037
    pmc: PMC8728202
    pubmed: '34788826'
    title: 'PHI-base in 2022: a multi-species phenotype database for Pathogen-Host
      Interactions'
    year: 2022
  - doi: null
    pmc: null
    pubmed: '34788826'
    title: 'PHI-base in 2022: a multi-species phenotype database for Pathogen-Host
      Interactions'
    year: null
  uri_format: http://purl.obolibrary.org/obo/PHIPO_$1
phosphopoint.kinase:
  biocontext:
    prefix: PHOSPHOPOINT.KINASE
  mappings:
    biocontext: PHOSPHOPOINT.KINASE
    miriam: phosphopoint.kinase
    n2t: phosphopoint.kinase
  miriam:
    deprecated: false
    description: PhosphoPOINT is a database of the human kinase and phospho-protein
      interactome. It describes the interactions among kinases, their potential substrates
      and their interacting (phospho)-proteins. It also incorporates gene expression
      and uses gene ontology (GO) terms to annotate interactions. This collection
      references kinase information.
    homepage: http://kinase.bioinformatics.tw/
    id: 00000385
    name: PhosphoPoint Kinase
    namespaceEmbeddedInLui: false
    pattern: ^\w+$
    prefix: phosphopoint.kinase
    sampleId: AURKA
    uri_format: http://kinase.bioinformatics.tw/showall.jsp?type=Kinase&info=Gene&name=$1&drawing=0&sorting=0&kinome=1
  n2t:
    description: PhosphoPOINT is a database of the human kinase and phospho-protein
      interactome. It describes the interactions among kinases, their potential substrates
      and their interacting (phospho)-proteins. It also incorporates gene expression
      and uses gene ontology (GO) terms to annotate interactions. This collection
      references kinase information.
    example: AURKA
    homepage: http://kinase.bioinformatics.tw/
    name: PhosphoPoint Kinase at National Taiwan University
    namespaceEmbeddedInLui: false
    pattern: ^\w+$
    prefix: phosphopoint.kinase
    uri_format: http://kinase.bioinformatics.tw/showall.jsp?type=Kinase&info=Gene&name=$1&drawing=0&sorting=0&kinome=1
  prefix: phosphopoint.kinase
phosphopoint.protein:
  biocontext:
    prefix: PHOSPHOPOINT.PROTEIN
  mappings:
    biocontext: PHOSPHOPOINT.PROTEIN
    miriam: phosphopoint.protein
    n2t: phosphopoint.protein
  miriam:
    deprecated: true
    description: PhosphoPOINT is a database of the human kinase and phospho-protein
      interactome. It describes the interactions among kinases, their potential substrates
      and their interacting (phospho)-proteins. It also incorporates gene expression
      and uses gene ontology (GO) terms to annotate interactions. This collection
      references phosphoprotein information.
    homepage: http://kinase.bioinformatics.tw/
    id: 00000386
    name: PhosphoPoint Phosphoprotein
    namespaceEmbeddedInLui: false
    pattern: ^\w+$
    prefix: phosphopoint.protein
    sampleId: AURKA
    uri_format: http://kinase.bioinformatics.tw/showall.jsp?type=PhosphoProtein&info=Gene&name=$1&drawing=0&sorting=0&kinome=0
  n2t:
    description: PhosphoPOINT is a database of the human kinase and phospho-protein
      interactome. It describes the interactions among kinases, their potential substrates
      and their interacting (phospho)-proteins. It also incorporates gene expression
      and uses gene ontology (GO) terms to annotate interactions. This collection
      references phosphoprotein information.
    example: AURKA
    homepage: http://kinase.bioinformatics.tw/
    name: PhosphoPoint Phosphoprotein at National Taiwan University
    namespaceEmbeddedInLui: false
    pattern: ^\w+$
    prefix: phosphopoint.protein
    uri_format: http://kinase.bioinformatics.tw/showall.jsp?type=PhosphoProtein&info=Gene&name=$1&drawing=0&sorting=0&kinome=0
  prefix: phosphopoint.protein
phosphosite.curation:
  contributor:
    email: b.gyori@northeastern.edu
    github: bgyori
    name: Benjamin M. Gyori
    orcid: 0000-0001-9439-5346
  description: PhosphoSite is a mammalian protein database that provides information
    about in vivo phosphorylation sites. This datatype refers to curation records
    that collect information extracted from specific publications.
  example: '34665743'
  github_request_issue: 1136
  homepage: https://www.phosphosite.org
  name: PhosphoSite Curation
  pattern: ^\d+$
  prefix: phosphosite.curation
  reviewer:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  uri_format: https://www.phosphosite.org/curatedInfoAction.action?record=$1
phosphosite.protein:
  biocontext:
    prefix: PHOSPHOSITE.PROTEIN
  mappings:
    biocontext: PHOSPHOSITE.PROTEIN
    miriam: phosphosite.protein
    n2t: phosphosite.protein
  miriam:
    deprecated: false
    description: PhosphoSite is a mammalian protein database that provides information
      about in vivo phosphorylation sites. This datatype refers to protein-level information,
      providing a list of phosphorylation sites for each protein in the database.
    homepage: http://www.phosphosite.org/homeAction.do
    id: '00000105'
    name: PhosphoSite Protein
    namespaceEmbeddedInLui: false
    pattern: ^\d{5}$
    prefix: phosphosite.protein
    sampleId: '12300'
    uri_format: http://www.phosphosite.org/proteinAction.do?id=$1
  n2t:
    description: PhosphoSite is a mammalian protein database that provides information
      about in vivo phosphorylation sites. This datatype refers to protein-level information,
      providing a list of phosphorylation sites for each protein in the database.
    example: '12300'
    homepage: http://www.phosphosite.org/homeAction.do
    name: PhosphoSite
    namespaceEmbeddedInLui: false
    pattern: ^\d{5}$
    prefix: phosphosite.protein
    uri_format: http://www.phosphosite.org/proteinAction.do?id=$1
  prefix: phosphosite.protein
phosphosite.residue:
  biocontext:
    prefix: PHOSPHOSITE.RESIDUE
  mappings:
    biocontext: PHOSPHOSITE.RESIDUE
    miriam: phosphosite.residue
    n2t: phosphosite.residue
  miriam:
    deprecated: false
    description: PhosphoSite is a mammalian protein database that provides information
      about in vivo phosphorylation sites. This datatype refers to residue-level information,
      providing a information about a single modification position in a specific protein
      sequence.
    homepage: http://www.phosphosite.org/homeAction.do
    id: '00000125'
    name: PhosphoSite Residue
    namespaceEmbeddedInLui: false
    pattern: ^\d+$
    prefix: phosphosite.residue
    sampleId: '2842'
    uri_format: http://www.phosphosite.org/siteAction.do?id=$1
  n2t:
    description: PhosphoSite is a mammalian protein database that provides information
      about in vivo phosphorylation sites. This datatype refers to residue-level information,
      providing a information about a single modification position in a specific protein
      sequence.
    example: '2842'
    homepage: http://www.phosphosite.org/homeAction.do
    name: PhosphoSite Residue
    namespaceEmbeddedInLui: false
    pattern: ^\d+$
    prefix: phosphosite.residue
    uri_format: http://www.phosphosite.org/siteAction.do?id=$1
  prefix: phosphosite.residue
phosphosite.sitegroup:
  comment: Potentially could use a URI format like https://www.phosphosite.org/siteGroupAction.action?protOrg=1156&id=$1,
    but it's not obvious what the protOrg does.
  contributor:
    email: benjamin_gyori@hms.harvard.edu
    github: bgyori
    name: Benjamin M. Gyori
    orcid: 0000-0001-9439-5346
  description: Site groups are orthologous positions in human, mouse, rat, etc. where
    phosphorylations or other PTMs occur.
  example: '447860'
  github_request_issue: 432
  homepage: https://www.phosphosite.org
  keywords:
  - biochemistry
  - grouping
  - post-translational modification
  name: PhosphoSite Site Group
  pattern: ^\d+$
  prefix: phosphosite.sitegroup
  reviewer:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
phrr:
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: The Philippine Health Research Registry (PHRR), managed by the Philippine
    Council for Health Research and Development, is a tool for good governance to
    promote transparency and accountability in health research. PHRR is a publicly
    accessible database on newly approved health researches. It includes clinical
    trials and non-clinical studies conducted in the Philippines. The registry is
    compliant with the World Health Organization (WHO) standard for clinical trials
    registry. [from website]
  example: '4195'
  homepage: https://registry.healthresearch.ph
  name: Philippine Health Research Registry
  prefix: phrr
  uri_format: https://registry.healthresearch.ph/index.php/registry?view=research&layout=details&cid=$1
phylomedb:
  biocontext:
    prefix: PHYLOMEDB
  contact:
    email: toni.gabaldon@crg.eu
    github: tgabaldon
    name: Toni Gabaldón
    orcid: 0000-0003-0019-1735
  fairsharing:
    abbreviation: PhylomeDB
    description: 'PhylomeDB is a unique knowledge base providing public access to
      minable and browsable catalogues of pre-computed, genome-wide collections of
      annotated sequences, alignments and phylogenies (i.e. phylomes) of homologous
      genes, as well as to their corresponding phylogeny-based orthology and paralogy
      relationships. In addition, PhylomeDB trees and alignments can be downloaded
      for further processing to detect and date gene duplication events, infer past
      events of inter-species hybridization and horizontal gene transfer, as well
      as to uncover footprints of selection, introgression, gene conversion, or other
      relevant evolutionary processes in the genes and organisms of interests. The
      v5 release also represents a significant core data expansion, with the database
      providing access to 534 phylomes, comprising over 8 million trees, and homology
      relationships for genes in over 6000 species. This makes PhylomeDB the largest
      and most comprehensive public repository of gene phylogenies '
    homepage: http://phylomedb.org
    license: CC BY-NC-SA 2.0
    name: PhylomeDB
    prefix: FAIRsharing.7hxxc4
    publications:
    - doi: 10.1093/nar/gkm899
      pubmed_id: 17962297
      title: 'PhylomeDB: a database for genome-wide collections of gene phylogenies.'
    - doi: 10.1093/nar/gkq1109
      pubmed_id: 21075798
      title: 'PhylomeDB v3.0: an expanding repository of genome-wide collections of
        trees, alignments and phylogeny-based orthology and paralogy predictions.'
    - doi: 10.1093/nar/gkt1177
      pubmed_id: 24275491
      title: 'PhylomeDB v4: zooming into the plurality of evolutionary histories of
        a genome.'
    - doi: 10.1093/nar/gkab966
      pubmed_id: 34718760
      title: 'PhylomeDB V5: an expanding repository for genome-wide catalogues of
        annotated gene phylogenies.'
    subjects:
    - Taxonomy
    - Phylogeny
    - Phylogenetics
    - Phylogenomics
    - Life Science
    twitter: phylomedb
  integbio:
    description: PhylomeDB is a unique knowledge base providing public access to minable
      and browsable catalogues of pre-computed, genome-wide collections of annotated
      sequences, alignments and phylogenies (i.e. phylomes) of homologous genes, as
      well as to their corresponding phylogeny-based orthology and paralogy relationships.
      In addition, PhylomeDB trees and alignments can be downloaded for further processing
      to detect and date gene duplication events, infer past events of inter-species
      hybridization and horizontal gene transfer, as well as to uncover footprints
      of selection, introgression, gene conversion, or other relevant evolutionary
      processes in the genes and organisms of interests. The v5 release also represents
      a significant core data expansion, with the database providing access to 534
      phylomes, comprising over 8 million trees, and homology relationships for genes
      in over 6000 species. This makes PhylomeDB the largest and most comprehensive
      public repository of gene phylogenies
    fairsharing: FAIRsharing.7hxxc4
    homepage: http://phylomedb.org
    information_keywords:
    - Classification
    - Sequence
    maintainer: CRG (Comparative Genomics Group)
    name: PhylomeDB
    prefix: nbdc01764
    pubmeds:
    - '17962297'
    - '21075798'
    - '24275491'
    status: Active
    target_keywords:
    - Genome/Gene
  mappings:
    biocontext: PHYLOMEDB
    fairsharing: FAIRsharing.7hxxc4
    integbio: nbdc01764
    miriam: phylomedb
    n2t: phylomedb
    prefixcommons: phylomedb
    uniprot: DB-0144
  miriam:
    deprecated: false
    description: PhylomeDB is a database of complete phylomes derived for different
      genomes within a specific taxonomic range. It provides alignments, phylogentic
      trees and tree-based orthology predictions for all encoded proteins.
    homepage: http://phylomedb.org/
    id: '00000223'
    name: PhylomeDB
    namespaceEmbeddedInLui: false
    pattern: ^\w+$
    prefix: phylomedb
    sampleId: Phy000CLXM_RAT
    uri_format: http://phylomedb.org/?seqid=$1
  n2t:
    description: PhylomeDB is a database of complete phylomes derived for different
      genomes within a specific taxonomic range. It provides alignments, phylogentic
      trees and tree-based orthology predictions for all encoded proteins.
    example: Phy000CLXM_RAT
    homepage: http://phylomedb.org/
    name: PhylomeDB at Centro de Investigaci&#xF3;n Pr&#xED;ncipe Felipe
    namespaceEmbeddedInLui: false
    pattern: ^\w+$
    prefix: phylomedb
    uri_format: http://phylomedb.org/?seqid=$1
  prefix: phylomedb
  prefixcommons:
    description: PhylomeDB is a public database for complete collections of gene phylogenies
      (phylomes). It allows users to interactively explore the evolutionary history
      of genes through the visualization of phylogenetic trees and multiple sequence
      alignments.
    example: Phy000CLXM_RAT
    homepage: http://phylomedb.bioinfo.cipf.es
    keywords:
    - genome
    - protein
    - taxonomy
    name: Database for complete collections of gene phylogenies
    pattern: ^\w+$
    prefix: phylomedb
    pubmed_ids:
    - '17962297'
    uri_format: http://phylomedb.org/?seqid=$1
  publications:
  - doi: 10.1093/nar/gkab966
    pmc: PMC8728271
    pubmed: '34718760'
    title: 'PhylomeDB V5: an expanding repository for genome-wide catalogues of annotated
      gene phylogenies'
    year: 2022
  - doi: 10.1093/nar/gkt1177
    pmc: PMC3964985
    pubmed: '24275491'
    title: 'PhylomeDB v4: zooming into the plurality of evolutionary histories of
      a genome'
    year: 2013
  - doi: 10.1093/nar/gkq1109
    pmc: PMC3013701
    pubmed: '21075798'
    title: 'PhylomeDB v3.0: an expanding repository of genome-wide collections of
      trees, alignments and phylogeny-based orthology and paralogy predictions'
    year: 2010
  - doi: 10.1093/nar/gkm899
    pmc: PMC2238872
    pubmed: '17962297'
    title: 'PhylomeDB: a database for genome-wide collections of gene phylogenies'
    year: 2007
  - doi: 10.1093/nar/gkm899
    pmc: null
    pubmed: null
    title: 'PhylomeDB: a database for genome-wide collections of gene phylogenies.'
    year: null
  - doi: 10.1093/nar/gkq1109
    pmc: null
    pubmed: null
    title: 'PhylomeDB v3.0: an expanding repository of genome-wide collections of
      trees, alignments and phylogeny-based orthology and paralogy predictions.'
    year: null
  - doi: 10.1093/nar/gkt1177
    pmc: null
    pubmed: null
    title: 'PhylomeDB v4: zooming into the plurality of evolutionary histories of
      a genome.'
    year: null
  - doi: 10.1093/nar/gkab966
    pmc: null
    pubmed: null
    title: 'PhylomeDB V5: an expanding repository for genome-wide catalogues of annotated
      gene phylogenies.'
    year: null
  - doi: null
    pmc: null
    pubmed: '17962297'
    title: null
    year: null
  - doi: 10.1093/nar/gkab966
    pmc: null
    pubmed: '34718760'
    title: null
    year: null
  uniprot:
    abbreviation: PhylomeDB
    category: Phylogenomic databases
    homepage: https://phylomedb.org/
    name: Database for complete collections of gene phylogenies
    prefix: DB-0144
    publications:
    - doi: 10.1093/nar/gkab966
      pubmed: '34718760'
    uri_format: https://phylomedb.org/search_phylome/?seqid=$1
physh:
  bartoc:
    abbreviation: PhySH
    description: 'PhySH (Physics Subject Headings) is a physics classification scheme
      developed by the American Physical Society to organize journals, meetings, and
      other content by topic. The development of PhySH is motivated by the lack of
      a fully open, high quality classification scheme for physics. It is intended
      initially to meet the specific goals of the APS for our journal, meeting, and
      other content. A longer term goal is to make it available for use by the broader
      community. (...) Right now, the main use of PhySH is to classify manuscripts
      within the APS peer-review process and, ultimately, published journal articles.
      The assigned concepts will be used for ensuring articles are routed to the most
      appropriate handling editor who is knowledgeable in that area. They also help
      editors in finding similar articles previously submitted and in finding suitable
      referees.


      As one might expect with something so new, the refinement of PhySH is still
      very much underway. The facets and disciplines have been identified and almost
      3,000 concepts have been added to PhySH through an iterative process that is
      still ongoing. Many APS journal editors are involved in this process, primarily
      by lending their expertise in the various subfields in physics. The assignment
      of concepts to the various facets can be rather subjective. Thus, we expect
      to make many adjustments to PhySH as we receive feedback from the community
      (especially authors using PhySH to classify their submissions) and as we incorporate
      PhySH into the APS journal websites. As we iteratively refine PhySH over the
      coming months, the rate of new concept additions, concept reassignments within
      facets, and new relationships among concepts should abate significantly.'
    homepage: https://physh.aps.org/
    license: CC0-1.0
    name: Physics Subject Headings
    pattern: ^[0-9a-z-]+$
    prefix: '1899'
    wikidata_database: Q30523272
  example: 0003fc3f-1522-4fca-bf3f-bcef0dcec405
  mappings:
    bartoc: '1899'
    tib: physh
  name: Physics Subject Headings
  prefix: physh
  tib:
    description: PhySH (Physics Subject Headings) is a physics classification scheme
      developed by APS to organize journal, meeting, and other content by topic.
    download_rdf: https://raw.githubusercontent.com/physh-org/PhySH/master/physh.ttl
    homepage: https://physh.org/
    keywords:
    - NFDI4ING
    - physics
    name: PhySH - Physics Subject Headings
    prefix: physh
    tracker: https://github.com/physh-org/PhySH/issues
    uri_format: https://doi.org/10.29172/$1
phytozome.locus:
  biocontext:
    prefix: PHYTOZOME.LOCUS
  mappings:
    biocontext: PHYTOZOME.LOCUS
    miriam: phytozome.locus
    n2t: phytozome.locus
    ncbi: Phytozome
  miriam:
    deprecated: false
    description: Phytozome is a project to facilitate comparative genomic studies
      amongst green plants. Famlies of orthologous and paralogous genes that represent
      the modern descendents of ancestral gene sets are constructed at key phylogenetic
      nodes. These families allow easy access to clade specific orthology/paralogy
      relationships as well as clade specific genes and gene expansions. This collection
      references locus information.
    homepage: http://www.phytozome.net/
    id: '00000432'
    name: Phytozome Locus
    namespaceEmbeddedInLui: false
    pattern: ^[A-Za-z0-9]+$
    prefix: phytozome.locus
    sampleId: Glyma0021s00410
    uri_format: http://www.phytozome.net/genePage.php?crown&method=0&search=1&detail=1&searchText=locusname:$1
  n2t:
    description: Phytozome is a project to facilitate comparative genomic studies
      amongst green plants. Famlies of orthologous and paralogous genes that represent
      the modern descendents of ancestral gene sets are constructed at key phylogenetic
      nodes. These families allow easy access to clade specific orthology/paralogy
      relationships as well as clade specific genes and gene expansions. This collection
      references locus information.
    example: Glyma0021s00410
    homepage: http://www.phytozome.net/
    name: Phytozome Locus at Joint Genome Institute
    namespaceEmbeddedInLui: false
    pattern: ^[A-Za-z0-9]+$
    prefix: phytozome.locus
    uri_format: http://www.phytozome.net/genePage.php?crown&method=0&search=1&detail=1&searchText=locusname:$1
  ncbi:
    example: Glyma0021s00410
    homepage: http://phytozome.jgi.doe.gov/pz/portal.html
    name: Plant Genome Network
    prefix: Phytozome
  prefix: phytozome.locus
  synonyms:
  - JGI Phytozome
pibase:
  mappings:
    pathguide: '183'
    prefixcommons: pibase
  name: Database of structurally defined protein interfaces
  pathguide:
    abbreviation: PIBASE
    homepage: http://modbase.compbio.ucsf.edu/pibase/introduction.html
    name: PIBASE
    prefix: '183'
  prefix: pibase
  prefixcommons:
    description: PIBASE is a collection of all protein structural interfaces extracted
      from the Protein Data Bank and PQS structure databases. Both chain-chain and
      domain-domain (SCOP and CATH definitions) interfaces are detected.
    example: '21692'
    homepage: http://salilab.org/pibase
    keywords:
    - protein
    - structure
    name: 'PIBASE: a database of structurally defined protein interfaces'
    pattern: ^\d+$
    prefix: pibase
    uri_format: http://modbase.compbio.ucsf.edu/pibase-cgi/get_details.pl?object_type=complexes&bdp_id=$1
  reviewer:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
pictar:
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  deprecated: true
  example: hsa-let-7a
  homepage: https://pictar.mdc-berlin.de/
  name: PicTar
  prefix: pictar
  synonyms:
  - pictar-vert
pid.pathway:
  biocontext:
    prefix: PID.PATHWAY
  contact:
    email: schaefec@mail.nih.gov
    github: null
    name: Carl F. Schaefer
    orcid: 0000-0002-5941-3390
  domain: pathway
  edam:
    description: Identifier of a pathway from the NCI-Nature pathway database.
    name: Pathway ID (NCI-Nature)
    obsolete: false
    prefix: '2344'
  example: eff796f3-6195-11e5-8ac5-06603eb7f303
  fairsharing:
    abbreviation: PID
    description: The Pathway Interaction Database is a highly-structured, curated
      collection of information about known biomolecular interactions and key cellular
      processes assembled into signaling pathways.
    homepage: http://pid.nci.nih.gov/
    name: Pathway Interaction Database
    prefix: FAIRsharing.ncgh1j
    publications:
    - doi: 10.1093/nar/gkn653
      pubmed_id: 18832364
      title: 'PID: the Pathway Interaction Database.'
    subjects:
    - Life Science
  homepage: https://www.ndexbio.org/index.html#/networkset/8a2d7ee9-1513-11e9-bb6a-0ac135e8bacf
  logo: https://home.ndexbio.org/img/pid-logo-ndex.jpg
  mappings:
    biocontext: PID.PATHWAY
    edam: '2344'
    fairsharing: FAIRsharing.ncgh1j
    miriam: pid.pathway
    n2t: pid.pathway
    pathguide: '119'
    prefixcommons: pid
  miriam:
    deprecated: true
    description: The Pathway Interaction Database is a highly-structured, curated
      collection of information about known human biomolecular interactions and key
      cellular processes assembled into signaling pathways. This datatype provides
      access to pathway information.
    homepage: http://pid.nci.nih.gov/
    id: '00000133'
    name: 'NCI Pathway Interaction Database: Pathway'
    namespaceEmbeddedInLui: false
    pattern: ^\w+$
    prefix: pid.pathway
    sampleId: pi3kcipathway
    uri_format: http://pid.nci.nih.gov/search/pathway_landing.shtml?what=graphic&jpg=on&pathway_id=$1
  n2t:
    description: The Pathway Interaction Database is a highly-structured, curated
      collection of information about known human biomolecular interactions and key
      cellular processes assembled into signaling pathways. This datatype provides
      access to pathway information.
    example: pi3kcipathway
    homepage: http://pid.nci.nih.gov/
    name: NCI Pathway Interaction Database (Pathway)
    namespaceEmbeddedInLui: false
    pattern: ^\w+$
    prefix: pid.pathway
    uri_format: http://pid.nci.nih.gov/search/pathway_landing.shtml?what=graphic&jpg=on&pathway_id=$1
  pathguide:
    abbreviation: PID
    homepage: http://pid.nci.nih.gov/
    keywords:
    - BioPAX
    name: NCI-Nature Pathway Interaction Database
    prefix: '119'
  pattern: ^\b[0-9a-f]{8}\b-[0-9a-f]{4}-[0-9a-f]{4}-[0-9a-f]{4}-\b[0-9a-f]{12}\b$
  prefix: pid.pathway
  prefixcommons:
    description: The Pathway Interaction Database is a highly-structured, curated
      collection of information about known biomolecular interactions and key cellular
      processes assembled into signaling pathways
    example: p38alphabetadownstreampathway
    homepage: http://pid.nci.nih.gov/
    keywords:
    - pathway
    - small molecule
    - gene
    - protein
    license: http://www.cancer.gov/global/web/policies/allpages#5
    name: Pathway Interaction Database
    pattern: ^\w+$
    prefix: pid
    pubmed_ids:
    - '18832364'
    synonyms:
    - pid.pathway
    uri_format: http://pid.nci.nih.gov/search/pathway_landing.shtml?what=graphic&jpg=on&pathway_id=$1
  publications:
  - doi: 10.1093/nar/gkn653
    pmc: PMC2686461
    pubmed: '18832364'
    title: 'PID: the Pathway Interaction Database'
    year: 2008
  - doi: 10.1093/nar/gkn653
    pmc: null
    pubmed: null
    title: 'PID: the Pathway Interaction Database.'
    year: null
  - doi: null
    pmc: null
    pubmed: '18832364'
    title: null
    year: null
  - doi: 10.1093/nar/gkn653
    pmc: null
    pubmed: null
    title: 'PID: the Pathway Interaction Database.'
    year: null
  - doi: null
    pmc: null
    pubmed: '18832364'
    title: null
    year: null
  synonyms:
  - pid
pigqtldb:
  biocontext:
    prefix: PIGQTLDB
  mappings:
    biocontext: PIGQTLDB
    miriam: pigqtldb
    n2t: pigqtldb
    prefixcommons: pigqtldb
  miriam:
    deprecated: false
    description: The Animal Quantitative Trait Loci (QTL) database (Animal QTLdb)
      is designed to house publicly all available QTL and single-nucleotide polymorphism/gene
      association data on livestock animal species. This collection references pig
      QTLs.
    homepage: https://www.animalgenome.org/QTLdb
    id: '00000506'
    name: Animal Genome Pig QTL
    namespaceEmbeddedInLui: false
    pattern: ^\d+$
    prefix: pigqtldb
    sampleId: '14'
    uri_format: https://www.animalgenome.org/QTLdb/q?id=QTL_ID:$1
  n2t:
    description: The Animal Quantitative Trait Loci (QTL) database (Animal QTLdb)
      is designed to house publicly all available QTL and single-nucleotide polymorphism/gene
      association data on livestock animal species. This collection references pig
      QTLs.
    example: '14'
    homepage: http://www.animalgenome.org/cgi-bin/QTLdb/SS/index
    name: Animal QTL Pig at Iowa State University
    namespaceEmbeddedInLui: false
    pattern: ^\d+$
    prefix: pigqtldb
    uri_format: http://www.animalgenome.org/cgi-bin/QTLdb/SS/qdetails?QTL_ID=$1
  part_of: qtldb
  prefix: pigqtldb
  prefixcommons:
    description: This Pig Quantitative Trait Locus (QTL) database (Pig QTLdb) has
      gathered all pig QTL data published during the past 10+ years. The database
      and its peripheral tools make it possible to compare, confirm and locate on
      pig chromosomes the most feasible location for genes responsible for quantitative
      trait important to pig production.
    example: '66'
    homepage: http://www.animalgenome.org/cgi-bin/QTLdb/SS/index
    keywords:
    - DNA
    - genome
    name: Pig Quantitative Trait Locus database
    pattern: ^\d+$
    prefix: pigqtldb
    uri_format: http://www.animalgenome.org/cgi-bin/QTLdb/SS/qdetails?QTL_ID=$1
pii:
  appears_in:
  - pubmed
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: A combination of an ISBN and local unique identifier for articles and
    other published works. Please see the [Wikipedia page](https://en.wikipedia.org/wiki/Publisher_Item_Identifier)
    for a detailed explanation. Some PIIs are used as the local identifiers in DOIs,
    such as https://doi.org/10.1136/S0003-4967(24)38620-0.
  example: S0960-9822(11)01319-4
  example_extras:
  - B0-123-12345-1/12345-1
  github_request_issue: 1447
  homepage: https://en.wikipedia.org/wiki/Publisher_Item_Identifier
  name: Publisher Item Identifier
  pattern: ^((S\d{4}-\d{4}\(\d{2}\)\d{5})|(B\d-\d{3}-\d{5}-\d/\d{5}))-[\d|X]$
  prefix: pii
pina:
  biocontext:
    prefix: PINA
  fairsharing:
    abbreviation: PINA
    contact:
      email: wujm@bjmu.edu.cn
      name: Jianmin Wu
      orcid: 0000-0002-8876-128X
    description: Protein Interaction Network Analysis (PINA) platform is an integrated
      platform for protein interaction network construction, filtering, analysis,
      visualization, and management. It integrates protein-protein interaction (PPI)
      data from public curated databases and builds a complete, non-redundant protein
      interaction dataset for six model organisms. In particular, it provides a variety
      of built-in tools to filter and analyze the networks for gaining biological
      and functional insights into the network.
    homepage: http://omics.bjcancer.org/pina/
    name: Protein Interaction Network Analysis platform
    prefix: FAIRsharing.7q4gsz
    publications:
    - doi: 10.1038/nmeth.1282
      pubmed_id: 19079255
      title: Integrated network analysis platform for protein-protein interactions.
    - doi: 10.1093/nar/gkr967
      pubmed_id: 22067443
      title: 'PINA v2.0: mining interactome modules.'
    - doi: 10.1093/nar/gkaa1075
      pubmed_id: null
      title: 'PINA 3.0: mining cancer interactome'
    subjects:
    - Life Science
    - Data Visualization
  mappings:
    biocontext: PINA
    fairsharing: FAIRsharing.7q4gsz
    miriam: pina
    n2t: pina
    pathguide: '348'
  miriam:
    deprecated: false
    description: Protein Interaction Network Analysis (PINA) platform is an integrated
      platform for protein interaction network construction, filtering, analysis,
      visualization and management. It integrates protein-protein interaction data
      from six public curated databases and builds a complete, non-redundant protein
      interaction dataset for six model organisms.
    homepage: https://omics.bjcancer.org/pina/
    id: 00000359
    name: PINA
    namespaceEmbeddedInLui: false
    pattern: ^([A-N,R-Z][0-9][A-Z][A-Z, 0-9][A-Z, 0-9][0-9])|([O,P,Q][0-9][A-Z, 0-9][A-Z,
      0-9][A-Z, 0-9][0-9])$
    prefix: pina
    sampleId: Q13485
    uri_format: https://omics.bjcancer.org/pina/quickSearch.action?keyword=$1
  n2t:
    description: Protein Interaction Network Analysis (PINA) platform is an integrated
      platform for protein interaction network construction, filtering, analysis,
      visualization and management. It integrates protein-protein interaction data
      from six public curated databases and builds a complete, non-redundant protein
      interaction dataset for six model organisms.
    example: Q13485
    homepage: http://cbg.garvan.unsw.edu.au/pina/
    name: Protein Interaction Network Analysis (PINA) at Garvan Institute
    namespaceEmbeddedInLui: false
    pattern: ^([A-N,R-Z][0-9][A-Z][A-Z, 0-9][A-Z, 0-9][0-9])|([O,P,Q][0-9][A-Z, 0-9][A-Z,
      0-9][A-Z, 0-9][0-9])$
    prefix: pina
    uri_format: http://cbg.garvan.unsw.edu.au/pina/interactome.oneP.do?ac=$1&showExtend=null
  name: Protein Interaction Network Analysis
  pathguide:
    abbreviation: PINA
    homepage: http://omics.bjcancer.org/pina/
    name: Protein Interaction Network Analysis
    prefix: '348'
  prefix: pina
  provides: uniprot
  publications:
  - doi: 10.1093/nar/gkaa1075
    pmc: PMC7779002
    pubmed: '33231689'
    title: 'PINA 3.0: mining cancer interactome'
    year: 2021
  - doi: 10.1093/nar/gkr967
    pmc: PMC3244997
    pubmed: '22067443'
    title: 'PINA v2.0: mining interactome modules'
    year: 2011
  - doi: 10.1038/nmeth.1282
    pmc: null
    pubmed: '19079255'
    title: Integrated network analysis platform for protein-protein interactions
    year: 2008
  - doi: 10.1038/nmeth.1282
    pmc: null
    pubmed: null
    title: Integrated network analysis platform for protein-protein interactions.
    year: null
  - doi: 10.1093/nar/gkr967
    pmc: null
    pubmed: null
    title: 'PINA v2.0: mining interactome modules.'
    year: null
  - doi: 10.1093/nar/gkaa1075
    pmc: null
    pubmed: null
    title: 'PINA 3.0: mining cancer interactome'
    year: null
  uri_format: http://cbg.garvan.unsw.edu.au/pina/interactome.oneP.do?showExtend=null&ac=$1
piroplasma:
  biocontext:
    prefix: PIROPLASMA
  mappings:
    biocontext: PIROPLASMA
    miriam: piroplasma
    n2t: piroplasma
  miriam:
    deprecated: false
    description: PiroplasmaDB is one of the databases that can be accessed through
      the EuPathDB (http://EuPathDB.org; formerly ApiDB) portal, covering eukaryotic
      pathogens of the genera Cryptosporidium, Giardia, Leishmania, Neospora, Plasmodium,
      Toxoplasma, Trichomonas and Trypanosoma. While each of these groups is supported
      by a taxon-specific database built upon the same infrastructure, the EuPathDB
      portal offers an entry point to all these resources, and the opportunity to
      leverage orthology for searches across genera.
    homepage: http://piroplasmadb.org/
    id: '00000351'
    name: PiroplasmaDB
    namespaceEmbeddedInLui: false
    pattern: ^TA\d+$
    prefix: piroplasma
    sampleId: TA14985
    uri_format: http://piroplasmadb.org/piro/showRecord.do?name=GeneRecordClasses.GeneRecordClass&source_id=$1
  n2t:
    description: PiroplasmaDB is one of the databases that can be accessed through
      the EuPathDB (http://EuPathDB.org; formerly ApiDB) portal, covering eukaryotic
      pathogens of the genera Cryptosporidium, Giardia, Leishmania, Neospora, Plasmodium,
      Toxoplasma, Trichomonas and Trypanosoma. While each of these groups is supported
      by a taxon-specific database built upon the same infrastructure, the EuPathDB
      portal offers an entry point to all these resources, and the opportunity to
      leverage orthology for searches across genera.
    example: TA14985
    homepage: http://piroplasmadb.org/
    name: PiroplasmaBD at EuPathDB
    namespaceEmbeddedInLui: false
    pattern: ^TA\d+$
    prefix: piroplasma
    uri_format: http://piroplasmadb.org/piro/showRecord.do?name=GeneRecordClasses.GeneRecordClass&source_id=$1
  prefix: piroplasma
pirsf:
  biocontext:
    prefix: PIRSF
  contact:
    email: wuc@udel.edu
    github: null
    name: Cathy H. Wu
    orcid: 0000-0001-6379-8601
  edam:
    description: Unique identifier of an entry from the PIRSF database.
    name: PIRSF
    obsolete: false
    prefix: '1136'
  fairsharing:
    abbreviation: PIRSF
    description: The PIR SuperFamily concept is being used as a guiding principle
      to provide comprehensive and non-overlapping clustering of UniProtKB sequences
      into a hierarchical order to reflect their evolutionary relationships.
    homepage: https://proteininformationresource.org/pirwww/dbinfo/pirsf.shtml
    license: http://opendatacommons.org/licenses/pddl/1.0
    name: PIR SuperFamily
    prefix: FAIRsharing.vssch2
    publications:
    - doi: 10.1093/nar/gkh097
      pubmed_id: 14681371
      title: 'PIRSF: family classification system at the Protein Information Resource.'
    subjects:
    - Proteomics
    - Life Science
  go:
    homepage: http://pir.georgetown.edu/pirsf/
    name: PIR Superfamily Classification System
    prefix: PIRSF
    uri_format: http://pir.georgetown.edu/cgi-bin/ipcSF?id=$1
  mappings:
    biocontext: PIRSF
    edam: '1136'
    fairsharing: FAIRsharing.vssch2
    go: PIRSF
    miriam: pirsf
    n2t: pirsf
    prefixcommons: pirsf
    uniprot: DB-0079
  miriam:
    deprecated: false
    description: The PIR SuperFamily concept is being used as a guiding principle
      to provide comprehensive and non-overlapping clustering of UniProtKB sequences
      into a hierarchical order to reflect their evolutionary relationships.
    homepage: https://pir.georgetown.edu/
    id: '00000017'
    name: PIRSF
    namespaceEmbeddedInLui: false
    pattern: ^PIRSF\d{6}$
    prefix: pirsf
    sampleId: PIRSF000100
    uri_format: https://pir.georgetown.edu/cgi-bin/ipcSF?id=$1
  n2t:
    description: The PIR SuperFamily concept is being used as a guiding principle
      to provide comprehensive and non-overlapping clustering of UniProtKB sequences
      into a hierarchical order to reflect their evolutionary relationships.
    example: PIRSF000100
    homepage: https://pir.georgetown.edu/
    name: PIRSF
    namespaceEmbeddedInLui: false
    pattern: ^PIRSF\d{6}$
    prefix: pirsf
    uri_format: https://pir.georgetown.edu/cgi-bin/ipcSF?id=$1
  prefix: pirsf
  prefixcommons:
    description: The PIR SuperFamily concept is being used as a guiding principle
      to provide comprehensive and non-overlapping clustering of UniProtKB sequences
      into a hierarchical order to reflect their evolutionary relationships.
    example: PIRSF000100
    homepage: http://pir.georgetown.edu/pirsf/
    keywords:
    - protein
    - structure
    name: PIRSF; a whole-protein classification database
    pattern: ^PIRSF\d{6}$
    prefix: pirsf
    pubmed_ids:
    - '14681371'
    uri_format: http://pir.georgetown.edu/cgi-bin/ipcSF?id=$1
  publications:
  - doi: 10.1093/nar/gkh097
    pmc: PMC308831
    pubmed: '14681371'
    title: 'PIRSF: family classification system at the Protein Information Resource'
    year: 2004
  - doi: 10.1093/nar/gkh097
    pmc: null
    pubmed: null
    title: 'PIRSF: family classification system at the Protein Information Resource.'
    year: null
  - doi: null
    pmc: null
    pubmed: '14681371'
    title: null
    year: null
  - doi: 10.1093/nar/gkh097
    pmc: null
    pubmed: '14681371'
    title: null
    year: null
  uniprot:
    abbreviation: PIRSF
    category: Family and domain databases
    homepage: https://proteininformationresource.org/pirwww/dbinfo/pirsf.shtml
    name: PIRSF; a whole-protein classification database
    prefix: DB-0079
    publications:
    - doi: 10.1093/nar/gkh097
      pubmed: '14681371'
    uri_format: https://www.ebi.ac.uk/interpro/entry/pirsf/$1
pkdb:
  fairsharing:
    abbreviation: PK-DB
    contact:
      email: konigmatt@googlemail.com
      name: Matthias König
      orcid: 0000-0003-1725-179X
    description: PK-DB an open database for pharmacokinetics information from clinical
      trials as well as pre-clinical research. The focus of PK-DB is to provide high-quality
      pharmacokinetics data enriched with the required meta-information for computational
      modeling and data integration.
    homepage: https://pk-db.com
    name: Pharmacokinetics Database
    prefix: FAIRsharing.AYegqK
    publications:
    - doi: 10.1093/nar/gkaa990
      pubmed_id: 33151297
      title: 'PK-DB: pharmacokinetics database for individualized and stratified computational
        modeling'
    repository: https://github.com/matthiaskoenig/pkdb/issues
    subjects:
    - Clinical Veterinary Medicine
    - Clinical Studies
    - Personalized Medicine
    - Pharmacology
    - Life Science
    - Pharmacogenomics
    - Preclinical Studies
  mappings:
    fairsharing: FAIRsharing.AYegqK
    miriam: pkdb
  miriam:
    deprecated: false
    description: 'PK-DB an open database for pharmacokinetics information from clinical
      trials as well as pre-clinical research. The focus of PK-DB is to provide high-quality
      pharmacokinetics data enriched with the required meta-information for computational
      modeling and data integration. '
    homepage: https://www.hu-berlin.de/?set_language=en&cl=en
    id: 00000708
    name: PK-DB
    namespaceEmbeddedInLui: false
    pattern: ^PKDB[0-9]{5}$
    prefix: pkdb
    sampleId: PKDB00198
    uri_format: https://pk-db.com/data/$1
  prefix: pkdb
  publications:
  - doi: 10.1093/nar/gkaa990
    pmc: PMC7779054
    pubmed: '33151297'
    title: 'PK-DB: pharmacokinetics database for individualized and stratified computational
      modeling'
    year: 2021
plana:
  aberowl:
    description: PLANA, the planarian anatomy ontology, encompasses the anatomy and
      life cycle stages for both __Schmidtea mediterranea__ biotypes.
    download_owl: http://aber-owl.net/media/ontologies/PLANA/28/plana.owl
    homepage: https://github.com/obophenotype/planaria-ontology
    name: planaria-ontology
    prefix: PLANA
  biocontext:
    prefix: PLANA
  bioportal:
    contact:
      email: smr@stowers.org
      name: Sofia Robb
    description: Anatomy ontology for planaria and terms specific to the developmental
      stages of the planarian Schmidtea mediterranea.
    homepage: https://github.com/obophenotype/planaria-ontology
    name: Planarian Anatomy and Developmental Stage Ontolgoy
    prefix: PLANA
    version: '2023-03-13'
  example: '0000001'
  fairsharing:
    abbreviation: PLANA
    description: Anatomy ontology for planaria and terms specific to the developmental
      stages of the planarian Schmidtea mediterranea. As the regenerative flatworm
      Schmidtea mediterranea gains popularity as a developmental research organism
      the need for standard nomenclature and a centralized repository of anatomical
      terms has become increasingly apparent. Utilization of a controlled vocabulary
      creates opportunities to catalogue genes and expression data for computational
      searches across research groups and cross-species comparisons, all while establishing
      a framework for integration of new terms. We created a Planarian Anatomy Ontology
      containing 327 terms and definitions for cellular organelles, cell types, tissues,
      organ systems, anatomical entities, life cycle stages and developmental processes
      described in the literature. Where possible, extant terms and definitions from
      Uberon and other open source anatomy ontologies were imported into the ontology
      to strengthen cross-species queries.
    domains:
    - organelle
    - organ
    - tissue
    homepage: https://planosphere.stowers.org/anatomyontology
    license: CC-BY-3.0
    name: Planarian Anatomy and Developmental Stage Ontology
    prefix: FAIRsharing.g1qrqs
    repository: https://github.com/obophenotype/planaria-ontology
    subjects:
    - Life Science
    - Anatomy
    - Developmental Biology
  mappings:
    aberowl: PLANA
    biocontext: PLANA
    bioportal: PLANA
    fairsharing: FAIRsharing.g1qrqs
    obofoundry: plana
    ols: plana
    ontobee: PLANA
    wikidata.entity: Q81661781
  name: Planarian Anatomy and Schmidtea mediterranean Developmental Stage Ontology
  obofoundry:
    appears_in:
    - planp
    contact: smr@stowers.org
    contact.github: srobb1
    contact.label: Sofia Robb
    contact.orcid: 0000-0002-3528-5267
    depends_on:
    - ro
    - uberon
    deprecated: false
    description: PLANA, the planarian anatomy ontology, encompasses the anatomy and
      life cycle stages for both __Schmidtea mediterranea__ biotypes.
    domain: anatomy and development
    download.obo: http://purl.obolibrary.org/obo/plana.obo
    download.owl: http://purl.obolibrary.org/obo/plana.owl
    homepage: https://github.com/obophenotype/planaria-ontology
    license: CC BY 3.0
    license.url: http://creativecommons.org/licenses/by/3.0/
    name: planaria-ontology
    preferredPrefix: PLANA
    prefix: plana
    publications:
    - id: https://www.ncbi.nlm.nih.gov/pubmed/34318308
      title: 'Planarian Anatomy Ontology: a resource to connect data within and across
        experimental platforms'
    repository: https://github.com/obophenotype/planaria-ontology
  ols:
    description: PLANA, the PLANarian Anatomy Ontology, encompasses the anatomy of
      developmental stages and adult biotypes of Schmidtea mediterranea.
    download_owl: http://purl.obolibrary.org/obo/plana.owl
    homepage: https://github.com/obophenotype/planaria-ontology
    name: Planarian Anatomy Ontology (PLANA)
    prefix: plana
    tracker: https://github.com/obophenotype/planaria-ontology/issues
    version: '2023-03-13'
    version.iri: http://purl.obolibrary.org/obo/plana/releases/2023-03-13
  ontobee:
    library: Library
    name: planaria-ontology
    prefix: PLANA
  pattern: ^\d{7}$
  prefix: plana
  publications:
  - doi: 10.1242/dev.196097
    pmc: PMC8353266
    pubmed: '34318308'
    title: 'Planarian Anatomy Ontology: a resource to connect data within and across
      experimental platforms'
    year: 2021
  uri_format: http://purl.obolibrary.org/obo/PLANA_$1
planp:
  aberowl:
    description: Planarian Phenotype Ontology is an ontology of phenotypes observed
      in the planarian Schmidtea mediterranea.
    download_owl: http://aber-owl.net/media/ontologies/PLANP/6/planp.owl
    homepage: https://github.com/obophenotype/planarian-phenotype-ontology
    name: Planarian Phenotype Ontology
    prefix: PLANP
  bioportal:
    contact:
      email: smr@stowers.org
      name: Sofia Robb
    description: Planarian Phenotype Ontology is an ontology of phenotypes observed
      in the planarian Schmidtea mediterranea. Many of the phenotypes were seen durning
      RNAi experiments.
    homepage: https://github.com/obophenotype/planarian-phenotype-ontology
    name: Planarian Phenotype Ontology
    prefix: PLANP
  example: '0000001'
  mappings:
    aberowl: PLANP
    bioportal: PLANP
    obofoundry: planp
    ols: planp
    ontobee: PLANP
    wikidata.entity: Q81661782
  obofoundry:
    contact: smr@stowers.org
    contact.github: srobb1
    contact.label: Sofia Robb
    contact.orcid: 0000-0002-3528-5267
    depends_on:
    - go
    - pato
    - plana
    - ro
    deprecated: false
    description: Planarian Phenotype Ontology is an ontology of phenotypes observed
      in the planarian Schmidtea mediterranea.
    domain: phenotype
    download.obo: http://purl.obolibrary.org/obo/planp.obo
    download.owl: http://purl.obolibrary.org/obo/planp.owl
    homepage: https://github.com/obophenotype/planarian-phenotype-ontology
    license: CC BY 3.0
    license.url: http://creativecommons.org/licenses/by/3.0/
    name: Planarian Phenotype Ontology
    preferredPrefix: PLANP
    prefix: planp
    repository: https://github.com/obophenotype/planarian-phenotype-ontology
  ols:
    description: Planarian Phenotype Ontology is an ontology of phenotypes observed
      in the planarian Schmidtea mediterranea.
    download_owl: http://purl.obolibrary.org/obo/planp.owl
    homepage: https://github.com/obophenotype/planarian-phenotype-ontology
    name: Planarian Phenotype Ontology (PLANP)
    prefix: planp
    tracker: https://github.com/obophenotype/planarian-phenotype-ontology/issues
    version: '2020-03-28'
    version.iri: http://purl.obolibrary.org/obo/planp/releases/2020-03-28/planp.owl
  ontobee:
    library: Library
    name: Planarian Phenotype Ontology
    prefix: PLANP
  pattern: ^\d+$
  prefix: planp
  uri_format: http://purl.obolibrary.org/obo/PLANP_$1
plant_reactome:
  mappings:
    miriam: plant_reactome
    pathguide: '587'
  miriam:
    deprecated: false
    description: PLANT REACTOME is an open-source, open access, manually curated and
      peer-reviewed pathway database. Pathway annotations are authored by expert biologists,
      in collaboration with the Reactome editorial staff and cross-referenced to many
      bioinformatics databases. These include project databases like Gramene, Ensembl,
      UniProt, ChEBI small molecule databases, PubMed, and Gene Ontology.
    homepage: https://www.gramene.org
    id: '00001111'
    name: Plant Reactome
    namespaceEmbeddedInLui: false
    pattern: ^R-[A-Z]{3}-\d+(-\d+)?(\.\d+)?$
    prefix: plant_reactome
    sampleId: R-ACH-1120024
    uri_format: https://plantreactome.gramene.org/content/detail/$1
  pathguide:
    abbreviation: Plant Reactome
    homepage: http://plantreactome.gramene.org/
    keywords:
    - BioPAX
    - PSI-MI
    - SBML
    name: Plant Reactome Pathway Database
    prefix: '587'
  prefix: plant_reactome
planttfdb:
  biocontext:
    prefix: PLANTTFDB
  contact:
    email: gaog@mail.cbi.pku.edu.cn
    github: gao-ge
    name: Ge Gao
    orcid: 0000-0001-6470-8815
  fairsharing:
    abbreviation: PlantTFDB
    description: Plant Transcription Factor Database (PlantTFDB) provides a comprehensive,
      high-quality resource of plant transcription factors (TFs), regulatory elements
      and interactions between them. In the latest version, It contains 320 370 TFs,
      classified into 58 families, from 165 species. Abundant functional and evolutionary
      annotations (e.g., GO, functional description, binding motifs, cis-element,
      regulation, references, orthologous groups and phylogenetic tree, etc.) are
      provided for identified TFs. In addition, multiple online tools are set up for
      TF identification, regulation prediction and functional enrichment analyses.
    homepage: http://planttfdb.cbi.pku.edu.cn
    name: Plant Transcription Factor Database
    prefix: FAIRsharing.ex3fqk
    publications:
    - doi: 10.1093/molbev/msv058
      pubmed_id: 25750178
      title: An Arabidopsis Transcriptional Regulatory Map Reveals Distinct Functional
        and Evolutionary Features of Novel Transcription Factors
    - doi: 10.1093/nar/gkt1016
      pubmed_id: 24174544
      title: 'PlantTFDB 3.0: a portal for the functional and evolutionary study of
        plant transcription factors'
    - doi: 10.1093/nar/gkw982
      pubmed_id: null
      title: 'PlantTFDB 4.0: toward a central hub for transcription factors and regulatory
        interactions in plants'
    subjects:
    - Life Science
  mappings:
    biocontext: PLANTTFDB
    fairsharing: FAIRsharing.ex3fqk
    miriam: planttfdb
    n2t: planttfdb
    pathguide: '497'
    prefixcommons: planttfdb
    re3data: r3d100011301
  miriam:
    deprecated: false
    description: The Plant TF database (PlantTFDB) systematically identifies transcription
      factors for plant species. It includes annotation for identified TFs, including
      information on expression, regulation, interaction, conserved elements, phenotype
      information. It also provides curated descriptions and cross-references to other
      life science databases, as well as identifying evolutionary relationship among
      identified factors.
    homepage: http://planttfdb.cbi.pku.edu.cn
    id: 00000579
    name: Plant Transcription Factor Database
    namespaceEmbeddedInLui: false
    pattern: ^[A-Z][a-z]{2}_([A-Za-z]{3}[0-9]{6})|([A-Za-z0-9\._\-#]*)$
    prefix: planttfdb
    sampleId: Ath_AT1G01030.1
    uri_format: http://planttfdb.cbi.pku.edu.cn/tf.php?uid=$1
  n2t:
    description: The Plant TF database (PlantTFDB) systematically identifies transcription
      factors for plant species. It includes annotation for identified TFs, including
      information on expression, regulation, interaction, conserved elements, phenotype
      information. It also provides curated descriptions and cross-references to other
      life science databases, as well as identifying evolutionary relationship among
      identified factors.
    example: Ath_AT1G01030.1
    homepage: http://planttfdb.cbi.pku.edu.cn
    name: PlantTFDB at Peking University
    namespaceEmbeddedInLui: false
    pattern: ^[A-Z][a-z]{2}_([A-Za-z]{3}[0-9]{6})|([A-Za-z0-9\._\-#]*)$
    prefix: planttfdb
    uri_format: http://planttfdb.cbi.pku.edu.cn/tf.php?uid=$1
  pathguide:
    abbreviation: PlantTFDB
    homepage: http://planttfdb.cbi.pku.edu.cn/
    name: Plant Transcription Factor Database
    prefix: '497'
  prefix: planttfdb
  prefixcommons:
    description: Plant Transcription Factor Database collected 40976 transcription
      factors from 39 species, and they are classified into 58 families.
    example: Ath005712
    homepage: http://planttfdb.cbi.pku.edu.cn
    keywords:
    - regulation
    - DNA
    - RNA
    - small molecule
    - protein
    - gene
    name: Plant Transcription Factor Database
    pattern: ^[a-z]+\d+$
    prefix: planttfdb
    uri_format: http://planttfdb.cbi.pku.edu.cn/tf.php?sp=[?species_name]&did=$1
  publications:
  - doi: 10.1093/nar/gkw982
    pmc: PMC5210657
    pubmed: '27924042'
    title: 'PlantTFDB 4.0: toward a central hub for transcription factors and regulatory
      interactions in plants'
    year: 2016
  - doi: 10.1093/molbev/msv058
    pmc: PMC4476157
    pubmed: '25750178'
    title: An Arabidopsis Transcriptional Regulatory Map Reveals Distinct Functional
      and Evolutionary Features of Novel Transcription Factors
    year: 2015
  - doi: 10.1093/nar/gkt1016
    pmc: PMC3965000
    pubmed: '24174544'
    title: 'PlantTFDB 3.0: a portal for the functional and evolutionary study of plant
      transcription factors'
    year: 2013
  - doi: 10.1093/molbev/msv058
    pmc: null
    pubmed: null
    title: An Arabidopsis Transcriptional Regulatory Map Reveals Distinct Functional
      and Evolutionary Features of Novel Transcription Factors
    year: null
  - doi: 10.1093/nar/gkt1016
    pmc: null
    pubmed: null
    title: 'PlantTFDB 3.0: a portal for the functional and evolutionary study of plant
      transcription factors'
    year: null
  - doi: 10.1093/nar/gkw982
    pmc: null
    pubmed: null
    title: 'PlantTFDB 4.0: toward a central hub for transcription factors and regulatory
      interactions in plants'
    year: null
  re3data:
    description: 'Species included in PlantTFDB 4.0 covers the main lineages of green
      plants. Therefore, PlantTFDB provides genomic TF repertoires across Viridiplantae.
      To provide comprehensive information for the TF family, a brief introduction
      and key references are presented for each family. Comprehensive annotations
      are made for each identified TF, including functional domains, 3D structures,
      gene ontology (GO), plant ontology (PO), expression information, expert-curated
      functional description, regulation information, interaction, conserved elements,
      references, and annotations in various databases such as UniProt, RefSeq, TransFac,
      STRING, and VISTA.

      By inferring orthologous groups and constructing phylogenetic trees, evolutionary
      relationships among identified TFs were inferred. In addition, PlantTFDB has
      a simple and user-friendly interface to allow users to query based on combined
      conditions or make sequence similarity search using BLAST.

      The new version PlantTFDB 5.0 has been incorporated into PlantRegMap http://plantregmap.gao-lab.org/.'
    doi: 10.17616/R35D1V
    homepage: http://planttfdb.gao-lab.org/
    name: Plant Transcription Factor Database
    prefix: r3d100011301
    synonyms:
    - PlantTFDB
    xrefs:
      nif: 0000-03311
      omics: '00560'
plasmodb:
  biocontext:
    prefix: PLASMODB
  contact:
    email: oharb@upenn.edu
    github: ramobrah
    name: Omar S. Harb
    orcid: 0000-0003-4446-6200
  fairsharing:
    abbreviation: PlasmoDB
    description: PlasmoDB is a genome database for the genus Plasmodium, a set of
      single-celled eukaryotic pathogens that cause human and animal diseases, including
      malaria.
    homepage: https://plasmodb.org
    name: PlasmoDB
    prefix: FAIRsharing.g4n8sw
    publications:
    - doi: 10.1093/nar/gkn814
      pubmed_id: 18957442
      title: 'PlasmoDB: a functional genomic database for malaria parasites.'
    subjects:
    - Genomics
    - Infectious Disease Medicine
    twitter: VEuPathDB
  go:
    homepage: https://plasmodb.org
    name: PlasmoDB
    prefix: PlasmoDB
    uri_format: https://plasmodb.org/plasmo/app/record/gene/$1
  integbio:
    description: PlasmoDB is a genome database for the genus Plasmodium, a set of
      single-celled eukaryotic pathogens that cause human and animal diseases, including
      malaria.
    fairsharing: FAIRsharing.g4n8sw
    homepage: https://plasmodb.org
    information_keywords:
    - Sequence
    - Expression
    - Ontology/Terminology/Nomenclature
    name: PlasmoDB
    prefix: nbdc01783
    pubmeds:
    - '18957442'
    status: Active
    target_keywords:
    - Genome/Gene
    - Health/Disease
    - Organism
    - cDNA/EST
  logo: https://sites.psu.edu/llinaslab/files/2020/05/plasmodb_logogif-e1590176740521.jpg
  mappings:
    biocontext: PLASMODB
    fairsharing: FAIRsharing.g4n8sw
    go: PlasmoDB
    integbio: nbdc01783
    miriam: plasmodb
    n2t: plasmodb
    ncbi: ApiDB_PlasmoDB
    pathguide: '514'
    prefixcommons: plasmodb
    re3data: r3d100011569
  miriam:
    deprecated: false
    description: AmoebaDB is one of the databases that can be accessed through the
      EuPathDB (http://EuPathDB.org; formerly ApiDB) portal, covering eukaryotic pathogens
      of the genera Cryptosporidium, Giardia, Leishmania, Neospora, Plasmodium, Toxoplasma,
      Trichomonas and Trypanosoma. While each of these groups is supported by a taxon-specific
      database built upon the same infrastructure, the EuPathDB portal offers an entry
      point to all these resources, and the opportunity to leverage orthology for
      searches across genera.
    homepage: http://plasmodb.org/plasmo/
    id: '00000150'
    name: PlasmoDB
    namespaceEmbeddedInLui: false
    pattern: ^\w+$
    prefix: plasmodb
    sampleId: PF11_0344
    uri_format: http://plasmodb.org/plasmo/showRecord.do?name=GeneRecordClasses.GeneRecordClass&source_id=$1
  n2t:
    description: AmoebaDB is one of the databases that can be accessed through the
      EuPathDB (http://EuPathDB.org; formerly ApiDB) portal, covering eukaryotic pathogens
      of the genera Cryptosporidium, Giardia, Leishmania, Neospora, Plasmodium, Toxoplasma,
      Trichomonas and Trypanosoma. While each of these groups is supported by a taxon-specific
      database built upon the same infrastructure, the EuPathDB portal offers an entry
      point to all these resources, and the opportunity to leverage orthology for
      searches across genera.
    example: PF11_0344
    homepage: http://plasmodb.org/plasmo/
    name: PlasmoDB at EuPathDB
    namespaceEmbeddedInLui: false
    pattern: ^\w+$
    prefix: plasmodb
    uri_format: http://plasmodb.org/plasmo/showRecord.do?name=GeneRecordClasses.GeneRecordClass&source_id=$1
  ncbi:
    example: PF11_0344
    homepage: http://www.plasmodb.org/plasmo/home.jsp
    name: Plasmodium Genome Resources
    prefix: ApiDB_PlasmoDB
  pathguide:
    abbreviation: PlasmoDB
    homepage: http://plasmodb.org/plasmo/
    name: Plasmodium Genomics Resource
    prefix: '514'
  prefix: plasmodb
  prefixcommons:
    description: PlasmoDB is a genome database for the genus Plasmodium, a set of
      single-celled eukaryotic pathogens that cause human and animal diseases, including
      malaria.
    example: PFA0765c
    homepage: http://PlasmoDB.org
    keywords:
    - genome
    name: PlasmoDB
    pattern: ^PF[A-Z,0-9]+$
    prefix: plasmodb
    pubmed_ids:
    - '18957442'
    uri_format: http://plasmodb.org/plasmo/showRecord.do?name=GeneRecordClasses.GeneRecordClass&source_id=$1&project_id=PlasmoDB
  publications:
  - doi: 10.1093/nar/gkn814
    pmc: PMC2686598
    pubmed: '18957442'
    title: 'PlasmoDB: a functional genomic database for malaria parasites'
    year: 2008
  - doi: 10.1093/nar/gkn814
    pmc: null
    pubmed: null
    title: 'PlasmoDB: a functional genomic database for malaria parasites.'
    year: null
  - doi: null
    pmc: null
    pubmed: '18957442'
    title: null
    year: null
  re3data:
    description: PlasmoDB is a genome database for the genus Plasmodium, a set of
      single-celled eukaryotic pathogens that cause human and animal diseases, including
      malaria.
    doi: 10.17616/R3C04Q
    homepage: https://plasmodb.org/plasmo/app/
    name: PlasmoDB
    prefix: r3d100011569
    synonyms:
    - Plasmodium Genomics Resource
    xrefs:
      nif: 0000-03314
      omics: '02765'
  synonyms:
  - ApiDB_PlasmoDB
plo:
  biocontext:
    prefix: PLO
  mappings:
    biocontext: PLO
    obofoundry: plo
    wikidata.entity: Q114677908
  name: Plasmodium Life Cycle
  obofoundry:
    contact: mb4@sanger.ac.uk
    contact.label: Matt Berriman
    deprecated: true
    domain: anatomy and development
    homepage: http://www.sanger.ac.uk/Users/mb4/PLO/
    name: Plasmodium life cycle
    prefix: plo
  prefix: plo
plos:
  aberowl:
    description: The PLOS Thesaurus includes over 10,000 Subject Area terms covering
      the wide range of research topics included the PLOS journals. It was initially
      built for PLOS in 2012 by Access Innovations (http://www.accessinn.com/). The
      entire corpus of PLOS articles was analysed to ensure that the thesaurus covers
      relevant research domains comprehensively. Updates are released several times
      a year.
    homepage: https://github.com/PLOS/plos-thesaurus
    name: PLOS Thesaurus
    prefix: PLOSTHES
    version: plosthes.2017-1
  bioportal:
    contact:
      email: subjectareas@plos.org
      name: PLOS Taxonomy Team
    description: The PLOS Thesaurus includes over 10,000 Subject Area terms covering
      the wide range of research topics included the PLOS journals. It was initially
      built for PLOS in 2012 by Access Innovations (http://www.accessinn.com/). The
      entire corpus of PLOS articles was analysed to ensure that the thesaurus covers
      relevant research domains comprehensively. Updates are released several times
      a year.
    homepage: https://github.com/PLOS/plos-thesaurus
    name: PLOS Thesaurus
    prefix: PLOSTHES
    publications:
    - http://www.plos.org/
    version: plosthes.2017-1
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: An ontologization of Public Library of Science (PLOS) journal keywords
    and topics. It's not clear how the IDs correspond to the actual pages. Appears
    in ADCAD.
  example: '1443'
  fairsharing:
    abbreviation: PLOSTHES
    description: The PLOS Thesaurus includes over 10,000 Subject Area terms covering
      the wide range of research topics included the PLOS journals. The terms are
      applied programmatically to publications to aid record search and discovery.
    homepage: https://github.com/PLOS/plos-thesaurus
    license: CC0-1.0
    name: PLOS Thesaurus
    prefix: FAIRsharing.2ndf9r
    subjects:
    - Subject Agnostic
  github_request_issue: 1318
  homepage: http://journals.plos.org
  mappings:
    aberowl: PLOSTHES
    bioportal: PLOSTHES
    fairsharing: FAIRsharing.2ndf9r
  name: PLOS Thesaurus
  pattern: ^\d+$
  prefix: plos
  synonyms:
  - PLOSTHES
  uri_format: http://localhost/plosthes.2017-1#$1
pmap.cutdb:
  biocontext:
    prefix: PMAP.CUTDB
  contact:
    email: adam@burnham.org
    github: null
    name: Adam Godzik
    orcid: 0000-0002-2425-852X
  mappings:
    biocontext: PMAP.CUTDB
    miriam: pmap.cutdb
    n2t: pmap.cutdb
    prefixcommons: pmap.cutdb
  miriam:
    deprecated: true
    description: The Proteolysis MAP is a resource for proteolytic networks and pathways.
      PMAP is comprised of five databases, linked together in one environment. CutDB
      is a database of individual proteolytic events (cleavage sites).
    homepage: http://cutdb.burnham.org
    id: '00000225'
    name: CutDB
    namespaceEmbeddedInLui: false
    pattern: ^\d+$
    prefix: pmap.cutdb
    sampleId: '25782'
    uri_format: http://cutdb.burnham.org/relation/show/$1
  n2t:
    description: The Proteolysis MAP is a resource for proteolytic networks and pathways.
      PMAP is comprised of five databases, linked together in one environment. CutDB
      is a database of individual proteolytic events (cleavage sites).
    example: '25782'
    homepage: http://cutdb.burnham.org
    name: CutDB at The Burnham Institute for Medical Research
    namespaceEmbeddedInLui: false
    pattern: ^\d+$
    prefix: pmap.cutdb
    uri_format: http://cutdb.burnham.org/relation/show/$1
  prefix: pmap.cutdb
  prefixcommons:
    description: The Proteolysis MAP is a resource for proteolytic networks and pathways.
      PMAP is comprised of five databases, linked together in one environment. CutDB
      is a database of individual proteolytic events (cleavage sites).
    example: pmap.21243
    homepage: http://www.proteolysis.org/
    keywords:
    - pathway
    - protein
    - enzyme
    name: CutDB - Proteolytic event database
    pattern: ^pmap.\d+$
    prefix: pmap.cutdb
    pubmed_ids:
    - '17142225'
    uri_format: http://www.proteolysis.org/proteases/m_summarypg/$1
  publications:
  - doi: 10.1093/nar/gkl813
    pmc: PMC1669773
    pubmed: '17142225'
    title: 'CutDB: a proteolytic event database'
    year: 2006
  - doi: null
    pmc: null
    pubmed: '17142225'
    title: null
    year: null
  - doi: null
    pmc: null
    pubmed: '17142225'
    title: null
    year: null
  - doi: null
    pmc: null
    pubmed: '17142225'
    title: null
    year: null
  - doi: null
    pmc: null
    pubmed: '17142225'
    title: null
    year: null
pmap.substratedb:
  biocontext:
    prefix: PMAP.SUBSTRATEDB
  contact:
    email: eroshkin@burnham.org
    github: null
    name: Alexey M. Eroshkin
    orcid: 0000-0003-2023-4608
  mappings:
    biocontext: PMAP.SUBSTRATEDB
    miriam: pmap.substratedb
    n2t: pmap.substratedb
    prefixcommons: pmap.substratedb
  miriam:
    deprecated: false
    description: The Proteolysis MAP is a resource for proteolytic networks and pathways.
      PMAP is comprised of five databases, linked together in one environment. SubstrateDB
      contains molecular information on documented protease substrates.
    homepage: http://substrate.burnham.org/
    id: '00000224'
    name: SubstrateDB
    namespaceEmbeddedInLui: false
    pattern: ^\d+$
    prefix: pmap.substratedb
    sampleId: '1915'
    uri_format: http://substrate.burnham.org/protein/annotation/$1/html
  n2t:
    description: The Proteolysis MAP is a resource for proteolytic networks and pathways.
      PMAP is comprised of five databases, linked together in one environment. SubstrateDB
      contains molecular information on documented protease substrates.
    example: '1915'
    homepage: http://substrate.burnham.org/
    name: SubstrateDB at The Burnham Institute for Medical Research
    namespaceEmbeddedInLui: false
    pattern: ^\d+$
    prefix: pmap.substratedb
    uri_format: http://substrate.burnham.org/protein/annotation/$1/html
  prefix: pmap.substratedb
  prefixcommons:
    description: The Proteolysis MAP is a resource for proteolytic networks and pathways.
      PMAP is comprised of five databases, linked together in one environment. SubstrateDB
      contains molecular information on documented protease substrates.
    example: '1915'
    keywords:
    - domain
    - protein
    - reaction
    name: SubstrateDB - Protease substrates
    pattern: ^\w+$
    prefix: pmap.substratedb
    pubmed_ids:
    - '18842634'
    uri_format: http://substrate.burnham.org/protein/annotation/$1/html
  publications:
  - doi: 10.1093/nar/gkn683
    pmc: PMC2686432
    pubmed: '18842634'
    title: 'PMAP: databases for analyzing proteolytic events and pathways'
    year: 2008
  - doi: null
    pmc: null
    pubmed: '18842634'
    title: null
    year: null
pmc:
  biocontext:
    prefix: PMCID
    uri_format: http://www.ncbi.nlm.nih.gov/pmc/$1
  biolink:
    is_identifiers: false
    is_obo: false
    prefix: PMC
    uri_format: http://europepmc.org/articles/PMC$1
  cellosaurus:
    category: Reference resources
    homepage: https://www.ncbi.nlm.nih.gov/pmc/
    name: PubMed Central
    prefix: PMCID
    uri_format: https://www.ncbi.nlm.nih.gov/pmc/articles/$1
  comment: Note that the Europe PMC instance redirects canonical local unique identifiers
    from https://europepmc.org/articles/PMC3084216 to https://europepmc.org/article/PMC/3084216.
    However, this is an implementation detail and does not reflect the official format
    of a PMC identifier, which indeed does include `PMC` at the beginning of the local
    unique identifier
  contact:
    email: beck@ncbi.nlm.nih.gov
    github: jeffbeckncbi
    name: Jeff Beck
    orcid: 0000-0002-1798-9797
  example_extras:
  - PMC7418728
  - PMC7418728.1
  - PMC7418728.2
  fairsharing:
    abbreviation: PMCID
    description: 'Identifier schema for PubMed Central, a U.S. National Institutes
      of Health''s National Library of Medicine (NIH/NLM) free full-text archive of
      biomedical and life sciences journal literature, which gives the public access
      to papers at no cost. Papers collected under the NIH or participating funder''s
      public access policy are archived in PMC. Each paper in PMC is assigned a unique
      identification number. A PMCID may be used by authors and awardees to demonstrate
      compliance with a funder''s public access policy. A PMCID is assigned to an
      NIHMS submission when the following two criteria are met: the Final Approval
      step is complete, and the article has been matched to a PubMed record.'
    domains:
    - centrally registered identifier
    homepage: https://www.nihms.nih.gov/help/glossary/#pmcid
    name: PubMed Central Identifier
    prefix: FAIRsharing.2b4316
    subjects:
    - Biomedical Science
  go:
    homepage: https://www.ncbi.nlm.nih.gov/pmc/
    name: Pubmed Central
    prefix: PMCID
    synonyms:
    - PMC
    uri_format: https://www.ncbi.nlm.nih.gov/pmc/articles/$1
  mappings:
    biocontext: PMCID
    biolink: PMC
    cellosaurus: PMCID
    fairsharing: FAIRsharing.2b4316
    go: PMCID
    miriam: pmc
    n2t: pmc
    prefixcommons: pmc
    togoid: Pmc
    wikidata: P932
    wikidata.entity: Q11801904
  miriam:
    deprecated: false
    description: PMC International (PMCI) is a free full-text archive of biomedical
      and life sciences journal literature. PMCI is a collaborative effort between
      the U.S. National Institutes of Health and the National Library of Medicine,
      the publishers whose journal content makes up the PMC archive, and organizations
      in other countries that share NIH's and NLM's interest in archiving life sciences
      literature.
    homepage: http://europepmc.org/
    id: '00000147'
    name: PMC International
    namespaceEmbeddedInLui: false
    pattern: ^PMC\d+$
    prefix: pmc
    sampleId: PMC3084216
    uri_format: http://europepmc.org/articles/$1
  n2t:
    description: PMC International (PMCI) is a free full-text archive of biomedical
      and life sciences journal literature. PMCI is a collaborative effort between
      the U.S. National Institutes of Health and the National Library of Medicine,
      the publishers whose journal content makes up the PMC archive, and organizations
      in other countries that share NIH's and NLM's interest in archiving life sciences
      literature.
    example: PMC3084216
    homepage: http://europepmc.org/
    name: Europe PMC
    namespaceEmbeddedInLui: false
    pattern: PMC\d+
    prefix: pmc
    uri_format: http://europepmc.org/articles/$1
  name: PubMed Central
  pattern: ^PMC\d+(\.\d+)?$
  prefix: pmc
  prefixcommons:
    description: PubMed Central (PMC) is the U.S. National Institutes of Health (NIH)
      digital archive of biomedical and life sciences journal literature.
    example: PMC3084216
    homepage: http://www.pubmedcentral.nih.gov/
    keywords:
    - bibliography
    name: Pubmed Central
    pattern: ^PMC\d+$
    prefix: pmc
    synonyms:
    - pmcid
    uri_format: http://www.ncbi.nlm.nih.gov/pmc/articles/$1/?tool=pmcentrez
  providers:
  - code: ncbi.pmc
    description: PubMed Central
    example: null
    first_party: null
    homepage: https://www.ncbi.nlm.nih.gov/pmc/
    name: PubMed Central
    publications: null
    status: null
    uri_format: https://www.ncbi.nlm.nih.gov/pmc/articles/$1
  publications:
  - doi: 10.1093/nar/gkr1184
    pmc: PMC3245031
    pubmed: '22140104'
    title: Database resources of the National Center for Biotechnology Information
    year: 2011
  - doi: 10.1093/nar/gkq1172
    pmc: PMC3013733
    pubmed: '21097890'
    title: Database resources of the National Center for Biotechnology Information
    year: 2010
  references:
  - https://github.com/biopragmatics/bioregistry/issues/965
  synonyms:
  - PMC
  - PMCID
  togoid:
    catalog: nbdc01836
    examples:
    - PMC7857752
    - PMC10139720
    - PMC3815299
    - PMC4990340
    - PMC6885017
    - PMC5286597
    - PMC8035296
    - PMC46450
    - PMC11138896
    - PMC9528096
    keywords:
    - Literature
    name: PMC
    pattern: ^(?:PMC)?(?\d+)$
    prefix: Pmc
    uri_format: http://identifiers.org/pmc/PMC$1
  wikidata:
    database: Q11801904
    description: identifier for a scientific work issued by PubMed Central (without
      "PMC" prefix)
    example:
    - '1201091'
    - '3682911'
    homepage: https://www.ncbi.nlm.nih.gov/pmc/
    name: PMC publication ID
    pattern: ^[1-9]\d+$
    prefix: P932
    uri_format: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC$1
pmdb:
  biocontext:
    prefix: PMDB
  fairsharing:
    abbreviation: PMDB
    description: The Protein Model DataBase (PMDB) is a database that stores three
      dimensional protein models obtained by structure prediction techniques.
    homepage: http://srv00.recas.ba.infn.it/PMDB/main.php
    name: Protein Model Database
    prefix: FAIRsharing.wkaakq
    publications:
    - doi: 10.1093/nar/gkj105
      pubmed_id: 16381873
      title: The PMDB Protein Model Database.
    subjects:
    - Structural Biology
  mappings:
    biocontext: PMDB
    fairsharing: FAIRsharing.wkaakq
    miriam: pmdb
    n2t: pmdb
    prefixcommons: pmdb
  miriam:
    deprecated: false
    description: The Protein Model DataBase (PMDB), is a database that collects manually
      built three dimensional protein models, obtained by different structure prediction
      techniques.
    homepage: https://bioinformatics.cineca.it/PMDB/
    id: 00000190
    name: Protein Model Database
    namespaceEmbeddedInLui: false
    pattern: ^PM\d{7}$
    prefix: pmdb
    sampleId: PM0012345
    uri_format: https://bioinformatics.cineca.it/PMDB/user//search.php?idsearch=$1
  n2t:
    description: The Protein Model DataBase (PMDB), is a database that collects manually
      built three dimensional protein models, obtained by different structure prediction
      techniques.
    example: PM0012345
    homepage: https://bioinformatics.cineca.it/PMDB/
    name: Protein Model Database at University of Rome
    namespaceEmbeddedInLui: false
    pattern: ^PM\d{7}
    prefix: pmdb
    uri_format: https://bioinformatics.cineca.it/PMDB/user//search.php?idsearch=$1
  prefix: pmdb
  prefixcommons:
    description: The Protein Model DataBase (PMDB), is a database that collects manually
      built three dimensional protein models, obtained by different structure prediction
      techniques.
    example: PM0012345
    homepage: http://www.caspur.it/PMDB/
    keywords:
    - protein
    - structure
    name: Protein Model Database
    pattern: ^PM\d{7}$
    prefix: pmdb
    uri_format: http://mi.caspur.it/PMDB/user/search.php?idsearch=$1
  publications:
  - doi: 10.1093/nar/gkj105
    pmc: PMC1347467
    pubmed: '16381873'
    title: The PMDB Protein Model Database
    year: 2006
  - doi: 10.1093/nar/gkj105
    pmc: null
    pubmed: null
    title: The PMDB Protein Model Database.
    year: null
pmdco:
  example: '0000000'
  mappings:
    tib: pmd
  name: Platform Material Digital Core Ontology
  prefix: pmdco
  repository: https://github.com/materialdigital/core-ontology
  tib:
    description: 'The PMD Core Ontology (PMDco) is a comprehensive framework for representing
      knowledge that encompasses fundamental concepts from the domains of materials
      science and engineering (MSE). The PMDco has been designed as a mid-level ontology
      to establish a connection between specific MSE application ontologies and the
      domain neutral concepts found in established top-level ontologies. The primary
      goal of the PMDco is to promote interoperability between diverse domains. PMDco''s
      class structure is both understandable and extensible, making it an efficient
      tool for organizing MSE knowledge. It serves as a semantic intermediate layer
      that unifies MSE knowledge representations, enabling data and metadata to be
      systematically integrated on key terms within the MSE domain. With PMDco, it
      is possible to seamlessly trace data generation. By building on this foundation,
      PMDco facilitates the integration of data from various sources and the creation
      of complex workflows. In summary, PMDco is a valuable tool for researchers and
      practitioners in the MSE domains. It provides a common language for representing
      and sharing knowledge, allowing for efficient collaboration and promoting interoperability
      between diverse domains. Its design allows for the systematic integration of
      data and metadata, enabling seamless traceability of data generation. Overall,
      PMDco is a crucial step towards a unified and comprehensive understanding of
      the MSE domain. PMDco at GitHub: https://github.com/materialdigital/core-ontology
      Documentation: https://materialdigital.github.io/core-ontology/docs/'
    download_rdf: https://materialdigital.github.io/core-ontology/ontology.ttl
    homepage: https://materialdigital.github.io/core-ontology/
    keywords:
    - NFDI4ING
    - material science
    - mechanical engineering, energy technology
    - chemical and environmental engineering
    name: PMD Core Ontology
    prefix: pmd
    tracker: https://github.com/materialdigital/core-ontology/issues
    uri_format: https://w3id.org/pmd/co/PMD_$1
    version.iri: https://w3id.org/pmd/co/3.0.0-alpha4
pmp:
  biocontext:
    prefix: PMP
  contact:
    email: torsten.schwede@unibas.ch
    github: null
    name: Torsten Schwede
    orcid: 0000-0003-2715-335X
  mappings:
    biocontext: PMP
    miriam: pmp
    n2t: pmp
    pathguide: '438'
    prefixcommons: pmp
  miriam:
    deprecated: true
    description: The number of known protein sequences exceeds those of experimentally
      solved protein structures. Homology (or comparative) modeling methods make use
      of experimental protein structures to build models for evolutionary related
      proteins. The Protein Model Portal (PMP) provides a single portal to access
      these models, which are accessed through their UniProt identifiers.
    id: '00000227'
    name: PMP
    namespaceEmbeddedInLui: false
    pattern: ^([A-N,R-Z][0-9][A-Z][A-Z, 0-9][A-Z, 0-9][0-9])|([O,P,Q][0-9][A-Z, 0-9][A-Z,
      0-9][A-Z, 0-9][0-9])$
    prefix: pmp
    sampleId: Q0VCA6
  n2t:
    description: The number of known protein sequences exceeds those of experimentally
      solved protein structures. Homology (or comparative) modeling methods make use
      of experimental protein structures to build models for evolutionary related
      proteins. The Protein Model Portal (PMP) provides a single portal to access
      these models, which are accessed through their UniProt identifiers.
    example: Q0VCA6
    homepage: http://www.proteinmodelportal.org/
    name: PMP at University of Basel
    namespaceEmbeddedInLui: false
    pattern: ^([A-N,R-Z][0-9][A-Z][A-Z, 0-9][A-Z, 0-9][0-9])|([O,P,Q][0-9][A-Z, 0-9][A-Z,
      0-9][A-Z, 0-9][0-9])$
    prefix: pmp
    uri_format: http://www.proteinmodelportal.org/query/uniprot/$1
  name: Protein Model Portal
  pathguide:
    abbreviation: PMP
    homepage: http://www.proteinmodelportal.org/
    name: The Protein Model Portal
    prefix: '438'
  prefix: pmp
  prefixcommons:
    description: The number of known protein sequences exceeds those of experimentally
      solved protein structures. Homology (or comparative) modeling methods make use
      of experimental protein structures to build models for evolutionary related
      proteins. The Protein Model Portal (PMP) provides a single portal to access
      these models.
    example: Q0VCA6
    homepage: http://www.proteinmodelportal.org/
    keywords:
    - prediction
    - protein
    - structure
    name: Protein Model Portal
    pattern: ^\d+$
    prefix: pmp
    pubmed_ids:
    - '19037750'
    synonyms:
    - proteinmodelportal
    uri_format: http://www.proteinmodelportal.org/query/uniprot/$1
  provides: uniprot
  publications:
  - doi: 10.1007/s10969-008-9048-5
    pmc: PMC2704613
    pubmed: '19037750'
    title: The Protein Model Portal
    year: 2008
  - doi: null
    pmc: null
    pubmed: '19037750'
    title: null
    year: null
pmr.exposure:
  aberowl:
    description: Knowledge representation related to computer-based decision support
      in rehabilitation; concepts and relationships in the rehabilitation domain,
      integrating clinical practice, the ICD (specifically its 11th revision), the
      clinical investigator record ontology, the ICF and SNOMED CT.
    download_owl: http://aber-owl.net/media/ontologies/PMR/4/pmr.owl
    homepage: https://sites.google.com/site/laiasubirats
    name: Physical Medicine and Rehabilitation
    prefix: PMR
    version: '1.6'
  bioportal:
    contact:
      email: laia.subirats@gmail.com
      name: Laia Subirats
    description: Knowledge representation related to computer-based decision support
      in rehabilitation; concepts and relationships in the rehabilitation domain,
      integrating clinical practice, the ICD (specifically its 11th revision), the
      clinical investigator record ontology, the ICF and SNOMED CT.
    homepage: https://sites.google.com/site/laiasubirats
    name: Physical Medicine and Rehabilitation
    prefix: PMR
    publications:
    - https://sites.google.com/site/laiasubirats/publications
    version: '1.6'
  contact:
    email: laia.subirats@gmail.com
    github: null
    name: Laia Subirats
    orcid: 0000-0001-8646-5463
  fairsharing:
    abbreviation: PMR
    description: The Physiome Model Repository (PMR) is the main online repository
      for the IUPS Physiome Project, providing version and access controlled repositories,
      called workspaces, for users to store their data. PMR also provides a mechanism
      to create persistent access to specific revisions of a workspace, termed exposures.
      Exposure plugins are available for specific types of data (e.g., CellML or FieldML
      documents) which enable customizable views of the data when browsing the repository
      via a web browser, or an application accessing the repository’s content via
      web services.
    homepage: https://models.physiomeproject.org
    name: Physiome Model Repository
    prefix: FAIRsharing.bcjrnq
    publications:
    - doi: 10.1093/bioinformatics/btq723
      pubmed_id: 21216774
      title: The Physiome Model Repository 2.
    - doi: 10.1093/bioinformatics/btn390
      pubmed_id: 18658182
      title: The CellML Model Repository.
    - doi: 10.1098/rsta.2008.0310
      pubmed_id: 19380315
      title: CellML metadata standards, associated tools and repositories.
    - doi: 10.1186/1471-2105-12-22
      pubmed_id: 21235804
      title: Revision history aware repositories of computational models of biological
        systems.
    - doi: 10.1109/IEMBS.2006.260202
      pubmed_id: 17947072
      title: Toward a curated CellML model repository.
    - doi: 10.1098/rsfs.2015.0103
      pubmed_id: 27051515
      title: 'The Human Physiome: how standards, software and innovative service infrastructures
        are providing the building blocks to make it achievable.'
    subjects:
    - Mathematics
    - Life Science
    - Physiology
    - Biomedical Science
    - Systems Biology
    twitter: physiomeproject
  mappings:
    aberowl: PMR
    bioportal: PMR
    fairsharing: FAIRsharing.bcjrnq
    miriam: pmr
  miriam:
    deprecated: false
    description: Resource for the community to store, retrieve, search, reference,
      and reuse CellML models.
    homepage: https://www.auckland.ac.nz/en.html
    id: 00000845
    name: Physiome Model Repository
    namespaceEmbeddedInLui: false
    pattern: ^[a-z0-9]{32,32}$
    prefix: pmr
    sampleId: ebf69ca24298b28b2361e7d43eb52d6c
    uri_format: https://models.physiomeproject.org/exposure/$1
  part_of_database: pmr
  prefix: pmr.exposure
  publications:
  - doi: 10.1098/rsfs.2015.0103
    pmc: PMC4759754
    pubmed: '27051515'
    title: 'The Human Physiome: how standards, software and innovative service infrastructures
      are providing the building blocks to make it achievable'
    year: 2016
  - doi: 10.1186/1471-2105-12-22
    pmc: PMC3033326
    pubmed: '21235804'
    title: Revision history aware repositories of computational models of biological
      systems
    year: 2011
  - doi: 10.1093/bioinformatics/btq723
    pmc: null
    pubmed: '21216774'
    title: The Physiome Model Repository 2
    year: 2011
  - doi: 10.1098/rsta.2008.0310
    pmc: PMC3268215
    pubmed: '19380315'
    title: CellML metadata standards, associated tools and repositories
    year: 2009
  - doi: 10.1093/bioinformatics/btn390
    pmc: null
    pubmed: '18658182'
    title: The CellML Model Repository
    year: 2008
  - doi: 10.1109/iembs.2006.260202
    pmc: null
    pubmed: '17947072'
    title: Toward a curated CellML model repository
    year: 2006
  synonyms:
  - pmr
pmr.workspace:
  mappings:
    miriam: pmr.workspace
  miriam:
    deprecated: false
    description: Workspace (Git repository) for modeling projects managed by the Physiome
      Model Repository
    homepage: https://www.auckland.ac.nz/en.html
    id: 00000948
    name: Physiome Model Repository workspace
    namespaceEmbeddedInLui: false
    pattern: ^[a-zA-Z0-9_\-]+(/.*?)?$
    prefix: pmr.workspace
    sampleId: modularmassactionprimer
    uri_format: https://models.physiomeproject.org/workspace/$1
  part_of_database: pmr
  prefix: pmr.workspace
po:
  aberowl:
    description: The Plant Ontology is a structured vocabulary and database resource
      that links plant anatomy, morphology and growth and development to plant genomics
      data.
    download_owl: http://aber-owl.net/media/ontologies/PO/28/po.owl
    homepage: http://browser.planteome.org/amigo
    name: Plant Ontology
    prefix: PO
  agroportal:
    contact:
      email: jaiswalp@science.oregonstate.edu
      name: Pankaj Jaiswal
    description: The Plant Ontology is a structured vocabulary and database resource
      that links plant anatomy, morphology and growth and development to plant genomics
      data., An ontology that describes plant anatomy, morphology, and growth and
      development in plants.
    example_uri: http://purl.obolibrary.org/obo/PO_0025270
    homepage: https://planteome.org/
    license: CC-BY-4.0
    name: Plant Ontology
    prefix: PO
    publications:
    - https://doi.org/10.1007/978-1-4939-3167-5_5
    - https://planteome.org/references
    repository: https://github.com/Planteome/plant-ontology
    version: July 2023
  biocontext:
    prefix: PO
  bioportal:
    contact:
      email: jaiswalp@oregonstate.edu
      name: Pankaj Jaiswal
    description: The Plant Ontology is a structured vocabulary and database resource
      that links plant anatomy, morphology and growth and development to plant genomics
      data. The PO is under active development to expand to encompass terms and annotations
      from all plants., An ontology that describes plant anatomy, morphology, and
      growth and development in plants.
    homepage: http://planteome.org
    license: CC-BY-4.0
    name: Plant Ontology
    prefix: PO
    publications:
    - http://planteome.org/pub
    version: releases/2024-04-17
  cellosaurus:
    category: Anatomy/cell type resources
    homepage: https://browser.planteome.org/amigo
    name: Plant Ontology
    prefix: PO
  edam:
    description: An identifier of a concept from the Plant Ontology (PO).
    name: Plant Ontology concept
    obsolete: false
    prefix: '1180'
  fairsharing:
    abbreviation: PO
    contact:
      email: jaiswalp@science.oregonstate.edu
      name: Pankaj Jaiswal
      orcid: 0000-0002-1005-8383
    description: The Plant Ontology is a structured vocabulary and database resource
      that links plant anatomy, morphology and growth and development to plant genomics
      data. The PO is under active development to expand to encompass terms and annotations
      from all plants.
    domains:
    - Expression data
    - whole plant development stage
    - life cycle
    homepage: http://plantontology.org/
    license: CC-BY-4.0
    name: Plant Ontology
    prefix: FAIRsharing.3ngg40
    publications:
    - doi: 10.1002/cfg.496
      pubmed: '18629207'
      title: 'Plant Ontology (PO): a Controlled Vocabulary of Plant Structures and
        Growth Stages'
      year: 2008
    - doi: 10.1002/cfg.154
      pubmed: '18628842'
      title: The Plant Ontology Consortium and plant ontologies
      year: 2008
    - doi: 10.1007/978-1-4939-3167-5_5
      pubmed: '26519402'
      title: 'The Plant Ontology: A Tool for Plant Genomics'
      year: 2015
    - doi: 10.1093/pcp/pcs163
      pubmed: '23220694'
      title: The plant ontology as a tool for comparative plant anatomy and genomic
        analyses
      year: 2012
    - doi: 10.1093/nar/gkm908
      pubmed: '18194960'
      title: 'The Plant Ontology Database: a community resource for plant structure
        and developmental stages controlled vocabulary and annotations'
      year: 2008
    - doi: 10.1371/journal.pbio.1002033
      pubmed: '25562316'
      title: Finding our way through phenotypes
      year: 2015
    repository: https://github.com/Planteome/plant-ontology
    subjects:
    - Life Science
    - Botany
    - Plant Anatomy
  go:
    homepage: http://www.planteome.org/
    name: Plant Ontology
    prefix: PO
  mappings:
    aberowl: PO
    agroportal: PO
    biocontext: PO
    bioportal: PO
    cellosaurus: PO
    edam: '1180'
    fairsharing: FAIRsharing.3ngg40
    go: PO
    miriam: po
    n2t: po
    obofoundry: po
    ols: po
    ontobee: PO
    prefixcommons: po
    tib: po
    wikidata.entity: Q7201529
  miriam:
    deprecated: false
    description: The Plant Ontology is a structured vocabulary and database resource
      that links plant anatomy, morphology and growth and development to plant genomics
      data.
    homepage: http://bioportal.bioontology.org/ontologies/PO
    id: '00000307'
    name: Plant Ontology
    namespaceEmbeddedInLui: true
    pattern: ^PO:\d+$
    prefix: po
    providers:
    - code: amigo
      description: Plant Ontology through Amigo
      homepage: http://www.plantontology.org/
      name: Plant Ontology through Amigo
      uri_format: http://www.plantontology.org/amigo/go.cgi?view=details&query=PO:$1
    sampleId: 0009089
    uri_format: http://purl.bioontology.org/ontology/PO/PO:$1
  n2t:
    description: The Plant Ontology is a structured vocabulary and database resource
      that links plant anatomy, morphology and growth and development to plant genomics
      data.
    example: 0009089
    homepage: http://bioportal.bioontology.org/ontologies/PO
    name: Plant Ontology through BioPortal
    namespaceEmbeddedInLui: true
    pattern: ^PO:\d+$
    prefix: po
    uri_format: http://purl.bioontology.org/ontology/PO/PO:$1
  obofoundry:
    appears_in:
    - agro
    - ecocore
    - envo
    - gallont
    - genepio
    contact: jaiswalp@science.oregonstate.edu
    contact.github: jaiswalp
    contact.label: Pankaj Jaiswal
    contact.orcid: 0000-0002-1005-8383
    deprecated: false
    description: The Plant Ontology is a structured vocabulary and database resource
      that links plant anatomy, morphology and growth and development to plant genomics
      data.
    domain: anatomy and development
    download.obo: http://purl.obolibrary.org/obo/po.obo
    download.owl: http://purl.obolibrary.org/obo/po.owl
    homepage: http://browser.planteome.org/amigo
    license: CC BY 4.0
    license.url: https://creativecommons.org/licenses/by/4.0/
    logo: https://raw.githubusercontent.com/Planteome/plant-ontology/refs/heads/master/Planteome_profile.jpg
    name: Plant Ontology
    preferredPrefix: PO
    prefix: po
    publications:
    - id: https://www.ncbi.nlm.nih.gov/pubmed/23220694
      title: The plant ontology as a tool for comparative plant anatomy and genomic
        analyses.
    - id: https://www.ncbi.nlm.nih.gov/pubmed/29186578
      title: 'The Planteome database: an integrated resource for reference ontologies,
        plant genomics and phenomics.'
    repository: https://github.com/Planteome/plant-ontology
    twitter: planteome
  ols:
    description: The Plant Ontology is a structured vocabulary and database resource
      that links plant anatomy, morphology and growth and development to plant genomics
      data.
    download_owl: http://purl.obolibrary.org/obo/po.owl
    homepage: http://browser.planteome.org/amigo
    name: Plant Ontology
    prefix: po
    tracker: https://github.com/Planteome/plant-ontology/issues
    version: '2025-10-31'
    version.iri: http://purl.obolibrary.org/obo/po/releases/2025-10-31/po.owl
  ontobee:
    library: Foundry
    name: Plant Ontology
    prefix: PO
  pattern: ^\d+$
  prefix: po
  prefixcommons:
    bioportal: '1587'
    description: The Plant Ontology is a structured vocabulary and database resource
      that links plant anatomy, morphology and growth and development to plant genomics
      data. The PO is under active development to expand to encompass terms and annotations
      from all plants.
    example: PO:0006220
    homepage: http://www.plantontology.org/
    keywords:
    - ontology
    - structure
    - classification
    name: Plant Ontology
    pattern: ^PO:\d+$
    prefix: po
    synonyms:
    - poc
    uri_format: http://www.plantontology.org/amigo/go.cgi?view=details&search_constraint=terms&depth=0&query=$1
  providers:
  - code: amigo
    description: Plant Ontology through Amigo
    example: null
    first_party: null
    homepage: http://www.plantontology.org/
    name: Plant Ontology through Amigo
    publications: null
    status: null
    uri_format: https://browser.planteome.org/amigo/term/PO:$1
  publications:
  - doi: 10.1093/nar/gkx1152
    pmc: PMC5753347
    pubmed: '29186578'
    title: 'The Planteome database: an integrated resource for reference ontologies,
      plant genomics and phenomics'
    year: 2018
  - doi: 10.1007/978-1-4939-3167-5_5
    pmc: null
    pubmed: '26519402'
    title: 'The Plant Ontology: A Tool for Plant Genomics'
    year: 2016
  - doi: 10.1371/journal.pbio.1002033
    pmc: PMC4285398
    pubmed: '25562316'
    title: Finding our way through phenotypes
    year: 2015
  - doi: 10.1093/pcp/pcs163
    pmc: PMC3583023
    pubmed: '23220694'
    title: The plant ontology as a tool for comparative plant anatomy and genomic
      analyses
    year: 2012
  - doi: 10.1093/nar/gkm908
    pmc: PMC2238838
    pubmed: '18194960'
    title: 'The Plant Ontology Database: a community resource for plant structure
      and developmental stages controlled vocabulary and annotations'
    year: 2008
  - doi: 10.1002/cfg.496
    pmc: PMC2447502
    pubmed: '18629207'
    title: 'Plant Ontology (PO): a Controlled Vocabulary of Plant Structures and Growth
      Stages'
    year: 2005
  - doi: 10.1002/cfg.154
    pmc: PMC2447263
    pubmed: '18628842'
    title: The Plant Ontology Consortium and plant ontologies
    year: 2002
  - doi: null
    pmc: null
    pubmed: '23220694'
    title: The plant ontology as a tool for comparative plant anatomy and genomic
      analyses
    year: null
  - doi: null
    pmc: null
    pubmed: '29186578'
    title: 'The Planteome database: an integrated resource for reference ontologies,
      plant genomics and phenomics'
    year: null
  - doi: 10.1002/cfg.496
    pmc: null
    pubmed: '18629207'
    title: 'Plant Ontology (PO): a Controlled Vocabulary of Plant Structures and Growth
      Stages'
    year: 2008
  - doi: 10.1002/cfg.154
    pmc: null
    pubmed: '18628842'
    title: The Plant Ontology Consortium and plant ontologies
    year: 2008
  - doi: 10.1007/978-1-4939-3167-5_5
    pmc: null
    pubmed: '26519402'
    title: 'The Plant Ontology: A Tool for Plant Genomics'
    year: 2015
  - doi: 10.1093/pcp/pcs163
    pmc: null
    pubmed: '23220694'
    title: The plant ontology as a tool for comparative plant anatomy and genomic
      analyses
    year: 2012
  - doi: 10.1093/nar/gkm908
    pmc: null
    pubmed: '18194960'
    title: 'The Plant Ontology Database: a community resource for plant structure
      and developmental stages controlled vocabulary and annotations'
    year: 2008
  - doi: 10.1371/journal.pbio.1002033
    pmc: null
    pubmed: '25562316'
    title: Finding our way through phenotypes
    year: 2015
  tib:
    description: An ontology that describes plant anatomy, morphology, and growth
      and development in plants.
    download_owl: http://purl.obolibrary.org/obo/po.owl
    homepage: https://www.plantontology.org/
    keywords:
    - ESS
    - DataPLANT
    - earth sciences
    name: Plant Ontology
    prefix: po
    tracker: https://github.com/Planteome/plant-ontology/issues
    version.iri: http://purl.obolibrary.org/obo/po/releases/2025-10-31/po.owl
  uri_format: http://purl.obolibrary.org/obo/PO_$1
pocketome:
  biocontext:
    prefix: POCKETOME
  contact:
    email: ikufareva@ucsd.edu
    github: null
    name: Ruben Abagyan
    orcid: 0000-0001-9309-2976
  fairsharing:
    abbreviation: Pocketome
    description: The Pocketome is an encyclopedia of conformational ensembles of druggable
      binding sites that can be identified experimentally from co-crystal structures
      in the Protein Data Bank. Each Pocketome entry describes a site on a protein
      surface that is involved in transient interactions with small molecules and
      peptides.
    homepage: http://pocketome.org
    name: 'Pocketome: an encyclopedia of small-molecule binding sites in 4D'
    prefix: FAIRsharing.tc6df8
    publications:
    - doi: 10.1093/nar/gkr825
      pubmed_id: 22080553
      title: 'Pocketome: an encyclopedia of small-molecule binding sites in 4D.'
    - doi: 10.1007/978-1-60761-274-2_11
      pubmed_id: 19727619
      title: The flexible pocketome engine for structural chemogenomics.
    subjects:
    - Life Science
  mappings:
    biocontext: POCKETOME
    fairsharing: FAIRsharing.tc6df8
    miriam: pocketome
    n2t: pocketome
    pathguide: '537'
  miriam:
    deprecated: false
    description: Pocketome is an encyclopedia of conformational ensembles of all druggable
      binding sites that can be identified experimentally from co-crystal structures
      in the Protein Data Bank. Each Pocketome entry corresponds to a small molecule
      binding site in a protein which has been co-crystallized in complex with at
      least one drug-like small molecule, and is represented in at least two PDB entries.
    homepage: http://www.pocketome.org/sfSearch.cgi?act=browseall
    id: '00000400'
    name: Pocketome
    namespaceEmbeddedInLui: false
    pattern: ^[A-Za-z_0-9]+$
    prefix: pocketome
    sampleId: 1433C_TOBAC_1_252
    uri_format: http://www.pocketome.org/files/$1.html
  n2t:
    description: Pocketome is an encyclopedia of conformational ensembles of all druggable
      binding sites that can be identified experimentally from co-crystal structures
      in the Protein Data Bank. Each Pocketome entry corresponds to a small molecule
      binding site in a protein which has been co-crystallized in complex with at
      least one drug-like small molecule, and is represented in at least two PDB entries.
    example: 1433C_TOBAC_1_252
    homepage: http://www.pocketome.org/sfSearch.cgi?act=browseall
    name: Pocketome at UCSD Skaggs School
    namespaceEmbeddedInLui: false
    pattern: ^[A-Za-z_0-9]+
    prefix: pocketome
    uri_format: http://www.pocketome.org/files/$1.html
  pathguide:
    abbreviation: Pocketome
    homepage: http://www.pocketome.org/
    name: Pocketome
    prefix: '537'
  prefix: pocketome
  publications:
  - doi: 10.1093/nar/gkr825
    pmc: PMC3245087
    pubmed: '22080553'
    title: 'Pocketome: an encyclopedia of small-molecule binding sites in 4D'
    year: 2011
  - doi: 10.1007/978-1-60761-274-2_11
    pmc: PMC2975493
    pubmed: '19727619'
    title: The flexible pocketome engine for structural chemogenomics
    year: 2009
polbase:
  biocontext:
    prefix: POLBASE
  contact:
    email: lreha@ualberta.ca
    github: null
    name: Linda Reha-Krantz
    orcid: 0000-0003-4497-423X
  fairsharing:
    abbreviation: Polbase
    description: Polbase is an open and searchable database providing information
      from published and unpublished sources on the biochemical, genetic, and structural
      information of DNA polymerases.
    homepage: http://polbase.neb.com
    name: Polbase
    prefix: FAIRsharing.s9ztmd
    publications:
    - doi: 10.1093/nar/gkr847
      pubmed_id: 21993301
      title: 'Polbase: a repository of biochemical, genetic and structural information
        about DNA polymerases.'
    subjects:
    - Biochemistry
    - Genetics
  integbio:
    description: Polbase is an open and searchable database providing information
      from published and unpublished sources on the biochemical, genetic, and structural
      information of DNA polymerases.
    fairsharing: FAIRsharing.s9ztmd
    homepage: https://polbase.neb.com/
    information_keywords:
    - Sequence
    - 3D structure
    - Repository
    maintainer: New England Biolabs
    name: Polbase
    prefix: nbdc02079
    pubmeds:
    - '21993301'
    target_keywords:
    - Genetic variation
    - Protein
  mappings:
    biocontext: POLBASE
    fairsharing: FAIRsharing.s9ztmd
    integbio: nbdc02079
    miriam: polbase
    n2t: polbase
  miriam:
    deprecated: false
    description: Polbase is a database of DNA polymerases providing information on
      polymerase protein sequence, target DNA sequence, enzyme structure, sequence
      mutations and details on polymerase activity.
    homepage: http://polbase.neb.com/
    id: '00000355'
    name: PolBase
    namespaceEmbeddedInLui: false
    pattern: ^[A-Za-z-0-9]+$
    prefix: polbase
    sampleId: 19-T4
    uri_format: https://polbase.neb.com/polymerases/$1#sequences
  n2t:
    description: Polbase is a database of DNA polymerases providing information on
      polymerase protein sequence, target DNA sequence, enzyme structure, sequence
      mutations and details on polymerase activity.
    example: 19-T4
    homepage: http://polbase.neb.com/
    name: PolBase at New England BioLabs
    namespaceEmbeddedInLui: false
    pattern: ^[A-Za-z-0-9]+$
    prefix: polbase
    uri_format: https://polbase.neb.com/polymerases/$1#sequences
  prefix: polbase
  publications:
  - doi: 10.1093/nar/gkr847
    pmc: PMC3245023
    pubmed: '21993301'
    title: 'Polbase: a repository of biochemical, genetic and structural information
      about DNA polymerases'
    year: 2011
  - doi: 10.1093/nar/gkr847
    pmc: null
    pubmed: null
    title: 'Polbase: a repository of biochemical, genetic and structural information
      about DNA polymerases.'
    year: null
polymat:
  example: 4PointResistanceSetup
  mappings:
    tib: pmat
  name: PolyMat Ontology
  prefix: polymat
  tib:
    description: PolyMat is a domain ontology designed for polymer membrane research
      and tailored for immediate integration within Electronic Laboratory Notebooks
      (ELNs), facilitating efficient documentation of laboratory experiments and advancing
      the domain's FAIRification process.
    homepage: https://gitlab.com/dlr-dw/poly-ontologies/polymat-ontology
    keywords:
    - NFDI4ING
    - chemistry
    - material science
    name: The PolyMat ontology
    prefix: pmat
    tracker: https://gitlab.com/dlr-dw/poly-ontologies/polymat-ontology/-/issues
    uri_format: https://w3id.org/polymat/$1
    version.iri: https://w3id.org/polymat/1.1.0
polytraits.trait:
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: Reproductive and behavioural traits of both adult and larval stages,
    as well as information on environmental preferences and a few morphological traits.
  example: PRED
  github_request_issue: 1422
  homepage: http://polytraits.lifewatchgreece.eu/terms
  name: Polytraits Trait Definitions
  prefix: polytraits.trait
  rdf_uri_format: http://polytraits.lifewatchgreece.eu/terms/$1
  uri_format: http://polytraits.lifewatchgreece.eu/traitspublic_traitdefinitions.php#$1
pombase:
  biocontext:
    prefix: PomBase
    uri_format: https://www.pombase.org/spombe/result/$1
  biolink:
    is_identifiers: false
    is_obo: false
    prefix: PomBase
    uri_format: https://www.pombase.org/gene/$1
  contact:
    email: vw253@cam.ac.uk
    github: ValWood
    name: Valerie Wood
    orcid: 0000-0001-6330-7526
  domain: gene
  fairsharing:
    abbreviation: PomBase
    description: PomBase is a model organism database that provides organization of
      and access to scientific data for the fission yeast Schizosaccharomyces pombe.
      PomBase supports genomic sequence and features, genome-wide datasets and manual
      literature curation as well as providing structural and functional annotation
      and access to large-scale data sets.
    homepage: http://www.pombase.org
    license: CC-BY-4.0
    name: PomBase
    prefix: FAIRsharing.8jsya3
    publications:
    - doi: 10.1093/nar/gkr853
      pubmed_id: 22039153
      title: 'PomBase: a comprehensive online resource for fission yeast.'
    - doi: 10.1093/nar/gkr1028
      pubmed_id: 22102568
      title: 'The Gene Ontology: enhancements for 2011.'
    - doi: 10.1093/bioinformatics/btt266
      pubmed_id: 23658422
      title: 'FYPO: the fission yeast phenotype ontology.'
    - doi: 10.1093/nar/gku1040
      pubmed_id: 25361970
      title: 'PomBase 2015: updates to the fission yeast database.'
    - doi: 10.1093/bioinformatics/btu103
      pubmed_id: 24574118
      title: 'Canto: an online tool for community literature curation.'
    - doi: 10.1186/1471-2105-15-155
      pubmed_id: 24885854
      title: A method for increasing expressivity of Gene Ontology annotations using
        a compositional approach.
    - doi: 10.1093/nar/gks1050
      pubmed_id: 23161678
      title: Gene Ontology annotations and resources.
    - doi: 10.1186/s12915-016-0276-z
      pubmed_id: 27334346
      title: 'Model organism databases: essential resources that need the support
        of both funders and users.'
    subjects:
    - Life Science
  go:
    homepage: https://www.pombase.org/
    name: PomBase
    prefix: PomBase
  integbio:
    description: "PomBase is a scientific resource for genomic information on the\
      \ fission yeast Schizosaccharomyces pombe. \nThis database offers extensive\
      \ information on the structural and functional aspects of the yeast genome.\n\
      The sequenced size of the genome, not including rRNA is 12.57Mbp.\nThe nucleus\
      \ of the yeast cell contains 3 chromosomes of which the size ranges from 2.45Mbp\
      \ to 5.58Mbp\nThere are 5124 protein coding genes that have been counted and\
      \ they are packed on the DNA molecules at a density of 554.49 genes per Mb.\
      \ \nA comprehensive number of datasets are available for download.\nSearch options\
      \ available are a Simple keyword search, an Advanced search, a gene list search,\
      \ a Blast search and a Genome Browser."
    fairsharing: biodbcore-000139
    homepage: http://www.pombase.org/
    information_keywords:
    - Sequence
    - Repository
    maintainer: Wellcome Sanger Institute
    name: PomBase
    prefix: nbdc00332
    pubmeds:
    - '22039153'
    status: Active
    target_keywords:
    - Genome/Gene
  license: CC-BY-4.0
  logo: https://www.pombase.org/assets/pombase-logo.png
  mappings:
    biocontext: PomBase
    biolink: PomBase
    fairsharing: FAIRsharing.8jsya3
    go: PomBase
    integbio: nbdc00332
    miriam: pombase
    n2t: pombase
    ncbi: PomBase
    prefixcommons: pombase
    re3data: r3d100011478
    uniprot: DB-0031
    wikidata: P6245
  miriam:
    deprecated: false
    description: PomBase is a model organism database established to provide access
      to molecular data and biological information for the fission yeast Schizosaccharomyces
      pombe. It encompasses annotation of genomic sequence and features, comprehensive
      manual literature curation and genome-wide data sets.
    homepage: https://www.pombase.org/
    id: '00000335'
    name: PomBase
    namespaceEmbeddedInLui: false
    pattern: ^S\w+(\.)?\w+(\.)?$
    prefix: pombase
    sampleId: SPCC13B11.01
    uri_format: https://www.pombase.org/gene/$1
  n2t:
    description: PomBase is a model organism database established to provide access
      to molecular data and biological information for the fission yeast Schizosaccharomyces
      pombe. It encompasses annotation of genomic sequence and features, comprehensive
      manual literature curation and genome-wide data sets.
    example: SPCC13B11.01
    homepage: http://www.pombase.org/
    name: PomBase at University of Cambridge
    namespaceEmbeddedInLui: false
    pattern: ^S\w+(\.)?\w+(\.)?$
    prefix: pombase
    uri_format: http://www.pombase.org/spombe/result/$1
  name: PomBase
  ncbi:
    example: SPBC11B10.09
    homepage: http://www.pombase.org/
    name: Database of Structural and Functional Data for Schizosaccaromyces pombe
    prefix: PomBase
  prefix: pombase
  prefixcommons:
    description: PomBase is a model organism database for the fission yeast Schizosaccharomyces
      pombe. PomBase  supports genomic sequence and features, genome-wide datasets
      and manual literature curation.
    example: SPCC13B11.01
    homepage: http://www.pombase.org
    name: Schizosaccharomyces pombe database
    pattern: ^S\w+(\.)?\w+(\.)?$
    prefix: pombase
    pubmed_ids:
    - '22039153'
  publications:
  - doi: 10.1093/nar/gky961
    pmc: PMC6324063
    pubmed: '30321395'
    title: 'PomBase 2018: user-driven reimplementation of the fission yeast database
      provides rapid and intuitive access to diverse, interconnected information'
    year: 2019
  - doi: 10.1186/s12915-016-0276-z
    pmc: PMC4918006
    pubmed: '27334346'
    title: 'Model organism databases: essential resources that need the support of
      both funders and users'
    year: 2016
  - doi: 10.1186/1471-2105-15-155
    pmc: PMC4039540
    pubmed: '24885854'
    title: A method for increasing expressivity of Gene Ontology annotations using
      a compositional approach
    year: 2014
  - doi: 10.1093/bioinformatics/btu103
    pmc: PMC4058955
    pubmed: '24574118'
    title: 'Canto: an online tool for community literature curation'
    year: 2014
  - doi: 10.1093/nar/gku1040
    pmc: PMC4383888
    pubmed: '25361970'
    title: 'PomBase 2015: updates to the fission yeast database'
    year: 2014
  - doi: 10.1093/bioinformatics/btt266
    pmc: PMC3694669
    pubmed: '23658422'
    title: 'FYPO: the fission yeast phenotype ontology'
    year: 2013
  - doi: 10.1093/nar/gks1050
    pmc: PMC3531070
    pubmed: '23161678'
    title: Gene Ontology annotations and resources
    year: 2012
  - doi: 10.1093/nar/gkr853
    pmc: PMC3245111
    pubmed: '22039153'
    title: 'PomBase: a comprehensive online resource for fission yeast'
    year: 2011
  - doi: 10.1093/nar/gkr1028
    pmc: PMC3245151
    pubmed: '22102568'
    title: 'The Gene Ontology: enhancements for 2011'
    year: 2011
  re3data:
    description: PomBase is a comprehensive database for the fission yeast Schizosaccharomyces
      pombe, providing structural and functional annotation, literature curation and
      access to large-scale data sets.
    doi: 10.17616/R3NS78
    homepage: https://www.pombase.org/
    license: other
    name: Pombase
    prefix: r3d100011478
    synonyms:
    - The scientific resource for fission yeast
    xrefs:
      omics: 06183
  synonyms:
  - PomBase
  uniprot:
    abbreviation: PomBase
    category: Organism-specific databases
    homepage: https://www.pombase.org/
    name: Schizosaccharomyces pombe database
    prefix: DB-0031
    publications:
    - doi: 10.1093/genetics/iyae007
      pubmed: '38376816'
    uri_format: https://www.pombase.org/gene/$1
  wikidata:
    description: Identifier for a coding gene in the Schizosaccharomyces pombe model
      organism database PomBase
    example:
    - SPAC24H6.05
    - SPAC2F7.03c
    - SPAC57A10.02
    - SPCC18B5.03
    name: PomBase systematic ID
    prefix: P6245
    uri_format: https://www.pombase.org/gene/$1
poro:
  aberowl:
    description: An ontology covering the anatomy of the taxon Porifera (sponges)
    download_owl: http://aber-owl.net/media/ontologies/PORO/10/poro.owl
    homepage: https://github.com/obophenotype/porifera-ontology
    name: Porifera Ontology
    prefix: PORO
  biocontext:
    prefix: PORO
  bioportal:
    contact:
      email: thacker@uab.edu
      name: Bob Thacker
    description: An ontology covering the anatomy of Porifera (sponges)
    name: Porifera Ontology
    prefix: PORO
    version: unknown
  ecoportal:
    contact:
      email: thacker@uab.edu
      name: Bob Thacker
    description: An ontology describing the anatomical structures and characteristics
      of Porifera (sponges).
    homepage: https://github.com/obophenotype/porifera-ontology
    license: CC0-1.0
    name: Porifera Ontology
    prefix: PORO
  example: '0000550'
  fairsharing:
    abbreviation: PORO
    description: An ontology covering the anatomy of Porifera (sponges)
    domains:
    - Taxonomic classification
    homepage: http://bioportal.bioontology.org/ontologies/PORO
    name: Porifera Ontology
    prefix: FAIRsharing.93g1th
    subjects:
    - Phylogeny
    - Taxonomy
    - Anatomy
  mappings:
    aberowl: PORO
    biocontext: PORO
    bioportal: PORO
    ecoportal: PORO
    fairsharing: FAIRsharing.93g1th
    obofoundry: poro
    ols: poro
    ontobee: PORO
    wikidata.entity: Q55118578
  obofoundry:
    appears_in:
    - gallont
    contact: robert.thacker@stonybrook.edu
    contact.github: bobthacker
    contact.label: Bob Thacker
    contact.orcid: 0000-0002-9654-0073
    depends_on:
    - ro
    - uberon
    deprecated: false
    description: An ontology covering the anatomy of the taxon Porifera (sponges)
    domain: anatomy and development
    download.obo: http://purl.obolibrary.org/obo/poro.obo
    download.owl: http://purl.obolibrary.org/obo/poro.owl
    homepage: https://github.com/obophenotype/porifera-ontology
    license: CC BY 3.0
    license.url: http://creativecommons.org/licenses/by/3.0/
    name: Porifera Ontology
    preferredPrefix: PORO
    prefix: poro
    publications:
    - id: https://www.ncbi.nlm.nih.gov/pubmed/25276334
      title: 'The Porifera Ontology (PORO): enhancing sponge systematics with an anatomy
        ontology'
    repository: https://github.com/obophenotype/porifera-ontology
  ols:
    description: An ontology describing the anatomical structures and characteristics
      of Porifera (sponges)
    download_owl: http://purl.obolibrary.org/obo/poro.owl
    homepage: https://github.com/obophenotype/porifera-ontology
    name: Porifera (sponge) ontology
    prefix: poro
    tracker: https://github.com/obophenotype/porifera-ontology/issues
    version: '2016-10-06'
    version.iri: http://purl.obolibrary.org/obo/poro/releases/2016-10-06/poro.owl
  ontobee:
    library: Library
    name: Porifera Ontology
    prefix: PORO
  pattern: ^\d{7}$
  prefix: poro
  publications:
  - doi: 10.1186/2041-1480-5-39
    pmc: PMC4177528
    pubmed: '25276334'
    title: 'The Porifera Ontology (PORO): enhancing sponge systematics with an anatomy
      ontology'
    year: 2014
  uri_format: http://purl.obolibrary.org/obo/PORO_$1
ppdb:
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: PPDB is a comprehensive source of data on pesticide chemical, physical
    and biological properties.
  example: '1484'
  fairsharing:
    abbreviation: ppdb
    contact:
      email: ppdb@gifu-u.ac.jp
      name: Yoshiharu Y. Yamamoto
      orcid: 0000-0002-9667-0572
    description: Genome-wide plant promoter database for several plant species, including
      Arabidopsis thaliana, rice, poplar, and Physcomitrella patens.
    homepage: http://ppdb.agr.gifu-u.ac.jp
    name: Plant Promoter Database
    prefix: FAIRsharing.7k8zh0
    publications:
    - doi: 10.1093/nar/gkm785
      pubmed_id: 17947329
      title: 'ppdb: a plant promoter database.'
    - doi: 10.1093/nar/gkt1027
      pubmed_id: 24194597
      title: 'ppdb: plant promoter database version 3.0.'
    subjects:
    - Life Science
  homepage: https://sitem.herts.ac.uk/aeru/ppdb/
  integbio:
    alt_name: PlantPromoterDB
    description: PPDB is a database of plant promoter elements. This database contains
      position, motif, and sequence information for promoters from four major plant
      species. The promoters can be searched by gene name, ID, or model ID, and cross-species
      homology analyses can be performed.
    fairsharing: biodbcore-000603
    homepage: http://ppdb.agr.gifu-u.ac.jp/ppdb/cgi-bin/index.cgi
    information_keywords:
    - Sequence
    maintainer: Gifu University
    name: PPDB
    prefix: nbdc01041
    pubmeds:
    - '17947329'
    - '24194597'
    target_keywords:
    - Genome/Gene
  mappings:
    fairsharing: FAIRsharing.7k8zh0
    integbio: nbdc01041
  name: Pesticide Properties DataBase
  pattern: ^\d+$
  prefix: ppdb
  publications:
  - doi: 10.1093/nar/gkt1027
    pmc: PMC3965062
    pubmed: '24194597'
    title: 'ppdb: plant promoter database version 3.0'
    year: 2013
  - doi: 10.1093/nar/gkm785
    pmc: PMC2238996
    pubmed: '17947329'
    title: 'ppdb: a plant promoter database'
    year: 2007
  - doi: 10.1093/nar/gkm785
    pmc: null
    pubmed: null
    title: 'ppdb: a plant promoter database.'
    year: null
  - doi: 10.1093/nar/gkt1027
    pmc: null
    pubmed: null
    title: 'ppdb: plant promoter database version 3.0.'
    year: null
  uri_format: https://sitem.herts.ac.uk/aeru/ppdb/en/Reports/$1.htm
ppeo:
  agroportal:
    contact:
      email: cyril.pommier@inrae.fr
      name: Cyril Pommier
    description: The Plant Phenotyping Experiment Ontology (PPEO) is an implementation
      of the Minimal Information About Plant Phenotyping Experiment. It lists and
      organises all the informations necessary to describe and reuse a phenotyping
      dataset following FAIR principles (Findable Interoperable Accessible Reusable).
      It has been initiated with experts from Elixir, Emphasis, Bioversity International
      - CGIAR and RDA.
    example_uri: https://raw.githubusercontent.com/MIAPPE/MIAPPE-ontology/master/MIAPPE.owl#MIAPPE_000011
    homepage: http://purl.org/ppeo
    license: CC-BY-4.0
    name: Plant Phenotype Experiment Ontology
    prefix: PPEO
    repository: https://github.com/MIAPPE/MIAPPE-ontology
    version: 1.1-beta
  example: GPS_location
  mappings:
    agroportal: PPEO
    tib: ppeo
  prefix: ppeo
  tib:
    description: The Plant Phenotyping Experiment Ontology (PPEO) is an implementation
      of the Minimal Information About Plant Phenotyping Experiment. It lists and
      organises all the informations necessary to describe and reuse a phenotyping
      dataset following FAIR principles (Findable Interoperable Accessible Reusable).
      It has been initiated with experts from Elixir, Emphasis, Bioversity International
      - CGIAR and RDA.
    download_owl: https://www.purl.org/ppeo/ppeo.owl
    homepage: http://purl.org/ppeo
    keywords:
    - DataPLANT
    - life sciences, biology
    name: Plant Phenotyping Experiment Ontology
    prefix: ppeo
    tracker: https://github.com/MIAPPE/MIAPPE-ontology/issues/
    uri_format: http://purl.org/ppeo/PPEO.owl#$1
ppo:
  aberowl:
    description: An ontology for describing the phenology of individual plants and
      populations of plants, and for integrating plant phenological data across sources
      and scales.
    download_owl: http://aber-owl.net/media/ontologies/PPO/12/ppo.owl
    homepage: https://github.com/PlantPhenoOntology/PPO
    name: Plant Phenology Ontology
    prefix: PPO
  agroportal:
    contact:
      email: stucky.brian@gmail.com
      name: Brian J. Stucky
    description: Plant phenology — the timing of plant life-cycle events, such as
      flowering or leafing-out — has cascading effects on multiple levels of biological
      organization, from individuals to ecosystems, and is crucial for understanding
      the links between climate and biological communities. Plant phenology data are
      collected and used by many different types of researchers, from plant breeders
      to ecosystem ecologists. Today, thanks to data digitization and aggregation
      initiatives, phenology monitoring networks, and the efforts of citizen scientists,
      more phenologically relevant data is available than ever before. Unfortunately,
      combining these data in large-scale analyses remains prohibitively difficult,
      mostly because the individuals and organizations producing the data are using
      non-standardized terminologies and metrics during data collection and processing.
      Lack of standardization remains particularly problematic for historical datasets,
      which are crucial for time-based analyses. The Plant Phenology Ontology (PPO)
      is a collaborative effort to help solve these problems by developing the standardized
      terminology, definitions, and relations that are needed for large-scale data
      integration. The PPO builds on the widely used Plant Ontology (PO) and Phenotype
      and Trait Ontology (PATO) to promote broad reuse of phenological data. The initial
      use case for the PPO is integration of citizen science data from the USA National
      Phenology Network (USA-NPN) and the Pan-European Phenology Network (PEP), but
      work is also planned for integrating data from herbaria., An ontology that defines
      plant phenological classes and is used to run the plantphenology.org data portal.
      Reuses terms from PO and PATO where possible.
    example_uri: http://purl.obolibrary.org/obo/PPO_0007001
    homepage: http://www.obofoundry.org/ontology/ppo.html
    license: http://purl.obolibrary.org/obo/ppo.owl#Unspecified
    name: Plant Phenology Ontology
    prefix: PPO
    repository: https://github.com/PlantPhenoOntology
    version: '2025-06-16'
  biocontext:
    prefix: PPO
  bioportal:
    contact:
      email: rlwalls2008@gmail.com
      name: Ramona Walls
    description: An ontology for describing the phenology of individual plants and
      populations of plants, and for integrating plant phenological data across sources
      and scales.
    homepage: https://github.com/PlantPhenoOntology/PPO
    name: Plant Phenology Ontology
    prefix: PPO
    version: '2025-06-16'
  contact:
    email: rlwalls2008@gmail.com
    github: ramonawalls
    name: Ramona Walls
    orcid: 0000-0001-8815-0078
  example: 0002058
  fairsharing:
    abbreviation: PPO
    description: An ontology for describing the phenology of individual plants and
      populations of plants, and for integrating plant phenological data across sources
      and scales.
    domains:
    - phenotype
    - life cycle
    homepage: https://github.com/PlantPhenoOntology/PPO
    license: CC-BY-3.0
    name: Plant Phenology Ontology
    prefix: FAIRsharing.hakg7c
    publications:
    - doi: 10.3389/fpls.2018.00517
      pubmed: '29765382'
      title: 'The Plant Phenology Ontology: A New Informatics Resource for Large-Scale
        Integration of Plant Phenology Data'
      year: 2018
    repository: https://github.com/PlantPhenoOntology/ppo/raw/master/documentation/ppo.pdf
    subjects:
    - Botany
    user_defined_tags:
    - Phenology
  mappings:
    aberowl: PPO
    agroportal: PPO
    biocontext: PPO
    bioportal: PPO
    fairsharing: FAIRsharing.hakg7c
    obofoundry: ppo
    ols: ppo
    ontobee: PPO
    tib: ppo
    wikidata.entity: Q65057180
  obofoundry:
    contact: rlwalls2008@gmail.com
    contact.github: ramonawalls
    contact.label: Ramona Walls
    contact.orcid: 0000-0001-8815-0078
    deprecated: false
    description: An ontology for describing the phenology of individual plants and
      populations of plants, and for integrating plant phenological data across sources
      and scales.
    domain: phenotype
    download.owl: http://purl.obolibrary.org/obo/ppo.owl
    homepage: https://github.com/PlantPhenoOntology/PPO
    license: CC BY 3.0
    license.url: http://creativecommons.org/licenses/by/3.0/
    name: Plant Phenology Ontology
    preferredPrefix: PPO
    prefix: ppo
    repository: https://github.com/PlantPhenoOntology/PPO
  ols:
    contact: ppo-discuss@googlegroups.com
    description: An ontology for describing the phenology of individual plants and
      populations of plants, and for integrating plant phenological data across sources
      and scales.
    download_owl: http://purl.obolibrary.org/obo/ppo.owl
    homepage: https://github.com/PlantPhenoOntology/PPO
    name: Plant Phenology Ontology
    prefix: ppo
    tracker: https://github.com/PlantPhenoOntology/PPO/issues
    version: '2025-06-16'
    version.iri: http://purl.obolibrary.org/obo/ppo/releases/2025-06-16/ppo.owl
  ontobee:
    library: Library
    name: Plant Phenology Ontology
    prefix: PPO
  pattern: ^\d{7}$
  prefix: ppo
  publications:
  - doi: 10.3389/fpls.2018.00517
    pmc: PMC5938398
    pubmed: '29765382'
    title: 'The Plant Phenology Ontology: A New Informatics Resource for Large-Scale
      Integration of Plant Phenology Data'
    year: 2018
  tib:
    contact: ppo-discuss@googlegroups.com
    description: An ontology for describing the phenology of individual plants and
      populations of plants, and for integrating plant phenological data across sources
      and scales.
    download_owl: http://purl.obolibrary.org/obo/ppo.owl
    homepage: https://github.com/PlantPhenoOntology/PPO/
    keywords:
    - DataPLANT
    - life sciences, biology
    name: Plant Phenology Ontology
    prefix: ppo
    tracker: https://github.com/PlantPhenoOntology/ppo/issues/
    version.iri: http://purl.obolibrary.org/obo/ppo/releases/2025-06-16/ppo.owl
  uri_format: http://purl.obolibrary.org/obo/PPO_$1
ppr:
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  contributor_extras:
  - email: egon.willighagen@gmail.com
    github: egonw
    name: Egon Willighagen
    orcid: 0000-0001-7542-0286
  - email: javier.millanacosta@maastrichtuniversity.nl
    github: jmillanacosta
    name: Javier Millán Acosta
    orcid: 0000-0002-4166-7093
  description: Preprints are articles which have not been peer-reviewed from various
    preprint servers and open research platforms such as bioRxiv, ChemRxiv, PeerJ
    Preprints and F1000.
  example: PPR103739
  homepage: https://europepmc.org/Preprints
  keywords:
  - bibliometrics
  - preprints
  - publishing
  name: Europe PMC Preprints
  pattern: ^PPR\d+$
  prefix: ppr
  references:
  - https://github.com/bridgedb/tiwid/pull/21
  uri_format: https://europepmc.org/article/ppr/$1
pr:
  aberowl:
    description: An ontological representation of protein-related entities
    download_owl: http://aber-owl.net/media/ontologies/PR/87/pr.owl
    homepage: http://proconsortium.org
    name: PRotein Ontology (PRO)
    prefix: PR
  agroportal:
    contact:
      email: dan5@georgetown.edu
      name: Darren Natale
    description: 'An ontological representation of protein-related entities. The PRotein
      Ontology (PRO) formally defines taxon-specific and taxon-neutral protein-related
      entities in three major areas: proteins related by evolution; proteins produced
      from a given gene; and protein-containing complexes., The PRotein Ontology (PRO)
      formally defines taxon-specific and taxon-neutral protein-related entities in
      three major areas: proteins related by evolution; proteins produced from a given
      gene; and protein-containing complexes.'
    example_uri: http://purl.obolibrary.org/obo/PR_Q9UIG8-3
    license: CC-BY-4.0
    name: Protein Ontology
    prefix: PR
  biocontext:
    prefix: PR
  bioportal:
    contact:
      email: dan5@georgetown.edu
      name: Darren Natale
    description: 'PRO provides an ontological representation of protein-related entities
      by explicitly defining them and showing the relationships between them. Each
      PRO term represents a distinct class of entities (including specific modified
      forms, orthologous isoforms, and protein complexes) ranging from the taxon-neutral
      to the taxon-specific. The ontology has a meta-structure encompassing three
      areas: proteins based on evolutionary relatedness (ProEvo); protein forms produced
      from a given gene locus (ProForm); and protein-containing complexes (ProComp).,
      The PRotein Ontology (PRO) formally defines taxon-specific and taxon-neutral
      protein-related entities in three major areas: proteins related by evolution;
      proteins produced from a given gene; and protein-containing complexes.'
    homepage: http://proconsortium.org
    license: CC-BY-4.0
    name: Protein Ontology
    prefix: PR
    publications:
    - https://proconsortium.org/pro_pub.shtml
    version: '71.0'
  contributor_extras:
  - email: dan5@georgetown.edu
    github: nataled
    name: Darren A. Natale
    orcid: 0000-0001-5809-9523
  domain: protein
  example_extras:
  - P0DP23
  - Q15796
  - Q15796-1
  - A0A0G2QC33
  - A0A0G2QC33-2
  fairsharing:
    abbreviation: PRO
    contact:
      email: dan5@georgetown.edu
      name: Darren Natale
      orcid: 0000-0001-5809-9523
    description: 'Protein Ontology (PRO) provides an ontological representation of
      protein-related entities by explicitly defining them and showing the relationships
      between them. Each PRO term represents a distinct class of entities (including
      specific modified forms, orthologous isoforms, and protein complexes) ranging
      from the taxon-neutral to the taxon-specific. The ontology has a meta-structure
      encompassing three areas: proteins based on evolutionary relatedness (ProEvo);
      protein forms produced from a given gene locus (ProForm); and protein-containing
      complexes (ProComp).'
    domains:
    - Annotation
    - Post-translational modification site prediction
    - Data analysis
    - enhancer
    - protein acetylation
    - phosphorylation
    - methylation
    - protein-containing complex
    - glycosylation
    - craniofacial phenotype
    - phenotype
    - disease phenotype
    - microbe-host interaction phenotype
    - protein
    - QTL
    - Biocuration
    homepage: https://proconsortium.org/
    license: CC-BY-4.0
    logo: https://api.fairsharing.org/rails/active_storage/blobs/redirect/eyJfcmFpbHMiOnsibWVzc2FnZSI6IkJBaHBBWTA9IiwiZXhwIjpudWxsLCJwdXIiOiJibG9iX2lkIn19--7796769110d5d35906d68221bdd275782255a676/PROlogofinal300.png?disposition=inline
    name: PRotein Ontology
    prefix: FAIRsharing.4ndncv
    publications:
    - doi: 10.1093/nar/gkt1173
      pubmed: '24270789'
      title: 'Protein Ontology: a controlled structured network of protein entities'
      year: 2013
    - doi: 10.1093/nar/gkq907
      pubmed: '20935045'
      title: 'The Protein Ontology: a structured representation of protein forms and
        complexes'
      year: 2010
    - doi: 10.1186/1471-2105-8-s9-s1
      pubmed: '18047702'
      title: Framework for a protein ontology
      year: 2007
    - doi: 10.1186/1471-2105-12-371
      pubmed: '21929785'
      title: The representation of protein complexes in the Protein Ontology (PRO)
      year: 2011
    - doi: 10.1093/nar/gkw1075
      pubmed: '27899649'
      title: 'Protein Ontology (PRO): enhancing and scaling up the representation
        of protein entities'
      year: 2016
    repository: https://github.com/PROconsortium/PRoteinOntology
    subjects:
    - Functional Genomics
    - Phenomics
    - Omics
    - Biology
    - Proteomics
    - Metaproteomics
    user_defined_tags:
    - Phenology
    - Plant Phenotypes and Traits
  go:
    homepage: https://proconsortium.org/
    name: Protein Ontology
    prefix: PR
    synonyms:
    - PRO
  integbio:
    alt_name: Protein Ontology
    description: PRO provides an ontological representation of protein-related entities
      by unambiguously defining them and showing the relationships between them. Each
      PRO term describes a distinct class of entities (including specific modified
      forms, orthologous isoforms, and protein complexes) ranging from the taxon-neutral
      to the taxon-specific.
    homepage: https://proconsortium.org/pro.shtml
    information_keywords:
    - Ontology/Terminology/Nomenclature
    maintainer: University of Delaware||Georgetown University Medical Center
    name: PRO
    prefix: nbdc01630
    pubmeds:
    - '20935045'
    status: Active
    target_keywords:
    - Protein
  lov:
    description: A vocabulary for describing the ontology design pattern of property
      reification.
    homepage: http://purl.org/ontology/prv/core#
    keywords:
    - RDF
    modified: '2011-02-19'
    name: Property Reification Vocabulary
    prefix: pr
    uri_prefix: http://purl.org/ontology/prv/core#$1
  mappings:
    aberowl: PR
    agroportal: PR
    biocontext: PR
    bioportal: PR
    fairsharing: FAIRsharing.4ndncv
    go: PR
    integbio: nbdc01630
    lov: pr
    miriam: pr
    n2t: pr
    obofoundry: pr
    ols: pr
    ontobee: PR
    prefixcommons: pr
    uniprot: DB-0181
    wikidata: P4926
    wikidata.entity: Q55118584
  miriam:
    deprecated: false
    description: The PRotein Ontology (PRO) has been designed to describe the relationships
      of proteins and protein evolutionary classes, to delineate the multiple protein
      forms of a gene locus (ontology for protein forms), and to interconnect existing
      ontologies.
    homepage: http://bioportal.bioontology.org/ontologies/PR
    id: '00000141'
    name: Protein Ontology
    namespaceEmbeddedInLui: true
    pattern: ^PR:P?\d+$
    prefix: pr
    providers:
    - code: ''
      description: Protein Ontology at Georgetown
      homepage: https://proconsortium.org/
      name: Protein Ontology at Georgetown
      uri_format: https://proconsortium.org/cgi-bin/entry_pro?id=PR:$1
    sampleId: '000000024'
    uri_format: http://purl.bioontology.org/ontology/PR/PR:$1
  n2t:
    description: The PRotein Ontology (PRO) has been designed to describe the relationships
      of proteins and protein evolutionary classes, to delineate the multiple protein
      forms of a gene locus (ontology for protein forms), and to interconnect existing
      ontologies.
    example: '000000024'
    homepage: https://proconsortium.org/
    name: Protein Ontology at Georgetown
    namespaceEmbeddedInLui: true
    pattern: ^PR\:P?\d+$
    prefix: pr
    uri_format: https://proconsortium.org/app/entry/PR:$1
  name: Protein Ontology
  obofoundry:
    appears_in:
    - chiro
    - cl
    - pcl
    - uberon
    - scdo
    contact: dan5@georgetown.edu
    contact.github: nataled
    contact.label: Darren Natale
    contact.orcid: 0000-0001-5809-9523
    deprecated: false
    description: An ontological representation of protein-related entities
    domain: chemistry and biochemistry
    download.obo: http://purl.obolibrary.org/obo/pr.obo
    download.owl: http://purl.obolibrary.org/obo/pr.owl
    homepage: http://proconsortium.org
    license: CC BY 4.0
    license.url: http://creativecommons.org/licenses/by/4.0/
    logo: https://raw.githubusercontent.com/PROconsortium/logo/master/PROlogo_small.png
    name: PRotein Ontology (PRO)
    preferredPrefix: PR
    prefix: pr
    publications:
    - id: https://www.ncbi.nlm.nih.gov/pubmed/27899649
      title: 'Protein Ontology (PRO): enhancing and scaling up the representation
        of protein entities'
    repository: https://github.com/PROconsortium/PRoteinOntology
  ols:
    description: An ontological representation of protein-related entities
    download_owl: http://purl.obolibrary.org/obo/pr.owl
    homepage: http://proconsortium.org
    name: PRotein Ontology (PRO)
    prefix: pr
    tracker: https://github.com/PROconsortium/PRoteinOntology/issues
    version: '72.0'
    version.iri: http://purl.obolibrary.org/obo/pr/72.0/pr.owl
  ontobee:
    library: Foundry
    name: PRotein Ontology (PRO)
    prefix: PR
  pattern: ^(?:\d{9}|[OPQ][0-9][A-Z0-9]{3}[0-9](?:-\d+)?|[A-NR-Z][0-9](?:[A-Z][A-Z0-9]{2}[0-9]){1,2}(?:-\d+)?)$
  prefix: pr
  prefixcommons:
    alt_uri_formats:
    - http://purl.org/obo/owl/PR#$1
    bioportal: '1062'
    description: 'PRO provides an ontological representation of protein-related entities
      by explicitly defining them and showing the relationships between them. Each
      PRO term represents a distinct class of entities (including specific modified
      forms, orthologous isoforms, and protein complexes) ranging from the taxon-neutral
      to the taxon-specific. The ontology has a meta-structure encompassing three
      areas: proteins based on evolutionary relatedness (ProEvo); protein forms produced
      from a given gene locus (ProForm); and protein-containing complexes (ProComp).'
    example: PR:000000024
    homepage: http://pir.georgetown.edu/pro/
    keywords:
    - obo
    - protein
    name: PRotein Ontology (PRO)
    pattern: ^PR\:\d+$
    prefix: pr
    pubmed_ids:
    - '18047702'
    synonyms:
    - obo.pr
    - pro
    uri_format: http://pir.georgetown.edu/cgi-bin/pro/entry_pro?id=$1
  providers:
  - code: ontorat
    description: Misguided re-labeling of IRIs from ontorat tool
    example: null
    first_party: null
    homepage: http://purl.obolibrary.org/obo/vo/ontorat
    name: OntoRat
    publications: null
    status: null
    uri_format: http://purl.obolibrary.org/obo/vo/ontorat/PR_$1
  publications:
  - doi: 10.1093/nar/gkw1075
    pmc: PMC5210558
    pubmed: '27899649'
    title: 'Protein Ontology (PRO): enhancing and scaling up the representation of
      protein entities'
    year: 2016
  - doi: 10.1093/nar/gkt1173
    pmc: PMC3964965
    pubmed: '24270789'
    title: 'Protein Ontology: a controlled structured network of protein entities'
    year: 2013
  - doi: 10.1186/1471-2105-12-371
    pmc: PMC3189193
    pubmed: '21929785'
    title: The representation of protein complexes in the Protein Ontology (PRO)
    year: 2011
  - doi: 10.1093/nar/gkq907
    pmc: PMC3013777
    pubmed: '20935045'
    title: 'The Protein Ontology: a structured representation of protein forms and
      complexes'
    year: 2010
  - doi: 10.1186/1471-2105-8-s9-s1
    pmc: PMC2217659
    pubmed: '18047702'
    title: Framework for a protein ontology
    year: 2007
  - doi: null
    pmc: null
    pubmed: '27899649'
    title: 'Protein Ontology (PRO): enhancing and scaling up the representation of
      protein entities'
    year: null
  - doi: 10.1093/nar/gkt1173
    pmc: null
    pubmed: '24270789'
    title: 'Protein Ontology: a controlled structured network of protein entities'
    year: 2013
  - doi: 10.1093/nar/gkq907
    pmc: null
    pubmed: '20935045'
    title: 'The Protein Ontology: a structured representation of protein forms and
      complexes'
    year: 2010
  - doi: 10.1186/1471-2105-8-s9-s1
    pmc: null
    pubmed: '18047702'
    title: Framework for a protein ontology
    year: 2007
  - doi: 10.1186/1471-2105-12-371
    pmc: null
    pubmed: '21929785'
    title: The representation of protein complexes in the Protein Ontology (PRO)
    year: 2011
  - doi: 10.1093/nar/gkw1075
    pmc: null
    pubmed: '27899649'
    title: 'Protein Ontology (PRO): enhancing and scaling up the representation of
      protein entities'
    year: 2016
  - doi: null
    pmc: null
    pubmed: '18047702'
    title: null
    year: null
  - doi: 10.1093/nar/gkw1075
    pmc: null
    pubmed: '27899649'
    title: null
    year: null
  references:
  - https://github.com/biopragmatics/bioregistry/issues/959
  synonyms:
  - PR
  - PRO
  uniprot:
    abbreviation: PRO
    category: Miscellaneous databases
    homepage: https://proconsortium.org/
    name: Protein Ontology
    prefix: DB-0181
    publications:
    - doi: 10.1093/nar/gkw1075
      pubmed: '27899649'
    uri_format: https://proconsortium.org/cgi-bin/entry_pro?id=$1
  uri_format: http://purl.obolibrary.org/obo/PR_$1
  wikidata:
    description: Identifier for an entry in the PRotein Ontology (PRO)
    example:
    - PR:000013246
    - PR:000023661
    - PR:000049515
    homepage: https://pir.georgetown.edu/pro/pro.shtml
    name: PRotein Ontology ID
    pattern: ^PR:\d*$
    prefix: P4926
    uri_format: https://proconsortium.org/app/entry/$1/
prefixcommons:
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: A registry of life science prefxes
  example: ChEBI
  homepage: https://prefixcommons.org
  name: Prefix Commons
  prefix: prefixcommons
  uri_format: https://bioregistry.io/metaregistry/prefixcommons/$1
premis:
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: Ontology for PREMIS 3, the international standard for metadata to support
    the preservation of digital objects and ensure their long-term usability.
  example: Agent
  homepage: https://id.loc.gov/ontologies/premis-3-0-0.html
  lov:
    description: This ontology identifies the classes and properties used to describe
      preservation metadata in RDF.
    homepage: http://id.loc.gov/ontologies/premis.html
    keywords:
    - Catalogs
    modified: '2018-10-12'
    name: PREMIS Ontology
    prefix: premis
    uri_prefix: http://www.loc.gov/premis/rdf/v1#$1
  mappings:
    lov: premis
    tib: premis3
  name: PREMIS 3 Ontology
  prefix: premis
  rdf_uri_format: http://www.loc.gov/premis/rdf/v3/$1
  synonyms:
  - premis3
  tib:
    description: PREMIS is based on a data model that defines the entities that are
      described (Objects, Events, Agents and Rights), the properties of those entities
      (semantic units), and relationships between them.  The PREMIS OWL ontology provides
      an RDF encoding reflecting that model. This revised version replaces the earlier
      PREMIS OWL ontology, which was based on version 2.2. The PREMIS OWL Ontology
      Revision Working Group, appointed by the PREMIS Editorial Committee, worked
      on the ontology between early 2016 and September 2018. This revision is based
      on the PREMIS Data Dictionary, version 3.0 and has substantially remodeled the
      previous ontology, incorporating emerging Linked Data best practices and connections
      to other relevant RDF ontologies, e.g. PROV-O (Provenance ontology), Dublin
      Core metadata terms, and the preservation vocabularies at http://id.loc.gov/vocabulary/preservation,
      among others.
    download_owl: https://raw.githubusercontent.com/lcnetdev/PREMIS/master/premis3.owl
    homepage: https://www.loc.gov/standards/premis/ontology/owl-version3.html
    keywords:
    - NFDI4CULTURE
    name: PREMIS
    prefix: premis3
    uri_format: http://www.loc.gov/premis/rdf/v3/$1
    version.iri: https://id.loc.gov/ontologies/premis-3-0-0
  uri_format: http://www.loc.gov/premis/rdf/v3/$1
pride:
  aberowl:
    name: PRIDE Controlled Vocabulary
    prefix: PRIDE
  biocontext:
    prefix: PRIDE
  contact:
    email: yperez@ebi.ac.uk
    github: ypriverol
    name: Yasset Perez-Riverol
    orcid: 0000-0001-6579-6941
  example: '0000006'
  fairsharing:
    abbreviation: PRIDE
    description: 'The PRIDE PRoteomics IDEntifications (PRIDE) Archive database is
      a centralized, standards compliant, public data repository for mass spectrometry
      proteomics data, including protein and peptide identifications and the corresponding
      expression values, post-translational modifications and supporting mass spectra
      evidence (both as raw data and peak list files). PRIDE is a core member in the
      ProteomeXchange (PX) consortium, which provides a standardised way for submitting
      mass spectrometry based proteomics data to public-domain repositories. '
    homepage: http://www.ebi.ac.uk/pride/
    license: http://opendatacommons.org/licenses/pddl/1.0
    name: PRoteomics IDEntifications database
    prefix: FAIRsharing.e1byny
    publications:
    - doi: 10.1038/nbt.2839
      pubmed_id: 24727771
      title: ProteomeXchange provides globally coordinated proteomics data submission
        and dissemination.
    - doi: 10.1002/pmic.201400120
      pubmed_id: 25047258
      title: How to submit MS proteomics data to ProteomeXchange via the PRIDE database.
    - doi: 10.1002/pmic.200401303
      pubmed_id: 16041671
      title: 'PRIDE: the proteomics identifications database.'
    - doi: 10.1093/nar/gkv1145
      pubmed_id: 26527722
      title: 2016 update of the PRIDE database and its related tools.
    - doi: 10.1002/0471250953.bi1308s21
      pubmed_id: 18428683
      title: Using the Proteomics Identifications Database (PRIDE).
    - doi: 10.1093/nar/gkj138
      pubmed_id: 16381953
      title: 'PRIDE: a public repository of protein and peptide identifications for
        the proteomics community.'
    - doi: 10.1093/nar/gks1262
      pubmed_id: 23203882
      title: 'The PRoteomics IDEntifications (PRIDE) database and associated tools:
        status in 2013.'
    - doi: 10.1093/nar/gkm1021
      pubmed_id: 18033805
      title: 'PRIDE: new developments and new datasets.'
    - doi: 10.1093/nar/gky1106
      pubmed_id: 30395289
      title: 'The PRIDE database and related tools and resources in 2019: improving
        support for quantification data.'
    - doi: 10.1093/nar/gkab1038
      pubmed_id: null
      title: 'The PRIDE database resources in 2022: a hub for mass spectrometry-based
        proteomics evidences'
    subjects:
    - Proteomics
    twitter: pride_ebi
  integbio:
    alt_name: PSC-RIKEN Database of EST/Gene Expression
    description: "This database contains information on the way genes are expressed\
      \ in plants like Zinnia elegans and also its EST's. This information was collected\
      \ by applying a tool called Silicon genetics (genet).\nIt is planned to add\
      \ the same data for other organisms, for instance Arabidopsis, Lotus japonica\
      \ and BY-2 in the future. \nA Blast search option is provided."
    homepage: http://mrg.psc.riken.go.jp/PRIDE/index.html
    information_keywords:
    - Sequence
    - Expression
    maintainer: RIKEN Yokohama Institute
    name: PRIDE
    prefix: nbdc00630
    status: Inactive
    target_keywords:
    - cDNA/EST
  logo: https://www.proteomexchange.org/pride_logo.png
  mappings:
    aberowl: PRIDE
    biocontext: PRIDE
    fairsharing: FAIRsharing.e1byny
    integbio: nbdc00630
    miriam: pride
    n2t: pride
    ols: pride
    prefixcommons: pride
    re3data: r3d100010137
    uniprot: DB-0130
  miriam:
    deprecated: true
    description: The PRIDE PRoteomics IDEntifications database is a centralized, standards
      compliant, public data repository that provides protein and peptide identifications
      together with supporting evidence. This collection references experiments and
      assays.
    homepage: https://www.ebi.ac.uk/pride/
    id: '00000065'
    name: PRIDE
    namespaceEmbeddedInLui: false
    pattern: ^\d+$
    prefix: pride
    sampleId: '1'
    uri_format: https://www.ebi.ac.uk/pride/archive/assays/$1
  n2t:
    description: The PRIDE PRoteomics IDEntifications database is a centralized, standards
      compliant, public data repository that provides protein and peptide identifications
      together with supporting evidence. This collection references experiments and
      assays.
    example: '1'
    homepage: https://www.ebi.ac.uk/pride/
    name: PRIDE at EBI
    namespaceEmbeddedInLui: false
    pattern: ^\d+$
    prefix: pride
    uri_format: https://www.ebi.ac.uk/pride/archive/assays/$1
  ols:
    description: Proteomics Identification Database Ontology, terms describing proteomics
      data and experimental metadata
    download_owl: https://raw.githubusercontent.com/PRIDE-Utilities/pride-ontology/master/pride_cv.owl
    homepage: https://github.com/PRIDE-Utilities/pride-ontology
    name: Proteomics Identification Database Ontology
    prefix: pride
    uri_format: http://purl.obolibrary.org/obo/PRIDE_$1
    version: '2025-02-17'
    version.iri: http://purl.obolibrary.org/obo/pride/releases/2025-02-17/pride.owl
  part_of_database: pride
  pattern: ^\d{7}$
  prefix: pride
  prefixcommons:
    description: The PRIDE PRoteomics IDEntifications database is a centralized, standards
      compliant, public data repository that provides protein and peptide identifications
      together with supporting evidence.
    example: '1'
    homepage: http://www.ebi.ac.uk/pride/
    keywords:
    - protein
    license: http://www.ebi.ac.uk/Information/termsofuse.html
    name: PRoteomics IDEntifications database
    pattern: ^\d+$
    prefix: pride
    pubmed_ids:
    - '16381953'
    - '16041671'
    - '18033805'
    - '18428683'
    uri_format: http://www.ebi.ac.uk/pride/experimentLink.do?experimentAccessionNumber=$1
  publications:
  - doi: 10.1093/nar/gkab1038
    pmc: PMC8728295
    pubmed: '34723319'
    title: 'The PRIDE database resources in 2022: a hub for mass spectrometry-based
      proteomics evidences'
    year: 2022
  - doi: 10.1093/nar/gky1106
    pmc: PMC6323896
    pubmed: '30395289'
    title: 'The PRIDE database and related tools and resources in 2019: improving
      support for quantification data'
    year: 2019
  - doi: 10.1093/nar/gkv1145
    pmc: PMC4702828
    pubmed: '26527722'
    title: 2016 update of the PRIDE database and its related tools
    year: 2015
  - doi: 10.1002/pmic.201400120
    pmc: null
    pubmed: '25047258'
    title: How to submit MS proteomics data to ProteomeXchange via the PRIDE database
    year: 2014
  - doi: 10.1038/nbt.2839
    pmc: PMC3986813
    pubmed: '24727771'
    title: ProteomeXchange provides globally coordinated proteomics data submission
      and dissemination
    year: 2014
  - doi: 10.1093/nar/gks1262
    pmc: PMC3531176
    pubmed: '23203882'
    title: 'The PRoteomics IDEntifications (PRIDE) database and associated tools:
      status in 2013'
    year: 2012
  - doi: 10.1002/0471250953.bi1308s21
    pmc: null
    pubmed: '18428683'
    title: Using the Proteomics Identifications Database (PRIDE)
    year: 2008
  - doi: 10.1093/nar/gkm1021
    pmc: PMC2238846
    pubmed: '18033805'
    title: 'PRIDE: new developments and new datasets'
    year: 2007
  - doi: 10.1093/nar/gkj138
    pmc: PMC1347500
    pubmed: '16381953'
    title: 'PRIDE: a public repository of protein and peptide identifications for
      the proteomics community'
    year: 2006
  - doi: 10.1002/pmic.200401303
    pmc: null
    pubmed: '16041671'
    title: 'PRIDE: the proteomics identifications database'
    year: 2005
  re3data:
    description: The PRIDE PRoteomics IDEntifications database is a centralized, standards
      compliant, public data repository for proteomics data, including protein and
      peptide identifications, post-translational modifications and supporting spectral
      evidence. PRIDE encourages and welcomes direct user submissions of mass spectrometry
      data to be published in peer-reviewed publications.
    doi: 10.17616/R3JG6V
    homepage: https://www.ebi.ac.uk/pride/
    license: other
    name: PRoteomics IDEntifications Database
    prefix: r3d100010137
    synonyms:
    - PRIDE
    xrefs:
      nif: 0000-03336
      omics: '02456'
  repository: https://github.com/PRIDE-Utilities/pride-ontology
  uniprot:
    abbreviation: PRIDE
    category: Proteomic databases
    homepage: https://www.ebi.ac.uk/pride
    name: PRoteomics IDEntifications database
    prefix: DB-0130
    publications:
    - doi: 10.1093/nar/gky1106
      pubmed: '30395289'
    uri_format: https://www.ebi.ac.uk/pride/searchSummary.do?queryTypeSelected=identification%20accession%20number&identificationAccessionNumber=$1
  uri_format: http://purl.obolibrary.org/obo/PRIDE_$1
pride.project:
  biocontext:
    prefix: PRIDE.PROJECT
  cellosaurus:
    category: Proteomic databases
    homepage: https://www.ebi.ac.uk/pride/archive/
    name: PRoteomics IDEntifications archive
    prefix: PRIDE
    uri_format: https://www.ebi.ac.uk/pride/archive/projects/$1
  mappings:
    biocontext: PRIDE.PROJECT
    cellosaurus: PRIDE
    miriam: pride.project
    n2t: pride.project
  miriam:
    deprecated: false
    description: The PRIDE PRoteomics IDEntifications database is a centralized, standards
      compliant, public data repository that provides protein and peptide identifications
      together with supporting evidence. This collection references projects.
    homepage: https://www.ebi.ac.uk/pride/
    id: '00000515'
    name: PRIDE Project
    namespaceEmbeddedInLui: false
    pattern: ^P(X|R|A)D\d{6}$
    prefix: pride.project
    providers:
    - code: omicsdi
      description: PRIDE Project through OmicsDI
      homepage: https://www.omicsdi.org/
      name: PRIDE Project through OmicsDI
      uri_format: https://www.omicsdi.org/dataset/pride/$1
    sampleId: PXD000440
    uri_format: https://www.ebi.ac.uk/pride/archive/projects/$1
  n2t:
    description: The PRIDE PRoteomics IDEntifications database is a centralized, standards
      compliant, public data repository that provides protein and peptide identifications
      together with supporting evidence. This collection references projects.
    example: PXD000440
    homepage: https://www.ebi.ac.uk/pride/
    name: PRIDE Project at EBI
    namespaceEmbeddedInLui: false
    pattern: ^P(X|R)D\d{6}$
    prefix: pride.project
    uri_format: https://www.ebi.ac.uk/pride/archive/projects/$1
  part_of_database: pride
  prefix: pride.project
prints:
  biocontext:
    prefix: PRINTS
  contact:
    email: teresa.k.attwood@manchester.ac.uk
    github: null
    name: Teresa K. Attwood
    orcid: 0000-0003-2409-4235
  fairsharing:
    abbreviation: PRINTS
    description: PRINTS is a collection of groups of conserved protein motifs, called
      fingerprints, used to define a protein family. A fingerprint is a group of conserved
      motifs used to characterize a protein family. Usually, the motifs do not overlap,
      though they may be contiguous in 3D space. Fingerprints can encode protein folds
      and functionalities more flexibly than single motifs. Please note that the last
      release of this database on the PRINTS website was in 2007.
    homepage: http://www.bioinf.manchester.ac.uk/dbbrowser/PRINTS/PRINTS.html
    name: PRINTS
    prefix: FAIRsharing.h8r843
    publications:
    - doi: 10.1093/bioinformatics/15.10.799
      pubmed_id: 10705433
      title: 'FingerPRINTScan: intelligent searching of the PRINTS motif database.'
    - doi: 10.1093/nar/gkg030
      pubmed_id: 12520033
      title: PRINTS and its automatic supplement, prePRINTS.
    - doi: 10.1093/database/bas019
      pubmed_id: 22508994
      title: 'The PRINTS database: a fine-grained protein sequence annotation and
        analysis resource--its status in 2012.'
    subjects:
    - Structural Biology
    - Biology
  go:
    homepage: http://www.bioinf.manchester.ac.uk/dbbrowser/PRINTS/
    name: PRINTS compendium of protein fingerprints
    prefix: PRINTS
    uri_format: http://www.bioinf.manchester.ac.uk/cgi-bin/dbbrowser/sprint/searchprintss.cgi?display_opts=Prints&category=None&queryform=false&regexpr=off&prints_accn=$1
  integbio:
    description: 'PRINTS Version 42.0 is a collection of motifs called ''fingerprints'',
      because they are applied to define the character of protein families. To obtain
      these protein fingerprints the SWISS-PROT and TrEMBL databases were scanned
      repetitively. The motifs are usually located on the protein sequence as separate,
      but consecutive units with no overlaps. They are more effective in encoding
      protein folds and determining their function than are single motifs. The database
      contains 2,156 fingerprints and 12,444 single motifs.

      This repository can be search by means of entering an accession number, a PRINTS
      code, a database code, a sequence or by making use of the provided keyword search
      option. A Blast sequence search option as well as a BLOCKS search option is
      provided. This database was created on 2 February 2012.'
    fairsharing: biodbcore-000568
    homepage: http://www.bioinf.manchester.ac.uk/dbbrowser/PRINTS/index.php
    information_keywords:
    - Sequence
    maintainer: University of Manchester
    name: PRINTS
    prefix: nbdc00039
    pubmeds:
    - '7937065'
    - '7971946'
    - '2330366'
    status: Inactive
    target_keywords:
    - Protein
  mappings:
    biocontext: PRINTS
    fairsharing: FAIRsharing.h8r843
    go: PRINTS
    integbio: nbdc00039
    miriam: prints
    n2t: prints
    prefixcommons: sprint
    uniprot: DB-0082
  miriam:
    deprecated: true
    description: PRINTS is a compendium of protein fingerprints. A fingerprint is
      a group of conserved motifs used to characterise a protein family; its diagnostic
      power is refined by iterative scanning of a SWISS-PROT/TrEMBL composite. Usually
      the motifs do not overlap, but are separated along a sequence, though they may
      be contiguous in 3D-space. Fingerprints can encode protein folds and functionalities
      more flexibly and powerfully than can single motifs, full diagnostic potency
      deriving from the mutual context provided by motif neighbours.
    homepage: http://www.bioinf.manchester.ac.uk/dbbrowser/sprint/
    id: '00000061'
    name: PRINTS
    namespaceEmbeddedInLui: false
    pattern: ^PR\d{5}$
    prefix: prints
    sampleId: PR00001
    uri_format: http://www.bioinf.manchester.ac.uk/cgi-bin/dbbrowser/sprint/searchprintss.cgi?prints_accn=$1&display_opts=Prints&category=None&queryform=false&regexpr=off
  n2t:
    description: PRINTS is a compendium of protein fingerprints. A fingerprint is
      a group of conserved motifs used to characterise a protein family; its diagnostic
      power is refined by iterative scanning of a SWISS-PROT/TrEMBL composite. Usually
      the motifs do not overlap, but are separated along a sequence, though they may
      be contiguous in 3D-space. Fingerprints can encode protein folds and functionalities
      more flexibly and powerfully than can single motifs, full diagnostic potency
      deriving from the mutual context provided by motif neighbours.
    example: PR00001
    homepage: http://www.bioinf.manchester.ac.uk/dbbrowser/sprint/
    name: PRINTS through SPRINT
    namespaceEmbeddedInLui: false
    pattern: ^PR\d{5}$
    prefix: prints
    uri_format: http://www.bioinf.manchester.ac.uk/cgi-bin/dbbrowser/sprint/searchprintss.cgi?prints_accn=$1&display_opts=Prints&category=None&queryform=false&regexpr=off
  prefix: prints
  prefixcommons:
    description: SPRINT provides search access to the data bank of protein family
      fingerprints (PRINTS).
    example: PR00001
    homepage: http://www.bioinf.manchester.ac.uk/dbbrowser/sprint/
    keywords:
    - domain
    - protein
    name: SPRINT
    pattern: ^PR\d{5}$
    prefix: sprint
    pubmed_ids:
    - '10592232'
    uri_format: http://www.bioinf.manchester.ac.uk/cgi-bin/dbbrowser/sprint/searchprintss.cgi?prints_accn=$1&display_opts=Prints&category=None&queryform=false&regexpr=off
  providers:
  - code: prints.alt1
    description: Alternative access
    example: null
    first_party: null
    homepage: http://130.88.97.239/dbbrowser/sprint/
    name: PRINTS Alt. 1
    publications: null
    status: null
    uri_format: http://130.88.97.239/cgi-bin/dbbrowser/sprint/searchprintss.cgi?display_opts=Prints&category=None&queryform=false&regexpr=off&prints_accn=$1
  publications:
  - doi: 10.1093/database/bas019
    pmc: PMC3326521
    pubmed: '22508994'
    title: 'The PRINTS database: a fine-grained protein sequence annotation and analysis
      resource--its status in 2012'
    year: 2012
  - doi: 10.1093/nar/gkg030
    pmc: PMC165477
    pubmed: '12520033'
    title: PRINTS and its automatic supplement, prePRINTS
    year: 2003
  - doi: 10.1093/nar/28.1.225
    pmc: PMC102408
    pubmed: '10592232'
    title: 'PRINTS-S: the database formerly known as PRINTS'
    year: 2000
  - doi: 10.1093/bioinformatics/15.10.799
    pmc: null
    pubmed: '10705433'
    title: 'FingerPRINTScan: intelligent searching of the PRINTS motif database'
    year: 1999
  - doi: 10.1093/bioinformatics/15.10.799
    pmc: null
    pubmed: null
    title: 'FingerPRINTScan: intelligent searching of the PRINTS motif database.'
    year: null
  - doi: 10.1093/nar/gkg030
    pmc: null
    pubmed: null
    title: PRINTS and its automatic supplement, prePRINTS.
    year: null
  - doi: 10.1093/database/bas019
    pmc: null
    pubmed: null
    title: 'The PRINTS database: a fine-grained protein sequence annotation and analysis
      resource--its status in 2012.'
    year: null
  - doi: null
    pmc: null
    pubmed: '10592232'
    title: null
    year: null
  - doi: 10.1093/database/bas019
    pmc: null
    pubmed: '22508994'
    title: null
    year: null
  synonyms:
  - sprint
  uniprot:
    abbreviation: PRINTS
    category: Family and domain databases
    homepage: http://www.bioinf.manchester.ac.uk/dbbrowser/PRINTS/
    name: Protein Motif fingerprint database; a protein domain database
    prefix: DB-0082
    publications:
    - doi: 10.1093/database/bas019
      pubmed: '22508994'
    uri_format: https://www.ebi.ac.uk/interpro/entry/prints/$1
probesanddrugs:
  contact:
    email: ctibor.skuta@img.cas.cz
    github: null
    name: Ctibor Škuta
    orcid: 0000-0001-5325-4934
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: The Probes & Drugs portal (P&D) is a hub for the integration of high-quality
    bioactive compound sets enabling their analysis and comparison. Its main focus
    is on chemical probes and drugs but it also includes additional relevant sets
    from specialist databases/scientific publications, and vendor sets. Upon these,
    established bioactive chemistry sources (such as ChEMBL, BindingDB, Guide To Pharmacology,
    DrugCentral or DrugBank) are utilized for compounds' biological annotation.
  example: PD000596
  homepage: https://www.probes-drugs.org
  license: CC BY-SA 4.0
  mappings:
    wikidata: P11199
  name: Probes and Drugs
  pattern: ^PD\d{6}$
  prefix: probesanddrugs
  uri_format: https://www.probes-drugs.org/compound/$1
  wikidata:
    description: ID of a chemical compound in Probes And Drugs
    example:
    - PD000003
    - PD000100
    - PD000596
    homepage: https://www.probes-drugs.org
    name: Probes And Drugs ID
    pattern: ^PD\d{6}$
    prefix: P11199
    uri_format: https://www.probes-drugs.org/compound/$1
probonto:
  banana: PROB
  banana_peel: _
  biocontext:
    prefix: PROBONTO
  contact:
    email: pierre.grenon@ifomis.uni-saarland.de
    github: pgrenon
    name: Pierre Grenon
    orcid: 0000-0003-4614-562X
  example: c0000005
  example_extras:
  - k0001285
  fairsharing:
    abbreviation: ProbOnto
    description: ProbOnto, is an ontology-based knowledge base of probability distributions,
      featuring more than 150 uni- and multivariate distributions with their defining
      functions, characteristics, relationships and re-parameterization formulas.
      It can be used for model annotation and facilitates the encoding of distribution-based
      models, related functions and quantities. ProbOnto is both an ontology and a
      knowledge base, however its primary focus is the knowledge base.
    homepage: http://www.probonto.org
    license: CC-BY-4.0
    name: Ontology and Knowledge Base of Probability Distributions
    prefix: FAIRsharing.8zqzm9
    publications:
    - doi: 10.1093/bioinformatics/btw170
      pubmed_id: 27153608
      title: 'ProbOnto: ontology and knowledge base of probability distributions'
    repository: https://github.com/probonto/ontology/issues
    subjects:
    - Statistics
    - Mathematics
    - Computational Biology
    - Systems Biology
  mappings:
    biocontext: PROBONTO
    fairsharing: FAIRsharing.8zqzm9
    miriam: probonto
    n2t: probonto
    ols: probonto
  miriam:
    deprecated: false
    description: ProbOnto, is an ontology-based knowledge base of probability distributions,
      featuring uni- and multivariate distributions with their defining functions,
      characteristics, relationships and reparameterisation formulae.  It can be used
      for annotation of models, facilitating the encoding of distribution-based models,
      related functions and quantities.
    homepage: https://www.ebi.ac.uk/ols4/ontologies/probonto
    id: '00000575'
    name: ProbOnto
    namespaceEmbeddedInLui: false
    pattern: ^PROB_c\d+$
    prefix: probonto
    sampleId: PROB_c0000005
    uri_format: https://www.ebi.ac.uk/ols4/ontologies/probonto/terms/http%253A%252F%252Fwww.probonto.org%252Fontology%2523$1
  n2t:
    description: ProbOnto, is an ontology-based knowledge base of probability distributions,
      featuring uni- and multivariate distributions with their defining functions,
      characteristics, relationships and reparameterisation formulae.  It can be used
      for annotation of models, facilitating the encoding of distribution-based models,
      related functions and quantities.
    example: PROB_c0000005
    homepage: https://www.ebi.ac.uk/ols/ontologies/probonto
    name: ProbOnto through OLS
    namespaceEmbeddedInLui: false
    pattern: ^PROB_c\d+$
    prefix: probonto
    uri_format: https://www.ebi.ac.uk/ols/ontologies/probonto/terms?short_form=$1
  ols:
    contact: probonto.dev@gmail.com
    description: ProbOnto, is an ontology-based knowledge base of probability distributions,
      featuring more than eighty uni- and multivariate distributions with their defining
      functions, characteristics, relationships and reparameterisation formulas.
    homepage: http://probonto.org
    name: Probability Distribution Ontology
    prefix: probonto
    uri_format: http://www.probonto.org/core$1
    version: 2.5.0
  pattern: ^(c|k)\d{7}$
  prefix: probonto
  publications:
  - doi: 10.1093/bioinformatics/btw170
    pmc: PMC5013898
    pubmed: '27153608'
    title: 'ProbOnto: ontology and knowledge base of probability distributions'
    year: 2016
  - doi: 10.1093/bioinformatics/btw170
    pmc: null
    pubmed: null
    title: 'ProbOnto: ontology and knowledge base of probability distributions'
    year: null
  repository: https://github.com/probonto/ontology
  uri_format: http://www.probonto.org/ontology#PROB_$1
proco:
  aberowl:
    description: PROCO covers process chemistry, the chemical field concerned with
      scaling up laboratory syntheses to commercially viable processes.
    download_owl: http://aber-owl.net/media/ontologies/PROCO/1/proco.owl
    homepage: https://github.com/proco-ontology/PROCO
    name: Process Chemistry Ontology
    prefix: PROCO
  bioportal:
    contact:
      email: wes_schafer@merck.com
      name: Wes Schafer
    description: PROCO covers process chemistry, the chemical field concerned with
      scaling up laboratory syntheses to commercially viable processes.
    homepage: https://github.com/proco-ontology/PROCO
    name: Process Chemistry Ontology
    prefix: PROCO
    version: PROCO release 20220414
  example: '0000001'
  mappings:
    aberowl: PROCO
    bioportal: PROCO
    obofoundry: proco
    ols: proco
    ontobee: PROCO
    tib: proco
    wikidata.entity: Q113014436
  obofoundry:
    contact: wes_schafer@merck.com
    contact.github: schaferw
    contact.label: Wes Schafer
    contact.orcid: 0000-0002-8786-1756
    depends_on:
    - chebi
    - cheminf
    - obi
    - pato
    - ro
    - sbo
    deprecated: false
    description: PROCO covers process chemistry, the chemical field concerned with
      scaling up laboratory syntheses to commercially viable processes.
    domain: chemistry and biochemistry
    download.owl: http://purl.obolibrary.org/obo/proco.owl
    homepage: https://github.com/proco-ontology/PROCO
    license: CC BY 4.0
    license.url: https://creativecommons.org/licenses/by/4.0/
    name: Process Chemistry Ontology
    preferredPrefix: PROCO
    prefix: proco
    repository: https://github.com/proco-ontology/PROCO
  ols:
    description: PROCO (PROcess Chemistry Ontology) is a formal ontology that aims
      to standardly represent entities and relations among entities in the domain
      of process chemistry.
    download_owl: http://purl.obolibrary.org/obo/proco.owl
    homepage: https://github.com/proco-ontology/PROCO
    name: 'PROCO: PROcess Chemistry Ontology'
    prefix: proco
    tracker: https://github.com/proco-ontology/PROCO/issues
    version: '2022-04-11'
    version.iri: http://purl.obolibrary.org/obo/proco/releases/2022-04-11/proco.owl
  ontobee:
    library: Library
    name: Process Chemistry Ontology
    prefix: PROCO
  pattern: ^\d{7}$
  prefix: proco
  tib:
    description: PROCO (PROcess Chemistry Ontology) is a formal ontology that aims
      to standardly represent entities and relations among entities in the domain
      of process chemistry.
    download_owl: https://raw.githubusercontent.com/proco-ontology/PROCO/main/src/ontology/proco.owl
    homepage: https://github.com/proco-ontology/PROCO
    keywords:
    - NFDI4CHEM
    - chemistry
    - chemical and environmental engineering
    name: 'PROCO: PROcess Chemistry Ontology'
    prefix: proco
    tracker: https://github.com/proco-ontology/PROCO/issues
    version.iri: http://purl.obolibrary.org/obo/proco/releases/2022-04-11/proco.owl
  uri_format: http://purl.obolibrary.org/obo/PROCO_$1
prodom:
  biocontext:
    prefix: PRODOM
  contact:
    email: Daniel.Kahn@toulouse.inra.fr
    github: null
    name: Daniel Kahn
    orcid: 0000-0003-1644-0169
  fairsharing:
    abbreviation: ProDom
    description: ProDom is a comprehensive set of protein domain families automatically
      generated from the UniProt Knowledge Database.
    homepage: http://prodom.prabi.fr/
    name: ProDom
    prefix: FAIRsharing.a8z6gz
    publications:
    - doi: 10.1093/nar/gki034
      pubmed_id: 15608179
      title: 'The ProDom database of protein domain families: more emphasis on 3D'
    - doi: 10.1093/bib/3.3.246
      pubmed_id: 12230033
      title: 'ProDom: automated clustering of homologous domains.'
    subjects:
    - Life Science
  integbio:
    description: 'ProDom is an extensive database providing information on protein
      domain families.

      It was created automatically by performing a global comparison of all the protein
      sequences that could be found.

      The database can be searched by means of accession number, SWISS-PROT/TrEMBL
      identifier, or keywords.

      The site also provides access to related databases namely InterPro, PROSITE,
      PFAM and PDB.

      The ProDom domains may also be viewed on 3D structures created by the graphical
      interface.'
    fairsharing: biodbcore-000375
    homepage: http://prodom.prabi.fr/prodom/current/html/home.php
    information_keywords:
    - Classification
    maintainer: Rhone-Alpes Bioinformatics Center
    name: ProDom
    prefix: nbdc00174
    pubmeds:
    - '9009835'
    - '9399865'
    - '9847197'
    - '10592243'
    - '12230033'
    - '15608179'
    status: Inactive
    target_keywords:
    - Protein
  mappings:
    biocontext: PRODOM
    fairsharing: FAIRsharing.a8z6gz
    integbio: nbdc00174
    miriam: prodom
    n2t: prodom
    prefixcommons: prodom
  miriam:
    deprecated: true
    description: ProDom is a database of protein domain families generated from the
      global comparison of all available protein sequences.
    homepage: http://prodom.prabi.fr/prodom/current/html/home.php
    id: '00000117'
    name: ProDom
    namespaceEmbeddedInLui: false
    pattern: ^PD\d+$
    prefix: prodom
    sampleId: PD10000
    uri_format: http://prodom.prabi.fr/prodom/current/cgi-bin/request.pl?question=DBEN&query=$1
  n2t:
    description: ProDom is a database of protein domain families generated from the
      global comparison of all available protein sequences.
    example: PD10000
    homepage: http://prodom.prabi.fr/prodom/current/html/home.php
    name: ProDom Protein Domain Database
    namespaceEmbeddedInLui: false
    pattern: ^PD\d+$
    prefix: prodom
    uri_format: http://prodom.prabi.fr/prodom/current/cgi-bin/request.pl?question=DBEN&query=$1
  prefix: prodom
  prefixcommons:
    description: ProDom is a comprehensive set of protein domain families automatically
      generated from the UniProt Knowledge Database
    example: PD10000
    homepage: http://prodom.prabi.fr/
    keywords:
    - protein
    - classification
    name: ProDom; a protein domain database
    pattern: ^PD\d+$
    prefix: prodom
    pubmed_ids:
    - '15608179'
    uri_format: http://prodom.prabi.fr/prodom/current/cgi-bin/request.pl?question=DBEN&query=$1
  publications:
  - doi: 10.1093/nar/gki034
    pmc: PMC539988
    pubmed: '15608179'
    title: 'The ProDom database of protein domain families: more emphasis on 3D'
    year: 2005
  - doi: 10.1093/bib/3.3.246
    pmc: null
    pubmed: '12230033'
    title: 'ProDom: automated clustering of homologous domains'
    year: 2002
proglyc:
  biocontext:
    prefix: PROGLYC
  mappings:
    biocontext: PROGLYC
    miriam: proglyc
    n2t: proglyc
  miriam:
    deprecated: true
    description: ProGlycProt (Prokaryotic Glycoprotein) is a repository of bacterial
      and archaeal glycoproteins with at least one experimentally validated glycosite
      (glycosylated residue). Each entry in the database is fully cross-referenced
      and enriched with available published information about source organism, coding
      gene, protein, glycosites, glycosylation type, attached glycan, associated oligosaccharyl/glycosyl
      transferases (OSTs/GTs), supporting references, and applicable additional information.
    homepage: http://www.proglycprot.org/
    id: '00000354'
    name: ProGlycProt
    namespaceEmbeddedInLui: false
    pattern: ^[A-Z]C\d{1,3}$
    prefix: proglyc
    sampleId: AC119
    uri_format: http://www.proglycprot.org/detail.aspx?ProId=$1
  n2t:
    description: ProGlycProt (Prokaryotic Glycoprotein) is a repository of bacterial
      and archaeal glycoproteins with at least one experimentally validated glycosite
      (glycosylated residue). Each entry in the database is fully cross-referenced
      and enriched with available published information about source organism, coding
      gene, protein, glycosites, glycosylation type, attached glycan, associated oligosaccharyl/glycosyl
      transferases (OSTs/GTs), supporting references, and applicable additional information.
    example: AC119
    homepage: http://www.proglycprot.org/
    name: ProGlycProt at IMT
    namespaceEmbeddedInLui: false
    pattern: ^[A-Z]C\d{1,3}$
    prefix: proglyc
    uri_format: http://www.proglycprot.org/detail.aspx?ProId=$1
  prefix: proglyc
propreo:
  aberowl:
    description: A comprehensive proteomics data and process provenance ontology.
    download_owl: http://aber-owl.net/media/ontologies/PROPREO/2/propreo.owl
    homepage: http://knoesis.wright.edu/research/semsci/application_domain/sem_life_sci/glycomics/resources/ontologies/propreo/
    name: Proteomics Data and Process Provenance Ontology
    prefix: PROPREO
    version: '1.1'
  biocontext:
    prefix: PROPREO
  bioportal:
    contact:
      email: satyasahoo@ieee.org
      name: Satya S. Sahoo
    description: A comprehensive proteomics data and process provenance ontology.
    homepage: http://knoesis.wright.edu/research/semsci/application_domain/sem_life_sci/glycomics/resources/ontologies/propreo/
    name: Proteomics Data and Process Provenance Ontology
    prefix: PROPREO
    publications:
    - http://knoesis.wright.edu/research/semsci/application_domain/sem_life_sci/glycomics/resources/ontologies/propreo/
    version: '1.1'
  contact:
    email: satyasahoo@ieee.org
    github: null
    name: Satya S. Sahoo
    orcid: 0000-0001-9190-4256
  mappings:
    aberowl: PROPREO
    biocontext: PROPREO
    bioportal: PROPREO
    obofoundry: propreo
    prefixcommons: propreo
    wikidata.entity: Q114677909
  obofoundry:
    contact: satya30@uga.edu
    contact.label: Satya S. Sahoo
    deprecated: true
    domain: chemistry and biochemistry
    homepage: http://lsdis.cs.uga.edu/projects/glycomics/propreo/
    name: Proteomics data and process provenance
    prefix: propreo
  prefix: propreo
  prefixcommons:
    bioportal: '1039'
    description: A comprehensive proteomics data and process provenance ontology.
    example: protein
    homepage: http://knoesis.wright.edu/research/semsci/application_domain/sem_life_sci/glycomics/resources/ontologies/propreo/
    keywords:
    - owl
    - proteomics
    name: Proteomics data and process provenance
    pattern: ^\w+$
    prefix: propreo
    rdf_uri_format: http://lsdis.cs.uga.edu/projects/glycomics/propreo#$1
prosite:
  biocontext:
    prefix: PROSITE
  contact:
    email: Ioannis.Xenarios@unil.ch
    github: null
    name: Ioannis Xenarios
    orcid: 0000-0002-3413-6841
  fairsharing:
    abbreviation: PROSITE
    description: PROSITE is a database of protein families and domains. PROSITE consists
      of documentation entries describing protein domains, families and functional
      sites as well as associated patterns and profiles to identify them.
    homepage: https://prosite.expasy.org/
    name: PROSITE
    prefix: FAIRsharing.vwc6bd
    publications:
    - doi: 10.1093/nar/gkj063
      pubmed_id: 16381852
      title: The PROSITE database.
    - doi: 10.1093/bioinformatics/btt129
      pubmed_id: 23505298
      title: 'pfsearchV3: a code acceleration and heuristic to search PROSITE profiles.'
    - doi: 10.1093/nar/gks1067
      pubmed_id: 23161676
      title: New and continuing developments at PROSITE.
    subjects:
    - Biology
  go:
    homepage: https://prosite.expasy.org/
    name: Prosite database of protein families and domains
    prefix: Prosite
    uri_format: https://prosite.expasy.org/$1
  integbio:
    alt_name: Database of protein domains, families and functional sites
    description: 'ExPASy PROSITE is a database of protein domains, protein families
      and their functional sites.

      This repository also provides profiles and associated patterns, which can be
      used to identify the above.

      This version (20.91) was made available on 4 March 2013.

      It contains 1,661 documentation entries, 1,053 profiles and 1,308 patterns.

      The database can be searched by entering a document number, a ProRule description,
      a taxonomic series or by calling up a page, whereupon the proteins are listed
      according to the number of positive UniProtKB hits, from most to least.

      The option is also provided to have a sequence scanned against PROSITE patterns
      and profiles.

      In the Advanced search option that is available, additional criteria may be
      added when a scan request is entered to specify the results more accurately.'
    fairsharing: biodbcore-000527
    homepage: http://prosite.expasy.org/
    information_keywords:
    - Sequence
    - Classification
    maintainer: SIB (Swiss Institute of Bioinformatics)
    name: PROSITE
    prefix: nbdc00241
    pubmeds:
    - '12230035'
    - '19858104'
    - '12230035'
    - '16845026'
    - '16091411'
    status: Active
    target_keywords:
    - Protein
  mappings:
    biocontext: PROSITE
    fairsharing: FAIRsharing.vwc6bd
    go: Prosite
    integbio: nbdc00241
    miriam: prosite
    n2t: prosite
    prefixcommons: prosite
    togoid: Prosite
    uniprot: DB-0084
    wikidata: P4355
  miriam:
    deprecated: false
    description: PROSITE consists of documentation entries describing protein domains,
      families and functional sites as well as associated patterns and profiles to
      identify them.
    homepage: https://www.expasy.org/prosite/
    id: '00000032'
    name: PROSITE
    namespaceEmbeddedInLui: false
    pattern: ^PS\d{5}$
    prefix: prosite
    sampleId: PS00001
    uri_format: https://prosite.expasy.org/$1
  n2t:
    description: PROSITE consists of documentation entries describing protein domains,
      families and functional sites as well as associated patterns and profiles to
      identify them.
    example: PS00001
    homepage: https://www.expasy.org/prosite/
    name: ExPASy PROSITE
    namespaceEmbeddedInLui: false
    pattern: ^PS\d{5}$
    prefix: prosite
    uri_format: https://prosite.expasy.org/$1
  name: PROSITE
  prefix: prosite
  prefixcommons:
    description: PROSITE consists of documentation entries describing protein domains,
      families and functional sites as well as associated patterns and profiles to
      identify them
    example: PS00001
    homepage: http://www.expasy.org/prosite
    keywords:
    - protein
    - structure
    license: http://www.isb-sib.ch/disclaimer.html
    name: PROSITE; a protein domain and family database
    pattern: ^PS\d{5}$
    prefix: prosite
    pubmed_ids:
    - '16381852'
    synonyms:
    - prositedoc
    uri_format: http://www.expasy.org/cgi-bin/nicesite.pl?$1
  publications:
  - doi: 10.1093/bioinformatics/btt129
    pmc: PMC3634184
    pubmed: '23505298'
    title: 'pfsearchV3: a code acceleration and heuristic to search PROSITE profiles'
    year: 2013
  - doi: 10.1093/nar/gks1067
    pmc: PMC3531220
    pubmed: '23161676'
    title: New and continuing developments at PROSITE
    year: 2012
  - doi: 10.1093/nar/gkj063
    pmc: PMC1347426
    pubmed: '16381852'
    title: The PROSITE database
    year: 2006
  togoid:
    catalog: nbdc00241
    description: ExPASy PROSITE is a database of protein domains, protein families
      and their functional sites. This repository also provides profiles and associated
      patterns, which can be used to identify the above. This version (20.91) was
      made available on 4 March 2013. It contains 1,661 documentation entries, 1,053
      profiles and 1,308 patterns. The database can be searched by entering a document
      number, a ProRule description, a taxonomic series or by calling up a page, whereupon
      the proteins are listed according to the number of positive UniProtKB hits,
      from most to least. The option is also provided to have a sequence scanned against
      PROSITE patterns and profiles. In the Advanced search option that is available,
      additional criteria may be added when a scan request is entered to specify the
      results more accurately.
    examples:
    - PS01177
    - PS00516
    - PS01065
    - PS00418
    - PS01085
    - PS01086
    - PS01293
    - PS00355
    - PS01253
    - PS00992
    keywords:
    - Domain
    name: PROSITE
    pattern: ^(?PS\d{5})$
    prefix: Prosite
    uri_format: http://identifiers.org/prosite/$1
  uniprot:
    abbreviation: PROSITE
    category: Family and domain databases
    homepage: https://prosite.expasy.org/
    name: PROSITE; a protein domain and family database
    prefix: DB-0084
    publications:
    - doi: 10.1093/nar/gks1067
      pubmed: '23161676'
    uri_format: https://prosite.expasy.org/doc/$1
  wikidata:
    description: identifier for a protein family, domain or functional site, in the
      PROSITE database
    example:
    - PDOC00263
    - PDOC00550
    - PDOC51055
    name: PROSITE documentation ID
    pattern: ^PDOC\d{5}$
    prefix: P4355
    uri_format: https://prosite.expasy.org/$1
protclustdb:
  biocontext:
    prefix: PROTCLUSTDB
  contact:
    email: klimke@ncbi.nlm.nih.gov
    github: null
    name: William Klimke
    orcid: null
  fairsharing:
    abbreviation: ProtClustDB
    description: ProtClustDB is a collection of related protein sequences (clusters)
      consisting of Reference Sequence proteins encoded by complete genomes. This
      database contains both curated and non-curated clusters.
    homepage: https://www.ncbi.nlm.nih.gov/proteinclusters
    license: http://opendatacommons.org/licenses/pddl/1.0
    name: NCBI Protein Clusters Database
    prefix: FAIRsharing.da493y
    publications:
    - doi: 10.1093/nar/gkn734
      pubmed_id: 18940865
      title: The National Center for Biotechnology Information's Protein Clusters
        Database.
    subjects:
    - Genomics
    - Genetics
    - Life Science
  mappings:
    biocontext: PROTCLUSTDB
    fairsharing: FAIRsharing.da493y
    miriam: protclustdb
    n2t: protclustdb
    prefixcommons: protclustdb
  miriam:
    deprecated: false
    description: ProtClustDB is a collection of related protein sequences (clusters)
      consisting of Reference Sequence proteins encoded by complete genomes. This
      database contains both curated and non-curated clusters.
    homepage: https://www.ncbi.nlm.nih.gov/proteinclusters?db=proteinclusters
    id: '00000226'
    name: ProtClustDB
    namespaceEmbeddedInLui: false
    pattern: ^\w+$
    prefix: protclustdb
    sampleId: O80725
    uri_format: https://www.ncbi.nlm.nih.gov/sites/entrez?Db=proteinclusters&Cmd=DetailsSearch&Term=$1
  n2t:
    description: ProtClustDB is a collection of related protein sequences (clusters)
      consisting of Reference Sequence proteins encoded by complete genomes. This
      database contains both curated and non-curated clusters.
    example: O80725
    homepage: https://www.ncbi.nlm.nih.gov/proteinclusters?db=proteinclusters
    name: ProtClustDB at NCBI
    namespaceEmbeddedInLui: false
    pattern: ^\w+$
    prefix: protclustdb
    uri_format: https://www.ncbi.nlm.nih.gov/sites/entrez?Db=proteinclusters&Cmd=DetailsSearch&Term=$1
  prefix: protclustdb
  prefixcommons:
    description: ProtClustDB is a collection of related protein sequences (clusters)
      consisting of Reference Sequence proteins encoded by complete genomes. This
      database contains both curated and non-curated clusters.
    example: '2728498'
    homepage: http://www.ncbi.nlm.nih.gov/sites/entrez?db=proteinclusters
    keywords:
    - protein
    - structure
    name: ProtClustDB
    pattern: ^\d+$
    prefix: protclustdb
    pubmed_ids:
    - '18940865'
    synonyms:
    - protein_clusters
    uri_format: http://www.ncbi.nlm.nih.gov/sites/entrez?Db=proteinclusters&Cmd=ShowDetailView&TermToSearch=$1
  publications:
  - doi: 10.1093/nar/gkn734
    pmc: PMC2686591
    pubmed: '18940865'
    title: The National Center for Biotechnology Information's Protein Clusters Database
    year: 2008
protcom:
  comment: This resource doesn't exist on the web anymore
  deprecated: true
  mappings:
    pathguide: '242'
    prefixcommons: protcom
  pathguide:
    abbreviation: PROTCOM
    homepage: http://www.ces.clemson.edu/compbio/protcom
    name: Database of Protein Complexes
    prefix: '242'
  prefix: protcom
  prefixcommons:
    description: This database is a collection of protein-protein homo- and hetero-complexes
      as well as domain-domain structures. This issue of the database contains 17.024
      entries (as of October 2007) of which 1350 are two-chain protein hetero-complexes,
      7773 homodimers and 1589 are one-chain proteins parsed into two domains (domain
      structures).
    example: 12e8LH
    homepage: http://www.ces.clemson.edu/compbio/protcom
    keywords:
    - protein
    - structure
    name: Database of protein-protein complexes
    pattern: ^[A-Z,0-9]+$
    prefix: protcom
    uri_format: http://www.ces.clemson.edu/compbio/protcom/print_file.cgi?pdbid=$1
  reviewer:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
protege:
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: An ontology of metadata from protege
  download_rdf: https://protege.stanford.edu/plugins/owl/protege
  example: defaultLanguage
  github_request_issue: 1317
  homepage: http://protege.stanford.edu
  name: Protege Ontology
  prefix: protege
  uri_format: http://protege.stanford.edu/plugins/owl/protege#$1
proteomicsdb.peptide:
  biocontext:
    prefix: PROTEOMICSDB.PEPTIDE
  comment: The fact that this has .peptide as a subspace is a bit of a misnomer. Its
    original registration with MIRIAM uses a subview over the protein to point to
    peptides, but the identifiers in this semantic space seem to be about proteins.
  mappings:
    biocontext: PROTEOMICSDB.PEPTIDE
    miriam: proteomicsdb.peptide
    n2t: proteomicsdb.peptide
  miriam:
    deprecated: false
    description: ProteomicsDB is an effort dedicated to expedite the identification
      of the human proteome and its use across the scientific community. This human
      proteome data is assembled primarily using information from liquid chromatography
      tandem-mass-spectrometry (LC-MS/MS) experiments involving human tissues, cell
      lines and body fluids. Information is accessible for individual proteins, or
      on the basis of protein coverage on the encoding chromosome, and for peptide
      components of a protein. This collection provides access to the peptides identified
      for a given protein.
    homepage: https://www.proteomicsdb.org/#peptideSearch
    id: '00000525'
    name: ProteomicsDB Peptide
    namespaceEmbeddedInLui: false
    pattern: ^\d+$
    prefix: proteomicsdb.peptide
    sampleId: '53504'
    uri_format: https://www.proteomicsdb.org/#human/proteinDetails/$1/peptides/
  n2t:
    description: ProteomicsDB is an effort dedicated to expedite the identification
      of the human proteome and its use across the scientific community. This human
      proteome data is assembled primarily using information from liquid chromatography
      tandem-mass-spectrometry (LC-MS/MS) experiments involving human tissues, cell
      lines and body fluids. Information is accessible for individual proteins, or
      on the basis of protein coverage on the encoding chromosome, and for peptide
      components of a protein. This collection provides access to the peptides identified
      for a given protein.
    example: '53504'
    homepage: https://www.proteomicsdb.org/#peptideSearch
    name: Proteomics DB Peptide at Center for Integrated Protein Science
    namespaceEmbeddedInLui: false
    pattern: ^\d+$
    prefix: proteomicsdb.peptide
    uri_format: https://www.proteomicsdb.org/#human/proteinDetails/$1/peptides/
  prefix: proteomicsdb.peptide
  uri_format: https://www.proteomicsdb.org/#human/proteinDetails/$1
proteomicsdb.protein:
  biocontext:
    prefix: PROTEOMICSDB.PROTEIN
  mappings:
    biocontext: PROTEOMICSDB.PROTEIN
    miriam: proteomicsdb.protein
    n2t: proteomicsdb.protein
  miriam:
    deprecated: false
    description: ProteomicsDB is an effort dedicated to expedite the identification
      of the human proteome and its use across the scientific community. This human
      proteome data is assembled primarily using information  from liquid chromatography
      tandem-mass-spectrometry (LC-MS/MS) experiments involving human tissues, cell
      lines and body fluids. Information is accessible for individual proteins, or
      on the basis of protein coverage on the encoding chromosome, and for peptide
      components of a protein. This collection provides access to individual proteins.
    homepage: https://www.proteomicsdb.org/#human
    id: '00000524'
    name: ProteomicsDB Protein
    namespaceEmbeddedInLui: false
    pattern: ^\d+$
    prefix: proteomicsdb.protein
    sampleId: '53504'
    uri_format: https://www.proteomicsdb.org/#human/proteinDetails/$1/summary
  n2t:
    description: ProteomicsDB is an effort dedicated to expedite the identification
      of the human proteome and its use across the scientific community. This human
      proteome data is assembled primarily using information  from liquid chromatography
      tandem-mass-spectrometry (LC-MS/MS) experiments involving human tissues, cell
      lines and body fluids. Information is accessible for individual proteins, or
      on the basis of protein coverage on the encoding chromosome, and for peptide
      components of a protein. This collection provides access to individual proteins.
    example: '53504'
    homepage: https://www.proteomicsdb.org/#human
    name: Proteomics DB Protein at Center for Integrated Protein Science
    namespaceEmbeddedInLui: false
    pattern: ^\d+$
    prefix: proteomicsdb.protein
    uri_format: https://www.proteomicsdb.org/#human/proteinDetails/$1/summary
  prefix: proteomicsdb.protein
protonet.cluster:
  biocontext:
    prefix: PROTONET.CLUSTER
  contact:
    email: michall@cc.huji.ac.il
    github: LinialLab
    name: Michal Linial
    orcid: 0000-0002-9357-4526
  mappings:
    biocontext: PROTONET.CLUSTER
    miriam: protonet.cluster
    n2t: protonet.cluster
    prefixcommons: protonet.cluster
  miriam:
    deprecated: true
    description: ProtoNet provides automatic hierarchical classification of protein
      sequences in the UniProt database, partitioning the protein space into clusters
      of similar proteins. This collection references cluster information.
    homepage: http://www.protonet.cs.huji.ac.il/
    id: 00000229
    name: ProtoNet Cluster
    namespaceEmbeddedInLui: false
    pattern: ^\d+$
    prefix: protonet.cluster
    sampleId: '4349895'
    uri_format: http://www.protonet.cs.huji.ac.il/requested/cluster_card.php?cluster=$1
  n2t:
    description: ProtoNet provides automatic hierarchical classification of protein
      sequences in the UniProt database, partitioning the protein space into clusters
      of similar proteins. This collection references cluster information.
    example: '4349895'
    homepage: http://www.protonet.cs.huji.ac.il/
    name: ProtoNet at Hebrew University
    namespaceEmbeddedInLui: false
    pattern: ^\d+$
    prefix: protonet.cluster
    uri_format: http://www.protonet.cs.huji.ac.il/requested/cluster_card.php?cluster=$1
  prefix: protonet.cluster
  prefixcommons:
    description: ProtoNet provides automatic hierarchical classification of protein
      sequences in the UniProt database, partitioning the protein space into clusters
      of similar proteins. This collection references cluster information.
    example: '4349895'
    keywords:
    - classification
    - clustering
    - protein
    name: ProtoNet Cluster
    pattern: ^\d+$
    prefix: protonet.cluster
    pubmed_ids:
    - '16672244'
    uri_format: http://www.protonet.cs.huji.ac.il/requested/cluster_card.php?cluster=$1
  publications:
  - doi: 10.1110/ps.062185706
    pmc: PMC2242553
    pubmed: '16672244'
    title: 'Functional annotation prediction: all for one and one for all'
    year: 2006
protonet.proteincard:
  biocontext:
    prefix: PROTONET.PROTEINCARD
  contact:
    email: michall@cc.huji.ac.il
    github: LinialLab
    name: Michal Linial
    orcid: 0000-0002-9357-4526
  mappings:
    biocontext: PROTONET.PROTEINCARD
    miriam: protonet.proteincard
    n2t: protonet.proteincard
    prefixcommons: protonet.proteincard
  miriam:
    deprecated: true
    description: ProtoNet provides automatic hierarchical classification of protein
      sequences in the UniProt database, partitioning the protein space into clusters
      of similar proteins. This collection references protein information.
    homepage: http://www.protonet.cs.huji.ac.il/
    id: 00000228
    name: ProtoNet ProteinCard
    namespaceEmbeddedInLui: false
    pattern: ^\d+$
    prefix: protonet.proteincard
    sampleId: '16941567'
    uri_format: http://www.protonet.cs.huji.ac.il/requested/protein_card.php?protein_id=$1
  n2t:
    description: ProtoNet provides automatic hierarchical classification of protein
      sequences in the UniProt database, partitioning the protein space into clusters
      of similar proteins. This collection references protein information.
    example: '16941567'
    homepage: http://www.protonet.cs.huji.ac.il/
    name: ProtoNet at Hebrew University
    namespaceEmbeddedInLui: false
    pattern: ^\d+$
    prefix: protonet.proteincard
    uri_format: http://www.protonet.cs.huji.ac.il/requested/protein_card.php?protein_id=$1
  prefix: protonet.proteincard
  prefixcommons:
    description: ProtoNet provides automatic hierarchical classification of protein
      sequences in the UniProt database, partitioning the protein space into clusters
      of similar proteins. This collection references protein information.
    example: '16941567'
    keywords:
    - protein
    name: ProtoNet ProteinCard
    pattern: ^\d+$
    prefix: protonet.proteincard
    pubmed_ids:
    - '16672244'
    uri_format: http://www.protonet.cs.huji.ac.il/requested/protein_card.php?protein_id=$1
  publications:
  - doi: 10.1110/ps.062185706
    pmc: PMC2242553
    pubmed: '16672244'
    title: 'Functional annotation prediction: all for one and one for all'
    year: 2006
prov:
  aberowl:
    description: PROV is a superset of PROV (the Provenance Ontology). The relationship
      between these two ontologies is described at http://www.w3.org/ns/prov
    download_owl: http://aber-owl.net/media/ontologies/PROV/1/prov.owl
    homepage: http://www.w3.org/TR/prov-o/
    name: Superset of Provenance Ontology
    prefix: PROV
    version: Recommendation version 2013-04-30
  biocontext:
    prefix: prov
    uri_format: http://www.w3.org/ns/prov#$1
  biolink:
    is_identifiers: false
    is_obo: false
    prefix: prov
    uri_format: http://www.w3.org/ns/prov#$1
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: The namespace name http://www.w3.org/ns/prov# is intended for use with
    the PROV family of documents that support the interchange of provenance on the
    web.
  example: Activity
  homepage: https://www.w3.org/ns/prov
  lov:
    description: The namespace name http://www.w3.org/ns/prov# is intended for use
      with the PROV family of documents that support the interchange of provenance
      on the web.
    homepage: http://www.w3.org/TR/prov-o/
    keywords:
    - W3C Rec
    modified: '2015-01-11'
    name: W3C PROVenance Interchange
    prefix: prov
    uri_prefix: http://www.w3.org/ns/prov#$1
  mappings:
    aberowl: PROV
    biocontext: prov
    biolink: prov
    lov: prov
    ols: prov
    tib: prov
    zazuko: prov
  name: PROV Namespace
  ols:
    homepage: https://www.w3.org/TR/prov-o/
    name: Provenance Ontology (PROV-O)
    prefix: prov
    uri_format: http://www.bioassayontology.org/bao#$1
  preferred_prefix: prov
  prefix: prov
  tib:
    description: The PROV Ontology provides a set of classes, properties, and restrictions
      that can be used to represent and interchange provenance information generated
      in different systems and under different contexts. It can also be specialized
      to create new classes and properties to model provenance information for different
      applications and domains.
    download_owl: https://www.w3.org/ns/prov-o.owl
    homepage: https://www.w3.org/TR/prov-o/
    keywords:
    - NFDI4ING
    - NFDI4CHEM
    - ESS
    name: The PROV Ontology
    prefix: prov
    uri_format: http://www.w3.org/ns/prov#$1
    version.iri: http://www.w3.org/ns/prov-o-20130430
  uri_format: http://www.w3.org/ns/prov#$1
  zazuko:
    prefix: prov
    uri_format: http://www.w3.org/ns/prov#$1
pscdb:
  biocontext:
    prefix: PSCDB
  contact:
    email: mota@i.nagoya-u.ac.jp
    github: null
    name: Motonori Ota
    orcid: 0000-0001-9090-668X
  fairsharing:
    abbreviation: PSCDB
    description: The Protein Structural Change DataBase (PSCDB) presents the structural
      changes found in proteins, represented by pairs of ligand-free and ligand-bound
      structures of identical proteins, and links these changes to ligand-binding.
    homepage: http://idp1.force.cs.is.nagoya-u.ac.jp/pscdb/
    name: Protein Structure Change Database
    prefix: FAIRsharing.3d4jx0
    publications:
    - doi: 10.1016/j.jmb.2011.02.058
      pubmed_id: 21376729
      title: Classification and annotation of the relationship between protein structural
        change and ligand binding.
    - doi: 10.1093/nar/gkr966
      pubmed_id: 22080505
      title: 'PSCDB: a database for protein structural change upon ligand binding.'
    subjects:
    - Life Science
  integbio:
    alt_name: Protein Structural Change DataBase
    description: The PSCDB contains information on the relationship between protein
      structural changes and ligand binding. Structural changes are classified into
      seven distinct classes based on the location of the ligand binding site and
      the mechanism underlying the structural change.
    homepage: https://www.ideal-db.org/pscdb/
    information_keywords:
    - 3D structure
    - Interaction/Pathway
    maintainer: Nagoya University, Graduate School of Information Science
    name: PSCDB
    prefix: nbdc01636
    pubmeds:
    - '22080505'
    - '21376729'
    status: Active
    target_keywords:
    - Protein
  mappings:
    biocontext: PSCDB
    fairsharing: FAIRsharing.3d4jx0
    integbio: nbdc01636
    miriam: pscdb
    n2t: pscdb
  miriam:
    deprecated: false
    description: The PSCDB (Protein Structural Change DataBase) collects information
      on the relationship between protein structural change upon ligand binding. Each
      entry page provides detailed information about this structural motion.
    homepage: http://idp1.force.cs.is.nagoya-u.ac.jp/pscdb/index.html
    id: '00000370'
    name: PSCDB
    namespaceEmbeddedInLui: false
    pattern: ^\d+$
    prefix: pscdb
    sampleId: '051'
    uri_format: http://idp1.force.cs.is.nagoya-u.ac.jp/pscdb/$1.html
  n2t:
    description: The PSCDB (Protein Structural Change DataBase) collects information
      on the relationship between protein structural change upon ligand binding. Each
      entry page provides detailed information about this structural motion.
    example: '051'
    homepage: http://idp1.force.cs.is.nagoya-u.ac.jp/pscdb/index.html
    name: PSCDB at Nagoya University
    namespaceEmbeddedInLui: false
    pattern: ^\d+$
    prefix: pscdb
    uri_format: http://idp1.force.cs.is.nagoya-u.ac.jp/pscdb/$1.html
  name: Protein Structural Change Database
  prefix: pscdb
  publications:
  - doi: 10.1016/j.jmb.2011.02.058
    pmc: null
    pubmed: '21376729'
    title: Classification and annotation of the relationship between protein structural
      change and ligand binding
    year: 2011
  - doi: 10.1093/nar/gkr966
    pmc: PMC3245091
    pubmed: '22080505'
    title: 'PSCDB: a database for protein structural change upon ligand binding'
    year: 2011
  - doi: 10.1016/j.jmb.2011.02.058
    pmc: null
    pubmed: null
    title: Classification and annotation of the relationship between protein structural
      change and ligand binding.
    year: null
  - doi: 10.1093/nar/gkr966
    pmc: null
    pubmed: null
    title: 'PSCDB: a database for protein structural change upon ligand binding.'
    year: null
  - doi: 10.1016/j.jmb.2011.02.058
    pmc: null
    pubmed: null
    title: Classification and annotation of the relationship between protein structural
      change and ligand binding.
    year: null
  - doi: 10.1093/nar/gkr966
    pmc: null
    pubmed: null
    title: 'PSCDB: a database for protein structural change upon ligand binding.'
    year: null
psdo:
  aberowl:
    description: Ontology to reproducibly study visualizations of clinical performance
    download_owl: http://aber-owl.net/media/ontologies/PSDO/3/psdo.owl
    homepage: https://github.com/Display-Lab/psdo
    name: Performance Summary Display Ontology
    prefix: PSDO
  bioportal:
    contact:
      email: zachll@umich.edu
      name: Zach Landis-Lewis
    description: 'The Performance Summary Display Ontology (PSDO) is a lightweight
      application ontology used to reproducibly study visualizations of clinical performance
      and their associated outcomes in healthcare quality improvement settings. PSDO
      extends boundaries of visual representation artifacts by the IAO in the domain
      of distributed representations. PSDO describes dimensional representations of
      relational information displays that can be used to study the influence of feedback
      interventions on clinical practice., Performance Summary Display Ontology (PSDO)
      is an application ontology about motivating information in performance summaries
      and the visual and textual entities that are used to communicate about performance.
      Motivating information includes performance comparisons and changes that motivate
      improvement or sustainment, such as improvement towards a goal, loss of high
      performer status, or the presence of a performance gap. Visual and textual entities
      include charts, tables, and graphs that display performance information. PSDO''s
      domain focus is healthcare organizations that use clinical quality dashboards
      and feedback interventions for healthcare professionals and teams. Performance
      information is commonly about the quality of care and health outcomes that have
      been derived from clinical data using performance measures (aka metrics, process
      indicators, quality measures, etc). PSDO uses Basic Formal Ontology as its upper
      level ontology. This work is supported by the NIH, National Library of Medicine
      (1K01LM012528-01, 1R01LM013894-01).


      Landis-Lewis Z, Stansbury C, Rincón J, Gross C. Performance Summary Display
      Ontology: Feedback intervention content, delivery, and interpreted information.
      International Conference on Biomedical Ontology 2022 (ICBO 2022). https://icbo-conference.github.io/icbo2022/papers/ICBO-2022_paper_2172.pdf'
    homepage: https://github.com/Display-Lab/psdo
    license: CC-BY-4.0
    name: Performance Summary Display Ontology
    prefix: PSDO
    publications:
    - https://icbo-conference.github.io/icbo2022/papers/ICBO-2022_paper_2172.pdf
    - https://pubmed.ncbi.nlm.nih.gov/39949869/
    version: 1.0.1
  example: '0000055'
  mappings:
    aberowl: PSDO
    bioportal: PSDO
    obofoundry: psdo
    ols: psdo
    ontobee: PSDO
    wikidata.entity: Q81661788
  obofoundry:
    contact: zachll@umich.edu
    contact.github: zachll
    contact.label: Zach Landis-Lewis
    contact.orcid: 0000-0002-9117-9338
    depends_on:
    - bfo
    - iao
    - ro
    - stato
    deprecated: false
    description: Ontology to reproducibly study visualizations of clinical performance
    domain: information
    download.owl: http://purl.obolibrary.org/obo/psdo.owl
    homepage: https://github.com/Display-Lab/psdo
    license: CC BY 3.0
    license.url: http://creativecommons.org/licenses/by/3.0/
    name: Performance Summary Display Ontology
    preferredPrefix: PSDO
    prefix: psdo
    repository: https://github.com/Display-Lab/psdo
  ols:
    description: 'Performance Summary Display Ontology (PSDO) is an application ontology
      about motivating information in performance summaries and the visual and textual
      entities that are used to communicate about performance. Motivating information
      includes performance comparisons and changes that motivate improvement or sustainment,
      such as improvement towards a goal, loss of high performer status, or the presence
      of a performance gap. Visual and textual entities include charts, tables, and
      graphs that display performance information. PSDO''s domain focus is healthcare
      organizations that use clinical quality dashboards and feedback interventions
      for healthcare professionals and teams. Performance information is commonly
      about the quality of care and health outcomes that have been derived from clinical
      data using performance measures (aka metrics, process indicators, quality measures,
      etc). PSDO uses Basic Formal Ontology as its upper level ontology. This work
      is supported by the NIH, National Library of Medicine (1K01LM012528-01, 1R01LM013894-01).


      Landis-Lewis Z, Stansbury C, Rincón J, Gross C. Performance Summary Display
      Ontology: Feedback intervention content, delivery, and interpreted information.
      International Conference on Biomedical Ontology 2022 (ICBO 2022). https://icbo-conference.github.io/icbo2022/papers/ICBO-2022_paper_2172.pdf'
    download_owl: http://purl.obolibrary.org/obo/psdo.owl
    homepage: https://github.com/Display-Lab/psdo
    name: Performance Summary Display Ontology
    prefix: psdo
    tracker: https://github.com/Display-Lab/psdo/issues
    version: 1.0.1
    version.iri: http://purl.obolibrary.org/obo/2022-02-23/psdo.owl
  ontobee:
    library: Library
    name: Performance Summary Display Ontology
    prefix: PSDO
  pattern: ^\d{7}$
  prefix: psdo
  uri_format: http://purl.obolibrary.org/obo/PSDO_$1
pseudogene:
  bioportal:
    contact:
      email: yhl3@gersteinlab.org
      name: Gerstein Lab
    name: Pseudogene
    prefix: pseudo
    version: '0.1'
  contact:
    email: mark@gersteinlab.org
    github: null
    name: Mark Gerstein
    orcid: 0000-0002-9746-3719
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: This site contains a comprehensive database of identified pseudogenes,
    utilities used to find pseudogenes, various publication data sets and a pseudogene
    knowledgebase.
  example: PGOHUM00000289843
  homepage: http://www.pseudogene.org
  integbio:
    description: 'Pseudogene.org is a comprehensive database of identified pseudogenes,
      utilities used to find pseudogenes, various publication data sets and a pseudogene
      knowledgebase. It contains annotations, nucleotide sequences, amino acid sequence,
      individual sequence alignment about Eukaryote and Prokaryote pseudogenes and
      pseudomotifs.

      Pseudogenes are analyzed using sequence alignment programs (such as FASTA or
      BLAST) to detect matching regions in the nucleotide sequence.'
    homepage: http://www.pseudogene.org/
    information_keywords:
    - Sequence
    maintainer: Yale University
    name: Pseudogene.org
    prefix: nbdc00178
    pubmeds:
    - '17099229'
    status: Active
    target_keywords:
    - Genome/Gene
  mappings:
    bioportal: pseudo
    integbio: nbdc00178
    prefixcommons: pseudogene
    wikidata.entity: Q7254809
  name: PseudoGene
  prefix: pseudogene
  prefixcommons:
    description: Pseudogene is a comprehensive database of identified pseudogenes,
      utilities used to find pseudogenes, various publication data sets and a pseudogene
      knowledgebase.
    example: '4'
    homepage: http://www.pseudogene.org/
    keywords:
    - gene
    name: PseudoGene
    pattern: ^\d+$
    prefix: pseudogene
    uri_format: http://tables.pseudogene.org/[?species_name]/$1
  synonyms:
  - pseudogene.org
  wikidata:
    database: Q7254809
pseudomonas:
  biocontext:
    prefix: PSEUDOMONAS
  mappings:
    biocontext: PSEUDOMONAS
    miriam: pseudomonas
    n2t: pseudomonas
  miriam:
    deprecated: false
    description: The Pseudomonas Genome Database is a resource for peer-reviewed,
      continually updated annotation for all Pseudomonas species. It includes gene
      and protein sequence information, as well as regulation and predicted function
      and annotation.
    homepage: http://www.pseudomonas.com/
    id: 00000180
    name: Pseudomonas Genome Database
    namespaceEmbeddedInLui: false
    pattern: ^P\w+$
    prefix: pseudomonas
    sampleId: PSEEN0001
    uri_format: http://www.pseudomonas.com/feature/show/?locus_tag=$1
  n2t:
    description: The Pseudomonas Genome Database is a resource for peer-reviewed,
      continually updated annotation for all Pseudomonas species. It includes gene
      and protein sequence information, as well as regulation and predicted function
      and annotation.
    example: PSEEN0001
    homepage: http://www.pseudomonas.com/
    name: Pseudomonas Genome Database at Simon Fraser University
    namespaceEmbeddedInLui: false
    pattern: ^P\w+$
    prefix: pseudomonas
    uri_format: http://www.pseudomonas.com/feature/show/?locus_tag=$1
  prefix: pseudomonas
psipar:
  banana: PAR
  biocontext:
    prefix: PSIPAR
  comment: This resource is no longer loaded on XML and the sourceforge link from
    the HUPO website to the psi-par.obo artifact is dead.
  deprecated: true
  example: '0116'
  homepage: https://www.psidev.info/psi-par
  mappings:
    biocontext: PSIPAR
    miriam: psipar
    n2t: psipar
  miriam:
    deprecated: false
    description: Protein Affinity Reagents (PSI-PAR) provides a structured controlled
      vocabulary for the annotation of experiments concerned with interactions, and
      interactor production methods. PAR is developed by the HUPO Proteomics Standards
      Initiative and contains the majority of the terms from the PSI-MI controlled
      vocabular, as well as additional terms.
    homepage: https://www.ebi.ac.uk/ontology-lookup/browse.do?ontName=PAR
    id: '00000533'
    name: Protein Affinity Reagents
    namespaceEmbeddedInLui: false
    pattern: ^PAR:\d+$
    prefix: psipar
    sampleId: PAR:0116
    uri_format: https://www.ebi.ac.uk/ontology-lookup/?termId=$1
  n2t:
    description: Protein Affinity Reagents (PSI-PAR) provides a structured controlled
      vocabulary for the annotation of experiments concerned with interactions, and
      interactor production methods. PAR is developed by the HUPO Proteomics Standards
      Initiative and contains the majority of the terms from the PSI-MI controlled
      vocabular, as well as additional terms.
    example: PAR:0116
    homepage: https://www.ebi.ac.uk/ontology-lookup/browse.do?ontName=PAR
    name: Protein Affinity Reagents through OLS
    namespaceEmbeddedInLui: false
    pattern: ^PAR:\d+$
    prefix: psipar
    uri_format: https://www.ebi.ac.uk/ontology-lookup/?termId=$1
  pattern: ^\d+$
  prefix: psipar
  uri_format: https://www.ebi.ac.uk/ontology-lookup/?termId=PAR:$1
pso:
  aberowl:
    description: The Plant Stress Ontology describes biotic and abiotic stresses that
      a plant may encounter.
    download_owl: http://aber-owl.net/media/ontologies/PSO/5/pso.owl
    homepage: https://github.com/Planteome/plant-stress-ontology
    name: Plant Stress Ontology
    prefix: PSO
  agroportal:
    contact:
      email: cooperl@oregonstate.edu
      name: Laurel Cooper
    description: The Plant Stress Ontology (PSO) describes biotic and abiotic stresses
      that a plant may encounter. An ontology containing biotic and abiotic plant
      stresses. Part of the Planteome suite of reference ontologies., An ontology
      describing biotic and abiotic plant stresses.
    example_uri: http://purl.obolibrary.org/obo/PSO_0000013
    homepage: https://planteome.org/
    license: CC-BY-4.0
    name: Plant Stress Ontology
    prefix: PSO
    publications:
    - https://doi.org/10.1093/nar/gkx1152
    - https://planteome.org/references
    repository: https://github.com/Planteome/plant-stress-ontology
    version: '2025-12-16'
  bioportal:
    contact:
      email: schrader@th-brandenburg.de
      name: Thomas Schrader
    description: It is the ontology embedding PRIME (Prospective Risk Analysis in
      Medical Environments) in related issues of patient safety research and activities.
      It classifies terms and express relations between them. The ontology building
      in an ongoing process. Any comments are welcome.
    name: PatientSafetyOntology
    prefix: PSO
    version: '008:2017-08-04: Einarbeitung der Zustände'
  example: '0000013'
  fairsharing:
    abbreviation: PSO
    description: It is the ontology embedding PRIME (Prospective Risk Analysis in
      Medical Environments) in related issues of patient safety research and activities.
      It classifies terms and express relations between them. The ontology building
      in an ongoing process. Any comments are welcome.
    domains:
    - Monitoring
    - Hospital
    homepage: http://bioportal.bioontology.org/ontologies/PSO
    name: PatientSafetyOntology
    prefix: FAIRsharing.dyj433
    subjects:
    - Medical Informatics
    - Occupational Medicine
  mappings:
    aberowl: PSO
    agroportal: PSO
    bioportal: PSO
    fairsharing: FAIRsharing.dyj433
    obofoundry: pso
    ols: pso
    ontobee: PSO
    tib: pso
    wikidata.entity: Q113014437
  obofoundry:
    contact: cooperl@oregonstate.edu
    contact.github: cooperl09
    contact.label: Laurel Cooper
    contact.orcid: 0000-0002-6379-8932
    depends_on:
    - ro
    deprecated: false
    description: The Plant Stress Ontology describes biotic and abiotic stresses that
      a plant may encounter.
    domain: agriculture
    download.obo: http://purl.obolibrary.org/obo/pso.obo
    download.owl: http://purl.obolibrary.org/obo/pso.owl
    homepage: https://github.com/Planteome/plant-stress-ontology
    license: CC BY 3.0
    license.url: http://creativecommons.org/licenses/by/3.0/
    name: Plant Stress Ontology
    preferredPrefix: PSO
    prefix: pso
    publications:
    - id: https://www.ncbi.nlm.nih.gov/pubmed/29186578
      title: 'The Planteome database: an integrated resource for reference ontologies,
        plant genomics and phenomics.'
    repository: https://github.com/Planteome/plant-stress-ontology
  ols:
    description: The Plant Stress Ontology describes biotic and abiotic stresses that
      a plant may encounter.
    download_owl: http://purl.obolibrary.org/obo/pso.owl
    homepage: https://github.com/Planteome/plant-stress-ontology
    name: Plant Stress Ontology
    prefix: pso
    tracker: https://github.com/Planteome/plant-stress-ontology/issues
    version: '2025-12-16'
    version.iri: http://purl.obolibrary.org/obo/pso/releases/2025-12-16/pso.owl
  ontobee:
    library: Library
    name: Plant Stress Ontology
    prefix: PSO
  pattern: ^\d{7}$
  prefix: pso
  publications:
  - doi: 10.1093/nar/gkx1152
    pmc: PMC5753347
    pubmed: '29186578'
    title: 'The Planteome database: an integrated resource for reference ontologies,
      plant genomics and phenomics'
    year: 2018
  tib:
    description: The Plant Stress Ontology describes biotic and abiotic stresses that
      a plant may encounter.
    download_owl: http://purl.obolibrary.org/obo/pso.owl
    homepage: https://github.com/Planteome/plant-stress-ontology/
    keywords:
    - DataPLANT
    - life sciences, biology
    name: Plant Stress Ontology
    prefix: pso
    tracker: https://github.com/Planteome/plant-stress-ontology/issues/
    version.iri: http://purl.obolibrary.org/obo/pso/releases/2023-11-14/pso.owl
  uri_format: http://purl.obolibrary.org/obo/PSO_$1
pspub:
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: Documentation of the Phenoscape Curation Workflow
  homepage: https://wiki.phenoscape.org/wiki/Curation_workflow
  name: Phenoscape Publication
  prefix: pspub
psskb:
  contact:
    email: kaysheva1@gmail.com
    github: null
    name: Anna L. Kaysheva
    orcid: 0000-0003-4472-2016
  contributor:
    email: palayoor.n@northeastern.edu
    github: nalikapalayoor
    name: Nalika Palayoor
    orcid: 0009-0008-8406-631X
  description: PSSKB allows researchers to model post translational modifications
    and amino acid substitutions in proteins, providing 3D structural representations.
    Identifiers represent protein motifs on which PSSKB provides data.
  example: 2VM6_A55_A135
  github_request_issue: 1398
  homepage: https://psskb.org/
  name: Protein Structure and Stability Knowledge Base
  pattern: ^[A-Za-z0-9_]+$
  prefix: psskb
  publications:
  - doi: 10.1002/jcc.70046
    pmc: null
    pubmed: '39876062'
    title: 'PSSKB: A Web Application to Study Protein Structures'
    year: 2025
  reviewer:
    email: b.gyori@northeastern.edu
    github: bgyori
    name: Benjamin M. Gyori
    orcid: 0000-0001-9439-5346
  uri_format: https://psskb.org/motif/card/$1
pto:
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: Identifiers for product types (product, price, and company data) based
    on Wikipedia
  example: Atlas
  homepage: http://www.productontology.org/
  license: CC-BY-SA-3.0
  name: Product Types Ontology
  prefix: pto
  uri_format: http://www.productontology.org/id/$1
ptr:
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: This specification contains a framework for representing pointers -
    entities that permit identifying a portion or segment of a piece of content -
    making use of the Resource Description Framework (RDF). It also describes a number
    of specific types of pointers that permit portions of a document to be referred
    to in different ways. When referring to a specific part of, say, a piece of web
    content, it is useful to be able to have a consistent manner by which to refer
    to a particular segment of a web document, to have a variety of ways by which
    to refer to that same segment, and to make the reference robust in the face of
    changes to that document. This specification is part of the Evaluation And Report
    Language (EARL) but can be reused in other contexts too. [from homepage]
  download_rdf: https://www.w3.org/2009/pointers
  example: Pointer
  homepage: https://www.w3.org/TR/Pointers-in-RDF/
  name: Pointer Methods in RDF
  prefix: ptr
  rdf_uri_format: https://www.w3.org/2009/pointers#$1
  references:
  - https://www.w3.org/blog/2009/pointer-methods-in-rdf-first-draft/
  uri_format: https://www.w3.org/2009/pointers#$1
  version: '2009'
pubchem.bioassay:
  biocontext:
    prefix: PUBCHEM.BIOASSAY
  contact:
    email: pruitt@ncbi.nlm.nih.gov
    github: null
    name: Kim Dixon Pruitt
    orcid: 0000-0001-7950-1374
  edam:
    description: Identifier of an assay from the PubChem database.
    name: PubChem bioassay
    obsolete: false
    prefix: '2638'
  go:
    homepage: https://pubchem.ncbi.nlm.nih.gov
    name: NCBI PubChem database of bioassay records
    prefix: PubChem_BioAssay
    uri_format: https://pubchem.ncbi.nlm.nih.gov/bioassay/$1
  integbio:
    description: PubChem BioAssay is a database of the biological activity characteristics
      of various PubChem substances. The database contains readouts and descriptions
      of experiments analyzing a number of compounds. Users can submit results and
      download via FTP.
    homepage: http://www.ncbi.nlm.nih.gov/pcassay
    information_keywords:
    - Method
    - Image/Movie
    - Bibliography/Documents
    - Repository
    maintainer: NCBI (National Center for Biotechnology Information)
    name: PubChem BioAssay
    prefix: nbdc00640
    pubmeds:
    - '22140110'
    status: Active
    target_keywords:
    - Metabolite
    - Chemical compound
  logo: https://pubchem.ncbi.nlm.nih.gov/pcfe/logo/PubChem_logo_splash.png
  mappings:
    biocontext: PUBCHEM.BIOASSAY
    edam: '2638'
    go: PubChem_BioAssay
    integbio: nbdc00640
    miriam: pubchem.bioassay
    n2t: pubchem.bioassay
    prefixcommons: pubchem.bioassay
  miriam:
    deprecated: false
    description: PubChem provides information on the biological activities of small
      molecules. It is a component of NIH's Molecular Libraries Roadmap Initiative.
      PubChem bioassay archives active compounds and bioassay results.
    homepage: https://www.ncbi.nlm.nih.gov/sites/entrez?db=pcassay
    id: '00000072'
    name: PubChem-bioassay
    namespaceEmbeddedInLui: false
    pattern: ^\d+$
    prefix: pubchem.bioassay
    sampleId: '1018'
    uri_format: https://pubchem.ncbi.nlm.nih.gov/bioassay/$1
  n2t:
    description: PubChem provides information on the biological activities of small
      molecules. It is a component of NIH's Molecular Libraries Roadmap Initiative.
      PubChem bioassay archives active compounds and bioassay results.
    example: '1018'
    homepage: 'https://www.ncbi.nlm.nih.gov/sites/entrez?db=pcassay '
    name: PubChem Bioassay at NCBI
    namespaceEmbeddedInLui: false
    pattern: ^\d+$
    prefix: pubchem.bioassay
    uri_format: https://pubchem.ncbi.nlm.nih.gov/assay/assay.cgi?aid=$1
  part_of_database: pubchem
  prefix: pubchem.bioassay
  prefixcommons:
    description: PubChem provides information on the biological activities of small
      molecules. It is a component of NIH's Molecular Libraries Roadmap Initiative.
      PubChem bioassay archives active compounds and bioassay results.
    example: '1018'
    homepage: http://www.ncbi.nlm.nih.gov/sites/entrez?db=pcassay
    keywords:
    - small molecule
    license: http://www.nlm.nih.gov/copyright.html
    name: 'Pubchem: Bioassays'
    pattern: ^\d+$
    prefix: pubchem.bioassay
    pubmed_ids:
    - '17170002'
    uri_format: http://pubchem.ncbi.nlm.nih.gov/assay/assay.cgi?aid=$1
  publications:
  - doi: 10.1093/nar/gkl1031
    pmc: PMC1781113
    pubmed: '17170002'
    title: Database resources of the National Center for Biotechnology Information
    year: 2006
  - doi: null
    pmc: null
    pubmed: '17170002'
    title: null
    year: null
  - doi: null
    pmc: null
    pubmed: '17170002'
    title: null
    year: null
  synonyms:
  - pubchem.aid
  - pubchem.assay
  twitter: pubchem
pubchem.cell:
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: Cell Lines in PubChem
  example: '31'
  homepage: https://pubchem.ncbi.nlm.nih.gov
  keywords:
  - bioactivities
  - cell lines
  - chemistry
  logo: https://pubchem.ncbi.nlm.nih.gov/pcfe/logo/PubChem_logo_splash.png
  name: PubChem Cell Line
  part_of_database: pubchem
  pattern: ^\d+$
  prefix: pubchem.cell
  twitter: pubchem
  uri_format: https://pubchem.ncbi.nlm.nih.gov/cell/$1
pubchem.classification:
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: The PubChem Classification Browser allows you to browse the distribution
    of PubChem data among nodes in the hierarchy of interest, thereby providing an
    aggregate view of PubChem data. It also allows you to search for PubChem records
    annotated with the desired hierarchy/term, providing a powerful way to quickly
    find the subset of PubChem records.
  example: '87'
  homepage: https://pubchem.ncbi.nlm.nih.gov/classification/
  keywords:
  - chemistry
  logo: https://pubchem.ncbi.nlm.nih.gov/pcfe/logo/PubChem_logo_splash.png
  name: PubChem Classification
  part_of_database: pubchem
  pattern: ^\d+$
  prefix: pubchem.classification
  twitter: pubchem
  uri_format: https://pubchem.ncbi.nlm.nih.gov/classification/#hid=$1
pubchem.compound:
  biocontext:
    prefix: PUBCHEM.COMPOUND
  biolink:
    is_identifiers: false
    is_obo: false
    prefix: CID
    uri_format: http://pubchem.ncbi.nlm.nih.gov/compound/$1
  cellosaurus:
    category: Chemistry resources
    homepage: https://pubchem.ncbi.nlm.nih.gov
    name: PubChem compound database
    prefix: PubChem
    uri_format: https://pubchem.ncbi.nlm.nih.gov/compound/$1
  cheminf:
    description: []
    name: PubChem compound identifier (CID)
    obsolete: false
    prefix: '000140'
  contact:
    email: bolton@ncbi.nlm.nih.gov
    github: null
    name: Evan E Bolton
    orcid: 0000-0002-5959-6190
  domain: chemical
  edam:
    description: Identifier of an entry from the PubChem database.
    name: PubChem
    obsolete: false
    prefix: '2639'
  fairsharing:
    abbreviation: PubChem
    description: 'PubChem is the world''s largest collection of freely accessible
      chemical information. Searches can be performed via a number of descriptors
      such as name, molecular formula and structure. Information is provided for chemical
      and physical properties, biological activities, safety and toxicity information,
      patents, literature citations and more. PubChem is organized as three linked
      databases within the NCBI''s Entrez information retrieval system. These are
      PubChem Substance, PubChem Compound, and PubChem BioAssay. PubChem also provides
      a fast chemical structure similarity search tool. '
    homepage: https://pubchem.ncbi.nlm.nih.gov/
    license: http://opendatacommons.org/licenses/pddl/1.0
    name: PubChem
    prefix: FAIRsharing.qt3w7z
    publications:
    - doi: 10.1016/j.drudis.2010.10.003
      pubmed_id: 20970519
      title: PubChem as a public resource for drug discovery.
    - doi: 10.1093/nar/gkp456
      pubmed_id: 19498078
      title: 'PubChem: a public information system for analyzing bioactivities of
        small molecules.'
    - doi: 10.1093/nar/gkl1031
      pubmed_id: 17170002
      title: Database resources of the National Center for Biotechnology Information.
    - doi: 10.1093/nar/gky1033
      pubmed_id: 30371825
      title: 'PubChem 2019 update: improved access to chemical data.'
    - doi: 10.1093/nar/gkw1118
      pubmed_id: 27899599
      title: 'PubChem BioAssay: 2017 update.'
    - doi: 10.1093/nar/gkt978
      pubmed_id: 24198245
      title: 'PubChem BioAssay: 2014 update.'
    - doi: 10.1093/nar/gkr1132
      pubmed_id: 22140110
      title: PubChem's BioAssay Database.
    - doi: 10.1093/nar/gkaa971
      pubmed_id: null
      title: 'PubChem in 2021: new data content and improved web interfaces'
    subjects:
    - Chemistry
    - Virology
    - Epidemiology
  go:
    homepage: https://pubchem.ncbi.nlm.nih.gov
    name: NCBI PubChem database of chemical structures
    prefix: PubChem_Compound
    uri_format: https://pubchem.ncbi.nlm.nih.gov/compound/$1
  integbio:
    description: PubChem is the world's largest collection of freely accessible chemical
      information. Searches can be performed via a number of descriptors such as name,
      molecular formula and structure. Information is provided for chemical and physical
      properties, biological activities, safety and toxicity information, patents,
      literature citations and more. PubChem is organized as three linked databases
      within the NCBI's Entrez information retrieval system. These are PubChem Substance,
      PubChem Compound, and PubChem BioAssay. PubChem also provides a fast chemical
      structure similarity search tool.
    fairsharing: FAIRsharing.qt3w7z
    homepage: https://pubchem.ncbi.nlm.nih.gov/
    information_keywords:
    - Method
    - Chemical structure
    - Bibliography/Documents
    - Repository
    maintainer: NCBI (National Center for Biotechnology Information)
    name: PubChem
    prefix: nbdc02626
    pubmeds:
    - '33151290'
    status: Active
    target_keywords:
    - Protein
    - Metabolite
    - Chemical compound
  logo: https://pubchem.ncbi.nlm.nih.gov/pcfe/logo/PubChem_logo_splash.png
  mappings:
    biocontext: PUBCHEM.COMPOUND
    biolink: CID
    cellosaurus: PubChem
    cheminf: '000140'
    edam: '2639'
    fairsharing: FAIRsharing.qt3w7z
    go: PubChem_Compound
    integbio: nbdc02626
    miriam: pubchem.compound
    n2t: pubchem.compound
    pathguide: '361'
    prefixcommons: pubchem.compound
    re3data: r3d100010129
    togoid: PubchemCompound
    wikidata: P662
  miriam:
    deprecated: false
    description: PubChem provides information on the biological activities of small
      molecules. It is a component of NIH's Molecular Libraries Roadmap Initiative.
      PubChem Compound archives chemical structures and records.
    homepage: https://pubchem.ncbi.nlm.nih.gov/
    id: '00000034'
    name: PubChem-compound
    namespaceEmbeddedInLui: false
    pattern: ^\d+$
    prefix: pubchem.compound
    providers:
    - code: scholia
      description: Scholia is a service that creates visual scholarly profiles for
        topic, people, organizations, species, chemicals, etc using bibliographic
        and other information in Wikidata.
      homepage: https://scholia.toolforge.org/
      name: Scholia
      uri_format: https://scholia.toolforge.org/pubchem/$1
    sampleId: '100101'
    uri_format: https://pubchem.ncbi.nlm.nih.gov/compound/$1
  n2t:
    description: PubChem provides information on the biological activities of small
      molecules. It is a component of NIH's Molecular Libraries Roadmap Initiative.
      PubChem Compound archives chemical structures and records.
    example: '100101'
    homepage: https://pubchem.ncbi.nlm.nih.gov/
    name: NCBI PubChem Compound
    namespaceEmbeddedInLui: false
    pattern: ^\d+$
    prefix: pubchem.compound
    uri_format: https://pubchem.ncbi.nlm.nih.gov/summary/summary.cgi?cid=$1
  name: PubChem compound
  part_of_database: pubchem
  pathguide:
    abbreviation: CID
    homepage: http://cisban-silico.cs.ncl.ac.uk/cid.html
    name: CISBAN Cross-Species Interactome Database
    prefix: '361'
  prefix: pubchem.compound
  prefixcommons:
    alt_uri_formats:
    - http://rdf.ncbi.nlm.nih.gov/pubchem/compound/$1
    description: PubChem provides information on the biological activities of small
      molecules. It is a component of NIH's Molecular Libraries Roadmap Initiative.
      PubChem Compound archives chemical structures and records.
    example: '100101'
    keywords:
    - chemical
    - metabolite
    - structure
    name: 'Pubchem: Compounds'
    pattern: ^\d+$
    prefix: pubchem.compound
    synonyms:
    - pubchemcompound
    uri_format: http://pubchem.ncbi.nlm.nih.gov/summary/summary.cgi?db=pccompound&term=$1
  publications:
  - doi: 10.1093/nar/gkaa971
    pmc: PMC7778930
    pubmed: '33151290'
    title: 'PubChem in 2021: new data content and improved web interfaces'
    year: 2021
  - doi: 10.1093/nar/gky1033
    pmc: PMC6324075
    pubmed: '30371825'
    title: 'PubChem 2019 update: improved access to chemical data'
    year: 2019
  - doi: 10.1093/nar/gkw1118
    pmc: PMC5210581
    pubmed: '27899599'
    title: 'PubChem BioAssay: 2017 update'
    year: 2016
  - doi: 10.1093/nar/gkt978
    pmc: PMC3965008
    pubmed: '24198245'
    title: 'PubChem BioAssay: 2014 update'
    year: 2013
  - doi: 10.1093/nar/gkr1132
    pmc: PMC3245056
    pubmed: '22140110'
    title: PubChem's BioAssay Database
    year: 2011
  - doi: 10.1016/j.drudis.2010.10.003
    pmc: PMC3010383
    pubmed: '20970519'
    title: PubChem as a public resource for drug discovery
    year: 2010
  - doi: 10.1093/nar/gkp456
    pmc: PMC2703903
    pubmed: '19498078'
    title: 'PubChem: a public information system for analyzing bioactivities of small
      molecules'
    year: 2009
  - doi: 10.1093/nar/gkl1031
    pmc: PMC1781113
    pubmed: '17170002'
    title: Database resources of the National Center for Biotechnology Information
    year: 2006
  - doi: 10.1016/j.drudis.2010.10.003
    pmc: null
    pubmed: null
    title: PubChem as a public resource for drug discovery.
    year: null
  - doi: 10.1093/nar/gkp456
    pmc: null
    pubmed: null
    title: 'PubChem: a public information system for analyzing bioactivities of small
      molecules.'
    year: null
  - doi: 10.1093/nar/gkl1031
    pmc: null
    pubmed: null
    title: Database resources of the National Center for Biotechnology Information.
    year: null
  - doi: 10.1093/nar/gky1033
    pmc: null
    pubmed: null
    title: 'PubChem 2019 update: improved access to chemical data.'
    year: null
  - doi: 10.1093/nar/gkw1118
    pmc: null
    pubmed: null
    title: 'PubChem BioAssay: 2017 update.'
    year: null
  - doi: 10.1093/nar/gkt978
    pmc: null
    pubmed: null
    title: 'PubChem BioAssay: 2014 update.'
    year: null
  - doi: 10.1093/nar/gkr1132
    pmc: null
    pubmed: null
    title: PubChem's BioAssay Database.
    year: null
  - doi: 10.1093/nar/gkaa971
    pmc: null
    pubmed: null
    title: 'PubChem in 2021: new data content and improved web interfaces'
    year: null
  - doi: 10.1016/j.drudis.2010.10.003
    pmc: null
    pubmed: null
    title: PubChem as a public resource for drug discovery.
    year: null
  - doi: 10.1093/nar/gkp456
    pmc: null
    pubmed: null
    title: 'PubChem: a public information system for analyzing bioactivities of small
      molecules.'
    year: null
  - doi: 10.1093/nar/gkl1031
    pmc: null
    pubmed: null
    title: Database resources of the National Center for Biotechnology Information.
    year: null
  - doi: 10.1093/nar/gky1033
    pmc: null
    pubmed: null
    title: 'PubChem 2019 update: improved access to chemical data.'
    year: null
  - doi: 10.1093/nar/gkw1118
    pmc: null
    pubmed: null
    title: 'PubChem BioAssay: 2017 update.'
    year: null
  - doi: 10.1093/nar/gkt978
    pmc: null
    pubmed: null
    title: 'PubChem BioAssay: 2014 update.'
    year: null
  - doi: 10.1093/nar/gkr1132
    pmc: null
    pubmed: null
    title: PubChem's BioAssay Database.
    year: null
  - doi: 10.1093/nar/gkaa971
    pmc: null
    pubmed: null
    title: 'PubChem in 2021: new data content and improved web interfaces'
    year: null
  re3data:
    description: 'Pubchem contains 3 databases. 1. PubChem BioAssay: The PubChem BioAssay
      Database contains bioactivity screens of chemical substances described in PubChem
      Substance. It provides searchable descriptions of each bioassay, including descriptions
      of the conditions and readouts specific to that screening procedure. 2. PubChem
      Compound: The PubChem Compound Database contains validated chemical depiction
      information provided to describe substances in PubChem Substance. Structures
      stored within PubChem Compounds are pre-clustered and cross-referenced by identity
      and similarity groups. 3. PubChem Substance. The PubChem Substance Database
      contains descriptions of samples, from a variety of sources, and links to biological
      screening results that are available in PubChem BioAssay. If the chemical contents
      of a sample are known, the description includes links to PubChem Compound.'
    doi: 10.17616/R3KG65
    homepage: https://pubchem.ncbi.nlm.nih.gov/
    name: PubChem
    prefix: r3d100010129
    xrefs:
      omics: '02734'
  synonyms:
  - CID
  - DSSTox_CID
  - PUBCHEM_CID
  - PubChem_Compound_CID
  - Pubchem
  - pubchem_id
  togoid:
    catalog: nbdc00641
    description: PubChem Compound is a database of chemical structrues of validated
      small molecules. The dataase contains entries for PubChem entities which are
      grouped by structural identity and similarity. Users can submit compounds and
      download via FTP.
    examples:
    - '9548669'
    - '160419'
    - '9869929'
    - '76333303'
    - '9868491'
    - '27854'
    - '76329169'
    - '3448'
    - '296'
    - '10371227'
    keywords:
    - Compound
    name: PubChem compound
    pattern: ^(?:CID)?(?\d+)$
    prefix: PubchemCompound
    uri_format: http://rdf.ncbi.nlm.nih.gov/pubchem/compound/CID$1
  twitter: pubchem
  wikidata:
    description: identifier from database of chemical molecules and their activities
      in biological assays (Compound ID number)
    example:
    - '11125'
    - '5284603'
    - '5426'
    homepage: http://pubchem.ncbi.nlm.nih.gov
    miriam: pubchem.compound
    name: PubChem CID
    pattern: ^[1-9]\d{0,8}$
    prefix: P662
    uri_format: https://pubchem.ncbi.nlm.nih.gov/compound/$1
    uri_format_rdf: http://rdf.ncbi.nlm.nih.gov/pubchem/compound/CID$1
pubchem.element:
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: PubChem Element gives information on chemical elements like Hydrogen,
    with the local identifier corresponding to the atomic number.
  example: '1'
  homepage: https://pubchem.ncbi.nlm.nih.gov/periodic-table
  keywords:
  - chemistry
  logo: https://pubchem.ncbi.nlm.nih.gov/pcfe/logo/PubChem_logo_splash.png
  name: PubChem Element
  part_of_database: pubchem
  pattern: ^\d+$
  prefix: pubchem.element
  twitter: pubchem
  uri_format: https://pubchem.ncbi.nlm.nih.gov/element/$1
pubchem.substance:
  biocontext:
    prefix: PUBCHEM.SUBSTANCE
  cheminf:
    description: []
    name: PubChem substance identifier (SID)
    obsolete: false
    prefix: '000141'
  go:
    homepage: https://pubchem.ncbi.nlm.nih.gov
    name: NCBI PubChem database of chemical substances
    prefix: PubChem_Substance
    uri_format: https://pubchem.ncbi.nlm.nih.gov/substance/$1
  integbio:
    description: PubChem Substance is a database of samples of chemical entities which
      links to the biological activity of those samples in PubChem BioAssay. The database
      contains structural information on substances with links to further information
      in cases where the substance has been more fully characterized. It consists
      of records of chemical entities deposited by various contributors, so a chemical
      entity may be described different records with different data in this database.
    homepage: http://www.ncbi.nlm.nih.gov/pcsubstance
    information_keywords:
    - Bibliography/Documents
    - Chemical structure
    - Repository
    maintainer: NCBI (National Center for Biotechnology Information)
    name: PubChem Substance
    prefix: nbdc00642
    pubmeds:
    - '22140110'
    status: Active
    target_keywords:
    - Chemical compound
    - Drug
    - Metabolite
  logo: https://pubchem.ncbi.nlm.nih.gov/pcfe/logo/PubChem_logo_splash.png
  mappings:
    biocontext: PUBCHEM.SUBSTANCE
    cheminf: '000141'
    go: PubChem_Substance
    integbio: nbdc00642
    miriam: pubchem.substance
    n2t: pubchem.substance
    prefixcommons: pubchem.substance
    togoid: PubchemSubstance
    wikidata: P2153
  miriam:
    deprecated: false
    description: PubChem provides information on the biological activities of small
      molecules. It is a component of NIH's Molecular Libraries Roadmap Initiative.
      PubChem Substance archives chemical substance records.
    homepage: https://pubchem.ncbi.nlm.nih.gov/
    id: '00000033'
    name: PubChem-substance
    namespaceEmbeddedInLui: false
    pattern: ^\d+$
    prefix: pubchem.substance
    sampleId: '100101'
    uri_format: https://pubchem.ncbi.nlm.nih.gov/substance/$1
  n2t:
    description: PubChem provides information on the biological activities of small
      molecules. It is a component of NIH's Molecular Libraries Roadmap Initiative.
      PubChem Substance archives chemical substance records.
    example: '100101'
    homepage: https://pubchem.ncbi.nlm.nih.gov/
    name: NCBI PubChem Substance
    namespaceEmbeddedInLui: false
    pattern: ^\d+$
    prefix: pubchem.substance
    uri_format: https://pubchem.ncbi.nlm.nih.gov/summary/summary.cgi?sid=$1
  part_of_database: pubchem
  prefix: pubchem.substance
  prefixcommons:
    alt_uri_formats:
    - http://rdf.ncbi.nlm.nih.gov/pubchem/substance/$1
    description: PubChem provides information on the biological activities of small
      molecules. It is a component of NIH's Molecular Libraries Roadmap Initiative.
      PubChem Substance archives chemical substance records.
    example: '100101'
    keywords:
    - small molecule
    - protein
    - structure
    name: 'Pubchem: Substances'
    pattern: ^\d+$
    prefix: pubchem.substance
    pubmed_ids:
    - '17170002'
    synonyms:
    - pubchemsubstance
    uri_format: http://www.ncbi.nlm.nih.gov/sites/entrez?cmd=search&db=pcsubstance&term=$1
  publications:
  - doi: 10.1093/nar/gkl1031
    pmc: PMC1781113
    pubmed: '17170002'
    title: Database resources of the National Center for Biotechnology Information
    year: 2006
  synonyms:
  - DSSTox_Generic_SID
  togoid:
    catalog: nbdc00642
    description: PubChem Substance is a database of samples of chemical entities which
      links to the biological activity of those samples in PubChem BioAssay. The database
      contains structural information on substances with links to further information
      in cases where the substance has been more fully characterized. It consists
      of records of chemical entities deposited by various contributors, so a chemical
      entity may be described different records with different data in this database.
    examples:
    - '15229855'
    - '15277848'
    - '15782795'
    - '16076657'
    - '16035895'
    - '12012900'
    - '15378994'
    - '14850434'
    - '14847540'
    - '15271473'
    keywords:
    - Compound
    name: PubChem substance
    pattern: ^(?:SID)?(?\d+)$
    prefix: PubchemSubstance
    uri_format: http://rdf.ncbi.nlm.nih.gov/pubchem/substance/SID$1
  twitter: pubchem
  wikidata:
    description: substance (e.g. mixtures, undefined stereochemistry, ...) identifier
      in the PubChem database
    example:
    - '135307179'
    - '7069'
    - '830551'
    homepage: https://www.ncbi.nlm.nih.gov/pcsubstance
    miriam: pubchem.substance
    name: PubChem Substance ID (SID)
    pattern: ^[1-9]\d*$
    prefix: P2153
    uri_format: https://pubchem.ncbi.nlm.nih.gov/substance/$1
    uri_format_rdf: http://rdf.ncbi.nlm.nih.gov/pubchem/substance/SID$1
publons.publication:
  homepage: https://publons.com
  mappings:
    wikidata: P3431
  name: Publons publication
  prefix: publons.publication
  wikidata:
    description: identifier for the defunct/merged Publons website; URL redirects
      to Web of Science's P8372 (WOSID)
    example:
    - '18466622'
    - '4917112'
    - '507568'
    name: Publons publication ID
    prefix: P3431
    uri_format: https://publons.com/publon/$1
publons.researcher:
  biolink:
    is_identifiers: false
    is_obo: false
    prefix: ResearchID
    uri_format: https://publons.com/researcher/$1
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: Database of researchers to track publications, citation metrics, peer
    reviews, and journal editing work.
  example: '1981638'
  homepage: https://publons.com/researcher
  mappings:
    biolink: ResearchID
    wikidata: P3829
  name: Publons Researcher
  pattern: ^\d+$
  prefix: publons.researcher
  uri_format: https://publons.com/researcher/$1
  wikidata:
    description: identifier of an author or reviewer, in Publons that redirects, along
      with P1053, to an ID in Clarivate's Web of Science
    example:
    - '2388520'
    - '2544783'
    - '654601'
    name: Publons author ID
    pattern: ^\d+$
    prefix: P3829
    uri_format: https://publons.com/researcher/$1/
pubmed:
  biocontext:
    prefix: PUBMED
  cellosaurus:
    category: Reference resources
    homepage: https://www.ncbi.nlm.nih.gov/pubmed
    name: PubMed
    prefix: PubMed
    uri_format: https://www.ncbi.nlm.nih.gov/pubmed/$1
  cheminf:
    description: []
    name: PubChem Identifier
    obsolete: false
    prefix: '000302'
  contact:
    email: beck@ncbi.nlm.nih.gov
    github: jeffbeckncbi
    name: Jeff Beck
    orcid: 0000-0002-1798-9797
  edam:
    description: PubMed unique identifier of an article.
    name: PubMed
    obsolete: false
    prefix: '1187'
  fairsharing:
    abbreviation: PMID
    description: 'The PubMed Unique Identifier (PMID) is a 1- to 8-digit accession
      number with no leading zeros for managing and disseminating records at the PubMed
      repository. PubMed is a citation and abstract database for biomedical literature,
      life science journals, and online books. Citations may include links to full-text
      content from PubMed Central and publisher websites. The PMID is a unique reference
      number for PubMed citations and is a distinctly different number from the PMCID
      and is used only for PubMed records. PMIDs are not reused after records are
      deleted. Prior to the 2004 version of PubMed (available December 3, 2003), many
      records contained a MEDLINE Unique Identifier in addition to the PMID. NLM no
      longer displays the MEDLINE Unique Identifier. The PMID has become the unique
      identifier for the MEDLINE record. Each citation record in PubMed is assigned
      a unique identification number. A PMID is not the same as a PMCID and cannot
      be used to demonstrate compliance with the NIH or another participating funder''s
      public access policy. '
    homepage: https://www.nihms.nih.gov/help/glossary/#pmid
    name: PubMed Unique Identifier
    prefix: FAIRsharing.2b9b61
    subjects:
    - Biomedical Science
  go:
    homepage: https://pubmed.ncbi.nlm.nih.gov/
    name: PubMed
    prefix: PMID
    synonyms:
    - PUBMED
    uri_format: https://pubmed.ncbi.nlm.nih.gov/$1
  integbio:
    description: This database contains bibliographic information from journal articles
      in the field of life science as well as MEDLINE (title, authors, journal name,
      abstracts). Links are provided for articles with free access to the full article.
    fairsharing: biodbcore-000456
    homepage: http://www.ncbi.nlm.nih.gov/pubmed
    information_keywords:
    - Bibliography/Documents
    maintainer: NCBI (National Center for Biotechnology Information)
    name: PubMed
    prefix: nbdc00179
    status: Active
  mappings:
    biocontext: PUBMED
    cellosaurus: PubMed
    cheminf: '000302'
    edam: '1187'
    fairsharing: FAIRsharing.2b9b61
    go: PMID
    integbio: nbdc00179
    miriam: pubmed
    n2t: pubmed
    prefixcommons: pubmed
    togoid: Pubmed
    wikidata: P698
    wikidata.entity: Q2082879
  miriam:
    deprecated: false
    description: PubMed is a service of the U.S. National Library of Medicine that
      includes citations from MEDLINE and other life science journals for biomedical
      articles back to the 1950s.
    homepage: https://www.ncbi.nlm.nih.gov/PubMed/
    id: '00000015'
    name: PubMed
    namespaceEmbeddedInLui: false
    pattern: ^\d+$
    prefix: pubmed
    providers:
    - code: epmc
      description: Europe PMC
      homepage: http://europepmc.org/
      name: Europe PMC
      uri_format: http://europepmc.org/abstract/MED/$1
    - code: hubmed
      description: HubMed
      homepage: http://www.hubmed.org/
      name: HubMed
      uri_format: https://www.hubmed.org/?term=$1
    - code: scholia
      description: Scholia is a service that creates visual scholarly profiles for
        topic, people, organizations, species, chemicals, etc using bibliographic
        and other information in Wikidata.
      homepage: https://scholia.toolforge.org/
      name: Scholia
      uri_format: https://scholia.toolforge.org/pubmed/$1
    sampleId: '16333295'
    uri_format: https://pubmed.ncbi.nlm.nih.gov/$1/
  n2t:
    description: PubMed is a service of the U.S. National Library of Medicine that
      includes citations from MEDLINE and other life science journals for biomedical
      articles back to the 1950s.
    example: '16333295'
    homepage: https://www.ncbi.nlm.nih.gov/PubMed/
    name: NCBI PubMed
    namespaceEmbeddedInLui: false
    pattern: ^\d+$
    prefix: pubmed
    uri_format: https://www.ncbi.nlm.nih.gov/pubmed/$1
  name: PubMed
  prefix: pubmed
  prefixcommons:
    alt_uri_formats:
    - http://europepmc.org/abstract/MED/#$1
    - http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-view+MedlineFull+[medline-PMID:#]$1
    - http://www.hubmed.org/display.cgi?uids=#$1
    description: PubMed is a service of the U.S. National Library of Medicine that
      includes citations from MEDLINE and other life science journals for biomedical
      articles back to the 1950s.
    example: '23735196'
    homepage: http://www.ncbi.nlm.nih.gov/pubmed/
    keywords:
    - bibliography
    name: PubMed
    pattern: ^\d+$
    prefix: pubmed
    pubmed_ids:
    - '16381840'
    synonyms:
    - pmid
    - medline
    uri_format: http://www.ncbi.nlm.nih.gov/pubmed/$1
  providers:
  - code: uniprot.citation
    description: UniProt mints PURLs for citations identifiers
    example: null
    first_party: null
    homepage: https://uniprot.org/
    name: UniProt
    publications: null
    status: null
    uri_format: http://purl.uniprot.org/citations/$1
  - code: uniprot.pubmed
    description: UniProt mints PURLs for PubMed identifiers
    example: null
    first_party: null
    homepage: https://uniprot.org/
    name: UniProt
    publications: null
    status: null
    uri_format: http://purl.uniprot.org/pubmed/$1
  - code: pubmed.new
    description: New-style link for pubmed
    example: null
    first_party: null
    homepage: https://pubmed.ncbi.nlm.nih.gov
    name: PubMed (new)
    publications: null
    status: null
    uri_format: https://pubmed.ncbi.nlm.nih.gov/$1
  publications:
  - doi: 10.1093/nar/gkj158
    pmc: PMC1347520
    pubmed: '16381840'
    title: Database resources of the National Center for Biotechnology Information
    year: 2006
  synonyms:
  - MEDLINE
  - PMID
  - PubMed
  - PubMed ID
  - pmid
  togoid:
    catalog: nbdc00179
    description: This database contains bibliographic information from journal articles
      in the field of life science as well as MEDLINE (title, authors, journal name,
      abstracts). Links are provided for articles with free access to the full article.
    examples:
    - '19281226'
    - '19879151'
    - '20858243'
    - '10773016'
    - '16527252'
    - '28499733'
    - '10397770'
    - '15149666'
    - '23861362'
    - '10577920'
    keywords:
    - Literature
    name: PubMed
    pattern: ^(?:pmid:|PMID:)?(?\d+)$
    prefix: Pubmed
    uri_format: http://rdf.ncbi.nlm.nih.gov/pubmed/$1
  wikidata:
    database: Q2082879
    description: identifier for journal articles/abstracts in PubMed
    example:
    - '17246615'
    - '32768924'
    - '4388'
    - '823'
    homepage: https://pubmed.ncbi.nlm.nih.gov
    name: PubMed publication ID
    pattern: ^([1-4]\d{7}|[1-9]\d{0,6})$
    prefix: P698
    uri_format: https://pubmed.ncbi.nlm.nih.gov/$1
    uri_format_rdf: http://rdf.ncbi.nlm.nih.gov/pubchem/reference/$1
puro:
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: An ontology for the characterisation of the roles of agents – people,
    corporate bodies and computational agents in the publication process. These agents
    can be, e.g. authors, editors, reviewers, publishers or librarians.
  example: RoleInTime
  fairsharing:
    abbreviation: PRO
    contact:
      email: silvio.peroni@unibo.it
      name: Silvio Peroni
      orcid: 0000-0003-0530-4305
    description: The Publishing Roles Ontology (PRO) is an ontology for the characterisation
      of the roles of agents – people, corporate bodies and computational agents in
      the publication process. These agents can be, e.g. authors, editors, reviewers,
      publishers or librarians.
    homepage: http://www.sparontologies.net/ontologies/pro
    license: CC-BY-4.0
    name: Publishing Roles Ontology
    prefix: FAIRsharing.3e88d6
    publications:
    - doi: 10.1145/2362499.2362502
      title: 'Scholarly publishing and Linked Data: describing roles, statuses, temporal
        and contextual extents'
      year: 2012
    repository: https://github.com/sparontologies/pro
    subjects:
    - Subject Agnostic
    twitter: sparontologies
  homepage: http://www.sparontologies.net/ontologies/pro
  mappings:
    fairsharing: FAIRsharing.3e88d6
  name: Publishing Roles Ontology
  preferred_prefix: PuRO
  prefix: puro
  publications:
  - doi: 10.1145/2362499.2362502
    pmc: null
    pubmed: null
    title: Scholarly publishing and linked data
    year: 2012
  repository: https://github.com/sparontologies/pro
  uri_format: http://purl.org/spar/pro/$1
pw:
  aberowl:
    description: A controlled vocabulary for annotating gene products to pathways.
    download_owl: http://aber-owl.net/media/ontologies/PW/97/pw.owl
    homepage: http://rgd.mcw.edu/rgdweb/ontology/search.html
    name: Pathway ontology
    prefix: PW
  biocontext:
    prefix: PW
  bioportal:
    contact:
      email: gthayman@mcw.edu
      name: G. Thomas Hayman
    description: 'The goal of the Pathway Ontology is to cover all types of biological
      pathways, including altered and disease pathways, and to capture the relationships
      between them within the hierarchical structure of a Directed Acyclic Graph (DAG).
      The five nodes of the ontology are: classic metabolic, regulatory, signaling,
      drug and disease pathways. An extensive survey of the review literature along
      with searches of existing pathway databases have been used to choose terms and
      their position within the tree. The ontology is continually expanding along
      with the development of Pathway and Disease Portals at RGD. Mapping of pathways
      in other databases to terms in PW as synonyms further increased the content
      of the ontology. It also provided the means to bring in annotations made by
      these databases and link to their sites via automatic pipelines built at RGD.
      The ontology allows for the standardized annotation of rat as well as human
      and mouse genes to pathway terms. It also serves as a vehicle to connect between
      genes and ontology reports, between reports and interactive pathway diagrams,
      between pathways that directly connect to one another within a diagram or between
      pathways that in some fashion are globally related in pathway suites and suite
      networks. Metabolic, regulatory or signaling pathway terms have associated terms
      for the altered version of the pathway and the level at which the alteration(s)
      may occur. Proteins with mutations known to affect a particular pathway can
      be annotated to the normal and altered version(s) of the pathway and to a disease
      pathway, if known. Both the provision of terms for the altered versions of pathways
      and the representation of disease pathway diagrams as a collection of altered
      pathways are unique to the PW ontology and RGD''s pathway data. The Pathway
      ontology is distributed under the terms of the Creative Commons Attribution
      license version 3.0 Unported (CC BY 3.0), see http://creativecommons.org/licenses/by/3.0
      for details.'
    homepage: https://rgd.mcw.edu/rgdweb/ontology/search.html
    name: Pathway Ontology
    prefix: PW
    publications:
    - http://rgd.mcw.edu/wg/home/pathway2/molecular-pathways/#pwrpubs
    version: '7.93'
  download_obo: https://download.rgd.mcw.edu/pub/data_release/ontology_obo_files/pathway/pathway.obo
  example: '0000423'
  fairsharing:
    abbreviation: PW
    contact:
      email: vpetri@mcw.edu
      name: Victoria Petri
      orcid: 0000-0002-5540-8498
    description: 'The goal of the Pathway Ontology is to cover all types of biological
      pathways, including altered and disease pathways, and to capture the relationships
      between them within the hierarchical structure of a Directed Acyclic Graph (DAG).
      The five nodes of the ontology are: classic metabolic, regulatory, signaling,
      drug and disease pathways. An extensive survey of the review literature along
      with searches of existing pathway databases have been used to choose terms and
      their position within the tree. The ontology is continually expanding along
      with the development of Pathway and Disease Portals at RGD.'
    domains:
    - molecular entity
    - drug
    - signaling
    - biological regulation
    - enzymatic reaction
    - disease
    - pathway
    homepage: https://rgd.mcw.edu/rgdweb/ontology/view.html?acc_id=PW:0000001
    license: CC-BY-4.0
    name: Pathway Ontology
    prefix: FAIRsharing.f73xhd
    publications:
    - doi: 10.1186/2041-1480-5-7
      pubmed: '24499703'
      title: The pathway ontology - updates and applications
      year: 2014
    - doi: 10.1186/s40246-014-0017-8
      pubmed: '25265995'
      title: 'Disease pathways at the Rat Genome Database Pathway Portal: genes in
        context-a network approach to understanding the molecular mechanisms of disease'
      year: 2014
    subjects:
    - Life Science
    - Drug Metabolism
  mappings:
    aberowl: PW
    biocontext: PW
    bioportal: PW
    fairsharing: FAIRsharing.f73xhd
    miriam: pw
    n2t: pw
    obofoundry: pw
    ols: pw
    ontobee: PW
    prefixcommons: pw
    wikidata: P7333
    wikidata.entity: Q28864280
  miriam:
    deprecated: false
    description: 'The Pathway Ontology captures information on biological networks,
      the relationships between netweorks and the alterations or malfunctioning of
      such networks within a hierarchical structure. The five main branches of the
      ontology are: classic metabolic pathways, regulatory, signaling, drug, and disease
      pathwaysfor complex human conditions.'
    homepage: https://www.ebi.ac.uk/ols4/ontologies/pw
    id: '00000242'
    name: Pathway Ontology
    namespaceEmbeddedInLui: true
    pattern: ^PW:\d{7}$
    prefix: pw
    providers:
    - code: ''
      description: Pathway Ontology at Rat Genome Database
      homepage: http://rgd.mcw.edu/rgdweb/ontology/search.html
      name: Pathway Ontology at Rat Genome Database
      uri_format: http://rgd.mcw.edu/rgdweb/ontology/annot.html?acc_id=PW:$1
    sampleId: 0000208
    uri_format: https://www.ebi.ac.uk/ols4/ontologies/pw/terms?obo_id=PW:$1
  n2t:
    description: 'The Pathway Ontology captures information on biological networks,
      the relationships between netweorks and the alterations or malfunctioning of
      such networks within a hierarchical structure. The five main branches of the
      ontology are: classic metabolic pathways, regulatory, signaling, drug, and disease
      pathwaysfor complex human conditions.'
    example: 0000208
    homepage: http://bioportal.bioontology.org/ontologies/PW
    name: Pathway Ontology through BioPortal
    namespaceEmbeddedInLui: true
    pattern: ^PW:\d{7}$
    prefix: pw
    uri_format: http://purl.bioontology.org/ontology/PW/PW:$1
  obofoundry:
    contact: gthayman@mcw.edu
    contact.github: gthayman
    contact.label: G. Thomas Hayman
    contact.orcid: 0000-0002-9553-7227
    deprecated: false
    description: A controlled vocabulary for annotating gene products to pathways.
    domain: biological systems
    download.obo: http://purl.obolibrary.org/obo/pw.obo
    download.owl: http://purl.obolibrary.org/obo/pw.owl
    homepage: http://rgd.mcw.edu/rgdweb/ontology/search.html
    license: CC BY 4.0
    license.url: https://creativecommons.org/licenses/by/4.0/
    logo: http://rgd.mcw.edu/common/images/rgd_LOGO_blue_rgd.gif
    name: Pathway ontology
    preferredPrefix: PW
    prefix: pw
    publications:
    - id: https://www.ncbi.nlm.nih.gov/pubmed/21478484
      title: The Rat Genome Database pathway portal.
    - id: https://www.ncbi.nlm.nih.gov/pubmed/24499703
      title: The pathway ontology - updates and applications.
    repository: https://github.com/rat-genome-database/PW-Pathway-Ontology
  ols:
    description: A controlled vocabulary for annotating gene products to pathways.
    download_owl: http://purl.obolibrary.org/obo/pw.owl
    homepage: http://rgd.mcw.edu/rgdweb/ontology/search.html
    name: Pathway ontology
    prefix: pw
    tracker: https://github.com/rat-genome-database/PW-Pathway-Ontology/issues
    version: '7.96'
    version.iri: http://purl.obolibrary.org/obo/pw/7.96/pw.owl
  ontobee:
    library: Library
    name: Pathway ontology
    prefix: PW
  pattern: ^\d{7}$
  prefix: pw
  prefixcommons:
    bioportal: '1035'
    description: 'The goal of the Pathway Ontology is to capture the various kinds
      of biological networks, the relationships between them and the alterations or
      malfunctioning of such networks within a hierarchical structure. The five nodes
      are: classic metabolic pathways, regulatory pathways, signaling pathways, drug
      pathways and disease pathways for complex human conditions.'
    example: PW_0000002
    homepage: ftp://rgd.mcw.edu/pub/data_release/ontology_obo_files/
    keywords:
    - obo
    - pathway
    - human
    name: Pathway ontology
    pattern: ^PW_\d{7}$
    prefix: pw
    pubmed_ids:
    - '21478484'
    synonyms:
    - obo.pw
    uri_format: http://rgd.mcw.edu/rgdweb/ontology/annot.html?acc_id=$1
  providers:
  - code: miriam_obo_legacy
    description: An old URI style for MIRIAM
    example: null
    first_party: null
    homepage: https://identifiers.org/
    name: MIRIAM OBO Legacy
    publications: null
    status: null
    uri_format: http://identifiers.org/obo.pw/PW:$1
  publications:
  - doi: 10.1186/s40246-014-0017-8
    pmc: PMC4191248
    pubmed: '25265995'
    title: 'Disease pathways at the Rat Genome Database Pathway Portal: genes in context-a
      network approach to understanding the molecular mechanisms of disease'
    year: 2014
  - doi: 10.1186/2041-1480-5-7
    pmc: PMC3922094
    pubmed: '24499703'
    title: The pathway ontology - updates and applications
    year: 2014
  - doi: 10.1093/database/bar010
    pmc: PMC3072770
    pubmed: '21478484'
    title: The Rat Genome Database pathway portal
    year: 2011
  twitter: ratgenome
  uri_format: http://purl.obolibrary.org/obo/PW_$1
  wikidata:
    database: Q28864280
    description: identifier in the Pathway Ontology database
    example:
    - PW:0000003
    - PW:0000125
    - PW:0000624
    homepage: http://bioportal.bioontology.org/ontologies/PW
    name: Pathway Ontology ID
    pattern: ^PW:([0-9]{7})$
    prefix: P7333
    uri_format: https://purl.bioontology.org/ontology/PW/$1
pwo:
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: An ontology for describing the steps in the workflow associated with
    the publication of a document or other publication entity.
  example: Workflow
  fairsharing:
    abbreviation: PWO
    contact:
      email: silvio.peroni@unibo.it
      name: Silvio Peroni
      orcid: 0000-0003-0530-4305
    description: The Publishing Workflow Ontology (PWO) is a simple ontology for describing
      the steps in the workflow associated with the publication of a document or other
      publication entity.
    homepage: http://www.sparontologies.net/ontologies/pwo
    license: CC-BY-4.0
    name: ' Publishing Workflow Ontology '
    prefix: FAIRsharing.c4e46c
    publications:
    - doi: 10.3233/sw-160230
      title: The Publishing Workflow Ontology (PWO)
      year: 2014
    repository: https://github.com/sparontologies/pwo
    subjects:
    - Subject Agnostic
    twitter: sparontologies
  homepage: http://www.sparontologies.net/ontologies/pwo
  lov:
    description: An ontology for describing the workflow associated with the publication
      of a document.
    homepage: http://purl.org/spar/pwo
    keywords:
    - SPAR
    modified: '2015-06-18'
    name: The Publishing Workflow Ontology
    prefix: pwo
    uri_prefix: http://purl.org/spar/pwo/$1
  mappings:
    fairsharing: FAIRsharing.c4e46c
    lov: pwo
  name: Publishing Workflow Ontology
  preferred_prefix: PWO
  prefix: pwo
  publications:
  - doi: 10.3233/sw-160230
    pmc: null
    pubmed: null
    title: The Publishing Workflow Ontology (PWO)
    year: 2017
  - doi: 10.3233/sw-160230
    pmc: null
    pubmed: null
    title: The Publishing Workflow Ontology (PWO)
    year: 2014
  repository: https://github.com/sparontologies/pwo
  uri_format: http://purl.org/spar/pwo/$1
px:
  biocontext:
    prefix: PX
  mappings:
    biocontext: PX
    miriam: px
    n2t: px
  miriam:
    deprecated: false
    description: The ProteomeXchange provides a single point of submission of Mass
      Spectrometry (MS) proteomics data for the main existing proteomics repositories,
      and encourages the data exchange between them for optimal data dissemination.
    homepage: http://www.proteomexchange.org/
    id: '00000513'
    name: ProteomeXchange
    namespaceEmbeddedInLui: false
    pattern: ^(R)?PXD\d{6}$
    prefix: px
    sampleId: PXD000500
    uri_format: http://proteomecentral.proteomexchange.org/cgi/GetDataset?ID=$1
  n2t:
    description: The ProteomeXchange provides a single point of submission of Mass
      Spectrometry (MS) proteomics data for the main existing proteomics repositories,
      and encourages the data exchange between them for optimal data dissemination.
    example: PXD000500
    homepage: http://www.proteomexchange.org/
    name: ProteomeXchange at Seattle
    namespaceEmbeddedInLui: false
    pattern: ^(R)?PXD\d{6}$
    prefix: px
    uri_format: http://proteomecentral.proteomexchange.org/cgi/GetDataset?ID=$1
  prefix: px
pypi:
  mappings:
    miriam: pypi
  miriam:
    deprecated: false
    description: The Python Package Index (PyPI) is a repository for Python packages.
    homepage: https://www.python.org/psf/
    id: 00000863
    name: PyPI
    namespaceEmbeddedInLui: false
    pattern: ^[a-zA-Z_][a-zA-Z0-9\-_]+$
    prefix: pypi
    sampleId: numpy
    uri_format: https://pypi.org/project/$1/
  prefix: pypi
  uri_format: https://pypi.org/project/$1
qb:
  contact:
    email: richard@cyganiak.de
    github: cygri
    name: Richard Cyganiak
    orcid: 0000-0001-9950-5209
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: This vocabulary allows multi-dimensional data, such as statistics,
    to be published in RDF. It is based on the core information model from SDMX (and
    thus also DDI).
  download_rdf: http://purl.org/linked-data/cube#
  example: Observation
  homepage: https://www.w3.org/TR/vocab-data-cube
  lov:
    description: This vocabulary allows multi-dimensional data, such as statistics,
      to be published in RDF.
    homepage: http://www.w3.org/TR/vocab-data-cube/
    keywords:
    - Methods
    - W3C Rec
    modified: '2014-07-31'
    name: The data cube vocabulary
    prefix: qb
    uri_prefix: http://purl.org/linked-data/cube#$1
  mappings:
    lov: qb
    zazuko: qb
  name: The data cube vocabulary
  pattern: ^\w+$
  preferred_prefix: qb
  prefix: qb
  repository: https://github.com/UKGovLD/publishing-statistical-data
  uri_format: http://purl.org/linked-data/cube#$1
  zazuko:
    prefix: qb
    uri_format: http://purl.org/linked-data/cube#$1
qtldb:
  mappings:
    miriam: qtldb
  miriam:
    deprecated: false
    description: The Animal Quantitative Trait Loci (QTL) database (Animal QTLdb)
      is designed to house publicly all available QTL and single-nucleotide polymorphism/gene
      association data on livestock animal species. This collection is species-independent.
    homepage: https://www.animalgenome.org/QTLdb
    id: 00000798
    name: Animal Genome QTL
    namespaceEmbeddedInLui: false
    pattern: ^\d+$
    prefix: qtldb
    sampleId: '4685'
    uri_format: https://www.animalgenome.org/QTLdb/q?id=QTL_ID:$1
  prefix: qtldb
qualo:
  contact:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: An ontology of qualifications, distinctions, and certifications that
    uses the Phenotype And Trait Ontology term quality (PATO:0000001) as a root term.
  example: '0000001'
  homepage: https://github.com/cthoyt/qualo
  license: CC0-1.0
  name: Qualification Ontology
  pattern: ^\d{7}$
  prefix: qualo
  rdf_uri_format: https://w3id.org/qualo/id/$1
  repository: https://github.com/cthoyt/qualo
  uri_format: https://w3id.org/qualo/id/$1
qudt:
  aberowl:
    description: The QUDT, or 'Quantity, Unit, Dimension and Type' collection of ontologies
      define the base classes properties, and restrictions used for modeling physical
      quantities, units of measure, and their dimensions in various measurement systems.
      The goal of the QUDT ontology is to provide a unified model of, measurable quantities,
      units for measuring different kinds of quantities, the numerical values of quantities
      in different units of measure and the data structures and data types used to
      store and manipulate these objects in software. This OWL schema is a foundation
      for a basic treatment of units.
    download_owl: http://aber-owl.net/media/ontologies/QUDT/4/qudt.owl
    homepage: http://qudt.org/
    name: Quantities, Units, Dimensions, and Types Ontology
    prefix: QUDT
    version: '$Id: OSG_qudt-(v1.1).ttl 4989 2011-06-01 21:56:40Z RalphHodgson $'
  bartoc:
    abbreviation: QUDT
    description: 'QUDT is more than a set of vocabularies representing the various
      quantity and unit standards:


      Main QUDT Ontology

      QUDT Datatype Ontology

      QUDT Units Vocabulary

      QUDT QuantityKinds Vocabulary

      QUDT DimensionVectors Vocabulary

      QUDT Physical Constants Vocabulary

      QUDT Systems of Units Vocabulary'
    homepage: http://qudt.org/
    name: Quantities, Units, Dimensions and Types
    prefix: '18206'
  biolink:
    is_identifiers: false
    is_obo: false
    prefix: qud
    uri_format: http://qudt.org/1.1/schema/qudt#$1
  bioportal:
    contact:
      email: noreply@bioontology.org
      name: Unknown
    description: The QUDT, or 'Quantity, Unit, Dimension and Type' collection of ontologies
      define the base classes properties, and restrictions used for modeling physical
      quantities, units of measure, and their dimensions in various measurement systems.
      The goal of the QUDT ontology is to provide a unified model of, measurable quantities,
      units for measuring different kinds of quantities, the numerical values of quantities
      in different units of measure and the data structures and data types used to
      store and manipulate these objects in software. This OWL schema is a foundation
      for a basic treatment of units.
    homepage: http://qudt.org/
    name: Quantities, Units, Dimensions, and Types Ontology
    prefix: QUDT
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: Ontologies that aim to provide semantic specifications for units of
    measure, quantity kind, dimensions and data types.
  download_rdf: http://qudt.org/schema/qudt/
  example: baseDimensionEnumeration
  fairsharing:
    abbreviation: QUDT
    description: The QUDT, or 'Quantity, Unit, Dimension and Type' collection of ontologies
      define the base classes properties, and restrictions used for modeling physical
      quantities, units of measure, and their dimensions in various measurement systems.
      QUDT provides a unified model of measurable quantities, units for measuring
      different kinds of quantities, the numerical values of quantities in different
      units of measure and the data structures and data types used to store and manipulate
      these objects in software. This schema, expressed in both SHACL and OWL, is
      a foundation for a basic treatment of units. Originally developed by TopQuadrant
      for the NASA Exploration Initiatives Ontology Models (NExIOM) project, they
      now form the basis of the NASA QUDT Handbook. QUDT aims to improve interoperability
      of data and the specification of information structures through industry standards
      for Units of Measure, Quantity Kinds, Dimensions and Data Types.
    domains:
    - Experimental measurement
    - Quantification
    - unit
    homepage: https://qudt.org/
    license: CC-BY-4.0
    name: 'Quantities, Units, Dimensions and Types '
    prefix: FAIRsharing.d3pqw7
    repository: https://github.com/qudt/qudt-public-repo/blob/master/docs/2020-04-28%20Intro%20to%20QUDT.pdf
    subjects:
    - Measurement Systems
  homepage: https://qudt.org
  keywords:
  - unit
  - units
  lov:
    description: The QUDT, or 'Quantity, Unit, Dimension and Type' collection of ontologies
      define the base classes properties, and restrictions used for modeling physical
      quantities, units of measure, and their dimensions in various measurement systems.
    homepage: http://qudt.org
    keywords:
    - Methods
    modified: '2020-04-20'
    name: Quantities, Units, Dimensions and Types
    prefix: qudt
    uri_prefix: http://qudt.org/schema/qudt/$1
  mappings:
    aberowl: QUDT
    bartoc: '18206'
    biolink: qud
    bioportal: QUDT
    fairsharing: FAIRsharing.d3pqw7
    lov: qudt
    zazuko: qudt
  name: Quantities, Units, Dimensions, and Types Ontology
  preferred_prefix: qudt
  prefix: qudt
  providers:
  - code: v11
    description: Version 1.1 provider
    example: null
    first_party: null
    homepage: http://qudt.org
    name: Version 1.1
    publications: null
    status: null
    uri_format: http://qudt.org/1.1/schema/qudt#$1
  repository: https://github.com/qudt/qudt-public-repo
  uri_format: http://qudt.org/schema/qudt#$1
  zazuko:
    prefix: qudt
    uri_format: http://qudt.org/schema/qudt/$1
radiomics:
  bioportal:
    contact:
      email: alberto.traverso@maastro.nl
      name: Alberto Traverso
    description: The Radiomics Ontology aims to cover the radiomics feature domain
      with a strong focus on first order, shape, textural radiomics features. In addition,
      in the original version. it includes classes about segmentation algorithms and
      imaging filters. Due to a recent collaboration with the IBSI (International
      Biomarkers Standardization Initiative), the ontology has been expanded (v 1.6)
      and it includes all the entities presented in the IBSI document. Therefore,
      a broad coverage of not only radiomics features, but also every entity (e.g.
      software properties, filter properties, features extraction parameters) involved
      into radiomics computation has been added. In the latest version (v2.0), the
      ontology URIs have been updated to reflect the codes avaialble in the IBSI latest
      manual
    name: Radiomics Ontology
    prefix: RO
    version: '2.1'
  contact:
    email: alberto.traverso@maastro.nl
    github: null
    name: Alberto Traverso
    orcid: 0000-0001-6183-4429
  description: The Radiomics Ontology aims to cover the radiomics feature domain with
    a strong focus on first order, shape, textural radiomics features. In addition,
    in the original version. it includes classes about segmentation algorithms and
    imaging filters. Due to a recent collaboration with the IBSI (International Biomarkers
    Standardization Initiative), the ontology has been expanded (v 1.6) and it includes
    all the entities presented in the IBSI document. Therefore, a broad coverage of
    not only radiomics features, but also every entity (e.g. software properties,
    filter properties, features extraction parameters) involved into radiomics computation
    has been added. In the latest version (v2.0), the ontology URIs have been updated
    to reflect the codes avaialble in the IBSI latest manual. [bioportal]
  example: LK99
  homepage: http://www.radiomics.org/RO
  mappings:
    bioportal: RO
  prefix: radiomics
  uri_format: http://www.radiomics.org/RO/$1
radlex:
  aberowl:
    description: 'RadLex is a controlled terminology for radiology-a single unified
      source of radiology terms for radiology practice, education, and research. For
      license information see : <a href="http://www.rsna.org/uploadedFiles/RSNA/Content/Informatics/RadLex_License_Agreement_and_Terms_of_Use_V2_Final.pdf">http://www.rsna.org/uploadedFiles/RSNA/Content/Informatics/RadLex_License_Agreement_and_Terms_of_Use_V2_Final.pdf</a>
      Converted to use OWL format submissions'
    download_owl: http://aber-owl.net/media/ontologies/RADLEX/37/radlex.owl
    homepage: http://www.rsna.org/RadLex.aspx
    name: Radiology Lexicon
    prefix: RADLEX
    version: '3.14'
  bartoc:
    abbreviation: RadLex
    description: We recognize the benefits that come from radiologists using common
      language to communicate diagnostic results. For this reason, RSNA produced RadLex®,
      a comprehensive set of radiology terms for use in radiology reporting, decision
      support, data mining, data registries, education and research.
    homepage: https://radlex.org/
    name: Radiology Lexicon
    prefix: '20689'
  bioportal:
    contact:
      email: radlex-feedback@lists.rsna.org
      name: Radiological Society of North America
    description: RadLex OWL, as downloaded from BioPortal, includes a set of puns
      in order to facilitate browsing and display. For the base RadLex ontology alone,
      without puns, and release notes for the latest version, please see http://radlex.org/
    homepage: https://www.rsna.org/practice-tools/data-tools-and-standards/radlex-radiology-lexicon
    name: Radiology Lexicon
    prefix: RADLEX
    version: '4.2'
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: 'A comprehensive set of radiology terms for use in radiology reporting,
    decision support, data mining, data registries, education and research.


    RadLex provides the foundation for vital data resources used in radiology:


    - The LOINC/RSNA Radiology Playbook

    - RadElement Common Data Elements

    -RadReport Radiology Reporting Templates


    The development of RadLex has been supported by the National Institute of Biomedical
    Imaging and Bioengineering (NIBIB) and the cancer Biomedical Informatics Grid
    (caBIG) project.'
  example: RID1
  fairsharing:
    abbreviation: RadLex
    description: RadLex is a comprehensive lexicon—a unified language of radiology
      terms—for standardized indexing and retrieval of radiology information resources.
      With more than 68,000 terms, RadLex satisfies the needs of software developers,
      system vendors and radiology users by adopting the best features of existing
      terminology systems while producing new terms to fill critical gaps. RadLex
      also provides a comprehensive and technology-friendly replacement for the ACR
      Index for Radiological Diagnoses. It unifies and supplements other lexicons
      and standards, such as SNOMED-CT and DICOM. RadLex development has received
      support from both the National Institute of Biomedical Imaging and Bioengineering
      (NIBIB) and the cancer Biomedical Informatics Grid (caBIG) project.
    domains:
    - Medical imaging
    - diagnosis
    homepage: https://www.rsna.org/en/practice-tools/data-tools-and-standards/radlex-radiology-lexicon
    name: Radiology Lexicon
    prefix: FAIRsharing.shm2f2
    publications:
    - doi: 10.2214/ajr.174.5.1741463
      pubmed: '10789815'
      title: Radiology lexicon
      year: 2000
    - doi: 10.1016/j.jvir.2008.10.022
      pubmed: '19081735'
      title: 'The IR RadLex project: an interventional radiology lexicon--a collaborative
        project of the Radiological Society of North America and the Society of Interventional
        Radiology'
      year: 2008
    - doi: 10.1016/j.jvir.2009.04.031
      pubmed: '19560008'
      title: 'The IR Radlex Project: an interventional radiology lexicon--a collaborative
        project of the Radiological Society of North America and the Society of Interventional
        Radiology'
      year: 2009
    subjects:
    - Anatomy
    - Biomedical Science
    - Clinical Studies
    - Medical Informatics
    - Radiology
  hl7:
    description: RadLex terminology comprises coded terms used in the acquisition
      and management of diagnostic images and related data, and in the representation
      of imaging-related findings and results.  RadLex terms would be used in both
      Orders and Observations, appearing in HL7 V2 OBX segments and in HL7 V3 Acts
      describing both imaging procedures and the observations derived therefrom.  RadLex
      codes will also be used in HL7 CDA documents, as they will be in related DICOM
      Structured Reporting (SR) objects used in imaging applications.
    homepage: http://www.radlex.org
    name: RadLex
    organization: Radiological Society of North America
    preferred_prefix: radLex
    prefix: 2.16.840.1.113883.6.256
    status: Complete
  homepage: https://radlex.org
  license: http://www.rsna.org/uploadedFiles/RSNA/Content/Informatics/RadLex_License_Agreement_and_Terms_of_Use_V2_Final.pdf
  mappings:
    aberowl: RADLEX
    bartoc: '20689'
    bioportal: RADLEX
    fairsharing: FAIRsharing.shm2f2
    hl7: 2.16.840.1.113883.6.256
  name: RSNA Informatics RadLex
  pattern: ^RID\d+$
  prefix: radlex
  publications:
  - doi: 10.1016/j.jvir.2009.04.031
    pmc: null
    pubmed: '19560008'
    title: 'The IR Radlex Project: an interventional radiology lexicon--a collaborative
      project of the Radiological Society of North America and the Society of Interventional
      Radiology'
    year: 2009
  - doi: 10.1016/j.jvir.2008.10.022
    pmc: null
    pubmed: '19081735'
    title: 'The IR RadLex project: an interventional radiology lexicon--a collaborative
      project of the Radiological Society of North America and the Society of Interventional
      Radiology'
    year: 2008
  - doi: 10.2214/ajr.174.5.1741463
    pmc: null
    pubmed: '10789815'
    title: Radiology lexicon
    year: 2000
  uri_format: https://radlex.org/RID/$1
  version: '4.1'
raid:
  fairsharing:
    abbreviation: RAiD
    description: 'Research Activity Identifier (RAiD) is an identifier mechanism designed
      for research projects and activities. It is persistent and connects existing
      PIDs for researchers, institutions, outputs and tools together to create a timeline
      of research activity which makes connecting digital infrastructure, reporting
      on impact and establishing data provenance clear and easy. RAiD is one of the
      Identifier Services owned and offered by the Australia Research Data Commons
      (ARDC), and can be accessed for machine-to-machine service by API integration,
      using a RAiD service point designated platform, or by manually minting via the
      RAiD user Dashboard. '
    domains:
    - Resource metadata
    - centrally registered identifier
    - Knowledge representation
    - FAIR
    homepage: https://raid.org/
    logo: https://api.fairsharing.org/rails/active_storage/blobs/redirect/eyJfcmFpbHMiOnsibWVzc2FnZSI6IkJBaHBBZ0VIIiwiZXhwIjpudWxsLCJwdXIiOiJibG9iX2lkIn19--c5438876bbbcd4c68044b1e22d159b57bc79513f/RAID%20Logo.png?disposition=inline
    name: Research Activity Identifier
    prefix: FAIRsharing.dc702a
    repository: https://github.com/ResearchDataServices
    subjects:
    - Subject Agnostic
  mappings:
    fairsharing: FAIRsharing.dc702a
    miriam: raid
  miriam:
    deprecated: false
    description: RAiD is an identifier and global system, governed by ISO 23527:2022,
      to uniquely identifiy research projects, collaboratively, collect and publicly
      share information about them.
    homepage: https://ardc.edu.au/
    id: '00001107'
    name: Research Activity Identifier
    namespaceEmbeddedInLui: false
    pattern: ^102?\.\d+\/.+$
    prefix: raid
    sampleId: 10.26259/0e59e9a5
    uri_format: https://raid.org/$1
  prefix: raid
rapdb.locus:
  mappings:
    miriam: rapdb.locus
  miriam:
    deprecated: false
    description: Rice Annotation Project Database (RAP-DB) is a primary rice (Oryza
      sativa) annotation database established in 2004 upon the completion of the Oryza
      sativa ssp. japonica cv. Nipponbare genome sequencing by the International Rice
      Genome Sequencing Project. RAP-DB provides comprehensive resources (e.g. genome
      annotation, gene expression, DNA markers, genetic diversity, etc.) for biological
      and agricultural research communities. This collection provides locus information
      in RAP-DB.
    homepage: https://rapdb.dna.affrc.go.jp/
    id: '00000702'
    name: RAP-DB Locus
    namespaceEmbeddedInLui: false
    pattern: ^Os\S+g\d{7}$
    prefix: rapdb.locus
    sampleId: Os01g0883800
    uri_format: https://rapdb.dna.affrc.go.jp/locus/?name=$1
  prefix: rapdb.locus
  synonyms:
  - irgsp
rapdb.transcript:
  go:
    homepage: https://rapdb.dna.affrc.go.jp
    name: Rice annotation Project database
    prefix: RAP-DB
    uri_format: https://rapdb.dna.affrc.go.jp/viewer/gene_detail/irgsp1?name=$1
  mappings:
    go: RAP-DB
    miriam: rapdb.transcript
    ncbi: RAP-DB
    prefixcommons: rapdb
  miriam:
    deprecated: false
    description: Rice Annotation Project Database (RAP-DB) is a primary rice (Oryza
      sativa) annotation database established in 2004 upon the completion of the Oryza
      sativa ssp. japonica cv. Nipponbare genome sequencing by the International Rice
      Genome Sequencing Project. RAP-DB provides comprehensive resources (e.g. genome
      annotation, gene expression, DNA markers, genetic diversity, etc.) for biological
      and agricultural research communities. This collection provides transcript information
      in RAP-DB.
    homepage: https://rapdb.dna.affrc.go.jp/
    id: '00000762'
    name: RAP-DB Transcript
    namespaceEmbeddedInLui: false
    pattern: ^Os\S+t\d{7}-\d{2}$
    prefix: rapdb.transcript
    sampleId: Os01t0883800-02
    uri_format: https://rapdb.dna.affrc.go.jp/viewer/gene_detail/irgsp1?name=$1
  ncbi:
    example: Os01g1234567
    homepage: http://rapdb.dna.affrc.go.jp/
    name: Rice Annotation Project Database
    prefix: RAP-DB
  prefix: rapdb.transcript
  prefixcommons:
    description: The Rice Annotation Project (RAP) was conceptualized upon the completion
      of the rice genome sequencing in 2004 with the aim of providing the scientific
      community with an accurate and timely annotation of the rice genome sequence.
    example: Os01g0102600
    homepage: http://rapdb.dna.affrc.go.jp/
    keywords:
    - genome
    - DNA
    name: The Rice Annotation Project Database
    pattern: ^[A-Z,0-9]+$
    prefix: rapdb
    uri_format: http://rapdb.dna.affrc.go.jp/viewer/gbrowse_details/build5?name=[$1
ratmap:
  comment: This resource doesn't exist on the web anymore
  deprecated: true
  mappings:
    ncbi: RATMAP
    prefixcommons: ratmap
  name: Rat Genome Database RatMap
  ncbi:
    example: '5'
    name: Rat Genome Database
    prefix: RATMAP
  part_of_database: rgd
  prefix: ratmap
  prefixcommons:
    description: The Rat Genome Database RatMap is focused on presenting rat genes,
      DNA-markers, QTL:s etc that is localized to chromosome. The database is dedicated
      to rat gene nomenclature and should be consulted for queries in such matters
    example: ENSRNOG00000008380
    homepage: http://ratmap.org
    keywords:
    - genome
    - gene
    - DNA
    name: RatMap, the rat genome database
    pattern: ^[A-Z]+\d+$
    prefix: ratmap
    uri_format: http://ratmap.org/Showgene.php?gene_stable_id=$1
  provides: ensembl
  reviewer:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
rbk:
  biocontext:
    prefix: RBK
  contact:
    email: oxburl@mmc.org
    github: null
    name: Leif Oxburgh
    orcid: 0000-0002-2825-7663
  fairsharing:
    abbreviation: RBK
    description: This site contains data generated by (Re)Building a Kidney (RBK),
      an NIDDK-funded consortium of research projects working to optimize approaches
      for the isolation, expansion, and differentiation of appropriate kidney cell
      types and their integration into complex structures that replicate human kidney
      function. RBK's goal is to coordinate and support studies that will result in
      the ability to generate or repair nephrons that can function within the kidney.
      This resource includes data from both the RBK project and the GenitoUrinary
      Development Molecular Anatomy Project (GUDMAP). Data submission is restricted
      to members of the Consortium only.
    homepage: https://rebuildingakidney.org
    name: (Re)Building a Kidney
    prefix: FAIRsharing.78d3ad
    publications:
    - doi: 10.1681/ASN.2016101077
      pubmed_id: 28096308
      title: (Re)Building a Kidney.
    repository: https://github.com/informatics-isi-edu/gudmap-rbk/wiki/Create-citable-datasets
    subjects:
    - Molecular biology
    - Genomics
    - Developmental Biology
    - Cell Biology
  mappings:
    biocontext: RBK
    fairsharing: FAIRsharing.78d3ad
    miriam: rbk
    n2t: rbk
  miriam:
    deprecated: false
    description: (Re)Building a Kidney is an NIDDK-funded consortium of research projects
      working to optimize approaches for the isolation, expansion, and differentiation
      of appropriate kidney cell types and their integration into complex structures
      that replicate human kidney function.
    homepage: https://www.rebuildingakidney.org/
    id: 00000659
    name: Rebuilding a Kidney
    namespaceEmbeddedInLui: false
    pattern: ^[-0-9a-zA-Z]+(@[-0-9a-zA-Z]+)?$
    prefix: rbk
    sampleId: Q-2958
    uri_format: https://www.rebuildingakidney.org/id/$1
  n2t:
    description: (Re)Building a Kidney is an NIDDK-funded consortium of research projects
      working to optimize approaches for the isolation, expansion, and differentiation
      of appropriate kidney cell types and their integration into complex structures
      that replicate human kidney function.
    example: Q-2958
    homepage: https://www.rebuildingakidney.org/
    name: Rebuilding a Kidney
    namespaceEmbeddedInLui: false
    pattern: ^[-0-9a-zA-Z]+(@[-0-9a-zA-Z]+)?$
    prefix: rbk
    uri_format: https://www.rebuildingakidney.org/id/$1
  prefix: rbk
  publications:
  - doi: 10.1681/asn.2016101077
    pmc: PMC5407737
    pubmed: '28096308'
    title: (Re)Building a Kidney
    year: 2017
  - doi: 10.1681/ASN.2016101077
    pmc: null
    pubmed: null
    title: (Re)Building a Kidney.
    year: null
rbo:
  aberowl:
    description: RBO is an ontology for the effects of radiation on biota in terrestrial
      and space environments.
    download_owl: http://aber-owl.net/media/ontologies/RBO/39/rbo.owl
    homepage: https://github.com/Radiobiology-Informatics-Consortium/RBO
    name: Radiation Biology Ontology
    prefix: RBO
  bioportal:
    contact:
      email: kristen.m.peach@nasa.gov
      name: Kristen Peach
    description: RBO is an ontology for the effects of radiation on biota in terrestrial
      and space environments.
    homepage: https://github.com/Radiobiology-Informatics-Consortium/RBO/tree/master/src/ontology
    license: CC-BY-3.0
    name: Radiation Biology Ontology
    prefix: RBO
    publications:
    - https://doi.org/10.1080/09553002.2023.2173823
    version: '2025-11-26'
  example: '00000105'
  example_extras:
  - '010007'
  mappings:
    aberowl: RBO
    bioportal: RBO
    obofoundry: rbo
    ols: rbo
    ontobee: RBO
    wikidata.entity: Q113014438
  obofoundry:
    contact: daniel.c.berrios@nasa.gov
    contact.github: DanBerrios
    contact.label: Daniel C. Berrios
    contact.orcid: 0000-0003-4312-9552
    depends_on:
    - bfo
    - chmo
    - envo
    - obi
    - pato
    - ro
    - uo
    deprecated: false
    description: RBO is an ontology for the effects of radiation on biota in terrestrial
      and space environments.
    domain: environment
    download.json: http://purl.obolibrary.org/obo/rbo.json
    download.obo: http://purl.obolibrary.org/obo/rbo.obo
    download.owl: http://purl.obolibrary.org/obo/rbo.owl
    homepage: https://github.com/Radiobiology-Informatics-Consortium/RBO
    license: CC BY 3.0
    license.url: http://creativecommons.org/licenses/by/3.0/
    name: Radiation Biology Ontology
    preferredPrefix: RBO
    prefix: rbo
    repository: https://github.com/Radiobiology-Informatics-Consortium/RBO
  ols:
    description: RBO is an ontology for the effects of radiation on biota in terrestrial
      and space environments.
    download_owl: http://purl.obolibrary.org/obo/rbo.owl
    homepage: https://github.com/Radiobiology-Informatics-Consortium/RBO
    name: Radiation Biology Ontology
    prefix: rbo
    tracker: https://github.com/Radiobiology-Informatics-Consortium/RBO/issues
    version: '2025-12-11'
    version.iri: http://purl.obolibrary.org/obo/rbo/releases/2025-12-11/rbo.owl
  ontobee:
    library: Library
    name: Radiation Biology Ontology
    prefix: RBO
  pattern: ^\d{6,8}$
  prefix: rbo
  uri_format: http://purl.obolibrary.org/obo/RBO_$1
rcb:
  cellosaurus:
    category: Cell line collections (Providers)
    homepage: https://cell.brc.riken.jp/en/rcb
    name: RIKEN Bioresource Center Cell Bank
    prefix: RCB
    uri_format: https://cellbank.brc.riken.jp/cell_bank/CellInfo/?cellNo=$1&lang=En
  contact:
    email: atsushi.yoshiki@riken.jp
    github: null
    name: Atsushi Yoshiki
    orcid: 0000-0002-9450-5151
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: Collection of many cell lines derived from human and other various
    animals, preserved by the RIKEN BioResource Research Center.
  example: RCB0002
  homepage: https://cell.brc.riken.jp/en/rcb
  mappings:
    cellosaurus: RCB
    rrid: IMSR_RBRC
  name: RIKEN Bioresource Center Cell Bank
  pattern: ^RCB\d+$
  prefix: rcb
  rrid:
    abbreviation: BRC, RIKEN BRC
    homepage: http://www.brc.riken.jp/inf/en
    keywords:
    - FASEB list
    - animal
    - bioresource
    - cell
    - cell line
    - cultured cell
    - cultured cell line
    - dna
    - embryo
    - experimental animal
    - experimental plant
    - gene
    - genetic material
    - organ
    - plant
    - recombinant host
    - seed
    - sperm
    - tissue
    - virus
    name: RIKEN BioResource Center
    prefix: IMSR_RBRC
    pubmeds:
    - '19448331'
    - '34532769'
    scr: '003250'
  uri_format: https://cellbank.brc.riken.jp/cell_bank/CellInfo/?cellNo=$1
rdbsb:
  contact:
    email: gqzhang@sinh.ac.cn
    github: null
    name: Guoqing Zhang
    orcid: 0000-0001-8827-7546
  contributor:
    email: m.naguthana@hotmail.com
    github: nagutm
    name: Mufaddal Naguthanawala
    orcid: 0009-0009-5240-7463
  description: This database provides identifiers for catalytic bioparts which are
    fundamental to the design, construction, and optimization of biological systems
    for specific metabolic pathways. It provides basic information, function information
    (including catalytic functions, qualitative and quantitative parameters, and biopart
    expression), and sequence information (nucleotide sequence and amino acid sequence)
  example: OENC205
  github_request_issue: 1473
  homepage: https://www.biosino.org/rdbsb
  name: Registry and database of bioparts for synthetic biology
  pattern: ^OENC\d+$
  prefix: rdbsb
  publications:
  - doi: 10.1093/nar/gkae844
    pmc: PMC11701600
    pubmed: '39360609'
    title: 'RDBSB: a database for catalytic bioparts with experimental evidence'
    year: 2024
  reviewer:
    email: b.gyori@northeastern.edu
    github: bgyori
    name: Benjamin M. Gyori
    orcid: 0000-0001-9439-5346
  uri_format: https://www.biosino.org/rdbsb/bioparts_detail/$1
rdf:
  biocontext:
    prefix: rdf
    uri_format: http://www.w3.org/1999/02/22-rdf-syntax-ns#$1
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: This is the RDF Schema for the RDF vocabulary terms in the RDF Namespace,
    defined in RDF 1.1 Concepts
  example: type
  fairsharing:
    abbreviation: RDF
    contact:
      email: rmrich5@gmail.com
      name: Rafael Richards
      orcid: 0000-0001-5699-0515
    description: 'The Resource Description Framework (RDF) is a framework for representing
      information in the Web. This document defines an abstract syntax (a data model)
      which serves to link all RDF-based languages and specifications. The abstract
      syntax has two key data structures: RDF graphs are sets of subject-predicate-object
      triples, where the elements may be IRIs, blank nodes, or datatyped literals.
      They are used to express descriptions of resources. RDF datasets are used to
      organize collections of RDF graphs, and comprise a default graph and zero or
      more named graphs. RDF 1.1 Concepts and Abstract Syntax also introduces key
      concepts and terminology, and discusses datatyping and the handling of fragment
      identifiers in IRIs within RDF graphs.'
    homepage: http://www.w3.org/TR/2014/REC-rdf11-concepts-20140225/
    name: Resource Description Framework
    prefix: FAIRsharing.p77ph9
    publications: []
    subjects:
    - Computer Science
    - Subject Agnostic
  homepage: http://www.w3.org/1999/02/22-rdf-syntax-ns
  lov:
    description: This is the RDF Schema for the RDF vocabulary terms in the RDF Namespace,
      defined in RDF 1.1 Concepts.
    homepage: http://www.w3.org/TR/rdf11-concepts/
    keywords:
    - W3C Rec
    modified: '2019-12-16'
    name: The RDF Concepts Vocabulary
    prefix: rdf
    uri_prefix: http://www.w3.org/1999/02/22-rdf-syntax-ns#$1
  mappings:
    biocontext: rdf
    fairsharing: FAIRsharing.p77ph9
    lov: rdf
    zazuko: rdf
  name: Resource Description Framework
  preferred_prefix: rdf
  prefix: rdf
  uri_format: http://www.w3.org/1999/02/22-rdf-syntax-ns#$1
  zazuko:
    prefix: rdf
    uri_format: http://www.w3.org/1999/02/22-rdf-syntax-ns#$1
rdfa:
  contact:
    email: ivan@w3.org
    github: iherman
    name: Ivan Herman
    orcid: 0000-0003-0782-2704
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: RDFa Core is a specification for attributes to express structured data
    in any markup language. The embedded data already available in the markup language
    (e.g., HTML) can often be reused by the RDFa markup, so that publishers don't
    need to repeat significant data in the document content. (from https://www.w3.org/TR/rdfa-core/)
  download_rdf: http://www.w3.org/ns/rdfa.ttl
  example: PrefixOrTermMapping
  homepage: http://www.w3.org/ns/rdfa
  lov:
    description: This document describes the RDFa Vocabulary for Term and Prefix Assignment.
      The Vocabulary is used to modify RDFa 1.1 processing behavior
    homepage: http://www.w3.org/ns/rdfa#
    keywords:
    - RDF
    modified: '2013-03-11'
    name: RDFa Vocabulary for Term and Prefix Assignment, and for Processor Graph
      Reporting
    prefix: rdfa
    uri_prefix: http://www.w3.org/ns/rdfa#$1
  mappings:
    lov: rdfa
    zazuko: rdfa
  name: RDFa Vocabulary for Term and Prefix Assignment, and for Processor Graph Reporting
  prefix: rdfa
  uri_format: http://www.w3.org/ns/rdfa#$1
  zazuko:
    prefix: rdfa
    uri_format: http://www.w3.org/ns/rdfa#$1
rdfs:
  aberowl:
    description: RDF Schema provides a data-modelling vocabulary for RDF data
    download_owl: http://aber-owl.net/media/ontologies/RDFS/4/rdfs.owl
    name: The RDF Schema vocabulary
    prefix: RDFS
    version: '1.1'
  biocontext:
    prefix: rdfs
    uri_format: http://www.w3.org/2000/01/rdf-schema#$1
  bioportal:
    contact:
      email: danbri@w3.org
      name: Dan Brickley
    description: RDF Schema provides a data-modelling vocabulary for RDF data
    name: The RDF Schema vocabulary
    prefix: RDFS
    version: '1.1'
  contact:
    email: danbri@w3.org
    github: null
    name: Dan Brickley
    orcid: 0000-0002-6450-7041
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: RDF Schema provides a data-modelling vocabulary for RDF data. RDF Schema
    is an extension of the basic RDF vocabulary.
  download_owl: https://triplydb.com/w3c/rdfs/download.trig.gz
  example: label
  fairsharing:
    abbreviation: RDFS
    description: RDF Schema (RDFS) is the RDF vocabulary description language. RDFS
      defines classes and properties that may be used to describe classes, properties
      and other resources.
    homepage: https://www.w3.org/TR/rdf-schema/
    name: Resource Description Framework Schema
    prefix: FAIRsharing.v9n3gk
    publications: []
    subjects:
    - Bioinformatics
    - Life Science
    - Ontology and Terminology
    - Linguistics
  homepage: https://www.w3.org/TR/rdf-schema/
  lov:
    description: RDF Schema provides a data-modelling vocabulary for RDF data. RDF
      Schema is an extension of the basic RDF vocabulary.
    homepage: http://www.w3.org/TR/rdf-schema/
    keywords:
    - W3C Rec
    modified: '2014-02-25'
    name: The RDF Schema vocabulary
    prefix: rdfs
    uri_prefix: http://www.w3.org/2000/01/rdf-schema#$1
  mappings:
    aberowl: RDFS
    biocontext: rdfs
    bioportal: RDFS
    fairsharing: FAIRsharing.v9n3gk
    lov: rdfs
    ols: rdfs
    zazuko: rdfs
  name: RDF Schema
  ols:
    name: The RDF Schema vocabulary (RDFS)
    prefix: rdfs
    uri_format: http://www.w3.org/2000/01/rdf-schema#$1
  preferred_prefix: rdfs
  prefix: rdfs
  uri_format: http://www.w3.org/2000/01/rdf-schema#$1
  zazuko:
    prefix: rdfs
    uri_format: http://www.w3.org/2000/01/rdf-schema#$1
rdo:
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: Ontologies of diseases that integrates many types of data for Rattus
    Norvegicus, Homo Sapiens, Mus Musculus and other organisms.
  download_obo: https://download.rgd.mcw.edu/pub/data_release/ontology_obo_files/disease/RDO.obo
  download_owl: https://download.rgd.mcw.edu/pub/data_release/ontology_obo_files/disease/RDO.owl
  example: '9002859'
  homepage: https://ratmine.mcw.edu/ontology/disease/
  name: RGD Disease Ontology
  pattern: ^\d{7}$
  prefix: rdo
  uri_format: http://www.semanticweb.org/mca/ontologies/2018/8/untitled-ontology-47#$1
re3data:
  bartoc:
    description: The re3data.org schema is a list of metadata properties describing
      a research data repository regarding its general scope, content and infrastructure
      as well as its compliance with technical, metadata and quality standards. The
      schema includes required metadata properties and optional properties providing
      additional information. The schema is designed to recommend a standard for describing
      a research data repository; provide the basis for interoperability between research
      data repositories and re3data.org; be one of the first steps towards the goal
      of a certificate for research data repositories.
    homepage: http://www.re3data.org/schema/
    license: CC-BY-3.0
    name: Schema for the description of research data repositories
    prefix: '822'
  mappings:
    bartoc: '822'
    miriam: re3data
  miriam:
    deprecated: false
    description: Re3data is a global registry of research data repositories that covers
      research data repositories from different academic disciplines.
    homepage: https://datacite.org
    id: 00000861
    name: re3data
    namespaceEmbeddedInLui: false
    pattern: ^r3d\d{9,9}$
    prefix: re3data
    sampleId: r3d100010772
    uri_format: https://www.re3data.org/repository/$1
  prefix: re3data
reactome:
  biocontext:
    prefix: REACTOME
  cheminf:
    description: Database identifier used by Reactome.
    name: Reactome
    obsolete: false
    prefix: '000411'
  contact:
    email: deustp01@med.nyu.edu
    github: deustp01
    name: Peter D'Eustachio
    orcid: 0000-0002-5494-626X
  contributor_extras:
  - email: smoxon@lbl.gov
    github: sierra-moxon
    name: Sierra Moxon
    orcid: 0000-0002-8719-7760
  domain: pathway
  edam:
    description: Identifier of an entry from the Reactome database.
    name: Pathway ID (reactome)
    obsolete: false
    prefix: '1155'
  example: R-BTA-418592
  go:
    homepage: https://www.reactome.org/
    name: Reactome - a curated knowledgebase of biological pathways
    prefix: Reactome
    synonyms:
    - REACTOME
    - REAC
    uri_format: https://www.reactome.org/content/detail/$1
  integbio:
    description: REACTOME is a database of human pathways for basic research, genome
      analysis, pathway modeling, systems biology and education. It contains manually
      curated and peer-reviewed pathway data which are annotated by expert biologists,
      in collaboration with Reactome editorial staff and cross-referenced to many
      bioinformatics databases. This database provides an intuitive website to navigate
      pathway knowledge and a suite of data analysis tools to support the pathway-based
      analysis of complex experimental and computational data sets. The curated  human
      pathway data are available to infer orthologous events in 20 non-human species
      including mouse, rat, chicken, worm, fly, yeast, plant and bacteria. Using species
      comparison tool, users are able to compare predicted pathways with those of
      human to find reactions and pathways common to a selected species and human.
    fairsharing: biodbcore-000329
    homepage: https://reactome.org
    information_keywords:
    - Expression
    - Interaction/Pathway
    maintainer: Reactome team
    name: REACTOME
    prefix: nbdc00185
    pubmeds:
    - '15608231'
    - '29145629'
    status: Active
    target_keywords:
    - Protein
  license: CC0-1.0
  logo: https://reactome.org/templates/favourite/images/logo/logo.png
  mappings:
    biocontext: REACTOME
    cheminf: '000411'
    edam: '1155'
    go: Reactome
    integbio: nbdc00185
    miriam: reactome
    n2t: reactome
    pathguide: '103'
    prefixcommons: reactome
    re3data: r3d100010861
    togoid: ReactomePathway
    wikidata: P3937
  miriam:
    deprecated: false
    description: The Reactome project is a collaboration to develop a curated resource
      of core pathways and reactions in human biology.
    homepage: https://www.reactome.org/
    id: 00000018
    name: Reactome
    namespaceEmbeddedInLui: false
    pattern: ^(R-[A-Z]{3}-\d+(-\d+)?(\.\d+)?)|(REACT_\d+(\.\d+)?)$
    prefix: reactome
    sampleId: R-HSA-201451
    uri_format: https://reactome.org/content/detail/$1
  n2t:
    description: The Reactome project is a collaboration to develop a curated resource
      of core pathways and reactions in human biology.
    example: R-HSA-201451
    homepage: https://www.reactome.org/
    name: Reactome, a curated knowledgebase of biological pathways
    namespaceEmbeddedInLui: false
    pattern: (^R-[A-Z]{3}-\d+(-\d+)?(\.\d+)?$)|(^REACT_\d+(\.\d+)?$)
    prefix: reactome
    uri_format: https://reactome.org/content/detail/$1
  name: Reactome
  pathguide:
    abbreviation: Reactome
    homepage: http://www.reactome.org
    keywords:
    - BioPAX
    - PSI-MI
    - SBML
    name: Reactome KnowledgeBase
    prefix: '103'
  pattern: ^R-[A-Z]{3}-\d+(-\d+)?(\.\d+)?$
  prefix: reactome
  prefixcommons:
    description: The Reactome project is a collaboration to develop a curated resource
      of core pathways and reactions in human biology.
    example: REACT_1590
    homepage: http://www.reactome.org
    keywords:
    - human
    - pathway
    - reaction
    name: Reactome - a curated knowledgebase of biological pathways
    pattern: ^REACT_\d+(\.\d+)?$
    prefix: reactome
    pubmed_ids:
    - '15608231'
    synonyms:
    - identifier.reactome
    uri_format: http://www.reactome.org/cgi-bin/eventbrowser_st_id?FROM_REACTOME=1&ST_ID=$1
  providers:
  - code: pathwaycommons
    description: Pathway diagram drawn with Cytoscape
    example: null
    first_party: null
    homepage: https://www.pathwaycommons.org
    name: Pathway Commons
    publications: null
    status: null
    uri_format: https://apps.pathwaycommons.org/pathways?uri=http%3A%2F%2Fidentifiers.org%2Freactome%2F$1
  - code: browser
    description: An interactive view over pathways.
    example: null
    first_party: null
    homepage: https://reactome.org/PathwayBrowser/
    name: Reactome Pathway Browser
    publications: null
    status: null
    uri_format: https://reactome.org/PathwayBrowser/#/$1
  publications:
  - doi: 10.1093/nar/gki072
    pmc: PMC540026
    pubmed: '15608231'
    title: 'Reactome: a knowledgebase of biological pathways'
    year: 2005
  - doi: null
    pmc: null
    pubmed: '15608231'
    title: null
    year: null
  re3data:
    description: Reactome is a manually curated, peer-reviewed pathway database, annotated
      by expert biologists and cross-referenced to bioinformatics databases. Its aim
      is to share information in the visual representations of biological pathways
      in a computationally accessible format. Pathway annotations are authored by
      expert biologists, in collaboration with Reactome editorial staff and cross-referenced
      to many bioinformatics databases. These include NCBI Gene, Ensembl and UniProt
      databases, the UCSC and HapMap Genome Browsers, the KEGG Compound and ChEBI
      small molecule databases, PubMed, and Gene Ontology.
    doi: 10.17616/R3TS52
    homepage: https://reactome.org/
    license: CC0
    name: Reactome
    prefix: r3d100010861
    synonyms:
    - a curated pathway database
    xrefs:
      nif: 0000-03390
      omics: '02771'
  references:
  - https://github.com/biopragmatics/bioregistry/pull/1086
  synonyms:
  - RE
  - REACT
  - Reactome
  - reactome.pathway
  togoid:
    catalog: nbdc00185
    description: REACTOME is a database of human pathways for basic research, genome
      analysis, pathway modeling, systems biology and education. It contains manually
      curated and peer-reviewed pathway data which are annotated by expert biologists,
      in collaboration with Reactome editorial staff and cross-referenced to many
      bioinformatics databases. This database provides an intuitive website to navigate
      pathway knowledge and a suite of data analysis tools to support the pathway-based
      analysis of complex experimental and computational data sets. The curated  human
      pathway data are available to infer orthologous events in 20 non-human species
      including mouse, rat, chicken, worm, fly, yeast, plant and bacteria. Using species
      comparison tool, users are able to compare predicted pathways with those of
      human to find reactions and pathways common to a selected species and human.
    examples:
    - R-HSA-165159
    - R-DRE-1630316
    - R-SCE-9634635
    - R-DRE-140834
    - R-HSA-2142753
    - R-BTA-383280
    - R-MMU-5218900
    - R-RNO-5654219
    - R-MMU-8875791
    - R-MMU-9648025
    keywords:
    - Pathway
    name: Reactome pathway
    pattern: ^(?R-[A-Z]{3}-\d+)(?:\.\d+)?$
    prefix: ReactomePathway
    uri_format: http://identifiers.org/reactome/$1
  wikidata:
    description: Identifier used in Reactome to uniquely identify a biological pathway
    example:
    - R-HSA-191273
    - R-HSA-6807047
    - R-HSA-71403
    homepage: http://www.reactome.org/
    name: Reactome ID
    prefix: P3937
    uri_format: https://reactome.org/content/detail/$1
reaxys:
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: Reaxys is a web-based tool for the retrieval of chemistry information
    and data from published literature, including journals and patents. The information
    includes chemical compounds, chemical reactions, chemical properties, related
    bibliographic data, substance data with synthesis planning information, as well
    as experimental procedures from selected journals and patents. It is licensed
    by Elsevier.
  edam:
    description: Beilstein registry number of a chemical compound.
    name: Chemical registry number (Beilstein)
    obsolete: false
    prefix: '1003'
  example: '1257009'
  homepage: https://www.reaxys.com
  mappings:
    edam: '1003'
    wikidata: P1579
  name: Reaxys
  pattern: ^\d+$
  prefix: reaxys
  synonyms:
  - Beilstein
  - Reaxys
  wikidata:
    description: identifier for chemical substance in Reaxys
    example:
    - '2018'
    - '635680'
    - '93704'
    name: Reaxys registry number
    pattern: ^\d+$
    prefix: P1579
rebase:
  biocontext:
    prefix: REBASE
  contact:
    email: roberts@neb.com
    github: null
    name: Richard John Roberts
    orcid: 0000-0002-4348-0169
  edam:
    description: Identifier of an enzyme from the REBASE enzymes database.
    name: REBASE enzyme number
    obsolete: false
    prefix: '2325'
  fairsharing:
    abbreviation: REBASE
    description: A collection of information about restriction enzymes and related
      proteins. It contains published and unpublished references, recognition and
      cleavage sites, isoschizomers, commercial availability, methylation sensitivity,
      crystal, genome, and sequence data.
    homepage: http://rebase.neb.com
    license: http://opendatacommons.org/licenses/pddl/1.0
    name: Restriction enzymes and methylases database
    prefix: FAIRsharing.9sb9qh
    publications:
    - doi: 10.1093/nar/gku1046
      pubmed_id: 25378308
      title: 'REBASE-a database for DNA restriction and modification: enzymes, genes
        and genomes.'
    - doi: 10.1093/nar/gkp874
      pubmed_id: 19846593
      title: 'REBASE--a database for DNA restriction and modification: enzymes, genes
        and genomes.'
    subjects:
    - Life Science
  go:
    homepage: http://rebase.neb.com/rebase/rebase.html
    name: REBASE restriction enzyme database
    prefix: REBASE
    uri_format: http://rebase.neb.com/rebase/enz/$1.html
  integbio:
    alt_name: The Restriction Enzyme Database
    description: REBASE is a database of restriction enzymes. The database contains
      entries by publication authors, and the database can be searched by identifiers
      such as name and number. Tools for digests and comparison of sequences are provided.
    fairsharing: biodbcore-000475
    homepage: http://rebase.neb.com/rebase/rebase.html
    information_keywords:
    - Bioresource
    - Sequence
    - Repository
    maintainer: New England Biolabs Inc.
    name: REBASE
    prefix: nbdc00648
    pubmeds:
    - '19846593'
    status: Active
    target_keywords:
    - RNA
    - Protein
  logo: https://rebase.neb.com/rebase/rebase_header_crop3_gray_url_use.png
  mappings:
    biocontext: REBASE
    edam: '2325'
    fairsharing: FAIRsharing.9sb9qh
    go: REBASE
    integbio: nbdc00648
    miriam: rebase
    n2t: rebase
    pathguide: '72'
    prefixcommons: rebase
    re3data: r3d100012171
    uniprot: DB-0089
    wikidata: P4866
  miriam:
    deprecated: false
    description: REBASE is a comprehensive database of information about restriction
      enzymes, DNA methyltransferases and related proteins involved in the biological
      process of restriction-modification (R-M). It contains fully referenced information
      about recognition and cleavage sites, isoschizomers, neoschizomers, commercial
      availability, methylation sensitivity, crystal and sequence data.
    homepage: http://rebase.neb.com/rebase/
    id: '00000230'
    name: REBASE
    namespaceEmbeddedInLui: false
    pattern: ^\d+$
    prefix: rebase
    sampleId: '101'
    uri_format: http://rebase.neb.com/rebase/enz/$1.html
  n2t:
    description: REBASE is a comprehensive database of information about restriction
      enzymes, DNA methyltransferases and related proteins involved in the biological
      process of restriction-modification (R-M). It contains fully referenced information
      about recognition and cleavage sites, isoschizomers, neoschizomers, commercial
      availability, methylation sensitivity, crystal and sequence data.
    example: '101'
    homepage: http://rebase.neb.com/rebase/
    name: REBASE at New England Biolabs
    namespaceEmbeddedInLui: false
    pattern: ^\d+$
    prefix: rebase
    uri_format: http://rebase.neb.com/rebase/enz/$1.html
  pathguide:
    abbreviation: REBASE
    homepage: http://rebase.neb.com/rebase/rebase.html
    name: Restriction Enzyme Database
    prefix: '72'
  prefix: rebase
  prefixcommons:
    description: A collection of information about restriction enzymes and related
      proteins. It contains published and unpublished references, recognition and
      cleavage sites, isoschizomers, commercial availability, methylation sensitivity,
      crystal, genome, and sequence data.
    example: '101'
    homepage: http://rebase.neb.com
    keywords:
    - enzyme
    - protein
    - structure
    - small molecule
    - genome
    - DNA
    - RNA
    name: Restriction enzymes and methylases database
    pattern: ^\d+$
    prefix: rebase
    pubmed_ids:
    - '19846593'
    uri_format: http://rebase.neb.com/rebase/enz/$1.html
  publications:
  - doi: 10.1093/nar/gku1046
    pmc: PMC4383893
    pubmed: '25378308'
    title: 'REBASE--a database for DNA restriction and modification: enzymes, genes
      and genomes'
    year: 2014
  - doi: 10.1093/nar/gkp874
    pmc: PMC2808884
    pubmed: '19846593'
    title: 'REBASE--a database for DNA restriction and modification: enzymes, genes
      and genomes'
    year: 2009
  - doi: 10.1093/nar/gku1046
    pmc: null
    pubmed: null
    title: 'REBASE-a database for DNA restriction and modification: enzymes, genes
      and genomes.'
    year: null
  - doi: 10.1093/nar/gkp874
    pmc: null
    pubmed: null
    title: 'REBASE--a database for DNA restriction and modification: enzymes, genes
      and genomes.'
    year: null
  - doi: null
    pmc: null
    pubmed: '19846593'
    title: null
    year: null
  - doi: 10.1093/nar/gkac975
    pmc: null
    pubmed: '36318248'
    title: null
    year: null
  - doi: 10.1093/nar/gku1046
    pmc: null
    pubmed: null
    title: 'REBASE-a database for DNA restriction and modification: enzymes, genes
      and genomes.'
    year: null
  - doi: 10.1093/nar/gkp874
    pmc: null
    pubmed: null
    title: 'REBASE--a database for DNA restriction and modification: enzymes, genes
      and genomes.'
    year: null
  - doi: null
    pmc: null
    pubmed: '19846593'
    title: null
    year: null
  - doi: 10.1093/nar/gkac975
    pmc: null
    pubmed: '36318248'
    title: null
    year: null
  - doi: 10.1093/nar/gku1046
    pmc: null
    pubmed: null
    title: 'REBASE-a database for DNA restriction and modification: enzymes, genes
      and genomes.'
    year: null
  - doi: 10.1093/nar/gkp874
    pmc: null
    pubmed: null
    title: 'REBASE--a database for DNA restriction and modification: enzymes, genes
      and genomes.'
    year: null
  - doi: null
    pmc: null
    pubmed: '19846593'
    title: null
    year: null
  - doi: 10.1093/nar/gkac975
    pmc: null
    pubmed: '36318248'
    title: null
    year: null
  - doi: 10.1093/nar/gku1046
    pmc: null
    pubmed: null
    title: 'REBASE-a database for DNA restriction and modification: enzymes, genes
      and genomes.'
    year: null
  - doi: 10.1093/nar/gkp874
    pmc: null
    pubmed: null
    title: 'REBASE--a database for DNA restriction and modification: enzymes, genes
      and genomes.'
    year: null
  - doi: null
    pmc: null
    pubmed: '19846593'
    title: null
    year: null
  - doi: 10.1093/nar/gkac975
    pmc: null
    pubmed: '36318248'
    title: null
    year: null
  re3data:
    description: The Restriction Enzyme Database is a collection of information about
      restriction enzymes, methylases, the microorganisms from which they have been
      isolated, recognition sequences, cleavage sites, methylation specificity, the
      commercial availability of the enzymes, and references - both published and
      unpublished observations (dating back to 1952).  REBASE is updated daily and
      is constantly expanding.
    doi: 10.17616/R3J930
    homepage: http://rebase.neb.com/rebase/rebase.html
    name: REBASE
    prefix: r3d100012171
    synonyms:
    - The Restriction Enzyme Database
    xrefs:
      nif: 0000-03391
  uniprot:
    abbreviation: REBASE
    category: Protein family/group databases
    homepage: https://rebase.neb.com/rebase/rebase.html
    name: Restriction enzymes and methylases database
    prefix: DB-0089
    publications:
    - doi: 10.1093/nar/gkac975
      pubmed: '36318248'
    uri_format: https://rebase.neb.com/rebase/enz/$1.html
  wikidata:
    database: Q7301611
    description: ID in REBASE (Restriction Enzyme Database)
    example:
    - '1'
    - '6974'
    - '993'
    name: REBASE Enzyme Number
    pattern: ^[1-9]\d*$
    prefix: P4866
    uri_format: http://rebase.neb.com/cgi-bin/reb_get.pl?enzname=$1
rebec:
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: Presents the new fast tracks for clinical research and observational
    studies on INDIGENOUS PEOPLE AND TRADITIONAL COMMUNITIES and on NEGLECTED TROPICAL
    DISEASES (NTDs). Fast-track can reduce the normal approval period for clinical
    trials to less than 48 hours, if the documentation, information and any mandatory
    changes requested are provided by the registrant.
  example: RBR-6qvdftm
  homepage: https://ensaiosclinicos.gov.br
  name: Brazilian Registry of Clinical Trials
  pattern: ^RBR-\w+$
  prefix: rebec
  uri_format: https://ensaiosclinicos.gov.br/rg/$1
rec:
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: The Recommendation Ontology specification provides basic concepts and
    properties for describing recommendations on/for the Semantic Web.
  download_owl: https://web.archive.org/web/20250116013621/https://smiy.sourceforge.net/rec/rdf/recommendationontology.owl
  example: Recommendation
  homepage: https://web.archive.org/web/20250105164652/https://smiy.sourceforge.net/rec/spec/recommendationontology.html
  license: CC-BY-3.0
  lov:
    description: The Recommendation Ontology specification provides basic concepts
      and properties for describing recommendations on/ for the Semantic Web.
    homepage: http://purl.org/ontology/rec/core#
    keywords:
    - Rec
    modified: '2010-08-02'
    name: Recommendation Ontology
    prefix: rec
    uri_prefix: http://purl.org/ontology/rec/core#$1
  mappings:
    lov: rec
  name: Recommendation Ontology
  prefix: rec
  rdf_uri_format: http://purl.org/ontology/rec/core#$1
  uri_format: http://purl.org/ontology/rec/core#$1
receptome.family:
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: The human receptor families involved in signaling (with the exception
    of channels) are presented in the Human Plasma Membrane Receptome database.
  example: '5.1'
  homepage: http://www.receptome.org
  mappings:
    prefixcommons: hpmr
  name: Human Plasma Membrane Receptome Families
  prefix: receptome.family
  prefixcommons:
    description: Plasma membrane protein sequences, literature, and expression database
    example: '14'
    homepage: http://www.receptome.org/HPMR/
    keywords:
    - protein
    name: Human Plasma Membrane Receptome
    pattern: ^\d+$
    prefix: hpmr
    uri_format: http://www.receptome.org/HPMR/Families/Frameset_family.asp?FamId=$1
  uri_format: http://www.receptome.org/families/Frameset_family.asp?ProtType=Receptor&FamId=$1
redfly:
  comment: This resource doesn't exist on the web anymore
  deprecated: true
  mappings:
    pathguide: '265'
    prefixcommons: redfly
  pathguide:
    abbreviation: REDfly
    homepage: http://redfly.ccr.buffalo.edu/
    name: Regulatory Element Database for Drosophila
    prefix: '265'
  prefix: redfly
  prefixcommons:
    description: REDflyis a curated collection of known Drosophila transcriptional
      cis-regulatory modules (CRMs) and transcription factor binding sites (TFBSs).
    example: '8'
    homepage: http://redfly.ccr.buffalo.edu
    keywords:
    - regulation
    name: Regulatory Elements Database for Drosophila
    pattern: ^\d+$
    prefix: redfly
    uri_format: http://redfly.ccr.buffalo.edu/?content=/view_detail.php&crm_id=$1
  reviewer:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
refseq:
  biocontext:
    prefix: RefSeq
    uri_format: http://www.ncbi.nlm.nih.gov/refseq/?term=$1
  contact:
    email: pruitt@ncbi.nlm.nih.gov
    github: null
    name: Kim Dixon Pruitt
    orcid: 0000-0001-7950-1374
  contributor_extras:
  - email: null
    github: slobentanzer
    name: Sebastian Lobentanzer
    orcid: 0000-0003-3399-6695
  edam:
    description: Accession number of a RefSeq database entry.
    name: RefSeq
    obsolete: false
    prefix: '1098'
  example_extras:
  - WP_029104145.1
  fairsharing:
    abbreviation: RefSeq
    description: The Reference Sequence (RefSeq) collection aims to provide a comprehensive,
      integrated, non-redundant, well-annotated set of sequences, including genomic
      DNA, transcripts, and proteins.
    homepage: http://www.ncbi.nlm.nih.gov/RefSeq/
    license: http://opendatacommons.org/licenses/pddl/1.0
    name: Reference Sequence Database
    prefix: FAIRsharing.4jg0qw
    publications:
    - doi: 10.1093/nar/gkl842
      pubmed_id: 17130148
      title: 'NCBI reference sequences (RefSeq): a curated non-redundant sequence
        database of genomes, transcripts and proteins.'
    subjects:
    - Genetics
    - Computational Biology
    - Life Science
  go:
    homepage: http://www.ncbi.nlm.nih.gov/RefSeq/
    name: RefSeq
    prefix: RefSeq
  has_canonical: ncbiprotein
  hl7:
    description: 'The Reference Sequence (RefSeq) is one of the NCBI projects, the
      RefSeq collection aims to provide a comprehensive, integrated, non-redundant,
      well-annotated set of sequences, including genomic DNA, transcripts, and proteins.
      ReqSeq is accessible via BLAST, Entrez, and the NCBI FTP site.  Information
      is also available in Entrez Genomes and Entrez Gene, and for some genomes additional
      information is available in the Map Viewer. RefSeq entries can be used with
      the HL7 coded data type.  For example, in the HL7 messages specified according
      to the HL7 V2 Clinical Genomics Fully LOINC-Qualified Genetic Variation Model,
      RefSeq entries can be used to as the observation values for genomic reference
      sequence identifiers (LOINC #: 48013-7).  More information may be found at:
      http://www.ncbi.nlm.nih.gov/RefSeqVersioning informaiton:The latest release
      of RefSeq was released on May 13, 2009 with the release number of 35.RefSeq
      generates new releases roughly every two months.  The dates of the three previous
      releases were:Release 34, March 12, 2009Release 33, January 20, 2009Release
      32, November 17, 2008RefSeq is a free database for the public.'
    homepage: http://www.ncbi.nlm.nih.gov
    organization: National Center for Biotechnology Information,National Center for
      Biotechnology Information
    preferred_prefix: refSeq
    prefix: 2.16.840.1.113883.6.280
    status: Complete
  integbio:
    alt_name: Reference Sequence
    description: RefSeq is a database of standard reference genomic, transcript, and
      protein sequences. The database contains consensus sequence data for over 20,000
      organisms and over 27 million proteins and is designed to provide a common basis
      for experimental studies that can be searched using accession ID, keyword, or
      BLAST. Bulk data is available for FTP download.
    fairsharing: biodbcore-000457
    homepage: https://www.ncbi.nlm.nih.gov/refseq/
    information_keywords:
    - Sequence
    maintainer: NCBI (National Center for Biotechnology Information)
    name: RefSeq
    prefix: nbdc00187
    pubmeds:
    - '22121212'
    - '18927115'
    - '10592200'
    status: Active
    target_keywords:
    - Genome/Gene
    - cDNA/EST
    - RNA
    - Protein
    - Cell/Organelle
  mappings:
    biocontext: RefSeq
    edam: '1098'
    fairsharing: FAIRsharing.4jg0qw
    go: RefSeq
    hl7: 2.16.840.1.113883.6.280
    integbio: nbdc00187
    miriam: refseq
    n2t: refseq
    prefixcommons: refseq
    re3data: r3d100010285
    uniprot: DB-0117
  miriam:
    deprecated: false
    description: The Reference Sequence (RefSeq) collection aims to provide a comprehensive,
      integrated, non-redundant set of sequences, including genomic DNA, transcript
      (RNA), and protein products.
    homepage: https://www.ncbi.nlm.nih.gov/projects/RefSeq/
    id: 00000039
    name: RefSeq
    namespaceEmbeddedInLui: false
    pattern: ^(((WP|AC|AP|NC|NG|NM|NP|NR|NT|NW|XM|XP|XR|YP|ZP)_\d+)|(NZ\_[A-Z]{2,4}\d+))(\.\d+)?$
    prefix: refseq
    sampleId: NP_012345
    uri_format: https://www.ncbi.nlm.nih.gov/protein/$1
  n2t:
    description: The Reference Sequence (RefSeq) collection aims to provide a comprehensive,
      integrated, non-redundant set of sequences, including genomic DNA, transcript
      (RNA), and protein products.
    example: NP_012345
    homepage: https://www.ncbi.nlm.nih.gov/projects/RefSeq/
    name: The NCBI Reference Sequence database
    namespaceEmbeddedInLui: false
    pattern: ^((AC|AP|NC|NG|NM|NP|NR|NT|NW|XM|XP|XR|YP|ZP)_\d+|(NZ\_[A-Z]{4}\d+))(\.\d+)?$
    prefix: refseq
    uri_format: https://www.ncbi.nlm.nih.gov/protein/$1
  name: Reference Sequence Collection
  pattern: ^(((AC|AP|NC|NG|NM|NP|NR|NT|NW|WP|XM|XP|XR|YP|ZP)_\d+)|(NZ_[A-Z]{2,4}\d+))(\.\d+)?$
  prefix: refseq
  prefixcommons:
    description: The Reference Sequence (RefSeq) collection aims to provide a comprehensive,
      integrated, non-redundant, well-annotated set of sequences, including genomic
      DNA, transcripts, and proteins.
    example: NP_012345
    homepage: http://www.ncbi.nlm.nih.gov/RefSeq/
    keywords:
    - protein
    - DNA
    - RNA
    name: Reference Sequence Database
    pattern: ^(NC|AC|NG|NT|NW|NZ|NM|NR|XM|XR|NP|AP|XP|ZP)_\d+(\.\d+)?$
    prefix: refseq
    pubmed_ids:
    - '17130148'
    uri_format: http://www.ncbi.nlm.nih.gov/nuccore/$1
  publications:
  - doi: 10.1093/nar/gkae1038
    pmc: null
    pubmed: '39526381'
    title: 'NCBI RefSeq: reference sequence standards through 25 years of curation
      and annotation'
    year: 2024
  - doi: 10.1093/nar/gkv1189
    pmc: PMC4702849
    pubmed: '26553804'
    title: 'Reference sequence (RefSeq) database at NCBI: current status, taxonomic
      expansion, and functional annotation'
    year: 2015
  - doi: 10.1093/nar/gkl842
    pmc: PMC1716718
    pubmed: '17130148'
    title: 'NCBI reference sequences (RefSeq): a curated non-redundant sequence database
      of genomes, transcripts and proteins'
    year: 2006
  - doi: 10.1093/nar/gkl842
    pmc: null
    pubmed: null
    title: 'NCBI reference sequences (RefSeq): a curated non-redundant sequence database
      of genomes, transcripts and proteins.'
    year: null
  - doi: null
    pmc: null
    pubmed: '17130148'
    title: null
    year: null
  - doi: 10.1093/nar/gkv1189
    pmc: null
    pubmed: '26553804'
    title: null
    year: null
  re3data:
    description: The Reference Sequence (RefSeq) collection provides a comprehensive,
      integrated, non-redundant, well-annotated set of sequences, including genomic
      DNA, transcripts, and proteins. RefSeq sequences form a foundation for medical,
      functional, and diversity studies. They provide a stable reference for genome
      annotation, gene identification and characterization, mutation and polymorphism
      analysis (especially RefSeqGene records), expression studies, and comparative
      analyses.
    doi: 10.17616/R3V59P
    homepage: https://www.ncbi.nlm.nih.gov/refseq/
    license: Copyrights
    name: NCBI Reference Sequence Database
    prefix: r3d100010285
    synonyms:
    - RefSeq
    xrefs:
      nif: 0000-03397
      omics: 01659
  references:
  - https://github.com/biopragmatics/bioregistry/issues/545
  synonyms:
  - REFSEQ_PROT
  uniprot:
    abbreviation: RefSeq
    category: Sequence databases
    homepage: https://www.ncbi.nlm.nih.gov/refseq/
    name: NCBI Reference Sequences
    prefix: DB-0117
    publications:
    - doi: 10.1093/nar/gkv1189
      pubmed: '26553804'
    uri_format: https://www.ncbi.nlm.nih.gov/protein/$1
reo:
  comment: 'From James O.: It was an ontology for "reagents" developed by @Matthew
    Brush. Since OBI was interested in reagents, Matt developed it in coordination
    with OBI and had plans to submit it to OBO. I believe that REO was once included
    in Ontobee, and OBI even started using some REO terms. But REO was never submitted
    to OBO. I believe it was abandoned.'
  contact:
    email: matt@tislab.org
    github: mbrush
    name: Matthew Brush
    orcid: 0000-0002-1048-5019
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: The Reagent Ontology (ReO) adheres to OBO Foundry principles (obofoundry.org)
    to model the domain of biomedical research reagents, considered broadly to include
    materials applied “chemically” in scientific techniques to facilitate generation
    of data and research materials. ReO is a modular ontology that re-uses existing
    ontologies to facilitate cross-domain interoperability. It consists of reagents
    and their properties, linking diverse biological and experimental entities to
    which they are related. ReO supports community use cases by providing a flexible,
    extensible, and deeply integrated framework that can be adapted and extended with
    more specific modeling to meet application needs.
  download_owl: https://github.com/tis-lab/reagent-ontology/raw/master/reo/ontology_files/reo_pre-merged_or_reasoned_files/reo_reasoned_9-6-12.owl
  example: 0000079
  homepage: https://github.com/tis-lab/reagent-ontology
  mappings:
    ontobee: REO
  name: Reagent Ontology
  ontobee:
    library: Not Specified/No
    name: Reagent Ontology
    prefix: REO
  pattern: ^\d{7}$
  prefix: reo
  references:
  - https://github.com/obi-ontology/obi/issues/1015
  - https://code.google.com/archive/p/reagent-ontology/
  - https://github.com/obi-ontology/obi/issues/1135
  repository: https://github.com/tis-lab/reagent-ontology
  uri_format: http://purl.obolibrary.org/obo/REO_$11
repeatsdb.protein:
  mappings:
    miriam: repeatsdb.protein
  miriam:
    deprecated: false
    description: RepeatsDB is a database of annotated tandem repeat protein structures.
      This collection references protein entries in the database.
    homepage: https://repeatsdb.org/
    id: 00000792
    name: RepeatsDB Protein
    namespaceEmbeddedInLui: false
    pattern: ^[OPQopq][0-9][A-Za-z0-9]{3}[0-9]|[A-Na-nR-Zr-z][0-9]([A-Za-z][A-Za-z0-9]{2}[0-9]){1,2}$
    prefix: repeatsdb.protein
    sampleId: P29894
    uri_format: https://repeatsdb.org/protein/$1
  prefix: repeatsdb.protein
  provides: uniprot
repeatsdb.structure:
  mappings:
    miriam: repeatsdb.structure
  miriam:
    deprecated: false
    description: RepeatsDB is a database of annotated tandem repeat protein structures.
      This collection references structural entries in the database.
    homepage: https://repeatsdb.org/
    id: '00000764'
    name: RepeatsDB Structure
    namespaceEmbeddedInLui: false
    pattern: ^[0-9][A-Za-z0-9]{3}[A-Za-z0-9][A-Za-z0-9]?[0-9]?[0-9]?$
    prefix: repeatsdb.structure
    sampleId: 2gc4E
    uri_format: https://repeatsdb.org/structure/$1
  prefix: repeatsdb.structure
repec:
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: The Peruvian Clinical Trials Registry - REPEC is a non-profit online
    information system developed in 2007 by INS. It is a publicly accessible prospective
    registry aimed at providing information about clinical trials underway in Peru.
    REPEC also includes Registries for Trial Sites, Institutional Research Ethics
    Committees, Sponsors and Contract Research Organizations. REPEC contains records
    of clinical trials since 1995. Since December 14, 2012, the Peruvian National
    Institute of Health, by means of the General Office for Research and Technological
    Transfer (OGITT), has started a process to improve REPEC and to join the WHO International
    Clinical Trials Registry Platform (ICTRP) and to be acknowledged as a Primary
    Registry. More information about primary registries is available in ICRTP at http://apps.who.int/trialsearch/.
    (from website)
  domain: clinical trial
  example: 046-19
  homepage: https://ensayosclinicos-repec.ins.gob.pe/en/
  logo: https://ensayosclinicos-repec.ins.gob.pe/images/plantilla/img_logo_principal_repec_en.png
  name: Peruvian Clinical Trial Registry
  pattern: ^\d+-\d+(-[A-Z])?$
  prefix: repec
  providers:
  - code: who
    description: WHO Clinical Trials Search
    example: null
    first_party: null
    homepage: https://trialsearch.who.int
    name: WHO Clinical Trials Search
    publications: null
    status: null
    uri_format: https://trialsearch.who.int/Trial2.aspx?TrialID=PER-$1
  uri_format: https://www.ins.gob.pe/ensayosclinicos/rpec/recuperarECPBNuevo.asp?val=&NroPag=1&flg=0&ver=EN&numEC=$1
reproduceme:
  aberowl:
    description: The REPRODUCE-ME ontology is an extension of the PROV-O and the P-Plan
      ontology to describe a complete path of a scientific experiment. It expresses
      the REPRODUCE-ME Data Model using the OWL2 Web Ontology Language (OWL2). It
      provides a set of classes and properties to represent a scientific experiment
      including its computational and non-computational steps to track the provenance
      of results. It describes an experiment and its data, agents, activities, plans,
      steps, variables, instruments, materials and settings required for its reproducibility.
    download_owl: http://aber-owl.net/media/ontologies/REPRODUCE-ME/7/reproduce-me.owl
    homepage: https://w3id.org/reproduceme/research
    name: REPRODUCE-ME
    prefix: REPRODUCE-ME
    version: '1.1'
  bioportal:
    contact:
      email: sheeba.samuel@uni-jena.de
      name: Sheeba Samuel
    description: The REPRODUCE-ME ontology is an extension of the PROV-O and the P-Plan
      ontology to describe a complete path of a scientific experiment. It expresses
      the REPRODUCE-ME Data Model using the OWL2 Web Ontology Language (OWL2). It
      provides a set of classes and properties to represent a scientific experiment
      including its computational and non-computational steps to track the provenance
      of results. It describes an experiment and its data, agents, activities, plans,
      steps, variables, instruments, materials and settings required for its reproducibility.
    homepage: https://w3id.org/reproduceme/research
    name: REPRODUCE-ME
    prefix: REPRODUCE-ME
    publications:
    - https://w3id.org/reproduceme/research
    version: '1.1'
  contact:
    email: sheeba.samuel@uni-jena.de
    github: null
    name: Sheeba Samuel
    orcid: 0000-0002-7981-8504
  example: MicrobeamManipulation
  mappings:
    aberowl: REPRODUCE-ME
    bioportal: REPRODUCE-ME
    ols: reproduceme
    tib: repr
  ols:
    contact: sheeba.samuel@uni-jena.de
    description: The REPRODUCE-ME ontology is an extension of the PROV-O and the P-Plan
      ontology to describe a complete path of a scientific experiment. It expresses
      the REPRODUCE-ME Data Model using the OWL2 Web Ontology Language (OWL2). It
      provides a set of classes and properties to represent a scientific experiment
      including its computational and non-computational steps to track the provenance
      of results. It describes a complete path of a scientific experiment considering
      the use-case of biological imaging and microscopy experiments, computational
      experiments, including Jupyter notebooks and scripts. It describes an experiment
      and its data, agents, activities, plans, steps, variables, instruments, materials,
      and settings required for its reproducibility.
    homepage: https://w3id.org/reproduceme/research
    name: REPRODUCE-ME Ontology
    prefix: reproduceme
    uri_format: https://w3id.org/reproduceme#$1
    version: '1.1'
  prefix: reproduceme
  tib:
    description: The REPRODUCE-ME ontology is an extension of the PROV-O and the P-Plan
      ontology to describe a complete path of a scientific experiment. It expresses
      the REPRODUCE-ME Data Model using the OWL2 Web Ontology Language (OWL2). It
      provides a set of classes and properties to represent a scientific experiment
      including its computational and non-computational steps to track the provenance
      of results. It describes an experiment and its data, agents, activities, plans,
      steps, variables, instruments, materials and settings required for its reproducibility.
    download_owl: https://raw.githubusercontent.com/Sheeba-Samuel/REPRODUCE-ME/gh-pages/doc/reproduce-me.owl
    homepage: https://sheeba-samuel.github.io/REPRODUCE-ME/doc/index-en.html
    keywords:
    - NFDI4CHEM
    name: REPRODUCEME Ontology
    prefix: repr
    tracker: https://github.com/Sheeba-Samuel/REPRODUCE-ME/issues
    uri_format: https://w3id.org/reproduceme#$1
  uri_format: https://w3id.org/reproduceme#$1
researchgate.profile:
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  homepage: https://www.researchgate.net
  keywords:
  - person
  - researcher
  mappings:
    wikidata: P2038
  prefix: researchgate.profile
  references:
  - https://github.com/biopragmatics/bioregistry/pull/1171
  wikidata:
    description: identifier for a person, used by ResearchGate profiles
    example:
    - Rita-Heuser
    - William-White-32
    name: ResearchGate profile ID
    pattern: ^[0-9A-Za-z_-]+$
    prefix: P2038
    uri_format: https://www.researchgate.net/profile/$1
resid:
  biocontext:
    prefix: RESID
  edam:
    description: Identifier of a protein modification catalogued in the RESID database.
    name: RESID
    obsolete: false
    prefix: '2619'
  go:
    homepage: https://proteininformationresource.org/resid/resid.shtml
    name: RESID Database of Protein Modifications
    prefix: RESID
    uri_format: https://proteininformationresource.org/cgi-bin/resid?id=$1
  homepage: https://proteininformationresource.org/resid/
  mappings:
    biocontext: RESID
    edam: '2619'
    go: RESID
    miriam: resid
    n2t: resid
    obofoundry: resid
    prefixcommons: resid
    wikidata.entity: Q114677910
  miriam:
    deprecated: false
    description: The RESID Database of Protein Modifications is a comprehensive collection
      of annotations and structures for protein modifications including amino-terminal,
      carboxyl-terminal and peptide chain cross-link post-translational modifications.
    homepage: https://proteininformationresource.org/resid/
    id: '00000046'
    name: RESID
    namespaceEmbeddedInLui: false
    pattern: ^AA\d{4}$
    prefix: resid
    sampleId: AA0001
    uri_format: https://proteininformationresource.org/cgi-bin/resid?id=$1
  n2t:
    description: The RESID Database of Protein Modifications is a comprehensive collection
      of annotations and structures for protein modifications including amino-terminal,
      carboxyl-terminal and peptide chain cross-link post-translational modifications.
    example: AA0001
    homepage: http://pir0.georgetown.edu/resid/
    name: RESID at Georgetown University
    namespaceEmbeddedInLui: false
    pattern: ^AA\d{4}$
    prefix: resid
    uri_format: http://pir0.georgetown.edu/cgi-bin/resid?id=$1
  obofoundry:
    contact: john.garavelli@ebi.ac.uk
    contact.label: John Garavelli
    contact.orcid: 0000-0002-4131-735X
    deprecated: true
    description: For the description of covalent bonds in proteins.
    domain: chemistry and biochemistry
    homepage: http://www.ebi.ac.uk/RESID/
    name: Protein covalent bond
    prefix: resid
  prefix: resid
  prefixcommons:
    description: The RESID Database of Protein Modifications is a comprehensive collection
      of annotations and structures for protein modifications including amino-terminal,
      carboxyl-terminal and peptide chain cross-link post-translational modifications.
    example: AA0001
    homepage: http://www.ebi.ac.uk/RESID/
    keywords:
    - protein
    - small molecule
    - structure
    license: http://www.ebi.ac.uk/Information/termsofuse.html
    name: RESID Database of Protein Modifications
    pattern: ^AA\d{4}$
    prefix: resid
    pubmed_ids:
    - '15174124'
    uri_format: http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-id+6JSUg1NA6u4+-e+[RESID:'$1']
  publications:
  - doi: 10.1002/pmic.200300764
    pmc: null
    pubmed: '15174124'
    title: Annotation of post-translational modifications in the Swiss-Prot knowledge
      base
    year: 2004
  uri_format: https://proteininformationresource.org/cgi-bin/resid?id=$1
reto:
  aberowl:
    description: An application ontology for the domain of gene transcription regulation.
      The ontology integrates fragments of GO and MI with data from GOA, IntAct, UniProt,
      NCBI and orthological properties from RO and SIO.
    download_obo: http://aber-owl.net/media/ontologies/RETO/7/reto.obo
    homepage: http://www.semantic-systems-biology.org/apo/
    name: Regulation of Transcription Ontology
    prefix: RETO
    version: '2015'
  bioportal:
    contact:
      email: vladimir.n.mironov@gmail.com
      name: Vladimir Mironov
    description: An application ontology for the domain of gene transcription regulation.
      The ontology integrates fragments of GO and MI with data from GOA, IntAct, UniProt,
      NCBI and orthological properties from RO and SIO.
    homepage: http://www.semantic-systems-biology.org/apo/
    name: Regulation of Transcription Ontology
    prefix: RETO
    publications:
    - http://bmcbioinformatics.biomedcentral.com/articles/10.1186/s12859-014-0386-y
    version: '2015'
  download_obo: https://www.bio.ntnu.no/ontology/ReTO/reto.obo
  download_owl: https://www.bio.ntnu.no/ontology/ReTO/reto.owl
  fairsharing:
    abbreviation: ReTO
    description: An application ontology for the domain of gene transcription regulation.
      The ontology integrates fragments of GO and MI with data from GOA, IntAct, UniProt,
      NCBI and orthological properties from RO and SIO.
    domains:
    - regulation of gene expression
    - transcript
    homepage: https://bioportal.bioontology.org/ontologies/RETO
    name: Regulation of Transcription Ontolology
    prefix: FAIRsharing.4qyf0f
    subjects:
    - Life Science
    - Transcriptomics
  mappings:
    aberowl: RETO
    bioportal: RETO
    fairsharing: FAIRsharing.4qyf0f
    ols: reto
  no_own_terms: true
  ols:
    contact: vladimir.n.mironov@gmail.com
    description: Regulation of Transcription
    download_rdf: http://www.bio.ntnu.no/ontology/ReTO/reto.rdf
    homepage: http://www.semantic-systems-biology.org/apo
    name: Regulation of Transcription Ontology
    prefix: reto
    uri_format: http://purl.obolibrary.org/obo/ReTO_$1
  prefix: reto
rex:
  aberowl:
    description: An ontology of physico-chemical processes, i.e. physico-chemical
      changes occurring in course of time.
    download_owl: http://aber-owl.net/media/ontologies/REX/1/rex.owl
    name: Physico-chemical process
    prefix: REX
  biocontext:
    prefix: REX
  bioportal:
    contact:
      email: chebi-help@ebi.ac.uk
      name: Chebi Administrators
    description: REX is an ontology of physico-chemical processes, i.e. physico-chemical
      changes occurring in course of time. REX includes both microscopic processes
      (involving molecular entities or subatomic particles) and macroscopic processes.
      Some biochemical processes from Gene Ontology (GO Biological process) can be
      described as instances of REX.
    homepage: http://www.ebi.ac.uk/~kirill/REX/
    name: Physico-Chemical Process
    prefix: REX
    version: '1.13'
  contact:
    email: amalik@ebi.ac.uk
    github: amalik01
    name: Adnan Malik
    orcid: 0000-0001-8123-5351
  contact_group_email: chebi-help@ebi.ac.uk
  download_owl: http://purl.obolibrary.org/obo/rex.owl
  example: '0000512'
  fairsharing:
    abbreviation: REX
    description: REX is an ontology of physico-chemical processes, i.e. physico-chemical
      changes occurring in course of time. REX includes both microscopic processes
      (involving molecular entities or subatomic particles) and macroscopic processes.
      Some biochemical processes from Gene Ontology (GO Biological process) can be
      described as instances of REX.
    domains:
    - Reaction data
    - enzymatic reaction
    homepage: http://purl.bioontology.org/ontology/REX
    name: Physico-chemical process
    prefix: FAIRsharing.g0a7s0
    subjects:
    - Life Science
    - Chemistry
  homepage: https://www.ebi.ac.uk/chebi/
  mappings:
    aberowl: REX
    biocontext: REX
    bioportal: REX
    fairsharing: FAIRsharing.g0a7s0
    obofoundry: rex
    ols: rex
    ontobee: REX
    prefixcommons: rex
    tib: rex
  obofoundry:
    deprecated: true
    description: An ontology of physico-chemical processes, i.e. physico-chemical
      changes occurring in course of time.
    domain: chemistry and biochemistry
    download.owl: http://purl.obolibrary.org/obo/rex.owl
    name: Physico-chemical process
    prefix: rex
  ols:
    description: An ontology of physico-chemical processes, i.e. physico-chemical
      changes occurring in course of time.
    download_owl: http://purl.obolibrary.org/obo/rex.owl
    name: Physico-chemical process
    prefix: rex
  ontobee:
    library: Library
    name: Physico-chemical process
    prefix: REX
  part_of_database: chebi
  pattern: ^\d{7}$
  prefix: rex
  prefixcommons:
    bioportal: '1043'
    description: REX is an ontology of physico-chemical processes and includes microscopic
      processes (involving molecular entities or subatomic particles) and macroscopic
      processes.
    example: REX_0000517
    homepage: http://www.ebi.ac.uk/~kirill/REX/
    keywords:
    - obo
    - biochemistry
    name: Physico-chemical process
    pattern: ^REX_\d{8}$
    prefix: rex
  tib:
    description: REX is an ontology of physico-chemical processes, i.e. physico-chemical
      changes occurring in course of time. REX includes both microscopic processes
      (involving molecular entities or subatomic particles) and macroscopic processes.
      Some biochemical processes from Gene Ontology (GO Biological process) can be
      described as instances of REX.
    download_owl: http://purl.obolibrary.org/obo/rex.owl
    keywords:
    - NFDI4CHEM
    - NFDI4CAT
    - chemistry
    name: Physico-chemical process
    prefix: rex
    version.iri: http://purl.obolibrary.org/obo/rex/releases/2017-11-19/rex.owl
rexo:
  aberowl:
    description: An application ontology for the domain of gene expression regulation.
      The ontology integrates fragments of GO and MI with data from GOA, IntAct, UniProt,
      NCBI, and orthology relations using ontological properties from RO and ISO.
    download_owl: http://aber-owl.net/media/ontologies/REXO/6/rexo.owl
    homepage: http://www.semantic-systems-biology.org/apo
    name: Regulation of Gene Expression Ontolology
    prefix: REXO
    version: '2015'
  bioportal:
    contact:
      email: vladimir.n.mironov@gmail.com
      name: Vladimir Mironov
    description: An application ontology for the domain of gene expression regulation.
      The ontology integrates fragments of GO and MI with data from GOA, IntAct, UniProt,
      NCBI, and orthology relations using ontological properties from RO and ISO.
    homepage: http://www.semantic-systems-biology.org/apo
    name: Regulation of Gene Expression Ontolology
    prefix: REXO
    publications:
    - http://bmcbioinformatics.biomedcentral.com/articles/10.1186/s12859-014-0386-y
    version: '2015'
  contact:
    email: kuiper@bio.ntnu.no
    github: makuintnu
    name: Martin Kuiper
    orcid: 0000-0002-1171-9876
  download_obo: https://www.bio.ntnu.no/ontology/ReXO/rexo.obo
  download_owl: https://www.bio.ntnu.no/ontology/ReXO/rexo.owl
  fairsharing:
    abbreviation: ReXO
    contact:
      email: kuiper@bio.ntnu.no
      name: Martin Kuiper
      orcid: 0000-0002-1171-9876
    description: An application ontology for the domain of gene expression regulation.
      The ontology integrates fragments of GO and MI with data from GOA, IntAct, UniProt,
      NCBI, and orthology relations using ontological properties from RO and ISO.
    domains:
    - Expression data
    - regulation of gene expression
    - orthologous
    homepage: https://bioportal.bioontology.org/ontologies/REXO
    name: Regulation of Gene Expression Ontolology
    prefix: FAIRsharing.recas1
    publications:
    - doi: 10.1186/s12859-014-0386-y
      pubmed: '25490885'
      title: Finding gene regulatory network candidates using the gene expression
        knowledge base
      year: 2014
    subjects:
    - Life Science
  mappings:
    aberowl: REXO
    bioportal: REXO
    fairsharing: FAIRsharing.recas1
    ols: rexo
  no_own_terms: true
  ols:
    contact: vladimir.n.mironov@gmail.com
    description: Regulation of Gene Expression
    download_rdf: http://www.bio.ntnu.no/ontology/ReXO/rexo.rdf
    homepage: http://www.semantic-systems-biology.org/apo
    name: Regulation of Gene Expression Ontology
    prefix: rexo
    uri_format: http://purl.obolibrary.org/obo/ReXO_$1
  prefix: rexo
  publications:
  - doi: 10.1186/s12859-014-0386-y
    pmc: PMC4279962
    pubmed: '25490885'
    title: Finding gene regulatory network candidates using the gene expression knowledge
      base
    year: 2014
rfam:
  biocontext:
    prefix: RFAM
  contact:
    email: apetrov@ebi.ac.uk
    github: AntonPetrov
    name: Anton I Petrov
    orcid: 0000-0001-7279-2682
  edam:
    description: Stable accession number of an entry (RNA family) from the RFAM database.
    name: RFAM
    obsolete: false
    prefix: '2356'
  fairsharing:
    abbreviation: Rfam
    description: 'The Rfam database is a collection of RNA families, each represented
      by multiple sequence alignments, consensus secondary structures and covariance
      models (CMs). The families in Rfam break down into three broad functional classes:
      non-coding RNA genes, structured cis-regulatory elements and self-splicing RNAs.
      Typically these functional RNAs often have a conserved secondary structure which
      may be better preserved than the RNA sequence.'
    homepage: http://rfam.xfam.org/
    name: Rfam
    prefix: FAIRsharing.fex4c8
    publications:
    - doi: 10.1093/nar/gku1063
      pubmed_id: 25392425
      title: 'Rfam 12.0: updates to the RNA families database.'
    - doi: 10.1093/nar/gkx1038
      pubmed_id: 29112718
      title: 'Rfam 13.0: shifting to a genome-centric resource for non-coding RNA
        families.'
    subjects:
    - Genetics
    twitter: RfamDB
  go:
    homepage: https://rfam.org
    name: Rfam database of RNA families
    prefix: Rfam
    uri_format: https://rfam.org/family/$1
  integbio:
    alt_name: RNA family database
    description: Rfam is a database of RNA sequence and structure families. The database
      contains information on families and sequences of constituent members which
      can be searched by keyword or taxonomy. Data can also be downloaded via FTP.
    homepage: http://rfam.xfam.org
    information_keywords:
    - Sequence
    - Bibliography/Documents
    - Classification
    maintainer: EMBL-EBI (European Bioinformatics Institute)
    name: Rfam
    prefix: nbdc00654
    pubmeds:
    - '12520045'
    - '15608160'
    - '18945806'
    - '18953034'
    - '21062808'
    - '25392425'
    status: Active
    target_keywords:
    - RNA
  mappings:
    biocontext: RFAM
    edam: '2356'
    fairsharing: FAIRsharing.fex4c8
    go: Rfam
    integbio: nbdc00654
    miriam: rfam
    n2t: rfam
    ncbi: RFAM
  miriam:
    deprecated: false
    description: 'The Rfam database is a collection of RNA families, each represented
      by multiple sequence alignments, consensus secondary structures and covariance
      models (CMs). The families in Rfam break down into three broad functional classes:
      non-coding RNA genes, structured cis-regulatory elements and self-splicing RNAs.
      Typically these functional RNAs often have a conserved secondary structure which
      may be better preserved than the RNA sequence. The CMs used to describe each
      family are a slightly more complicated relative of the profile hidden Markov
      models (HMMs) used by Pfam. CMs can simultaneously model RNA sequence and the
      structure in an elegant and accurate fashion.'
    homepage: https://rfam.org/
    id: 00000409
    name: RFAM
    namespaceEmbeddedInLui: false
    pattern: ^RF\d{5}$
    prefix: rfam
    sampleId: RF00230
    uri_format: https://rfam.org/family/$1
  n2t:
    description: 'The Rfam database is a collection of RNA families, each represented
      by multiple sequence alignments, consensus secondary structures and covariance
      models (CMs). The families in Rfam break down into three broad functional classes:
      non-coding RNA genes, structured cis-regulatory elements and self-splicing RNAs.
      Typically these functional RNAs often have a conserved secondary structure which
      may be better preserved than the RNA sequence. The CMs used to describe each
      family are a slightly more complicated relative of the profile hidden Markov
      models (HMMs) used by Pfam. CMs can simultaneously model RNA sequence and the
      structure in an elegant and accurate fashion.'
    example: RF00230
    homepage: https://rfam.xfam.org/
    name: Rfam at EMBL-EBI
    namespaceEmbeddedInLui: false
    pattern: ^RF\d{5}$
    prefix: rfam
    uri_format: https://rfam.xfam.org/family/$1
  ncbi:
    example: RF00230
    homepage: http://www.sanger.ac.uk/Software/Rfam/
    name: RNA families database of alignments and CMs
    prefix: RFAM
  prefix: rfam
  publications:
  - doi: 10.1093/nar/gkae1023
    pmc: null
    pubmed: '39526405'
    title: 'Rfam 15: RNA families database in 2025'
    year: 2024
  - doi: 10.1093/nar/gkx1038
    pmc: PMC5753348
    pubmed: '29112718'
    title: 'Rfam 13.0: shifting to a genome-centric resource for non-coding RNA families'
    year: 2018
  - doi: 10.1093/nar/gku1063
    pmc: PMC4383904
    pubmed: '25392425'
    title: 'Rfam 12.0: updates to the RNA families database'
    year: 2014
  - doi: 10.1093/nar/gku1063
    pmc: null
    pubmed: null
    title: 'Rfam 12.0: updates to the RNA families database.'
    year: null
  - doi: 10.1093/nar/gkx1038
    pmc: null
    pubmed: null
    title: 'Rfam 13.0: shifting to a genome-centric resource for non-coding RNA families.'
    year: null
  - doi: 10.1093/nar/gku1063
    pmc: null
    pubmed: null
    title: 'Rfam 12.0: updates to the RNA families database.'
    year: null
  - doi: 10.1093/nar/gkx1038
    pmc: null
    pubmed: null
    title: 'Rfam 13.0: shifting to a genome-centric resource for non-coding RNA families.'
    year: null
rfc:
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: Legacy site for IETF RFC proposals
  mappings:
    n2t: rfc
  n2t:
    example: '5013'
    homepage: https://www.ietf.org/
    name: Internet Standard -- IETF Request for Comments
    namespaceEmbeddedInLui: false
    prefix: rfc
    uri_format: https://tools.ietf.org/rfc/rfc$1
  pattern: ^\d+$
  prefix: rfc
rgd:
  aberowl:
    name: RRB Group D
    prefix: RGD
  biocontext:
    prefix: RGD
    uri_format: http://rgd.mcw.edu/rgdweb/report/gene/main.html?id=$1
  bioportal:
    name: RRB Group D
    prefix: RGD
  cellosaurus:
    category: Organism-specific databases
    homepage: https://rgd.mcw.edu
    name: Rat Genome Database
    prefix: RGD
    uri_format: https://rgd.mcw.edu/rgdweb/report/gene/main.html?id=$1
  domain: gene
  edam:
    description: Identifier of an entry from the RGD database.
    name: RGD
    obsolete: false
    prefix: '2620'
  example: '7499841'
  fairsharing:
    abbreviation: RGD
    contact:
      email: jrsmith@mcw.edu
      name: Jennifer R Smith
      orcid: 0000-0002-6443-9376
    description: The Rat Genome Database stores genetic, genomic, phenotype, and disease
      data generated from rat research. It provides access to corresponding data for
      eight other species, allowing cross-species comparison. Data curation is performed
      both manually and via an automated pipeline, giving RGD users integrated access
      to a wide variety of data to support their research.
    homepage: https://rgd.mcw.edu/
    license: https://rgd.mcw.edu/wg/disclaimer
    name: Rat Genome Database
    prefix: FAIRsharing.pfg82t
    publications:
    - doi: 10.1093/nar/gkl988
      pubmed_id: 17151068
      title: The Rat Genome Database, update 2007--easing the path from disease to
        data and back again.
    - doi: 10.1093/database/bat015
      pubmed_id: 23603846
      title: 'PhenoMiner: quantitative phenotype curation at the rat genome database.'
    - doi: 10.1186/s40246-014-0017-8
      pubmed_id: 25265995
      title: 'Disease pathways at the Rat Genome Database Pathway Portal: genes in
        context-a network approach to understanding the molecular mechanisms of disease.'
    - doi: 10.1093/nar/gku1026
      pubmed_id: 25355511
      title: 'The Rat Genome Database 2015: genomic, phenotypic and environmental
        variations and disease.'
    - doi: 10.1093/nar/gkz1041
      pubmed_id: 31713623
      title: 'The Year of the Rat: The Rat Genome Database at 20: a multi-species
        knowledgebase and analysis platform.'
    - doi: 10.1093/database/baw034
      pubmed_id: 27009807
      title: The Disease Portals, disease-gene annotation and the RGD disease ontology
        at the Rat Genome Database.
    - doi: null
      pubmed_id: 10400928
      title: A high-density integrated genetic linkage and radiation hybrid map of
        the laboratory rat.
    - doi: 10.1007/s00335-021-09932-x
      pubmed_id: null
      title: The Rat Genome Database (RGD) facilitates genomic and phenotypic data
        integration across multiple species for biomedical research
    - doi: 10.1093/genetics/iyac005
      pubmed_id: 35380657
      title: 'MOET: a web-based gene set enrichment tool at the Rat Genome Database
        for multiontology and multispecies analyses.'
    - doi: 10.1007/978-1-4939-9581-3_1
      pubmed_id: 31228150
      title: 'The Rat: A Model Used in Biomedical Research.'
    - doi: 10.1007/978-1-4939-9581-3_2
      pubmed_id: 31228151
      title: Rat Genome Assemblies, Annotation, and Variant Repository.
    - doi: 10.1007/978-1-4939-9581-3_3
      pubmed_id: 31228152
      title: Rat Genome Databases, Repositories, and Tools.
    - doi: 10.1093/database/baz037
      pubmed_id: 30938777
      title: Quantitative phenotype analysis to identify, validate and compare rat
        disease models.
    - doi: 10.1093/database/baz014
      pubmed_id: 30753478
      title: Integrated curation and data mining for disease and phenotype models
        at the Rat Genome Database.
    - doi: 10.1007/978-1-4939-7737-6_8
      pubmed_id: 29761460
      title: A Primer for the Rat Genome Database (RGD).
    - doi: 10.1093/ilar/ilw041
      pubmed_id: 28838068
      title: Rat Genome and Model Resources.
    - doi: null
      pubmed_id: 27736745
      title: Exploring human disease using the Rat Genome Database.
    - doi: 10.1016/j.csbj.2015.11.006
      pubmed_id: 27602200
      title: Disease, Models, Variants and Altered Pathways-Journeying RGD Through
        the Magnifying Glass.
    - doi: 10.1152/physiolgenomics.00046.2016
      pubmed_id: 27287925
      title: Comprehensive coverage of cardiovascular disease data in the disease
        portals at the Rat Genome Database.
    - doi: 10.1371/journal.pcbi.1000582
      pubmed_id: 19956751
      title: 'The rat genome database curators: who, what, where, why.'
    subjects:
    - Genomics
    - Quantitative Genetics
    - Veterinary Medicine
    - Phenomics
    - Molecular Medicine
    - Biomedical Science
    - Comparative Genomics
    - Translational Medicine
    twitter: ratgenome
  go:
    homepage: https://rgd.mcw.edu/
    name: Rat Genome Database
    prefix: RGD
    synonyms:
    - RAD
    - RGDID
    uri_format: https://rgd.mcw.edu/rgdweb/search/search.html?term=$1
  integbio:
    alt_name: The Rat Genome Database
    description: This is a comprehensive site for rat genome researches. In addition
      to information on rat genes, the site contains information on rat strains, data
      on rat models for disease, and publications.
    fairsharing: biodbcore-000417
    homepage: http://rgd.mcw.edu
    information_keywords:
    - Bioresource
    - Ontology/Terminology/Nomenclature
    - Sequence
    - Interaction/Pathway
    - Repository
    maintainer: Medical College of Wisconsin/Bioinformatics Research Center
    name: RGD
    prefix: nbdc00188
    pubmeds:
    - '21478484'
    - '17151068'
    status: Active
    target_keywords:
    - Genome/Gene
    - Genetic variation
    - DNA
    - Organism
    - Health/Disease
  license: CC-BY-4.0
  logo: https://rgd.mcw.edu/rgdweb//common/images/rgd_logo.jpg
  mappings:
    aberowl: RGD
    biocontext: RGD
    bioportal: RGD
    cellosaurus: RGD
    edam: '2620'
    fairsharing: FAIRsharing.pfg82t
    go: RGD
    integbio: nbdc00188
    miriam: rgd
    n2t: rgd
    ncbi: RGD
    pathguide: '267'
    prefixcommons: rgd
    re3data: r3d100010417
    rrid: RGD
    togoid: Rgd
    uniprot: DB-0091
    wikidata: P3853
  miriam:
    deprecated: false
    description: Rat Genome Database seeks to collect, consolidate, and integrate
      rat genomic and genetic data with curated functional and physiological data
      and make these data widely available to the scientific community. This collection
      references genes.
    homepage: http://rgd.mcw.edu/
    id: '00000047'
    name: Rat Genome Database
    namespaceEmbeddedInLui: false
    pattern: ^\d{4,}$
    prefix: rgd
    providers:
    - code: agr
      description: RGD through the Alliance of Genome Resources
      homepage: https://www.alliancegenome.org
      name: RGD through the Alliance of Genome Resources
      uri_format: https://www.alliancegenome.org/gene/RGD:$1
    sampleId: '2018'
    uri_format: http://rgd.mcw.edu/rgdweb/report/gene/main.html?id=$1
  n2t:
    description: Rat Genome Database seeks to collect, consolidate, and integrate
      rat genomic and genetic data with curated functional and physiological data
      and make these data widely available to the scientific community. This collection
      references genes.
    example: '2018'
    homepage: http://rgd.mcw.edu/
    name: Rat Genome Database
    namespaceEmbeddedInLui: false
    pattern: ^\d{4,}$
    prefix: rgd
    uri_format: http://rgd.mcw.edu/rgdweb/report/gene/main.html?id=$1
  name: Rat Genome Database
  ncbi:
    example: '620528'
    homepage: http://rgd.mcw.edu/rgdweb/search/search.html
    name: Rat Genome Database
    prefix: RGD
  pathguide:
    abbreviation: RGD
    homepage: http://rgd.mcw.edu/wg/home/pathway2/molecular-pathways2
    name: Rat Genome Database pathway resource
    prefix: '267'
  prefix: rgd
  prefixcommons:
    description: Rat Genome Database seeks to collect, consolidate, and integrate
      rat genomic and genetic data with curated functional and physiological data
      and make these data widely available to the scientific community.
    example: '2018'
    homepage: http://rgd.mcw.edu/genes/
    keywords:
    - genome
    - gene
    - DNA
    name: Rat Genome Database
    pattern: ^\d{4,7}$
    prefix: rgd
    pubmed_ids:
    - '17151068'
    uri_format: http://rgd.mcw.edu/tools/genes/genes_view.cgi?id=$1
  publications:
  - doi: 10.1093/genetics/iyac005
    pmc: PMC8982048
    pubmed: '35380657'
    title: 'MOET: a web-based gene set enrichment tool at the Rat Genome Database
      for multiontology and multispecies analyses'
    year: 2022
  - doi: 10.1007/s00335-021-09932-x
    pmc: PMC8570235
    pubmed: '34741192'
    title: The Rat Genome Database (RGD) facilitates genomic and phenotypic data integration
      across multiple species for biomedical research
    year: 2021
  - doi: 10.1093/nar/gkz1041
    pmc: PMC7145519
    pubmed: '31713623'
    title: 'The Year of the Rat: The Rat Genome Database at 20: a multi-species knowledgebase
      and analysis platform'
    year: 2020
  - doi: 10.1093/database/baz014
    pmc: PMC6369425
    pubmed: '30753478'
    title: Integrated curation and data mining for disease and phenotype models at
      the Rat Genome Database
    year: 2019
  - doi: 10.1093/database/baz037
    pmc: PMC6444380
    pubmed: '30938777'
    title: Quantitative phenotype analysis to identify, validate and compare rat disease
      models
    year: 2019
  - doi: 10.1007/978-1-4939-9581-3_2
    pmc: null
    pubmed: '31228151'
    title: Rat Genome Assemblies, Annotation, and Variant Repository
    year: 2019
  - doi: 10.1007/978-1-4939-9581-3_3
    pmc: null
    pubmed: '31228152'
    title: Rat Genome Databases, Repositories, and Tools
    year: 2019
  - doi: 10.1007/978-1-4939-9581-3_1
    pmc: null
    pubmed: '31228150'
    title: 'The Rat: A Model Used in Biomedical Research'
    year: 2019
  - doi: 10.1007/978-1-4939-7737-6_8
    pmc: PMC6487669
    pubmed: '29761460'
    title: A Primer for the Rat Genome Database (RGD)
    year: 2018
  - doi: 10.1093/ilar/ilw041
    pmc: PMC6057551
    pubmed: '28838068'
    title: Rat Genome and Model Resources
    year: 2017
  - doi: 10.1152/physiolgenomics.00046.2016
    pmc: PMC5005459
    pubmed: '27287925'
    title: Comprehensive coverage of cardiovascular disease data in the disease portals
      at the Rat Genome Database
    year: 2016
  - doi: 10.1242/dmm.026021
    pmc: PMC5087824
    pubmed: '27736745'
    title: Exploring human disease using the Rat Genome Database
    year: 2016
  - doi: 10.1093/database/baw034
    pmc: PMC4805243
    pubmed: '27009807'
    title: The Disease Portals, disease-gene annotation and the RGD disease ontology
      at the Rat Genome Database
    year: 2016
  - doi: 10.1016/j.csbj.2015.11.006
    pmc: PMC4700298
    pubmed: '27602200'
    title: Disease, Models, Variants and Altered Pathways-Journeying RGD Through the
      Magnifying Glass
    year: 2015
  - doi: 10.1186/s40246-014-0017-8
    pmc: PMC4191248
    pubmed: '25265995'
    title: 'Disease pathways at the Rat Genome Database Pathway Portal: genes in context-a
      network approach to understanding the molecular mechanisms of disease'
    year: 2014
  - doi: 10.1093/nar/gku1026
    pmc: PMC4383884
    pubmed: '25355511'
    title: 'The Rat Genome Database 2015: genomic, phenotypic and environmental variations
      and disease'
    year: 2014
  - doi: 10.1093/database/bat015
    pmc: PMC3630803
    pubmed: '23603846'
    title: 'PhenoMiner: quantitative phenotype curation at the rat genome database'
    year: 2013
  - doi: 10.1371/journal.pcbi.1000582
    pmc: PMC2775909
    pubmed: '19956751'
    title: 'The rat genome database curators: who, what, where, why'
    year: 2009
  - doi: 10.1093/nar/gkl988
    pmc: PMC1761441
    pubmed: '17151068'
    title: The Rat Genome Database, update 2007--easing the path from disease to data
      and back again
    year: 2006
  - doi: null
    pmc: null
    pubmed: '10400928'
    title: A high-density integrated genetic linkage and radiation hybrid map of the
      laboratory rat
    year: 1999
  - doi: 10.1093/database/baae132
    pmc: PMC11753291
    pubmed: '39841812'
    title: Standardized pipelines support and facilitate integration of diverse datasets
      at the Rat Genome Database
    year: null
  re3data:
    description: 'The Rat Genome Database is a collaborative effort between leading
      research institutions involved in rat genetic and genomic research. Its goal,
      as stated in RFA: HL-99-013 is the establishment of a Rat Genome Database, to
      collect, consolidate, and integrate data generated from ongoing rat genetic
      and genomic research efforts and make these data widely available to the scientific
      community. A secondary, but critical goal is to provide curation of mapped positions
      for quantitative trait loci, known mutations and other phenotypic data.'
    doi: 10.17616/R3WK60
    homepage: https://rgd.mcw.edu
    name: Rat Genome Database
    prefix: r3d100010417
    synonyms:
    - RGD
    xrefs:
      nif: 0000-00134
      omics: '01660'
  rrid:
    homepage: http://rgd.mcw.edu
    keywords:
    - FASEB list
    - behavior
    - comparative genomics
    - congenic rat
    - data analysis service
    - disease
    - est
    - function
    - gene
    - genetic
    - genome
    - genomic
    - genotype
    - gold standard
    - human
    - immunology
    - inbred rat strain
    - knockout
    - map
    - marker
    - model organism
    - mouse
    - mutant
    - ontology
    - organism supplier
    - pathway
    - phenotype
    - physiology
    - proteomics
    - qtl
    - rat
    - recombinant inbred rat
    - sequence
    - strain
    - variation
    name: Rat Genome Database (RGD)
    prefix: RGD
    pubmeds:
    - '23434633'
    - '18996890'
    - '17151068'
    scr: '006444'
  synonyms:
  - RGD
  togoid:
    catalog: nbdc00188
    description: This is a comprehensive site for rat genome researches. In addition
      to information on rat genes, the site contains information on rat strains, data
      on rat models for disease, and publications.
    examples:
    - '1308312'
    - '1311120'
    - '1309724'
    - '1565514'
    - '7683241'
    - '1307957'
    - '71036'
    - '1307876'
    - '1308965'
    - '1305482'
    keywords:
    - Gene
    name: RGD
    pattern: ^(?:(?:RGD|rgd):)?(?\d{4,})$
    prefix: Rgd
    uri_format: http://identifiers.org/rgd/$1
  twitter: ratgenome
  uniprot:
    abbreviation: RGD
    category: Organism-specific databases
    homepage: https://rgd.mcw.edu/
    name: Rat Genome Database
    prefix: DB-0091
    publications:
    - doi: 10.1093/nar/gkz1041
      pubmed: '31713623'
    uri_format: https://rgd.mcw.edu/rgdweb/report/gene/main.html?id=$1
  wikidata:
    description: Identifier for a genetic element in the Rat Genome Database
    example:
    - '1584682'
    - '2243'
    - '3754'
    homepage: https://rgd.mcw.edu/
    name: Rat Genome Database ID
    prefix: P3853
    uri_format: https://rgd.mcw.edu/rgdweb/report/gene/main.html?id=$1
rgd.qtl:
  biocontext:
    prefix: RGD.QTL
  mappings:
    biocontext: RGD.QTL
    miriam: rgd.qtl
    n2t: rgd.qtl
  miriam:
    deprecated: false
    description: Rat Genome Database seeks to collect, consolidate, and integrate
      rat genomic and genetic data with curated functional and physiological data
      and make these data widely available to the scientific community. This collection
      references quantitative trait loci (qTLs), providing phenotype and disease descriptions,
      mapping, and strain information as well as links to markers and candidate genes.
    homepage: http://rgd.mcw.edu/
    id: '00000451'
    name: Rat Genome Database qTL
    namespaceEmbeddedInLui: false
    pattern: ^\d+$
    prefix: rgd.qtl
    sampleId: '1354581'
    uri_format: http://rgd.mcw.edu/rgdweb/report/qtl/main.html?id=$1
  n2t:
    description: Rat Genome Database seeks to collect, consolidate, and integrate
      rat genomic and genetic data with curated functional and physiological data
      and make these data widely available to the scientific community. This collection
      references quantitative trait loci (qTLs), providing phenotype and disease descriptions,
      mapping, and strain information as well as links to markers and candidate genes.
    example: '1354581'
    homepage: http://rgd.mcw.edu/
    name: Rat Genome Database qTL at Medical College of Wisconsin
    namespaceEmbeddedInLui: false
    pattern: ^\d+$
    prefix: rgd.qtl
    uri_format: http://rgd.mcw.edu/rgdweb/report/qtl/main.html?id=$1
  part_of_database: rgd
  prefix: rgd.qtl
  twitter: ratgenome
rgd.strain:
  biocontext:
    prefix: RGD.STRAIN
  mappings:
    biocontext: RGD.STRAIN
    miriam: rgd.strain
    n2t: rgd.strain
  miriam:
    deprecated: false
    description: Rat Genome Database seeks to collect, consolidate, and integrate
      rat genomic and genetic data with curated functional and physiological data
      and make these data widely available to the scientific community. This collection
      references strain reports, which include a description of strain origin, disease,
      phenotype, genetics and immunology.
    homepage: http://rgd.mcw.edu/
    id: '00000452'
    name: Rat Genome Database strain
    namespaceEmbeddedInLui: false
    pattern: ^\d+$
    prefix: rgd.strain
    sampleId: '5688061'
    uri_format: http://rgd.mcw.edu/rgdweb/report/strain/main.html?id=$1
  n2t:
    description: Rat Genome Database seeks to collect, consolidate, and integrate
      rat genomic and genetic data with curated functional and physiological data
      and make these data widely available to the scientific community. This collection
      references strain reports, which include a description of strain origin, disease,
      phenotype, genetics and immunology.
    example: '5688061'
    homepage: http://rgd.mcw.edu/
    name: Rat Genome Database strain at Medical College of Wisconsin
    namespaceEmbeddedInLui: false
    pattern: ^\d+$
    prefix: rgd.strain
    uri_format: http://rgd.mcw.edu/rgdweb/report/strain/main.html?id=$1
  part_of_database: rgd
  prefix: rgd.strain
  twitter: ratgenome
rhea:
  biocontext:
    prefix: RHEA
  domain: reaction
  edam:
    description: Identifier of an enzyme-catalysed reaction from the Rhea database.
    name: Reaction ID (Rhea)
    obsolete: false
    prefix: '2644'
  fairsharing:
    abbreviation: Rhea
    contact:
      email: anne.morgat@sib.swiss
      name: Anne Morgat
      orcid: 0000-0002-1216-2969
    description: Rhea is a comprehensive and non-redundant resource of expert-curated
      chemical and transport reactions of biological interest. Rhea can be used for
      enzyme annotation, genome-scale metabolic modeling and omics-related analysis.
      Rhea describes enzyme-catalyzed reactions covering the IUBMB Enzyme Nomenclature
      list as well as additional reactions, including spontaneously occurring reactions.
      Rhea is built on ChEBI (Chemical Entities of Biological Interest) ontology of
      small molecules to describe its reaction participants. Since December 2018,
      Rhea is the standard for enzyme annotation in UniProt.
    homepage: http://www.rhea-db.org
    license: CC-BY-4.0
    name: Rhea
    prefix: FAIRsharing.pn1sr5
    publications:
    - doi: 10.1093/nar/gkw990
      pubmed_id: 27789701
      title: Updates in Rhea - an expert curated resource of biochemical reactions.
    - doi: 10.1093/nar/gku961
      pubmed_id: 25332395
      title: Updates in Rhea--a manually curated resource of biochemical reactions.
    - doi: 10.1093/nar/gkr1126
      pubmed_id: 22135291
      title: Rhea--a manually curated resource of biochemical reactions.
    - doi: 10.1093/nar/gky876
      pubmed_id: 30272209
      title: 'Updates in Rhea: SPARQLing biochemical reaction data.'
    - doi: 10.1093/bioinformatics/btz817
      pubmed_id: 31688925
      title: Enzyme annotation in UniProtKB using Rhea
    - doi: 10.1093/nar/gkab1016
      pubmed_id: 34755880
      title: Rhea, the reaction knowledgebase in 2022.
    subjects:
    - Biochemistry
    - Life Science
    twitter: rhea_db
  go:
    description: Rhea is a manually annotated database of chemical reactions. All
      data in Rhea is freely accessible and available for anyone to use.
    homepage: https://www.rhea-db.org
    name: Rhea, the Annotated Reactions Database
    prefix: RHEA
    uri_format: https://www.rhea-db.org/rhea/$1
  integbio:
    description: Rhea is a comprehensive and non-redundant resource of expert-curated
      chemical and transport reactions of biological interest. Rhea can be used for
      enzyme annotation, genome-scale metabolic modeling and omics-related analysis.
      Rhea describes enzyme-catalyzed reactions covering the IUBMB Enzyme Nomenclature
      list as well as additional reactions, including spontaneously occurring reactions.
      Rhea is built on ChEBI (Chemical Entities of Biological Interest) ontology of
      small molecules to describe its reaction participants. Since December 2018,
      Rhea is the standard for enzyme annotation in UniProt.
    fairsharing: FAIRsharing.pn1sr5
    homepage: http://www.rhea-db.org
    information_keywords:
    - Interaction/Pathway
    maintainer: SIB (Swiss Institute of Bioinformatics)
    name: Rhea
    prefix: nbdc02083
    pubmeds:
    - '25332395'
    - '22135291'
    - '27789701'
    status: Active
    target_keywords:
    - Protein
    - Metabolite
  license: CC-BY-4.0
  logo: https://www.rhea-db.org/style/images/rhea_logo.png
  mappings:
    biocontext: RHEA
    edam: '2644'
    fairsharing: FAIRsharing.pn1sr5
    go: RHEA
    integbio: nbdc02083
    miriam: rhea
    n2t: rhea
    pathguide: '310'
    prefixcommons: rhea
    re3data: r3d100010891
    togoid: Rhea
    wikidata.entity: Q24265951
  miriam:
    deprecated: false
    description: ' Rhea is an expert-curated knowledgebase of chemical and transport
      reactions of biological interest. Enzyme-catalyzed and spontaneously occurring
      reactions are curated from peer-reviewed literature and represented in a computationally
      tractable manner by using the ChEBI (Chemical Entities of Biological Interest)
      ontology to describe reaction participants.


      Rhea covers the reactions described by the IUBMB Enzyme Nomenclature as well
      as many additional reactions and can be used for enzyme annotation, genome-scale
      metabolic modeling and omics-related analyses. Rhea is the standard for enzyme
      and transporter annotation in UniProtKB.'
    homepage: https://www.rhea-db.org/
    id: 00000082
    name: Rhea
    namespaceEmbeddedInLui: false
    pattern: ^\d{5}$
    prefix: rhea
    sampleId: '12345'
    uri_format: https://www.rhea-db.org/rhea/$1
  n2t:
    description: Rhea is a manually annotated reaction database, where all reaction
      participants (reactants and products) are linked to the ChEBI database (Chemical
      Entities of Biological Interest), providing detailed information about structure,
      formulae and charge. It is populated with the reactions found in the EC list,
      IntEnz and ENZYME databases), as well as other biochemical reactions, including
      those that are often termed "spontaneous".
    example: '12345'
    homepage: https://www.rhea-db.org/
    name: Rhea
    namespaceEmbeddedInLui: false
    pattern: ^\d{5}$
    prefix: rhea
    uri_format: https://www.rhea-db.org/reaction?id=$1
  name: Rhea reaction
  pathguide:
    abbreviation: Rhea
    homepage: http://www.rhea-db.org/
    keywords:
    - BioPAX
    name: Reaction database
    prefix: '310'
  prefix: rhea
  prefixcommons:
    description: Rhea is a manually annotated reaction database, where all reaction
      participants (reactants and products) are linked to the ChEBI database (Chemical
      Entities of Biological Interest), providing detailed information about structure,
      formulae and charge. It is populated with the reactions found in the EC list,
      IntEnz and ENZYME databases), as well as other biochemical reactions, including
      those that are often termed "spontaneous".
    example: '12345'
    homepage: http://www.ebi.ac.uk/rhea/
    keywords:
    - reaction
    - small molecule
    license: http://www.ebi.ac.uk/Information/termsofuse.html
    name: Reaction database
    pattern: ^\d{5}$
    prefix: rhea
    uri_format: http://www.ebi.ac.uk/rhea//reaction.xhtml?id=$1
  publications:
  - doi: 10.1093/nar/gkab1016
    pmc: PMC8728268
    pubmed: '34755880'
    title: Rhea, the reaction knowledgebase in 2022
    year: 2022
  - doi: 10.1093/bioinformatics/btz817
    pmc: PMC7162351
    pubmed: '31688925'
    title: Enzyme annotation in UniProtKB using Rhea
    year: 2020
  - doi: 10.1093/nar/gky876
    pmc: PMC6324061
    pubmed: '30272209'
    title: 'Updates in Rhea: SPARQLing biochemical reaction data'
    year: 2019
  - doi: 10.1093/nar/gkw990
    pmc: PMC5210663
    pubmed: '27789701'
    title: Updates in Rhea - an expert curated resource of biochemical reactions
    year: 2016
  - doi: 10.1093/nar/gku961
    pmc: PMC4384025
    pubmed: '25332395'
    title: Updates in Rhea--a manually curated resource of biochemical reactions
    year: 2014
  - doi: 10.1093/nar/gkr1126
    pmc: PMC3245052
    pubmed: '22135291'
    title: Rhea--a manually curated resource of biochemical reactions
    year: 2011
  re3data:
    description: 'Rhea is a freely available and comprehensive resource of expert-curated
      biochemical reactions. It has been designed to provide a non-redundant set of
      chemical transformations for applications such as the functional annotation
      of enzymes, pathway inference and metabolic network reconstruction. There are
      three types of reaction participants (reactants and products): Small molecules,  Rhea
      polymers, Generic compounds.

      All three types of reaction participants are linked to the ChEBI database (Chemical
      Entities of Biological Interest) which provides detailed information about structure,
      formula and charge. Rhea provides built-in validations that ensure both mass
      and charge balance of the reactions. We have populated the database with the
      reactions found in the enzyme classification (i.e. in the IntEnz and ENZYME
      databases), extending it with additional known reactions of biological interest.
      While the main focus of Rhea is enzyme-catalysed reactions, other biochemical
      reactions (including those that are often termed "spontaneous") also are included.'
    doi: 10.17616/R3332H
    homepage: https://www.rhea-db.org/
    license: Apache License 2.0
    name: Rhea
    prefix: r3d100010891
    xrefs:
      omics: 06093
  synonyms:
  - RHEA
  togoid:
    catalog: nbdc02083
    examples:
    - '10253'
    - '10818'
    - '13517'
    - '11136'
    - '13729'
    - '10240'
    - '11728'
    - '16870'
    - '10732'
    - '11278'
    keywords:
    - Reaction
    name: Rhea
    pattern: ^(?\d{5})$
    prefix: Rhea
    uri_format: http://identifiers.org/rhea/$1
  uri_format: https://www.rhea-db.org/rhea/$1
  wikidata:
    database: Q24265951
ribocentre:
  contact:
    email: huanglin36@mail.sysu.edu.cn
    github: null
    name: Lin Huang
    orcid: 0000-0002-2121-365X
  contributor:
    email: benjamin_gyori@hms.harvard.edu
    github: bgyori
    name: Benjamin M. Gyori
    orcid: 0000-0001-9439-5346
  description: Ribocentre is designed to contain comprehensive information of all
    natural ribozymes.
  example: hammer
  github_request_issue: 611
  homepage: https://www.ribocentre.org/
  name: Ribocentre
  pattern: ^[a-zA-Z0-9-]+$
  prefix: ribocentre
  publications:
  - doi: 10.1093/nar/gkac840
    pmc: PMC9825448
    pubmed: '36177882'
    title: 'Ribocentre: a database of ribozymes'
    year: 2023
  repository: https://github.com/ribocentre/ribocentre.github.io
  reviewer:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  synonyms:
  - ribocenter
  uri_format: https://www.ribocentre.org/docs/$1
ricecyc:
  mappings:
    pathguide: '227'
    prefixcommons: ricecyc
  pathguide:
    abbreviation: RiceCyc
    homepage: http://pathway.gramene.org/gramene/ricecyc.shtml
    name: The rice metabolic pathway database
    prefix: '227'
  prefix: ricecyc
  prefixcommons:
    description: RiceCyc is a catalog of known and/or predicted biochemical pathways
      from rice (Oryza sativa). Pathways and genes presented in this catalog are primarily
      based on the annotations carried out by Gramene database project
    example: PWY-1042
    homepage: http://www.gramene.org/pathway/ricecyc.html
    keywords:
    - pathway
    - gene
    name: Rice Metabolic Pathways
    pattern: ^PWY-\d+$
    prefix: ricecyc
    uri_format: http://pathway.gramene.org/RICE/NEW-IMAGE?type=PATHWAY&object=$1
  reviewer:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
ricegap:
  biocontext:
    prefix: RICEGAP
  contact:
    email: Robin.Buell@uga.edu
    github: null
    name: C. Robin Buell
    orcid: 0000-0002-6727-4677
  homepage: https://rice.uga.edu
  mappings:
    biocontext: RICEGAP
    miriam: ricegap
    n2t: ricegap
    prefixcommons: rgap
  miriam:
    deprecated: false
    description: The objective of this project is to provide high quality annotation
      for the rice genome Oryza sativa spp japonica cv Nipponbare. All genes are annotated
      with functional annotation including expression data, gene ontologies, and tagged
      lines.
    homepage: http://rice.plantbiology.msu.edu/annotation_pseudo_current.shtml
    id: 00000358
    name: Rice Genome Annotation Project
    namespaceEmbeddedInLui: false
    pattern: ^LOC\_Os\d{1,2}g\d{5}$
    prefix: ricegap
    sampleId: LOC_Os02g13300
    uri_format: http://rice.plantbiology.msu.edu/cgi-bin/ORF_infopage.cgi?&orf=$1
  n2t:
    description: The objective of this project is to provide high quality annotation
      for the rice genome Oryza sativa spp japonica cv Nipponbare. All genes are annotated
      with functional annotation including expression data, gene ontologies, and tagged
      lines.
    example: LOC_Os02g13300
    homepage: http://rice.plantbiology.msu.edu/annotation_pseudo_current.shtml
    name: Rice Genome Annotation Project at TIGR
    namespaceEmbeddedInLui: false
    pattern: ^LOC\_Os\d{1,2}g\d{5}$
    prefix: ricegap
    uri_format: http://rice.plantbiology.msu.edu/cgi-bin/ORF_infopage.cgi?&orf=$1
  prefix: ricegap
  prefixcommons:
    description: This website provides genome sequence from the Nipponbare subspecies
      of rice and annotation of the 12 rice chromosomes. These data are available
      through search pages and the Genome Browser that provides an integrated display
      of annotation data.
    example: LOC_Os02g13300
    homepage: http://rice.plantbiology.msu.edu/
    keywords:
    - genome
    - DNA
    name: Rice Genome Annotation Project
    pattern: ^LOC\_Os\d{1,2}g\d{5}$
    prefix: rgap
    pubmed_ids:
    - '17145706'
    synonyms:
    - rice
    uri_format: http://rice.plantbiology.msu.edu/cgi-bin/gbrowse/rice/?name=$1
  publications:
  - doi: 10.1093/nar/gkae1061
    pmc: null
    pubmed: '39558187'
    title: 'The rice genome annotation project: an updated database for mining the
      rice genome'
    year: 2024
  - doi: 10.1093/nar/gkl976
    pmc: PMC1751532
    pubmed: '17145706'
    title: 'The TIGR Rice Genome Annotation Resource: improvements and new features'
    year: 2006
  - doi: null
    pmc: null
    pubmed: '17145706'
    title: null
    year: null
  - doi: null
    pmc: null
    pubmed: '17145706'
    title: null
    year: null
  - doi: null
    pmc: null
    pubmed: '17145706'
    title: null
    year: null
  synonyms:
  - rgap
ricenetdb.compound:
  biocontext:
    prefix: RICENETDB.COMPOUND
  mappings:
    biocontext: RICENETDB.COMPOUND
    miriam: ricenetdb.compound
    n2t: ricenetdb.compound
  miriam:
    deprecated: false
    description: 'RiceNetDB is currently the most comprehensive regulatory database
      on Oryza Sativa based on genome annotation. It was displayed in three levels:
      GEM, PPIs and GRNs to facilitate biomolecular regulatory analysis and gene-metabolite
      mapping.'
    homepage: http://bis.zju.edu.cn/ricenetdb
    id: '00000666'
    name: RiceNetDB Compound
    namespaceEmbeddedInLui: false
    pattern: ^OSC\d{4}$
    prefix: ricenetdb.compound
    sampleId: OSC1416
    uri_format: http://bis.zju.edu.cn/ricenetdb/compounddetails.php?ID=$1
  n2t:
    description: 'RiceNetDB is currently the most comprehensive regulatory database
      on Oryza Sativa based on genome annotation. It was displayed in three levels:
      GEM, PPIs and GRNs to facilitate biomolecular regulatory analysis and gene-metabolite
      mapping.'
    example: OSC1416
    homepage: http://bis.zju.edu.cn/ricenetdb
    name: RiceNetDB Compound
    namespaceEmbeddedInLui: false
    pattern: ^OSC\d{4}$
    prefix: ricenetdb.compound
    uri_format: http://bis.zju.edu.cn/ricenetdb/compounddetails.php?ID=$1
  prefix: ricenetdb.compound
ricenetdb.gene:
  biocontext:
    prefix: RICENETDB.GENE
  mappings:
    biocontext: RICENETDB.GENE
    miriam: ricenetdb.gene
    n2t: ricenetdb.gene
  miriam:
    deprecated: false
    description: 'RiceNetDB is currently the most comprehensive regulatory database
      on Oryza Sativa based on genome annotation. It was displayed in three levels:
      GEM, PPIs and GRNs to facilitate biomolecular regulatory analysis and gene-metabolite
      mapping.'
    homepage: http://bis.zju.edu.cn/ricenetdb/
    id: '00000664'
    name: RiceNetDB Gene
    namespaceEmbeddedInLui: false
    pattern: ^LOC\_Os\d{1,2}g\d{5}\.\d$
    prefix: ricenetdb.gene
    sampleId: LOC_Os01g49190.1
    uri_format: http://bis.zju.edu.cn/ricenetdb/genedetails.php?ID=$1
  n2t:
    description: 'RiceNetDB is currently the most comprehensive regulatory database
      on Oryza Sativa based on genome annotation. It was displayed in three levels:
      GEM, PPIs and GRNs to facilitate biomolecular regulatory analysis and gene-metabolite
      mapping.'
    example: LOC_Os01g49190.1
    homepage: http://bis.zju.edu.cn/ricenetdb/
    name: RiceNetDB
    namespaceEmbeddedInLui: false
    pattern: ^LOC\_Os\d{1,2}g\d{5}\.\d$
    prefix: ricenetdb.gene
    uri_format: http://bis.zju.edu.cn/ricenetdb/genedetails.php?ID=$1
  prefix: ricenetdb.gene
ricenetdb.mirna:
  biocontext:
    prefix: RICENETDB.MIRNA
  mappings:
    biocontext: RICENETDB.MIRNA
    miriam: ricenetdb.mirna
    n2t: ricenetdb.mirna
  miriam:
    deprecated: false
    description: 'RiceNetDB is currently the most comprehensive regulatory database
      on Oryza Sativa based on genome annotation. It was displayed in three levels:
      GEM, PPIs and GRNs to facilitate biomolecular regulatory analysis and gene-metabolite
      mapping.'
    homepage: http://bis.zju.edu.cn/ricenetdb
    id: 00000668
    name: RiceNetDB miRNA
    namespaceEmbeddedInLui: false
    pattern: ^osa-miR\d{3,5}[a-z]{0,1}$
    prefix: ricenetdb.mirna
    sampleId: osa-miR446
    uri_format: http://bis.zju.edu.cn/ricenetdb/miRNAdetails.php?ID=$1
  n2t:
    description: 'RiceNetDB is currently the most comprehensive regulatory database
      on Oryza Sativa based on genome annotation. It was displayed in three levels:
      GEM, PPIs and GRNs to facilitate biomolecular regulatory analysis and gene-metabolite
      mapping.'
    example: osa-miR446
    homepage: http://bis.zju.edu.cn/ricenetdb
    name: RiceNetDB miRNA
    namespaceEmbeddedInLui: false
    pattern: ^osa-miR\d{3,5}[a-z]{0,1}$
    prefix: ricenetdb.mirna
    uri_format: http://bis.zju.edu.cn/ricenetdb/miRNAdetails.php?ID=$1
  prefix: ricenetdb.mirna
ricenetdb.protein:
  biocontext:
    prefix: RICENETDB.PROTEIN
  mappings:
    biocontext: RICENETDB.PROTEIN
    miriam: ricenetdb.protein
    n2t: ricenetdb.protein
  miriam:
    deprecated: false
    description: 'RiceNetDB is currently the most comprehensive regulatory database
      on Oryza Sativa based on genome annotation. It was displayed in three levels:
      GEM, PPIs and GRNs to facilitate biomolecular regulatory analysis and gene-metabolite
      mapping.'
    homepage: http://bis.zju.edu.cn/ricenetdb/
    id: '00000665'
    name: RiceNetDB Protein
    namespaceEmbeddedInLui: false
    pattern: ^LOC\_Os\d{1,2}g\d{5}$
    prefix: ricenetdb.protein
    sampleId: LOC_Os01g49190
    uri_format: http://bis.zju.edu.cn/ricenetdb/proteindetails.php?ID=$1
  n2t:
    description: 'RiceNetDB is currently the most comprehensive regulatory database
      on Oryza Sativa based on genome annotation. It was displayed in three levels:
      GEM, PPIs and GRNs to facilitate biomolecular regulatory analysis and gene-metabolite
      mapping.'
    example: LOC_Os01g49190
    homepage: http://bis.zju.edu.cn/ricenetdb/
    name: RiceNetDB
    namespaceEmbeddedInLui: false
    pattern: ^LOC\_Os\d{1,2}g\d{5}$
    prefix: ricenetdb.protein
    uri_format: http://bis.zju.edu.cn/ricenetdb/proteindetails.php?ID=$1
  prefix: ricenetdb.protein
ricenetdb.reaction:
  biocontext:
    prefix: RICENETDB.REACTION
  mappings:
    biocontext: RICENETDB.REACTION
    miriam: ricenetdb.reaction
    n2t: ricenetdb.reaction
  miriam:
    deprecated: false
    description: 'RiceNetDB is currently the most comprehensive regulatory database
      on Oryza Sativa based on genome annotation. It was displayed in three levels:
      GEM, PPIs and GRNs to facilitate biomolecular regulatory analysis and gene-metabolite
      mapping.'
    homepage: http://bis.zju.edu.cn/ricenetdb
    id: '00000667'
    name: RiceNetDB Reaction
    namespaceEmbeddedInLui: false
    pattern: ^OSR\d{4}$
    prefix: ricenetdb.reaction
    sampleId: OSR0818
    uri_format: http://bis.zju.edu.cn/ricenetdb/reactiondetails.php?ID=$1
  n2t:
    description: 'RiceNetDB is currently the most comprehensive regulatory database
      on Oryza Sativa based on genome annotation. It was displayed in three levels:
      GEM, PPIs and GRNs to facilitate biomolecular regulatory analysis and gene-metabolite
      mapping.'
    example: OSR0818
    homepage: http://bis.zju.edu.cn/ricenetdb
    name: RiceNetDB Reaction
    namespaceEmbeddedInLui: false
    pattern: ^OSR\d{4}$
    prefix: ricenetdb.reaction
    uri_format: http://bis.zju.edu.cn/ricenetdb/reactiondetails.php?ID=$1
  prefix: ricenetdb.reaction
rism:
  mappings:
    miriam: rism
  miriam:
    deprecated: false
    description: RISM Online is a new service that will publish the bibliographic
      and authority data from the catalogue of the Répertoire International des Sources
      Musicales project.
    homepage: https://rism.digital/
    id: 00000911
    name: RISM Online
    namespaceEmbeddedInLui: false
    pattern: ^[a-z]+/[0-9]+$
    prefix: rism
    sampleId: people/11035
    uri_format: https://rism.online/$1
  prefix: rism
rna_sstrand:
  mappings:
    prefixcommons: rna_sstrand
  prefix: rna_sstrand
  prefixcommons:
    description: RNA STRAND contains known RNA secondary structures of any type and
      organism. The ultimate goal of this database is to incorporate a comprehensive
      collection of known RNA secondary structures, and to provide the scientific
      community with simple yet powerful ways of analysing, searching and updating
      the proposed database.
    example: CRW_00469
    homepage: http://www.rnasoft.ca/sstrand
    keywords:
    - RNA
    - structure
    name: RNA SSTRAND
    pattern: ^[A-Z]_\d+$
    prefix: rna_sstrand
    uri_format: http://www.rnasoft.ca/sstrand/show_results.php?molecule_ID=$1
  reviewer:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
rnacentral:
  biocontext:
    prefix: RNACENTRAL
  contact:
    email: bsweeney@ebi.ac.uk
    github: blakesweeney
    name: Blake A Sweeney
    orcid: 0000-0002-6497-2883
  edam:
    description: Identifier of an entry from the RNA central database of annotated
      human miRNAs.
    name: RNA central
    obsolete: false
    prefix: '3856'
  fairsharing:
    abbreviation: RNAcentral
    description: RNAcentral is a free, public resource that offers integrated access
      to a comprehensive and up-to-date set of non-coding RNA sequences provided by
      a collaborating group of databases representing a broad range of organisms and
      RNA types.
    homepage: https://rnacentral.org
    name: RNAcentral
    prefix: FAIRsharing.KcCjL7
    publications:
    - doi: 10.1093/nar/gky1034
      pubmed_id: 30395267
      title: 'RNAcentral: a hub of information for non-coding RNA sequences.'
    - doi: 10.1093/nar/gkw1008
      pubmed_id: 27794554
      title: 'RNAcentral: a comprehensive database of non-coding RNA sequences.'
    repository: https://github.com/RNAcentral/
    subjects:
    - Bioinformatics
    - Biology
    twitter: RNAcentral
  go:
    description: An international database of ncRNA sequences
    homepage: https://rnacentral.org
    name: RNAcentral
    prefix: RNAcentral
    uri_format: https://rnacentral.org/rna/$1
  integbio:
    alt_name: Long Non-Coding RNA Database
    description: lncRNAdb is a database providing comprehensive annotations of long
      non-coding RNAs (lncRNAs) in eukaryotes. Each record contains referenced information
      about the RNA, including sequences, structural information, genomic context,
      expression, subcellular localization, conservation, functional evidence and
      other relevant information. lncRNAdb allows to search by querying published
      RNA names and aliases, sequences, species and associated protein-coding genes,
      as well as terms contained in the annotations, such as the tissues in which
      the transcripts are expressed and associated diseases. Moreover, lncRNAdb is
      linked to the UCSC Genome Browser for visualization and Noncoding RNA Expression
      Database (NRED) for expression information from a variety of sources.
    homepage: http://www.lncrnadb.com
    information_keywords:
    - Sequence
    - Bibliography/Documents
    maintainer: Institute for Molecular Bioscience, The University of Queensland
    name: lncRNAdb
    prefix: nbdc01215
    pubmeds:
    - '21112873'
    target_keywords:
    - RNA
  mappings:
    biocontext: RNACENTRAL
    edam: '3856'
    fairsharing: FAIRsharing.KcCjL7
    go: RNAcentral
    integbio: nbdc01215
    miriam: rnacentral
    n2t: rnacentral
    ncbi: RNAcentral
    wikidata: P8697
  miriam:
    deprecated: false
    description: RNAcentral is a public resource that offers integrated access to
      a comprehensive and up-to-date set of non-coding RNA sequences provided by a
      collaborating group of Expert Databases.
    homepage: https://rnacentral.org/
    id: '00000630'
    name: RNAcentral
    namespaceEmbeddedInLui: false
    pattern: ^URS[0-9A-F]{10}(\_\d+)?$
    prefix: rnacentral
    sampleId: URS0000759CF4
    uri_format: https://rnacentral.org/rna/$1
  n2t:
    description: RNAcentral is a public resource that offers integrated access to
      a comprehensive and up-to-date set of non-coding RNA sequences provided by a
      collaborating group of Expert Databases.
    example: URS0000759CF4
    homepage: https://rnacentral.org/
    name: RNAcentral through EMBL-EBI
    namespaceEmbeddedInLui: false
    pattern: ^URS[0-9A-F]{10}(\_\d+)?$
    prefix: rnacentral
    uri_format: https://rnacentral.org/rna/$1
  name: RNACentral
  ncbi:
    example: URS00001B9622_9606
    homepage: http://rnacentral.org
    name: Noncoding RNA Sequence Database
    prefix: RNAcentral
  prefix: rnacentral
  publications:
  - doi: 10.1093/nar/gky1034
    pmc: PMC6324050
    pubmed: '30395267'
    title: 'RNAcentral: a hub of information for non-coding RNA sequences'
    year: 2019
  - doi: 10.1093/nar/gkw1008
    pmc: PMC5210518
    pubmed: '27794554'
    title: 'RNAcentral: a comprehensive database of non-coding RNA sequences'
    year: 2016
  - doi: 10.1093/nar/gky1034
    pmc: null
    pubmed: null
    title: 'RNAcentral: a hub of information for non-coding RNA sequences.'
    year: null
  - doi: 10.1093/nar/gkw1008
    pmc: null
    pubmed: null
    title: 'RNAcentral: a comprehensive database of non-coding RNA sequences.'
    year: null
  - doi: 10.1093/nar/gky1034
    pmc: null
    pubmed: null
    title: 'RNAcentral: a hub of information for non-coding RNA sequences.'
    year: null
  - doi: 10.1093/nar/gkw1008
    pmc: null
    pubmed: null
    title: 'RNAcentral: a comprehensive database of non-coding RNA sequences.'
    year: null
  synonyms:
  - LNCRNADB
  wikidata:
    description: ID in the RNA central database
    example:
    - URS0000413C32_559292
    - URS000080E36F_9606
    homepage: https://rnacentral.org/
    name: RNACentral ID
    prefix: P8697
    uri_format: https://rnacentral.org/rna/$1
rnajunction:
  contact:
    email: ygyingli@ncsu.edu
    github: null
    name: Yaroslava G Yingling
    orcid: 0000-0002-8557-9992
  example: '8668'
  fairsharing:
    abbreviation: RNAJunction
    description: 'RNAJunction is a database of RNA junctions and kissing loop structures.
      It contains structure and sequence information for RNA structural elements such
      as helical junctions, internal loops, bulges and loop–loop interactions. It
      allows searching by PDB code, structural classification, sequence, keyword or
      inter-helix angles. RNAJunction is designed to aid analysis of RNA structures
      as well as design of novel RNA structures on a nanoscale. '
    homepage: https://rnajunction.ncifcrf.gov/
    name: RNAJunction
    prefix: FAIRsharing.zzgvrv
    publications:
    - doi: 10.1093/nar/gkm842
      pubmed_id: 17947325
      title: 'RNAJunction: a database of RNA junctions and kissing loops for three-dimensional
        structural analysis and nanodesign.'
    subjects:
    - Structural Biology
  mappings:
    fairsharing: FAIRsharing.zzgvrv
    prefixcommons: rnajunction
  name: Database of RNA Junctions and Kissing loop Structures
  prefix: rnajunction
  prefixcommons:
    description: Within this database you will to able to find more than 12,000 extracted
      three-dimensional junction and kissing loop structures as well as detailed annotations
      for each.
    example: '10387'
    homepage: http://rnajunction.abcc.ncifcrf.gov
    keywords:
    - structure
    - RNA
    name: 'RNAJunction: A Database of RNA Junction and Kissing loop Structure'
    pattern: ^\d+$
    prefix: rnajunction
    uri_format: http://rnajunction.abcc.ncifcrf.gov/JunctionPage.php?jid=$1
  publications:
  - doi: 10.1093/nar/gkm842
    pmc: PMC2238914
    pubmed: '17947325'
    title: 'RNAJunction: a database of RNA junctions and kissing loops for three-dimensional
      structural analysis and nanodesign'
    year: 2007
  - doi: 10.1093/nar/gkm842
    pmc: null
    pubmed: null
    title: 'RNAJunction: a database of RNA junctions and kissing loops for three-dimensional
      structural analysis and nanodesign.'
    year: null
  reviewer:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  uri_format: https://rnajunction.ncifcrf.gov/JunctionPage.php?jid=$1
rnaloops:
  contact:
    email: Maciej.Antczak@cs.put.poznan.pl
    github: mantczak
    name: Maciej Antczak
    orcid: 0000-0002-5320-2023
  contributor:
    email: benjamin_gyori@hms.harvard.edu
    github: bgyori
    name: Benjamin M. Gyori
    orcid: 0000-0001-9439-5346
  description: Rnaloops stores the information about n-way junctions (where n≥3) found
    in experimentally determined rna 3d structures deposited in the protein data bank.
  example: '91792'
  github_request_issue: 601
  homepage: https://rnaloops.cs.put.poznan.pl
  keywords:
  - rna
  - structural bioinformatcs
  name: RNAloops
  pattern: ^\d+$
  prefix: rnaloops
  reviewer:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  uri_format: https://rnaloops.cs.put.poznan.pl/search/details/$1
rnamod:
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: A comprehensive listing of post-transcriptionally modified nucleosides
    from RNA -
  example: '051'
  homepage: http://rna.rega.kuleuven.be/rnamods/
  keywords:
  - post-transcriptional modification
  - rna
  - structural bioinformatcs
  name: The RNA Modification Database
  pattern: ^\d{3}$
  prefix: rnamod
  uri_format: http://rna.rega.kuleuven.be/cgi-bin/rnamods/rnashow.pl?$1
rnamods:
  biocontext:
    prefix: RNAMODS
  go:
    homepage: https://mods.rna.albany.edu/
    name: RNA Modification Database
    prefix: RNAmods
    synonyms:
    - RNAMDB
    uri_format: https://mods.rna.albany.edu/mods/modifications/view/$1
  mappings:
    biocontext: RNAMODS
    go: RNAmods
    miriam: rnamods
    n2t: rnamods
    prefixcommons: rnamods
  miriam:
    deprecated: false
    description: The RNA modification database provides a comprehensive listing of
      post-transcriptionally modified nucleosides from RNA. The database consists
      of all RNA-derived ribonucleosides of known structure, including those from
      established sequence positions, as well as those detected or characterized from
      hydrolysates of RNA.
    homepage: http://rna.rega.kuleuven.be/rnamods/
    id: 00000308
    name: RNA Modification Database
    namespaceEmbeddedInLui: false
    pattern: ^\d{3}$
    prefix: rnamods
    sampleId: '101'
    uri_format: http://rna.rega.kuleuven.be/rnamods/rnashow.pl?$1
  n2t:
    description: The RNA modification database provides a comprehensive listing of
      post-transcriptionally modified nucleosides from RNA. The database consists
      of all RNA-derived ribonucleosides of known structure, including those from
      established sequence positions, as well as those detected or characterized from
      hydrolysates of RNA.
    example: '101'
    homepage: http://rna-mdb.cas.albany.edu/RNAmods/rnaover.htm
    name: RNA Modification Database at University of Utah
    namespaceEmbeddedInLui: false
    pattern: ^\d{3}$
    prefix: rnamods
    uri_format: http://mods.rna.albany.edu/mods/modifications/view/$1
  prefix: rnamods
  prefixcommons:
    description: The RNA modification database provides a comprehensive listing of
      posttranscriptionally modified nucleosides from RNA and is maintained as an
      updated version of the initial printed report.
    example: 080
    homepage: http://medlib.med.utah.edu/RNAmods/
    keywords:
    - RNA
    - structure
    name: RNA Modification Database
    pattern: ^\d+$
    prefix: rnamods
    synonyms:
    - rnamod
    uri_format: http://s59.cas.albany.edu/RNAmods/cgi-bin/rnashow.cgi?$1
rnao:
  aberowl:
    description: The central aim of the RNA Ontology Consortium (ROC) is to develop
      an ontology to capture all aspects of RNA - from primary sequence to alignments,
      secondary and tertiary structure from base pairing and base stacking to sophisticated
      motifs.
    download_obo: http://aber-owl.net/media/ontologies/RNAO/4/rnao.obo
    homepage: https://github.com/BGSU-RNA/rnao
    name: RNA ontology
    prefix: RNAO
    version: r113
  biocontext:
    prefix: RNAO
  bioportal:
    contact:
      email: BatchelorC@rsc.org
      name: Colin Batchelor
    description: The central aim of the RNA Ontology Consortium (ROC) is to develop
      an ontology to capture all aspects of RNA - from primary sequence to alignments,
      secondary and tertiary structure from base pairing and base stacking to sophisticated
      motifs.
    homepage: https://github.com/BGSU-RNA/rnao
    name: RNA Ontology
    prefix: RNAO
    version: r113
  example: 0000128
  fairsharing:
    abbreviation: RNAO
    contact:
      email: BatchelorC@rsc.org
      name: Colin Batchelor
      orcid: 0000-0001-5985-7429
    description: RNAO is a controlled vocabulary pertaining to RNA function and based
      on RNA sequences, secondary and three-dimensional structures. The central aim
      of the RNA Ontology Consortium (ROC) is to develop an ontology to capture all
      aspects of RNA - from primary sequence to alignments, secondary and tertiary
      structure, and from base pairing and base stacking interactions to sophisticated
      motifs.
    domains:
    - RNA secondary structure
    - Structure
    - ribonucleic acid
    - sequence motif
    homepage: https://github.com/bgsu-rna/rnao
    name: RNA Ontology
    prefix: FAIRsharing.kqt2h2
    publications:
    - doi: 10.1261/rna.2343206
      pubmed: '16484377'
      title: 'The RNA Ontology Consortium: an open invitation to the RNA community'
      year: 2006
    - doi: 10.3233/ao-2011-0082
      title: 'The RNA Ontology (RNAO): An Ontology for Integrating RNA Sequence and
        Structure Data'
      year: 2011
    subjects:
    - Life Science
    - Biochemistry
  mappings:
    aberowl: RNAO
    biocontext: RNAO
    bioportal: RNAO
    fairsharing: FAIRsharing.kqt2h2
    obofoundry: rnao
    ols: rnao
    ontobee: RNAO
    prefixcommons: rnao
  obofoundry:
    contact: BatchelorC@rsc.org
    contact.label: Colin Batchelor
    contact.orcid: 0000-0001-5985-7429
    deprecated: true
    description: Controlled vocabulary pertaining to RNA function and based on RNA
      sequences, secondary and three-dimensional structures.
    domain: chemistry and biochemistry
    download.obo: http://purl.obolibrary.org/obo/rnao.obo
    download.owl: http://purl.obolibrary.org/obo/rnao.owl
    homepage: https://github.com/bgsu-rna/rnao
    license: CC0 1.0
    license.url: https://creativecommons.org/publicdomain/zero/1.0/
    name: RNA ontology
    prefix: rnao
    repository: https://github.com/BGSU-RNA/rnao
  ols:
    description: Controlled vocabulary pertaining to RNA function and based on RNA
      sequences, secondary and three-dimensional structures.
    download: http://purl.obolibrary.org/obo/rnao.owl
    homepage: https://github.com/bgsu-rna/rnao
    name: 'The RNA Ontology (RNAO): An Ontology for Integrating RNA Sequence and Structure
      Data'
    prefix: rnao
    version: '2019-04-15'
  ontobee:
    library: Library
    name: RNA ontology
    prefix: RNAO
  pattern: ^\d{7}$
  prefix: rnao
  prefixcommons:
    bioportal: '1500'
    description: The central aim of the RNA Ontology Consortium (ROC) is to develop
      an ontology to capture all aspects of RNA - from primary sequence to alignments,
      secondary and tertiary structure from base pairing and base stacking to sophisticated
      motifs.
    example: RNAO_0000112
    homepage: http://code.google.com/p/rnao/
    keywords:
    - obo
    name: RNA ontology
    pattern: ^RNAO_\d{7}$
    prefix: rnao
  publications:
  - doi: 10.3233/ao-2011-0082
    pmc: null
    pubmed: null
    title: 'The RNA Ontology (RNAO): An ontology for integrating RNA sequence and
      structure data'
    year: 2011
  - doi: 10.1261/rna.2343206
    pmc: PMC1421088
    pubmed: '16484377'
    title: 'The RNA Ontology Consortium: an open invitation to the RNA community'
    year: 2006
rnavdb:
  mappings:
    prefixcommons: rvd
  prefix: rnavdb
  prefixcommons:
    description: The RNA Virus Database is a database and web application describing
      the genome organization and providing analytical tools for the 938 known species
      of RNA virus. It can identify submitted nucleotide sequences, can place them
      into multiple whole-genome alignments and contains translated genome sequences
      for all species.
    example: '164750'
    homepage: http://virus.zoo.ox.ac.uk/rnavirusdb/
    keywords:
    - RNA
    - genome
    name: RNA Virus Database
    pattern: ^\d+$
    prefix: rvd
    uri_format: http://virus.zoo.ox.ac.uk/rnavirusdb/virus.php?id=$1
ro:
  aberowl:
    description: Relationship types shared across multiple ontologies
    download_owl: http://aber-owl.net/media/ontologies/RO/32/ro.owl
    homepage: https://oborel.github.io/
    name: Relation Ontology
    prefix: RO
  agroportal:
    contact:
      email: cjmungall@lbl.gov
      name: Chris Mungall
    description: The OBO Relations Ontology (RO) is a collection of OWL relations
      (ObjectProperties) intended for use across a wide variety of biological ontologies.,
      RO chemical module.
    example_uri: http://purl.obolibrary.org/obo/RO_0002533
    homepage: https://github.com/oborel/obo-relations/
    license: CC0-1.0
    name: Relations Ontology
    prefix: RO
    repository: http://purl.obolibrary.org/obo/ro.owl
    version: '2025-06-24'
  banana_peel: _
  biocontext:
    prefix: RO
  biolink:
    is_identifiers: false
    is_obo: true
    prefix: RO
    uri_format: http://purl.obolibrary.org/obo/RO_$1
  bioportal:
    contact:
      email: cjmungall@lbl.gov
      name: Chris Mungall
    description: A collection of relations intended primarily for standardization
      across ontologies in the OBO Foundry and wider OBO library. It incorporates
      ROCore upper-level relations such as part of as well as biology-specific relationship
      types such as develops from., The OBO Relations Ontology (RO) is a collection
      of OWL relations (ObjectProperties) intended for use across a wide variety of
      biological ontologies.
    homepage: https://github.com/oborel/obo-relations/
    license: CC0-1.0
    name: Relations Ontology
    prefix: OBOREL
    version: '2025-06-24'
  domain: relationship type
  example: '0002533'
  example_extras:
  - HOM0000022
  fairsharing:
    abbreviation: RO
    contact:
      email: cjmungall@lbl.gov
      name: Chris Mungall
      orcid: 0000-0002-6601-2165
    description: RO is a collection of relations intended primarily for standardization
      across ontologies in the OBO Foundry and wider OBO library. It incorporates
      ROCore upper-level relations such as part of as well as biology-specific relationship
      types such as develops from. The predecessor of RO was OBO_REL. Many of the
      relations in OBO_REL have been ceded to BFO.
    homepage: https://github.com/oborel/obo-relations/
    license: CC0-1.0
    name: OBO Relations Ontology
    prefix: FAIRsharing.9w8ea0
    repository: https://github.com/oborel/obo-relations/wiki/ROAndBFO
    subjects:
    - Subject Agnostic
    user_defined_tags:
    - Relations
  go:
    description: A collection of relations used across OBO ontologies
    name: OBO Relation Ontology Ontology
    prefix: RO
  mappings:
    aberowl: RO
    agroportal: RO
    biocontext: RO
    biolink: RO
    bioportal: OBOREL
    fairsharing: FAIRsharing.9w8ea0
    go: RO
    miriam: ro
    n2t: ro
    obofoundry: ro
    ols: ro
    ontobee: RO
    prefixcommons: ro
    tib: ro
    wikidata: P3590
    wikidata.entity: Q28729320
  miriam:
    deprecated: false
    description: The OBO Relation Ontology provides consistent and unambiguous formal
      definitions of the relational expressions used in biomedical ontologies.
    homepage: https://www.ebi.ac.uk/ols4/ontologies/ro
    id: '00000120'
    name: Relation Ontology
    namespaceEmbeddedInLui: false
    pattern: ^RO_\d{7}$
    prefix: ro
    providers:
    - code: ''
      description: OBO Relation Ontology through OntoBee
      homepage: http://obofoundry.org/ontology/ro.html
      name: OBO Relation Ontology through OntoBee
      uri_format: http://purl.obolibrary.org/obo/$1
    sampleId: RO_0002533
    uri_format: https://www.ebi.ac.uk/ols4/ontologies/ro/terms?short_form=$1
  n2t:
    description: The OBO Relation Ontology provides consistent and unambiguous formal
      definitions of the relational expressions used in biomedical ontologies.
    example: RO_0002533
    homepage: http://obofoundry.org/ontology/ro.html
    name: OBO Relation Ontology through OntoBee
    namespaceEmbeddedInLui: false
    pattern: ^RO_\d{7}$
    prefix: ro
    uri_format: http://purl.obolibrary.org/obo/$1
  name: Relation Ontology
  namespace_in_lui: true
  obofoundry:
    appears_in:
    - agro
    - aism
    - cdno
    - cl
    - clao
    - clyh
    - colao
    - cteno
    - ecao
    - ecocore
    - ecto
    - envo
    - foodon
    - fovt
    - gallont
    - genepio
    - go
    - hso
    - lepao
    - maxo
    - ons
    - ontoavida
    - pcl
    - pco
    - plana
    - planp
    - poro
    - proco
    - psdo
    - pso
    - rbo
    - uberon
    - xpo
    - zp
    - upa
    contact: cjmungall@lbl.gov
    contact.github: cmungall
    contact.label: Chris Mungall
    contact.orcid: 0000-0002-6601-2165
    deprecated: false
    description: Relationship types shared across multiple ontologies
    domain: upper
    download.json: http://purl.obolibrary.org/obo/ro.json
    download.obo: http://purl.obolibrary.org/obo/ro.obo
    download.owl: http://purl.obolibrary.org/obo/ro.owl
    homepage: https://oborel.github.io/
    license: CC0 1.0
    license.url: http://creativecommons.org/publicdomain/zero/1.0/
    name: Relation Ontology
    preferredPrefix: RO
    prefix: ro
    repository: https://github.com/oborel/obo-relations
  ols:
    description: Relationship types shared across multiple ontologies
    download_owl: http://purl.obolibrary.org/obo/ro.owl
    homepage: https://oborel.github.io/
    name: Relation Ontology
    prefix: ro
    tracker: https://github.com/oborel/obo-relations/issues
    uri_format: http://purl.obolibrary.org/obo/BFO_0000050$1
    version: '2025-06-24'
    version.iri: http://purl.obolibrary.org/obo/ro/releases/2025-06-24/ro.owl
  ontobee:
    library: Library
    name: Relation Ontology
    prefix: RO
  pattern: ^(HOM)?\d{7}$
  prefix: ro
  prefixcommons:
    alt_uri_formats:
    - http://purl.org/obo/owl/RO_REL#$1
    - http://purl.org/obo/owlapi/relationship#$1
    bioportal: '1042'
    description: The OBO Relation Ontology provides consistent and unambiguous formal
      definitions of the relational expressions used in biomedical ontologies.
    example: part_of
    homepage: http://www.obofoundry.org/ro
    keywords:
    - obo
    - relations
    license: CC-BY-3.0
    name: Relation Ontology
    pattern: ^\w+$
    prefix: ro
    pubmed_ids:
    - '15892874'
    synonyms:
    - obo_rel
    - obo.ro
    - ro_proposed_relation
  publications:
  - doi: 10.1186/2041-1480-5-41
    pmc: PMC4177597
    pubmed: '25276335'
    title: 'Structuring research methods and data with the research object model:
      genomics workflows as a case study'
    year: 2014
  - doi: 10.1186/gb-2005-6-5-r46
    pmc: PMC1175958
    pubmed: '15892874'
    title: Relations in biomedical ontologies
    year: 2005
  - doi: null
    pmc: null
    pubmed: '15892874'
    title: null
    year: null
  - doi: null
    pmc: null
    pubmed: '15892874'
    title: null
    year: null
  synonyms:
  - RO_proposed_relation
  - obo_rel
  - oborel
  tib:
    description: Relationship types shared across multiple ontologies.
    download_owl: http://purl.obolibrary.org/obo/ro.owl
    homepage: https://oborel.github.io/
    keywords:
    - NFDI4CHEM
    - DataPLANT
    - Foundational Ontologies
    - life sciences, biology
    name: Relation Ontology
    prefix: ro
    tracker: https://github.com/oborel/obo-relations/issues
    version.iri: http://purl.obolibrary.org/obo/ro/releases/2025-06-24/ro.owl
  uri_format: http://purl.obolibrary.org/obo/RO_$1
  wikidata:
    description: ID in the Relations Ontology
    homepage: https://github.com/oborel/obo-relations/
    name: Relations Ontology ID
    pattern: ^(RO|BFO)_[0-9]{7}$
    prefix: P3590
roleo:
  aberowl:
    description: The Role Ontology (RoleO) is a ontology in the domain of role classification.
      RoleO aims to standardize role classification and support computer-assisted
      reasoning. RoleO is a community-based ontology, and its development follows
      the OBO Foundry principles.
    download_owl: http://aber-owl.net/media/ontologies/ROLEO/1/roleo.owl
    homepage: http://sourceforge.net/projects/roleo
    name: Role Ontology
    prefix: ROLEO
    version: Vision Release; 1.0.11
  banana: RoleO
  banana_peel: _
  bioportal:
    contact:
      email: yongqunh@med.umich.edu
      name: Oliver He
    description: The Role Ontology (RoleO) is an ontology in the domain of role classification.
      RoleO aims to standardize role classification and support computer-assisted
      reasoning. RoleO development follows the OBO Foundry principles. RoleO has represented
      all the occupations defined in the Standard Occupational Classification (SOC)
      System from the USA Bureau of Labor Statistics.
    homepage: https://github.com/roleontology/roleo
    name: Role Ontology
    prefix: ROLEO
    version: 'Vision Release: 1.0.16'
  comment: This resource doesn't exist on the web anymore
  contact:
    email: yongqunh@med.umich.edu
    github: yongqunh
    name: Yongqun Oliver He
    orcid: 0000-0001-9189-9661
  deprecated: true
  example: '0000002'
  mappings:
    aberowl: ROLEO
    bioportal: ROLEO
    prefixcommons: roleo
  pattern: ^\d{7}$
  preferred_prefix: RoleO
  prefix: roleo
  prefixcommons:
    bioportal: '1538'
    description: The Role Ontology (RoleO) is a ontology in the domain of role classification.
      RoleO aims to standardize role classification and support computer-assisted
      reasoning.  RoleO is a community-based ontology, and its development follows
      the OBO Foundry principles.
    example: RoleO_0000002
    homepage: http://sourceforge.net/projects/roleo
    keywords:
    - obo
    name: Role Ontology
    pattern: ^RoleO_\d{7}$
    prefix: roleo
  reviewer:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  uri_format: http://purl.obolibrary.org/obo/RoleO_$1
ror:
  bartoc:
    abbreviation: ROR
    description: ROR is a global, community-led registry of open persistent identifiers
      for research organizations
    homepage: https://ror.org/
    license: CC-BY-4.0
    name: Research Organization Registry
    prefix: '20474'
    wikidata_database: Q110235640
  contact:
    email: maria.gould@ucop.edu
    github: mariagould
    name: Maria Gould
    orcid: 0000-0002-2916-3423
  contact_group_email: support@ror.org
  domain: organization
  download_owl: https://w3id.org/rorio/rorio.owl
  fairsharing:
    abbreviation: ROR
    contact:
      email: info@ror.org
      name: Maria Gould
      orcid: 0000-0002-2916-3423
    description: ROR is a community-led project to develop an open, sustainable, usable,
      and unique identifier for every research organization in the world. Implementation
      of ROR IDs in scholarly infrastructure and metadata will enable more efficient
      discovery and tracking of research outputs across institutions and funding bodies.
    homepage: https://ror.org
    license: CC0-1.0
    name: Research Organization Registry
    prefix: FAIRsharing.1jKfji
    publications: []
    repository: https://github.com/ror-community
    subjects:
    - Data Management
    twitter: ResearchOrgs
  license: CC0-1.0
  logo: https://ror.org/img/ror-logo.svg
  mappings:
    bartoc: '20474'
    fairsharing: FAIRsharing.1jKfji
    miriam: ror
    n2t: ror
    ols: ror
    wikidata.entity: Q110235640
  mastodon: ResearchOrgs@mastodon.social
  miriam:
    deprecated: false
    description: 'ROR (Research Organization Registry) is a global, community-led
      registry

      of open persistent identifiers for research organizations. ROR is jointly

      operated by California Digital Library, Crossref, and Datacite.'
    homepage: https://ror.org
    id: 00000961
    name: ROR
    namespaceEmbeddedInLui: false
    pattern: ^0[a-hj-km-np-tv-z|0-9]{6}[0-9]{2}$
    prefix: ror
    sampleId: 03yrm5c26
    uri_format: https://ror.org/$1
  n2t:
    example: 03yrm5c26
    homepage: http://ror.org
    name: Research Organization Registry
    namespaceEmbeddedInLui: false
    prefix: ror
    uri_format: https://ror.org/$1
  name: Research Organization Registry
  ols:
    contact: info@ror.org
    description: 'ROR (Research Organization Registry) is a global, community-led
      registry

      of open persistent identifiers for research organizations. ROR is jointly

      operated by California Digital Library, Crossref, and Datacite.'
    homepage: https://ror.org
    name: Research Organization Registry
    prefix: ror
    uri_format: https://ror.org/$1
    version.iri: https://w3id.org/biopragmatics/resources/ror/1.36/ror.ofn
  prefix: ror
rosetta:
  example: canBePerformedBy
  mappings:
    tib: rosetta
  prefix: rosetta
  repository: https://github.com/jacekmalec/Rosetta_ontology
  tib:
    description: The ROSETTA ontology of industrial robotics devices and robotic skills.
    download_owl: https://raw.githubusercontent.com/jacekmalec/Rosetta_ontology/master/rosetta.owl
    homepage: https://github.com/jacekmalec/Rosetta_ontology
    keywords:
    - NFDI4ING
    - engineering
    name: The ROSETTA ontology of industrial robotics devices and robotic skills.
    prefix: rosetta
    uri_format: http://kif.cs.lth.se/ontologies/rosetta.owl#$1
rouge:
  biocontext:
    prefix: ROUGE
  contact:
    email: ohara@kazusa.or.jp
    github: null
    name: Osamu Ohara
    orcid: 0000-0002-3328-9571
  fairsharing:
    abbreviation: ROUGE
    description: The ROUGE protein database is a sister database of HUGE protein database
      which has accumulated the results of comprehensive sequence analysis of human
      long cDNAs (KIAA cDNAs). The ROUGE protein database has been created to publicize
      the information obtained from mouse homologues of the KIAA cDNAs (mKIAA cDNAs).
    homepage: http://www.kazusa.or.jp/rouge/
    license: http://opendatacommons.org/licenses/pddl/1.0
    name: ROdent Unidentified Gene-Encoded large proteins
    prefix: FAIRsharing.vdbagq
    publications:
    - doi: 10.1093/nar/gkh035
      pubmed_id: 14681467
      title: 'HUGE: a database for human KIAA proteins, a 2004 update integrating
        HUGEppi and ROUGE.'
    subjects:
    - Life Science
  integbio:
    alt_name: A Database of Rodent Unidentified Gene-Encoded Large Proteins Analyzed
      by Kazusa Mouse cDNA Project
    description: ROUGE is a database of long rodent cDNA clones designed to compliment
      the HUGE database of long human cDNA clones. The database contains sequence
      information for mouse clones from the mKIAA sequencing project, which can be
      browsed or searched. ROUGE was conducted as part of the CREATE program.
    fairsharing: biodbcore-000408
    homepage: http://www.kazusa.or.jp/rouge/index.html
    information_keywords:
    - Bioresource
    - Sequence
    maintainer: Kazusa DNA Research Institute
    name: ROUGE
    prefix: nbdc00672
    pubmeds:
    - '15368895'
    - '15449545'
    - '15188409'
    - '14621295'
    - '12693553'
    - '12465718'
    status: Active
    target_keywords:
    - Genome/Gene
    - cDNA/EST
    - RNA
    - Protein
  mappings:
    biocontext: ROUGE
    fairsharing: FAIRsharing.vdbagq
    integbio: nbdc00672
    miriam: rouge
    n2t: rouge
    prefixcommons: rouge
    uniprot: DB-0092
  miriam:
    deprecated: false
    description: The Rouge protein database contains results from sequence analysis
      of novel large (>4 kb) cDNAs identified in the Kazusa cDNA sequencing project.
    homepage: http://www.kazusa.or.jp/rouge/
    id: 00000293
    name: Rouge
    namespaceEmbeddedInLui: false
    pattern: ^m\w+$
    prefix: rouge
    sampleId: mKIAA4200
    uri_format: http://www.kazusa.or.jp/rouge/gfpage/$1/
  n2t:
    description: The Rouge protein database contains results from sequence analysis
      of novel large (>4 kb) cDNAs identified in the Kazusa cDNA sequencing project.
    example: mKIAA4200
    homepage: http://www.kazusa.or.jp/rouge/
    name: Rouge at Kazusa DNA Research Institute
    namespaceEmbeddedInLui: false
    pattern: ^m\w+$
    prefix: rouge
    uri_format: http://www.kazusa.or.jp/rouge/gfpage/$1/
  name: Rodent Unidentified Gene-Encoded Large Proteins
  prefix: rouge
  prefixcommons:
    description: The ROUGE protein database is a sister database of HUGE protein database
      which has accumulated the results of comprehensive sequence analysis of human
      long cDNAs (KIAA cDNAs). The ROUGE protein database has been created to publicize
      the information obtained from mouse homologues of the KIAA cDNAs (mKIAA cDNAs).
    example: mKIAA0701
    homepage: http://www.kazusa.or.jp/rouge/
    keywords:
    - protein
    - DNA
    name: A Database of Rodent Unidentified Gene-Encoded Large Proteins Analyzed
    pattern: ^mKIAA\d+$
    prefix: rouge
    uri_format: http://www.kazusa.or.jp/rouge/gfpage/$1/
  publications:
  - doi: 10.1093/nar/gkh035
    pmc: PMC308769
    pubmed: '14681467'
    title: 'HUGE: a database for human KIAA proteins, a 2004 update integrating HUGEppi
      and ROUGE'
    year: 2004
  - doi: 10.1093/nar/gkh035
    pmc: null
    pubmed: null
    title: 'HUGE: a database for human KIAA proteins, a 2004 update integrating HUGEppi
      and ROUGE.'
    year: null
  - doi: 10.1093/nar/gkh035
    pmc: null
    pubmed: '14681467'
    title: null
    year: null
  - doi: 10.1093/nar/gkh035
    pmc: null
    pubmed: null
    title: 'HUGE: a database for human KIAA proteins, a 2004 update integrating HUGEppi
      and ROUGE.'
    year: null
  - doi: 10.1093/nar/gkh035
    pmc: null
    pubmed: '14681467'
    title: null
    year: null
  uniprot:
    abbreviation: Rouge
    category: Organism-specific databases
    homepage: http://www.kazusa.or.jp/rouge/
    name: Rodent Unidentified Gene-Encoded large proteins database
    prefix: DB-0092
    publications:
    - doi: 10.1093/nar/gkh035
      pubmed: '14681467'
    uri_format: http://www.kazusa.or.jp/rouge/gfpage/$1
  uri_format: https://www.kazusa.or.jp/rouge/gfpage/$1
rpcec:
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: The Cuban Public Registry of Clinical Trials (RPCEC) is a website with
    a database of clinical trials, with national coverage. It was established in 2007
    under the leadership of the National Coordinating Center of Clinical Trials (CENCEC)
    and with INFOMED collaboration. (from homepage)
  example: RPCEC00000423
  homepage: https://rpcec.sld.cu/en/home
  name: Cuban Registry of Clinical Trials
  pattern: ^RPCEC\d+$
  prefix: rpcec
  uri_format: https://rpcec.sld.cu/en/trials/$1
rrid:
  banana: RRID
  biocontext:
    prefix: RRID
  contact:
    email: bandrow@gmail.com
    github: bandrow
    name: Anita Bandrowski
    orcid: 0000-0002-5497-0243
  contributor_extras:
  - email: bandrow@gmail.com
    github: bandrow
    name: Anita Bandrowski
    orcid: 0000-0002-5497-0243
  fairsharing:
    abbreviation: RRID
    description: "Research Resource Identifiers (#RRID) are ID numbers assigned to\
      \ help researchers cite key resources (antibodies, model organisms and software\
      \ projects) in the biomedical literature to improve transparency of research\
      \ methods. \n\n\n\n"
    domains:
    - Resource metadata
    - Annotation
    - Data retrieval
    - centrally registered identifier
    - FAIR
    homepage: https://www.rrids.org/
    name: Research Resource Identifier
    prefix: FAIRsharing.ATwSZG
    publications:
    - doi: 10.12688/f1000research.6555.2
      pubmed: '26594330'
      title: 'The Resource Identification Initiative: A cultural shift in publishing'
      year: 2015
    - doi: 10.1016/j.neuron.2016.04.030
      pubmed: '27151636'
      title: 'RRIDs: A Simple Step toward Improving Reproducibility through Rigor
        and Transparency of Experimental Methods'
      year: 2016
    - doi: 10.1002/cne.23913
      pubmed: '26599696'
      title: 'The Resource Identification Initiative: A Cultural Shift in Publishing'
      year: 2015
    - doi: 10.7717/peerj.148
      pubmed: '24032093'
      title: 'On the reproducibility of science: unique identification of research
        resources in the biomedical literature'
      year: 2013
    - doi: 10.1038/nmeth.3995
      pubmed: '27595404'
      title: A proposal for validation of antibodies
      year: 2016
    subjects:
    - Life Science
    - Biochemistry
    - Omics
    - Biology
    - Chemistry
    user_defined_tags:
    - Resource Discovery
    - community resource
  homepage: https://rrid.site
  mappings:
    biocontext: RRID
    fairsharing: FAIRsharing.ATwSZG
    miriam: rrid
    n2t: rrid
  miriam:
    deprecated: false
    description: "The Research Resource Identification Initiative provides RRIDs to\
      \ 4 main classes of resources: Antibodies, Cell Lines, Model Organisms, and\
      \ Databases / Software tools.: Antibodies, Model Organisms, and Databases /\
      \ Software tools.\r\nThe initiative works with participating journals to intercept\
      \ manuscripts in the publication process that use these resources, and allows\
      \ publication authors to incorporate RRIDs within the methods sections. It also\
      \ provides resolver services that access curated data from 10 data sources:\
      \ the antibody registry (a curated catalog of antibodies), the SciCrunch registry\
      \ (a curated catalog of software tools and databases), and model organism nomenclature\
      \ authority databases (MGI, FlyBase, WormBase, RGD), as well as various stock\
      \ centers. These RRIDs are aggregated and can be searched through SciCrunch."
    homepage: https://scicrunch.org/resolver
    id: 00000558
    name: RRID
    namespaceEmbeddedInLui: true
    pattern: ^RRID:[a-zA-Z]+.+$
    prefix: rrid
    sampleId: AB_262044
    uri_format: https://scicrunch.org/resolver/RRID:$1
  n2t:
    description: 'The Research Resource Identification Initiative provides RRIDs to
      4 main classes of resources: Antibodies, Cell Lines, Model Organisms, and Databases
      / Software tools.: Antibodies, Model Organisms, and Databases / Software tools.
      The initiative works with participating journals to intercept manuscripts in
      the publication process that use these resources, and allows publication authors
      to incorporate RRIDs within the methods sections. It also provides resolver
      services that access curated data from 10 data sources: the antibody registry
      (a curated catalog of antibodies), the SciCrunch registry (a curated catalog
      of software tools and databases), and model organism nomenclature authority
      databases (MGI, FlyBase, WormBase, RGD), as well as various stock centers. These
      RRIDs are aggregated and can be searched through SciCrunch.'
    example: AB_262044
    homepage: https://scicrunch.org/resolver
    name: RRID at SciCrunch
    namespaceEmbeddedInLui: true
    pattern: ^RRID:[A-Z_a-z-0-9]+$
    prefix: rrid
    uri_format: https://scicrunch.org/resolver/RRID:$1
  name: Research Resource Identification
  pattern: ^[a-zA-Z]+.+$
  prefix: rrid
  publications:
  - doi: 10.1093/nar/gkac927
    pmc: PMC9825422
    pubmed: '36370112'
    title: 'The Antibody Registry: ten years of registering antibodies'
    year: 2023
  - doi: 10.1093/gigascience/giac058
    pmc: PMC9197678
    pubmed: '35701373'
    title: 'A decade of GigaScience: What can be learned from half a million RRIDs
      in the scientific literature?'
    year: 2022
  - doi: 10.1371/journal.pcbi.1008967
    pmc: PMC8189493
    pubmed: '34043624'
    title: 'Antibody Watch: Text mining antibody specificity from the literature'
    year: 2021
  - doi: 10.7554/elife.41676
    pmc: PMC6351100
    pubmed: '30693867'
    title: Incidences of problematic cell lines are lower in papers that use RRIDs
      to identify cell lines
    year: 2019
  - doi: 10.1002/cnr2.1150
    pmc: PMC7941525
    pubmed: '32721132'
    title: Improving transparency and scientific rigor in academic publishing
    year: 2018
  - doi: 10.1038/nmeth.3995
    pmc: PMC10335836
    pubmed: '27595404'
    title: A proposal for validation of antibodies
    year: 2016
  - doi: 10.1016/j.neuron.2016.04.030
    pmc: PMC5854161
    pubmed: '27151636'
    title: 'RRIDs: A Simple Step toward Improving Reproducibility through Rigor and
      Transparency of Experimental Methods'
    year: 2016
  - doi: 10.1002/cne.23913
    pmc: PMC4684178
    pubmed: '26599696'
    title: 'The Resource Identification Initiative: A Cultural Shift in Publishing'
    year: 2016
  - doi: 10.12688/f1000research.6555.2
    pmc: PMC4648211
    pubmed: '26594330'
    title: 'The Resource Identification Initiative: A cultural shift in publishing'
    year: 2015
  - doi: 10.7717/peerj.148
    pmc: PMC3771067
    pubmed: '24032093'
    title: 'On the reproducibility of science: unique identification of research resources
      in the biomedical literature'
    year: 2013
  - doi: 10.12688/f1000research.6555.2
    pmc: null
    pubmed: '26594330'
    title: 'The Resource Identification Initiative: A cultural shift in publishing'
    year: 2015
  - doi: 10.1016/j.neuron.2016.04.030
    pmc: null
    pubmed: '27151636'
    title: 'RRIDs: A Simple Step toward Improving Reproducibility through Rigor and
      Transparency of Experimental Methods'
    year: 2016
  - doi: 10.1002/cne.23913
    pmc: null
    pubmed: '26599696'
    title: 'The Resource Identification Initiative: A Cultural Shift in Publishing'
    year: 2015
  - doi: 10.7717/peerj.148
    pmc: null
    pubmed: '24032093'
    title: 'On the reproducibility of science: unique identification of research resources
      in the biomedical literature'
    year: 2013
  - doi: 10.1038/nmeth.3995
    pmc: null
    pubmed: '27595404'
    title: A proposal for validation of antibodies
    year: 2016
rrrc:
  description: Supplies biomedical investigators with rat models, embryonic stem cells,
    related reagents, and protocols they require for their research. In addition to
    repository, cryostorage and distribution functions, RRRC can facilitate acquisition
    of rat strains from other international repositories as well as provide consultation
    and technical training to investigators using rat models. [from RRID]
  example: '961'
  mappings:
    rrid: RRRC
  pattern: ^\d+$
  prefix: rrrc
  rrid:
    abbreviation: NRRRC, RRRC, NCRR RRRC
    homepage: http://www.rrrc.us/
    keywords:
    - animal
    - biomedical
    - catalog
    - cell line
    - cryopreserved
    - database
    - disease
    - drug
    - embryo
    - embryonic stem cell
    - gamete
    - genome
    - genotyping
    - germplasma
    - human
    - hybrid
    - inbred
    - infectious
    - molecular
    - mutant
    - nuclear
    - ovarian
    - pathogen
    - protocol
    - rat
    - rat model
    - reagent
    - research
    - stem cell
    - strain
    - tissue
    name: Rat Resource and Research Center
    prefix: RRRC
    scr: '002044'
  uri_format: https://www.rrrc.us/Strain/?x=$1
rs:
  aberowl:
    description: Ontology of rat strains
    download_owl: http://aber-owl.net/media/ontologies/RS/203/rs.owl
    homepage: http://rgd.mcw.edu/rgdweb/search/strains.html
    name: Rat Strain Ontology
    prefix: RS
  biocontext:
    prefix: RS
  bioportal:
    contact:
      email: akwitek@mcw.edu
      name: Anne Kwitek
    description: This ontology defines the hierarchical display of the different rat
      strains as derived from the parental strains
    homepage: http://rgd.mcw.edu/rgdweb/search/strains.html
    name: Rat Strain Ontology
    prefix: RS
    publications:
    - http://www.ncbi.nlm.nih.gov/pubmed/23603846
    version: '6.251'
  cellosaurus:
    category: Organism-specific databases
    homepage: https://github.com/rat-genome-database/RS-Rat-Strain-Ontology
    name: Rat Strain Ontology
    prefix: RS
  download_obo: https://download.rgd.mcw.edu/pub/data_release/ontology_obo_files/rat_strain/rat_strain.obo
  download_owl: https://download.rgd.mcw.edu/pub/data_release/ontology_obo_files/rat_strain/rat_strain.owl
  example: 0001807
  fairsharing:
    abbreviation: RS
    description: This ontology defines the hierarchical display of the different rat
      strains as derived from the parental strains.
    domains:
    - mutation
    - strain
    homepage: http://rgd.mcw.edu/rgdweb/ontology/view.html?acc_id=RS:0000457
    name: Rat Strain Ontology
    prefix: FAIRsharing.vajn3f
    publications:
    - doi: 10.1093/database/bat015
      pubmed: '23603846'
      title: 'PhenoMiner: quantitative phenotype curation at the rat genome database'
      year: 2013
    - doi: 10.1186/2041-1480-4-36
      pubmed: '24267899'
      title: 'Rat Strain Ontology: structured controlled vocabulary designed to facilitate
        access to strain data at RGD'
      year: 2013
    subjects:
    - Life Science
  mappings:
    aberowl: RS
    biocontext: RS
    bioportal: RS
    cellosaurus: RS
    fairsharing: FAIRsharing.vajn3f
    obofoundry: rs
    ols: rs
    ontobee: RS
    prefixcommons: rs
    wikidata.entity: Q81661797
  obofoundry:
    contact: sjwang@mcw.edu
    contact.github: shurjenw
    contact.label: Shur-Jen Wang
    contact.orcid: 0000-0001-5256-8683
    deprecated: false
    description: Ontology of rat strains
    domain: organisms
    download.obo: http://purl.obolibrary.org/obo/rs.obo
    download.owl: http://purl.obolibrary.org/obo/rs.owl
    homepage: http://rgd.mcw.edu/rgdweb/search/strains.html
    license: CC BY 4.0
    license.url: https://creativecommons.org/licenses/by/4.0/
    logo: http://rgd.mcw.edu/common/images/rgd_LOGO_blue_rgd.gif
    name: Rat Strain Ontology
    preferredPrefix: RS
    prefix: rs
    publications:
    - id: https://www.ncbi.nlm.nih.gov/pubmed/24267899
      title: 'Rat Strain Ontology: structured controlled vocabulary designed to facilitate
        access to strain data at RGD.'
    repository: https://github.com/rat-genome-database/RS-Rat-Strain-Ontology
  ols:
    description: Ontology of rat strains
    download_owl: http://purl.obolibrary.org/obo/rs.owl
    homepage: http://rgd.mcw.edu/rgdweb/search/strains.html
    name: Rat Strain Ontology
    prefix: rs
    tracker: https://github.com/rat-genome-database/RS-Rat-Strain-Ontology/issues
    version: '6.263'
    version.iri: http://purl.obolibrary.org/obo/rs/6.263/rs.owl
  ontobee:
    library: Library
    name: Rat Strain Ontology
    prefix: RS
  pattern: ^\d{7}$
  prefix: rs
  prefixcommons:
    bioportal: '1150'
    description: This ontology defines the hierarchical display of the different rat
      strains as derived from the parental strains
    example: RS_0000271
    homepage: http://rgd.mcw.edu/
    keywords:
    - obo
    name: Rat Strain Ontology
    pattern: ^RS_\d{7}$
    prefix: rs
  publications:
  - doi: 10.1093/database/bat015
    pmc: PMC3630803
    pubmed: '23603846'
    title: 'PhenoMiner: quantitative phenotype curation at the rat genome database'
    year: 2013
  - doi: 10.1186/2041-1480-4-36
    pmc: PMC4177145
    pubmed: '24267899'
    title: 'Rat Strain Ontology: structured controlled vocabulary designed to facilitate
      access to strain data at RGD'
    year: 2013
  - doi: null
    pmc: null
    pubmed: '24267899'
    title: 'Rat Strain Ontology: structured controlled vocabulary designed to facilitate
      access to strain data at RGD'
    year: null
  - doi: 10.1093/database/bat015
    pmc: null
    pubmed: '23603846'
    title: 'PhenoMiner: quantitative phenotype curation at the rat genome database'
    year: 2013
  - doi: 10.1186/2041-1480-4-36
    pmc: null
    pubmed: '24267899'
    title: 'Rat Strain Ontology: structured controlled vocabulary designed to facilitate
      access to strain data at RGD'
    year: 2013
  twitter: ratgenome
  uri_format: http://purl.obolibrary.org/obo/RS_$1
rtecs:
  cheminf:
    description: Identifier used by the RTECS database (http://www.cdc.gov/niosh/rtecs/).
    name: RTECS
    obsolete: false
    prefix: '000566'
  contact:
    email: vep1@cdc.gov
    github: null
    name: Vernon Putz-Anderson
    orcid: 0000-0002-3588-3259
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: 'RTECS is a compendium of data extracted from the open scientific literature.
    The data are recorded in the format developed by the RTECS staff and arranged
    in alphabetical order by prime chemical name. Six types of toxicity data are included
    in the file: (1) primary irritation; (2) mutagenic effects; (3) reproductive effects;
    (4) tumorigenic effects; (5) acute toxicity; and (6) other multiple dose toxicity.
    Specific numeric toxicity values such as LD50, LC50, TDLo, and TCLo are noted
    as well as species studied and route of administration used. For each citation,
    the bibliographic source is listed thereby enabling the user to access the actual
    studies cited. No attempt has been made to evaluate the studies cited in RTECS.
    The user has the responsibility of making such assessments.'
  example: AB1925000
  homepage: https://www.cdc.gov/niosh/rtecs/
  mappings:
    cheminf: '000566'
  name: Registry of Toxic Effects of Chemical Substances
  pattern: ^AB\d+$
  prefix: rtecs
  proprietary: true
  publications:
  - doi: 10.1016/s1074-9098%2899%2900058-1
    pmc: null
    pubmed: null
    title: 'An overview of the Registry of Toxic Effects of Chemical Substances (RTECS):
      Critical information on chemical hazards'
    year: 1999
  references:
  - https://www.cdc.gov/niosh/docs/97-119/pdfs/97-119.pdf
  - https://www.cdc.gov/niosh/npg/npgdrtec.html
rubygems:
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: A repository of software packages written in Ruby.
  example: bel
  homepage: https://rubygems.org
  name: RubyGems
  prefix: rubygems
  uri_format: https://rubygems.org/gems/$1
runbiosimulations:
  mappings:
    miriam: runbiosimulations
  miriam:
    deprecated: false
    description: runBioSimulations is a platform for sharing simulation experiments
      and their results. runBioSimulations enables investigators to use a wide range
      of simulation tools to execute a wide range of simulations. runBioSimulations
      permanently saves the results of these simulations, and investigators can share
      results by sharing URLs similar to sharing URLs for files with DropBox and Google
      Drive.
    homepage: https://icahn.mssm.edu/
    id: 00000897
    name: runBioSimulations
    namespaceEmbeddedInLui: false
    pattern: ^[0-9a-z]{24,24}$
    prefix: runbiosimulations
    sampleId: 5fde96bdc5f1aa9ff0cce18a
    uri_format: https://run.biosimulations.org/simulations/$1
  prefix: runbiosimulations
rxno:
  aberowl:
    description: Connects organic name reactions to their roles in an organic synthesis
      and to processes in MOP
    download_owl: http://aber-owl.net/media/ontologies/RXNO/40/rxno.owl
    homepage: https://github.com/rsc-ontologies/rxno
    name: Name Reaction Ontology
    prefix: RXNO
  bartoc:
    abbreviation: RXNO
    description: RXNO is the name reaction ontology. It contains more than 500 classes
      representing organic name reactions such as the Diels–Alder cyclization and
      the Cannizzaro reaction to their roles in an organic synthesis.
    homepage: https://github.com/rsc-ontologies/rxno
    license: CC-BY-4.0
    prefix: '20712'
  biocontext:
    prefix: RXNO
  bioportal:
    contact:
      email: batchelorc@rsc.org
      name: Colin Batchelor
    description: RXNO, the name reaction ontology, connects organic name reactions
      such as the Diels-Alder cyclization and the Cannizzaro reaction to their roles
      in an organic synthesis.
    homepage: https://code.google.com/p/rxno/
    name: Name Reaction Ontology
    prefix: RXNO
    version: releases/2021-12-16
  download_obo: https://github.com/rsc-ontologies/rxno/raw/master/rxno.obo
  example: '0000253'
  fairsharing:
    abbreviation: RXNO
    description: The Name Reaction Ontology (RXNO) connects organic name reactions
      such as the Diels-Alder cyclization and the Cannizzaro reaction to their roles
      in organic synthesis.
    domains:
    - Reaction data
    homepage: https://github.com/rsc-ontologies/rxno/
    license: CC-BY-4.0
    name: Name Reaction Ontology
    prefix: FAIRsharing.w4tncg
    subjects:
    - Molecular Chemistry
  mappings:
    aberowl: RXNO
    bartoc: '20712'
    biocontext: RXNO
    bioportal: RXNO
    fairsharing: FAIRsharing.w4tncg
    obofoundry: rxno
    ols: rxno
    ontobee: RXNO
    tib: rxno
    wikidata: P2106
  name: Name Reaction Ontology
  obofoundry:
    contact: batchelorc@rsc.org
    contact.github: batchelorc
    contact.label: Colin Batchelor
    contact.orcid: 0000-0001-5985-7429
    deprecated: false
    description: Connects organic name reactions to their roles in an organic synthesis
      and to processes in MOP
    domain: chemistry and biochemistry
    download.owl: http://purl.obolibrary.org/obo/rxno.owl
    homepage: https://github.com/rsc-ontologies/rxno
    license: CC BY 4.0
    license.url: https://creativecommons.org/licenses/by/4.0/
    name: Name Reaction Ontology
    preferredPrefix: RXNO
    prefix: rxno
    repository: https://github.com/rsc-ontologies/rxno
  ols:
    contact: chemistry-ontologies@googlegroups.com
    description: RXNO is the name reaction ontology. It contains more than 500 classes
      representing organic reactions such as the Diels–Alder cyclization.
    download_owl: http://purl.obolibrary.org/obo/rxno.owl
    homepage: https://github.com/rsc-ontologies/rxno
    name: RXNO
    prefix: rxno
    tracker: https://github.com/rsc-ontologies/rxno/issues
    version: '2021-12-16'
    version.iri: http://purl.obolibrary.org/obo/rxno/releases/2021-12-16/rxno.owl
  ontobee:
    library: Library
    name: Name Reaction Ontology
    prefix: RXNO
  pattern: ^\d{7}$
  prefix: rxno
  tib:
    contact: chemistry-ontologies@googlegroups.com
    description: RXNO is the name reaction ontology. It contains more than 500 classes
      representing organic reactions such as the Diels–Alder cyclization.
    download_owl: http://purl.obolibrary.org/obo/rxno.owl
    homepage: https://github.com/rsc-ontology/rxno
    keywords:
    - NFDI4CHEM
    - NFDI4CAT
    - chemistry
    name: RXNO
    prefix: rxno
    tracker: https://github.com/rsc-ontology/rxno/issues
    version.iri: http://purl.obolibrary.org/obo/rxno/releases/2021-12-16/rxno.owl
  uri_format: http://purl.obolibrary.org/obo/RXNO_$1
  wikidata:
    description: RSC ontology for organic reactions
    example:
    - RXNO:0000051
    - RXNO:0000135
    - RXNO:0000233
    homepage: https://github.com/rsc-ontologies/rxno
    name: RXNO Ontology
    prefix: P2106
    uri_format: https://www.rsc.org/publishing/journals/prospect/ontology.asp?id=$1
rxnorm:
  aberowl:
    description: RxNorm Vocabulary
    name: RxNORM
    prefix: RXNORM
    version: 2016AB
  biocontext:
    prefix: RXCUI
    uri_format: http://purl.bioontology.org/ontology/RXNORM/$1
  biolink:
    is_identifiers: false
    is_obo: false
    prefix: RXNORM
    uri_format: http://purl.bioontology.org/ontology/RXNORM/$1
  bioportal:
    contact:
      email: rxnorminfo@nlm.nih.gov
      name: RxNorm Customer Service
    description: <p>RxNorm is intended to cover all prescription medications approved
      for human use in the United States. Prescription medications from other countries
      may be included as opportunities allow, a principal consideration being that
      there be an authoritative source of information about these drugs. Drugs are
      added to the vocabulary as new products are put on the market. Over-the-counter
      (OTC) medications will be added and covered, as well, when reliable information
      about the medications can be found. Drugs are added to the vocabulary as new
      products are put on the market.</p> <p>An RxNorm clinical drug name reflects
      the active ingredients, strengths, and dose form composing that drug. When any
      of these elements vary, a new RxNorm drug name is created as a separate concept.
      Thus, an RxNorm name should exist for every strength and dose of every available
      combination of clinically significant ingredients.</p> <p>National Drug Codes
      (NDCs) for specific drug products are linked to that product in RxNorm. RxNorm
      links its names to many of the drug vocabularies commonly used in pharmacy management
      and drug interaction software, including those of First Databank, Micromedex®,
      Gold Standard Alchemy, and Multum. By providing links between these vocabularies,
      RxNorm can mediate messages between systems not using the same software and
      vocabulary.</p>
    homepage: https://www.nlm.nih.gov/research/umls/rxnorm/index.html
    name: RxNORM
    prefix: RXNORM
    version: RXNORM_20AA_240903F
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: RxNorm provides normalized names for clinical drugs and links its names
    to many of the drug vocabularies commonly used in pharmacy management and drug
    interaction software, including those of First Databank, Micromedex, and Gold
    Standard Drug Database. By providing links between these vocabularies, RxNorm
    can mediate messages between systems not using the same software and vocabulary.
  example: '221058'
  fairsharing:
    abbreviation: RxNORM
    description: RxNorm provides normalized names for clinical drugs and links its
      names to many of the drug vocabularies commonly used in pharmacy management
      and drug interaction software, including those of First Databank, Micromedex,
      MediSpan, Gold Standard Drug Database, and Multum. By providing links between
      these vocabularies, RxNorm can mediate messages between systems not using the
      same software and vocabulary. RxNorm now includes the National Drug File - Reference
      Terminology (NDF-RT) from the Veterans Health Administration. NDF-RT is a terminology
      used to code clinical drug properties, including mechanism of action, physiologic
      effect, and therapeutic category.
    domains:
    - Drug name
    - drug
    homepage: https://www.nlm.nih.gov/research/umls/rxnorm/
    name: RxNORM
    prefix: FAIRsharing.36pf8q
    publications:
    - pubmed: '18998891'
      title: RxTerms - a drug interface terminology derived from RxNorm
      year: 2008
    - doi: 10.1136/amiajnl-2011-000116
      pubmed: '21515544'
      title: 'Normalized names for clinical drugs: RxNorm at 6 years'
      year: 2011
    - doi: 10.1109/mitp.2005.122
      title: 'RxNorm: prescription for electronic drug information exchange'
      year: 2005
    subjects:
    - Preclinical Studies
    - Biomedical Science
  hl7:
    description: RxNorm provides standard names for clinical drugs (active ingredient
      + strength + dose form) and for dose forms as administered to a patient. It
      provides links from clinical drugs, both branded and generic, to their active
      ingredients, drug components (active ingredient + strength), and related brand
      names. NDCs (National Drug Codes) for specific drug products (where there are
      often many NDC codes for a single product) are linked to that product in RxNorm.
      RxNorm links its names to many of the drug vocabularies commonly used in pharmacy
      management and drug interaction software, including those of First Databank,
      Micromedex, MediSpan, and Multum. By providing links between these vocabularies,
      RxNorm can mediate messages between systems not using the same software and
      vocabulary.RxNorm is one of a suite of designated standards for use in U.S.
      Federal Government systems for the electronic exchange of clinical health information.
    homepage: http://www.nlm.nih.gov/
    name: RxNorm
    organization: National Library of Medicine
    preferred_prefix: rxNorm
    prefix: 2.16.840.1.113883.6.88
    status: Complete
  homepage: https://www.nlm.nih.gov/research/umls/rxnorm/
  license: https://uts.nlm.nih.gov/uts/assets/LicenseAgreement.pdf
  mappings:
    aberowl: RXNORM
    biocontext: RXCUI
    biolink: RXNORM
    bioportal: RXNORM
    fairsharing: FAIRsharing.36pf8q
    hl7: 2.16.840.1.113883.6.88
    wikidata: P3345
  name: RxNorm
  pattern: ^[0-9]{1,7}$
  prefix: rxnorm
  providers:
  - code: bp
    description: RxNorm in BioPortal
    example: null
    first_party: null
    homepage: http://purl.bioontology.org/ontology/RXNORM
    name: BioPortal
    publications: null
    status: null
    uri_format: http://purl.bioontology.org/ontology/RXNORM/$1
  publications:
  - doi: 10.1136/amiajnl-2011-000116
    pmc: PMC3128404
    pubmed: '21515544'
    title: 'Normalized names for clinical drugs: RxNorm at 6 years'
    year: 2011
  - doi: null
    pmc: PMC2655997
    pubmed: '18998891'
    title: RxTerms - a drug interface terminology derived from RxNorm
    year: 2008
  - doi: 10.1109/mitp.2005.122
    pmc: null
    pubmed: null
    title: 'RxNorm: prescription for electronic drug information exchange'
    year: 2005
  - doi: null
    pmc: null
    pubmed: '18998891'
    title: RxTerms - a drug interface terminology derived from RxNorm
    year: 2008
  - doi: 10.1136/amiajnl-2011-000116
    pmc: null
    pubmed: '21515544'
    title: 'Normalized names for clinical drugs: RxNorm at 6 years'
    year: 2011
  - doi: 10.1109/mitp.2005.122
    pmc: null
    pubmed: null
    title: 'RxNorm: prescription for electronic drug information exchange'
    year: 2005
  synonyms:
  - RXCUI
  uri_format: https://mor.nlm.nih.gov/RxNav/search?searchBy=RXCUI&searchTerm=$1
  wikidata:
    description: identifier for the normalized clinical drug dictionary of the Unified
      Medical Language System
    example:
    - '11121'
    - '221058'
    - '6448'
    name: RxNorm CUI
    prefix: P3345
    uri_format: https://mor.nlm.nih.gov/RxNav/search?searchBy=RXCUI&searchTerm=$1
s_mart_db:
  integbio:
    alt_name: The S/MAR transaction DataBase
    description: S/MARt DB is a database of cellular scaffolds and matrix data. The
      database contains scaffold, matrix, and nuclear matrix information from species
      ranging from yeast to humans. genes with experimentally identified interactions
      with scaffold and matrix components are available in tabular or searchable formats.
    homepage: http://smartdb.bioinf.med.uni-goettingen.de/
    information_keywords:
    - Sequence
    maintainer: Gesellschaft fur Biotechnologische Forschung
    name: S/MARt DB
    prefix: nbdc00674
    pubmeds:
    - '11752340'
    status: Inactive
    target_keywords:
    - DNA
    - Protein
  mappings:
    integbio: nbdc00674
    pathguide: '47'
    prefixcommons: s_mart_db
  pathguide:
    abbreviation: S/MARt_DB
    homepage: http://smartdb.bioinf.med.uni-goettingen.de/
    name: The S/MAR transaction DataBase
    prefix: '47'
  prefix: s_mart_db
  prefixcommons:
    description: S/MARt DB collects information about scaffold/matrix attached regions
      and the nuclear matrix proteins that are supposed be involved in the interaction
      of these elements with the nuclear matrix.
    example: SM0000020
    homepage: http://smartdb.bioinf.med.uni-goettingen.de/
    keywords:
    - protein
    name: The S/MAR transaction DataBase
    pattern: ^SM\d$
    prefix: s_mart_db
    synonyms:
    - smartdb
    uri_format: http://smartdb.bioinf.med.uni-goettingen.de/cgi-bin/SMARtDB/getSMAR.cgi?$1
  reviewer:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
sabiork.compound:
  mappings:
    miriam: sabiork.compound
    n2t: sabiork.compound
  miriam:
    deprecated: false
    description: SABIO-RK is a relational database system that contains information
      about biochemical reactions, their kinetic equations with their parameters,
      and the experimental conditions under which these parameters were measured.
      The compound data set provides information regarding the reactions in which
      a compound participates as substrate, product or modifier (e.g. inhibitor, cofactor),
      and links to further information.
    homepage: http://sabiork.h-its.org/
    id: 00000688
    name: SABIO-RK Compound
    namespaceEmbeddedInLui: false
    pattern: ^\d+$
    prefix: sabiork.compound
    sampleId: '75'
    uri_format: http://sabiork.h-its.org/newSearch?q=$1
  n2t:
    description: SABIO-RK is a relational database system that contains information
      about biochemical reactions, their kinetic equations with their parameters,
      and the experimental conditions under which these parameters were measured.
      The compound data set provides information regarding the reactions in which
      a compound participates as substrate, product or modifier (e.g. inhibitor, cofactor),
      and links to further information.
    example: '75'
    homepage: http://sabiork.h-its.org/
    name: SABIO-RK Compound
    namespaceEmbeddedInLui: false
    pattern: ^\d+$
    prefix: sabiork.compound
    uri_format: http://sabiork.h-its.org/newSearch?q=$1
  prefix: sabiork.compound
sabiork.ec:
  biocontext:
    prefix: SABIORK.EC
  contact:
    email: ulrike.wittig@h-its.org
    github: null
    name: Ulrike Wittig
    orcid: 0000-0002-9077-5664
  mappings:
    biocontext: SABIORK.EC
    miriam: sabiork.ec
    n2t: sabiork.ec
    prefixcommons: sabiork.ec
  miriam:
    deprecated: false
    description: SABIO-RK is a relational database system that contains information
      about biochemical reactions, their kinetic equations with their parameters,
      and the experimental conditions under which these parameters were measured.
      The EC record provides for a given enzyme classification (EC) the associated
      list of enzyme-catalysed reactions and their corresponding kinetic data.
    homepage: http://sabiork.h-its.org/
    id: 00000128
    name: SABIO-RK EC Record
    namespaceEmbeddedInLui: false
    pattern: ^((\d+)|(\d+\.\d+)|(\d+\.\d+\.\d+)|(\d+\.\d+\.\d+\.\d+))$
    prefix: sabiork.ec
    sampleId: 2.7.1.1
    uri_format: http://sabiork.h-its.org/newSearch?q=ecnumber:$1
  n2t:
    description: SABIO-RK is a relational database system that contains information
      about biochemical reactions, their kinetic equations with their parameters,
      and the experimental conditions under which these parameters were measured.
      The EC record provides for a given enzyme classification (EC) the associated
      list of enzyme-catalysed reactions and their corresponding kinetic data.
    example: 2.7.1.1
    homepage: http://sabiork.h-its.org/
    name: SABIO-RK Reaction Kinetics Database - Enzyme Classification (EC)
    namespaceEmbeddedInLui: false
    pattern: ^((\d+)|(\d+\.\d+)|(\d+\.\d+\.\d+)|(\d+\.\d+\.\d+\.\d+))$
    prefix: sabiork.ec
    uri_format: http://sabiork.h-its.org/newSearch?q=ecnumber:$1
  prefix: sabiork.ec
  prefixcommons:
    description: The EC record provides for a given enzyme classification (EC) the
      associated list of enzyme-catalysed reactions and their corresponding kinetic
      data.
    example: 2.7.1.1
    keywords:
    - reaction
    name: SABIO-RK EC Record
    pattern: ^((\d+)|(\d+\.\d+)|(\d+\.\d+\.\d+)|(\d+\.\d+\.\d+\.\d+))$
    prefix: sabiork.ec
    pubmed_ids:
    - '17822389'
    uri_format: http://sabiork.h-its.org/index2.jsp?EC=$1
  provides: ec
  publications:
  - doi: null
    pmc: null
    pubmed: '17822389'
    title: Storing and annotating of kinetic data
    year: 2007
sabiork.kineticrecord:
  biocontext:
    prefix: SABIORK.KINETICRECORD
  contact:
    email: ulrike.wittig@h-its.org
    github: null
    name: Ulrike Wittig
    orcid: 0000-0002-9077-5664
  go:
    description: The SABIO-RK (System for the Analysis of Biochemical Pathways - Reaction
      Kinetics) is a web-based application based on the SABIO relational database
      that contains information about biochemical reactions, their kinetic equations
      with their parameters, and the experimental conditions under which these parameters
      were measured.
    homepage: http://sabio.villa-bosch.de/
    name: SABIO Reaction Kinetics
    prefix: SABIO-RK
    uri_format: http://sabio.villa-bosch.de/reacdetails.jsp?reactid=$1
  mappings:
    biocontext: SABIORK.KINETICRECORD
    go: SABIO-RK
    miriam: sabiork.kineticrecord
    n2t: sabiork.kineticrecord
    prefixcommons: sabiork.kinetic
  miriam:
    deprecated: false
    description: SABIO-RK is a relational database system that contains information
      about biochemical reactions, their kinetic equations with their parameters,
      and the experimental conditions under which these parameters were measured.
      The kinetic record data set provides information regarding the kinetic law,
      measurement conditions, parameter details and other reference information.
    homepage: http://sabiork.h-its.org/
    id: 00000086
    name: SABIO-RK Kinetic Record
    namespaceEmbeddedInLui: false
    pattern: ^\d+$
    prefix: sabiork.kineticrecord
    sampleId: '5046'
    uri_format: http://sabiork.h-its.org/kineticLawEntry.jsp?viewData=true&kinlawid=$1
  n2t:
    description: SABIO-RK is a relational database system that contains information
      about biochemical reactions, their kinetic equations with their parameters,
      and the experimental conditions under which these parameters were measured.
      The kinetic record data set provides information regarding the kinetic law,
      measurement conditions, parameter details and other reference information.
    example: '5046'
    homepage: http://sabiork.h-its.org/
    name: SABIO-RK Reaction Kinetics Database - Kinetic Dataset
    namespaceEmbeddedInLui: false
    pattern: ^\d+$
    prefix: sabiork.kineticrecord
    uri_format: http://sabiork.h-its.org/kineticLawEntry.jsp?viewData=true&kinlawid=$1
  prefix: sabiork.kineticrecord
  prefixcommons:
    description: The kinetic record data set provides information regarding the kinetic
      law, measurement conditions, parameter details and other reference information.
    example: '5046'
    keywords:
    - classification
    - enzyme
    - kinetics
    name: SABIO-RK Kinetic Record
    pattern: ^\d+$
    prefix: sabiork.kinetic
    pubmed_ids:
    - '17822389'
    synonyms:
    - sabiok
    - sabio-kr
    - sabiork.kineticrecord
    uri_format: http://sabiork.h-its.org/kineticLawEntry.jsp?kinlawid=$1
  publications:
  - doi: null
    pmc: null
    pubmed: '17822389'
    title: Storing and annotating of kinetic data
    year: 2007
sabiork.reaction:
  biocontext:
    prefix: SABIORK.REACTION
  contact:
    email: ulrike.wittig@h-its.org
    github: null
    name: Ulrike Wittig
    orcid: 0000-0002-9077-5664
  edam:
    description: Identifier of a biological reaction from the SABIO-RK reactions database.
    name: Reaction ID (SABIO-RK)
    obsolete: false
    prefix: '2309'
  fairsharing:
    abbreviation: SABIO-RK
    description: SABIO-RK is a database for biochemical reactions, their kinetic equations
      with their parameters, and the experimental conditions under which these parameters
      were measured.
    homepage: http://sabiork.h-its.org/
    license: http://opendatacommons.org/licenses/pddl/1.0
    name: SABIO-RK Biochemical Reaction Kinetics Database
    prefix: FAIRsharing.cwx04e
    publications:
    - doi: 10.1093/nar/gkr1046
      pubmed_id: 22102587
      title: SABIO-RK--database for biochemical reaction kinetics.
    subjects:
    - Biochemistry
    - Life Science
  mappings:
    biocontext: SABIORK.REACTION
    edam: '2309'
    fairsharing: FAIRsharing.cwx04e
    miriam: sabiork.reaction
    n2t: sabiork.reaction
    pathguide: '226'
    prefixcommons: sabiork.reaction
    re3data: r3d100011052
    uniprot: DB-0177
  miriam:
    deprecated: false
    description: SABIO-RK is a relational database system that contains information
      about biochemical reactions, their kinetic equations with their parameters,
      and the experimental conditions under which these parameters were measured.
      The reaction data set provides information regarding the organism in which a
      reaction is observed, pathways in which it participates, and links to further
      information.
    homepage: http://sabiork.h-its.org/
    id: 00000038
    name: SABIO-RK Reaction
    namespaceEmbeddedInLui: false
    pattern: ^\d+$
    prefix: sabiork.reaction
    sampleId: '75'
    uri_format: http://sabiork.h-its.org/newSearch?q=sabioreactionid:$1
  n2t:
    description: SABIO-RK is a relational database system that contains information
      about biochemical reactions, their kinetic equations with their parameters,
      and the experimental conditions under which these parameters were measured.
      The reaction data set provides information regarding the organism in which a
      reaction is observed, pathways in which it participates, and links to further
      information.
    example: '75'
    homepage: http://sabiork.h-its.org/
    name: SABIO-RK reaction
    namespaceEmbeddedInLui: false
    pattern: ^\d+$
    prefix: sabiork.reaction
    uri_format: http://sabiork.h-its.org/newSearch?q=sabioreactionid:$1
  pathguide:
    abbreviation: SABIO-RK
    homepage: http://sabio.villa-bosch.de/
    keywords:
    - BioPAX
    - SBML
    name: SABIO-Reaction Kinetics Database
    prefix: '226'
  prefix: sabiork.reaction
  prefixcommons:
    description: The reaction data set provides information regarding the organism
      in which a reaction is observed, pathways in which it participates, and links
      to further information.
    example: '75'
    keywords:
    - kinetics
    - pathway
    - reaction
    name: SABIO-RK Reaction Record
    pattern: ^\d+$
    prefix: sabiork.reaction
    synonyms:
    - sabior
    uri_format: http://sabiork.h-its.org/index2.jsp?reac=$1
  publications:
  - doi: 10.1093/nar/gkr1046
    pmc: PMC3245076
    pubmed: '22102587'
    title: SABIO-RK--database for biochemical reaction kinetics
    year: 2011
  - doi: 10.1093/nar/gkr1046
    pmc: null
    pubmed: null
    title: SABIO-RK--database for biochemical reaction kinetics.
    year: null
  - doi: 10.1093/nar/gkx1065
    pmc: null
    pubmed: '29092055'
    title: null
    year: null
  re3data:
    description: The SABIO-RK is a web-based application based on the SABIO relational
      database that contains information about biochemical reactions, their kinetic
      equations with their parameters, and the experimental conditions under which
      these parameters were measured. It aims to support modellers in the setting-up
      of models of biochemical networks, but it is also useful for experimentalists
      or researchers with interest in biochemical reactions and their kinetics. All
      the data are manually curated and annotated by biological experts, supported
      by automated consistency checks.
    doi: 10.17616/R33C9X
    homepage: https://sabiork.h-its.org/
    license: Copyrights
    name: SABIO-RK
    prefix: r3d100011052
    synonyms:
    - Biochemical reation kinetics database
    - System for the Analysis of Biochemical Pathways - Reaction Kinetics
    xrefs:
      nif: 0000-20912
  synonyms:
  - SABIO-RK
  uniprot:
    abbreviation: SABIO-RK
    category: Enzyme and pathway databases
    homepage: https://sabiork.h-its.org/
    name: SABIO-RK
    prefix: DB-0177
    publications:
    - doi: 10.1093/nar/gkx1065
      pubmed: '29092055'
    uri_format: https://sabiork.h-its.org/newSearch?q=UniProtKB_AC:$1
  uri_format: http://sabiork.h-its.org/reacdetails.jsp?reactid=$1
sael:
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  deprecated: true
  name: Standards and Ontologies for Functional Genomics (SOFG) Anatomy Entry List
  prefix: sael
  publications:
  - doi: 10.1002/cfg.434
    pmc: PMC2447422
    pubmed: '18629134'
    title: 'The SOFG Anatomy Entry List (SAEL): an annotation tool for functional
      genomics data'
    year: 2004
sage.socialsciencethesaurus:
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: 'The SAGE Social Science Thesaurus is a multidisciplinary vocabulary
    of the most important concepts in the social sciences. SAGE uses this vocabulary
    as its principal keyword vocabulary for automated tagging of content on SAGE Knowledge
    and SAGE Research Methods. You are welcome to browse, download, use and transform
    the vocabulary for any non-commercial purpose.


    The majority of concepts in the thesaurus have been mined from headwords in SAGE
    encyclopedias and other reference works. Relationships between concepts have been
    inferred from implicit structures in those works, for example subject indexes
    and readers'' guides. As such, the thesaurus is a structured representation of
    what the editors of those reference works consider to be the most important concepts
    in the social sciences.


    Additional scraping work has extracted and structured concept-specific metadata,
    such as dates (for events and people) and definitions. In addition to broader-narrower
    relationships, concepts are grouped by type: concepts, people, organizations,
    events, methods, theories or laws.'
  example: -LHR8P7WS-K
  homepage: https://loterre.istex.fr/N9J/en/
  license: CC BY-NC-SA 4.0
  name: SAGE Social Science Thesaurus
  prefix: sage.socialsciencethesaurus
  uri_format: http://data.loterre.fr/ark:/67375/N9J$1
salk:
  appears_in:
  - efo
  comment: spider stuff!
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: Scientific research institute for neuroscience, genetics, immunology,
    plant biology and more.
  example: '037727'
  homepage: https://www.salk.edu/
  name: Salk Institute for Biological Studies
  pattern: ^\d{6}$
  prefix: salk
  uri_format: https://abrc.osu.edu/stocks/number/SALK_$1
salmon:
  aberowl:
    description: An ontology representing knowledge about salmon, features of their
      habitats, salmon stakeholders, and related entities. This ontology is considered
      to be in the early stages of development, though it is based upon considerable
      previous work. Contributions of all kinds are welcome and encouraged, including
      alignments, updates to existing terms, and new terms.
    download_owl: http://aber-owl.net/media/ontologies/SALMON/2/salmon.owl
    homepage: https://github.com/DataONEorg/sem-prov-ontologies/
    name: Salmon Ontology
    prefix: SALMON
    version: 0.3.1
  bioportal:
    contact:
      email: jones@nceas.ucsb.edu
      name: Matthew Jones
    description: An ontology representing knowledge about salmon, features of their
      habitats, salmon stakeholders, and related entities. This ontology is considered
      to be in the early stages of development, though it is based upon considerable
      previous work. Contributions of all kinds are welcome and encouraged, including
      alignments, updates to existing terms, and new terms.
    homepage: https://github.com/DataONEorg/sem-prov-ontologies/
    name: Salmon Ontology
    prefix: SALMON
    version: 0.4.0
  contact:
    email: brycemecum@gmail.com
    github: amoeba
    name: Bryce Mecum
    orcid: 0000-0002-0381-3766
  example: '00000674'
  homepage: https://github.com/DataONEorg/sem-prov-ontologies/tree/main/salmon
  mappings:
    aberowl: SALMON
    bioportal: SALMON
  pattern: ^\d+$
  prefix: salmon
  uri_format: https://purl.dataone.org/odo/SALMON_$1
sao:
  aberowl:
    description: SAO describes structures from the dimensional range encompassing
      cellular and subcellular structure, supracellular domains, and macromolecules.
    download_owl: http://aber-owl.net/media/ontologies/SAO/2/sao.owl
    homepage: http://ccdb.ucsd.edu/SAO
    name: Subcellular Anatomy Ontology
    prefix: SAO
    version: Version 1.2
  biocontext:
    prefix: SAO
  bioportal:
    contact:
      email: mmartone@ucsd.edu
      name: Maryann Martone
    description: SAO describes structures from the dimensional range encompassing
      cellular and subcellular structure, supracellular domains, and macromolecules.
    name: Subcellular Anatomy Ontology
    prefix: SAO
    version: Version 1.2
  example: '5277619'
  mappings:
    aberowl: SAO
    biocontext: SAO
    bioportal: SAO
    obofoundry: sao
    prefixcommons: sao
    wikidata.entity: Q114677911
  name: Subcellular Anatomy Ontology
  obofoundry:
    contact: slarson@ncmir.ucsd.edu
    contact.label: Stephen Larson
    deprecated: true
    domain: anatomy and development
    homepage: http://ccdb.ucsd.edu/CCDBWebSite/sao.html
    name: Subcellular anatomy ontology
    prefix: sao
  pattern: ^\d+$
  prefix: sao
  prefixcommons:
    bioportal: '1068'
    description: SAO describes structures from the dimensional range encompassing
      cellular and subcellular structure, supracellular domains, and macromolecules.
    example: sao1289741256
    homepage: http://ccdb.ucsd.edu/SAO
    keywords:
    - owl
    - biochemistry
    name: Subcellular Anatomy Ontology (SAO)
    pattern: ^sao\d+$
    prefix: sao
    rdf_uri_format: http://ccdb.ucsd.edu/SAO/1.2#$1
    synonyms:
    - 'sao:'
  references:
  - http://www.ontobee.org/ontology/SAO
  uri_format: http://uri.neuinfo.org/nif/nifstd/sao$1
saref:
  agroportal:
    contact:
      email: maxime.lefrancois@emse.fr
      name: Maxime Lefrançois
    description: The Smart Applications REFerence ontology (SAREF) is intended to
      enable interoperability between solutions from different providers and among
      various activity sectors in the Internet of Things (IoT), thus contributing
      to the development of the global digital market.
    example_uri: https://saref.etsi.org/core/Command
    homepage: https://saref.etsi.org/
    license: https://forge.etsi.org/etsi-software-license
    name: Smart Applications REFerence ontology
    prefix: SAREF
    publications:
    - https://www.etsi.org/deliver/etsi_ts/103200_103299/103264/04.01.01_60/ts_103264v040101p.pdf
    version: v4.1.1
  example: Actuation
  lov:
    description: The Smart Appliances REFerence (SAREF) ontology is a shared model
      of consensus that facilitates the matching of existing assets (standards/protocols/datamodels/etc.)
      in the smart appliances domain. The SAREF ontology provides building blocks
      that allow separation and recombination of different parts of the ontology depending
      on specific needs.
    homepage: https://saref.etsi.org/core/
    keywords:
    - Industry
    - IoT
    - Services
    modified: '2020-05-29'
    name: 'SAREF: the Smart Appliances REFerence ontology'
    prefix: saref
    uri_prefix: https://saref.etsi.org/core/$1
  mappings:
    agroportal: SAREF
    lov: saref
    tib: saref
  name: Smart Applications Reference ontology
  prefix: saref
  tib:
    description: The Smart Applications REFerence ontology (SAREF) is intended to
      enable interoperability between solutions from different providers and among
      various activity sectors in the Internet of Things (IoT), thus contributing
      to the development of the global digital market.
    homepage: https://saref.etsi.org/core/
    keywords:
    - NFDI4ING
    - Digital Planning and Construction
    - FID BAUdigital
    - engineering
    name: 'SAREF: the Smart Applications REFerence ontology'
    prefix: saref
    tracker: https://saref.etsi.org/sources/saref-core/issues
    uri_format: https://saref.etsi.org/core/$1
    version.iri: https://saref.etsi.org/core/v4.1.1/
saref.agri:
  example: Animal
  lov:
    description: This ontology extends the SAREF ontology for the Agricultural domain.
      This work has been developed in the context of the STF 534 (https://portal.etsi.org/STF/STFs/STFHomePages/STF534.aspx),
      which was established with the goal to create three SAREF extensions, one of
      them for the Agricultural domain.
    homepage: https://saref.etsi.org/saref4agri/
    keywords:
    - Food
    - IoT
    modified: '2020-06-05'
    name: SAREF extension for Agriculture
    prefix: s4agri
    uri_prefix: https://saref.etsi.org/saref4agri/$1
  mappings:
    lov: s4agri
    tib: s4agri
  prefix: saref.agri
  synonyms:
  - s4agri
  tib:
    description: SAREF4AGRI is an extension of SAREF for the agriculture and food
      domain. SAREF4AGRI is specified and published by ETSI in the TS 103 410-6 associated
      to this ontology file. The list of use cases, standards and requirements that
      guided the creation of SAREF4AGRI are described in the associated ETSI TR 103
      511.
    homepage: https://saref.etsi.org/saref4agri/
    keywords:
    - TIB
    - agriculture
    name: 'SAREF4AGRI: an extension of SAREF for the agriculture and food domain'
    prefix: s4agri
    tracker: https://labs.etsi.org/rep/saref/saref4agri/-/issues
    uri_format: https://saref.etsi.org/saref4agri/$1
    version.iri: https://saref.etsi.org/saref4agri/v2.1.1/
saref.auto:
  example: AcousticSensor
  mappings:
    tib: s4auto
  prefix: saref.auto
  synonyms:
  - s4auto
  tib:
    description: This ontology extends the SAREF ontology for the automotive domain.
      This work has been developed in the context of the STF 566, which was established
      with the goal to create four SAREF extensions, one of them for the automotive
      domain.
    homepage: https://saref.etsi.org/saref4auto/
    keywords:
    - NFDI4ING
    - FID move
    - engineering
    - traffic engineering
    name: 'SAREF4AUTO: an extension of SAREF for the automotive domain'
    prefix: s4auto
    tracker: https://saref.etsi.org/sources/saref4auto/issues
    uri_format: https://saref.etsi.org/saref4auto/$1
    version.iri: https://saref.etsi.org/saref4auto/v2.1.1/
saref.building:
  example: Actuator
  lov:
    description: This ontology extends the SAREF ontology for the building domain
      by defining building devices and how they are located in a building. This extension
      is based on the ISO 16739:2013 Industry Foundation Classes (IFC) standard for
      data sharing in the construction and facility management industries. The descriptions
      of the classes and properties extracted from IFC have been taken from the IFC
      documentation.
    homepage: https://saref.etsi.org/saref4bldg/
    keywords:
    - IoT
    modified: '2020-06-05'
    name: SAREF extension for building devices
    prefix: s4bldg
    uri_prefix: https://saref.etsi.org/saref4bldg/$1
  mappings:
    lov: s4bldg
    tib: s4bldg
  prefix: saref.building
  synonyms:
  - s4bldg
  tib:
    description: This ontology extends the SAREF ontology for the building domain
      by defining building devices and how they are located in a building. This extension
      is based on the ISO 16739:2013 Industry Foundation Classes (IFC) standard for
      data sharing in the construction and facility management industries. The descriptions
      of the classes and properties extracted from IFC have been taken from the IFC
      documentation.
    homepage: https://saref.etsi.org/saref4bldg/
    keywords:
    - NFDI4ING
    - Digital Planning and Construction
    - FID BAUdigital
    - engineering
    name: 'SAREF4BLDG: an extension of SAREF for the building domain'
    prefix: s4bldg
    tracker: https://saref.etsi.org/sources/saref4bldg/issues
    uri_format: https://saref.etsi.org/saref4bldg/$1
    version.iri: https://saref.etsi.org/saref4bldg/v2.1.1/
saref.city:
  example: AccessibilityConcept
  lov:
    description: This ontology extends the SAREF ontology for the Smart City domain.
      This work has been developed in the context of the STF 534 (https://portal.etsi.org/STF/STFs/STFHomePages/STF534.aspx),
      which was established with the goal to create three SAREF extensions, one of
      them for the Smart City domain.
    homepage: https://saref.etsi.org/saref4city/
    keywords:
    - Government
    - IoT
    modified: '2020-06-05'
    name: SAREF extension for Smart City
    prefix: s4city
    uri_prefix: https://saref.etsi.org/saref4city/$1
  mappings:
    lov: s4city
    tib: s4city
  prefix: saref.city
  synonyms:
  - s4city
  tib:
    description: This ontology extends the SAREF ontology for the Smart City domain.
      This work has been developed in the context of the STF 534 (https://portal.etsi.org/STF/STFs/STFHomePages/STF534.aspx),
      which was established with the goal to create three SAREF extensions, one of
      them for the Smart City domain.
    homepage: https://saref.etsi.org/saref4city/
    keywords:
    - Digital Planning and Construction
    - FID move
    - civil engineering
    - traffic engineering
    - computer science
    name: 'SAREF4CITY: an extension of SAREF for the Smart City domain'
    prefix: s4city
    uri_format: https://saref.etsi.org/saref4city/$1
    version.iri: https://saref.etsi.org/saref4city/v2.1.1/
saref.ehaw:
  example: Activity
  lov:
    description: "The objective of SAREF4EHAW is to extend SAREF ontology for the\
      \ eHealth/Ageing-well (EHAW) vertical. Clause 4.1 of the present document shortly\
      \ introduces a high level view of the envisioned SAREF4EHAW semantic model and\
      \ modular ontology, with the retained concepts (i.e. classes) and their relations.\
      \ \nSAREF4EHAW extension has been specified and formalised by investigating\
      \ EHAW domain related resources, as reported in ETSI TR 103 509, such as: potential\
      \ stakeholders, standardization initiatives, alliances/associations, European\
      \ projects, EC directives, existing ontologies, and data repositories. Therefore,\
      \ SAREF4EHAW modular ontology shall both:\n - Allow the implementation of a\
      \ limited set of typical EHAW related use cases already identified in ETSI TR\
      \ 103 509, i.e.\n - Use case 1 ?elderly at home monitoring and support?,\n -\
      \ Use case 2 ?monitoring and support of healthy lifestyles for citizens?,\n\
      \ - Use case 3 ?Early Warning System (EWS) and Cardiovascular Accidents detection?.\n\
      \ - Fulfil the eHealth Ageing Well related requirements provided in ETSI TR\
      \ 103 509, mainly the ontological ones that were mostly taken as input for the\
      \ ontology specification.\n\nSAREF4EHAW mainly reuses the following existing\
      \ ontologies: SAREF, ETSI SmartBAN reference model, SAREF 4 Environment extension\
      \ and W3C SSN System module. The following figure presents the high level view\
      \ of SAREF4EHAW ontology.\n![SAREF4SYST overview](diagrams/SAREF4EHAW_Model.jpg)\n\
      For semantic interoperability handling purposes, an ontology based solution,\
      \ combined with sensing-as-a-service and WoT strategies, is retained for SAREF4EHAW.\
      \ Therefore, an upper level ontology, at service level, shall also behas been\
      \ fully modelled (Service class and sub-classes depicted in the previous figure).\n\
      For embedded semantic analytics purposes, SAREF4EHAW shall behas been designed\
      \ using the modularity principle (see ETSI TR 103 509) and can thus be mainly\
      \ described by the following self-contained knowledge sub-ontologies (or modules):\
      \ HealthActor, Ban, HealthDevice, Function (measured data related concepts included)\
      \ and Service."
    homepage: https://saref.etsi.org/saref4ehaw/
    keywords:
    - IoT
    modified: '2020-05-01'
    name: 'SAREF4EHAW: an extension of SAREF for eHealth Ageing Well domain'
    prefix: s4ehaw
    uri_prefix: https://saref.etsi.org/saref4ehaw/$1
  mappings:
    lov: s4ehaw
    tib: s4ehaw
  prefix: saref.ehaw
  synonyms:
  - s4ehaw
  tib:
    description: SAREF4EHAW extension has been specified and formalised by investigating
      EHAW domain related resources
    homepage: https://saref.etsi.org/saref4ehaw/
    keywords:
    - NFDI4ING
    - engineering
    name: 'SAREF4EHAW: an extension of SAREF for eHealth Ageing Well domain'
    prefix: s4ehaw
    tracker: https://saref.etsi.org/sources/saref4ehaw/issues
    uri_format: https://saref.etsi.org/saref4ehaw/$1
    version.iri: https://saref.etsi.org/saref4ehaw/v2.1.1/
saref.ener:
  example: ActuatorLevel
  lov:
    description: This is the extension of SAREF for the EEBus and Energy@Home project.
      The documentation of SAREF4EE is available at http://ontology.tno.nl/SAREF4EE_Documentation_v0.1.pdf.
      SAREF4EE represents 1) The configuration information exchanged in the use case
      'Remote Network Management' according to the EEBus Technical Report, Protocol
      Specification- Remote Network Management, version 1.0.0.2, 2015-09-19; 2) The
      scheduling information about power sequences exchanged in the use cases Appliance
      scheduling through CEM and remote start' and 'Automatic cycle rescheduling',
      according to the message structures described in General Message Structures,
      version 0.1.1, 2015-10-07; 3) The monitor and control information exchanged
      in the use case 'Communicate appliance status and info on manually planned cycles',
      according to the monitoring and control part of the Energy@Home Data Model,
      version 1.0; and 4) the event-based data exchanged in the use case 'Demand Response',
      according to General Message Structures, version 0.1.1, 2015-10-07.
    homepage: https://saref.etsi.org/saref4ener/
    keywords:
    - Environment
    - Services
    modified: '2020-06-04'
    name: 'SAREF4EE: the EEbus/Energy@home extension of SAREF'
    prefix: s4ener
    uri_prefix: https://saref.etsi.org/saref4ener/$1
  mappings:
    lov: s4ener
    tib: s4ener
  prefix: saref.ener
  synonyms:
  - s4ener
  tib:
    description: SAREF4ENER is an extension of SAREF for the Energy domain that was
      created in collaboration with Energy@Home (http://www.energy-home.it) and EEBus
      (http://www.eebus.org/en), the major Italy- and Germany-based industry associations,
      to enable the interconnection of their (different) data models. SAREF4ENER focuses
      on demand response scenarios, in which customers can offer flexibility to the
      Smart Grid to manage their smart home devices by means of a Customer Energy
      Manager (CEM). The CEM is a logical function for optimizing energy consumption
      and/or production that can reside either in the home gateway or in the cloud.
      SAREF4ENER is published as an ETSI tecnical specificatoion (ETSI TS 103 410-1).
    homepage: https://saref.etsi.org/saref4ener/
    keywords:
    - NFDI4ING
    - NFDI4Energy
    - Digital Planning and Construction
    - FID BAUdigital
    - engineering
    name: SAREF for Energy Flexibility
    prefix: s4ener
    tracker: https://saref.etsi.org/sources/saref4ener/issues
    uri_format: https://saref.etsi.org/saref4ener/$1
    version.iri: https://saref.etsi.org/saref4ener/v2.1.1/
saref.environment:
  example: AirEmissionKind
  lov:
    description: This ontology extends the SAREF ontology for the environment domain,
      specifically for the light pollution domain, including concepts like photometers,
      light, etc.
    homepage: https://saref.etsi.org/saref4envi/
    keywords:
    - Environment
    - IoT
    modified: '2021-02-25'
    name: SAREF extension for environment
    prefix: s4envi
    uri_prefix: https://saref.etsi.org/saref4envi/$1
  mappings:
    lov: s4envi
    tib: s4envi
  prefix: saref.environment
  synonyms:
  - s4envi
  tib:
    description: This ontology extends the SAREF ontology for the environment domain,
      specifically for the light pollution domain, including concepts like photometers,
      light, etc.
    homepage: https://saref.etsi.org/saref4envi/
    keywords:
    - NFDI4ING
    - engineering
    name: 'SAREF4ENVI: an extension of SAREF for the Environment domain'
    prefix: s4envi
    tracker: https://saref.etsi.org/sources/saref4envi/issues
    uri_format: https://saref.etsi.org/saref4envi/$1
    version.iri: https://saref.etsi.org/saref4envi/v2.1.1/
saref.grid:
  example: ActionOperation
  mappings:
    tib: s4grid
  prefix: saref.grid
  synonyms:
  - s4grid
  tib:
    description: This ontology extends the SAREF ontology for the smart grid domain.
    homepage: https://saref.etsi.org/saref4grid/
    keywords:
    - NFDI4Energy
    - engineering
    name: 'SAREF4GRID: an extension of SAREF for the Smart Grid domain'
    prefix: s4grid
    tracker: https://saref.etsi.org/sources/saref4grid/issues
    uri_format: https://saref.etsi.org/saref4grid/$1
    version.iri: https://saref.etsi.org/saref4grid/v2.1.1/
saref.industry:
  example: Area
  lov:
    description: SAREF4INMA is an extension of SAREF for the industry and manufacturing
      domain. SAREF4INMA focuses on extending SAREF for the industry and manufacturing
      domain to solve the lack of interoperability between various types of production
      equipment that produce items in a factory and, once outside the factory, between
      different organizations in the value chain to uniquely track back the produced
      items to the corresponding production equipment, batches, material and precise
      time in which they were manufactured. SAREF4INMA is specified and published
      by ETSI in the TS 103 410-5 associated to this ontology file. SAREF4INMA was
      created to be aligned with related initiatives in the smart industry and manufacturing
      domain in terms of modelling and standardization, such as the Reference Architecture
      Model for Industry 4.0 (RAMI), which combines several standards used by the
      various national initiatives in Europe that support digitalization in manufacturing.
      The full list of use cases, standards and requirements that guided the creation
      of SAREF4INMA are described in the associated ETSI TR 103 507.
    homepage: https://saref.etsi.org/saref4inma/
    keywords:
    - Industry
    - IoT
    modified: '2019-04-30'
    name: 'SAREF4INMA: an extension of SAREF for the industry and manufacturing domain'
    prefix: s4inma
    uri_prefix: https://saref.etsi.org/saref4inma/$1
  mappings:
    lov: s4inma
    tib: s4inma
  prefix: saref.industry
  synonyms:
  - s4inma
  tib:
    description: SAREF4INMA is an extension of SAREF for the industry and manufacturing
      domain. SAREF4INMA focuses on extending SAREF for the industry and manufacturing
      domain to solve the lack of interoperability between various types of production
      equipment that produce items in a factory and, once outside the factory, between
      different organizations in the value chain to uniquely track back the produced
      items to the corresponding production equipment, batches, material and precise
      time in which they were manufactured. SAREF4INMA is specified and published
      by ETSI in the TS 103 410-5 associated to this ontology file. SAREF4INMA was
      created to be aligned with related initiatives in the smart industry and manufacturing
      domain in terms of modelling and standardization, such as the Reference Architecture
      Model for Industry 4.0 (RAMI), which combines several standards used by the
      various national initiatives in Europe that support digitalization in manufacturing.
      The full list of use cases, standards and requirements that guided the creation
      of SAREF4INMA are described in the associated ETSI TR 103 507.
    homepage: https://saref.etsi.org/saref4inma/
    keywords:
    - NFDI4ING
    - engineering
    name: 'SAREF4INMA: an extension of SAREF for the industry and manufacturing domain'
    prefix: s4inma
    tracker: https://saref.etsi.org/sources/saref4inma/issues
    uri_format: https://saref.etsi.org/saref4inma/$1
    version.iri: https://saref.etsi.org/saref4inma/v2.1.1/
saref.lift:
  example: AlarmSignal
  mappings:
    tib: s4lift
  prefix: saref.lift
  synonyms:
  - s4lift
  tib:
    description: This ontology extends the SAREF ontology for the Smart Lifts domain.
    homepage: https://saref.etsi.org/saref4lift/
    keywords:
    - NFDI4ING
    - Digital Planning and Construction
    - FID BAUdigital
    - engineering
    name: 'SAREF4LIFT: an extension of SAREF for the Smart Lifts domain'
    prefix: s4lift
    tracker: https://saref.etsi.org/sources/saref4lift/issues
    uri_format: https://saref.etsi.org/saref4lift/$1
    version.iri: https://saref.etsi.org/saref4lift/v2.1.1/
saref.maritime:
  example: AISDevice
  mappings:
    tib: s4mari
  prefix: saref.maritime
  synonyms:
  - s4mari
  tib:
    description: SAREF4MARI is an extension of SAREF for the maritime domain.
    homepage: https://saref.etsi.org/saref4mari/
    keywords:
    - FID move
    - traffic engineering
    name: 'SAREF4MARI: an extension of SAREF for the maritime domain'
    prefix: s4mari
    tracker: https://labs.etsi.org/rep/saref/saref4mari/-/issues
    uri_format: https://saref.etsi.org/saref4mari/$1
    version.iri: https://saref.etsi.org/saref4mari/v1.1.1/
saref.system:
  example: Connection
  lov:
    description: "The present document is the technical specification of SAREF4SYST,\
      \ a generic extension of [ETSI TS 103 264 SAREF](https://www.etsi.org/deliver/etsi_ts/103200_103299/103264/02.01.01_60/ts_103264v020101p.pdf)\
      \ that defines an ontology pattern which can be instantiated for different domains.\
      \ SAREF4SYST defines Systems, Connections between systems, and Connection Points\
      \ at which systems may be connected. These core concepts can be used generically\
      \ to define the topology of features of interest, and can be specialized for\
      \ multiple domains. The topology of features of interest is highly important\
      \ in many use cases. If a room holds a lighting device, and if it is adjacent\
      \ with an open window to a room whose luminosity is low, then by turning on\
      \ the lighting device in the former room one may expect that the luminosity\
      \ in the latter room will rise.\n\nThe SAREF4SYST ontology pattern can be instantiated\
      \ for different domains. For example to describe zones inside a building (systems),\
      \ that share a frontier (connections). Properties of systems are typically state\
      \ variables (e.g. agent population, temperature), whereas properties of connections\
      \ are typically flows (e.g. heat flow).\n\nSAREF4SYST has two main aims: on\
      \ the one hand, to extend SAREF with the capability or representing general\
      \ topology of systems and how they are connected or interact and, on the other\
      \ hand, to exemplify how ontology patterns may help to ensure an homogeneous\
      \ structure of the overall SAREF ontology and speed up the development of extensions.\n\
      \nSAREF4SYST consists both of a core ontology, and guidelines to create ontologies\
      \ following the SAREF4SYST ontology pattern. The core ontology is a lightweight\
      \ OWL-DL ontology that defines 3 classes and 9 object properties.\n\nUse cases\
      \ for ontology patterns are described extensively in  [ETSI TR 103 549 Clauses\
      \ 4.2 and 4.3](https://www.etsi.org/deliver/etsi_tr/103500_103599/103549/01.01.01_60/tr_103549v010101p.pdf).\n\
      \nFor the Smart Energy domain:\n\n- Electric power systems can exchange electricity\
      \ with other electric power systems. The electric energy can flow both ways\
      \ in some cases (from the Public Grid to a Prosumer), or in only one way (from\
      \ the Public Grid to a Load). Electric power systems can be made up of different\
      \ sub-systems. Generic sub-types of electric power systems include producers,\
      \ consumers, storage systems, transmission systems. \n- Electric power systems\
      \ may be connected one to another through electrical connection points. An Electric\
      \ power system may have multiple connection points (Multiple Winding Transformer\
      \ generally have one single primary winding with two or more secondary windings).\
      \ Generic sub-types of electrical connection points include plugs, sockets,\
      \ direct-current, single-phase, three-phase, connection points. \n- An Electrical\
      \ connection may exist between two Electric power systems at two of their respective\
      \ connection points. Generic sub-types of electrical connections include Single-phase\
      \ Buses, Three-phase Buses. A single-phase electric power system can be connected\
      \ using different configurations at a three-phase bus (RN, SN, TN types).\n\n\
      For the Smart Building domain:\n\n- Buildings, Storeys, Spaces, are different\
      \ sub-types of Zones. Zones can contain sub-zones. Zones can be adjacent or\
      \ intersect with other zones. \n- Two zones may share one or more connections.\
      \ For example some fresh air may be created inside a storey if it has two controllable\
      \ openings to the exterior at different cardinal points. \n\nA graphical overview\
      \ of the SAREF4SYST ontology is provided in Figure 1. In such figure:\n\n- Rectangles\
      \ are used to denote Classes. The label of the rectangle is the identifier of\
      \ the Class.\n- Plain arrows are used to represent Object Properties between\
      \ Classes. The label of the arrow is the identifier of the Object Property.\
      \ The origin of the arrow is the domain Class of the property, and the target\
      \ of the arrow is the range Class of the property.\n- Dashed arrows with identifiers\
      \ between stereotype signs (i.e. \"`<< >>`\") refer to OWL axioms that are applied\
      \ to some property. Four pairs of properties are inverse one of the other; the\
      \ property `s4syst:connectedTo` is symmetric, and properties `s4syst:hasSubSystem`\
      \ and `s4syst:hasSubSystem` are transitive.\n- A symbol =1 near the target of\
      \ an arrow denotes that the associated property is functional. A symbol ? denotes\
      \ a local existential restriction.\n\n\n![SAREF4SYST overview](diagrams/overview.png)"
    homepage: https://saref.etsi.org/saref4syst/
    keywords:
    - IoT
    modified: '2020-06-14'
    name: 'SAREF4SYST: an extension of SAREF for typology of systems and their inter-connections'
    prefix: s4syst
    uri_prefix: https://saref.etsi.org/saref4syst/$1
  mappings:
    lov: s4syst
    tib: s4syst
  prefix: saref.system
  synonyms:
  - s4syst
  tib:
    description: SAREF4SYST defines Systems, Connections between systems, and Connection
      Points at which systems may be connected. These core concepts can be used generically
      to define the topology of features of interest, and can be specialized for multiple
      domains.
    homepage: https://saref.etsi.org/saref4syst/
    keywords:
    - NFDI4ING
    name: 'SAREF4SYST: an extension of SAREF for typology of systems and their inter-connections'
    prefix: s4syst
    tracker: https://labs.etsi.org/rep/saref/saref4syst/-/issues
    uri_format: https://saref.etsi.org/saref4syst/$1
    version.iri: https://saref.etsi.org/saref4syst/v1.1.2/
saref.water:
  example: AcceptabilityProperty
  lov:
    description: This ontology extends the SAREF ontology for the water domain. This
      work has been developed in the context of the STF 566, which was established
      with the goal to create three SAREF extensions, one of them for the water domain.
    homepage: https://saref.etsi.org/saref4watr/
    keywords:
    - Environment
    - IoT
    modified: '2020-06-03'
    name: SAREF extension for water
    prefix: s4watr
    uri_prefix: https://saref.etsi.org/saref4watr/$1
  mappings:
    lov: s4watr
    tib: s4watr
  prefix: saref.water
  synonyms:
  - s4watr
  tib:
    description: This ontology extends the SAREF ontology for the water domain. This
      work has been developed in the context of the STF 566, which was established
      with the goal to create three SAREF extensions, one of them for the water domain.
    homepage: https://saref.etsi.org/saref4watr/
    keywords:
    - NFDI4ING
    - engineering
    name: 'SAREF4WATR: an extension of SAREF for the water domain'
    prefix: s4watr
    tracker: https://saref.etsi.org/sources/saref4watr/issues
    uri_format: https://saref.etsi.org/saref4watr/$1
    version.iri: https://saref.etsi.org/saref4watr/v2.1.1/
saref.wearable:
  example: BiometricProperty
  lov:
    description: SAREF4WEAR is an extension of SAREF for Wearables
    homepage: https://saref.etsi.org/saref4wear/
    keywords:
    - IoT
    modified: '2020-02-01'
    name: 'SAREF4WEAR: an extension of SAREF for Wearables'
    prefix: s4wear
    uri_prefix: https://saref.etsi.org/saref4wear/$1
  mappings:
    lov: s4wear
    tib: s4wear
  prefix: saref.wearable
  synonyms:
  - s4wear
  tib:
    description: SAREF4WEAR is an extension of SAREF for Wearables
    homepage: https://saref.etsi.org/saref4wear/
    keywords:
    - NFDI4ING
    - engineering
    name: 'SAREF4WEAR: an extension of SAREF for the Wearables domain'
    prefix: s4wear
    tracker: https://saref.etsi.org/sources/saref4wear/issues
    uri_format: https://saref.etsi.org/saref4wear/$1
    version.iri: https://saref.etsi.org/saref4wear/v2.1.1/
sargon:
  example: AC-DC
  mappings:
    tib: sargon
  prefix: sargon
  tib:
    description: SARGON (SmArt eneRGy dOmain oNtology) is an open-source effort to
      define semantic descriptions of the smart assets in building automation and
      smart grid and the relationships between them. SARGON consists of an extensible
      dictionary of terms and concepts in and around building and smart grid, a set
      of relationships for linking and composing concepts together, and a flexible
      data model permitting seamless integration of SARGON with existing tools and
      databases. Through the use of powerful Semantic Web technology, SARGON can describe
      the broad set of Devices and custom features, assets and subsystems found across
      the building stock in a consistent matter.
    download_owl: https://sargon-n5geh.netlify.app/ontologies/Sargon.owl
    homepage: https://sargon-n5geh.netlify.app/
    keywords:
    - NFDI4Energy
    - engineering
    name: SARGON (SmArt eneRGy dOmain oNtology)
    prefix: sargon
    tracker: https://github.com/N5GEH/SARGON-Website/issues
    uri_format: https://sargon-n5geh.netlify.app/ontology/1.0/object_properties/$1
sasap:
  aberowl:
    description: An ontology which represents information about the State of Alaska's
      Salmon and People (SASAP) project, as well as knowledge about salmon, features
      of their habitats, salmon stakeholders, and related entities.
    download_owl: http://aber-owl.net/media/ontologies/SASAP/2/sasap.owl
    homepage: https://github.com/DataONEorg/sem-prov-ontologies
    name: The State of Alaska's Salmon and People Ontology
    prefix: SASAP
    version: 0.1.1
  bioportal:
    contact:
      email: mecum@nceas.ucsb.edu
      name: Bryce Mecum
    description: An ontology which represents information about the State of Alaska's
      Salmon and People (SASAP) project, as well as knowledge about salmon, features
      of their habitats, salmon stakeholders, and related entities.
    homepage: https://github.com/DataONEorg/sem-prov-ontologies
    name: The State of Alaska's Salmon and People Ontology
    prefix: SASAP
    version: 0.3.1
  contact:
    email: brycemecum@gmail.com
    github: amoeba
    name: Bryce Mecum
    orcid: 0000-0002-0381-3766
  example: '00000101'
  homepage: https://github.com/DataONEorg/sem-prov-ontologies/tree/main/salmon
  mappings:
    aberowl: SASAP
    bioportal: SASAP
  pattern: ^\d+$
  prefix: sasap
  uri_format: https://purl.dataone.org/odo/SASAP_$1
sasbdb:
  biocontext:
    prefix: SASBDB
  fairsharing:
    abbreviation: SASBDB
    contact:
      email: a.kikhney@embl-hamburg.de
      name: Al Kikhney
      orcid: 0000-0003-1321-3956
    description: Curated repository for small angle scattering data and models. SASBDB
      contains X-ray (SAXS) and neutron (SANS) scattering data from biological macromolecules
      in solution.
    homepage: https://www.sasbdb.org/
    name: Small angle scattering biological data bank
    prefix: FAIRsharing.i1F3Hb
    publications:
    - doi: 10.1093/nar/gku1047
      pubmed_id: 25352555
      title: SASBDB, a repository for biological small-angle scattering data
    subjects:
    - Molecular biology
    - Life Science
  mappings:
    biocontext: SASBDB
    fairsharing: FAIRsharing.i1F3Hb
    miriam: sasbdb
    n2t: sasbdb
    re3data: r3d100012273
    uniprot: DB-0258
  miriam:
    deprecated: false
    description: Small Angle Scattering Biological Data Bank (SASBDB) is a curated
      repository for small angle X-ray scattering (SAXS) and neutron scattering (SANS)
      data and derived models. Small angle scattering (SAS) of X-ray and neutrons
      provides structural information on biological macromolecules in solution at
      a resolution of 1-2 nm. SASBDB provides freely accessible and downloadable experimental
      data, which are deposited together with the relevant experimental conditions,
      sample details, derived models and their fits to the data.
    homepage: http://www.sasbdb.org/
    id: '00000572'
    name: SASBDB
    namespaceEmbeddedInLui: false
    pattern: ^[Ss][Aa][Ss][A-Za-z0-9]{3}[0-9]$
    prefix: sasbdb
    sampleId: SASDAX8
    uri_format: http://www.sasbdb.org/data/$1
  n2t:
    description: Small Angle Scattering Biological Data Bank (SASBDB) is a curated
      repository for small angle X-ray scattering (SAXS) and neutron scattering (SANS)
      data and derived models. Small angle scattering (SAS) of X-ray and neutrons
      provides structural information on biological macromolecules in solution at
      a resolution of 1-2 nm. SASBDB provides freely accessible and downloadable experimental
      data, which are deposited together with the relevant experimental conditions,
      sample details, derived models and their fits to the data.
    example: SASDAX8
    homepage: http://www.sasbdb.org/
    name: SASBDB at European Molecular Biology Laboratory
    namespaceEmbeddedInLui: false
    pattern: ^[Ss][Aa][Ss][A-Za-z0-9]{3}[0-9]$
    prefix: sasbdb
    uri_format: http://www.sasbdb.org/data/$1
  name: Small Angle Scattering Biological Data Bank
  prefix: sasbdb
  publications:
  - doi: 10.1002/pro.3731
    pmc: PMC6933840
    pubmed: '31576635'
    title: 'SASBDB: Towards an automatically curated and validated repository for
      biological scattering data'
    year: 2019
  - doi: 10.1093/nar/gku1047
    pmc: PMC4383894
    pubmed: '25352555'
    title: SASBDB, a repository for biological small-angle scattering data
    year: 2014
  - doi: 10.1093/nar/gku1047
    pmc: null
    pubmed: null
    title: SASBDB, a repository for biological small-angle scattering data
    year: null
  - doi: 10.1002/pro.3731
    pmc: null
    pubmed: '31576635'
    title: null
    year: null
  re3data:
    description: 'Small angle scattering (SAS) of X-ray and neutrons provides structural
      information on biological macromolecules in solution at a resolution of 1-2
      nm.

      SASBDB is a fully searchable curated repository of freely accessible and downloadable
      experimental data, which are deposited together with the relevant experimental
      conditions, sample details, derived models and their fits to the data.'
    doi: 10.17616/R36V1N
    homepage: https://www.sasbdb.org/
    name: SASBDB
    prefix: r3d100012273
    synonyms:
    - Small Angle Scattering Biological Data Bank
  uniprot:
    abbreviation: SASBDB
    category: 3D structure databases
    homepage: https://www.sasbdb.org/
    name: Small Angle Scattering Biological Data Bank
    prefix: DB-0258
    publications:
    - doi: 10.1002/pro.3731
      pubmed: '31576635'
    uri_format: https://www.sasbdb.org/uniprot/$1/
sbo:
  aberowl:
    description: Terms commonly used in Systems Biology, and in particular in computational
      modeling.
    download_owl: http://aber-owl.net/media/ontologies/SBO/816/sbo.owl
    homepage: http://www.ebi.ac.uk/sbo/
    name: Systems Biology Ontology
    prefix: SBO
  bartoc:
    abbreviation: SBO
    description: 'The Systems Biology Ontology is a set of controlled, relational
      vocabularies of terms commonly used in Systems Biology, and in particular in
      computational modelling. It consists of seven orthogonal vocabularies defining:
      reaction participants roles (e.g. „substrate“), quantitative parameters (e.g.
      „Michaelis constant“), classification of mathematical expressions describing
      the system (e.g. „mass action rate law“), modelling framework used (e.g. „logical
      framework“), the nature of the entity (e.g. „macromolecule“), the type of interaction
      (e.g. „process“), as well as a branch to define the different types of metadata
      that may be present within a model.'
    homepage: https://www.ebi.ac.uk/ols/ontologies/sbo
    name: Systems Biology Ontology
    prefix: '20713'
  biocontext:
    prefix: SBO
  bioportal:
    contact:
      email: sheriff@ebi.ac.uk
      name: Rahuman Sheriff
    description: 'The Systems Biology Ontology is a set of controlled, relational
      vocabularies of terms commonly used in Systems Biology, and in particular in
      computational modeling. The ontology consists of six orthogonal vocabularies
      defining: the roles of reaction participants (eg. "substrate"), quantitative
      parameters (eg. "Michaelis constant"), a precise classification of mathematical
      expressions that describe the system (eg. "mass action rate law"), the modeling
      framework used (eg. "logical framework"), and a branch each to describe entity
      (eg. "macromolecule") and interaction (eg. "process") types, and a branch to
      define the different types of metadata that may be present within a model. SBO
      terms can be used to introduce a layer of semantic information into the standard
      description of a model, or to annotate the results of biochemical experiments
      in order to facilitate their efficient reuse. SBO is an Open Biomedical Ontologies
      (OBO) candidate ontology, and is free for use. More information about SBO can
      be found from the project FAQ, at http://www.ebi.ac.uk/sbo/ SBO is a project
      of the BioModels.net effort and is developed through community collaboration.'
    homepage: https://github.com/EBI-BioModels/SBO
    name: Systems Biology Ontology
    prefix: SBO
    version: 28:08:2021 03:13
  download_obo: http://purl.obolibrary.org/obo/sbo.obo
  example: 0000485
  fairsharing:
    abbreviation: SBO
    description: 'The Systems Biology Ontology is a set of controlled, relational
      vocabularies of terms commonly used in Systems Biology, and in particular in
      computational modelling. It consists of seven orthogonal vocabularies defining:
      reaction participants roles (e.g. "substrate"), quantitative parameters (e.g.
      "Michaelis constant"), classification of mathematical expressions describing
      the system (e.g. "mass action rate law"), modelling framework used (e.g. "logical
      framework"), the nature of the entity (e.g. "macromolecule"), the type of interaction
      (e.g. "process"), as well as a branch to define the different types of metadata
      that may be present within a model. Use of such terms introduces a layer of
      semantic information into the standard description of a model, facilitating
      its interpretation and efficient reuse.'
    domains:
    - molecular interaction
    - pathway
    homepage: http://www.ebi.ac.uk/sbo/
    name: Systems Biology Ontology
    prefix: FAIRsharing.s19src
    publications:
    - doi: 10.1038/msb.2011.77
      pubmed: '22027554'
      title: Controlled vocabularies and semantics in systems biology
      year: 2011
    subjects:
    - Systems Biology
    twitter: biomodels
  logo: https://upload.wikimedia.org/wikipedia/commons/f/fd/SBO_logo.png
  mappings:
    aberowl: SBO
    bartoc: '20713'
    biocontext: SBO
    bioportal: SBO
    fairsharing: FAIRsharing.s19src
    miriam: sbo
    n2t: sbo
    obofoundry: sbo
    ols: sbo
    ontobee: SBO
    prefixcommons: sbo
    tib: sbo
    wikidata.entity: Q2377160
  miriam:
    deprecated: false
    description: The goal of the Systems Biology Ontology is to develop controlled
      vocabularies and ontologies tailored specifically for the kinds of problems
      being faced in Systems Biology, especially in the context of computational modeling.
      SBO is a project of the BioModels.net effort.
    homepage: https://www.ebi.ac.uk/ols4/ontologies/sbo
    id: '00000024'
    name: Systems Biology Ontology
    namespaceEmbeddedInLui: true
    pattern: ^SBO:\d{7}$
    prefix: sbo
    sampleId: '0000262'
    uri_format: https://www.ebi.ac.uk/ols4/ontologies/sbo/terms?obo_id=SBO:$1
  n2t:
    description: The goal of the Systems Biology Ontology is to develop controlled
      vocabularies and ontologies tailored specifically for the kinds of problems
      being faced in Systems Biology, especially in the context of computational modeling.
      SBO is a project of the BioModels.net effort.
    example: '0000262'
    homepage: https://www.ebi.ac.uk/sbo/
    name: SBO
    namespaceEmbeddedInLui: true
    pattern: ^SBO:\d{7}$
    prefix: sbo
    uri_format: https://www.ebi.ac.uk/sbo/main/SBO:$1
  obofoundry:
    appears_in:
    - proco
    - scdo
    contact: sheriff@ebi.ac.uk
    contact.github: rsmsheriff
    contact.label: Rahuman Sheriff
    contact.orcid: 0000-0003-0705-9809
    deprecated: false
    description: Terms commonly used in Systems Biology, and in particular in computational
      modeling.
    domain: chemistry and biochemistry
    download.owl: http://purl.obolibrary.org/obo/sbo.owl
    homepage: http://www.ebi.ac.uk/sbo/
    license: Artistic License 2.0
    license.url: http://opensource.org/licenses/Artistic-2.0
    name: Systems Biology Ontology
    preferredPrefix: SBO
    prefix: sbo
    repository: https://github.com/EBI-BioModels/SBO
  ols:
    description: Terms commonly used in Systems Biology, and in particular in computational
      modeling.
    download_owl: http://purl.obolibrary.org/obo/sbo.owl
    homepage: http://www.ebi.ac.uk/sbo/
    name: Systems Biology Ontology
    prefix: sbo
    tracker: https://github.com/EBI-BioModels/SBO/issues
    version: '2021-08-28'
  ontobee:
    library: Library
    name: Systems Biology Ontology
    prefix: SBO
  pattern: ^\d{7}$
  prefix: sbo
  prefixcommons:
    alt_uri_formats:
    - http://purl.org/obo/owl/SBO#$1
    bioportal: '1046'
    description: The Systems Biology Ontology is a set of controlled vocabularies
      and ontologies tailored specifically for the kinds of problems being faced in
      Systems Biology, especially in the context of computational modelling.
    example: SBO:0000262
    homepage: http://www.ebi.ac.uk/sbo/
    keywords:
    - obo
    - systems biology
    license: http://www.ebi.ac.uk/Information/termsofuse.html
    name: Systems Biology Ontology
    pattern: ^SBO:\d{7}$
    prefix: sbo
    pubmed_ids:
    - '17118155'
    synonyms:
    - biomodels.sbo
    - Systems_Biology_Ontology
    uri_format: http://www.ebi.ac.uk/sbo/main/$1
  providers:
  - code: biomodels
    description: Provider for SBO at BioModels
    example: null
    first_party: null
    homepage: http://biomodels.net
    name: BioModels
    publications: null
    status: null
    uri_format: http://biomodels.net/SBO/SBO_$1
  publications:
  - doi: 10.1038/msb.2011.77
    pmc: PMC3261705
    pubmed: '22027554'
    title: Controlled vocabularies and semantics in systems biology
    year: 2011
  - doi: 10.1186/1471-2202-7-s1-s11
    pmc: PMC1775041
    pubmed: '17118155'
    title: Model storage, exchange and integration
    year: 2006
  tib:
    description: SBO (Systems Biology Ontology) provides vocabularies for terms in
      Systems Biology, especially for computational modeling. It includes six orthogonal
      vocabularies defining roles of reaction participants (e.g., "substrate"), quantitative
      parameters (e.g., "Michaelis constant"), classifications of mathematical expressions
      (e.g., "mass action rate law"), the modeling framework (e.g., "logical framework"),
      and vocabularies describing entity (e.g., "macromolecule") and interaction (e.g.,
      "process") types.
    download_owl: http://purl.obolibrary.org/obo/sbo.owl
    homepage: http://www.ebi.ac.uk/sbo/
    keywords:
    - NFDI4CAT
    - ESS
    - life sciences, biology
    - earth sciences
    name: Systems Biology Ontology
    prefix: sbo
    tracker: https://github.com/EBI-BioModels/SBO/issues
    uri_format: http://purl.obolibrary.org/obo/SBO_$1
  uri_format: http://purl.obolibrary.org/obo/SBO_$1
scancerrna:
  contact:
    email: zty2009@hit.edu.cn
    github: null
    name: Tianyi Zhao
    orcid: 0000-0001-7352-2959
  contributor:
    email: m.naguthana@hotmail.com
    github: nagutm
    name: Mufaddal Naguthanawala
    orcid: 0009-0009-5240-7463
  description: SCancerRNA provides identifiers for non-coding RNA biomarkers, including
    long ncRNA, microRNA, PIWI-interacting RNA, small nucleolar RNA, and circular
    RNA, with data on their differential expression at the cellular level in cancer.
  example: '9530'
  github_request_issue: 1215
  homepage: http://www.scancerrna.com/
  name: SCancerRNA
  pattern: ^\d+$
  prefix: scancerrna
  publications:
  - doi: 10.1093/gpbjnl/qzae023
    pmc: null
    pubmed: '39341795'
    title: 'SCancerRNA: Expression at the Single-cell Level and Interaction Resource
      of Non-coding RNA Biomarkers for Cancers'
    year: 2024
  reviewer:
    email: b.gyori@northeastern.edu
    github: bgyori
    name: Benjamin M. Gyori
    orcid: 0000-0001-9439-5346
  uri_format: http://www.scancerrna.com/toDetail?id=$1
scdo:
  aberowl:
    description: An ontology for the standardization of terminology and integration
      of knowledge about Sickle Cell Disease.
    download_owl: http://aber-owl.net/media/ontologies/SCDO/18/scdo.owl
    homepage: https://scdontology.h3abionet.org/
    name: Sickle Cell Disease Ontology
    prefix: SCDO
  bioportal:
    contact:
      email: giant.plankton@gmail.com
      name: Jade Hotchkiss
    description: 'The Sickle Cell Disease Ontology (SCDO) project is a collaboration
      between H3ABioNet (Pan African Bioinformatics Network) and SPAN (Sickle Cell
      Disease Pan African Network). The SCDO is currently under development and its
      purpose is to: 1) establish community standardized SCD terms and descriptions,
      2) establish canonical and hierarchical representation of knowledge on SCD,
      3) links to other ontologies and bodies of work such as DO, PhenX, MeSH, ICD,
      NCI’s thesaurus, SNOMED and OMIM. Once complete, we anticipate that the ontology
      will: 1) be the most comprehensive collection of knowledge on SCD, 2) facilitate
      exploration of new scientific questions and ideas, 3) facilitate seamless data
      sharing and collaborations including meta-analysis within the SCD community,
      4) support the building of databasing and clinical informatics in SCD.'
    homepage: http://scdontology.h3abionet.org
    name: Sickle Cell Disease Ontology
    prefix: SCDO
    publications:
    - https://scdontology.h3abionet.org
    version: '2021-04-15'
  example: 0000728
  fairsharing:
    abbreviation: SCDO
    description: 'The Sickle Cell Disease Ontology (SCDO) project is a collaboration
      between H3ABioNet (Pan African Bioinformatics Network) and SPAN (Sickle Cell
      Disease Pan African Network). The SCDO is currently under development and its
      purpose is to: 1) establish community standardized SCD terms and descriptions,
      2) establish canonical and hierarchical representation of knowledge on SCD,
      3) links to other ontologies and bodies of work such as DO, PhenX MeSH, ICD,
      NCI’s thesaurus, SNOMED and OMIM. '
    domains:
    - genetic disorder
    homepage: http://scdontology.h3abionet.org
    logo: https://api.fairsharing.org/rails/active_storage/blobs/redirect/eyJfcmFpbHMiOnsibWVzc2FnZSI6IkJBaHBBbWtCIiwiZXhwIjpudWxsLCJwdXIiOiJibG9iX2lkIn19--69320a8be8ca6a407eaf142714307b4c7e6b5f45/cropped-Screenshot-from-2020-05-23-20-20-32-2.png?disposition=inline
    name: Sickle Cell Disease Ontology
    prefix: FAIRsharing.kkq6pw
    publications:
    - doi: 10.1093/database/baac014
      pubmed: '35363306'
      title: 'The Sickle Cell Disease Ontology: recent development and expansion of
        the universal sickle cell knowledge representation'
      year: 2022
    - doi: 10.1089/omi.2020.0153
      pubmed: '33021900'
      title: 'The Sickle Cell Disease Ontology: Enabling Collaborative Research and
        Co-Designing of New Planetary Health Applications'
      year: 2020
    - doi: 10.1093/database/baz118
      pubmed: '31769834'
      title: 'The Sickle Cell Disease Ontology: enabling universal sickle cell-based
        knowledge representation'
      year: 2019
    repository: https://github.com/scdodev/scdo-ontology
    subjects:
    - Biomedical Science
    user_defined_tags:
    - sickle cell disease
  mappings:
    aberowl: SCDO
    bioportal: SCDO
    fairsharing: FAIRsharing.kkq6pw
    obofoundry: scdo
    ols: scdo
    ontobee: SCDO
    wikidata.entity: Q108710019
  obofoundry:
    contact: giant.plankton@gmail.com
    contact.github: JadeHotchkiss
    contact.label: Jade Hotchkiss
    contact.orcid: 0000-0002-2193-0704
    depends_on:
    - apollo_sv
    - aro
    - chebi
    - chmo
    - cmo
    - doid
    - dron
    - duo
    - envo
    - eupath
    - exo
    - gaz
    - gsso
    - hp
    - hsapdv
    - ico
    - ido
    - idomal
    - mp
    - nbo
    - ncit
    - obi
    - ogms
    - opmi
    - pr
    - sbo
    - stato
    - symp
    - uo
    - vo
    - vt
    deprecated: false
    description: An ontology for the standardization of terminology and integration
      of knowledge about Sickle Cell Disease.
    domain: health
    download.obo: http://purl.obolibrary.org/obo/scdo.obo
    download.owl: http://purl.obolibrary.org/obo/scdo.owl
    homepage: https://scdontology.h3abionet.org/
    license: GPL-3.0
    license.url: https://www.gnu.org/licenses/gpl-3.0.en.html
    name: Sickle Cell Disease Ontology
    preferredPrefix: SCDO
    prefix: scdo
    publications:
    - id: https://www.ncbi.nlm.nih.gov/pubmed/35363306
      title: 'The Sickle Cell Disease Ontology: recent development and expansion of
        the universal sickle cell knowledge representation.'
    - id: https://www.ncbi.nlm.nih.gov/pubmed/33021900
      title: 'The Sickle Cell Disease Ontology: Enabling Collaborative Research and
        Co-Designing of New Planetary Health Applications.'
    - id: https://www.ncbi.nlm.nih.gov/pubmed/31769834
      title: 'The Sickle Cell Disease Ontology: enabling universal sickle cell-based
        knowledge representation.'
    repository: https://github.com/scdodev/scdo-ontology
  ols:
    description: An ontology for the standardization of terminology and integration
      of knowledge about Sickle Cell Disease.
    download_owl: http://purl.obolibrary.org/obo/scdo.owl
    homepage: https://scdontology.h3abionet.org/
    name: Sickle Cell Disease Ontology
    prefix: scdo
    tracker: https://github.com/scdodev/scdo-ontology/issues
    version: '2021-04-15'
    version.iri: http://purl.obolibrary.org/obo/scdo/releases/2021-04-15/scdo.owl
  ontobee:
    library: Library
    name: Sickle Cell Disease Ontology
    prefix: SCDO
  pattern: ^\d{7}$
  prefix: scdo
  publications:
  - doi: 10.1093/database/baac014
    pmc: PMC9216550
    pubmed: '35363306'
    title: 'The Sickle Cell Disease Ontology: recent development and expansion of
      the universal sickle cell knowledge representation'
    year: 2022
  - doi: 10.1089/omi.2020.0153
    pmc: PMC7549008
    pubmed: '33021900'
    title: 'The Sickle Cell Disease Ontology: Enabling Collaborative Research and
      Co-Designing of New Planetary Health Applications'
    year: 2020
  - doi: 10.1093/database/baz118
    pmc: PMC6878945
    pubmed: '31769834'
    title: 'The Sickle Cell Disease Ontology: enabling universal sickle cell-based
      knowledge representation'
    year: 2019
  uri_format: http://purl.obolibrary.org/obo/SCDO_$1
schem:
  contact:
    email: null
    github: ncatlett
    name: Natalie L Catlett
    orcid: null
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: Selventa legacy chemical namespace used with the Biological Expression
    Language
  domain: chemical
  example: A0001
  homepage: https://github.com/OpenBEL/resource-generator/blob/master/datasets/selventa-legacy-chemical-names.txt
  keywords:
  - bel
  - chemistry
  - selventa
  license: Apache-2.0
  logo: https://biological-expression-language.github.io/img/bel300.png
  name: Selventa Chemicals
  pattern: ^A\d{4}$
  prefix: schem
  uri_format: https://biopragmatics.github.io/providers/schem/$1
schema:
  aberowl:
    description: A collection of schemas that webmasters can use to markup HTML pages
      in ways recognized by major search providers, and that can also be used for
      structured data interoperability (e.g. in JSON).
    download_owl: http://aber-owl.net/media/ontologies/SCHEMAORG/2/schemaorg.owl
    homepage: https://schema.org/
    name: Schema.org core and all extension vocabularies
    prefix: SCHEMAORG
    version: '3.4'
  biolink:
    is_identifiers: false
    is_obo: false
    prefix: schema
    uri_format: http://schema.org/$1
  bioportal:
    contact:
      email: johardi@stanford.edu
      name: Josef Hardi
    description: A collection of schemas that webmasters can use to markup HTML pages
      in ways recognized by major search providers, and that can also be used for
      structured data interoperability (e.g. in JSON). This representation includes
      all layers, as presented in the experimental OWL file at https://schema.org/docs/schemaorg.owl.
      Versions containing -fixes in their names include the fixes described at https://github.com/schemaorg/schemaorg/issues/1611#issuecomment-299292010.
    homepage: http://schema.org/
    name: Schema.org core and all extension vocabularies
    prefix: SCHEMA
    version: 3.4 fixes
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: Schema.org is a collaborative, community activity with a mission to
    create, maintain, and promote schemas for structured data on the Internet, on
    web pages, in email messages, and beyond.
  download_rdf: https://schema.org/version/latest/schemaorg-current-https.ttl
  example: Person
  homepage: https://schema.org
  lov:
    description: The SALT Document Ontology captures the linear structure of the publication,
      in addition to the identification and revisioning information of the publication's
      content.
    homepage: http://salt.semanticauthoring.org/ontologies/sdo
    keywords:
    - Catalogs
    modified: '2009-06-16'
    name: SALT Document Ontology
    prefix: sdo
    uri_prefix: http://salt.semanticauthoring.org/ontologies/sdo#$1
  mappings:
    aberowl: SCHEMAORG
    biolink: schema
    bioportal: SCHEMA
    lov: sdo
    ols: schemaorg_http
    tib: schema
    zazuko: schema
  name: Schema.org
  ols:
    download_rdf: https://schema.org/version/latest/schemaorg-all-http.rdf
    prefix: schemaorg_http
    uri_format: http://schema.org/$1
  preferred_prefix: schema
  prefix: schema
  synonyms:
  - schemaorg
  - sdo
  tib:
    contact: public-schemaorg@w3.org
    description: A structured data vocabulary (schema) for the web. It was created
      by major search engines like Google, Bing, Yahoo!, and Yandex to help webmasters
      provide search engines with clear, structured information about their websites'
      content.
    download_owl: https://schema.org/docs/schemaorg.owl
    homepage: https://schema.org/
    keywords:
    - FAIR Data Spaces
    - ESS
    name: Schema.org Vocabulary
    prefix: schema
    tracker: https://github.com/schemaorg/schemaorg
    uri_format: https://schema.org/$1
  uri_format: https://schema.org/$1
  zazuko:
    prefix: schema
    uri_format: http://schema.org/$1
scholia.resource:
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: A frontend to Wikidata
  example: doi
  homepage: https://scholia.toolforge.org/
  keywords:
  - registry
  - wikidata
  name: Scholia Registry
  prefix: scholia.resource
  uri_format: https://bioregistry.io/metaregistry/scholia/$1
sciflection:
  mappings:
    miriam: sciflection
    re3data: r3d100013413
  miriam:
    deprecated: false
    description: Sciflection is a public repository for experiments and associated
      spectra, usually uploaded from Electronic Lab Notebooks, shared under FAIR conditions
    homepage: https://sciformation.com/sciflection.html
    id: 00000973
    name: Sciflection
    namespaceEmbeddedInLui: false
    pattern: ^[0-9a-f]{8}-[0-9a-f]{4}-[0-9a-f]{4}-[0-9a-f]{4}-[0-9a-f]{12}$
    prefix: sciflection
    sampleId: 5ede4273-b26c-4ea4-adb7-3ce294ab3397
    uri_format: https://sciflection.com/$1
  prefix: sciflection
  re3data:
    description: Sciflection accepts structured data directly uploaded from Electronic
      Laboratory Notebooks (open enventory, Sciformation ELN, open for others) in
      JSON format. Searchable by chemical structure, text parts, numeric parameters,
      etc.
    doi: 10.17616/R31NJMUD
    homepage: https://sciflection.com
    name: Sciflection
    prefix: r3d100013413
sciprofiles:
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  keywords:
  - person
  - researcher
  mappings:
    wikidata: P8159
  prefix: sciprofiles
  references:
  - https://github.com/biopragmatics/bioregistry/pull/1171
  wikidata:
    description: numerical identifier for an author in SciProfiles by MDPI
    example:
    - '118021'
    - '92927'
    - '94648'
    homepage: https://sciprofiles.com/
    name: SciProfiles ID
    pattern: ^[1-9]\d*$
    prefix: P8159
    uri_format: https://sciprofiles.com/profile/$1
scomp:
  contact:
    email: null
    github: ncatlett
    name: Natalie L Catlett
    orcid: null
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: Selventa legacy complex namespace used with the Biological Expression
    Language
  domain: protein complex
  example: C0001
  homepage: https://github.com/OpenBEL/resource-generator/blob/master/datasets/selventa-named-complexes.txt
  keywords:
  - bel
  - protein complexes
  - selventa
  license: Apache-2.0
  logo: https://biological-expression-language.github.io/img/bel300.png
  name: Selventa Complexes
  pattern: ^C\d{4}$
  prefix: scomp
  uri_format: https://biopragmatics.github.io/providers/scomp/$1
scop:
  biocontext:
    prefix: SCOP
  contact:
    email: JMChandonia@lbl.gov
    github: jmchandonia
    name: John-Marc Chandonia
    orcid: 0000-0002-5153-9079
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: SCOP(e) unique identifier. This is simply a number that may be used
    to reference any entry in the SCOP(e) hierarchy, from root to leaves (Fold, Superfamily,
    Family, etc.).
  edam:
    description: Unique identifier (number) of an entry in the SCOP hierarchy, for
      example 33229.
    name: SCOP sunid
    obsolete: false
    prefix: '1042'
  homepage: https://scop.berkeley.edu
  mappings:
    biocontext: SCOP
    edam: '1042'
    miriam: scop
    n2t: scop
    prefixcommons: scop
  miriam:
    deprecated: false
    description: The SCOP (Structural Classification of Protein) database is a comprehensive
      ordering of all proteins of known structure according to their evolutionary,
      functional and structural relationships. The basic classification unit is the
      protein domain. Domains are hierarchically classified into species, proteins,
      families, superfamilies, folds, and classes. This namespace is limited to SCOP
      v1 as the identifiers used by v2 are different.
    homepage: http://scop.berkeley.edu/
    id: '00000371'
    name: SCOP
    namespaceEmbeddedInLui: false
    pattern: ^\d+$
    prefix: scop
    sampleId: '47419'
    uri_format: http://scop.berkeley.edu/sunid=$1
  n2t:
    description: The SCOP (Structural Classification of Protein) database is a comprehensive
      ordering of all proteins of known structure according to their evolutionary,
      functional and structural relationships. The basic classification unit is the
      protein domain. Domains are hierarchically classified into species, proteins,
      families, superfamilies, folds, and classes.
    example: '47419'
    homepage: http://scop.berkeley.edu/
    name: SCOP at Berkeley
    namespaceEmbeddedInLui: false
    pattern: ^\d+$
    prefix: scop
    uri_format: http://scop.berkeley.edu/sunid=$1
  name: Structural Classification of Proteins - Unique Identifier
  prefix: scop
  prefixcommons:
    description: The SCOP database, created by manual inspection and abetted by a
      battery of automated methods, aims to provide a detailed and comprehensive description
      of the structural and evolutionary relationships between all proteins whose
      structure is known.
    example: '47419'
    homepage: http://scop.mrc-lmb.cam.ac.uk/scop
    keywords:
    - protein
    - structure
    name: Structural Classification Of Proteins
    pattern: ^\d+$
    prefix: scop
  providers:
  - code: mrc
    description: SCOP at UK Medical Research council (MRC)
    example: null
    first_party: null
    homepage: https://scop.mrc-lmb.cam.ac.uk
    name: SCOP at UK Medical Research council (MRC)
    publications: null
    status: null
    uri_format: https://scop.mrc-lmb.cam.ac.uk/term/$1
  - code: gendis
    description: GenDiS is a repository of SCOP-identified homologous sequences of
      structural superfamily members.
    example: null
    first_party: null
    homepage: https://caps.ncbs.res.in/gendis3/home
    name: Genomic Distribution of structural Superfamilies
    publications:
    - doi: 10.1093/database/baaf035
      pmc: PMC12063530
      pubmed: '40343712'
      title: 'GenDiS3 database: census on the prevalence of protein domain superfamilies
        of known structure in the entire sequence database'
      year: 2025
    status: null
    uri_format: https://caps.ncbs.res.in/gendis3/superfamily_display/$1
  publications:
  - doi: 10.1093/nar/28.1.257
    pmc: PMC102479
    pubmed: '10592240'
    title: 'SCOP: a structural classification of proteins database'
    year: 2000
  - doi: 10.1093/nar/27.1.254
    pmc: PMC148149
    pubmed: '9847194'
    title: 'SCOP: a Structural Classification of Proteins database'
    year: 1999
  - doi: 10.1107/s0907444998009172
    pmc: null
    pubmed: '10089491'
    title: 'SCOP, Structural Classification of Proteins database: applications to
      evaluation of the effectiveness of sequence alignment methods and statistics
      of protein structural data'
    year: 1998
  - doi: 10.1093/nar/25.1.236
    pmc: PMC146380
    pubmed: '9016544'
    title: 'SCOP: a structural classification of proteins database'
    year: 1997
  - doi: 10.1093/database/baaf035
    pmc: PMC12063530
    pubmed: '40343712'
    title: 'GenDiS3 database: census on the prevalence of protein domain superfamilies
      of known structure in the entire sequence database'
    year: 2025
  - doi: 10.1093/database/baaf035
    pmc: PMC12063530
    pubmed: '40343712'
    title: 'GenDiS3 database: census on the prevalence of protein domain superfamilies
      of known structure in the entire sequence database'
    year: 2025
  references:
  - https://scop.berkeley.edu/help/#stableidentifiers
  synonyms:
  - scop.sun
  - scop.sunid
  uri_format: http://scop.berkeley.edu/sunid=$1
scop.sccs:
  contact:
    email: JMChandonia@lbl.gov
    github: jmchandonia
    name: John-Marc Chandonia
    orcid: 0000-0002-5153-9079
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: This is a dot notation used to concisely describe a SCOP(e) class,
    fold, superfamily, and family. For example, a.39.1.1 references the 'Calbindin
    D9K' family, where 'a' represents the class, '39' represents the fold, '1' represents
    the superfamily, and the last '1' represents the family.
  edam:
    description: A SCOP concise classification string (sccs) is a compact representation
      of a SCOP domain classification.
    name: SCOP concise classification string (sccs)
    obsolete: false
    prefix: '1041'
  example: a.39.1.1
  example_extras:
  - a.39.1
  - a.39
  - a
  homepage: https://scop.berkeley.edu
  mappings:
    edam: '1041'
  name: SCOP(e) concise classification string
  part_of_database: scop
  prefix: scop.sccs
  references:
  - https://scop.berkeley.edu/help/#stableidentifiers
  uri_format: http://scop.berkeley.edu/sccs=$1
scop.sid:
  contact:
    email: JMChandonia@lbl.gov
    github: jmchandonia
    name: John-Marc Chandonia
    orcid: 0000-0002-5153-9079
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: A 7-character sid consists of "d" followed by the 4-character PDB ID
    of the file of origin, the PDB chain ID ('_' if none, '.' if multiple as is the
    case in genetic domains), and a single character (usually an integer) if needed
    to specify the domain uniquely ('_' if not). Sids are currently all lower case,
    even when the chain letter is upper case. Example sids include d4akea1, d9hvpa_,
    and d1cph.1.
  edam:
    description: Identifier of a protein domain (or other node) from the SCOP database.
    name: SCOP domain
    obsolete: false
    prefix: '1039'
  example: d4akea1
  example_extras:
  - d9hvpa_
  - d1cph.1
  homepage: https://scop.berkeley.edu
  mappings:
    edam: '1039'
  name: Structural Classification of Protein - Stable Domain Identifier
  part_of_database: scop
  prefix: scop.sid
  references:
  - https://scop.berkeley.edu/help/#stableidentifiers
  uri_format: http://scop.berkeley.edu/sid=$1
scopus:
  biolink:
    is_identifiers: false
    is_obo: false
    prefix: ScopusID
    uri_format: https://www.scopus.com/authid/detail.uri?authorId=$1
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: "Scopus is the largest abstract and citation database of peer-reviewed\
    \ literature: scientific journals, books and conference proceedings. \nDelivering\
    \ a comprehensive overview of the world's research output in  the fields of science,\
    \ technology, medicine, social sciences, and arts \nand humanities, Scopus features\
    \ smart tools to track, analyze and  visualize research."
  example: '56305849200'
  fairsharing:
    abbreviation: Scopus
    description: Scopus is an abstract and citation database of peer-reviewed literature
      across all research areas. It provides tools for visualization, tracking and
      analysis of its data.  Non-subscribed users access Scopus through Scopus Preview,
      which allows the searching of authors and source material (e.g. journal) titles.
    homepage: https://www.scopus.com/
    name: Scopus
    prefix: FAIRsharing.0a674c
    publications: []
    subjects:
    - Subject Agnostic
    twitter: Scopus
  homepage: https://www.scopus.com
  mappings:
    biolink: ScopusID
    fairsharing: FAIRsharing.0a674c
    wikidata: P1153
  name: Scopus Researcher
  part_of_database: scopus
  pattern: ^\d+$
  prefix: scopus
  synonyms:
  - scopus.author
  wikidata:
    description: identifier for an author assigned in Scopus bibliographic database
    example:
    - '25723615000'
    - '35247902700'
    - '37083905900'
    - '55765581600'
    - '7005487412'
    homepage: https://www.scopus.com/freelookup/form/author.uri
    name: Scopus author ID
    pattern: ^[1-9]\d{9,11}$
    prefix: P1153
    uri_format: https://www.scopus.com/authid/detail.uri?authorId=$1
scopus.affiliation:
  mappings:
    wikidata: P1155
  part_of_database: scopus
  prefix: scopus.affiliation
  wikidata:
    description: identifier for an organisation in author affiliations per Scopus
    example:
    - '60025709'
    - '60028651'
    homepage: http://info.sciencedirect.com/scopus/scopus-in-detail/tools/affiliationidentifier
    name: Scopus affiliation ID
    prefix: P1155
    uri_format: https://www.scopus.com/affil/profile.uri?afid=$1
scopus.publication:
  homepage: https://www.scopus.com/
  mappings:
    wikidata: P1156
  name: Scopus Publication
  part_of_database: scopus
  prefix: scopus.publication
  wikidata:
    description: identifier for a source/publication venue (journal, conference, etc)
      in Scopus
    example:
    - '16129'
    - '22380'
    - '25283'
    name: Scopus source ID
    pattern: ^[1-9]\d{0,11}$
    prefix: P1156
    uri_format: https://www.scopus.com/sourceid/$1
scopus.work:
  homepage: https://www.scopus.com/
  mappings:
    wikidata: P1154
  name: Scopus Work
  part_of_database: scopus
  prefix: scopus.work
  synonyms:
  - scopus.eid
  wikidata:
    description: unique academic work identifier assigned in Scopus bibliographic
      database
    example:
    - 2-s2.0-0030770923
    - 2-s2.0-41049112855
    homepage: https://plu.mx/
    name: Scopus EID
    pattern: ^2-s2\.0-\d+$
    prefix: P1154
    uri_format: http://www.scopus.com/record/display.url?origin=inward&eid=$1
scor:
  example: ActiviateOrArchiveContract
  mappings:
    tib: scor
  prefix: scor
  tib:
    description: The Supply Chain Operation Reference (SCOR) is a cross-industry approach
      to lay the groundwork for more efficient and effective information exchange
      in supply networks.
    download_rdf: https://raw.githubusercontent.com/vocol/scor/master/scor.ttl
    homepage: https://github.com/vocol/scor
    keywords:
    - CoyPu
    - economics
    name: Supply Chain Operation Reference
    prefix: scor
    tracker: https://github.com/vocol/scor/issues
    uri_format: http://purl.org/eis/vocab/scor#$1
scoro:
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: An ontology based on PRO for describing the contributions that may
    be made, and the roles that may be held by a person with respect to a journal
    article or other publication (e.g. the role of article guarantor or illustrator).
  example: IntellectualContribution
  fairsharing:
    abbreviation: SCoRO
    contact:
      email: silvio.peroni@unibo.it
      name: Silvio Peroni
      orcid: 0000-0003-0530-4305
    description: The Scholarly Contributions and Roles Ontology (SCoRO) is an ontology
      based on PRO for describing the contributions that may be made, and the roles
      that may be held by a person with respect to a journal article or other publication
      (e.g. the role of article guarantor or illustrator)
    homepage: http://www.sparontologies.net/ontologies/scoro
    license: CC-BY-4.0
    name: 'Scholarly Contributions and Roles Ontology '
    prefix: FAIRsharing.c86b48
    publications:
    - doi: 10.3233/sw-150177
      title: The Document Components Ontology (DoCO)
      year: 2016
    repository: https://github.com/sparontologies/deo
    subjects:
    - Subject Agnostic
    twitter: sparontologies
  homepage: http://www.sparontologies.net/ontologies/scoro
  lov:
    description: SCoRO, the Scholarly Contributions and Roles Ontology, is an ontology
      for use by authors and publishers for describing the contributions that may
      be made and the roles that may be held by a person with respect to a journal
      article or other publication, and by research administrators and others for
      describing contributions and roles with respect to other aspects of scholarly
      research.
    homepage: https://sparontologies.github.io/scoro/current/scoro.html
    keywords:
    - Academy
    modified: '2017-09-04'
    name: Scholarly Contributions and Roles Ontology
    prefix: scoro
    uri_prefix: http://purl.org/spar/scoro/$1
  mappings:
    fairsharing: FAIRsharing.c86b48
    lov: scoro
  name: Scholarly Contributions and Roles Ontology
  preferred_prefix: SCoRO
  prefix: scoro
  publications:
  - doi: 10.3233/sw-150177
    pmc: null
    pubmed: null
    title: The Document Components Ontology (DoCO)
    year: 2016
  - doi: 10.3233/sw-150177
    pmc: null
    pubmed: null
    title: The Document Components Ontology (DoCO)
    year: 2016
  - doi: 10.3233/sw-150177
    pmc: null
    pubmed: null
    title: The Document Components Ontology (DoCO)
    year: 2016
  repository: https://github.com/sparontologies/scoro
  uri_format: http://purl.org/spar/scoro/$1
scpd:
  comment: This resource doesn't exist on the web anymore
  deprecated: true
  mappings:
    pathguide: '130'
    prefixcommons: scpd
  pathguide:
    abbreviation: SCPD
    homepage: http://rulai.cshl.edu/SCPD/
    name: The Promoter Database of Saccharomyces cerevisiae
    prefix: '130'
  prefix: scpd
  prefixcommons:
    description: Database containing promotor sequences found in Saccharomyces cerevisiae.
    example: CDC2
    homepage: http://rulai.cshl.edu/SCPD/
    keywords:
    - DNA
    - RNA
    name: Saccharomyces cerevisiae promoter database
    pattern: ^[A-Z.0-9]+$
    prefix: scpd
    uri_format: http://rulai.cshl.edu/cgi-bin/SCPD/getgene2?$1
  reviewer:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
scr:
  contact:
    email: abandrowski@ncmir.ucsd.edu
    github: bandrow
    name: Anita Bandrowski
    orcid: 0000-0002-5497-0243
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: The SciCrunch Registry holds metadata records that describe digital
    resources, e.g., software, databases, projects and also services. Most of these
    are produced as a result of government funding and are available to the scientific
    community. Resources are manually curated to make sure the information is accurate.
    We also use a web crawler to find literature mentions for the resources.
  example: 022586
  fairsharing:
    abbreviation: SciCrunch
    description: 'The SciCrunch Data Dashboard is a data sharing and display platform
      that pulls information from primary data repositories. Anyone can create a custom
      portal where they can select searchable subsets of hundreds of data sources,
      brand their web pages and create their community. SciCrunch will push data updates
      automatically to all portals on a weekly basis. SciCrunch resource registry
      is the new name of the NIF registry. '
    homepage: https://scicrunch.org/browse/datadashboard
    name: SciCrunch Data Dashboard
    prefix: FAIRsharing.kj4pvk
    publications:
    - doi: 10.1002/cne.23913
      pubmed_id: 26599696
      title: 'The Resource Identification Initiative: A Cultural Shift in Publishing.'
    subjects:
    - Neurobiology
    - Life Science
  github_request_issue: 421
  homepage: https://scicrunch.org/browse/resourcedashboard
  integbio:
    description: SciCrunch resource registry is the new name of the NIF registry.
      SciCrunch is a data sharing and display platform. Anyone can create a custom
      portal where they can select searchable subsets of hundreds of data sources,
      brand their web pages and create their community. SciCrunch will push data updates
      automatically to all portals on a weekly basis.
    fairsharing: FAIRsharing.kj4pvk
    homepage: https://scicrunch.org/browse/datadashboard
    information_keywords:
    - Portal
    - Repository
    name: SciCrunch
    prefix: nbdc01937
    pubmeds:
    - '26599696'
    status: Active
    target_keywords:
    - Cell/Organelle
    - Health/Disease
  mappings:
    fairsharing: FAIRsharing.kj4pvk
    integbio: nbdc01937
    rrid: SCR
  name: SciCrunch Registry
  pattern: ^\d+$
  prefix: scr
  publications:
  - doi: 10.1002/cne.23913
    pmc: PMC4684178
    pubmed: '26599696'
    title: 'The Resource Identification Initiative: A Cultural Shift in Publishing'
    year: 2016
  - doi: 10.1002/cne.23913
    pmc: null
    pubmed: null
    title: 'The Resource Identification Initiative: A Cultural Shift in Publishing.'
    year: null
  - doi: null
    pmc: null
    pubmed: '22434839'
    title: null
    year: null
  rrid:
    homepage: https://scicrunch.org/scicrunch/about/sources/nlx_144509-1
    keywords:
    - interactive portal
    - nih initiative
    - rrid
    name: SciCrunch Registry
    prefix: SCR
    pubmeds:
    - '22434839'
    scr: '005400'
  synonyms:
  - scicrunch
  uri_format: http://scicrunch.org/resolver/SCR_$1
scretf:
  biocontext:
    prefix: SCRETF
  mappings:
    biocontext: SCRETF
    miriam: scretf
    n2t: scretf
  miriam:
    deprecated: true
    description: ScerTF is a database of position weight matrices (PWMs) for transcription
      factors in Saccharomyces species. It identifies a single matrix for each TF
      that best predicts in vivo data, providing metrics related to the performance
      of that matrix in accurately representing the DNA binding specificity of the
      annotated transcription factor.
    homepage: http://stormo.wustl.edu/ScerTF/
    id: '00000244'
    name: ScerTF
    namespaceEmbeddedInLui: false
    pattern: ^\w+$
    prefix: scretf
    sampleId: RSC3
    uri_format: http://stormo.wustl.edu/ScerTF/details/$1/
  n2t:
    description: ScerTF is a database of position weight matrices (PWMs) for transcription
      factors in Saccharomyces species. It identifies a single matrix for each TF
      that best predicts in vivo data, providing metrics related to the performance
      of that matrix in accurately representing the DNA binding specificity of the
      annotated transcription factor.
    example: RSC3
    homepage: http://stormo.wustl.edu/ScerTF/
    name: ScerTF at Washington University
    namespaceEmbeddedInLui: false
    pattern: ^\w+$
    prefix: scretf
    uri_format: http://stormo.wustl.edu/ScerTF/details/$1/
  prefix: scretf
  uri_format: http://stormo.wustl.edu/ScerTF/details/$1
sd:
  example: endpoint
  lov:
    description: Un vocabulaire pour décrire des services SPARQL publiés via le protocole
      SPARQL 1.1 pour RDF. Ces descriptions fournissent un mécanisme par lequel un
      client ou un utilisateur final peuvent obtenir des informations sur le service
      SPARQL, telles que les extensions de fonctions supportées ou les détails à propos
      des jeux de données disponibles.
    homepage: http://www.w3.org/TR/sparql11-service-description/
    keywords:
    - W3C Rec
    modified: '2013-03-21'
    name: SPARQL 1.1 Service Description
    prefix: sd
    uri_prefix: http://www.w3.org/ns/sparql-service-description#$1
  mappings:
    lov: sd
    zazuko: sd
  prefix: sd
  zazuko:
    prefix: sd
    uri_format: http://www.w3.org/ns/sparql-service-description#$1
sdap:
  mappings:
    prefixcommons: sdap
  prefix: sdap
  prefixcommons:
    description: SDAP is a Web server that integrates a database of allergenic proteins
      with various bioinformatics tools for performing structural studies related
      to allergens and characterization of their epitopes.
    example: '610'
    homepage: http://fermi.utmb.edu/SDAP
    keywords:
    - protein
    - structure
    name: Structural Database of Allergenic Proteins
    pattern: ^\d+$
    prefix: sdap
    uri_format: http://fermi.utmb.edu/cgi-bin/SDAP/sdap_02?dB_Type=0&allid=$1
  reviewer:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
sdbs:
  biocontext:
    prefix: SDBS
  integbio:
    alt_name: Spectral Database for Organic Compounds
    description: The SDBS database consists of of sensory characteristics of vision,
      hearing, and touch measured by National Institute of Advanced Industrial Science
      and Technology. To allow searches for conditions such as age and types of disability,
      target people with disabilities and/or older people, totaling more than 3,000,
      were subjected to measurement. Their characteristics data were adopted as Japanese
      Industrial Standards (JISs) "Guidelines for older persons and persons with disabilities".
    homepage: http://sdbs.db.aist.go.jp/sdbs/cgi-bin/direct_frame_top.cgi
    information_keywords:
    - Chemical structure
    maintainer: AIST (National Institute of Advanced Industrial Science and Technology)
    name: SDBS
    prefix: nbdc01520
    status: Active
    target_keywords:
    - Chemical compound
  mappings:
    biocontext: SDBS
    integbio: nbdc01520
    miriam: sdbs
    n2t: sdbs
  miriam:
    deprecated: false
    description: The Spectral Database for Organic Compounds (SDBS) is an integrated
      spectral database system for organic compounds. It provides access to 6 different
      types of spectra for each compound, including Mass spectrum (EI-MS), a Fourier
      transform infrared spectrum (FT-IR), and NMR spectra.
    homepage: https://sdbs.db.aist.go.jp
    id: 00000319
    name: Spectral Database for Organic Compounds
    namespaceEmbeddedInLui: false
    pattern: ^\d+$
    prefix: sdbs
    sampleId: '4544'
    uri_format: https://sdbs.db.aist.go.jp/CompoundView.aspx?sdbsno=$1
  n2t:
    description: The Spectral Database for Organic Compounds (SDBS) is an integrated
      spectral database system for organic compounds. It provides access to 6 different
      types of spectra for each compound, including Mass spectrum (EI-MS), a Fourier
      transform infrared spectrum (FT-IR), and NMR spectra.
    example: '4544'
    homepage: http://riodb01.ibase.aist.go.jp/sdbs/cgi-bin/direct_frame_top.cgi
    name: SDBS at AIST
    namespaceEmbeddedInLui: false
    pattern: \d+$
    prefix: sdbs
    uri_format: http://riodb01.ibase.aist.go.jp/sdbs/cgi-bin/cre_frame_disp.cgi?sdbsno=$1
  prefix: sdbs
sddo:
  contact:
    email: daniel.c.berrios@nasa.gov
    github: DanBerrios
    name: Dan Berrios
    orcid: 0000-0003-4312-9552
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: The Science Data Discovery Ontology (sddo) is being developed to provide
    a semantic foundation for the discovery of information managed by NASA's Science
    Mission Directorate. This information spans many scientific disciplines, fields
    and subfields, including heliophysics, earth science, planetary science, astrophysics,
    biology, astrobiology, and physical science. [from repository]
  download_json: https://github.com/NASA-IMPACT/sddo/raw/refs/heads/master/sddo.json
  download_obo: https://github.com/NASA-IMPACT/sddo/raw/refs/heads/master/sddo.obo
  download_owl: https://github.com/NASA-IMPACT/sddo/raw/refs/heads/master/sddo.owl
  example: '3000001'
  github_request_issue: 1556
  homepage: https://github.com/NASA-IMPACT/sddo
  license: CC-BY-3.0
  name: Science Data Discovery Ontology
  pattern: ^\d{7}$
  prefix: sddo
  repository: https://github.com/NASA-IMPACT/sddo
  uri_format: http://purl.obolibrary.org/obo/SDDO_$1
sdgio:
  agroportal:
    contact:
      email: pier.buttigieg@awi.de
      name: Pier Luigi Buttigieg
    description: The SDGIO aims to provide a semantic bridge between 1) the Sustainable
      Development Goals, their targets, and indicators and 2) the large array of entities
      they refer to. It will import classes from numerous exisitng ontologies and
      map to vocabularies such as GEMET to promote interoperability. New classes will
      be minted and defined where no external class exists.
    example_uri: http://purl.unep.org/sdg/SDGIO_00010073
    homepage: https://github.com/SDG-InterfaceOntology/sdgio
    name: Sustainable Development Goals Interface Ontology
    prefix: SDGIO
    publications:
    - http://ceur-ws.org/Vol-1747/IT201_ICBO2016.pdf
    repository: https://github.com/SDG-InterfaceOntology
    version: '2018-05-11'
  download_owl: https://github.com/SDG-InterfaceOntology/sdgio/raw/master/sdgio.owl
  example: '00020134'
  fairsharing:
    abbreviation: SDGIO
    contact:
      email: pier.buttigieg@awi.de
      name: Pier Luigi Buttigieg
      orcid: 0000-0002-4366-3088
    description: The Sustainable Development Goals Interface Ontology (SDGIO) aims
      to provide a semantic bridge between 1) the Sustainable Development Goals, their
      targets, and indicators and 2) the large array of entities they refer to. SDGIO
      will reuse existing ontologies where appropriate.
    domains:
    - Sustainability
    homepage: https://github.com/SDG-InterfaceOntology/sdgio
    name: Sustainable Development Goals Interface Ontology
    prefix: FAIRsharing.d5ff6e
    publications:
    - doi: 10.1186/s13326-016-0097-6
      pubmed: '27664130'
      title: 'The environment ontology in 2016: bridging domains with increased scope,
        semantic density, and interoperation'
      year: 2016
    repository: https://github.com/SDG-InterfaceOntology/sdgio/wiki
    subjects:
    - Environmental Science
  mappings:
    agroportal: SDGIO
    fairsharing: FAIRsharing.d5ff6e
    ols: sdgio
    ontobee: SDGIO
  ols:
    description: An OBO-compliant ontology representing the entities referenced by
      the SDGs, their targets, and indicators.
    download_owl: http://purl.unep.org/sdg/sdgio.owl
    homepage: https://github.com/SDG-InterfaceOntology/sdgio
    name: Sustainable Development Goals Interface Ontology
    prefix: sdgio
    version.iri: http://purl.unep.org/sdg/releases/2018-08-10/sdgio.owl
  ontobee:
    library: Not Specified/No
    name: Sustainable Development Goals Interface Ontology
    prefix: SDGIO
  pattern: ^\d{8}$
  prefix: sdgio
  publications:
  - doi: 10.1186/s13326-016-0097-6
    pmc: PMC5035502
    pubmed: '27664130'
    title: 'The environment ontology in 2016: bridging domains with increased scope,
      semantic density, and interoperation'
    year: 2016
  references:
  - https://github.com/SDG-InterfaceOntology/sdgio/issues/233
  repository: https://github.com/SDG-InterfaceOntology/sdgio
  uri_format: http://purl.unep.org/sdg/SDGIO_$1
sdis:
  contact:
    email: null
    github: ncatlett
    name: Natalie L Catlett
    orcid: null
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: Selventa legacy disease namespace used with the Biological Expression
    Language
  domain: disease
  example: D0001
  homepage: https://github.com/OpenBEL/resource-generator/blob/master/datasets/selventa-legacy-diseases.txt
  keywords:
  - bel
  - diseases
  - selventa
  license: Apache-2.0
  logo: https://biological-expression-language.github.io/img/bel300.png
  name: Selventa Diseases
  pattern: ^D\d{4}$
  prefix: sdis
  uri_format: https://biopragmatics.github.io/providers/sdis/$1
sdmx:
  download_rdf: http://purl.org/linked-data/sdmx
  example: EntityRole
  lov:
    description: This vocabulary extends the data cube vocabulary to support publication
      of statistical data in RDF, using an information model based on SDMX
    homepage: https://raw.githubusercontent.com/UKGovLD/publishing-statistical-data/master/specs/src/main/vocab/sdmx.ttl
    keywords:
    - Methods
    modified: '2010-07-22'
    name: SDMX-RDF vocabulary
    prefix: sdmx
    uri_prefix: http://purl.org/linked-data/sdmx#$1
  mappings:
    lov: sdmx
    zazuko: sdmx
  prefix: sdmx
  zazuko:
    prefix: sdmx
    uri_format: http://purl.org/linked-data/sdmx#$1
sedml.format:
  mappings:
    miriam: sedml.format
  miriam:
    deprecated: false
    description: Data format that can be used in conjunction with the Simulation Experimental
      Description Markup Language (SED-ML).
    homepage: http://sed-ml.org/
    id: 00000841
    name: SED-ML data format
    namespaceEmbeddedInLui: false
    pattern: ^[a-z]+(\..*?)?$
    prefix: sedml.format
    sampleId: csv
    uri_format: https://sed-ml.org/urns.html#format:$1
  prefix: sedml.format
sedml.language:
  mappings:
    miriam: sedml.language
  miriam:
    deprecated: false
    description: Model format that can be used in conjunction with the Simulation
      Experimental Description Markup Language (SED-ML).
    homepage: http://sed-ml.org/
    id: 00000843
    name: SED-ML model format
    namespaceEmbeddedInLui: false
    pattern: ^[a-z]+(\..*?)?$
    prefix: sedml.language
    sampleId: sbml.level-3.version-2
    uri_format: https://sed-ml.org/urns.html#language:$1
  prefix: sedml.language
seed.compound:
  biocontext:
    prefix: SEED.COMPOUND
  mappings:
    biocontext: SEED.COMPOUND
    miriam: seed.compound
    n2t: seed.compound
  miriam:
    deprecated: false
    description: This cooperative effort, which includes Fellowship for Interpretation
      of Genomes (FIG), Argonne National Laboratory, and the University of Chicago,
      focuses on the development of the comparative genomics environment called the
      SEED. It is a framework to support comparative analysis and annotation of genomes,
      and the development of curated genomic data (annotation). Curation is performed
      at the level of subsystems by an expert annotator, across many genomes, and
      not on a gene by gene basis. This collection references subsystems.
    homepage: http://modelseed.org/
    id: '00000553'
    name: SEED Compound
    namespaceEmbeddedInLui: false
    pattern: ^cpd\d+$
    prefix: seed.compound
    sampleId: cpd15380
    uri_format: http://modelseed.org/biochem/compounds/$1
  n2t:
    description: This cooperative effort, which includes Fellowship for Interpretation
      of Genomes (FIG), Argonne National Laboratory, and the University of Chicago,
      focuses on the development of the comparative genomics environment called the
      SEED. It is a framework to support comparative analysis and annotation of genomes,
      and the development of curated genomic data (annotation). Curation is performed
      at the level of subsystems by an expert annotator, across many genomes, and
      not on a gene by gene basis. This collection references subsystems.
    example: cpd15380
    homepage: http://modelseed.org/
    name: SEED Compound at Argonne National Laboratory
    namespaceEmbeddedInLui: false
    pattern: ^cpd\d+$
    prefix: seed.compound
    uri_format: http://modelseed.org/biochem/compounds/$1
  prefix: seed.compound
  repository: https://github.com/TheSEED
seed.reaction:
  biolink:
    is_identifiers: false
    is_obo: false
    prefix: SEED.REACTION
    uri_format: https://modelseed.org/biochem/reactions/$1
  mappings:
    biolink: SEED.REACTION
    miriam: seed.reaction
    n2t: seed.reaction
  miriam:
    deprecated: false
    description: ModelSEED is a platform for creating genome-scale metabolic network
      reconstructions for microbes and plants. As part of the platform, a biochemistry
      database is managed that contains reactions unique to ModelSEED as well as reactions
      aggregated from other databases or from manually-curated genome-scale metabolic
      network reconstructions.
    homepage: http://modelseed.org/biochem/reactions/
    id: 00000692
    name: SEED Reactions
    namespaceEmbeddedInLui: false
    pattern: ^rxn\d+$
    prefix: seed.reaction
    sampleId: rxn00001
    uri_format: http://modelseed.org/biochem/reactions/$1
  n2t:
    description: ModelSEED is a platform for creating genome-scale metabolic network
      reconstructions for microbes and plants. As part of the platform, a biochemistry
      database is managed that contains reactions unique to ModelSEED as well as reactions
      aggregated from other databases or from manually-curated genome-scale metabolic
      network reconstructions.
    example: rxn00001
    homepage: http://modelseed.org/biochem/reactions/
    name: SEED Reactions
    namespaceEmbeddedInLui: false
    pattern: ^rxn\d+$
    prefix: seed.reaction
    uri_format: http://modelseed.org/biochem/reactions/$1
  prefix: seed.reaction
seed.role:
  contributor:
    email: seaver@anl.gov
    github: samseaver
    name: Sam Seaver
    orcid: 0000-0002-7674-5194
  description: 'With the growing number of available genomes, the need for an environment
    to support effective comparative analysis increases. The original SEED Project
    was started in 2003 by the [Fellowship for Interpretation of Genomes (FIG)](http://thefig.info/)
    as a largely unfunded open source effort. Argonne National Laboratory and the
    University of Chicago joined the project, and now much of the activity occurs
    at those two institutions (as well as the University of Illinois at Urbana-Champaign,
    Hope college, San Diego State University, the Burnham Institute and a number of
    other institutions). The cooperative effort focuses on the development of the
    comparative genomics environment called the SEED and, more importantly, on the
    development of curated genomic data.

    This prefix provides identifiers for molecular roles that describe the function
    of one or more proteins in microbes and plants.'
  example: Histidinol dehydrogenase (EC 1.1.1.23)
  example_extras:
  - Archease
  - Xylan oligosaccharide ABC transporter, substrate-binding component
  github_request_issue: 1340
  homepage: https://theseed.org/
  license: MIT
  name: The SEED
  prefix: seed.role
  publications:
  - doi: 10.1093/nar/gki866
    pmc: PMC1251668
    pubmed: '16214803'
    title: The Subsystems Approach to Genome Annotation and its Use in the Project
      to Annotate 1000 Genomes
    year: 2005
  repository: https://github.com/orgs/TheSEED
  reviewer:
    email: b.gyori@northeastern.edu
    github: bgyori
    name: Benjamin M. Gyori
    orcid: 0000-0001-9439-5346
  reviewer_extras:
  - email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  uri_format: https://pubseed.theseed.org/SubsysEditor.cgi?page=FunctionalRolePage&fr=$1
seed.subsystem:
  biocontext:
    prefix: SEED
  contributor_extras:
  - email: aireland@lbl.gov
    github: ialarmedalien
    name: AJ Ireland
    orcid: 0000-0003-1982-9065
  - email: seaver@anl.gov
    github: samseaver
    name: Sam Seaver
    orcid: 0000-0002-7674-5194
  go:
    description: Project to annotate the first 1000 sequenced genomes, develop detailed
      metabolic reconstructions, and construct the corresponding stoichiometric matrices
    homepage: http://www.theseed.org
    name: The SEED;
    prefix: SEED
    uri_format: http://www.theseed.org/linkin.cgi?id=$1
  mappings:
    biocontext: SEED
    go: SEED
    miriam: seed
    n2t: seed
    ncbi: SEED
  miriam:
    deprecated: true
    description: This cooperative effort, which includes Fellowship for Interpretation
      of Genomes (FIG), Argonne National Laboratory, and the University of Chicago,
      focuses on the development of the comparative genomics environment called the
      SEED. It is a framework to support comparative analysis and annotation of genomes,
      and the development of curated genomic data (annotation). Curation is performed
      at the level of subsystems by an expert annotator, across many genomes, and
      not on a gene by gene basis. This collection references subsystems.
    id: '00000552'
    name: SEED Subsystem
    namespaceEmbeddedInLui: false
    pattern: ^\w+$
    prefix: seed
    sampleId: Biotin_biosynthesis
  n2t:
    description: This cooperative effort, which includes Fellowship for Interpretation
      of Genomes (FIG), Argonne National Laboratory, and the University of Chicago,
      focuses on the development of the comparative genomics environment called the
      SEED. It is a framework to support comparative analysis and annotation of genomes,
      and the development of curated genomic data (annotation). Curation is performed
      at the level of subsystems by an expert annotator, across many genomes, and
      not on a gene by gene basis. This collection references subsystems.
    example: Biotin_biosynthesis
    homepage: http://seed-viewer.theseed.org/seedviewer.cgi
    name: SEED Subsystem at Argonne National Laboratory
    namespaceEmbeddedInLui: false
    pattern: ^\w+$
    prefix: seed
    uri_format: http://seed-viewer.theseed.org/seedviewer.cgi?page=Subsystems&subsystem=$1
  name: SEED Subsystem
  ncbi:
    example: fig|83331.1.peg.1
    homepage: http://www.theseed.org
    name: The SEED Database
    prefix: SEED
  prefix: seed.subsystem
  publications:
  - doi: 10.1093/nar/gki866
    pmc: PMC1251668
    pubmed: '16214803'
    title: The Subsystems Approach to Genome Annotation and its Use in the Project
      to Annotate 1000 Genomes
    year: 2005
  repository: https://github.com/TheSEED
  synonyms:
  - seed
  uri_format: https://pubseed.theseed.org/SubsysEditor.cgi?page=ShowSubsystem&subsystem=$1
seinet:
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: A vocabulary about species to support the environmental research community
    in Arizona and New Mexico
  example: '762'
  github_request_issue: 653
  homepage: https://swbiodiversity.org/seinet/index.php
  mappings:
    wikidata: P6209
  name: Southwestern Environmental Information Network
  pattern: ^\d+$
  prefix: seinet
  reviewer:
    email: null
    github: callahantiff
    name: Tiffany J. Callahan
    orcid: 0000-0002-8169-9049
  uri_format: https://swbiodiversity.org/seinet/taxa/index.php?taxon=$1
  wikidata:
    description: identifier for a species on the SEINet website
    example:
    - '1522'
    - '3314'
    - '762'
    homepage: http://swbiodiversity.org/seinet/index.php
    name: SEINet ID
    pattern: ^[1-9]\d*$
    prefix: P6209
    uri_format: https://swbiodiversity.org/seinet/taxa/index.php?taxon=$1
semapv:
  bartoc:
    abbreviation: semapv
    description: The Semantic Mapping Vocabulary provides and defines terms used for
      creating and maintaining semantic mappings, in particular mapping metadata.
    homepage: https://mapping-commons.github.io/semantic-mapping-vocabulary/
    license: CC0-1.0
    name: Semantic Mapping Vocabulary
    prefix: '20428'
  contact:
    email: nicolas.matentzoglu@gmail.com
    github: matentzn
    name: Nicolas Matentzoglu
    orcid: 0000-0002-7356-1779
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: The Semantic Mapping Vocabulary provides and defines terms used for
    creating and maintaining semantic mappings, in particular mapping metadata.
  download_owl: https://raw.githubusercontent.com/mapping-commons/semantic-mapping-vocabulary/main/semapv.owl
  example: LexicalMatching
  homepage: https://mapping-commons.github.io/semantic-mapping-vocabulary/
  license: CC0-1.0
  mappings:
    bartoc: '20428'
    ols: semapv
  name: Semantic Mapping Vocabulary
  ols:
    description: The Semantic Mapping Vocabulary (SEMAPV) captures concepts and relations
      related to semantic matching, including types of matching (e.g. lexical, manually
      curated), preprocessing methods and specialised mapping relations.
    download_owl: https://raw.githubusercontent.com/mapping-commons/semantic-mapping-vocabulary/main/semapv.owl
    homepage: https://mapping-commons.github.io/semantic-mapping-vocabulary/
    name: Semantic Mapping Vocabulary
    prefix: semapv
    uri_format: https://w3id.org/semapv/vocab/$1
    version: '2025-01-06'
    version.iri: http://w3id.org/semapv/vocab/releases/2025-01-06/semapv.owl
  owners:
  - name: Semanticly
    partnered: true
    ror: null
    wikidata: Q115518213
  prefix: semapv
  publications:
  - doi: 10.5281/zenodo.7672103
    pmc: null
    pubmed: null
    title: 'A Simple Standard for Ontological Mappings 2022: Updates of data model
      and outlook'
    year: 2022
  references:
  - https://github.com/biopragmatics/bioregistry/pull/714
  repository: https://github.com/mapping-commons/semantic-mapping-vocabulary
  synonyms:
  - semapv_voc
  - sempav_voc
  uri_format: https://w3id.org/semapv/vocab/$1
semion:
  example: '22132778'
  mappings:
    wikidata: P7671
  prefix: semion
  wikidata:
    description: identifier of an author or reviewer, in Semion
    example:
    - '1085144'
    - '17963667'
    - '2975999'
    homepage: https://www.semion.io
    name: Semion author ID (archived)
    pattern: ^\d+$
    prefix: P7671
    uri_format: https://web.archive.org/web/1/https://www.semion.io/Author/$1
senso:
  aberowl:
    description: The SENSO ontology is designed to provide classification terms for
      labeling sensitive data for data archival and sharing.
    download_owl: http://aber-owl.net/media/ontologies/SENSO/1/senso.owl
    homepage: https://github.com/DataONEorg/sem-prov-ontologies
    name: Sensitive Data Ontology
    prefix: SENSO
    version: Version 0.1.0
  bioportal:
    contact:
      email: mecum@nceas.ucsb.edu
      name: Bryce Mecum
    description: The SENSO ontology is designed to provide classification terms for
      labeling sensitive data for data archival and sharing.
    homepage: https://github.com/DataONEorg/sem-prov-ontologies
    name: Sensitive Data Ontology
    prefix: SENSO
    version: Version 0.1.0
  contact:
    email: brycemecum@gmail.com
    github: amoeba
    name: Bryce Mecum
    orcid: 0000-0002-0381-3766
  download_rdf: https://ontologies.dataone.org/SENSO.ttl
  example: '00000003'
  homepage: https://github.com/DataONEorg/sem-prov-ontologies/tree/main/senso
  mappings:
    aberowl: SENSO
    bioportal: SENSO
  pattern: ^\d+$
  prefix: senso
  uri_format: http://purl.dataone.org/odo/SENSO_$1
seo:
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: The Scientific Event Ontology (SEO) is a reference ontology for modeling
    data about scientific events such as conferences, symposioums, and workshops.
  download_rdf: https://raw.githubusercontent.com/saidfathalla/SEOontology/master/SEO.ttl
  example: Symposium
  homepage: https://w3id.org/seo
  lov:
    description: The vocabulary allows for the description of data about scientific
      events such as conferences, symposiums and workshops.
    homepage: https://saidfathalla.github.io/SEOontology/Documentation/SEO.html
    keywords:
    - Academy
    - Events
    modified: '2019-04-10'
    name: The Scientific Events Ontology
    prefix: seo
    uri_prefix: https://w3id.org/seo#$1
  mappings:
    lov: seo
  name: Scientific Event Ontology
  prefix: seo
  uri_format: https://w3id.org/seo#$1
sep:
  aberowl:
    description: A structured controlled vocabulary for the annotation of sample processing
      and separation techniques in scientific experiments, such as, and including,
      gel electrophoresis, column chromatography, capillary electrophoresis, centrifugation
      and so on. Developed jointly by the HUPO Proteomics Standards Initiative and
      The Metabolomics Standards Initiative.
    download_obo: http://aber-owl.net/media/ontologies/SEP/4/sep.obo
    homepage: http://psidev.info/index.php?q=node/312
    name: Sample Processing and Separation Techniques Ontology
    prefix: SEP
    version: '1.070708'
  biocontext:
    prefix: SEP
  bioportal:
    contact:
      email: psidev-gps-dev@lists.sourceforge.net
      name: SEP developers
    description: A structured controlled vocabulary for the annotation of sample processing
      and separation techniques in scientific experiments, such as, and including,
      gel electrophoresis, column chromatography, capillary electrophoresis, centrifugation
      and so on. Developed jointly by the HUPO Proteomics Standards Initiative and
      The Metabolomics Standards Initiative.
    homepage: http://psidev.info/index.php?q=node/312
    name: Sample Processing and Separation Techniques Ontology
    prefix: SEP
    version: '1.070708'
  download_obo: https://raw.githubusercontent.com/HUPO-PSI/gelml/master/CV/sep.obo
  example: '00073'
  homepage: https://psidev.info/sepcv
  mappings:
    aberowl: SEP
    biocontext: SEP
    bioportal: SEP
    obofoundry: sep
    ontobee: SEP
    prefixcommons: sep
    wikidata.entity: Q114677913
  obofoundry:
    contact: psidev-gps-dev@lists.sourceforge.net
    contact.label: SEP developers via the PSI and MSI mailing lists
    deprecated: true
    description: A structured controlled vocabulary for the annotation of sample processing
      and separation techniques in scientific experiments.
    domain: investigations
    download.owl: http://purl.obolibrary.org/obo/sep.owl
    homepage: http://psidev.info/index.php?q=node/312
    name: Sample processing and separation techniques
    prefix: sep
  ontobee:
    library: Library
    name: Sample processing and separation techniques
    prefix: SEP
  pattern: ^\d{5,6}$
  prefix: sep
  prefixcommons:
    bioportal: '1044'
    description: A structured controlled vocabulary for the annotation of sample processing
      and separation techniques in scientific experiments, such as, and including,
      gel electrophoresis, column chromatography, capillary electrophoresis, centrifugation
      and so on. Developed jointly by the HUPO Proteomics Standards Initiative and
      The Metabolomics Standards Initiative.
    example: sep_00005
    homepage: http://psidev.info/index.php?q=node/312
    keywords:
    - obo
    - protein
    name: Sample processing and separation techniques
    pattern: ^sep_\d+$
    prefix: sep
sepio:
  aberowl:
    description: An ontology for representing the provenance of scientific claims
      and the evidence that supports them.
    download_owl: http://aber-owl.net/media/ontologies/SEPIO/4/sepio.owl
    homepage: https://github.com/monarch-initiative/SEPIO-ontology
    name: Scientific Evidence and Provenance Information Ontology
    prefix: SEPIO
  biocontext:
    prefix: SEPIO
  bioportal:
    contact:
      email: mhb120@gmail.com
      name: Matthew Brush
    description: The Scientific Evidence and Provenance Information Ontology (SEPIO)
      was developed to support description of evidence and provenance information
      for scientific claims. The core model represents the relationships between claims,
      their evidence lines, the information items that comprise these lines of evidence,
      and the methods, tools, and agents involved in the creation of these entities.
      Use cases driving SEPIO development include integration of scientific claims
      and their associated evidence/provenance metadata, and support for the discovery,
      analysis, and evaluation of claims based on this metadata.
    homepage: https://github.com/monarch-initiative/SEPIO-ontology
    name: Scientific Evidence and Provenance Information Ontology
    prefix: SEPIO
    version: '2023-06-13'
  example: 0000048
  mappings:
    aberowl: SEPIO
    biocontext: SEPIO
    bioportal: SEPIO
    obofoundry: sepio
    ols: sepio
    ontobee: SEPIO
    tib: sepio
    wikidata.entity: Q55118599
  obofoundry:
    contact: mhb120@gmail.com
    contact.github: mbrush
    contact.label: Matthew Brush
    contact.orcid: 0000-0002-1048-5019
    deprecated: false
    description: An ontology for representing the provenance of scientific claims
      and the evidence that supports them.
    domain: investigations
    download.owl: http://purl.obolibrary.org/obo/sepio.owl
    homepage: https://github.com/monarch-initiative/SEPIO-ontology
    license: CC BY 3.0
    license.url: https://creativecommons.org/licenses/by/3.0/
    logo: https://raw.githubusercontent.com/jmcmurry/closed-illustrations/master/logos/SEPIO-LOGOS/sepio_logo_black-banner.png
    name: Scientific Evidence and Provenance Information Ontology
    preferredPrefix: SEPIO
    prefix: sepio
    repository: https://github.com/monarch-initiative/SEPIO-ontology
  ols:
    description: An ontology for representing the provenance of scientific claims
      and the evidence that supports them.
    download_owl: http://purl.obolibrary.org/obo/sepio.owl
    homepage: https://github.com/monarch-initiative/SEPIO-ontology
    name: Ontology for Scientific Evidence and Provenance Information
    prefix: sepio
    tracker: https://github.com/monarch-initiative/SEPIO-ontology/issues
    version: '2023-06-13'
    version.iri: http://purl.obolibrary.org/obo/sepio/releases/2023-06-13/sepio.owl
  ontobee:
    library: Library
    name: Scientific Evidence and Provenance Information Ontology
    prefix: SEPIO
  pattern: ^\d{7}$
  prefix: sepio
  tib:
    description: 'The SEPIO ontology is in its early stages of development, undergoing
      iterative refinement as new requirements emerge and alignment with existing
      standards is explored. The SEPIO core file imports two files which can be resolved
      at the URLs below:


      IAO ontology-metadata import: https://raw.githubusercontent.com/monarch-initiative/SEPIO-ontology/master/src/ontology/imports/ontology-metadata.owl


      bfo mireot: https://raw.githubusercontent.com/monarch-initiative/SEPIO-ontology/master/src/ontology/mireots/bfo-mireot.owl'
    download_owl: http://purl.obolibrary.org/obo/sepio.owl
    homepage: https://github.com/monarch-initiative/SEPIO-ontology
    keywords:
    - NFDI4ING
    - NFDI4CHEM
    - mathematics
    name: Ontology for Scientific Evidence and Provenance Information
    prefix: sepio
    tracker: https://github.com/monarch-initiative/SEPIO-ontology/issues
    version.iri: http://purl.obolibrary.org/obo/sepio/releases/2023-06-13/sepio.owl
  uri_format: http://purl.obolibrary.org/obo/SEPIO_$1
sfam:
  contact:
    email: null
    github: ncatlett
    name: Natalie L Catlett
    orcid: null
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: Selventa legacy protein family namespace used with the Biological Expression
    Language
  domain: protein family
  example: F0001
  homepage: https://github.com/OpenBEL/resource-generator/blob/master/datasets/selventa-protein-families.txt
  keywords:
  - bel
  - protein families
  - selventa
  license: Apache-2.0
  logo: https://biological-expression-language.github.io/img/bel300.png
  name: Selventa Families
  pattern: ^F\d{4}$
  prefix: sfam
  uri_format: https://biopragmatics.github.io/providers/sfam/$1
sgd:
  biocontext:
    prefix: SGD
    uri_format: https://www.yeastgenome.org/locus/$1
  contact:
    email: cherry@genome.stanford.edu
    github: null
    name: J. Michael Cherry
    orcid: 0000-0001-9163-5180
  domain: gene
  edam:
    description: Identifier of an entry from the Saccharomyces genome database (SGD).
    name: SGD
    obsolete: false
    prefix: '2632'
  example: S000002493
  fairsharing:
    abbreviation: SGD
    description: The Saccharomyces Genome Database (SGD) provides comprehensive integrated
      biological information for the budding yeast Saccharomyces cerevisiae along
      with search and analysis tools to explore these data, enabling the discovery
      of functional relationships between sequence and gene products in fungi and
      higher organisms.
    homepage: http://www.yeastgenome.org/
    license: https://www.stanford.edu/site/terms
    name: Saccharomyces Genome Database
    prefix: FAIRsharing.pzvw40
    publications:
    - doi: 10.1093/database/bau075
      pubmed_id: 25052702
      title: Standardized description of scientific evidence using the Evidence Ontology
        (ECO).
    - doi: 10.1093/database/bat054
      pubmed_id: 23842463
      title: A guide to best practices for Gene Ontology (GO) manual annotation.
    - doi: 10.1093/database/bas001
      pubmed_id: 22434836
      title: CvManGO, a method for leveraging computational predictions to improve
        literature-based Gene Ontology annotations.
    - doi: 10.1093/nar/gkr1029
      pubmed_id: 22110037
      title: 'Saccharomyces Genome Database: the genomics resource of budding yeast.'
    - doi: 10.1002/9780470089941.et1104s01
      pubmed_id: null
      title: Using Model Organism Databases (MODs).
    - doi: 10.1093/database/bap001
      pubmed_id: 20157474
      title: New mutant phenotype data curation system in the Saccharomyces Genome
        Database.
    - doi: 10.1093/nar/gkl931
      pubmed_id: 17142221
      title: 'Expanded protein information at SGD: new pages and proteome browser.'
    - doi: 10.1002/yea.1400
      pubmed_id: 17001629
      title: 'Saccharomyces cerevisiae S288C genome annotation: a working hypothesis.'
    - doi: 10.1093/nar/gkj117
      pubmed_id: 16381907
      title: 'Genome Snapshot: a new resource at the Saccharomyces Genome Database
        (SGD) presenting an overview of the Saccharomyces cerevisiae genome.'
    - doi: 10.1093/bib/5.1.9
      pubmed_id: 15153302
      title: 'Saccharomyces genome database: underlying principles and organisation.'
    - doi: 10.1093/nar/gkt1158
      pubmed_id: 24265222
      title: Saccharomyces Genome Database provides new regulation data.
    - doi: 10.1534/g3.113.008995
      pubmed_id: 24374639
      title: 'The reference genome sequence of Saccharomyces cerevisiae: then and
        now.'
    - doi: 10.1093/database/bat012
      pubmed_id: 23487186
      title: 'The new modern era of yeast genomics: community sequencing and the resulting
        annotation of multiple Saccharomyces cerevisiae strains at the Saccharomyces
        Genome Database.'
    - doi: 10.1093/database/bat004
      pubmed_id: 23396302
      title: 'The YeastGenome app: the Saccharomyces Genome Database at your fingertips.'
    - doi: 10.1093/database/bar062
      pubmed_id: 22434830
      title: YeastMine - An integrated data warehouse for S. cerevisiae data as a
        multi-purpose tool-kit.
    - doi: 10.1093/database/bar057
      pubmed_id: 22434826
      title: 'Considerations for creating and annotating the budding yeast Genome
        Map at SGD: a progress report.'
    - doi: 10.1093/database/bar004
      pubmed_id: 21411447
      title: 'Using computational predictions to improve literature-based Gene Ontology
        annotations: a feasibility study.'
    - doi: 10.1093/nar/gkp917
      pubmed_id: 19906697
      title: Saccharomyces Genome Database provides mutant phenotype data.
    - doi: 10.1016/j.tim.2009.04.005
      pubmed_id: 19577472
      title: 'Functional annotations for the Saccharomyces cerevisiae genome: the
        knowns and the known unknowns.'
    - doi: 10.1093/nar/gkm909
      pubmed_id: 17982175
      title: 'Gene Ontology annotations at SGD: new data sources and annotation methods.'
    - doi: 10.1093/nar/gki023
      pubmed_id: 15608219
      title: 'Fungal BLAST and Model Organism BLASTP Best Hits: new comparison resources
        at the Saccharomyces Genome Database (SGD).'
    - doi: 10.1093/nar/gkh033
      pubmed_id: 14681421
      title: Saccharomyces Genome Database (SGD) provides tools to identify and analyze
        sequences from Saccharomyces cerevisiae and related sequences from other organisms.
    - doi: 10.1093/database/baw020
      pubmed_id: 26989152
      title: 'From one to many: expanding the Saccharomyces cerevisiae reference genome
        panel.'
    - doi: 10.1093/nar/gkg054
      pubmed_id: 12519985
      title: Saccharomyces Genome Database (SGD) provides biochemical and structural
        information for budding yeast proteins.
    - doi: 10.1016/s0076-6879(02)50972-1
      pubmed_id: 12073322
      title: Saccharomyces Genome Database
    - doi: 10.1101/pdb.top083840
      pubmed_id: 26631132
      title: 'The Saccharomyces Genome Database: A Tool for Discovery.'
    - doi: 10.1093/nar/30.1.69
      pubmed_id: 11752257
      title: Saccharomyces Genome Database (SGD) provides secondary gene annotation
        using the Gene Ontology (GO).
    - doi: 10.1093/nar/gkv1250
      pubmed_id: 26578556
      title: The Saccharomyces Genome Database Variant Viewer.
    - doi: 10.1101/pdb.prot088922
      pubmed_id: 26631126
      title: 'The Saccharomyces Genome Database: Exploring Genome Features and Their
        Annotations.'
    - doi: null
      pubmed_id: 9169866
      title: Genetic and physical maps of Saccharomyces cerevisiae.
    - doi: 10.1002/(SICI)1097-0061(199812)14:16<1453::AID-YEA348>3.0.CO;2-G
      pubmed_id: 9885151
      title: Expanding yeast knowledge online.
    - doi: 10.1101/pdb.prot088898
      pubmed_id: 26631123
      title: 'The Saccharomyces Genome Database: Exploring Biochemical Pathways and
        Mutant Phenotypes.'
    - doi: 10.1002/dvg.22862
      pubmed_id: 25997651
      title: Biocuration at the Saccharomyces Genome Database.
    - doi: 10.1371/journal.pone.0120671
      pubmed_id: 25781462
      title: AGAPE (Automated Genome Analysis PipelinE) for Pan-Genome Analysis of
        Saccharomyces cerevisiae.
    - doi: 10.1093/nar/gku975
      pubmed_id: 25313161
      title: The complex portal - an encyclopaedia of macromolecular complexes.
    - doi: 10.1101/pdb.prot088914
      pubmed_id: 26631125
      title: 'The Saccharomyces Genome Database: Gene Product Annotation of Function,
        Process, and Component.'
    - doi: 10.1101/pdb.prot088906
      pubmed_id: 26631124
      title: 'The Saccharomyces Genome Database: Advanced Searching Methods and Data
        Mining.'
    - doi: 10.1093/nar/29.1.80
      pubmed_id: 11125055
      title: Saccharomyces Genome Database provides tools to survey gene expression
        and functional analysis data.
    - doi: 10.1093/nar/26.1.73
      pubmed_id: 9399804
      title: 'SGD: Saccharomyces Genome Database.'
    - doi: 10.1093/nar/27.1.74
      pubmed_id: 9847146
      title: Using the Saccharomyces Genome Database (SGD) for analysis of protein
        similarities and structure.
    - doi: 10.1126/science.282.5396.2022
      pubmed_id: 9851918
      title: 'Comparison of the complete protein sets of worm and yeast: orthology
        and divergence.'
    - doi: 10.1126/science.277.5330.1259
      pubmed_id: 9297238
      title: Yeast as a model organism.
    - doi: 10.1093/nar/28.1.77
      pubmed_id: 10592186
      title: Integrating functional genomic information into the Saccharomyces genome
        database.
    - doi: 10.1073/pnas.94.11.5506
      pubmed_id: 9159100
      title: 'Molecular linguistics: extracting information from gene and protein
        sequences.'
    - doi: null
      pubmed_id: 7660459
      title: Genetic nomenclature guide. Saccharomyces cerevisiae.
    subjects:
    - Epigenetics
    - Proteomics
    - Life Science
    - Transcriptomics
    twitter: yeastgenome
  go:
    homepage: http://www.yeastgenome.org/
    name: Saccharomyces Genome Database
    prefix: SGD
    synonyms:
    - SGDID
    uri_format: https://www.yeastgenome.org/search?q=$1&is_quick=true
  integbio:
    alt_name: Saccharomyces Genome Database
    description: This is an integrated database for budding yeast Saccharomyces cerevisiae.
      It contains search and analysis tools based on genes, sequences, and functions,
      as well as information related to citations, and the community. The information
      is updated and maintained by curators. It enables users to find functional relationships
      to sequences and gene products of fungi and higher organisms can also be verified.
      The SGD also maintains all gene names for budding yeast through the gene Name
      Registry.
    fairsharing: biodbcore-000100
    homepage: http://www.yeastgenome.org/
    information_keywords:
    - Bioresource
    - Ontology/Terminology/Nomenclature
    - Sequence
    - Expression
    - Interaction/Pathway
    - Image/Movie
    - Bibliography/Documents
    maintainer: Stanford University
    name: SGD
    prefix: nbdc00202
    pubmeds:
    - '9399804'
    - '22110037'
    status: Active
    target_keywords:
    - Genome/Gene
    - RNA
    - Protein
    - Organism
  license: CC-BY-4.0
  logo: https://cherrylab.stanford.edu/sites/g/files/sbiybj20496/files/styles/card_1900x950/public/media/image/sgd-banner-higher_res_0.png
  mappings:
    biocontext: SGD
    edam: '2632'
    fairsharing: FAIRsharing.pzvw40
    go: SGD
    integbio: nbdc00202
    miriam: sgd
    n2t: sgd
    ncbi: SGD
    prefixcommons: sgd
    re3data: r3d100010419
    togoid: Sgd
    uniprot: DB-0095
    wikidata: P3406
  miriam:
    deprecated: false
    description: The Saccharomyces Genome Database (SGD) project collects information
      and maintains a database of the molecular biology of the yeast Saccharomyces
      cerevisiae.
    homepage: https://www.yeastgenome.org/
    id: '00000023'
    name: SGD
    namespaceEmbeddedInLui: false
    pattern: ^((S\d+$)|(Y[A-Z]{2}\d{3}[a-zA-Z](\-[A-Z])?))$
    prefix: sgd
    providers:
    - code: agr
      description: SGD through the Alliance of Genome Resources
      homepage: https://www.alliancegenome.org
      name: SGD through the Alliance of Genome Resources
      uri_format: https://www.alliancegenome.org/gene/SGD:$1
    - code: ''
      description: Bio2RDF
      homepage: http://bio2rdf.org
      name: Bio2RDF
      uri_format: http://bio2rdf.org/sgd:$1
    sampleId: S000003909
    uri_format: https://www.yeastgenome.org/locus/$1
  n2t:
    description: The Saccharomyces Genome Database (SGD) project collects information
      and maintains a database of the molecular biology of the yeast Saccharomyces
      cerevisiae.
    example: S000003909
    homepage: https://www.yeastgenome.org/
    name: SGD
    namespaceEmbeddedInLui: false
    pattern: ^((S\d+$)|(Y[A-Z]{2}\d{3}[a-zA-Z](\-[A-Z])?))$
    prefix: sgd
    uri_format: https://www.yeastgenome.org/locus/$1
  name: Saccharomyces Genome Database
  ncbi:
    example: L0000470
    homepage: http://www.yeastgenome.org/
    name: Saccharomyces Genome Database
    prefix: SGD
  part_of_database: sgd
  prefix: sgd
  prefixcommons:
    description: The Saccharomyces Genome Database (SGD) collects and organizes information
      about the molecular biology and genetics of the yeast Saccharomyces cerevisiae.
      SGD contains a variety of biological information and tools with which to search
      and analyze it.
    example: S000006169
    homepage: http://www.yeastgenome.org/
    keywords:
    - eukaryotic
    - genome
    - nucleotide
    name: Saccharomyces Genome Database
    pattern: ^S\d+$
    prefix: sgd
    pubmed_ids:
    - '14681421'
    uri_format: http://db.yeastgenome.org/cgi-bin/locus.pl?dbid=$1
  publications:
  - doi: 10.1101/2024.09.16.613348
    pmc: PMC11430078
    pubmed: '39345624'
    title: 'Saccharomyces Genome Database: Advances in Genome Annotation, Expanded
      Biochemical Pathways, and Other Key Enhancements'
    year: 2024
  - doi: 10.1093/database/baw020
    pmc: PMC4795930
    pubmed: '26989152'
    title: 'From one to many: expanding the Saccharomyces cerevisiae reference genome
      panel'
    year: 2016
  - doi: 10.1371/journal.pone.0120671
    pmc: PMC4363492
    pubmed: '25781462'
    title: AGAPE (Automated Genome Analysis PipelinE) for pan-genome analysis of Saccharomyces
      cerevisiae
    year: 2015
  - doi: 10.1002/dvg.22862
    pmc: PMC4545726
    pubmed: '25997651'
    title: Biocuration at the Saccharomyces genome database
    year: 2015
  - doi: 10.1093/nar/gkv1250
    pmc: PMC4702884
    pubmed: '26578556'
    title: The Saccharomyces Genome Database Variant Viewer
    year: 2015
  - doi: 10.1101/pdb.top083840
    pmc: PMC5673599
    pubmed: '26631132'
    title: 'The Saccharomyces Genome Database: A Tool for Discovery'
    year: 2015
  - doi: 10.1101/pdb.prot088906
    pmc: PMC5673598
    pubmed: '26631124'
    title: 'The Saccharomyces Genome Database: Advanced Searching Methods and Data
      Mining'
    year: 2015
  - doi: 10.1101/pdb.prot088898
    pmc: PMC5673601
    pubmed: '26631123'
    title: 'The Saccharomyces Genome Database: Exploring Biochemical Pathways and
      Mutant Phenotypes'
    year: 2015
  - doi: 10.1101/pdb.prot088922
    pmc: PMC5673602
    pubmed: '26631126'
    title: 'The Saccharomyces Genome Database: Exploring Genome Features and Their
      Annotations'
    year: 2015
  - doi: 10.1101/pdb.prot088914
    pmc: PMC5673600
    pubmed: '26631125'
    title: 'The Saccharomyces Genome Database: Gene Product Annotation of Function,
      Process, and Component'
    year: 2015
  - doi: 10.1093/database/bau075
    pmc: PMC4105709
    pubmed: '25052702'
    title: Standardized description of scientific evidence using the Evidence Ontology
      (ECO)
    year: 2014
  - doi: 10.1093/nar/gku975
    pmc: PMC4384031
    pubmed: '25313161'
    title: The complex portal--an encyclopaedia of macromolecular complexes
    year: 2014
  - doi: 10.1534/g3.113.008995
    pmc: PMC3962479
    pubmed: '24374639'
    title: 'The reference genome sequence of Saccharomyces cerevisiae: then and now'
    year: 2014
  - doi: 10.1093/database/bat054
    pmc: PMC3706743
    pubmed: '23842463'
    title: A guide to best practices for Gene Ontology (GO) manual annotation
    year: 2013
  - doi: 10.1093/nar/gkt1158
    pmc: PMC3965049
    pubmed: '24265222'
    title: Saccharomyces genome database provides new regulation data
    year: 2013
  - doi: 10.1093/database/bat012
    pmc: PMC3595989
    pubmed: '23487186'
    title: 'The new modern era of yeast genomics: community sequencing and the resulting
      annotation of multiple Saccharomyces cerevisiae strains at the Saccharomyces
      Genome Database'
    year: 2013
  - doi: 10.1093/database/bat004
    pmc: PMC3567487
    pubmed: '23396302'
    title: 'The YeastGenome app: the Saccharomyces Genome Database at your fingertips'
    year: 2013
  - doi: 10.1093/database/bar057
    pmc: PMC3308148
    pubmed: '22434826'
    title: 'Considerations for creating and annotating the budding yeast Genome Map
      at SGD: a progress report'
    year: 2012
  - doi: 10.1093/database/bas001
    pmc: PMC3308158
    pubmed: '22434836'
    title: CvManGO, a method for leveraging computational predictions to improve literature-based
      Gene Ontology annotations
    year: 2012
  - doi: 10.1093/database/bar062
    pmc: PMC3308152
    pubmed: '22434830'
    title: YeastMine--an integrated data warehouse for Saccharomyces cerevisiae data
      as a multipurpose tool-kit
    year: 2012
  - doi: 10.1093/nar/gkr1029
    pmc: PMC3245034
    pubmed: '22110037'
    title: 'Saccharomyces Genome Database: the genomics resource of budding yeast'
    year: 2011
  - doi: 10.1093/database/bar004
    pmc: PMC3067894
    pubmed: '21411447'
    title: 'Using computational predictions to improve literature-based Gene Ontology
      annotations: a feasibility study'
    year: 2011
  - doi: 10.1016/j.tim.2009.04.005
    pmc: PMC3057094
    pubmed: '19577472'
    title: 'Functional annotations for the Saccharomyces cerevisiae genome: the knowns
      and the known unknowns'
    year: 2009
  - doi: 10.1093/database/bap001
    pmc: PMC2790299
    pubmed: '20157474'
    title: New mutant phenotype data curation system in the Saccharomyces Genome Database
    year: 2009
  - doi: 10.1093/nar/gkp917
    pmc: PMC2808950
    pubmed: '19906697'
    title: Saccharomyces Genome Database provides mutant phenotype data
    year: 2009
  - doi: 10.1002/9780470089941.et1104s01
    pmc: null
    pubmed: null
    title: Using Model Organism Databases (MODs)
    year: 2009
  - doi: 10.1093/nar/gkm909
    pmc: PMC2238894
    pubmed: '17982175'
    title: 'Gene Ontology annotations at SGD: new data sources and annotation methods'
    year: 2007
  - doi: 10.1093/nar/gkl931
    pmc: PMC1669759
    pubmed: '17142221'
    title: 'Expanded protein information at SGD: new pages and proteome browser'
    year: 2006
  - doi: 10.1093/nar/gkj117
    pmc: PMC1347479
    pubmed: '16381907'
    title: 'Genome Snapshot: a new resource at the Saccharomyces Genome Database (SGD)
      presenting an overview of the Saccharomyces cerevisiae genome'
    year: 2006
  - doi: 10.1002/yea.1400
    pmc: PMC3040122
    pubmed: '17001629'
    title: 'Saccharomyces cerevisiae S288C genome annotation: a working hypothesis'
    year: 2006
  - doi: 10.1093/nar/gki023
    pmc: PMC539977
    pubmed: '15608219'
    title: 'Fungal BLAST and Model Organism BLASTP Best Hits: new comparison resources
      at the Saccharomyces Genome Database (SGD)'
    year: 2005
  - doi: 10.1093/nar/gkh033
    pmc: PMC308767
    pubmed: '14681421'
    title: Saccharomyces Genome Database (SGD) provides tools to identify and analyze
      sequences from Saccharomyces cerevisiae and related sequences from other organisms
    year: 2004
  - doi: 10.1093/bib/5.1.9
    pmc: PMC3037832
    pubmed: '15153302'
    title: 'Saccharomyces genome database: underlying principles and organisation'
    year: 2004
  - doi: 10.1093/nar/gkg054
    pmc: PMC165501
    pubmed: '12519985'
    title: Saccharomyces Genome Database (SGD) provides biochemical and structural
      information for budding yeast proteins
    year: 2003
  - doi: 10.1016/s0076-6879(02)50972-1
    pmc: null
    pubmed: '12073322'
    title: Saccharomyces Genome Database
    year: 2002
  - doi: 10.1093/nar/30.1.69
    pmc: PMC99086
    pubmed: '11752257'
    title: Saccharomyces Genome Database (SGD) provides secondary gene annotation
      using the Gene Ontology (GO)
    year: 2002
  - doi: 10.1093/nar/29.1.80
    pmc: PMC29796
    pubmed: '11125055'
    title: Saccharomyces Genome Database provides tools to survey gene expression
      and functional analysis data
    year: 2001
  - doi: 10.1093/nar/28.1.77
    pmc: PMC102447
    pubmed: '10592186'
    title: Integrating functional genomic information into the Saccharomyces genome
      database
    year: 2000
  - doi: 10.1093/nar/27.1.74
    pmc: PMC148101
    pubmed: '9847146'
    title: Using the Saccharomyces Genome Database (SGD) for analysis of protein similarities
      and structure
    year: 1999
  - doi: 10.1126/science.282.5396.2022
    pmc: PMC3057080
    pubmed: '9851918'
    title: 'Comparison of the complete protein sets of worm and yeast: orthology and
      divergence'
    year: 1998
  - doi: 10.1002/(sici)1097-0061(199812)14:16<1453::aid-yea348>3.0.co;2-g
    pmc: PMC3037831
    pubmed: '9885151'
    title: Expanding yeast knowledge online
    year: 1998
  - doi: 10.1093/nar/26.1.73
    pmc: PMC147204
    pubmed: '9399804'
    title: 'SGD: Saccharomyces Genome Database'
    year: 1998
  - doi: null
    pmc: PMC3057085
    pubmed: '9169866'
    title: Genetic and physical maps of Saccharomyces cerevisiae
    year: 1997
  - doi: 10.1073/pnas.94.11.5506
    pmc: PMC34160
    pubmed: '9159100'
    title: 'Molecular linguistics: extracting information from gene and protein sequences'
    year: 1997
  - doi: 10.1126/science.277.5330.1259
    pmc: PMC3039837
    pubmed: '9297238'
    title: Yeast as a model organism
    year: 1997
  - doi: null
    pmc: null
    pubmed: '7660459'
    title: Genetic nomenclature guide. Saccharomyces cerevisiae
    year: 1995
  - doi: 10.1093/database/bau075
    pmc: null
    pubmed: null
    title: Standardized description of scientific evidence using the Evidence Ontology
      (ECO).
    year: null
  - doi: 10.1093/database/bat054
    pmc: null
    pubmed: null
    title: A guide to best practices for Gene Ontology (GO) manual annotation.
    year: null
  - doi: 10.1093/database/bas001
    pmc: null
    pubmed: null
    title: CvManGO, a method for leveraging computational predictions to improve literature-based
      Gene Ontology annotations.
    year: null
  - doi: 10.1093/nar/gkr1029
    pmc: null
    pubmed: null
    title: 'Saccharomyces Genome Database: the genomics resource of budding yeast.'
    year: null
  - doi: 10.1002/9780470089941.et1104s01
    pmc: null
    pubmed: null
    title: Using Model Organism Databases (MODs).
    year: null
  - doi: 10.1093/database/bap001
    pmc: null
    pubmed: null
    title: New mutant phenotype data curation system in the Saccharomyces Genome Database.
    year: null
  - doi: 10.1093/nar/gkl931
    pmc: null
    pubmed: null
    title: 'Expanded protein information at SGD: new pages and proteome browser.'
    year: null
  - doi: 10.1002/yea.1400
    pmc: null
    pubmed: null
    title: 'Saccharomyces cerevisiae S288C genome annotation: a working hypothesis.'
    year: null
  - doi: 10.1093/nar/gkj117
    pmc: null
    pubmed: null
    title: 'Genome Snapshot: a new resource at the Saccharomyces Genome Database (SGD)
      presenting an overview of the Saccharomyces cerevisiae genome.'
    year: null
  - doi: 10.1093/bib/5.1.9
    pmc: null
    pubmed: null
    title: 'Saccharomyces genome database: underlying principles and organisation.'
    year: null
  - doi: 10.1093/nar/gkt1158
    pmc: null
    pubmed: null
    title: Saccharomyces Genome Database provides new regulation data.
    year: null
  - doi: 10.1534/g3.113.008995
    pmc: null
    pubmed: null
    title: 'The reference genome sequence of Saccharomyces cerevisiae: then and now.'
    year: null
  - doi: 10.1093/database/bat012
    pmc: null
    pubmed: null
    title: 'The new modern era of yeast genomics: community sequencing and the resulting
      annotation of multiple Saccharomyces cerevisiae strains at the Saccharomyces
      Genome Database.'
    year: null
  - doi: 10.1093/database/bat004
    pmc: null
    pubmed: null
    title: 'The YeastGenome app: the Saccharomyces Genome Database at your fingertips.'
    year: null
  - doi: 10.1093/database/bar062
    pmc: null
    pubmed: null
    title: YeastMine - An integrated data warehouse for S. cerevisiae data as a multi-purpose
      tool-kit.
    year: null
  - doi: 10.1093/database/bar057
    pmc: null
    pubmed: null
    title: 'Considerations for creating and annotating the budding yeast Genome Map
      at SGD: a progress report.'
    year: null
  - doi: 10.1093/database/bar004
    pmc: null
    pubmed: null
    title: 'Using computational predictions to improve literature-based Gene Ontology
      annotations: a feasibility study.'
    year: null
  - doi: 10.1093/nar/gkp917
    pmc: null
    pubmed: null
    title: Saccharomyces Genome Database provides mutant phenotype data.
    year: null
  - doi: 10.1016/j.tim.2009.04.005
    pmc: null
    pubmed: null
    title: 'Functional annotations for the Saccharomyces cerevisiae genome: the knowns
      and the known unknowns.'
    year: null
  - doi: 10.1093/nar/gkm909
    pmc: null
    pubmed: null
    title: 'Gene Ontology annotations at SGD: new data sources and annotation methods.'
    year: null
  - doi: 10.1093/nar/gki023
    pmc: null
    pubmed: null
    title: 'Fungal BLAST and Model Organism BLASTP Best Hits: new comparison resources
      at the Saccharomyces Genome Database (SGD).'
    year: null
  - doi: 10.1093/nar/gkh033
    pmc: null
    pubmed: null
    title: Saccharomyces Genome Database (SGD) provides tools to identify and analyze
      sequences from Saccharomyces cerevisiae and related sequences from other organisms.
    year: null
  - doi: 10.1093/database/baw020
    pmc: null
    pubmed: null
    title: 'From one to many: expanding the Saccharomyces cerevisiae reference genome
      panel.'
    year: null
  - doi: 10.1093/nar/gkg054
    pmc: null
    pubmed: null
    title: Saccharomyces Genome Database (SGD) provides biochemical and structural
      information for budding yeast proteins.
    year: null
  - doi: 10.1016/s0076-6879(02)50972-1
    pmc: null
    pubmed: null
    title: Saccharomyces Genome Database
    year: null
  - doi: 10.1101/pdb.top083840
    pmc: null
    pubmed: null
    title: 'The Saccharomyces Genome Database: A Tool for Discovery.'
    year: null
  - doi: 10.1093/nar/30.1.69
    pmc: null
    pubmed: null
    title: Saccharomyces Genome Database (SGD) provides secondary gene annotation
      using the Gene Ontology (GO).
    year: null
  - doi: 10.1093/nar/gkv1250
    pmc: null
    pubmed: null
    title: The Saccharomyces Genome Database Variant Viewer.
    year: null
  - doi: 10.1101/pdb.prot088922
    pmc: null
    pubmed: null
    title: 'The Saccharomyces Genome Database: Exploring Genome Features and Their
      Annotations.'
    year: null
  - doi: 10.1002/(SICI)1097-0061(199812)14:16<1453::AID-YEA348>3.0.CO;2-G
    pmc: null
    pubmed: null
    title: Expanding yeast knowledge online.
    year: null
  - doi: 10.1101/pdb.prot088898
    pmc: null
    pubmed: null
    title: 'The Saccharomyces Genome Database: Exploring Biochemical Pathways and
      Mutant Phenotypes.'
    year: null
  - doi: 10.1002/dvg.22862
    pmc: null
    pubmed: null
    title: Biocuration at the Saccharomyces Genome Database.
    year: null
  - doi: 10.1371/journal.pone.0120671
    pmc: null
    pubmed: null
    title: AGAPE (Automated Genome Analysis PipelinE) for Pan-Genome Analysis of Saccharomyces
      cerevisiae.
    year: null
  - doi: 10.1093/nar/gku975
    pmc: null
    pubmed: null
    title: The complex portal - an encyclopaedia of macromolecular complexes.
    year: null
  - doi: 10.1101/pdb.prot088914
    pmc: null
    pubmed: null
    title: 'The Saccharomyces Genome Database: Gene Product Annotation of Function,
      Process, and Component.'
    year: null
  - doi: 10.1101/pdb.prot088906
    pmc: null
    pubmed: null
    title: 'The Saccharomyces Genome Database: Advanced Searching Methods and Data
      Mining.'
    year: null
  - doi: 10.1093/nar/29.1.80
    pmc: null
    pubmed: null
    title: Saccharomyces Genome Database provides tools to survey gene expression
      and functional analysis data.
    year: null
  - doi: 10.1093/nar/26.1.73
    pmc: null
    pubmed: null
    title: 'SGD: Saccharomyces Genome Database.'
    year: null
  - doi: 10.1093/nar/27.1.74
    pmc: null
    pubmed: null
    title: Using the Saccharomyces Genome Database (SGD) for analysis of protein similarities
      and structure.
    year: null
  - doi: 10.1126/science.282.5396.2022
    pmc: null
    pubmed: null
    title: 'Comparison of the complete protein sets of worm and yeast: orthology and
      divergence.'
    year: null
  - doi: 10.1126/science.277.5330.1259
    pmc: null
    pubmed: null
    title: Yeast as a model organism.
    year: null
  - doi: 10.1093/nar/28.1.77
    pmc: null
    pubmed: null
    title: Integrating functional genomic information into the Saccharomyces genome
      database.
    year: null
  - doi: 10.1073/pnas.94.11.5506
    pmc: null
    pubmed: null
    title: 'Molecular linguistics: extracting information from gene and protein sequences.'
    year: null
  - doi: null
    pmc: null
    pubmed: '14681421'
    title: null
    year: null
  - doi: 10.1093/genetics/iyae185
    pmc: null
    pubmed: '39530598'
    title: null
    year: null
  re3data:
    description: The Saccharomyces Genome Database (SGD) provides comprehensive integrated
      biological information for the budding yeast Saccharomyces cerevisiae along
      with search and analysis tools to explore these data, enabling the discovery
      of functional relationships between sequence and gene products in fungi and
      higher organisms.
    doi: 10.17616/R3N313
    homepage: https://www.yeastgenome.org
    license: other
    name: Saccharomyces Genome Database
    prefix: r3d100010419
    synonyms:
    - SGD
    xrefs:
      nif: 0000-03456
      omics: '01661'
  togoid:
    catalog: nbdc00202
    description: This is an integrated database for budding yeast Saccharomyces cerevisiae.
      It contains search and analysis tools based on genes, sequences, and functions,
      as well as information related to citations, and the community. The information
      is updated and maintained by curators. It enables users to find functional relationships
      to sequences and gene products of fungi and higher organisms can also be verified.
      The SGD also maintains all gene names for budding yeast through the gene Name
      Registry.
    examples:
    - S000003096
    - S000003789
    - S000005770
    - S000028467
    - S000006377
    - S000001180
    - S000003769
    - S000001459
    - S000004428
    - S000006021
    keywords:
    - Gene
    name: SGD
    pattern: ^(?S\d{9})$
    prefix: Sgd
    uri_format: http://identifiers.org/sgd/$1
  uniprot:
    abbreviation: SGD
    category: Organism-specific databases
    homepage: https://www.yeastgenome.org/
    name: Saccharomyces Genome Database
    prefix: DB-0095
    publications:
    - doi: 10.1093/genetics/iyae185
      pubmed: '39530598'
    uri_format: https://www.yeastgenome.org/locus/$1
  wikidata:
    description: identifier for a genetic element in the Saccharomyces Genome Database
    example:
    - S000000944
    - S000001582
    - S000007279
    homepage: http://www.yeastgenome.org
    name: Saccharomyces Genome Database ID
    pattern: ^S\d{9}$
    prefix: P3406
    uri_format: http://www.yeastgenome.org/locus/$1/overview
sgd.pathways:
  biocontext:
    prefix: SGD.PATHWAYS
  contact:
    email: Karen.Christie@jax.org
    github: krchristie
    name: Karen R. Christie
    orcid: 0000-0001-5501-853X
  mappings:
    biocontext: SGD.PATHWAYS
    miriam: sgd.pathways
    n2t: sgd.pathways
    prefixcommons: sgd.pathways
  miriam:
    deprecated: false
    description: Curated biochemical pathways for Saccharomyces cerevisiae at Saccharomyces
      genome database (SGD).
    homepage: http://pathway.yeastgenome.org/
    id: '00000057'
    name: Saccharomyces genome database pathways
    namespaceEmbeddedInLui: false
    pattern: ^PWY\w{2}\-\d{3}$
    prefix: sgd.pathways
    sampleId: PWY3O-214
    uri_format: http://pathway.yeastgenome.org/YEAST/new-image?type=PATHWAY&object=$1
  n2t:
    description: Curated biochemical pathways for Saccharomyces cerevisiae at Saccharomyces
      genome database (SGD).
    example: PWY3O-214
    homepage: http://pathway.yeastgenome.org/
    name: Saccharomyces cerevisiae pathways at SGD.
    namespaceEmbeddedInLui: false
    pattern: ^PWY\w{2}\-\d{3}$
    prefix: sgd.pathways
    uri_format: http://pathway.yeastgenome.org/YEAST/new-image?type=PATHWAY&object=$1
  part_of_database: sgd
  prefix: sgd.pathways
  prefixcommons:
    description: Curated biochemical pathways for Saccharomyces cerevisiae at Saccharomyces
      genome database (SGD).
    example: PWY3O-214
    homepage: http://www.yeastgenome.org/
    keywords:
    - genome
    - pathway
    - sequence
    name: Saccharomyces genome database pathways
    pattern: ^PWY\w{2}\-\d{3}$
    prefix: sgd.pathways
    pubmed_ids:
    - '14681421'
    synonyms:
    - spt
    uri_format: http://pathway.yeastgenome.org/YEAST/new-image?type=PATHWAY&object=$1
  publications:
  - doi: 10.1101/2024.09.16.613348
    pmc: PMC11430078
    pubmed: '39345624'
    title: 'Saccharomyces Genome Database: Advances in Genome Annotation, Expanded
      Biochemical Pathways, and Other Key Enhancements'
    year: 2024
  - doi: 10.1093/nar/gkh033
    pmc: PMC308767
    pubmed: '14681421'
    title: Saccharomyces Genome Database (SGD) provides tools to identify and analyze
      sequences from Saccharomyces cerevisiae and related sequences from other organisms
    year: 2004
  - doi: null
    pmc: null
    pubmed: '14681421'
    title: null
    year: null
  - doi: null
    pmc: null
    pubmed: '14681421'
    title: null
    year: null
sgn:
  biocontext:
    prefix: SGN
  contact:
    email: lam87@cornell.edu
    github: lukasmueller
    name: Lukas A. Mueller
    orcid: 0000-0001-8640-1750
  fairsharing:
    abbreviation: SGN
    description: The Sol Genomics Network (SGN) is a database and website dedicated
      to the genomic information of the Solanaceae family, which includes species
      such as tomato, potato, pepper, petunia and eggplant.
    homepage: https://solgenomics.net
    name: Sol Genomics Network
    prefix: FAIRsharing.3zqvaf
    publications:
    - doi: 10.1093/nar/gkq866
      pubmed_id: 20935049
      title: 'The Sol Genomics Network (solgenomics.net): growing tomatoes using Perl.'
    - doi: 10.1093/nar/gku1195
      pubmed_id: 25428362
      title: The Sol Genomics Network (SGN)--from genotype to phenotype to breeding.
    subjects:
    - Botany
    - Genomics
    - Agriculture
    - Comparative Genomics
    twitter: solgenomics
  go:
    homepage: https://www.sgn.cornell.edu/
    name: Sol Genomics Network
    prefix: SGN
    synonyms:
    - SGN_gene
    uri_format: http://solgenomics.net/phenome/locus_display.pl?locus_id=$1
  integbio:
    alt_name: Sol Genomics Network
    description: SGN is a database of genome and phenotype data for species in the
      Solanaceae and their close relatives. It provides genome maps and sequences,
      QTLs, RNA-seq, and microarray data. Users can use tools, such as BLAST, Browse
      for browsing genomes, expression and map data viewers, a locus community annotation
      system and a QTL analysis tools.
    fairsharing: biodbcore-000301
    homepage: https://solgenomics.net
    information_keywords:
    - Sequence
    - Expression
    - Phenotype
    - Method
    - Repository
    maintainer: Boyce Thompson Institute for Plant Research
    name: SGN
    prefix: nbdc02414
    pubmeds:
    - '25428362'
    status: Active
    target_keywords:
    - Genome/Gene
    - cDNA/EST
  logo: https://solgenomics.net/documents/img/sgn_transparent_logo.png
  mappings:
    biocontext: SGN
    fairsharing: FAIRsharing.3zqvaf
    go: SGN
    integbio: nbdc02414
    miriam: sgn
    n2t: sgn
    ncbi: SGN
    pathguide: '433'
    prefixcommons: sgn
    re3data: r3d100012078
  miriam:
    deprecated: false
    description: The Sol Genomics Network (SGN) is a database and website dedicated
      to the genomic information of the nightshade family, which includes species
      such as tomato, potato, pepper, petunia and eggplant.
    homepage: http://solgenomics.net/
    id: 00000185
    name: Sol Genomics Network
    namespaceEmbeddedInLui: false
    pattern: ^\d+$
    prefix: sgn
    sampleId: '0001'
    uri_format: http://solgenomics.net/phenome/locus_display.pl?locus_id=$1
  n2t:
    description: The Sol Genomics Network (SGN) is a database and website dedicated
      to the genomic information of the nightshade family, which includes species
      such as tomato, potato, pepper, petunia and eggplant.
    example: '0001'
    homepage: http://solgenomics.net/
    name: Sol Genomics Network at Boyce Thompson Institute for Plant Research
    namespaceEmbeddedInLui: false
    pattern: ^\d+$
    prefix: sgn
    uri_format: http://solgenomics.net/phenome/locus_display.pl?locus_id=$1
  ncbi:
    example: E553090
    homepage: http://www.sgn.cornell.edu
    name: SOL Genomics Network
    prefix: SGN
  pathguide:
    abbreviation: SGN
    homepage: http://solgenomics.net/
    name: Sol Genomics Network
    prefix: '433'
  prefix: sgn
  prefixcommons:
    description: The Sol Genomics Network (SGN) is a database and website dedicated
      to the genomic information of the nightshade family, which includes species
      such as tomato, potato, pepper, petunia and eggplant.
    example: '1'
    homepage: http://www.sgn.cornell.edu
    keywords:
    - pathway
    - small molecule
    - genome
    - plant
    name: Sol Genomics Network
    pattern: ^\d+$
    prefix: sgn
    pubmed_ids:
    - '20935049'
    uri_format: http://solgenomics.net/phenome/locus_display.pl?locus_id=$1
  publications:
  - doi: 10.1093/nar/gku1195
    pmc: PMC4383978
    pubmed: '25428362'
    title: The Sol Genomics Network (SGN)--from genotype to phenotype to breeding
    year: 2014
  - doi: 10.1093/nar/gkq866
    pmc: PMC3013765
    pubmed: '20935049'
    title: 'The Sol Genomics Network (solgenomics.net): growing tomatoes using Perl'
    year: 2010
  - doi: 10.1093/nar/gkq866
    pmc: null
    pubmed: null
    title: 'The Sol Genomics Network (solgenomics.net): growing tomatoes using Perl.'
    year: null
  - doi: 10.1093/nar/gku1195
    pmc: null
    pubmed: null
    title: The Sol Genomics Network (SGN)--from genotype to phenotype to breeding.
    year: null
  - doi: null
    pmc: null
    pubmed: '20935049'
    title: null
    year: null
  re3data:
    description: 'The Sol Genomics Network (SGN) is a clade-oriented database dedicated
      to the biology of the Solanaceae family which includes a large number of closely
      related and many agronomically important species such as tomato, potato, tobacco,
      eggplant, pepper, and the ornamental Petunia hybrida.

      SGN is part of the International Solanaceae Initiative (SOL), which has the
      long-term goal of creating a network of resources and information to address
      key questions in plant adaptation and diversification'
    doi: 10.17616/R3FS95
    homepage: https://solgenomics.net/
    name: SOL Genomics Network
    prefix: r3d100012078
    synonyms:
    - SGN
    - Solanaceae Genomics Network
sh:
  contact:
    email: dr.shorthair@pm.me
    github: dr-shorthair
    name: Simon Cox
    orcid: 0000-0002-3884-3420
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: A language for validating RDF graphs against a set of conditions
  download_owl: https://triplydb.com/w3c/sh/download.trig.gz
  example: NodeShape
  fairsharing:
    abbreviation: SHACL
    description: This document defines the SHACL Shapes Constraint Language, a language
      for validating RDF graphs against a set of conditions. These conditions are
      provided as shapes and other constructs expressed in the form of an RDF graph.
      RDF graphs that are used in this manner are called "shapes graphs" in SHACL
      and the RDF graphs that are validated against a shapes graph are called "data
      graphs". As SHACL shape graphs are used to validate that data graphs satisfy
      a set of conditions they can also be viewed as a description of the data graphs
      that do satisfy these conditions. Such descriptions may be used for a variety
      of purposes beside validation, including user interface building, code generation
      and data integration.
    homepage: https://www.w3.org/TR/shacl/
    name: Shapes Constraint Language (SHACL)
    prefix: FAIRsharing.f1449d
    publications: []
    repository: https://github.com/w3c/data-shapes
    subjects:
    - Knowledge and Information Systems
    - Informatics
    - Ontology and Terminology
  homepage: https://www.w3.org/TR/shacl/
  lov:
    description: This vocabulary defines terms used in SHACL, the W3C Shapes Constraint
      Language.
    homepage: https://www.w3.org/TR/shacl/
    keywords:
    - Quality
    - W3C Rec
    modified: '2017-07-20'
    name: W3C Shapes Constraint Language (SHACL) Vocabulary
    prefix: sh
    uri_prefix: http://www.w3.org/ns/shacl#$1
  mappings:
    fairsharing: FAIRsharing.f1449d
    lov: sh
    tib: sh
    zazuko: sh
  name: Shapes Constraint Language
  preferred_prefix: sh
  prefix: sh
  synonyms:
  - shacl
  tib:
    description: This vocabulary defines terms used in SHACL, the W3C Shapes Constraint
      Language.
    download_rdf: https://www.w3.org/ns/shacl.rdf
    homepage: https://www.w3.org/TR/2017/REC-shacl-20170720/
    keywords:
    - NFDI4ING
    - computer science
    name: W3C Shapes Constraint Language (SHACL) Vocabulary
    prefix: sh
    tracker: https://github.com/w3c/data-shapes/issues
    uri_format: http://www.w3.org/ns/shacl#$1
  uri_format: http://www.w3.org/ns/shacl#$1
  zazuko:
    prefix: sh
    uri_format: http://www.w3.org/ns/shacl#$1
shareloc:
  example: '000004'
  homepage: https://shareloc.xyz
  mappings:
    ols: shareloc
  ols:
    description: 'ShareLoc defines terms to annotate data sets from single molecule
      localization microscopy, including but not limited to: imaging technique, biological
      structures or molecules of interest, cell types, experimental condition, labeling
      method, fixation protocol, etc.'
    download_owl: https://raw.githubusercontent.com/imodpasteur/ShareLoc.XYZ/ontology/shareloc.owl
    name: ShareLoc
    prefix: shareloc
  pattern: ^\d{6}$
  prefix: shareloc
  uri_format: https://shareloc.xyz/#/ontology/vocabulary/SHARELOC_$1
sharkipedia.species:
  contact:
    email: creeas@gmail.com
    github: creeas
    name: Christopher Mull
    orcid: 0000-0003-1710-8256
  contributor:
    email: benjamin_gyori@hms.harvard.edu
    github: bgyori
    name: Benjamin M. Gyori
    orcid: 0000-0001-9439-5346
  description: Sharkipedia is an open source research initiative to make all published
    biological traits and population trends on sharks, rays, and chimaeras accessible
    to everyone.
  example: '983'
  github_request_issue: 607
  homepage: https://www.sharkipedia.org/
  mappings:
    wikidata.entity: Q113989515
  name: Sharkipedia Species
  part_of_database: sharkipedia
  pattern: ^\d+$
  prefix: sharkipedia.species
  publications:
  - doi: 10.1038/s41597-022-01655-1
    pmc: PMC9464254
    pubmed: '36088355'
    title: 'Sharkipedia: a curated open access database of shark and ray life history
      traits and abundance time-series'
    year: 2022
  repository: https://github.com/sharkipedia/sharkipedia
  reviewer:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  uri_format: https://www.sharkipedia.org/species/$1
  wikidata:
    database: Q113989515
sharkipedia.trait:
  contact:
    email: creeas@gmail.com
    github: creeas
    name: Christopher Mull
    orcid: 0000-0003-1710-8256
  contributor:
    email: benjamin_gyori@hms.harvard.edu
    github: bgyori
    name: Benjamin M. Gyori
    orcid: 0000-0001-9439-5346
  description: Sharkipedia is an open source research initiative to make all published
    biological traits and population trends on sharks, rays, and chimaeras accessible
    to everyone.
  example: '13'
  github_request_issue: 607
  homepage: https://www.sharkipedia.org/
  mappings:
    wikidata.entity: Q113989515
  name: Sharkipedia Trait
  part_of_database: sharkipedia
  pattern: ^\d+$
  prefix: sharkipedia.trait
  publications:
  - doi: 10.1038/s41597-022-01655-1
    pmc: PMC9464254
    pubmed: '36088355'
    title: 'Sharkipedia: a curated open access database of shark and ray life history
      traits and abundance time-series'
    year: 2022
  repository: https://github.com/sharkipedia/sharkipedia
  reviewer:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  uri_format: https://www.sharkipedia.org/traits/$1
  wikidata:
    database: Q113989515
sharkipedia.trend:
  contact:
    email: creeas@gmail.com
    github: creeas
    name: Christopher Mull
    orcid: 0000-0003-1710-8256
  contributor:
    email: benjamin_gyori@hms.harvard.edu
    github: bgyori
    name: Benjamin M. Gyori
    orcid: 0000-0001-9439-5346
  description: Sharkipedia is an open source research initiative to make all published
    biological traits and population trends on sharks, rays, and chimaeras accessible
    to everyone.
  example: '3447'
  github_request_issue: 607
  homepage: https://www.sharkipedia.org/
  mappings:
    wikidata.entity: Q113989515
  name: Sharkipedia Trend
  part_of_database: sharkipedia
  pattern: ^\d+$
  prefix: sharkipedia.trend
  publications:
  - doi: 10.1038/s41597-022-01655-1
    pmc: PMC9464254
    pubmed: '36088355'
    title: 'Sharkipedia: a curated open access database of shark and ray life history
      traits and abundance time-series'
    year: 2022
  repository: https://github.com/sharkipedia/sharkipedia
  reviewer:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  uri_format: https://www.sharkipedia.org/trends/$1
  wikidata:
    database: Q113989515
sheepqtldb:
  biocontext:
    prefix: SHEEPQTLDB
  mappings:
    biocontext: SHEEPQTLDB
    miriam: sheepqtldb
    n2t: sheepqtldb
    prefixcommons: sheepqtldb
  miriam:
    deprecated: false
    description: The Animal Quantitative Trait Loci (QTL) database (Animal QTLdb)
      is designed to house publicly all available QTL and single-nucleotide polymorphism/gene
      association data on livestock animal species. This collection references sheep
      QTLs.
    homepage: https://www.animalgenome.org/QTLdb
    id: '00000507'
    name: Animal Genome Sheep QTL
    namespaceEmbeddedInLui: false
    pattern: ^\d+$
    prefix: sheepqtldb
    sampleId: '19803'
    uri_format: https://www.animalgenome.org/QTLdb/q?id=QTL_ID:$1
  n2t:
    description: The Animal Quantitative Trait Loci (QTL) database (Animal QTLdb)
      is designed to house publicly all available QTL and single-nucleotide polymorphism/gene
      association data on livestock animal species. This collection references sheep
      QTLs.
    example: '19803'
    homepage: http://www.animalgenome.org/cgi-bin/QTLdb/OA/index
    name: Animal QTL Sheep at Iowa State University
    namespaceEmbeddedInLui: false
    pattern: ^\d+$
    prefix: sheepqtldb
    uri_format: http://www.animalgenome.org/cgi-bin/QTLdb/OA/qdetails?QTL_ID=$1
  part_of: qtldb
  prefix: sheepqtldb
  prefixcommons:
    description: This Sheep Quantitative Trait Locus (QTL) database (Sheep QTLdb)
      has gathered all sheep QTL data published during the past 10+ years. The database
      and its peripheral tools make it possible to compare, confirm and locate on
      sheep chromosomes the most feasible location for genes responsible for quantitative
      trait important to sheep production.
    example: '66'
    homepage: http://www.animalgenome.org/cgi-bin/QTLdb/OA/index
    keywords:
    - DNA
    - genome
    name: Sheep Quantitative Trait Locus database
    pattern: ^\d+$
    prefix: sheepqtldb
    uri_format: http://www.animalgenome.org/cgi-bin/QTLdb/OA/qdetails?QTL_ID=$1
shex:
  contact:
    email: gregg@greggkellogg.net
    github: gkellogg
    name: Gregg Kellogg
    orcid: null
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: The Shape Expressions (ShEx) language describes RDF nodes and graph
    structures. A node constraint describes an RDF node (IRI, blank node or literal)
    and a shape describes the triples involving nodes in an RDF graph. These descriptions
    identify predicates and their associated cardinalities and datatypes. ShEx shapes
    can be used to communicate data structures associated with some process or interface,
    generate or validate data, or drive user interfaces.
  download_rdf: https://www.w3.org/ns/shex.ttl
  example: TripleExpression
  homepage: http://www.w3.org/ns/shex#
  keywords:
  - metadata
  - rdf
  - semantic web
  mappings:
    zazuko: shex
  name: Shape Expression Vocabulary
  pattern: ^\w+$
  preferred_prefix: shex
  prefix: shex
  repository: https://github.com/shexspec/shexspec.github.io
  uri_format: http://www.w3.org/ns/shex#$1
  zazuko:
    prefix: shex
    uri_format: http://www.w3.org/ns/shex#$1
shibase:
  comment: This resource doesn't exist on the web anymore
  deprecated: true
  mappings:
    prefixcommons: shibase
  prefix: shibase
  prefixcommons:
    description: The database focuses on the comparative genomics of Shigella and
      provides a way to summarize large volumes of genomic and comparison data in
      a visually intuitive format.
    example: SDY2614
    homepage: http://www.mgc.ac.cn/ShiBASE/
    keywords:
    - genome
    name: ShiBASE
    pattern: ^[A-Z]+\d+$
    prefix: shibase
    uri_format: http://www.mgc.ac.cn/cgi-bin/ShiBASE/ShiBASE_query.cgi?synonym=$1
  reviewer:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
shsh:
  description: This shapes graph can be used to validate SHACL shapes graphs against
    a subset of the syntax rules.
  download_rdf: http://www.w3.org/ns/shacl-shacl
  example: ListShape
  homepage: http://www.w3.org/ns/shacl-shacl
  mappings:
    zazuko: shsh
  name: SHACL in SHACL
  prefix: shsh
  zazuko:
    prefix: shsh
    uri_format: http://www.w3.org/ns/shacl-shacl#$1
sibo:
  aberowl:
    description: Social Behavior in insects
    download_owl: http://aber-owl.net/media/ontologies/SIBO/3/sibo.owl
    homepage: https://github.com/obophenotype/sibo
    name: Social Insect Behavior Ontology
    prefix: SIBO
  biocontext:
    prefix: SIBO
  bioportal:
    contact:
      email: cjmungall@lbl.gov
      name: Chris Mungall
    description: Social behavior in insects.
    homepage: https://github.com/obophenotype/sibo
    name: Social Insect Behavior Ontology
    prefix: SIBO
  ecoportal:
    contact:
      email: cjmungall@lbl.gov
      name: Chris Mungall
    description: The Social Insect Behavior Ontology (SIBO) was created by Chris Smith.
      This ontology will eventually be integrated into the NBO ando contains collected
      terms for Chemical, Anatomy, Behavior, Species. The most developed use cases
      are for Pogonomyrmex harvester ant foraging and apis mellifera honeybee colony
      defense.
    homepage: https://github.com/obophenotype/sibo
    license: CC-BY-3.0
    name: Social Insect Behavior Ontology
    prefix: SIBO
    repository: https://github.com/obophenotype/sibo
    version: '1.2'
  example: 0000509
  fairsharing:
    abbreviation: SIBO
    description: 'The Social Inset Behavior Ontology mostly contains terms related
      to Chemical, Anatomy, Behavior, Species. The most developed use cases are for
      Pogonomyrmex harvester ant foraging and apis mellifera honeybee colony defense.

      '
    homepage: https://github.com/obophenotype/sibo
    license: CC-BY-3.0
    name: Social Inset Behavior Ontology
    prefix: FAIRsharing.q09hck
    subjects:
    - Biology
  mappings:
    aberowl: SIBO
    biocontext: SIBO
    bioportal: SIBO
    ecoportal: SIBO
    fairsharing: FAIRsharing.q09hck
    obofoundry: sibo
    ols: sibo
    ontobee: SIBO
    wikidata.entity: Q114677952
  obofoundry:
    contact: cjmungall@lbl.gov
    contact.label: Chris Mungall
    contact.orcid: 0000-0002-6601-2165
    deprecated: true
    description: Social Behavior in insects
    domain: biological systems
    download.obo: http://purl.obolibrary.org/obo/sibo.obo
    download.owl: http://purl.obolibrary.org/obo/sibo.owl
    homepage: https://github.com/obophenotype/sibo
    license: CC BY 3.0
    license.url: http://creativecommons.org/licenses/by/3.0/
    name: Social Insect Behavior Ontology
    preferredPrefix: SIBO
    prefix: sibo
    repository: https://github.com/obophenotype/sibo
  ols:
    description: Social Behavior in insects
    download_owl: http://purl.obolibrary.org/obo/sibo.owl
    homepage: https://github.com/obophenotype/sibo
    name: Social Insect Behavior Ontology
    prefix: sibo
    tracker: https://github.com/obophenotype/sibo/issues
  ontobee:
    library: Library
    name: Social Insect Behavior Ontology
    prefix: SIBO
  pattern: ^\d{7}$
  prefix: sibo
sider.drug:
  biocontext:
    prefix: SIDER.DRUG
  mappings:
    biocontext: SIDER.DRUG
    miriam: sider.drug
    n2t: sider.drug
  miriam:
    deprecated: false
    description: SIDER (Side Effect Resource) is a public, computer-readable side
      effect resource that connects drugs to side effect terms. It aggregates dispersed
      public information on side effects. This collection references drugs in SIDER.
    homepage: http://sideeffects.embl.de/
    id: '00000435'
    name: SIDER Drug
    namespaceEmbeddedInLui: false
    pattern: ^\d+$
    prefix: sider.drug
    sampleId: '2244'
    uri_format: http://sideeffects.embl.de/drugs/$1/
  n2t:
    description: SIDER (Side Effect Resource) is a public, computer-readable side
      effect resource that connects drugs to side effect terms. It aggregates dispersed
      public information on side effects. This collection references drugs in SIDER.
    example: '2244'
    homepage: http://sideeffects.embl.de/
    name: SIDER Drug v2 at EMBL (Heidelberg)
    namespaceEmbeddedInLui: false
    pattern: ^\d+$
    prefix: sider.drug
    uri_format: http://sideeffects.embl.de/drugs/$1/
  prefix: sider.drug
  uri_format: http://sideeffects.embl.de/drugs/$1
sider.effect:
  biocontext:
    prefix: SIDER.EFFECT
  mappings:
    biocontext: SIDER.EFFECT
    miriam: sider.effect
    n2t: sider.effect
  miriam:
    deprecated: false
    description: SIDER (Side Effect Resource) is a public, computer-readable side
      effect resource that connects drugs to side effect terms. It aggregates dispersed
      public information on side effects. This collection references side effects
      of drugs as referenced in SIDER.
    homepage: http://sideeffects.embl.de/
    id: '00000436'
    name: SIDER Side Effect
    namespaceEmbeddedInLui: false
    pattern: ^C\d+$
    prefix: sider.effect
    sampleId: C0017565
    uri_format: http://sideeffects.embl.de/se/$1/
  n2t:
    description: SIDER (Side Effect Resource) is a public, computer-readable side
      effect resource that connects drugs to side effect terms. It aggregates dispersed
      public information on side effects. This collection references side effects
      of drugs as referenced in SIDER.
    example: C0017565
    homepage: http://sideeffects.embl.de/
    name: SIDER Side Effect v2 at EMBL (Heidelberg)
    namespaceEmbeddedInLui: false
    pattern: ^C\d+$
    prefix: sider.effect
    uri_format: http://sideeffects.embl.de/se/$1/
  prefix: sider.effect
  provides: umls
  uri_format: http://sideeffects.embl.de/se/$1
sigmaaldrich:
  cellosaurus:
    category: Cell line collections (Providers)
    homepage: https://www.sigmaaldrich.com
    name: Sigma-Aldrich cell line products
    prefix: Sigma-Aldrich
    uri_format: https://www.sigmaaldrich.com/catalog/product/sigma/$1
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: Sigma Aldrich is a life sciences supply vendor.
  example: HPA000698
  github_request_issue: 216
  homepage: https://www.sigmaaldrich.com
  keywords:
  - biology
  - chemistry
  - life sciences
  - vendor
  mappings:
    cellosaurus: Sigma-Aldrich
    pathguide: '236'
  name: Sigma Aldrich
  pathguide:
    abbreviation: SIGMA-ALDRICH
    homepage: http://www.sigmaaldrich.com/Area_of_Interest/Life_Science/Cell_Signaling/Scientific_Resources/Pathway_Slides___Charts.html
    name: Cell Signalling Pathway Slides & Charts
    prefix: '236'
  prefix: sigmaaldrich
  uri_format: https://www.sigmaaldrich.com/US/en/product/sigma/$1
signaling-gateway:
  biocontext:
    prefix: SIGNALING-GATEWAY
  contact:
    email: kenan@ucsd.edu
    github: null
    name: Kenan Azam
    orcid: 0000-0001-7016-8624
  mappings:
    biocontext: SIGNALING-GATEWAY
    miriam: signaling-gateway
    n2t: signaling-gateway
    pathguide: '87'
    prefixcommons: signaling-gateway
  miriam:
    deprecated: true
    description: The Signaling Gateway provides  information on  mammalian proteins
      involved in cellular signaling.
    homepage: http://www.signaling-gateway.org/molecule
    id: '00000045'
    name: Signaling Gateway
    namespaceEmbeddedInLui: false
    pattern: ^A\d{6}$
    prefix: signaling-gateway
    sampleId: A001094
    uri_format: http://www.signaling-gateway.org/molecule/query?afcsid=$1
  n2t:
    description: The Signaling Gateway provides  information on  mammalian proteins
      involved in cellular signaling.
    example: A001094
    homepage: http://www.signaling-gateway.org/molecule
    name: Signaling Gateway Molecule Pages
    namespaceEmbeddedInLui: false
    pattern: A\d{6}$
    prefix: signaling-gateway
    uri_format: http://www.signaling-gateway.org/molecule/query?afcsid=$1
  pathguide:
    abbreviation: Signaling Gateway
    homepage: http://www.signaling-gateway.org/molecule/
    keywords:
    - BioPAX
    - SBML
    name: UCSD-Nature Signaling Gateway Molecule Pages
    prefix: '87'
  prefix: signaling-gateway
  prefixcommons:
    description: The Signaling Gateway provides  information on  mammalian proteins
      involved in cellular signaling.
    example: A001094
    homepage: http://www.signaling-gateway.org/molecule/
    keywords:
    - pathway
    - protein
    - small molecule
    license: http://www.signaling-gateway.org/copyright/afcs.html
    name: The Signaling Gateway
    pattern: ^A\d{6}$
    prefix: signaling-gateway
    pubmed_ids:
    - '17965093'
    - '12478304'
    - '21505029'
    synonyms:
    - afcs
    - sgmp
    uri_format: http://www.signaling-gateway.org/molecule/query?afcsid=$1
  publications:
  - doi: 10.1093/bioinformatics/btr190
    pmc: PMC3106186
    pubmed: '21505029'
    title: Signaling gateway molecule pages--a data model perspective
    year: 2011
  - doi: 10.1093/nar/gkm907
    pmc: PMC2238911
    pubmed: '17965093'
    title: The Molecule Pages database
    year: 2007
  - doi: 10.1038/nature01307
    pmc: null
    pubmed: '12478304'
    title: The Molecule Pages database
    year: 2002
  - doi: null
    pmc: null
    pubmed: '17965093'
    title: null
    year: null
  - doi: null
    pmc: null
    pubmed: '12478304'
    title: null
    year: null
  - doi: null
    pmc: null
    pubmed: '21505029'
    title: null
    year: null
signor:
  domain: protein complex
  example: SIGNOR-C41
  fairsharing:
    abbreviation: SIGNOR
    contact:
      email: gianni.cesareni@torvergata.it
      name: Gianni Cesareni
      orcid: 0000-0002-9528-6018
    description: SIGNOR, the SIGnaling Network Open Resource, organizes and stores
      in a structured format signaling information published in the scientific literature.
      The captured information is stored as binary causative relationships between
      biological entities and can be represented graphically as activity flow. The
      entire network can be freely downloaded and used to support logic modeling or
      to interpret high content datasets. Each relationship is linked to the literature
      reporting the experimental evidence. In addition each node is annotated with
      the chemical inhibitors that modulate its activity. The signaling information
      is mapped to the human proteome even if the experimental evidence is based on
      experiments on mammalian model organisms.
    homepage: https://signor.uniroma2.it/user_guide.php
    name: SIGnaling Network Open Resource
    prefix: FAIRsharing.ss78t4
    publications:
    - doi: 10.1093/nar/gkv1048
      pubmed_id: 26467481
      title: 'SIGNOR: a database of causal relationships between biological entities.'
    subjects:
    - Biology
  license: CC-BY-NC-4.0
  logo: https://signor.uniroma2.it/img/signor_logo_noWhite.png
  mappings:
    fairsharing: FAIRsharing.ss78t4
    miriam: signor
    pathguide: '599'
    uniprot: DB-0206
  miriam:
    deprecated: false
    description: SIGNOR, the SIGnaling Network Open Resource, organizes and stores
      in a structured format signaling information published in the scientific literature.
    homepage: https://signor.uniroma2.it/
    id: 00000808
    name: SIGNOR
    namespaceEmbeddedInLui: false
    pattern: ^SIGNOR\-[A-Z]+\d+$
    prefix: signor
    sampleId: SIGNOR-C2
    uri_format: https://signor.uniroma2.it/relation_result.php?id=$1
  name: Signaling Network Open Resource
  part_of_database: signor
  pathguide:
    abbreviation: SIGNOR
    homepage: http://signor.uniroma2.it/
    keywords:
    - SBML
    name: The SIGnaling Network Open Resource
    prefix: '599'
  prefix: signor
  publications:
  - doi: 10.1093/nar/gkac883
    pmc: PMC9825604
    pubmed: '36243968'
    title: 'SIGNOR 3.0, the SIGnaling network open resource 3.0: 2022 update'
    year: 2022
  - doi: 10.1093/nar/gkv1048
    pmc: PMC4702784
    pubmed: '26467481'
    title: 'SIGNOR: a database of causal relationships between biological entities'
    year: 2015
  synonyms:
  - SIGNOR
  uniprot:
    abbreviation: SIGNOR
    category: Enzyme and pathway databases
    homepage: https://signor.uniroma2.it/
    name: SIGNOR Signaling Network Open Resource
    prefix: DB-0206
    publications:
    - doi: 10.1093/nar/gkac883
      pubmed: '36243968'
    uri_format: https://signor.uniroma2.it/relation_result.php?id=$1
signor.relation:
  comment: Currently, you can put a SIGNOR relation ID into the main page search box
    and it will resolve, but there is not currently a way to resolve them via a URL
    pattern
  contributor:
    email: benjamin_gyori@hms.harvard.edu
    github: bgyori
    name: Benjamin M. Gyori
    orcid: 0000-0001-9439-5346
  description: Identifiers for relationships between proteins and complexes, along
    with their type and provenance
  domain: relationship
  example: SIGNOR-252737
  github_request_issue: 604
  homepage: https://signor.uniroma2.it
  keywords:
  - protein-protein interactions
  logo: https://signor.uniroma2.it/img/signor_logo_noWhite.png
  name: SIGNOR Relation
  part_of_database: signor
  pattern: ^SIGNOR-\d+$
  prefix: signor.relation
  reviewer:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
silva.taxon:
  contact:
    email: lorenz.reimer@dsmz.de
    github: null
    name: Lorenz Reimer
    orcid: 0000-0002-7805-0660
  contact_group_email: contact@arb-silva.de
  contributor:
    email: jplfaria@anl.gov
    github: jplfaria
    name: Jose P. Faria
    orcid: 0000-0001-9302-7250
  description: 'SILVA is a resource of aligned ribosomal RNA (rRNA) gene sequences
    for Bacteria, Archaea, and Eukaryotes.


    It assigns internal, auto-incremented integer identifiers to taxa. However, these
    identifiers are not persistent nor unique - if the label for a taxon is changed,
    it assigned a new identifier and the old identifier is removed.'
  example: '11084'
  github_request_issue: 1306
  homepage: https://www.arb-silva.de
  license: CC-BY-SA-4.0
  logo: https://www.arb-silva.de/fileadmin/graphics_general/main/dissemination/silva-sticker-1_2_ext_33.png
  name: SILVA Taxon
  pattern: ^\d+$
  prefix: silva.taxon
  publications:
  - doi: 10.1093/nar/gkt1209
    pmc: PMC3965112
    pubmed: '24293649'
    title: The SILVA and "All-species Living Tree Project (LTP)" taxonomic frameworks
    year: 2014
  - doi: 10.1093/nar/gks1219
    pmc: PMC3531112
    pubmed: '23193283'
    title: 'The SILVA ribosomal RNA gene database project: improved data processing
      and web-based tools'
    year: 2012
  reviewer:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
sio:
  aberowl:
    description: The semanticscience integrated ontology (SIO) provides a simple,
      integrated upper level ontology (types, relations) for consistent knowledge
      representation across physical, processual and informational entities. It provides
      vocabulary for the Bio2RDF (http://bio2rdf.org) and SADI (http://sadiframework.org)
      projects.
    download_owl: http://aber-owl.net/media/ontologies/SIO/94/sio.owl
    homepage: http://sio.semanticscience.org
    name: Semanticscience Integrated Ontology
    prefix: SIO
    version: '1.59'
  agroportal:
    contact:
      email: michel.dumontier@gmail.com
      name: Michel Dumontier
    description: 'The semanticscience integrated ontology (SIO) provides a simple,
      integrated ontology (types, relations) for objects, processes and their attributes.
      This project provides foundational support for the Bio2RDF (http://bio2rdf.org)
      and SADI (http://sadiframework.org) projects. website: http://semanticscience.org
      email: sio-ontology@googlegroups.com mailing list: http://groups.google.com/group/sio-ontology
      , processes and their attributes. This project provides foundational support
      for the Bio2RDF (http://bio2rdf.org) and SADI (http://sadiframework.org) projects.'
    example_uri: http://semanticscience.org/resource/SIO_000837
    homepage: http://sio.semanticscience.org/
    license: CC-BY-4.0
    name: Semanticscience Integrated Ontology
    prefix: SIO
    publications:
    - http://www.jbiomedsem.com/content/5/1/14
    repository: https://github.com/micheldumontier/semanticscience
    version: '1.59'
  banana: SIO
  banana_peel: _
  biocontext:
    prefix: SIO
    uri_format: http://semanticscience.org/resource/SIO_$1
  biolink:
    is_identifiers: false
    is_obo: false
    prefix: SIO
    uri_format: http://semanticscience.org/resource/SIO_$1
  bioportal:
    contact:
      email: michel.dumontier@gmail.com
      name: Michel Dumontier
    description: The semanticscience integrated ontology (SIO) provides a simple,
      integrated upper level ontology (types, relations) for consistent knowledge
      representation across physical, processual and informational entities. It provides
      vocabulary for the Bio2RDF (http://bio2rdf.org) and SADI (http://sadiframework.org)
      projects.
    homepage: http://sio.semanticscience.org
    name: Semanticscience Integrated Ontology
    prefix: SIO
    publications:
    - http://sio.semanticscience.org
    version: '1.59'
  contact:
    email: michel.dumontier@gmail.com
    github: micheldumontier
    name: Michel Dumontier
    orcid: 0000-0003-4727-9435
  example: 000912
  fairsharing:
    abbreviation: SIO
    contact:
      email: michel.dumontier@gmail.com
      name: Michel Dumontier
      orcid: 0000-0003-4727-9435
    description: The semanticscience integrated ontology (SIO) provides a simple,
      integrated upper level ontology (types, relations) for consistent knowledge
      representation across physical, processual and informational entities. It provides
      vocabulary for the Bio2RDF (http://bio2rdf.org) and SADI (http://sadiframework.org)
      projects.
    domains:
    - Knowledge representation
    homepage: https://github.com/MaastrichtU-IDS/semanticscience
    license: CC-BY-4.0
    name: Semanticscience Integrated Ontology
    prefix: FAIRsharing.dpkb5f
    publications:
    - doi: 10.1186/2041-1480-5-14
      pubmed: '24602174'
      title: The Semanticscience Integrated Ontology (SIO) for biomedical research
        and knowledge discovery
      year: 2014
    repository: https://github.com/MaastrichtU-IDS/semanticscience/issues
    subjects:
    - Natural Science
    - Subject Agnostic
  lov:
    description: The semanticscience integrated ontology (SIO) provides a simple,
      integrated ontology (types, relations) for objects, processes and their attributes.
      This project provides foundational support for the Bio2RDF (http://bio2rdf.org)
      and SADI (http://sadiframework.org) projects.
    homepage: http://semanticscience.org
    keywords:
    - Biology
    modified: '2016-09-27'
    name: Semanticscience Integrated Ontology
    prefix: sio
    uri_prefix: http://semanticscience.org/resource/$1
  mappings:
    aberowl: SIO
    agroportal: SIO
    biocontext: SIO
    biolink: SIO
    bioportal: SIO
    fairsharing: FAIRsharing.dpkb5f
    lov: sio
    miriam: sio
    ols: sio
    ontobee: SIO
    tib: sio
  miriam:
    deprecated: false
    description: The semanticscience integrated ontology (SIO) provides a simple,
      integrated upper level ontology (types, relations) for consistent knowledge
      representation across physical, processual and informational entities.
    homepage: https://www.ebi.ac.uk/ols4/ontologies/sio
    id: 00000851
    name: Semanticscience Integrated Ontology
    namespaceEmbeddedInLui: false
    pattern: ^SIO_\d{6,6}$
    prefix: sio
    sampleId: SIO_000276
    uri_format: https://www.ebi.ac.uk/ols4/ontologies/sio/terms?short_form=$1
  ols:
    contact: sio-ontology@googlegroups.com
    description: The Semanticscience Integrated Ontology (SIO) provides a simple,
      integrated ontology of types and relations for rich description of objects,
      processes and their attributes.
    download_owl: https://raw.githubusercontent.com/micheldumontier/semanticscience/master/ontology/sio/release/sio-release.owl
    homepage: https://github.com/micheldumontier/semanticscience
    name: Semanticscience Integrated Ontology
    prefix: sio
    uri_format: http://semanticscience.org/resource/SIO_$1
    version: '1.59'
    version.iri: http://semanticscience.org/ontology/sio/v1.59/sio-release.owl
  ontobee:
    library: Not Specified/No
    name: Semanticscience Integrated Ontology
    prefix: SIO
  pattern: ^\d{6}$
  prefix: sio
  publications:
  - doi: 10.1186/2041-1480-5-14
    pmc: PMC4015691
    pubmed: '24602174'
    title: The Semanticscience Integrated Ontology (SIO) for biomedical research and
      knowledge discovery
    year: 2014
  repository: https://github.com/micheldumontier/semanticscience
  tib:
    description: The Semanticscience Integrated Ontology (SIO) provides a simple,
      integrated ontology of types and relations for rich description of objects,
      processes and their attributes.
    download_owl: https://raw.githubusercontent.com/micheldumontier/semanticscience/master/ontology/sio/release/sio-release.owl
    homepage: https://github.com/MaastrichtU-IDS/semanticscience
    keywords:
    - NFDI4ING
    - NFDI4CHEM
    - ESS
    name: Semanticscience Integrated Ontology (SIO)
    prefix: sio
    uri_format: http://semanticscience.org/resource/SIO_$1
    version.iri: http://semanticscience.org/ontology/sio/v1.59/sio-release.owl
  uri_format: https://semanticscience.org/resource/SIO_$1
sioc.access:
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: Extends the SIOC Core Ontology (Semantically-Interlinked Online Communities)
    by defining basic information on permissions and access rights.
  download_rdf: http://rdfs.org/sioc/access#
  example: Permission
  homepage: http://rdfs.org/sioc/spec/
  license: CC-BY-1.0
  name: Semantically-Interlinked Online Communities Access Ontology
  part_of_database: sioc
  prefix: sioc.access
  rdf_uri_format: http://rdfs.org/sioc/access#$1
  uri_format: http://rdfs.org/sioc/access#$1
sioc.actions:
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: An ontology of predicates for actions in SIOC
  download_rdf: http://rdfs.org/sioc/actions#
  example: DigitalArtifact
  homepage: http://rdfs.org/sioc/spec/
  license: CC-BY-1.0
  name: Semantically-Interlinked Online Communities Actions Ontology
  part_of_database: sioc
  prefix: sioc.actions
  rdf_uri_format: http://rdfs.org/sioc/actions#$1
  uri_format: http://rdfs.org/sioc/actions#$1
sioc.argument:
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: A vocabulary of argumentation predicates for SIOC
  download_rdf: http://rdfs.org/sioc/argument#
  example: decides
  homepage: http://rdfs.org/sioc/spec/
  license: CC-BY-1.0
  name: Semantically-Interlinked Online Communities Argumentation Ontology
  part_of_database: sioc
  prefix: sioc.argument
  rdf_uri_format: http://rdfs.org/sioc/argument#$1
  uri_format: http://rdfs.org/sioc/argument#$1
sioc.core:
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: Semantically-Interlinked Online Communities, or SIOC, is an attempt
    to link online community sites, to use Semantic Web technologies to describe the
    information that communities have about their structure and contents, and to find
    related information and new connections between content items and other community
    objects. SIOC is based around the use of machine-readable information provided
    by these sites.
  download_rdf: http://rdfs.org/sioc/ns#
  example: Item
  homepage: http://rdfs.org/sioc/spec/
  license: CC-BY-1.0
  lov:
    description: SIOC is an ontology for describing the information in online communities.
    homepage: http://rdfs.org/sioc/spec/
    keywords:
    - Society
    modified: '2010-03-25'
    name: Semantically-Interlinked Online Communities
    prefix: sioc
    uri_prefix: http://rdfs.org/sioc/ns#$1
  mappings:
    lov: sioc
    zazuko: sioc
  name: Semantically-Interlinked Online Communities Core Ontology
  part_of_database: sioc
  prefix: sioc.core
  rdf_uri_format: http://rdfs.org/sioc/ns#$1
  synonyms:
  - sioc
  uri_format: http://rdfs.org/sioc/ns#$1
  zazuko:
    prefix: sioc
    uri_format: http://rdfs.org/sioc/ns#$1
sioc.quote:
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: Extends the SIOC Core Ontology (Semantically-Interlinked Online Communities)
    by defining basic information on community-related web services.
  download_rdf: http://rdfs.org/sioc/services#
  example: has_service
  homepage: http://rdfs.org/sioc/spec/
  license: CC-BY-1.0
  name: Semantically-Interlinked Online Communities Services Ontology - Quote Ontology
  part_of_database: sioc
  prefix: sioc.quote
  rdf_uri_format: http://rdfs.org/sioc/services#$1
  uri_format: http://rdfs.org/sioc/services#$1
sioc.swan:
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: Mappings from SIOC to SWAN, with a small number of aux terms
  download_rdf: http://rdfs.org/sioc/swan#
  example: OnlineJournal
  homepage: http://rdfs.org/sioc/spec/
  license: CC-BY-1.0
  name: Semantically-Interlinked Online Communities Services Ontology - SWAN Mapping
  part_of_database: sioc
  prefix: sioc.swan
  rdf_uri_format: http://rdfs.org/sioc/swan#$1
  uri_format: http://rdfs.org/sioc/swan#$1
sioc.types:
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: Extends the SIOC Core Ontology (Semantically-Interlinked Online Communities)
    by defining subclasses and subproperties of SIOC terms.
  download_rdf: http://rdfs.org/sioc/types#
  example: AddressBook
  homepage: http://rdfs.org/sioc/spec/
  license: CC-BY-1.0
  name: Semantically-Interlinked Online Communities Types Ontology
  part_of_database: sioc
  prefix: sioc.types
  rdf_uri_format: http://rdfs.org/sioc/types#$1
  uri_format: http://rdfs.org/sioc/types#$1
siren:
  agroportal:
    contact:
      email: patrice.buche@inrae.fr
      name: Buche
    description: This ontology contains a OWL representation of SIREN food terms using
      Langual thesaurus. SIREN is the Scientific Information and Retrieval Exchange
      Network of the US Food and Drug administration.
    example_uri: http://purl.obolibrary.org/obo/FOODON_03306963
    name: SIREN
    prefix: SIREN
  comment: appears in FOODON, there is no website other than the spreadsheet referenced
    below on langual's site
  contact:
    email: patrice.buche@inrae.fr
    github: null
    name: Patrice Buche
    orcid: 0000-0002-9134-5404
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: A modern method of records management and an automated cross-referenced
    subject index for accurate and comprehensive information retrieval developed by
    the US FDA's Bureau of Foods
  example: F11903
  homepage: https://www.langual.org/langual_indexed_datasets.asp
  mappings:
    agroportal: SIREN
  name: Scientific Information Retrieval and Exchange Network
  pattern: ^F\d+$
  prefix: siren
  publications:
  - doi: 10.1093/jaoac/65.5.1268
    pmc: null
    pubmed: null
    title: 'SIREN: Data Base Approach to Scientific Information Handling in the Bureau
      of Foods, Food and Drug Administration'
    year: 1982
  references:
  - https://github.com/FoodOntology/foodon/issues/267
  - https://www.langual.org/download/IndexedDatasets/FDA/SIREN%20(updated).TXT
  synonyms:
  - SUBSET_SIREN
sisu:
  biocontext:
    prefix: SISU
  fairsharing:
    abbreviation: SISu
    contact:
      email: hannele.laivuori@helsinki.fi
      name: Hannele Laivuori
      orcid: 0000-0003-3212-7826
    description: The Sequencing Initiative Suomi (SISu) search engine offers a way
      to search for data on sequence variants in the Finnish population. It provides
      valuable summary data for researchers and clinicians as well as other researchers
      with an interest in genetics in Finland. With SISu, you can examine the attributes
      and appearance of different variants in Finnish cohorts and see their aggregate
      distribution in Finland visualized on a map. The SISu project is an international
      collaboration between multiple research groups aiming to build tools for genomic
      medicine.
    homepage: http://www.sisuproject.fi/
    name: Sequencing Initiative Suomi
    prefix: FAIRsharing.t1a232
    publications:
    - doi: 10.1371/journal.pone.0128524
      pubmed_id: 26030606
      title: Targeted resequencing of the pericentromere of chromosome 2 linked to
        constitutional delay of growth and puberty.
    - doi: 10.1371/journal.pgen.1004494
      pubmed_id: 25078778
      title: Distribution and medical impact of loss-of-function variants in the Finnish
        founder population.
    subjects:
    - Medicine
    - Genomics
    - Biomedical Science
    - Epidemiology
    - Preclinical Studies
  mappings:
    biocontext: SISU
    fairsharing: FAIRsharing.t1a232
    miriam: sisu
    n2t: sisu
  miriam:
    deprecated: false
    description: The Sequencing Initiative Suomi (SISu) project is an international
      collaboration to harmonize and aggregate whole genome and exome sequence data
      from Finnish samples, providing data for researchers and clinicians. The SISu
      project allows for the search of variants to determine their attributes and
      occurrence in Finnish cohorts, and provides summary data on single nucleotide
      variants and indels from exomes, sequenced in disease-specific and population
      genetic studies.
    homepage: http://www.sisuproject.fi/
    id: '00000624'
    name: SISu
    namespaceEmbeddedInLui: false
    pattern: ^[0-9]+:[0-9]+$
    prefix: sisu
    sampleId: 17:41223048
    uri_format: http://search.sisuproject.fi/#/variant/$1
  n2t:
    description: The Sequencing Initiative Suomi (SISu) project is an international
      collaboration to harmonize and aggregate whole genome and exome sequence data
      from Finnish samples, providing data for researchers and clinicians. The SISu
      project allows for the search of variants to determine their attributes and
      occurrence in Finnish cohorts, and provides summary data on single nucleotide
      variants and indels from exomes, sequenced in disease-specific and population
      genetic studies.
    example: 17:41223048
    homepage: http://www.sisuproject.fi/
    name: SISu
    namespaceEmbeddedInLui: false
    pattern: ^[0-9]+:[0-9]+$
    prefix: sisu
    uri_format: http://search.sisuproject.fi/#/variant/$1
  name: Sequencing Initiative Suomi
  prefix: sisu
  publications:
  - doi: 10.1371/journal.pone.0128524
    pmc: PMC4452275
    pubmed: '26030606'
    title: Targeted resequencing of the pericentromere of chromosome 2 linked to constitutional
      delay of growth and puberty
    year: 2015
  - doi: 10.1371/journal.pgen.1004494
    pmc: PMC4117444
    pubmed: '25078778'
    title: Distribution and medical impact of loss-of-function variants in the Finnish
      founder population
    year: 2014
  - doi: 10.1371/journal.pone.0128524
    pmc: null
    pubmed: null
    title: Targeted resequencing of the pericentromere of chromosome 2 linked to constitutional
      delay of growth and puberty.
    year: null
  - doi: 10.1371/journal.pgen.1004494
    pmc: null
    pubmed: null
    title: Distribution and medical impact of loss-of-function variants in the Finnish
      founder population.
    year: null
  - doi: 10.1371/journal.pone.0128524
    pmc: null
    pubmed: null
    title: Targeted resequencing of the pericentromere of chromosome 2 linked to constitutional
      delay of growth and puberty.
    year: null
  - doi: 10.1371/journal.pgen.1004494
    pmc: null
    pubmed: null
    title: Distribution and medical impact of loss-of-function variants in the Finnish
      founder population.
    year: null
sitex:
  biocontext:
    prefix: SITEX
  contact:
    email: imedvedeva@celgene.com
    github: imedvedeva-celgene
    name: Irina Medvedeva
    orcid: 0000-0003-2802-8198
  fairsharing:
    abbreviation: SitEx
    description: SitEx is a database containing information on eukaryotic protein
      functional sites. It stores the amino acid sequence positions in the functional
      site, in relation to the exon structure of encoding gene This can be used to
      detect the exons involved in shuffling in protein evolution, or to design protein-engineering
      experiments.
    homepage: http://www-bionet.sscc.ru/sitex/
    name: SitEx database of eukaryotic protein functional sites
    prefix: FAIRsharing.5mr9c5
    publications:
    - doi: 10.1093/nar/gkr1187
      pubmed_id: 22139920
      title: 'SitEx: a computer system for analysis of projections of protein functional
        sites on eukaryotic genes.'
    subjects:
    - Life Science
  mappings:
    biocontext: SITEX
    fairsharing: FAIRsharing.5mr9c5
    miriam: sitex
    n2t: sitex
    prefixcommons: sitex
  miriam:
    deprecated: true
    description: SitEx is a database containing information on eukaryotic protein
      functional sites. It stores the amino acid sequence positions in the functional
      site, in relation to the exon structure of encoding gene This can be used to
      detect the exons involved in shuffling in protein evolution, or to design protein-engineering
      experiments.
    homepage: http://www-bionet.sscc.ru/sitex/
    id: '00000252'
    name: SitEx
    namespaceEmbeddedInLui: false
    pattern: ^\d+$
    prefix: sitex
    sampleId: '1000'
    uri_format: http://www-bionet.sscc.ru/sitex/index.php?siteid=$1
  n2t:
    description: SitEx is a database containing information on eukaryotic protein
      functional sites. It stores the amino acid sequence positions in the functional
      site, in relation to the exon structure of encoding gene This can be used to
      detect the exons involved in shuffling in protein evolution, or to design protein-engineering
      experiments.
    example: '1000'
    homepage: http://www-bionet.sscc.ru/sitex/
    name: SitEx at Novosibirsk State University
    namespaceEmbeddedInLui: false
    pattern: ^\d+$
    prefix: sitex
    uri_format: http://www-bionet.sscc.ru/sitex/index.php?siteid=$1
  prefix: sitex
  prefixcommons:
    description: SitEx is a database containing information on eukaryotic protein
      functional sites. It stores the amino acid sequence positions in the functional
      site, in relation to the exon structure of encoding gene This can be used to
      detect the exons involved in shuffling in protein evolution, or to design protein-engineering
      experiments.
    example: '1000'
    homepage: http://www-bionet.sscc.ru/sitex/
    keywords:
    - domain
    - eukaryotic
    - sequence
    - structure
    name: SitEx database of eukaryotic protein functional sites
    pattern: ^\d+$
    prefix: sitex
    pubmed_ids:
    - '22139920'
    uri_format: http://www-bionet.sscc.ru/sitex/index.php?siteid=$1
  publications:
  - doi: 10.1093/nar/gkr1187
    pmc: PMC3245165
    pubmed: '22139920'
    title: 'SitEx: a computer system for analysis of projections of protein functional
      sites on eukaryotic genes'
    year: 2011
  - doi: 10.1093/nar/gkr1187
    pmc: null
    pubmed: null
    title: 'SitEx: a computer system for analysis of projections of protein functional
      sites on eukaryotic genes.'
    year: null
  - doi: null
    pmc: null
    pubmed: '22139920'
    title: null
    year: null
  - doi: 10.1093/nar/gkr1187
    pmc: null
    pubmed: null
    title: 'SitEx: a computer system for analysis of projections of protein functional
      sites on eukaryotic genes.'
    year: null
  - doi: null
    pmc: null
    pubmed: '22139920'
    title: null
    year: null
skip:
  cellosaurus:
    category: Cell line databases/resources
    homepage: https://www.skip.stemcellinformatics.org/en/
    name: Stemcell Knowledge and Information Portal
    prefix: SKIP
    uri_format: https://skip.stemcellinformatics.org/SKIPSearch/cell_line_detail?accession=$1
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: SKIP is aiming to promote the exchange of information and joint research
    between researchers by aggregating various information of stem cells (iPS cells,
    iPS cells derived from patients, etc.) to stimulate research on disease and regenerative
    medicine.
  example: SKIP001214
  homepage: https://skip.stemcellinformatics.org/en/
  mappings:
    cellosaurus: SKIP
  name: Stemcell Knowledge and Information Portal
  pattern: ^SKIP\d+$
  prefix: skip
  uri_format: https://skip.stemcellinformatics.org/SKIPSearch/cell_line_detail?accession=$1
skm:
  mappings:
    miriam: skm
  miriam:
    deprecated: false
    description: 'Stress Knowledge Map (SKM, available at https://skm.nib.si) is a
      knowledge graph resulting from the integration of dispersed published information
      on plant molecular responses to biotic and abiotic stressors. '
    homepage: http://www.nib.si/eng/
    id: 00000968
    name: Stress Knowledge Map
    namespaceEmbeddedInLui: false
    pattern: ^rx[0-9]{5}$
    prefix: skm
    sampleId: rx00408
    uri_format: https://skm.nib.si/api/pss/reactions?reaction_id=$1&return_field=summary
  prefix: skm
skos:
  aberowl:
    description: This file is imported by vivo-core-1.5.owl. It contains terms relating
      to concepts from the http://www.w3.org/2004/02/skos/core# namespace of the SKOS
      (Simple Knowledge Organization System) ontology that are included in the vivo
      ontology.
    download_owl: http://aber-owl.net/media/ontologies/skos/1/skos.owl
    homepage: http://sourceforge.net/apps/mediawiki/vivo/index.php?title=Ontology
    name: SKOS (concepts)
    prefix: skos
    version: '1.5'
  bartoc:
    abbreviation: skos
    homepage: http://www.w3.org/2004/02/skos/core
    name: Simple Knowledge Organization System
    prefix: '18274'
  biocontext:
    prefix: skos
    uri_format: http://www.w3.org/2004/02/skos/core#$1
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: SKOS is an area of work developing specifications and standards to
    support the use of knowledge organization systems (KOS) such as thesauri, classification
    schemes, subject heading lists and taxonomies within the framework of the Semantic
    Web
  example: prefLabel
  fairsharing:
    abbreviation: SKOS
    contact:
      email: alistair.miles@linacre.ox.ac.uk
      name: Alistair Miles
      orcid: 0000-0001-9018-4680
    description: Simple Knowledge Organization System (SKOS) is a common data model
      for sharing and linking knowledge organization systems via the Web. Many knowledge
      organization systems, such as thesauri, taxonomies, classification schemes and
      subject heading systems, share a similar structure, and are used in similar
      applications. SKOS captures much of this similarity and makes it explicit, to
      enable data and technology sharing across diverse applications. The SKOS data
      model provides a standard, low-cost migration path for porting existing knowledge
      organization systems to the Semantic Web. SKOS also provides a lightweight,
      intuitive language for developing and sharing new knowledge organization systems.
      It may be used on its own, or in combination with formal knowledge representation
      languages such as the Web Ontology language (OWL). The main objective of SKOS
      is to enable easy sharing and linking of controlled structured vocabularies
      for semantic web.
    homepage: http://www.w3.org/TR/skos-reference
    name: Simple Knowledge Organization System
    prefix: FAIRsharing.48e326
    publications: []
    subjects:
    - Subject Agnostic
  homepage: https://www.w3.org/2004/02/skos/
  lov:
    description: The Simple Knowledge Organization System (SKOS) is a common data
      model for sharing and linking knowledge organization systems via the Semantic
      Web.
    homepage: http://www.w3.org/2009/08/skos-reference/skos.html
    keywords:
    - W3C Rec
    modified: '2009-08-18'
    name: Simple Knowledge Organization System
    prefix: skos
    uri_prefix: http://www.w3.org/2004/02/skos/core#$1
  mappings:
    aberowl: skos
    bartoc: '18274'
    biocontext: skos
    fairsharing: FAIRsharing.48e326
    lov: skos
    ols: skos
    tib: skos
    zazuko: skos
  name: Simple Knowledge Organization System
  ols:
    download_rdf: http://www.w3.org/TR/skos-reference/skos.rdf
    prefix: skos
    uri_format: http://www.w3.org/2004/02/skos/core#$1
  preferred_prefix: skos
  prefix: skos
  tib:
    description: An RDF vocabulary for describing the basic structure and content
      of concept schemes such as thesauri, classification schemes, subject heading
      lists, taxonomies, 'folksonomies', other types of controlled vocabulary, and
      also concept schemes embedded in glossaries and terminologies.
    download_rdf: https://www.w3.org/2009/08/skos-reference/skos.rdf
    homepage: https://www.w3.org/TR/skos-reference/
    keywords:
    - TIB
    - computer science
    name: SKOS Vocabulary
    prefix: skos
    uri_format: http://www.w3.org/2004/02/skos/core#$1
  uri_format: http://www.w3.org/2004/02/skos/core#$1
  zazuko:
    prefix: skos
    uri_format: http://www.w3.org/2004/02/skos/core#$1
skos.thes:
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: 'SKOS-Thes: An extension to SKOS based on the ISO 25964 data model.
    The ISO 25964 standard, published in 2011, covers all aspects of developing thesauri
    and setting up mappings across vocabularies to encourage high quality information
    retrieval across networked resources. [from https://www.dublincore.org/specifications/skos-thes/]'
  download_rdf: https://www.dublincore.org/specifications/skos-thes/ns/skos-thes.ttl
  example: CompoundEquivalence
  homepage: https://www.dublincore.org/specifications/skos-thes/ns/
  name: SKOS Thesaurus Extension
  prefix: skos.thes
  rdf_uri_format: http://purl.org/iso25964/skos-thes#$1
  synonyms:
  - skos-thes
  - skosthes
  uri_format: https://www.dublincore.org/specifications/skos-thes/ns/#$1
skosxl:
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: The Simple Knowledge Organization System (SKOS) is a common data model
    for sharing and linking knowledge organization systems via the Semantic Web. SKOS-XL
    defines an extension for the Simple Knowledge Organization System, providing additional
    support for describing and linking lexical entities.This document provides a brief
    description of the SKOS-XL vocabulary.
  example: literalForm
  homepage: http://www.w3.org/2008/05/skos-xl#
  keywords:
  - data model
  - metadata
  - semantic web
  - skos
  lov:
    description: SKOS-XL defines an extension for the Simple Knowledge Organization
      System, providing additional support for describing and linking lexical entities.
    homepage: http://www.w3.org/TR/skos-reference/skos-xl.html
    keywords:
    - W3C Rec
    modified: '2009-08-18'
    name: SKOS eXtension for Labels
    prefix: skosxl
    uri_prefix: http://www.w3.org/2008/05/skos-xl#$1
  mappings:
    lov: skosxl
    tib: skosxl
    zazuko: skosxl
  name: Simple Knowledge Organization System eXtension for Labels
  preferred_prefix: skosxl
  prefix: skosxl
  synonyms:
  - skos-xl
  - skos.xl
  tib:
    description: An RDF vocabulary extending SKOS and allowing the description and
      linking of lexical entities.
    download_rdf: https://www.w3.org/2009/08/skos-reference/skos-xl.rdf
    homepage: https://www.w3.org/TR/skos-reference/skos-xl.html
    keywords:
    - TIB
    - computer science
    name: SKOS XL Vocabulary
    prefix: skosxl
    uri_format: http://www.w3.org/2008/05/skos-xl#$1
  uri_format: http://www.w3.org/2008/05/skos-xl#$1
  zazuko:
    prefix: skosxl
    uri_format: http://www.w3.org/2008/05/skos-xl#$1
slctr:
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: The Sri Lanka Clinical Trials Registry (SLCTR) is a Registry for clinical
    trials involving human subjects, conducted in Sri Lanka or overseas. The SLCTR
    is a Primary Registry linked to the Registry Network of the International Clinical
    Trials Registry Platform of the WHO (WHO-ICTRP). It is a not-for-profit Registry,
    with free and open access to researchers, clinicians, and the general public.
    (from homepage)
  example: SLCTR/2023/010
  homepage: https://slctr.lk/
  logo: https://slctr.lk/images/logo.png
  name: Sri Lanka Clinical Trials Registry
  pattern: ^SLCTR/\d{4}/\d+$
  prefix: slctr
  references:
  - https://slctr.lk/trials/slctr-2023-010
slkbase:
  cellosaurus:
    category: Cell line databases/resources
    homepage: https://sumlineknowledgebase.com/
    name: SUM Breast Cancer Cell Line Knowledge Base
    prefix: SLKBase
    uri_format: https://sumlineknowledgebase.com/?page_id=$1
  example: '3618'
  mappings:
    cellosaurus: SLKBase
  pattern: ^\d+$
  prefix: slkbase
slm:
  banana: SLM
  biocontext:
    prefix: SWISSLIPID
  domain: chemical
  example: '000000341'
  fairsharing:
    abbreviation: SwissLipids
    contact:
      email: swisslipids@isb-sib.ch
      name: Alan Bridge
      orcid: 0000-0003-2148-9135
    description: SwissLipids is an expert-curated resource that provides a framework
      for the integration of lipid and lipidomic data with biological knowledge and
      models. SwissLipids is updated daily.
    homepage: http://www.swisslipids.org/#/
    license: https://creativecommons.org/licenses/by-nc-nd/4.0
    name: SwissLipids
    prefix: FAIRsharing.pxr7x2
    publications:
    - doi: 10.1093/bioinformatics/btv285
      pubmed_id: 25943471
      title: The SwissLipids knowledgebase for lipid biology.
    subjects:
    - Life Science
    - Metabolomics
  integbio:
    description: SwissLipids is an expert-curated resource that provides a framework
      for the integration of lipid and lipidomic data with biological knowledge and
      models. SwissLipids is updated daily.
    fairsharing: FAIRsharing.pxr7x2
    homepage: http://www.swisslipids.org/#/
    information_keywords:
    - Chemical structure
    - Interaction/Pathway
    maintainer: Swiss-Prot group, SIB Swiss Institute of Bioinformatics||Vital-IT
      group, SIB Swiss Institute of Bioinformatics
    name: SwissLipids
    prefix: nbdc02026
    pubmeds:
    - '25943471'
    status: Active
    target_keywords:
    - Protein
    - Lipid
  license: CC-BY-4.0
  logo: https://www.swisslipids.org/images/SL_title_swiss.png
  mappings:
    biocontext: SWISSLIPID
    fairsharing: FAIRsharing.pxr7x2
    integbio: nbdc02026
    miriam: slm
    n2t: swisslipid
    ols: slm
    pathguide: '687'
    re3data: r3d100012603
    togoid: Swisslipids
    uniprot: DB-0197
    wikidata: P8691
  miriam:
    deprecated: false
    description: SwissLipids is a curated resource that provides information about
      known lipids, including lipid structure, metabolism, interactions, and subcellular
      and tissue localization. Information is curated from peer-reviewed literature
      and referenced using established ontologies, and provided with full provenance
      and evidence codes for curated assertions.
    homepage: http://www.swisslipids.org/#/
    id: '00000550'
    name: SwissLipids
    namespaceEmbeddedInLui: true
    pattern: ^SLM:\d+$
    prefix: slm
    sampleId: 000048885
    uri_format: http://www.swisslipids.org/#/entity/SLM:$1/
  n2t:
    description: SwissLipids is a curated resource that provides information about
      known lipids, including lipid structure, metabolism, interactions, and subcellular
      and tissue localization. Information is curated from peer-reviewed literature
      and referenced using established ontologies, and provided with full provenance
      and evidence codes for curated assertions.
    example: 000048885
    homepage: http://www.swisslipids.org/#/
    name: SwissLipids at Swiss Institute of Bioinformatics
    namespaceEmbeddedInLui: true
    pattern: ^SLM:\d+$
    prefix: swisslipid
    uri_format: http://www.swisslipids.org/#/entity/SLM:$1/
  name: SwissLipid
  ols:
    description: SwissLipids is a curated resource that provides information about
      known lipids, including lipid structure, metabolism, interactions, and subcellular
      and tissue localization. Information is curated from peer-reviewed literature
      and referenced using established ontologies, and provided with full provenance
      and evidence codes for curated assertions.
    name: SwissLipids
    prefix: slm
    uri_format: https://swisslipids.org/rdf/SLM_$1
  pathguide:
    abbreviation: SwissLipids
    homepage: http://www.swisslipids.org/#/
    name: A Knowledge Resource for Lipids and their Biology
    prefix: '687'
  pattern: ^\d+$
  preferred_prefix: SLM
  prefix: slm
  publications:
  - doi: 10.1093/bioinformatics/btv285
    pmc: PMC4547616
    pubmed: '25943471'
    title: The SwissLipids knowledgebase for lipid biology
    year: 2015
  - doi: 10.1093/bioinformatics/btv285
    pmc: null
    pubmed: null
    title: The SwissLipids knowledgebase for lipid biology.
    year: null
  - doi: 10.1093/bioinformatics/btv285
    pmc: null
    pubmed: '25943471'
    title: null
    year: null
  re3data:
    description: SwissLipids is an expert curated resource that provides a framework
      for the integration of lipid and lipidomic data with biological knowledge and
      models.
    doi: 10.17616/R3TZ18
    homepage: https://www.swisslipids.org/#/
    name: SwissLipids
    prefix: r3d100012603
    synonyms:
    - A knowledge resource for lipids and their biology
    - Swiss+Lipids
    xrefs:
      omics: 08652
  synonyms:
  - swisslipid
  - swisslipids
  togoid:
    catalog: nbdc02026
    examples:
    - SLM:000000002
    - SLM:000000003
    - SLM:000000006
    - SLM:000000007
    - SLM:000000035
    - SLM:000000042
    - SLM:000000043
    - SLM:000000044
    - SLM:000000047
    - SLM:000000048
    keywords:
    - Lipid
    name: SwissLipids
    pattern: ^SLM[:_](?\d+)$
    prefix: Swisslipids
    uri_format: http://identifiers.org/slm/SLM:$1
  uniprot:
    abbreviation: SwissLipids
    category: Chemistry databases
    homepage: https://www.swisslipids.org
    name: SwissLipids knowledge resource for lipid biology
    prefix: DB-0197
    publications:
    - doi: 10.1093/bioinformatics/btv285
      pubmed: '25943471'
    uri_format: https://www.swisslipids.org/#/entity/$1/
  uri_format: https://www.swisslipids.org/#/entity/SLM:$1
  wikidata:
    database: Q41165322
    description: identifier for lipids used by the SwissLipids database
    example:
    - SLM:000000274
    - SLM:000000510
    homepage: https://www.swisslipids.org/#/
    miriam: swisslipid
    name: SwissLipids ID
    prefix: P8691
    uri_format: https://www.swisslipids.org/#/entity/$1/
slso:
  aberowl:
    description: The Space Life Sciences Ontology is an application ontology and is
      intended to support the operation of NASA's Life Sciences Data Archive and other
      systems that contain space life science research data.
    download_owl: http://aber-owl.net/media/ontologies/SLSO/13/slso.owl
    homepage: https://github.com/nasa/LSDAO
    name: Space Life Sciences Ontology
    prefix: SLSO
  bioportal:
    contact:
      email: daniel.c.berrios@nasa.gov
      name: Dan Berrios
    description: The Space Life Sciences Ontology is an application ontology and is
      intended to support the operation of NASA's Life Sciences Data Archive (located
      at https://nlsp.nasa.gov) and other systems that contain space life science
      research data. Many kinds of scientific research in space involve specialized
      equipment, experimental procedures, specimens and specimen collection apparatus,
      supporting operational structures, and references to specific space environments
      and their characteristics. Often such research is extremely costly compared
      with planetary/terrestrial investigations, and the community supporting space
      life sciences is accustomed to the use of various specialized concepts and terminologies
      when dealing with this kind of research and data. However, the underlying conceptual
      models (and especially the specific labeled relationships in these models) have
      never been made explicit. The SLSO attempts to provide definition and organization
      of these models for the space research community. The SLSO was developed ab
      inicio using the Ontology Development Kit and imports an extends many concepts
      from the Basic Formal Ontology (BFO), the Ontology of Biomedical Investigations
      (OBI), the Environmental Ontology (ENVO), and other OBO Foundry ontologies.
      Projects at NASA such as the Open Science Data Repository (https://osdr.nasa.gov/)
      are already using many OBO ontologies, including the Radiation Biology Ontology
      (https://github.com/Radiobiology-Informatics-Consortium/RBO) and OBI, to index
      space biology investigation data. With the development of the SLSO, this practice
      can be extended to include all life science research in space or addressing
      space effects. Furthermore, the SLSO has a component that imports concepts from
      the Science Data Discovery Ontology, which was developed to support NASA's Science
      Discovery Engine (https://sciencediscoveryengine.nasa.gov). These links in the
      imported SDDO to concepts underlying a broad spectrum of space research (astrophysics,
      heliophysics, etc.) can ultimately be used to provide key capabilities for discovering
      and analyzing space life science data and how they relate to other kinds of
      scientific data regarding space environments., The Space Life Sciences Ontology
      is an application ontology and is intended to support the operation of NASA's
      Life Sciences Data Archive and other systems that contain space life science
      research data.
    homepage: https://github.com/nasa/LSDAO/tree/master/src/ontology
    license: CC-BY-3.0
    name: Space Life Sciences Ontology
    prefix: SLSO
    version: '2025-09-16'
  download_json: https://github.com/nasa/LSDAO/raw/refs/heads/master/slso.json
  example: '0000000'
  mappings:
    aberowl: SLSO
    bioportal: SLSO
    obofoundry: slso
    ols: slso
    ontobee: SLSO
  obofoundry:
    contact: daniel.c.berrios@nasa.gov
    contact.github: DanBerrios
    contact.label: Dan Berrios
    contact.orcid: 0000-0003-4312-9552
    deprecated: false
    description: The Space Life Sciences Ontology is an application ontology and is
      intended to support the operation of NASA's Life Sciences Data Archive and other
      systems that contain space life science research data.
    domain: investigations
    download.json: http://purl.obolibrary.org/obo/slso.json
    download.obo: http://purl.obolibrary.org/obo/slso.obo
    download.owl: http://purl.obolibrary.org/obo/slso.owl
    homepage: https://github.com/nasa/LSDAO
    license: CC BY 3.0
    license.url: http://creativecommons.org/licenses/by/3.0/
    name: Space Life Sciences Ontology
    preferredPrefix: SLSO
    prefix: slso
    repository: https://github.com/nasa/LSDAO
  ols:
    description: The Space Life Sciences Ontology is an application ontology and is
      intended to support the operation of NASA's Life Sciences Data Archive and other
      systems that contain space life science research data.
    download_owl: http://purl.obolibrary.org/obo/slso.owl
    homepage: https://github.com/nasa/LSDAO
    name: Space Life Sciences Ontology
    prefix: slso
    tracker: https://github.com/nasa/LSDAO/issues
    version: '2025-12-11'
    version.iri: http://purl.obolibrary.org/obo/slso/releases/2025-12-11/slso.owl
  ontobee:
    library: Library
    name: Space Life Sciences Ontology
    prefix: SLSO
  prefix: slso
smart:
  biocontext:
    prefix: SMART
  contact:
    email: chris.ponting@ed.ac.uk
    github: null
    name: Chris P. Ponting
    orcid: 0000-0003-0202-7816
  fairsharing:
    abbreviation: SMART
    description: SMART (Simple Modular Architecture Research Tool) is a web resource
      providing simple identification and extensive annotation of protein domains
      and the exploration of protein domain architectures. It allows the identification
      and annotation of genetically mobile domains and the analysis of domain architectures.
      More than 500 domain families found in signalling, extracellular and chromatin-associated
      proteins are detectable. These domains are extensively annotated with respect
      to phyletic distributions, functional class, tertiary structures and functionally
      important residues. Each domain found in a non-redundant protein database as
      well as search parameters and taxonomic information are stored in a relational
      database system. User interfaces to this database allow searches for proteins
      containing specific combinations of domains in defined taxa.
    homepage: http://smart.embl.de
    license: CC BY-SA 3.0
    name: Simple Modular Architecture Research Tool
    prefix: FAIRsharing.hsbpq3
    publications:
    - doi: 10.1093/nar/gkr931
      pubmed_id: 22053084
      title: 'SMART 7: recent updates to the protein domain annotation resource.'
    - doi: 10.1016/S0959-440X(99)80055-4
      pubmed_id: 10361098
      title: Protein families in multicellular organisms.
    - doi: 10.1093/nar/gkn808
      pubmed_id: 18978020
      title: 'SMART 6: recent updates and new developments.'
    - doi: 10.1093/nar/gkj079
      pubmed_id: 16381859
      title: 'SMART 5: domains in the context of genomes and networks.'
    - doi: 10.1093/nar/gkh088
      pubmed_id: 14681379
      title: 'SMART 4.0: towards genomic data integration.'
    - doi: 10.1093/nar/28.1.231
      pubmed_id: 10592234
      title: 'SMART: a web-based tool for the study of genetically mobile domains.'
    - doi: 10.1093/nar/27.1.229
      pubmed_id: 9847187
      title: 'SMART: identification and annotation of domains from signalling and
        extracellular protein sequences.'
    - doi: 10.1093/nar/30.1.242
      pubmed_id: 11752305
      title: Recent improvements to the SMART domain-based sequence annotation resource.
    - doi: 10.1093/nar/gkx922
      pubmed_id: 29040681
      title: 20 years of the SMART protein domain annotation resource.
    - doi: 10.1093/nar/gku949
      pubmed_id: 25300481
      title: 'SMART: recent updates, new developments and status in 2015.'
    subjects:
    - Life Science
  go:
    homepage: http://smart.embl-heidelberg.de/
    name: Simple Modular Architecture Research Tool
    prefix: SMART
    uri_format: http://smart.embl-heidelberg.de/smart/do_annotation.pl?BLAST=DUMMY&DOMAIN=$1
  integbio:
    alt_name: Simple Modular Architecture Research Tool
    description: SMART is a database of protein domains found in several different
      protein classes. The database contains classification information for domains
      and the proteins they can be found in. Users can search by sequence or domain
      information. The database can also be requested for local installation.
    fairsharing: FAIRsharing.hsbpq3
    homepage: http://smart.embl-heidelberg.de
    information_keywords:
    - 3D structure
    - Chemical structure
    - Classification
    maintainer: EMBL (European Molecular Biology Laboratory)
    name: SMART
    prefix: nbdc00682
    pubmeds:
    - '22053084'
    - '18978020'
    - '16381859'
    - '9600884'
    status: Active
    target_keywords:
    - Protein
  mappings:
    biocontext: SMART
    fairsharing: FAIRsharing.hsbpq3
    go: SMART
    integbio: nbdc00682
    miriam: smart
    n2t: smart
    prefixcommons: smart
    togoid: Smart
    uniprot: DB-0097
  miriam:
    deprecated: false
    description: The Simple Modular Architecture Research Tool (SMART) is an online
      tool for the identification and annotation of protein domains, and the analysis
      of domain architectures.
    homepage: http://smart.embl-heidelberg.de/
    id: 00000118
    name: SMART
    namespaceEmbeddedInLui: false
    pattern: ^SM\d{5}$
    prefix: smart
    sampleId: SM00015
    uri_format: http://smart.embl-heidelberg.de/smart/do_annotation.pl?DOMAIN=$1
  n2t:
    description: The Simple Modular Architecture Research Tool (SMART) is an online
      tool for the identification and annotation of protein domains, and the analysis
      of domain architectures.
    example: SM00015
    homepage: http://smart.embl-heidelberg.de/
    name: SMART (Simple Modular Architecture Research Tool)
    namespaceEmbeddedInLui: false
    pattern: ^SM\d{5}$
    prefix: smart
    uri_format: http://smart.embl-heidelberg.de/smart/do_annotation.pl?DOMAIN=$1
  prefix: smart
  prefixcommons:
    description: The Simple Modular Architecture Research Tool (SMART) is an online
      tool for the identification and annotation of protein domains, and the analysis
      of domain architectures.
    example: SM00015
    homepage: http://smart.embl.de/
    keywords:
    - domain
    - protein
    - structure
    license: CC BY-SA 3.0
    name: Simple Modular Architecture Research Tool; a protein domain database
    pattern: ^SM\d{5}$
    prefix: smart
    pubmed_ids:
    - '9847187'
    uri_format: http://smart.embl-heidelberg.de/smart/do_annotation.pl?DOMAIN=$1
  publications:
  - doi: 10.1093/nar/gkx922
    pmc: PMC5753352
    pubmed: '29040681'
    title: 20 years of the SMART protein domain annotation resource
    year: 2018
  - doi: 10.1093/nar/gku949
    pmc: PMC4384020
    pubmed: '25300481'
    title: 'SMART: recent updates, new developments and status in 2015'
    year: 2014
  - doi: 10.1093/nar/gkr931
    pmc: PMC3245027
    pubmed: '22053084'
    title: 'SMART 7: recent updates to the protein domain annotation resource'
    year: 2011
  - doi: 10.1093/nar/gkn808
    pmc: PMC2686533
    pubmed: '18978020'
    title: 'SMART 6: recent updates and new developments'
    year: 2008
  - doi: 10.1093/nar/gkj079
    pmc: PMC1347442
    pubmed: '16381859'
    title: 'SMART 5: domains in the context of genomes and networks'
    year: 2006
  - doi: 10.1093/nar/gkh088
    pmc: PMC308822
    pubmed: '14681379'
    title: 'SMART 4.0: towards genomic data integration'
    year: 2004
  - doi: 10.1093/nar/30.1.242
    pmc: PMC99073
    pubmed: '11752305'
    title: Recent improvements to the SMART domain-based sequence annotation resource
    year: 2002
  - doi: 10.1093/nar/28.1.231
    pmc: PMC102444
    pubmed: '10592234'
    title: 'SMART: a web-based tool for the study of genetically mobile domains'
    year: 2000
  - doi: 10.1016/s0959-440x(99)80055-4
    pmc: null
    pubmed: '10361098'
    title: Protein families in multicellular organisms
    year: 1999
  - doi: 10.1093/nar/27.1.229
    pmc: PMC148142
    pubmed: '9847187'
    title: 'SMART: identification and annotation of domains from signalling and extracellular
      protein sequences'
    year: 1999
  togoid:
    catalog: nbdc00682
    description: SMART is a database of protein domains found in several different
      protein classes. The database contains classification information for domains
      and the proteins they can be found in. Users can search by sequence or domain
      information. The database can also be requested for local installation.
    examples:
    - SM00130
    - SM00239
    - SM00043
    - SM00091
    - SM00104
    - SM01001
    - SM00135
    - SM00281
    - SM00996
    - SM00015
    keywords:
    - Domain
    name: SMART
    pattern: ^(?SM\d{5})$
    prefix: Smart
    uri_format: http://identifiers.org/smart/$1
  uniprot:
    abbreviation: SMART
    category: Family and domain databases
    homepage: https://smart.embl.de/
    name: Simple Modular Architecture Research Tool; a protein domain database
    prefix: DB-0097
    publications:
    - doi: 10.1093/nar/gkx922
      pubmed: '29040681'
    uri_format: https://smart.embl.de/smart/do_annotation.pl?DOMAIN=$1
smc.bgc:
  contact:
    email: dwudwary@lbl.gov
    github: null
    name: Daniel W Udwary
    orcid: 0000-0002-3491-0198
  contributor:
    email: m.naguthana@hotmail.com
    github: nagutm
    name: Mufaddal Naguthanawala
    orcid: 0009-0009-5240-7463
  description: The secondary metabolism collaboratory is a database for secondary
    metabolite biosynthetic gene clusters. This prefix represents identifiers for
    individual biosynthetic gene clusters (BGCs) linked to their corresponding bacterial
    or archaeal source.
  example: '12039302'
  github_request_issue: 1301
  homepage: https://smc.jgi.doe.gov
  name: Secondary Metabolism Collaboratory - biosynthetic gene cluster
  pattern: ^\d+$
  prefix: smc.bgc
  publications:
  - doi: 10.1093/nar/gkae1060
    pmc: null
    pubmed: '39540430'
    title: 'The secondary metabolism collaboratory: a database and web discussion
      portal for secondary metabolite biosynthetic gene clusters'
    year: 2024
  reviewer:
    email: b.gyori@northeastern.edu
    github: bgyori
    name: Benjamin M. Gyori
    orcid: 0000-0001-9439-5346
  uri_format: https://smc.jgi.doe.gov/bgc/$1
smc.source:
  contact:
    email: dwudwary@lbl.gov
    github: null
    name: Daniel W Udwary
    orcid: 0000-0002-3491-0198
  contributor:
    email: m.naguthana@hotmail.com
    github: nagutm
    name: Mufaddal Naguthanawala
    orcid: 0009-0009-5240-7463
  description: The secondary metabolism collaboratory is a database for secondary
    metabolite biosynthetic gene clusters. This prefix represents identifiers for
    bacteria and archaea sources linked to their associated set of biosynthetic gene
    clusters (BGCs).
  example: '1'
  github_request_issue: 1301
  homepage: https://smc.jgi.doe.gov
  name: Secondary Metabolism Collaboratory - taxon
  pattern: ^\d+$
  prefix: smc.source
  publications:
  - doi: 10.1093/nar/gkae1060
    pmc: null
    pubmed: '39540430'
    title: 'The secondary metabolism collaboratory: a database and web discussion
      portal for secondary metabolite biosynthetic gene clusters'
    year: 2024
  reviewer:
    email: b.gyori@northeastern.edu
    github: bgyori
    name: Benjamin M. Gyori
    orcid: 0000-0001-9439-5346
  uri_format: https://smc.jgi.doe.gov/sources/$1
smid:
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: SMIDs (Small Molecule Identifiers) represent gene-style identifiers
    for small molecules newly identified in C. elegans and other nematodes. SMIDs
    aim to make life easier for describing biogenic small molecules in metabolomic
    and genomic applications.
  example: '137'
  homepage: https://smid-db.org/
  name: C. elegans Small Molecule Identifier Database
  pattern: ^\d+$
  prefix: smid
  synonyms:
  - SMID-DB
  uri_format: https://smid-db.org/smid/$1
smiles:
  contact:
    email: tim.vandermeersch@gmail.com
    github: timvdm
    name: Tim Vandermeersch
    orcid: null
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  contributor_extras:
  - email: null
    github: NishaSharma14
    name: Nisha Sharma
    orcid: 0009-0006-4755-1039
  description: Documentation of SMILES (Simplified Molecular Input Line Entry System),
    a line notation (a typographical method using printable characters) for entering
    and representing molecules and reactions.
  example: CC2(C)C\1CCC(C)/C=C/12
  fairsharing:
    abbreviation: SMILES
    contact:
      email: egon.willighagen@maastrichtuniversity.nl
      name: Egon Willighagen
      orcid: 0000-0001-7542-0286
    description: This format is an open specification version of the SMILES language,
      a typographical line notation for specifying chemical structure. It is hosted
      under the banner of the Blue Obelisk project, with the intent to solicit contributions
      and comments from the entire computational chemistry community.
    domains:
    - Structure
    - Data analysis
    - molecular entity
    homepage: http://opensmiles.org/opensmiles.html
    logo: https://api.fairsharing.org/rails/active_storage/blobs/redirect/eyJfcmFpbHMiOnsibWVzc2FnZSI6IkJBaHBBazRFIiwiZXhwIjpudWxsLCJwdXIiOiJibG9iX2lkIn19--047d6c77b3abf77702d511a7e6a66acd8eb554b8/19335777.jpg?disposition=inline
    name: Simplified Molecular Input Line Entry Specification Format
    prefix: FAIRsharing.qv4b3c
    publications:
    - doi: 10.1021/ci00062a008
      title: SMILES. 2. Algorithm for generation of unique SMILES notation
      year: 1989
    - doi: 10.1186/1758-2946-4-24
      pubmed: '23031664'
      title: mol2chemfig, a tool for rendering chemical structures from molfile or
        SMILES format to LATE X code
      year: 2012
    - doi: 10.1021/ci00057a005
      title: SMILES, a chemical language and information system. 1. Introduction to
        methodology and encoding rules
      year: 1988
    - doi: 10.1021/ci00067a005
      title: SMILES, a chemical language and information system. 1. Introduction to
        methodology and encoding rules
      year: 1990
    repository: https://github.com/opensmiles
    subjects:
    - Life Science
    - Lipidomics
    - Metabolomics
    - Chemistry
    - Bioinformatics
  homepage: https://www.daylight.com/dayhtml/doc/theory/theory.smiles.html
  mappings:
    fairsharing: FAIRsharing.qv4b3c
    wikidata: P233
    wikidata.entity: Q466769
  name: Simplified molecular-input line-entry system
  prefix: smiles
  providers:
  - code: cms.descriptor
    description: Returns descriptors calculated from the molecule with RDKit
    example: null
    first_party: null
    homepage: https://api.naturalproducts.net/latest/docs#/chem/get_descriptors_chem_descriptors_get
    name: RDKit Descriptor via the Cheminformatics Microservice
    publications: null
    status: null
    uri_format: https://api.naturalproducts.net/latest/chem/descriptors?smiles=$1
  - code: cms.depict2d
    description: Generates a 2D depiction of a molecule using CDK or RDKit with the
      given parameters.
    example: null
    first_party: null
    homepage: https://api.naturalproducts.net/latest/docs#/depict/Depict2D_molecule_depict_2D_get
    name: Depict 2D via the Cheminformatics Microservice
    publications: null
    status: null
    uri_format: https://api.naturalproducts.net/latest/depict/2D?smiles=$1
  - code: cms.depict3d
    description: Generate 3D depictions of molecules using OpenBabel or RDKit.
    example: null
    first_party: null
    homepage: https://api.naturalproducts.net/latest/docs#/depict/Depict3D_Molecule_depict_3D_get
    name: Depict 3D via the Cheminformatics Microservice
    publications: null
    status: null
    uri_format: https://api.naturalproducts.net/latest/depict/3D?smiles=$1
  - code: cms.coordinates2d
    description: Generates 2D Coordinates using the CDK Structure diagram generator/RDKit/Open
      Babel and returns the mol block.
    example: null
    first_party: null
    homepage: https://api.naturalproducts.net/latest/docs#/convert/Create2D_Coordinates_convert_mol2D_get
    name: Generate 2D coordinates via the Cheminformatics Microservice
    publications: null
    status: null
    uri_format: https://api.naturalproducts.net/latest/convert/mol2D?smiles=$1
  - code: cms.coordinates3d
    description: Generates a random 3D conformer from SMILES using the specified molecule
      toolkit.
    example: null
    first_party: null
    homepage: https://api.naturalproducts.net/latest/docs#/convert/Create3D_Coordinates_convert_mol3D_get
    name: Generate 3D conformer via the Cheminformatics Microservice
    publications: null
    status: null
    uri_format: https://api.naturalproducts.net/latest/convert/mol3D?smiles=$1
  - code: cms.canonicalize
    description: Canonicalizes a given SMILES string according to the allowed toolkits.
    example: null
    first_party: null
    homepage: https://api.naturalproducts.net/latest/docs#/convert/SMILES_Canonicalise_convert_canonicalsmiles_get
    name: Canonicalizes a SMILES via the Cheminformatics Microservice
    publications: null
    status: null
    uri_format: https://api.naturalproducts.net/latest/convert/canonicalsmiles?smiles=$1
  - code: cms.cxsmiles
    description: Convert SMILES to CXSMILES. For more informations.
    example: null
    first_party: null
    homepage: https://api.naturalproducts.net/latest/docs#/convert/SMILES_to_CXSMILES_convert_cxsmiles_get
    name: Convert SMILES to CXSMILES via the Cheminformatics Microservice
    publications: null
    status: null
    uri_format: https://api.naturalproducts.net/latest/convert/cxsmiles?smiles=$1
  - code: cms.inchi
    description: Convert SMILES to InChI.
    example: null
    first_party: null
    homepage: https://api.naturalproducts.net/latest/docs#/convert/SMILES_to_InChI_convert_inchi_get
    name: Convert SMILES to InChI via the Cheminformatics Microservice
    publications: null
    status: null
    uri_format: https://api.naturalproducts.net/latest/convert/inchi?smiles=$1
  - code: cms.inchikey
    description: Convert SMILES to InChIKey.
    example: null
    first_party: null
    homepage: https://api.naturalproducts.net/latest/docs#/convert/SMILES_to_InChIKey_convert_inchikey_get
    name: Convert SMILES to InChIKey via the Cheminformatics Microservice
    publications: null
    status: null
    uri_format: https://api.naturalproducts.net/latest/convert/inchikey?smiles=$1
  - code: cms.iupac
    description: Generates IUPAC name for given SMILES using [STOUT](https://jcheminf.biomedcentral.com/articles/10.1186/s13321-021-00512-4)
      package.
    example: null
    first_party: null
    homepage: https://api.naturalproducts.net/latest/docs#/convert/SMILES_to_IUPACname_convert_iupac_get
    name: Generate IUPAC name from SMILES via the Cheminformatics Microservice
    publications: null
    status: null
    uri_format: https://api.naturalproducts.net/latest/convert/iupac?smiles=$1
  - code: cms.selfies
    description: Generates SELFIES string for a given SMILES string.
    example: null
    first_party: null
    homepage: https://api.naturalproducts.net/latest/docs#/convert/encode_SELFIES_convert_selfies_get
    name: Generates SELFIES for a SMILES via the Cheminformatics Microservice
    publications: null
    status: null
    uri_format: https://api.naturalproducts.net/latest/convert/selfies?smiles=$1
  - code: cms.convert
    description: Convert SMILES to various molecular formats using different toolkits.
    example: null
    first_party: null
    homepage: https://api.naturalproducts.net/latest/docs#/convert/SMILES_convert_to_Formats_convert_formats_get
    name: Convert SMILES to various molecular formats via the Cheminformatics Microservice
    publications: null
    status: null
    uri_format: https://api.naturalproducts.net/latest/convert/formats?smiles=$1
  publications:
  - doi: 10.1186/1758-2946-4-24
    pmc: PMC3551648
    pubmed: '23031664'
    title: mol2chemfig, a tool for rendering chemical structures from molfile or SMILES
      format to LATE X code
    year: 2012
  - doi: 10.1021/ci00067a005
    pmc: null
    pubmed: null
    title: SMILES. 3. DEPICT. Graphical depiction of chemical structures
    year: 1990
  - doi: 10.1021/ci00062a008
    pmc: null
    pubmed: null
    title: SMILES. 2. Algorithm for generation of unique SMILES notation
    year: 1989
  - doi: 10.1021/ci00057a005
    pmc: null
    pubmed: null
    title: SMILES, a chemical language and information system. 1. Introduction to
      methodology and encoding rules
    year: 1988
  - doi: 10.1021/ci00062a008
    pmc: null
    pubmed: null
    title: SMILES. 2. Algorithm for generation of unique SMILES notation
    year: 1989
  - doi: 10.1186/1758-2946-4-24
    pmc: null
    pubmed: '23031664'
    title: mol2chemfig, a tool for rendering chemical structures from molfile or SMILES
      format to LATE X code
    year: 2012
  - doi: 10.1021/ci00057a005
    pmc: null
    pubmed: null
    title: SMILES, a chemical language and information system. 1. Introduction to
      methodology and encoding rules
    year: 1988
  - doi: 10.1021/ci00067a005
    pmc: null
    pubmed: null
    title: SMILES, a chemical language and information system. 1. Introduction to
      methodology and encoding rules
    year: 1990
  references:
  - https://github.com/biopragmatics/bioregistry/issues/931
  wikidata:
    database: Q466769
    description: Simplified Molecular Input Line Entry Specification (canonical format)
    example:
    - CC2(C)C\1CCC(C)/C=C/12
    - CCO
    - '[Au]'
    name: canonical SMILES
    pattern: ^[A-Za-z0-9+\-\*=#$:().>/\\\[\]%]+$
    prefix: P233
    uri_format: https://www.simolecule.com/cdkdepict/depict/bow/svg?smi=$1&zoom=2.0&annotate=cip
smpdb:
  biocontext:
    prefix: SMPDB
    uri_format: http://smpdb.ca/view/$1
  biolink:
    is_identifiers: false
    is_obo: false
    prefix: PathWhiz
    uri_format: http://smpdb.ca/pathways/#$1
  contact:
    email: david.wishart@ualberta.ca
    github: DavidWishartLab
    name: David S. Wishart
    orcid: 0000-0002-3207-2434
  edam:
    description: Identifier of a pathway from the Small Molecule Pathway Database
      (SMPDB).
    name: Pathway ID (SMPDB)
    obsolete: false
    prefix: '2659'
  example: SMP0000219
  fairsharing:
    abbreviation: SMPDB
    description: The Small Molecule Pathway Database (SMPDB) contains small molecule
      pathways found in humans, which are presented visually. All SMPDB pathways include
      information on the relevant organs, subcellular compartments, protein cofactors,
      protein locations, metabolite locations, chemical structures and protein quaternary
      structures. Accompanying data includes detailed descriptions and references,
      providing an overview of the pathway, condition or processes depicted in each
      diagram.
    homepage: http://www.smpdb.ca/
    name: Small Molecule Pathway Database
    prefix: FAIRsharing.y1zyaq
    publications:
    - doi: doi:10.1093/nar/gkp1002
      pubmed_id: 19948758
      title: 'SMPDB: The Small Molecule Pathway Database.'
    - doi: 10.1093/nar/gkt1067
      pubmed_id: 24203708
      title: 'SMPDB 2.0: big improvements to the Small Molecule Pathway Database.'
    subjects:
    - Life Science
    twitter: WishartLab
  integbio:
    alt_name: Small Molecule Pathway Database
    description: SMPDB is a database of the biological pathways of small molecules.
      The database contains pathway information on hundreds of small molecules, many
      unique to SMPDB. Users can browse pathways by category, search the database,
      or use structure, sequence, and small molecule tools to explore pathways.
    fairsharing: biodbcore-000352
    homepage: http://www.smpdb.ca/
    information_keywords:
    - Interaction/Pathway
    - Image/Movie
    maintainer: University of Alberta
    name: SMPDB
    prefix: nbdc00908
    pubmeds:
    - '19948758'
    status: Active
    target_keywords:
    - Protein
    - Metabolite
  mappings:
    biocontext: SMPDB
    biolink: PathWhiz
    edam: '2659'
    fairsharing: FAIRsharing.y1zyaq
    integbio: nbdc00908
    miriam: smpdb
    n2t: smpdb
    pathguide: '311'
    prefixcommons: smpdb
  miriam:
    deprecated: false
    description: The Small Molecule Pathway Database (SMPDB) contains small molecule
      pathways found in humans, which are presented visually. All SMPDB pathways include
      information on the relevant organs, subcellular compartments, protein cofactors,
      protein locations, metabolite locations, chemical structures and protein quaternary
      structures. Accompanying data includes detailed descriptions and references,
      providing an overview of the pathway, condition or processes depicted in each
      diagram.
    homepage: https://smpdb.ca/
    id: '00000104'
    name: Small Molecule Pathway Database
    namespaceEmbeddedInLui: false
    pattern: ^SMP\d+$
    prefix: smpdb
    sampleId: SMP00001
    uri_format: http://smpdb.ca/view/$1
  n2t:
    description: The Small Molecule Pathway Database (SMPDB) contains small molecule
      pathways found in humans, which are presented visually. All SMPDB pathways include
      information on the relevant organs, subcellular compartments, protein cofactors,
      protein locations, metabolite locations, chemical structures and protein quaternary
      structures. Accompanying data includes detailed descriptions and references,
      providing an overview of the pathway, condition or processes depicted in each
      diagram.
    example: SMP00001
    homepage: http://www.smpdb.ca/pathways
    name: Small Molecule Pathway Database
    namespaceEmbeddedInLui: false
    pattern: ^SMP\d+$
    prefix: smpdb
    uri_format: http://smpdb.ca/view/$1
  name: Small Molecule Pathway Database
  pathguide:
    abbreviation: SMPDB
    homepage: http://www.smpdb.ca/
    keywords:
    - BioPAX
    - SBML
    name: Small Molecule Pathway Database
    prefix: '311'
  pattern: ^SMP\d+$
  prefix: smpdb
  prefixcommons:
    description: The Small Molecule Pathway Database (SMPDB) contains small molecule
      pathways found in humans, which are presented visually. All SMPDB pathways include
      information on the relevant organs, subcellular compartments, protein cofactors,
      protein locations, metabolite locations, chemical structures and protein quaternary
      structures. Accompanying data includes detailed descriptions and references,
      providing an overview of the pathway, condition or processes depicted in each
      diagram.
    example: SMP00001
    homepage: http://www.smpdb.ca/
    keywords:
    - chemical
    - human
    - metabolite
    - pathway
    license: http://www.smpdb.ca/about#cite
    name: Small Molecule Pathway Database
    pattern: ^SMP\d{5}$
    prefix: smpdb
    uri_format: http://pathman.smpdb.ca/pathways/$1/pathway
  publications:
  - doi: 10.1093/nar/gkt1067
    pmc: PMC3965088
    pubmed: '24203708'
    title: 'SMPDB 2.0: big improvements to the Small Molecule Pathway Database'
    year: 2013
  - doi: 10.1093/nar/gkp1002
    pmc: PMC2808928
    pubmed: '19948758'
    title: 'SMPDB: The Small Molecule Pathway Database'
    year: 2009
  synonyms:
  - SMP
  uri_format: https://smpdb.ca/view/$1
snap:
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: Theoretical explanation of a purely spatial ontology supporting snapshot
    views of the world at successive instants of time, as part of a modular ontology
    of the dynamic features of reality.
  example: Quality
  homepage: http://ontology.buffalo.edu/smith/articles/SNAP_SPAN.pdf
  mappings:
    pathguide: '494'
    prefixcommons: snap
  name: Snapshot
  pathguide:
    abbreviation: Snap
    homepage: http://snap.genomics.org.cn/
    name: a Single Nucleotide Polymorphism Annotation Platform
    prefix: '494'
  prefix: snap
  prefixcommons:
    description: Snap is a sequence analysis tool providing a simple but detailed
      analysis of human genes and their variations. For each gene, a gene-gene relationship
      network can be generated based on protein-protein interaction data, metabolic
      pathway connections and extended through phylogenetic relations.
    example: ENSG00000187634
    homepage: http://snap.humgen.au.dk
    keywords:
    - gene
    - protein
    - interaction
    - pathway
    name: 'SNAP: a SNP Annotation Platform'
    pattern: ^ENSG\d+$
    prefix: snap
    uri_format: http://snap.humgen.au.dk/views/geneview.cgi?gene=$1
  synonyms:
  - bfo11snap
  uri_format: http://www.ifomis.org/bfo/1.1/snap#$1
snctp:
  comment: it appears they cede information into WHO
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: 'The SNCTP (Swiss National Clinical Trials Portal) is the portal where
    clinical trials in Switzerland are published. It contains data from two sources:
    from BASEC, the national platform for submitting applications for research projects
    to ethics committees, and from the ICTRP (the WHO International Clinical Trials
    Registry Platform), which covers the 17 primary registries worldwide. The ICTRP
    clinical trials shown on the SNCTP are limited to those conducted in Switzerland;
    there is also an option to display trials conducted in one of Switzerland''s neighbouring
    countries. [from homepage]'
  example: SNCTP000005580
  homepage: https://kofam.ch/en/snctp-portal
  name: Swiss National Clinical Trials Portal
  prefix: snctp
snodb:
  contact:
    email: michelle.scott@usherbrooke.ca
    github: null
    name: Michelle S Scott
    orcid: 0000-0001-6231-7714
  contributor:
    email: maaya.m466@gmail.com
    github: maayamanoj466
    name: Maaya Manoj
    orcid: 0009-0000-6974-6386
  description: Contains identifiers for human small nucleolar RNAs (snoRNAs) from
    snoDB, an interactive database of human small nucleolar RNAs (snoRNAs) that includes
    up-to-date information on snoRNA features, genomic location, conservation, host
    gene, snoRNA–RNA targets and snoRNA abundance and provides links to other resources.
  example: snoDB0001
  github_request_issue: 1655
  homepage: https://bioinfo-scottgroup.med.usherbrooke.ca/snoDB
  integbio:
    description: snoDB is a database of human snoRNA, which data are collected from
      other established databases, publications and experimental data generated by
      the group. Each entry contains information about synonym, box type, location,
      conservation, genomic sequence and expression data.
    homepage: https://bioinfo-scottgroup.med.usherbrooke.ca/snoDB/
    information_keywords:
    - Sequence
    - Expression
    - Localization
    - Interaction/Pathway
    maintainer: Department of Biochemistry, University of Sherbrooke
    name: snoDB
    prefix: nbdc02602
    pubmeds:
    - '31598696'
    status: Active
    target_keywords:
    - Genome/Gene
    - RNA
    - Health/Disease
  keywords:
  - human nucleolar rna
  - rna
  - snorna-protein
  mappings:
    integbio: nbdc02602
  name: snoDB
  pattern: ^snoDB\d{4}$
  prefix: snodb
  publications:
  - doi: 10.1093/nar/gkac835
    pmc: PMC9825428
    pubmed: '36165892'
    title: 'snoDB 2.0: an enhanced interactive database, specializing in human snoRNAs'
    year: 2023
  - doi: 10.1093/nar/gkz884
    pmc: PMC6943035
    pubmed: '31598696'
    title: 'snoDB: an interactive database of human snoRNA sequences, abundance and
      interactions'
    year: 2020
  reviewer:
    email: b.gyori@northeastern.edu
    github: bgyori
    name: Benjamin M. Gyori
    orcid: 0000-0001-9439-5346
  uri_format: https://bioinfo-scottgroup.med.usherbrooke.ca/snoDB/detailed_view/$1
snomedct:
  aberowl:
    description: SNOMED Clinical Terms
    homepage: http://www.snomed.org
    name: SNOMED CT
    prefix: SNOMEDCT
    version: 2016AB
  bartoc:
    abbreviation: SNOMED CT
    homepage: https://www.snomed.org/
    name: Systematized Nomenclature of Human and Veterinary Medicine Clinical Termns
    prefix: '20686'
  biocontext:
    prefix: SNOMEDCT
  biolink:
    is_identifiers: false
    is_obo: false
    prefix: SNOMEDCT
    uri_format: http://snomed.info/id/$1
  bioportal:
    contact:
      email: custserv@nlm.nih.gov
      name: NLM Customer Service
    description: <p>The US Edition of SNOMED CT combines the International Release
      of SNOMED CT and the US Extension of SNOMED CT</p> <p>SNOMED CT provides the
      core general terminology for the electronic health record (EHR). The concepts
      have unique meanings and formal logic-based definitions organized into hierarchies.
      Each International Release includes the core of the terminology (concepts, descriptions,
      and relationships), together with works to support the implementation and use
      of SNOMED CT, including subsets, cross maps to existing classifications and
      coding schemes, and an extensive set of guidelines.</p> <p>The US Extension
      to SNOMED CT included the concepts, descriptions, and relationships accepted
      by NLM as a formal extension to the SNOMED CT International Release. NLM no
      longer releases the standalone US Extension.</p> The US Edition of SNOMED CT
      includes more than 300,000 unique concepts. There are over 1,000,000 descriptions
      in SNOMED CT, including synonyms that can be used to refer to a concept. In
      addition, there are approximately 903,000 links or semantic relationships between
      the SNOMED CT concepts.</p>
    homepage: http://www.snomed.org
    name: SNOMED CT
    prefix: SNOMEDCT
    publications:
    - http://www.snomed.org
    version: SNOMEDCT_US_2024_09_01
  contributor_extras:
  - email: nicolas.matentzoglu@gmail.com
    github: matentzn
    name: Nicolas Matentzoglu
    orcid: 0000-0002-7356-1779
  fairsharing:
    abbreviation: SNOMED CT
    description: The Systematized Nomenclature of Medicine Clinical Terms is a reference
      terminology that can be used to cross-map standardized healthcare languages
      across healthcare disciplines.
    homepage: https://www.snomed.org/what-is-snomed-ct
    name: Systematized Nomenclature of Medicine-Clinical Terms
    prefix: FAIRsharing.d88s6e
    publications:
    - doi: 10.1097/00024665-200609000-00011
      pubmed: '16980782'
      title: 'Standardized nursing language in the systematized nomenclature of medicine
        clinical terms: A cross-mapping validation method'
      year: 2006
    subjects:
    - Preclinical Studies
    - Biomedical Science
    - Health Science
    - Medicine
  hl7:
    description: 'SNOMED CT is a concept-based, scientifically validated terminology
      that provides a unique and permanent concept identifier that can be included
      in multiple HL7 data types including CD and CE.  The concepts are managed to
      avoid "semantic drift" so the meaning remains constant.  If the concept is found
      to be ambiguous or the meaning changes, the concept is inactivated but still
      retained and the identifier is never reused.  SNOMED CT''s concepts are interrelated
      hierarchically and using description logic.  SNOMED CT concepts have a unique
      "fully-specified name", a preferred term, and, optionally, synonyms.  The description
      languages include English and Spanish.   '
    homepage: http://www.ihtsdo.org
    name: SNOMED Clinical Terms
    organization: 'International Health Terminology Standards Development Organisation '
    preferred_prefix: snomed-CT
    prefix: 2.16.840.1.113883.6.96
    status: Complete
  license: https://uts.nlm.nih.gov/uts/assets/LicenseAgreement.pdf
  mappings:
    aberowl: SNOMEDCT
    bartoc: '20686'
    biocontext: SNOMEDCT
    biolink: SNOMEDCT
    bioportal: SNOMEDCT
    fairsharing: FAIRsharing.d88s6e
    hl7: 2.16.840.1.113883.6.96
    miriam: snomedct
    n2t: snomedct
    ols: snomed
    prefixcommons: snomedct
    wikidata: P5806
  miriam:
    deprecated: false
    description: SNOMED CT (Systematized Nomenclature of Medicine -- Clinical Terms),
      is a systematically organized computer processable collection of medical terminology
      covering most areas of clinical information such as diseases, findings, procedures,
      microorganisms, pharmaceuticals, etc.
    homepage: https://browser.ihtsdotools.org/
    id: 00000269
    name: SNOMED CT
    namespaceEmbeddedInLui: false
    pattern: ^(\w+)?\d+$
    prefix: snomedct
    sampleId: '284196006'
    uri_format: https://browser.ihtsdotools.org/?perspective=full&conceptId1=$1
  n2t:
    description: SNOMED CT (Systematized Nomenclature of Medicine -- Clinical Terms),
      is a systematically organized computer processable collection of medical terminology
      covering most areas of clinical information such as diseases, findings, procedures,
      microorganisms, pharmaceuticals, etc.
    example: '284196006'
    homepage: http://www.snomedbrowser.com/
    name: SNOMED-CT at The National Pathology Exchange
    namespaceEmbeddedInLui: false
    pattern: ^(\w+)?\d+$
    prefix: snomedct
    uri_format: http://www.snomedbrowser.com/Codes/Details/$1
  ols:
    description: SNOMED CT or SNOMED Clinical Terms is a systematically organized
      computer processable collection of medical terms providing codes, terms, synonyms
      and definitions used in clinical documentation and reporting.
    name: SNOMED CT (International Edition)
    prefix: snomed
    uri_format: http://snomed.info/id/$1
    version: '20251017'
    version.iri: http://snomed.info/sct/900000000000207008/version/20251017
  prefix: snomedct
  prefixcommons:
    bioportal: '1353'
    description: SNOMED Clinical Terms
    example: '284196006'
    homepage: http://ihtsdo.org
    name: Systematized Nomenclature of Medicine - Clinical Terms
    pattern: ^(\w+)?\d+$
    prefix: snomedct
    synonyms:
    - snomed
    - snomedct_2010_1_31
    - snomedct_2013_01_31
  providers:
  - code: snomed.info
    description: Stopped working sometime in 2020's
    example: null
    first_party: null
    homepage: null
    name: null
    publications: null
    status: null
    uri_format: http://snomed.info/id/$1
  publications:
  - doi: 10.1097/00024665-200609000-00011
    pmc: null
    pubmed: '16980782'
    title: 'Standardized nursing language in the systematized nomenclature of medicine
      clinical terms: A cross-mapping validation method'
    year: 2006
  - doi: 10.1097/00024665-200609000-00011
    pmc: null
    pubmed: '16980782'
    title: 'Standardized nursing language in the systematized nomenclature of medicine
      clinical terms: A cross-mapping validation method'
    year: 2006
  synonyms:
  - SCTID
  - SCTID_2010_1_31
  - SNOMECT
  - SNOMED
  - SNOMEDCT
  - SNOMEDCTCT
  - SNOMEDCTCT_2018_03_01
  - SNOMEDCTCT_2019_03_01
  - SNOMEDCT_2005_07_31
  - SNOMEDCT_2010_1_31
  - SNOMEDCT_2020_03_01
  - SNOMEDCT_US
  - SNOMEDCT_US_2015_03_01
  - SNOMEDCT_US_2016_03_01
  - SNOMEDCT_US_2018_03_01
  - SNOMEDCT_US_2018_09_01
  - SNOMEDCT_US_2019_03_01
  - SNOMEDCT_US_2019_09_01
  - SNOMEDCT_US_2020_03_01
  - SNOMEDCT_US_2020_09_01
  - SNOMEDCT_US_2021_03_01
  - SNOMEDCT_US_2021_07_31
  - SNOMEDCT_US_2021_09_01
  - SNOMEDCT_US_2022_07_31
  - SNOMEDCT_US_2022_09_01
  - SNOMEDCT_US_2022_12_31
  - SNOMEDCT_US_2023_02_28
  - SNOMEDCT_US_2023_03_01
  - SNOMEDCT_US_2023_09_01
  - SNOMEDCT_US_2023_10_01
  - SNOMEDCT_US_2023_11_01
  - SNOMEDCT_US_2024_03_01
  - SNOMED_CT
  - SNOMED_CT_US_2018_03_01
  - SNOWMEDCT
  - SNOWMEDCT_US
  - SNOWMEDCT_US_2018_03_01
  uri_format: http://purl.bioontology.org/ontology/SNOMEDCT/$1
  wikidata:
    description: identifier in the SNOMED CT catalogue codes for diseases, symptoms
      and procedures
    example:
    - '267718000'
    - '464035001'
    - '64859006'
    homepage: https://browser.ihtsdotools.org/
    name: SNOMED CT ID
    pattern: ^[0-9]*$
    prefix: P5806
    uri_format: https://browser.ihtsdotools.org/?perspective=full&conceptId1=$1&languages=en
    uri_format_rdf: http://snomed.info/id/$1
snornabase:
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: 'A comprehensive database of


    human H/ACA and C/D box snoRNAs.'
  example: SR0000178
  homepage: https://www-snorna.biotoul.fr/
  integbio:
    description: "SnoRNABase is an extensive database of human small nucleolar RNAs\
      \ (snoRNAs) constructed with the invaluable assistance of Laboratoire de Biologie\
      \ Mol?culaire Eucaryote (LBME) and Jean-Pierre Bachellerie in particular. \n\
      This repository provides the sequences of both snoRNA classes, namely C/D box\
      \ snoRNAs and H/ACA box snoRNAs.\nIn version 2 of the database each class contains\
      \ information on a set of four proteins.\nIn the updated version 3 of the database\
      \ different sequences are used and the nucleotides are numbered differently.\n\
      Keyword search and Blast search options are available."
    homepage: http://www-snorna.biotoul.fr/
    information_keywords:
    - Sequence
    - Bibliography/Documents
    maintainer: Laboratoire de Biologie Moleculaire des Eucaryotes
    name: snoRNABase
    prefix: nbdc00323
    pubmeds:
    - '16381836'
    status: Active
    target_keywords:
    - RNA
  mappings:
    integbio: nbdc00323
    prefixcommons: snornalbmedb
  name: snoRNABase
  prefix: snornabase
  prefixcommons:
    description: This is a database of human C/D box and H/ACA modification guide
      RNAs
    example: HBII-240
    homepage: http://www-snorna.biotoul.fr/
    keywords:
    - RNA
    name: snoRNA-LBME-db
    pattern: ^[A-Z,0-9]+$
    prefix: snornalbmedb
    synonyms:
    - snornabase
    uri_format: http://www-snorna.biotoul.fr/plus.php?id=$1
  wikidata:
    paper: Q24675417
snp2tfbs:
  mappings:
    miriam: snp2tfbs
  miriam:
    deprecated: false
    description: SNP2TFBS is aimed at studying variations (SNPs/indels) that affect
      transcription factor binding (TFB) in the Human genome.
    homepage: https://ccg.epfl.ch/snp2tfbs/
    id: '00000766'
    name: SNP2TFBS
    namespaceEmbeddedInLui: false
    pattern: ^rs[0-9]+$
    prefix: snp2tfbs
    sampleId: rs11603840
    uri_format: https://ccg.epfl.ch/cgi-bin/snp2tfbs/snpviewer_form_parser.cgi?snpid=$1
  name: SNP to Transcription Factor Binding Sites
  prefix: snp2tfbs
  provides: dbsnp
snp500cancer:
  comment: This resource doesn't exist on the web anymore
  deprecated: true
  mappings:
    prefixcommons: snp500cancer
  prefix: snp500cancer
  prefixcommons:
    description: The goal of the SNP500Cancer project is to resequence 102 reference
      samples to find known or newly discovered single nucleotide polymorphisms (SNPs)
      which are of immediate importance to molecular epidemiology studies in cancer.
    example: TP53-47
    homepage: http://snp500cancer.nci.nih.gov
    keywords:
    - DNA
    name: SNP500Cancer
    pattern: ^TP\d+-\d+$
    prefix: snp500cancer
    uri_format: http://snp500cancer.nci.nih.gov/snp.cfm?both_snp_id=$1
  reviewer:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
so:
  aberowl:
    description: A structured controlled vocabulary for sequence annotation, for the
      exchange of annotation data and for the description of sequence objects in databases.
    download_owl: http://aber-owl.net/media/ontologies/SO/292/so.owl
    homepage: http://www.sequenceontology.org/
    name: Sequence types and features ontology
    prefix: SO
  agroportal:
    contact:
      email: karen.eilbeck@genetics.utah.edu
      name: Karen Eilbeck (PI)
    description: A structured controlled vocabulary for sequence annotation, for the
      exchange of annotation data and for the description of sequence objects in databases.
    example_uri: http://purl.obolibrary.org/obo/SO_0001673
    homepage: http://www.sequenceontology.org/
    name: Sequence Types and Features Ontology
    prefix: SO
    publications:
    - http://www.sequenceontology.org/?page_id=296
    repository: https://github.com/The-Sequence-Ontology/SO-Ontologies
  biocontext:
    prefix: SO
  bioportal:
    contact:
      email: song-devel@lists.sourceforge.net
      name: SO Administrators
    description: 'SO is a collaborative ontology project for the definition of sequence
      features used in biological sequence annotation. SO was initially developed
      by the Gene Ontology Consortium. Contributors to SO include the GMOD community,
      model organism database groups such as WormBase, FlyBase, Mouse Genome Informatics
      group, and institutes such as the Sanger Institute and the EBI. Input to SO
      is welcomed from the sequence annotation community. The OBO revision is available
      here: http://sourceforge.net/p/song/svn/HEAD/tree/'
    homepage: http://www.sequenceontology.org
    name: Sequence Types and Features Ontology
    prefix: SO
    version: unknown
  download_obo: https://github.com/The-Sequence-Ontology/SO-Ontologies/raw/master/Ontology_Files/so.obo
  example: '0001157'
  fairsharing:
    abbreviation: SO
    contact:
      email: keilbeck@fruitfly.org
      name: Karen Eilbeck
      orcid: 0000-0002-0831-6427
    description: SO is a collaborative ontology project for the definition of sequence
      features used in biological sequence annotation. The Sequence Ontology is a
      set of terms and relationships used to describe the features and attributes
      of biological sequence. SO includes different kinds of features which can be
      located on the sequence.
    domains:
    - Sequence annotation
    - deoxyribonucleic acid
    - ribonucleic acid
    - region
    - sequence feature
    - gene
    - genome
    homepage: http://www.sequenceontology.org/
    license: CC-BY-4.0
    name: Sequence Ontology
    prefix: FAIRsharing.6bc7h9
    publications:
    - doi: 10.1186/gb-2010-11-8-r88
      pubmed: '20796305'
      title: A standard variation file format for human genome sequences
      year: 2010
    - doi: 10.1186/gb-2005-6-5-r44
      pubmed: '15892872'
      title: 'The Sequence Ontology: a tool for the unification of genome annotations'
      year: 2005
    - doi: 10.1016/j.jbi.2010.03.002
      pubmed: '20226267'
      title: Evolution of the Sequence Ontology terms and relationships
      year: 2010
    repository: https://github.com/The-Sequence-Ontology/SO-Ontologies
    subjects:
    - Life Science
    - Transcriptomics
    - Biology
    - Bioinformatics
    - Genomics
  go:
    homepage: http://www.sequenceontology.org/
    name: Sequence Ontology
    prefix: SO
  mappings:
    aberowl: SO
    agroportal: SO
    biocontext: SO
    bioportal: SO
    fairsharing: FAIRsharing.6bc7h9
    go: SO
    miriam: so
    n2t: so
    obofoundry: so
    ols: so
    ontobee: SO
    prefixcommons: so
    wikidata.entity: Q81661803
  miriam:
    deprecated: false
    description: The Sequence Ontology (SO) is a structured controlled vocabulary
      for the parts of a genomic annotation. It provides a common set of terms and
      definitions to facilitate the exchange, analysis and management of genomic data.
    homepage: http://bioportal.bioontology.org/ontologies/SO
    id: 00000081
    name: Sequence Ontology
    namespaceEmbeddedInLui: true
    pattern: ^SO:\d{7}$
    prefix: so
    providers:
    - code: ''
      description: Sequence Ontology
      homepage: http://www.sequenceontology.org/
      name: Sequence Ontology
      uri_format: http://www.sequenceontology.org/miso/current_release/term/SO:$1
    sampleId: '0000704'
    uri_format: http://purl.bioontology.org/ontology/SO/SO:$1
  n2t:
    description: The Sequence Ontology (SO) is a structured controlled vocabulary
      for the parts of a genomic annotation. It provides a common set of terms and
      definitions to facilitate the exchange, analysis and management of genomic data.
    example: '0000704'
    homepage: http://bioportal.bioontology.org/ontologies/SO
    name: Sequence Ontology through BioPortal
    namespaceEmbeddedInLui: true
    pattern: ^SO:\d{7}$
    prefix: so
    uri_format: http://purl.bioontology.org/ontology/SO/SO:$1
  obofoundry:
    appears_in:
    - pcl
    contact: keilbeck@genetics.utah.edu
    contact.github: keilbeck
    contact.label: Karen Eilbeck
    contact.orcid: 0000-0002-0831-6427
    deprecated: false
    description: A structured controlled vocabulary for sequence annotation, for the
      exchange of annotation data and for the description of sequence objects in databases.
    domain: chemistry and biochemistry
    download.obo: http://purl.obolibrary.org/obo/so.obo
    download.owl: http://purl.obolibrary.org/obo/so.owl
    homepage: http://www.sequenceontology.org/
    license: CC BY 4.0
    license.url: https://creativecommons.org/licenses/by/4.0/
    logo: https://obofoundry.org/images/so_logo.png
    name: Sequence types and features ontology
    preferredPrefix: SO
    prefix: so
    publications:
    - id: https://www.ncbi.nlm.nih.gov/pubmed/15892872
      title: 'The Sequence Ontology: a tool for the unification of genome annotations.'
    - id: https://www.ncbi.nlm.nih.gov/pubmed/20226267
      title: Evolution of the Sequence Ontology terms and relationships.
    repository: https://github.com/The-Sequence-Ontology/SO-Ontologies
  ols:
    description: A structured controlled vocabulary for sequence annotation, for the
      exchange of annotation data and for the description of sequence objects in databases.
    download_owl: http://purl.obolibrary.org/obo/so.owl
    homepage: http://www.sequenceontology.org/
    name: Sequence types and features ontology
    prefix: so
    tracker: https://github.com/The-Sequence-Ontology/SO-Ontologies/issues
    version: '2024-11-18'
    version.iri: http://purl.obolibrary.org/obo/so/2024-11-18/so.owl
  ontobee:
    library: Library
    name: Sequence types and features ontology
    prefix: SO
  pattern: ^\d{7}$
  prefix: so
  prefixcommons:
    alt_uri_formats:
    - http://purl.org/obo/owl/SO#$1
    bioportal: '1109'
    description: The Sequence Ontology is a set of terms and relationships used to
      describe the features and attributes of biological sequence. SO includes different
      kinds of features which can be located on the sequence.
    example: SO:0000704
    homepage: http://www.sequenceontology.org/
    keywords:
    - obo
    - ontology
    - DNA
    - RNA
    - structure
    license: http://www.sequenceontology.org/about/citing.html
    name: Sequence Ontology
    pattern: ^SO:\d{7}$
    prefix: so
    pubmed_ids:
    - '15892872'
    synonyms:
    - obo.so
    uri_format: http://www.sequenceontology.org/miso/current_release/term/$1
  publications:
  - doi: 10.1186/gb-2010-11-8-r88
    pmc: PMC2945790
    pubmed: '20796305'
    title: A standard variation file format for human genome sequences
    year: 2010
  - doi: 10.1016/j.jbi.2010.03.002
    pmc: PMC3052763
    pubmed: '20226267'
    title: Evolution of the Sequence Ontology terms and relationships
    year: 2010
  - doi: 10.1186/gb-2005-6-5-r44
    pmc: PMC1175956
    pubmed: '15892872'
    title: 'The Sequence Ontology: a tool for the unification of genome annotations'
    year: 2005
  uri_format: http://purl.obolibrary.org/obo/SO_$1
sopharm:
  aberowl:
    description: SO-Pharm (Suggested Ontology for Pharmacogenomics) is a domain ontology
      implemented in OWL-DL, which proposes a formal description of pharmacogenomic
      knowledge. SO-Pharm articulates different ontologies that represent complementary
      sub-domains of pharmacogenomics, i.e. related to genotype, phenotype, drugs,
      and clinical trials. SO-Pharm enables to represent pharmacogenomic relationships
      between a drug, a genomic variation and a phenotype trait. In addition, it enables
      to represent patient and more largely panel included in trials, and populations.
      SO-Pharm enables the representation of measured items on this patients such
      as results from the observation of a phenotype trait or of genomic variations.
      SO-Pharm supports knowledge about pharmacogenomic hypothesis, case study, and
      investigations in pharmacogenomics. SO-Pharm is designed to facilitate data
      integration and knowledge discovery in pharmacogenomics. In addition it provides
      a consistent articulation of ontologies of pharmacogenomic sub-domains.
    download_owl: http://aber-owl.net/media/ontologies/SOPHARM/18/sopharm.owl
    homepage: https://members.loria.fr/ACoulet/files/sopharm2.0_description.php
    name: Suggested Ontology for Pharmacogenomics
    prefix: SOPHARM
    version: 'The new release (March 02, 2017) 2.2 includes concept and properties
      labels in French.

      Imports have been abandoned in favor of simple references to distant URI'
  biocontext:
    prefix: SOPHARM
  bioportal:
    contact:
      email: adrien.coulet@loria.fr
      name: Adrien Coulet
    description: SO-Pharm (Suggested Ontology for Pharmacogenomics) is a domain ontology
      implemented in OWL-DL, which proposes a formal description of pharmacogenomic
      knowledge. SO-Pharm articulates different ontologies that represent complementary
      sub-domains of pharmacogenomics, i.e. related to genotype, phenotype, drugs,
      and clinical trials. SO-Pharm enables to represent pharmacogenomic relationships
      between a drug, a genomic variation and a phenotype trait. In addition, it enables
      to represent patient and more largely panel included in trials, and populations.
      SO-Pharm enables the representation of measured items on this patients such
      as results from the observation of a phenotype trait or of genomic variations.
      SO-Pharm supports knowledge about pharmacogenomic hypothesis, case study, and
      investigations in pharmacogenomics. SO-Pharm is designed to facilitate data
      integration and knowledge discovery in pharmacogenomics. In addition it provides
      a consistent articulation of ontologies of pharmacogenomic sub-domains.
    name: Suggested Ontology for Pharmacogenomics
    prefix: SOPHARM
    version: 'Version: SO-Pharm 2.2

      Release: 02 Mar 2017'
  contact:
    email: adrien.coulet@loria.fr
    github: null
    name: Adrien Coulet
    orcid: 0000-0002-1466-062X
  mappings:
    aberowl: SOPHARM
    biocontext: SOPHARM
    bioportal: SOPHARM
    obofoundry: sopharm
  obofoundry:
    contact: Adrien.Coulet@loria.fr
    contact.label: Adrien Coulet
    deprecated: true
    domain: chemistry and biochemistry
    homepage: http://www.loria.fr/~coulet/sopharm2.0_description.php
    name: Suggested Ontology for Pharmacogenomics
    prefix: sopharm
  prefix: sopharm
sosa:
  agroportal:
    contact:
      email: simon.cox@csiro.au
      name: Simon Cox
    description: This ontology is based on the SSN Ontology by the W3C Semantic Sensor
      Networks Incubator Group (SSN-XG), together with considerations from the W3C/OGC
      Spatial Data on the Web Working Group.
    example_uri: http://www.w3.org/ns/sosa/Observation
    homepage: https://www.w3.org/TR/vocab-ssn/
    license: http://www.w3.org/Consortium/Legal/2015/copyright-software-and-document
    name: Sensor, Observation, Sample, and Actuator Ontology
    prefix: SOSA
    publications:
    - http://www.semantic-web-journal.net/system/files/swj1804.pdf
    - https://doi.org/10.1016/j.websem.2018.06.003
    repository: https://github.com/w3c/sdw
    version: V-2017
  contact:
    email: dr.shorthair@pm.me
    github: dr-shorthair
    name: Simon Cox
    orcid: 0000-0002-3884-3420
  contributor:
    email: philip.stroemert@tib.eu
    github: StroemPhi
    name: Philip Strömert
    orcid: 0000-0002-1595-3213
  description: This ontology is based on the SSN Ontology by the W3C Semantic Sensor
    Networks Incubator Group (SSN-XG), together with considerations from the W3C/OGC
    Spatial Data on the Web Working Group.
  download_rdf: https://www.w3.org/ns/sosa/
  example: FeatureOfInterest
  github_request_issue: 1274
  homepage: https://www.w3.org/TR/vocab-ssn/
  license: http://www.w3.org/Consortium/Legal/2015/copyright-software-and-document
  lov:
    description: This ontology is based on the SSN Ontology by the W3C Semantic Sensor
      Networks Incubator Group (SSN-XG), together with considerations from the W3C/OGC
      Spatial Data on the Web Working Group.
    homepage: http://www.w3.org/ns/sosa/
    keywords:
    - Environment
    - IoT
    modified: '2017-04-17'
    name: Sensor, Observation, Sample, and Actuator (SOSA) Ontology
    prefix: sosa
    uri_prefix: http://www.w3.org/ns/sosa/$1
  mappings:
    agroportal: SOSA
    lov: sosa
    tib: sosa
    zazuko: sosa
  name: Sensor, Observation, Sample, and Actuator Ontology
  prefix: sosa
  publications:
  - doi: 10.1016/j.websem.2018.06.003
    pmc: null
    pubmed: null
    title: 'SOSA: A lightweight ontology for sensors, observations, samples, and actuators'
    year: 2019
  repository: https://github.com/w3c/sdw
  reviewer:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  tib:
    contact: public-sdw-comments@w3.org
    description: This ontology is based on the SSN Ontology by the W3C Semantic Sensor
      Networks Incubator Group (SSN-XG), together with considerations from the W3C/OGC
      Spatial Data on the Web Working Group.
    homepage: https://www.w3.org/TR/vocab-ssn/
    keywords:
    - NFDI4ING
    - NFDI4CHEM
    - ESS
    - engineering
    name: Sensor, Observation, Sample, and Actuator (SOSA) Ontology
    prefix: sosa
    tracker: https://github.com/w3c/sdw/issues
    uri_format: http://www.w3.org/ns/sosa/$1
  uri_format: http://www.w3.org/ns/sosa/$1
  zazuko:
    prefix: sosa
    uri_format: http://www.w3.org/ns/sosa/$1
soybase:
  biocontext:
    prefix: SOYBASE
  fairsharing:
    abbreviation: SoyBase
    contact:
      email: Jacqueline.Campbell@usda.gov
      name: Jacqueline Campbell
      orcid: 0000-0003-2787-3955
    description: SoyBase, the USDA-ARS soybean genetic database, is a comprehensive
      repository for professionally curated genetics, genomics and related data resources
      for soybean. SoyBase contains genetic, physical and genomic sequence maps integrated
      with qualitative and quantitative traits. The quantitative trait loci (QTL)
      represent more than 18 years of QTL mapping of more than 90 unique traits. SoyBase
      also contains the well-annotated 'Williams 82' genomic sequence and associated
      data mining tools. The genetic and sequence views of the soybean chromosomes
      and the extensive data on traits and phenotypes are extensively interlinked.
      This allows entry to the database using almost any kind of available information,
      such as genetic map symbols, soybean gene names or phenotypic traits. SoyBase
      is the repository for controlled vocabularies for soybean growth, development
      and trait terms, which are also linked to the more general plant ontologies.
    homepage: https://soybase.org/
    name: SoyBase
    prefix: FAIRsharing.z4agsr
    publications:
    - doi: 10.1093/nar/gkp798
      pubmed_id: 20008513
      title: SoyBase, the USDA-ARS soybean genetics and genomics database.
    subjects:
    - Plant Breeding
    - Agriculture
    - Life Science
    - Comparative Genomics
    twitter: SoyBaseDatabase
  integbio:
    description: SoyBase, the USDA-ARS soybean genetic database, is a comprehensive
      repository for professionally curated genetics, genomics and related data resources
      for soybean. SoyBase contains genetic, physical and genomic sequence maps integrated
      with qualitative and quantitative traits. The quantitative trait loci (QTL)
      represent more than 18 years of QTL mapping of more than 90 unique traits. SoyBase
      also contains the well-annotated 'Williams 82' genomic sequence and associated
      data mining tools. The genetic and sequence views of the soybean chromosomes
      and the extensive data on traits and phenotypes are extensively interlinked.
      This allows entry to the database using almost any kind of available information,
      such as genetic map symbols, soybean gene names or phenotypic traits. SoyBase
      is the repository for controlled vocabularies for soybean growth, development
      and trait terms, which are also linked to the more general plant ontologies.
    fairsharing: FAIRsharing.z4agsr
    homepage: https://soybase.org/
    information_keywords:
    - Phenotype
    - Ontology/Terminology/Nomenclature
    - Expression
    - Image/Movie
    - Interaction/Pathway
    - Sequence
    - Method
    maintainer: Iowa State University
    name: SoyBase
    prefix: nbdc01817
    pubmeds:
    - '20008513'
    status: Active
    target_keywords:
    - Organism
    - Genome/Gene
    - Genetic variation
    - DNA
    - Protein
  mappings:
    biocontext: SOYBASE
    fairsharing: FAIRsharing.z4agsr
    integbio: nbdc01817
    miriam: soybase
    n2t: soybase
    ncbi: SoyBase
    pathguide: '44'
    prefixcommons: soy
    re3data: r3d100010846
  miriam:
    deprecated: false
    description: SoyBase is a repository for curated genetics, genomics and related
      data resources for soybean.
    homepage: http://soybase.org/
    id: 00000291
    name: SoyBase
    namespaceEmbeddedInLui: false
    pattern: ^\w+(\-)?\w+(\-)?\w+$
    prefix: soybase
    sampleId: BARC-013845-01256
    uri_format: https://legacy.soybase.org/sbt/search/search_results.php?category=SNP&search_term=$1
  n2t:
    description: SoyBase is a repository for curated genetics, genomics and related
      data resources for soybean.
    example: BARC-013845-01256
    homepage: http://soybase.org/
    name: SoyBase at Iowa State University
    namespaceEmbeddedInLui: false
    pattern: ^\w+(\-)?\w+(\-)?\w+$
    prefix: soybase
    uri_format: http://www.soybase.org/sbt/search/search_results.php?category=SNP&search_term=$1
  name: SoyBase
  ncbi:
    example: Satt005
    homepage: http://soybase.org
    name: Glycine max Genome Database
    prefix: SoyBase
  pathguide:
    abbreviation: SoyBase
    homepage: http://soybase.org/
    name: USDA-ARS Soybean Genetics and Genome Database
    prefix: '44'
  prefix: soybase
  prefixcommons:
    bioportal: '3028'
    description: Growth, trait and development ontology for soybean
    example: SOY_0001650
    homepage: http://soybase.org
    keywords:
    - obo
    - development
    - phenotype
    - spider
    name: SoyOntology
    pattern: ^SOY_\d{7}$
    prefix: soy
  publications:
  - doi: 10.1093/nar/gkp798
    pmc: PMC2808871
    pubmed: '20008513'
    title: SoyBase, the USDA-ARS soybean genetics and genomics database
    year: 2009
  re3data:
    description: SoyBase is a professionally curated repository for genetics, genomics
      and related data resources for soybean. It contains current genetic, physical
      and genomic sequence maps integrated with qualitative and quantitative traits.
      SoyBase includes annotated "Williams 82" genomic sequence and associated data
      mining tools. The repository maintains controlled vocabularies for soybean growth,
      development, and traits that are linked to more general plant ontologies.
    doi: 10.17616/R3S032
    homepage: https://www.soybase.org/
    name: SoyBase
    prefix: r3d100010846
    synonyms:
    - SoyBase and the Soybean Breeder's Toolbox
    xrefs:
      nif: 0000-03483
span:
  comment: see also snap. This ontology only exists in description in the paper and
    does not have an associated web resource
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: Theoretical explanation of to a purely spatiotemporal ontology of change
    and process, as part of a modular ontology of the dynamic features of reality.
  homepage: http://ontology.buffalo.edu/smith/articles/SNAP_SPAN.pdf
  keywords:
  - ontology
  - upper-level ontology
  name: Span
  prefix: span
  synonyms:
  - bfo11span
sparcdrs:
  mappings:
    miriam: sparc.drs
  miriam:
    deprecated: false
    description: The SPARC Data Repository Service (DRS) is an implementation of the
      Global Alliance for Genomics and Health (GA4GH) DRS specification that provides
      a standardized API that enables researchers and other data consumers to access
      and retrieve data objects from various data repositories in a consistent and
      cloud-agnostic way. This implementation provides information for data objects
      in the SPARC repository (sparc.science).
    homepage: https://www.fdilab.org
    id: '00001102'
    name: SPARC DRS
    namespaceEmbeddedInLui: false
    pattern: (?:[a-zA-Z]+\/)?[0-9a-fA-F]{8}-[0-9a-fA-F]{4}-[0-9a-fA-F]{4}-[0-9a-fA-F]{4}-[0-9a-fA-F]{12}
    prefix: sparc.drs
    sampleId: package/8ca67504-3167-4cc8-ba74-98137bb7cd0a
    uri_format: https://services.scicrunch.io/sparc/drs/v1/package/$1
  prefix: sparcdrs
spbase:
  comment: This resource doesn't exist on the web anymore
  deprecated: true
  integbio:
    alt_name: Strongylocentrotus purpuratus database
    description: SpBase is a database of the sea urchin genome. In addition to a genome
      browser, the database contains several types of sequence and gene expression
      information as well as links to external resources. Bulk data is available for
      download.
    homepage: http://www.spbase.org/SpBase/
    information_keywords:
    - Sequence
    - Expression
    maintainer: California Institute of Technology
    name: SpBase
    prefix: nbdc00686
    pubmeds:
    - '19010966'
    target_keywords:
    - Genome/Gene
    - cDNA/EST
  mappings:
    integbio: nbdc00686
    prefixcommons: spbase
  prefix: spbase
  prefixcommons:
    description: SpBase, is designed to present the results of the genome sequencing
      project for the purple sea urchin. THe sequences and annotations emerging from
      this effort are organized in a database that provides the research community
      access to those data not normally presented through NCBI and other large databases.
    example: SPU_000001
    homepage: http://spbase.org
    keywords:
    - genome
    - DNA
    - RNA
    name: SpBase
    pattern: ^SPU_\d+$
    prefix: spbase
    uri_format: http://www.spbase.org/SpBase/search/viewAnnoGeneInfo.php?spu_id=$1
  reviewer:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
spd:
  aberowl:
    description: An ontology for spider comparative biology including anatomical parts
      (e.g. leg, claw), behavior (e.g. courtship, combing) and products (i.g. silk,
      web, borrow).
    download_owl: http://aber-owl.net/media/ontologies/SPD/26/spd.owl
    homepage: http://research.amnh.org/atol/files/
    name: Spider Ontology
    prefix: SPD
  biocontext:
    prefix: SPD
  bioportal:
    contact:
      email: michalik@uni-greifswald.de
      name: Peter Michalik
    description: An ontology for spider anatomy.
    name: Spider Anatomy Ontology
    prefix: SPD
    version: '1.1'
  download_obo: http://purl.obolibrary.org/obo/spd.obo
  example: '0000001'
  fairsharing:
    abbreviation: SPD
    contact:
      email: ramirez@macn.gov.ar
      name: Martin Ramirez
      orcid: 0000-0002-0358-0130
    description: An ontology for spider comparative biology including anatomical parts
      (e.g. leg, claw), behavior (e.g. courtship, combing) and products (i.g. silk,
      web, borrow).
    domains:
    - behavior
    homepage: https://github.com/obophenotype/spider-ontology
    license: CC-BY-3.0
    name: Spider Anatomy Ontology
    prefix: FAIRsharing.yecp83
    publications:
    - doi: 10.3390/d11100202
      title: The Spider Anatomy Ontology (SPD)—A Versatile Tool to Link Anatomy with
        Cross-Disciplinary Data
      year: 2019
    subjects:
    - Life Science
    - Anatomy
  mappings:
    aberowl: SPD
    biocontext: SPD
    bioportal: SPD
    fairsharing: FAIRsharing.yecp83
    obofoundry: spd
    ols: spd
    ontobee: SPD
    prefixcommons: spdo
    wikidata: P4537
    wikidata.entity: Q42404539
  obofoundry:
    contact: ramirez@macn.gov.ar
    contact.github: martinjramirez
    contact.label: Martin Ramirez
    contact.orcid: 0000-0002-0358-0130
    deprecated: false
    description: An ontology for spider comparative biology including anatomical parts
      (e.g. leg, claw), behavior (e.g. courtship, combing) and products (i.g. silk,
      web, borrow).
    domain: anatomy and development
    download.owl: http://purl.obolibrary.org/obo/spd.owl
    homepage: http://research.amnh.org/atol/files/
    license: CC BY 3.0
    license.url: https://creativecommons.org/licenses/by/3.0/
    name: Spider Ontology
    preferredPrefix: SPD
    prefix: spd
    publications:
    - id: https://doi.org/10.3390/d11100202
      title: The Spider Anatomy Ontology (SPD)—A Versatile Tool to Link Anatomy with
        Cross-Disciplinary Data
    repository: https://github.com/obophenotype/spider-ontology
  ols:
    description: An ontology for spider comparative biology including anatomical parts
      (e.g. leg, claw), behavior (e.g. courtship, combing) and products (i.g. silk,
      web, borrow).
    download_owl: http://purl.obolibrary.org/obo/spd.owl
    homepage: http://research.amnh.org/atol/files/
    name: Spider Ontology
    prefix: spd
    tracker: https://github.com/obophenotype/spider-ontology/issues
  ontobee:
    library: Library
    name: Spider Ontology
    prefix: SPD
  pattern: ^\d{7}$
  prefix: spd
  prefixcommons:
    bioportal: '1091'
    description: An ontology for spider comparative biology including anatomical parts
      (e.g. leg, claw), behavior (e.g. courtship, combing) and products (i.g. silk,
      web, borrow).
    example: SPD_0000464
    homepage: http://research.amnh.org/atol/files/
    keywords:
    - obo
    - anatomy
    - spider
    name: Spider Ontology
    pattern: ^SPD_\d{7}$
    prefix: spdo
  publications:
  - doi: 10.3390/d11100202
    pmc: null
    pubmed: null
    title: The Spider Anatomy Ontology (SPD)—A Versatile Tool to Link Anatomy with
      Cross-Disciplinary Data
    year: 2019
  uri_format: http://purl.obolibrary.org/obo/SPD_$1
  wikidata:
    description: identifier for the Spider Ontology which provides a controlled vocabulary
      for spider comparative biology including anatomical parts (e.g. leg, claw),
      behavior (e.g. courtship, combing) and products (i.g. silk, web, borrow)
    example:
    - '0000200'
    - '0000623'
    miriam: SPD
    name: Spider Ontology ID
    pattern: ^[0-9]{7}$
    prefix: P4537
    uri_format: http://purl.obolibrary.org/obo/SPD_$1
    uri_format_rdf: http://purl.obolibrary.org/obo/SPD_$1
spdx:
  bartoc:
    description: 'The SPDX License List is an integral part of the SPDX Specification.
      The SPDX License List itself is a list of commonly found licenses and exceptions
      used in free and open or collaborative software, data, hardware, or documentation.
      The SPDX License List includes a standardized short identifier, the full name,
      the license text, and a canonical permanent URL for each license and exception.


      The purpose of the SPDX License List is to enable efficient and reliable identification
      of such licenses and exceptions in an SPDX document, in source files or elsewhere.'
    homepage: https://spdx.org/licenses/
    license: CC0-1.0
    name: SPDX License List
    pattern: ^.+$
    prefix: '20514'
  contact:
    email: gary@sourceauditor.com
    github: goneall
    name: Gary O'Neall
    orcid: null
  domain: license
  example_extras:
  - GPL-1.0+
  homepage: https://spdx.org/licenses
  keywords:
  - license
  logo: https://spdx.dev/wp-content/uploads/sites/31/2023/08/logo-color.svg
  mappings:
    bartoc: '20514'
    miriam: spdx
    n2t: spdx
  miriam:
    deprecated: false
    description: The SPDX License List is a list of commonly found licenses and exceptions
      used in free and open source and other collaborative software or documentation.
      The purpose of the SPDX License List is to enable easy and efficient identification
      of such licenses and exceptions in an SPDX document, in source files or elsewhere.
      The SPDX License List includes a standardized short identifier, full name, vetted
      license text including matching guidelines markup as appropriate, and a canonical
      permanent URL for each license and exception.
    homepage: https://spdx.org
    id: 00000687
    name: SPDX License List
    namespaceEmbeddedInLui: false
    pattern: ^[0-9A-Za-z\-.]+$
    prefix: spdx
    sampleId: CC-BY-1.0
    uri_format: https://spdx.org/licenses/$1
  n2t:
    description: The SPDX License List is a list of commonly found licenses and exceptions
      used in free and open source and other collaborative software or documentation.
      The purpose of the SPDX License List is to enable easy and efficient identification
      of such licenses and exceptions in an SPDX document, in source files or elsewhere.
      The SPDX License List includes a standardized short identifier, full name, vetted
      license text including matching guidelines markup as appropriate, and a canonical
      permanent URL for each license and exception.
    example: CC-BY-1.0
    homepage: https://spdx.org
    name: SPDX License List
    namespaceEmbeddedInLui: false
    pattern: ^[0-9A-Za-z\-.]+$
    prefix: spdx
    uri_format: https://spdx.org/licenses/$1
  name: Software Package Data Exchange License
  pattern: ^[0-9A-Za-z\-.\+]+$
  prefix: spdx
  repository: https://github.com/spdx/license-list-data
  synonyms:
  - spdx.license
  - spdx.licenses
spdx.term:
  contact:
    email: gary@sourceauditor.com
    github: goneall
    name: Gary O'Neall
    orcid: null
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: A dictionary of named properties and classes for Software Package Data
    Exchange (SPDX) - an open standard for communicating software bill of material
    information, including components, licenses, copyrights, and security references.
    SPDX reduces redundant work by providing a common format for companies and communities
    to share important data, thereby streamlining and improving compliance. [from
    homepage]
  domain: schema
  example: annotation
  github_request_issue: 1598
  homepage: https://spdx.org/rdf/terms/
  logo: https://spdx.dev/wp-content/uploads/sites/31/2023/08/logo-color.svg
  name: Software Package Data Exchange RDF Vocabulary
  prefix: spdx.term
  rdf_uri_format: http://spdx.org/rdf/terms#$1
  synonyms:
  - spdx.terms
  uri_format: http://spdx.org/rdf/terms#$1
sphn:
  contact:
    email: Sabine.Oesterle@sib.swiss
    github: null
    name: Sabine Oesterle
    orcid: 0000-0003-3248-7899
  contributor:
    email: deepak.unni3@gmail.com
    github: deepakunni3
    name: Deepak Unni
    orcid: 0000-0002-3583-7340
  description: The Swiss Personalized Health Network is a national infrastructure
    initiative with the aim to develop, implement, and validate coordinated data infrastructures
    in order to make health-relevant data interoperable and shareable for research
    in Switzerland. The sphn RDF schema builds the foundation for all data exchanges
    within the sphn by integrating semantic information defined in the [sphn dataset](https://sphn.ch/document/sphn-dataset/).
  download_owl: https://git.dcc.sib.swiss/sphn-semantic-framework/sphn-ontology/-/raw/master/rdf_schema/sphn_rdf_schema.owl
  download_rdf: https://git.dcc.sib.swiss/sphn-semantic-framework/sphn-ontology/-/raw/master/rdf_schema/sphn_rdf_schema.ttl
  example: Allergy
  github_request_issue: 535
  homepage: https://www.sphn.ch
  license: CC-BY-4.0
  name: Swiss Personalized Health Network Schema
  pattern: ^\S+$
  prefix: sphn
  repository: https://git.dcc.sib.swiss/sphn-semantic-framework/sphn-ontology
  reviewer:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  uri_format: https://biomedit.ch/rdf/sphn-ontology/sphn#$1
spike.map:
  biocontext:
    prefix: SPIKE.MAP
  contact:
    email: Yossih@tauex.tau.ac.il
    github: null
    name: Yosef Shiloh
    orcid: 0000-0002-1538-6060
  mappings:
    biocontext: SPIKE.MAP
    miriam: spike.map
    n2t: spike.map
    prefixcommons: spike
  miriam:
    deprecated: false
    description: SPIKE (Signaling Pathways Integrated Knowledge Engine) is a repository
      that can store, organise and allow retrieval of pathway information in a way
      that will be useful for the research community. The database currently focuses
      primarily on pathways describing DNA damage response, cell cycle, programmed
      cell death and hearing related pathways. Pathways are regularly updated, and
      additional pathways are gradually added. The complete database and the individual
      maps are freely exportable in several formats. This collection references pathway
      maps.
    homepage: http://www.cs.tau.ac.il/~spike/
    id: '00000321'
    name: SPIKE Map
    namespaceEmbeddedInLui: false
    pattern: ^spike\d{5}$
    prefix: spike.map
    sampleId: spike00001
    uri_format: http://www.cs.tau.ac.il/~spike/maps/$1.html
  n2t:
    description: SPIKE (Signaling Pathways Integrated Knowledge Engine) is a repository
      that can store, organise and allow retrieval of pathway information in a way
      that will be useful for the research community. The database currently focuses
      primarily on pathways describing DNA damage response, cell cycle, programmed
      cell death and hearing related pathways. Pathways are regularly updated, and
      additional pathways are gradually added. The complete database and the individual
      maps are freely exportable in several formats. This collection references pathway
      maps.
    example: spike00001
    homepage: http://www.cs.tau.ac.il/~spike/
    name: SPIKE database at Tel Aviv University
    namespaceEmbeddedInLui: false
    pattern: ^spike\d{5}$
    prefix: spike.map
    uri_format: http://www.cs.tau.ac.il/~spike/maps/$1.html
  prefix: spike.map
  prefixcommons:
    description: SPIKE (Signaling Pathway Integrated Knowledge Engine) is an interactive
      software environment that graphically displays biological signaling networks,
      allows dynamic layout and navigation through these networks, and enables the
      superposition of DNA microarray and other functional genomics data on interaction
      maps.
    example: spike00001
    homepage: http://www.cs.tau.ac.il/~spike/
    keywords:
    - pathway
    - DNA
    - gene expression
    name: Signaling Pathway Integrated Knowledge Engine
    pattern: ^spike\d{5}$
    prefix: spike
    pubmed_ids:
    - '18289391'
    - '21097778'
    synonyms:
    - spike.map
  publications:
  - doi: 10.1093/nar/gkq1167
    pmc: PMC3014840
    pubmed: '21097778'
    title: 'SPIKE: a database of highly curated human signaling pathways'
    year: 2010
  - doi: 10.1186/1471-2105-9-110
    pmc: PMC2263022
    pubmed: '18289391'
    title: SPIKE--a database, visualization and analysis tool of cellular signaling
      pathways
    year: 2008
splash:
  biocontext:
    prefix: SPLASH
  fairsharing:
    abbreviation: SPLASH
    contact:
      email: ofiehn@ucdavis.edu
      name: Oliver Fiehn
      orcid: 0000-0002-6261-8928
    description: The SPLASH (SPectraL hASH) identifier is a unique and unambiguous
      database-independent spectral identifier for chemical structures. It contains
      four separate blocks that define different layers of information, separated
      by dashes. The first block is the SPLASH identifier, the second and third are
      spectral summary blocks, and the fourth is the full spectrum hash block. The
      first block (splash10) encodes the SPLASH identifier, starting with letters
      for semantic web compatibility, followed by a number representing the measurement
      type (1 for MS, 2 and above for other data types to be included in the future)
      and the SPLASH version number, starting at 0, to allow future specification
      updates. The the second and third blocks are , intensities are summed over fixed
      (but different) bin sizes and wrapped over ten bins. The second block (0002)
      is formed using a reduced spectrum (the top ten or fewer ions greater than 10%
      of the base peak). This reduced spectrum is summed over bins of 5 Da. Each bin
      is then scaled to a single-digit integral value in base 3 (0–2), and the resulting
      10 digit histogram is converted to a base 36 number, resulting in a 4-digit
      block. In the third block (0900000000) the intensities are summed over 100-Da
      bin sizes, each bin is then scaled to a single-digit, integral base-10 digit
      (0–9). The fourth block (full spectrum hash) is represented by a Secure Hash
      Algorithm SHA256 (numbers and lowercase letters only), calculated in hexadecimal
      notation and truncated to 20 characters. The full spectrum string of m/z and
      relative intensity pairs are sorted by ascending m/z and then by descending
      intensity. The m/z value is multiplied by 10^6, cast to a long (64-bit) integer
      and joined with the normalized intensity as strings separated by a colon. The
      resulting ion pairs are then joined, delimited by a single space.
    domains:
    - Mass spectrum
    homepage: https://splash.fiehnlab.ucdavis.edu/
    name: The Spectral Hash Identifier
    prefix: FAIRsharing.f31b8f
    publications:
    - doi: 10.1038/nbt.3689
      pubmed: '27824832'
      title: SPLASH, a hashed identifier for mass spectra
      year: 2016
    repository: https://github.com/berlinguyinca/spectra-hash
    subjects:
    - Lipidomics
    - Metabolomics
    - Proteomics
  mappings:
    biocontext: SPLASH
    fairsharing: FAIRsharing.f31b8f
    miriam: splash
    n2t: splash
  miriam:
    deprecated: false
    description: The spectra hash code (SPLASH) is a unique and non-proprietary identifier
      for spectra, and is independent of how the spectra were acquired or processed.
      It can be easily calculated for a wide range of spectra, including Mass spectroscopy,  infrared
      spectroscopy, ultraviolet and nuclear magnetic resonance.
    homepage: http://mona.fiehnlab.ucdavis.edu/
    id: '00000566'
    name: SPLASH
    namespaceEmbeddedInLui: false
    pattern: ^splash\d[A-Z-a-z0-9]-[A-Za-z0-9]+-[A-Za-z0-9]+$
    prefix: splash
    sampleId: splash10-0zq2000000-77302b0326a418630a84
    uri_format: http://mona.fiehnlab.ucdavis.edu/#/spectra/splash/$1
  n2t:
    description: The spectra hash code (SPLASH) is a unique and non-proprietary identifier
      for spectra, and is independent of how the spectra were acquired or processed.
      It can be easily calculated for a wide range of spectra, including Mass spectroscopy,  infrared
      spectroscopy, ultraviolet and nuclear magnetic resonance.
    example: splash10-0zq2000000-77302b0326a418630a84
    homepage: http://mona.fiehnlab.ucdavis.edu/
    name: Mass Bank of North America (MoNA)
    namespaceEmbeddedInLui: false
    pattern: ^splash\d[A-Z-a-z0-9]-[A-Za-z0-9]+-[A-Za-z0-9]+$
    prefix: splash
    uri_format: http://mona.fiehnlab.ucdavis.edu/#/spectra/splash/$1
  name: Spectra Hash Code
  prefix: splash
splicenest:
  comment: This resource doesn't exist on the web anymore
  deprecated: true
  mappings:
    prefixcommons: splicenest
  prefix: splicenest
  prefixcommons:
    description: SpliceNest [1] is a web based graphical tool to explore gene structure,
      including alternative splicing, based on a mapping on the EST consensus sequences
      (contigs) from GeneNest [2] to the complete human genome.
    example: Hs635
    homepage: http://splicenest.molgen.mpg.de/
    keywords:
    - gene
    - DNA
    - genome
    name: SpliceNest
    pattern: ^[a-z]+\d+$
    prefix: splicenest
    uri_format: http://splicenest.molgen.mpg.de/cgi-bin/splicegraph.cgi?cluster=$1
  reviewer:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
spp:
  fairsharing:
    abbreviation: SPP
    contact:
      email: nmckenna@bcm.edu
      name: Neil McKenna
      orcid: 0000-0001-6689-0104
    description: The Signaling Pathways Project is an integrated 'omics knowledgebase
      based upon public, manually curated transcriptomic and cistromic (ChIP-Seq)
      datasets involving genetic and small molecule manipulations of cellular receptors,
      enzymes and transcription factors. Our goal is to create a resource where scientists
      can routinely generate research hypotheses or validate bench data relevant to
      cellular signaling pathways.
    homepage: https://www.signalingpathways.org/index.jsf
    license: CC-BY-4.0
    name: Signaling Pathways Project
    prefix: FAIRsharing.WxI96O
    publications:
    - doi: 10.1038/s41597-019-0193-4
      pubmed_id: null
      title: The Signaling Pathways Project, an integrated ‘omics knowledgebase for
        mammalian cellular signaling pathways
    subjects:
    - Transcriptomics
    - Omics
    twitter: sigpathproject
  mappings:
    fairsharing: FAIRsharing.WxI96O
    miriam: spp
    re3data: r3d100013650
  miriam:
    deprecated: false
    description: The Signaling Pathways Project is an integrated 'omics knowledgebase
      based upon public, manually curated transcriptomic and cistromic (ChIP-Seq)
      datasets involving genetic and small molecule manipulations of cellular receptors,
      enzymes and transcription factors. Our goal is to create a resource where scientists
      can routinely generate research hypotheses or validate bench data relevant to
      cellular signaling pathways.
    homepage: https://www.signalingpathways.org/index.jsf
    id: '00000726'
    name: Signaling Pathways Project
    namespaceEmbeddedInLui: false
    pattern: ^10.\w{4}/\w{10}$
    prefix: spp
    sampleId: 10.1621/vwN2g2HaX3
    uri_format: https://www.signalingpathways.org/datasets/dataset.jsf?doi=$1
  prefix: spp
  publications:
  - doi: 10.1038/s41597-019-0193-4
    pmc: PMC6823428
    pubmed: '31672983'
    title: The Signaling Pathways Project, an integrated 'omics knowledgebase for
      mammalian cellular signaling pathways
    year: 2019
  re3data:
    description: 'The goal of the Signaling Pathways Project knowledgebase is to allow
      bench researchers to routinely ask sophisticated questions of the universe of
      multi-omics data points generated by the cellular signaling community.

      SPP is dedicated to helping researchers to make sense of the often overwhelming
      volume of multi-omics information in the field of cellular signaling.'
    doi: 10.17616/R31NJN0Y
    homepage: https://www.signalingpathways.org/datasets/index.jsf
    name: Signaling Pathways Project
    prefix: r3d100013650
    synonyms:
    - SSP
srao:
  contact:
    email: allyson.lister@oerc.ox.ac.uk
    github: allysonlister
    name: Allyson Lister
    orcid: 0000-0002-7702-4495
  download_obo: https://github.com/FAIRsharing/subject-ontology/raw/refs/heads/master/SRAO.obo
  download_owl: https://github.com/FAIRsharing/subject-ontology/raw/refs/heads/master/SRAO.owl
  example: '0000400'
  fairsharing:
    abbreviation: SRAO
    description: The Subject Resource Application Ontology (SRAO) is an application
      ontology describing subject areas / academic disciplines used within FAIRsharing
      records by curators and the user community. It is built in conjunction with
      the Domain Resource Application Ontology (DRAO), which contains more specific
      domain terms and other descriptors. All classes within SRAO come from publicly-available
      ontologies and controlled vocabularies.
    domains:
    - Resource metadata
    - Classification
    - FAIR
    homepage: https://github.com/FAIRsharing/subject-ontology
    license: CC BY-SA 4.0
    name: Subject Resource Application Ontology
    prefix: FAIRsharing.b1xD9f
    repository: https://github.com/FAIRsharing/subject-ontology/issues
    subjects:
    - Agriculture
    - Environmental Science
    - Life Science
    - Computer Science
    - Biomedical Science
    - Humanities
    - Natural Science
    - Earth Science
    twitter: FAIRsharing_org
    user_defined_tags:
    - Metadata standardization
  keywords:
  - metascience
  - topics
  mappings:
    fairsharing: FAIRsharing.b1xD9f
    ols: srao
  name: FAIRsharing Subject Ontology
  ols:
    contact: contact@fairsharing.org
    description: The FAIRsharing Subject Ontology (SRAO) is an application ontology
      for the categorization of research disciplines across all research domains,
      from the humanities to the natural sciences. It utilizes multiple external vocabularies.
    download_owl: https://github.com/FAIRsharing/subject-ontology/raw/master/SRAO.owl
    homepage: https://github.com/FAIRsharing/subject-ontology
    name: FAIRsharing Subject Ontology (SRAO)
    prefix: srao
    uri_format: http://www.fairsharing.org/ontology/subject$1
    version: '2025-06-01'
    version.iri: http://www.fairsharing.org/ontology/subject/SRAO/releases/2025-06-01/SRAO.owl
  part_of_database: fairsharing
  pattern: ^\d{7}$
  prefix: srao
  repository: https://github.com/FAIRsharing/subject-ontology
  uri_format: http://www.fairsharing.org/ontology/subject/SRAO_$1
ssbd.dataset:
  contact:
    email: sonami@riken.jp
    github: null
    name: Shuichi Onami
    orcid: 0000-0002-8255-1724
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: Systems Science of Biological Dynamics database (SSBD:database) is
    an added-value database for biological dynamics. It provides a rich set of open
    resources for analyzing quantitative data and microscopy images of biological
    objects, such as single-molecule, cell, tissue, individual, etc., and software
    tools for analysis. Quantitative biological data and microscopy images are collected
    from a variety of species, sources, and methods. These include data obtained from
    both experiments and computational simulations.
  example: '1'
  fairsharing:
    abbreviation: SSBD
    description: SSBD is a database that collects and shares quantitative biological
      dynamics data, microscopy images, and software tools. SSBD provides a rich set
      of resources for analyzing quantitative biological data, such as single-molecule,
      cell, and gene expression nuclei. Quantitative biological data are collected
      from a variety of species, sources and methods. These include data obtained
      from both experiment and computational simulation.
    homepage: http://ssbd.qbic.riken.jp
    license: http://ssbd.qbic.riken.jp/copyright
    name: 'SSBD: Systems Science of Biological Dynamics'
    prefix: FAIRsharing.we2r5a
    publications:
    - doi: 10.1093/bioinformatics/btw417
      pubmed_id: 27412095
      title: 'SSBD: a database of quantitative data of spatiotemporal dynamics of
        biological phenomena.'
    subjects:
    - Molecular Dynamics
    - Developmental Biology
    - Cell Biology
  homepage: https://ssbd.riken.jp
  mappings:
    fairsharing: FAIRsharing.we2r5a
  name: System Science of Biological Dynamics dataset
  pattern: ^\d+$
  prefix: ssbd.dataset
  publications:
  - doi: 10.1093/bioinformatics/btw417
    pmc: PMC5181557
    pubmed: '27412095'
    title: 'SSBD: a database of quantitative data of spatiotemporal dynamics of biological
      phenomena'
    year: 2016
  - doi: 10.1093/bioinformatics/btw417
    pmc: null
    pubmed: null
    title: 'SSBD: a database of quantitative data of spatiotemporal dynamics of biological
      phenomena.'
    year: null
  uri_format: https://ssbd.riken.jp/database/dataset/$1
ssbd.project:
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: Systems Science of Biological Dynamics database (SSBD:database) is
    an added-value database for biological dynamics. It provides a rich set of open
    resources for analyzing quantitative data and microscopy images of biological
    objects, such as single-molecule, cell, tissue, individual, etc., and software
    tools for analysis. Quantitative biological data and microscopy images are collected
    from a variety of species, sources, and methods. These include data obtained from
    both experiments and computational simulations.
  example: '1'
  homepage: https://ssbd.riken.jp
  name: System Science of Biological Dynamics project
  pattern: ^\d+$
  prefix: ssbd.project
  uri_format: https://ssbd.riken.jp/database/project/$1
ssn:
  aberowl:
    description: This ontology describes sensors, actuators and observations, and
      related concepts. It does not describe domain concepts, time, locations, etc.
      these are intended to be included from other ontologies via OWL imports.
    download_owl: http://aber-owl.net/media/ontologies/SSN/2/ssn.owl
    homepage: https://www.w3.org/TR/vocab-ssn/
    name: Semantic Sensor Network Ontology
    prefix: SSN
    version: "New modular version of the SSN ontology. \n\nThis ontology was originally\
      \ developed in 2009-2011 by the W3C Semantic Sensor Networks Incubator Group\
      \ (SSN-XG). For more information on the group's activities see: http://www.w3.org/2005/Incubator/ssn/.\
      \ The ontology was revised and modularized in 2015-2017 by the W3C/OGC Spatial\
      \ Data on the Web Working Group, see: https://www.w3.org/2015/spatial/wiki/Semantic_Sensor_Network_Ontology.\
      \ \n\nIn particular, (a) the scope is extended to include actuation and sampling;\
      \ (b) the core concepts and properties are factored out into the SOSA ontology.\
      \ The SSN ontology imports SOSA and adds formal axiomatization consistent with\
      \ the text definitions in SOSA, and adds classes and properties to accommodate\
      \ the scope of the original SSN ontology."
  agroportal:
    contact:
      email: simon.cox@csiro.au
      name: Simon Cox
    description: This ontology describes sensors, actuators and observations, and
      related concepts. It does not describe domain concepts, time, locations, etc.
      these are intended to be included from other ontologies via OWL imports.
    example_uri: http://www.w3.org/ns/ssn/Stimulus
    homepage: https://www.w3.org/TR/vocab-ssn/
    license: http://www.w3.org/Consortium/Legal/2015/copyright-software-and-document
    name: Semantic Sensor Network Ontology
    prefix: SSN
    publications:
    - https://doi.org/10.3233/SW-180320
    repository: https://github.com/w3c/sdw
    version: "New modular version of the SSN ontology. \n\nThis ontology was originally\
      \ developed in 2009-2011 by the W3C Semantic Sensor Networks Incubator Group\
      \ (SSN-XG). For more information on the group's activities see: http://www.w3.org/2005/Incubator/ssn/.\
      \ The ontology was revised and modularized in 2015-2017 by the W3C/OGC Spatial\
      \ Data on the Web Working Group, see: https://www.w3.org/2015/spatial/wiki/Semantic_Sensor_Network_Ontology.\
      \ \n\nIn particular, (a) the scope is extended to include actuation and sampling;\
      \ (b) the core concepts and properties are factored out into the SOSA ontology.\
      \ The SSN ontology imports SOSA and adds formal axiomatization consistent with\
      \ the text definitions in SOSA, and adds classes and properties to accommodate\
      \ the scope of the original SSN ontology."
  bioportal:
    contact:
      email: jgraybeal@stanford.edu
      name: John Graybeal
    description: This ontology describes sensors, actuators and observations, and
      related concepts. It does not describe domain concepts, time, locations, etc.
      these are intended to be included from other ontologies via OWL imports.
    name: Semantic Sensor Network Ontology
    prefix: SSN
    version: "New modular version of the SSN ontology. \n\nThis ontology was originally\
      \ developed in 2009-2011 by the W3C Semantic Sensor Networks Incubator Group\
      \ (SSN-XG). For more information on the group's activities see: http://www.w3.org/2005/Incubator/ssn/.\
      \ The ontology was revised and modularized in 2015-2017 by the W3C/OGC Spatial\
      \ Data on the Web Working Group, see: https://www.w3.org/2015/spatial/wiki/Semantic_Sensor_Network_Ontology.\
      \ \n\nIn particular, (a) the scope is extended to include actuation and sampling;\
      \ (b) the core concepts and properties are factored out into the SOSA ontology.\
      \ The SSN ontology imports SOSA and adds formal axiomatization consistent with\
      \ the text definitions in SOSA, and adds classes and properties to accommodate\
      \ the scope of the original SSN ontology."
  contact:
    email: dr.shorthair@pm.me
    github: dr-shorthair
    name: Simon Cox
    orcid: 0000-0002-3884-3420
  contributor:
    email: philip.stroemert@tib.eu
    github: StroemPhi
    name: Philip Strömert
    orcid: 0000-0002-1595-3213
  description: This ontology describes sensors, actuators and observations, and related
    concepts. It does not describe domain concepts, time, locations, etc. these are
    intended to be included from other ontologies via OWL imports.
  download_rdf: https://www.w3.org/ns/ssn/
  example: hasProperty
  fairsharing:
    abbreviation: SSN
    description: 'The Semantic Sensor Network (SSN) ontology is an ontology for describing
      sensors and their observations, the involved procedures, the studied features
      of interest, the samples used to do so, and the observed properties, as well
      as actuators. SSN follows a horizontal and vertical modularization architecture
      by including a lightweight but self-contained core ontology called SOSA (Sensor,
      Observation, Sample, and Actuator) for its elementary classes and properties.
      With their different scope and different degrees of axiomatization, SSN (http://www.w3.org/ns/ssn/)
      and SOSA (http://www.w3.org/ns/sosa/) are able to support a wide range of applications
      and use cases, including satellite imagery, large-scale scientific monitoring,
      industrial and household infrastructures, social sensing, citizen science, observation-driven
      ontology engineering, and the Web of Things. '
    domains:
    - Resource metadata
    - Imaging
    - Monitoring
    homepage: https://www.w3.org/TR/vocab-ssn/
    name: Semantic Sensor Network Ontology
    prefix: FAIRsharing.c0bvcy
    publications:
    - doi: 10.1016/j.websem.2012.05.003
      title: The SSN ontology of the W3C semantic sensor network incubator group
      year: 2012
    - doi: 10.3233/sw-180320
      title: 'The Modular SSN Ontology: A Joint W3C and OGC Standard Specifying the
        Semantics of Sensors, Observations, Sampling, and Actuation'
      year: 2019
    - doi: 10.1016/j.websem.2018.06.003
      title: 'SOSA: A lightweight ontology for sensors, observations, samples, and
        actuators'
      year: 2018
    repository: https://github.com/w3c/sdw/issues
    subjects:
    - Remote Sensing
    user_defined_tags:
    - Sensor data
    - Web of Things
  github_request_issue: 1272
  homepage: https://www.w3.org/TR/vocab-ssn
  license: http://www.w3.org/Consortium/Legal/2015/copyright-software-and-document
  lov:
    description: This ontology describes sensors and observations, and related concepts.  It
      does not describe domain concepts, time, locations, etc. these are intended
      to be included from other ontologies via OWL imports.
    homepage: http://www.w3.org/ns/ssn/
    keywords:
    - IoT
    - Methods
    - W3C Rec
    modified: '2017-04-17'
    name: Semantic Sensor Network Ontology
    prefix: ssn
    uri_prefix: http://www.w3.org/ns/ssn/$1
  mappings:
    aberowl: SSN
    agroportal: SSN
    bioportal: SSN
    fairsharing: FAIRsharing.c0bvcy
    lov: ssn
    tib: ssn
    zazuko: ssn
  name: Semantic Sensor Network Ontology
  prefix: ssn
  repository: https://github.com/w3c/sdw-sosa-ssn
  reviewer:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  tib:
    description: This ontology describes sensors, actuators and observations, and
      related concepts. It does not describe domain concepts, time, locations, etc.
      these are intended to be included from other ontologies via OWL imports.
    download_rdf: https://www.w3.org/ns/ssn/ssn.ttl
    homepage: https://www.w3.org/TR/vocab-ssn/
    keywords:
    - NFDI4ING
    - NFDI4CHEM
    - ESS
    - engineering
    name: Semantic Sensor Network Ontology
    prefix: ssn
    tracker: https://github.com/w3c/sdw/issues
    uri_format: http://www.w3.org/ns/ssn/$1
  uri_format: http://www.w3.org/ns/ssn/$1
  zazuko:
    prefix: ssn
    uri_format: http://www.w3.org/ns/ssn/$1
ssn.system:
  contact:
    email: dr.shorthair@pm.me
    github: dr-shorthair
    name: Simon Cox
    orcid: 0000-0002-3884-3420
  contributor:
    email: philip.stroemert@tib.eu
    github: StroemPhi
    name: Philip Strömert
    orcid: 0000-0002-1595-3213
  description: This ontology describes system capabilities, operating ranges, and
    survival ranges. Please report any errors to the W3C Spatial Data on the Web Working
    Group via the SDW WG Public List public-sdw-wg@w3.org
  download_rdf: http://www.w3.org/ns/ssn/systems
  example: qualityOfObservation
  github_request_issue: 1270
  homepage: https://www.w3.org/TR/vocab-ssn/
  license: http://www.w3.org/Consortium/Legal/2015/copyright-software-and-document
  mappings:
    tib: ssnsystem
  name: System capabilities, operating ranges, and survival ranges ontology
  prefix: ssn.system
  reviewer:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  tib:
    contact: public-sdw-comments@w3.org
    description: This ontology describes system capabilities, operating ranges, and
      survival ranges.
    download_rdf: https://www.w3.org/ns/ssn/systems/ssn-system.rdf
    homepage: https://www.w3.org/TR/vocab-ssn/#System-capabilities
    keywords:
    - NFDI4ING
    - NFDI4CHEM
    - engineering
    name: System capabilities, operating ranges, and survival ranges ontology
    prefix: ssnsystem
    tracker: https://github.com/w3c/sdw/issues
    uri_format: http://www.w3.org/ns/ssn/systems/$1
  uri_format: http://www.w3.org/ns/ssn/systems/$1
ssrn.article:
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  homepage: https://ssrn.com
  mappings:
    wikidata: P893
  name: Social Science Research Network Article
  prefix: ssrn.article
  references:
  - https://github.com/biopragmatics/bioregistry/pull/1171
  wikidata:
    description: identifier for an article/paper at the SSRN
    example:
    - '1667659'
    - '3345366'
    - '956170'
    name: SSRN article ID
    prefix: P893
    uri_format: https://ssrn.com/abstract=$1
ssrn.author:
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  homepage: https://ssrn.com
  keywords:
  - person
  - researcher
  mappings:
    wikidata: P3747
  name: Social Science Research Network Author
  prefix: ssrn.author
  references:
  - https://github.com/biopragmatics/bioregistry/pull/1171
  wikidata:
    description: identifier for an author at the Social Science Research Network
    example:
    - '112517'
    - '1585413'
    - '9'
    name: SSRN author ID
    pattern: ^[1-9]\d{0,6}$
    prefix: P3747
    uri_format: https://ssrn.com/author=$1
sssom:
  contact:
    email: nicolas.matentzoglu@gmail.com
    github: matentzn
    name: Nicolas Matentzoglu
    orcid: 0000-0002-7356-1779
  contributor:
    email: nicolas.matentzoglu@gmail.com
    github: matentzn
    name: Nicolas Matentzoglu
    orcid: 0000-0002-7356-1779
  description: SSSOM is a Simple Standard for Sharing Ontological Mappings, providing
    - a TSV-based representation for ontology term mappings - a comprehensive set
    of standard metadata elements to describe mappings and - a standard translation
    between the TSV and the Web Ontology Language (OWL). Most metadata elements, such
    as "sssom:mapping_justification" are defined in the sssom namespace.
  example: mapping_justification
  example_extras:
  - superClassOf
  github_request_issue: 759
  homepage: https://w3id.org/sssom
  license: BSD-3-Clause
  name: Simple Standard for Sharing Ontological Mappings
  pattern: ^[A-Za-z_]+$
  prefix: sssom
  repository: https://github.com/mapping-commons/sssom
  reviewer:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  uri_format: https://w3id.org/sssom/$1
sstoss:
  comment: This resource doesn't exist on the web anymore
  deprecated: true
  mappings:
    prefixcommons: sstoss
  prefix: sstoss
  prefixcommons:
    description: SSToSS is a database which provides sequence-structural templates
      of single member protein domain superfamilies like PASS2. Sequence-structural
      templates are recognized by considering the content and overlap of sequence
      similarity and structural parameters like, solvent inaccessibility, secondary
      structural content, hydrogen bonding and spatial packing of the residues among
      the protein of single member superfamilies.
    example: 01.01.005
    homepage: http://caps.ncbs.res.in/SSTOSS/index.htm
    keywords:
    - protein
    - structure
    name: Sequence-Structural Templates of Single-member Superfamilies
    pattern: ^\d+.\d+.\d+$
    prefix: sstoss
    uri_format: http://caps.ncbs.res.in/cgi-bin/mini/databases/SSTOSS/sstoss.cgi?code=$1
  reviewer:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
stap:
  biocontext:
    prefix: STAP
  contact:
    email: bhsung@kribb.re.kr
    github: null
    name: Bong Hyun Sung
    orcid: 0000-0002-8992-1118
  fairsharing:
    abbreviation: STAP
    description: The STAP database contains refined versions of the NMR structures
      deposited in PDB. These refinements have been performed using statistical torsion
      angle potential and structurally- or experimentally- derived distance potential.
      The refined structures have a significantly improved structural quality compared
      to their initial NMR structure.
    homepage: http://psb.kobic.re.kr/stap/refinement/
    name: Statistical Torsional Angles Potentials of NMR Refinement Database
    prefix: FAIRsharing.ja9cdq
    publications:
    - doi: 10.1093/nar/gkr1021
      pubmed_id: 22102572
      title: 'STAP Refinement of the NMR database: a database of 2405 refined solution
        NMR structures.'
    - doi: 10.1002/prot.24265
      pubmed_id: 23408564
      title: 'Statistical torsion angle potential energy functions for protein structure
        modeling: a bicubic interpolation approach.'
    - doi: 10.1371/journal.pone.0108888
      pubmed_id: 25279564
      title: Protein NMR structures refined without NOE data.
    - doi: 10.1093/bioinformatics/btv595
      pubmed_id: 26504145
      title: 'NMRe: a web server for NMR protein structure refinement with high-quality
        structure validation scores.'
    subjects:
    - Statistics
    - Life Science
  mappings:
    biocontext: STAP
    fairsharing: FAIRsharing.ja9cdq
    miriam: stap
    n2t: stap
  miriam:
    deprecated: true
    description: STAP (Statistical Torsional Angles Potentials) was developed since,
      according to several studies, some nuclear magnetic resonance (NMR) structures
      are of lower quality, are less reliable and less suitable for structural analysis
      than high-resolution X-ray crystallographic structures. The refined NMR solution
      structures (statistical torsion angle potentials; STAP) in the database are
      refined from the Protein Data Bank (PDB).
    homepage: http://psb.kobic.re.kr/STAP/refinement/
    id: 00000399
    name: STAP
    namespaceEmbeddedInLui: false
    pattern: ^[0-9][A-Za-z0-9]{3}$
    prefix: stap
    sampleId: 1a24
    uri_format: http://psb.kobic.re.kr/STAP/refinement1/result.php?search=$1
  n2t:
    description: STAP (Statistical Torsional Angles Potentials) was developed since,
      according to several studies, some nuclear magnetic resonance (NMR) structures
      are of lower quality, are less reliable and less suitable for structural analysis
      than high-resolution X-ray crystallographic structures. The refined NMR solution
      structures (statistical torsion angle potentials; STAP) in the database are
      refined from the Protein Data Bank (PDB).
    example: 1a24
    homepage: http://psb.kobic.re.kr/STAP/refinement/
    name: STAP at Korean Bioinformation Center
    namespaceEmbeddedInLui: false
    pattern: ^[0-9][A-Za-z0-9]{3}$
    prefix: stap
    uri_format: http://psb.kobic.re.kr/STAP/refinement1/result.php?search=$1
  name: Statistical Torsional Angles Potentials
  prefix: stap
  publications:
  - doi: 10.1093/bioinformatics/btv595
    pmc: null
    pubmed: '26504145'
    title: 'NMRe: a web server for NMR protein structure refinement with high-quality
      structure validation scores'
    year: 2015
  - doi: 10.1371/journal.pone.0108888
    pmc: PMC4184813
    pubmed: '25279564'
    title: Protein NMR structures refined without NOE data
    year: 2014
  - doi: 10.1002/prot.24265
    pmc: null
    pubmed: '23408564'
    title: 'Statistical torsion angle potential energy functions for protein structure
      modeling: a bicubic interpolation approach'
    year: 2013
  - doi: 10.1093/nar/gkr1021
    pmc: PMC3245188
    pubmed: '22102572'
    title: 'STAP Refinement of the NMR database: a database of 2405 refined solution
      NMR structures'
    year: 2011
stato:
  aberowl:
    description: STATO is a general-purpose STATistics Ontology. Its aim is to provide
      coverage for processes such as statistical tests, their conditions of application,
      and information needed or resulting from statistical methods, such as probability
      distributions, variables, spread and variation metrics. STATO also covers aspects
      of experimental design and description of plots and graphical representations
      commonly used to provide visual cues of data distribution or layout and to assist
      review of the results.
    download_owl: http://aber-owl.net/media/ontologies/STATO/16/stato.owl
    homepage: http://stato-ontology.org/
    name: The Statistical Methods Ontology
    prefix: STATO
  biocontext:
    prefix: STATO
  bioportal:
    contact:
      email: alejandra.gonzalez.beltran@gmail.com
      name: Alejandra Gonzalez-Beltran
    description: STATO is a general-purpose STATistics Ontology. Its aim is to provide
      coverage for processes such as statistical tests, their conditions of applications,
      and information needed or resulting from statistical methods, such as probability
      distributions, variable, spread and variation metrics. STATO also covers aspects
      of experimental design and description of plots and graphical representations
      commonly used to provide visual cues of data distribution or layout and to assist
      review of the results.
    homepage: http://stato-ontology.org/
    name: Statistics Ontology
    prefix: STATO
    publications:
    - http://stato-ontology.org/
    version: '2025-02-23'
  example: 0000288
  fairsharing:
    abbreviation: STATO
    contact:
      email: philippe.rocca-serra@oerc.ox.ac.uk
      name: Philippe Rocca-Serra
      orcid: 0000-0001-9853-5668
    description: STATO is a general-purpose STATistics Ontology. Its aim is to provide
      coverage for processes such as statistical tests, their conditions of applications,
      and information needed or resulting from statistical methods, such as probability
      distributions, variable, spread and variation metrics. STATO also covers aspects
      of experimental design and description of plots and graphical representations
      commonly used to provide visual cues of data distribution or layout and to assist
      review of the results.
    domains:
    - Experimental measurement
    - Data analysis
    - graph
    - study design
    homepage: http://stato-ontology.org/
    license: CC-BY-3.0
    name: Statistics Ontology
    prefix: FAIRsharing.na5xp
    repository: https://github.com/ISA-tools/stato
    subjects:
    - Omics
    - Statistics
    - data visualization
  mappings:
    aberowl: STATO
    biocontext: STATO
    bioportal: STATO
    fairsharing: FAIRsharing.na5xp
    miriam: stato
    obofoundry: stato
    ols: stato
    ontobee: STATO
    tib: stato
    wikidata.entity: Q83428681
  miriam:
    deprecated: false
    description: STATO is the statistical methods ontology. It contains concepts and
      properties related to statistical methods, probability distributions and other
      concepts related to statistical analysis, including relationships to study designs
      and plots.
    homepage: https://www.ebi.ac.uk
    id: '00001051'
    name: Statistical Ontology
    namespaceEmbeddedInLui: true
    pattern: ^STATO:\d+$
    prefix: stato
    sampleId: 0000138
    uri_format: https://www.ebi.ac.uk/ols4/ontologies/stato/classes?obo_id=STATO:$1
  obofoundry:
    appears_in:
    - ontoavida
    - psdo
    - scdo
    contact: proccaserra@gmail.com
    contact.github: proccaserra
    contact.label: Philippe Rocca-Serra
    contact.orcid: 0000-0001-9853-5668
    deprecated: false
    description: STATO is a general-purpose STATistics Ontology. Its aim is to provide
      coverage for processes such as statistical tests, their conditions of application,
      and information needed or resulting from statistical methods, such as probability
      distributions, variables, spread and variation metrics. STATO also covers aspects
      of experimental design and description of plots and graphical representations
      commonly used to provide visual cues of data distribution or layout and to assist
      review of the results.
    domain: information technology
    download.owl: http://purl.obolibrary.org/obo/stato.owl
    homepage: http://stato-ontology.org/
    license: CC BY 3.0
    license.url: http://creativecommons.org/licenses/by/3.0/
    logo: https://raw.githubusercontent.com/ISA-tools/stato/dev/images/stato-logo-3.png
    name: The Statistical Methods Ontology
    preferredPrefix: STATO
    prefix: stato
    publications:
    - id: https://www.ncbi.nlm.nih.gov/pubmed/31831744
      title: Experiment design driven FAIRification of omics data matrices, an exemplar
    - id: https://www.ncbi.nlm.nih.gov/pubmed/32109232
      title: Semantic concept schema of the linear mixed model of experimental observations
    repository: https://github.com/ISA-tools/stato
  ols:
    description: STATO is the statistical methods ontology. It contains concepts and
      properties related to statistical methods, probability distributions and other
      concepts related to statistical analysis, including relationships to study designs
      and plots.
    download_owl: http://purl.obolibrary.org/obo/stato.owl
    homepage: http://stato-ontology.org/
    name: 'STATO: the statistical methods ontology'
    prefix: stato
    tracker: https://github.com/ISA-tools/stato/issues
    version: '2025-02-23'
    version.iri: http://purl.obolibrary.org/obo/stato/releases/2025-02-23/stato.owl
  ontobee:
    library: Library
    name: The Statistical Methods Ontology
    prefix: STATO
  pattern: ^\d{7}$
  prefix: stato
  tib:
    contact: stat-ontology@googlegroups.com
    description: STATO is the statistical methods ontology. It contains concepts and
      properties related to statistical methods, probability distributions and other
      concepts related to statistical analysis, including relationships to study designs
      and plots.
    download_owl: http://purl.obolibrary.org/obo/stato.owl
    homepage: https://stato-ontology.org/
    keywords:
    - ESS
    - DataPLANT
    name: 'STATO: the statistical methods ontology'
    prefix: stato
    tracker: https://github.com/ISA-tools/stato/issues/
    version.iri: http://purl.obolibrary.org/obo/stato/releases/2025-02-23/stato.owl
  uri_format: http://purl.obolibrary.org/obo/STATO_$1
stitch:
  biocontext:
    prefix: STITCH
  contact:
    email: bork@embl.de
    github: null
    name: Peer Bork
    orcid: 0000-0002-2627-833X
  fairsharing:
    abbreviation: STITCH
    description: STITCH is a resource to explore known and predicted interactions
      of chemicals and proteins. Chemicals are linked to other chemicals and proteins
      by evidence derived from experiments, databases and the literature.
    homepage: http://stitch.embl.de
    license: CC BY-NC-SA 4.0
    name: Search Tool for Interactions of Chemicals
    prefix: FAIRsharing.zhwa8x
    publications:
    - doi: 10.1093/nar/gkm795
      pubmed_id: 18084021
      title: 'STITCH: interaction networks of chemicals and proteins.'
    - doi: 10.1093/nar/gkp937
      pubmed_id: 19897548
      title: 'STITCH 2: an interaction network database for small molecules and proteins.'
    - doi: 10.1093/nar/gkt1207
      pubmed_id: 24293645
      title: 'STITCH 4: integration of protein-chemical interactions with user data.'
    - doi: 10.1093/nar/gkr1011
      pubmed_id: 22075997
      title: 'STITCH 3: zooming in on protein-chemical interactions.'
    subjects:
    - Life Science
  mappings:
    biocontext: STITCH
    fairsharing: FAIRsharing.zhwa8x
    miriam: stitch
    n2t: stitch
    pathguide: '313'
    prefixcommons: stitch
    re3data: r3d100012165
  miriam:
    deprecated: false
    description: STITCH is a resource to explore known and predicted interactions
      of chemicals and proteins. Chemicals are linked to other chemicals and proteins
      by evidence derived from experiments, databases and the literature.
    homepage: http://stitch.embl.de/
    id: '00000266'
    name: STITCH
    namespaceEmbeddedInLui: false
    pattern: ^\w{14}$
    prefix: stitch
    sampleId: BQJCRHHNABKAKU
    uri_format: http://stitch.embl.de/interactions/$1
  n2t:
    description: STITCH is a resource to explore known and predicted interactions
      of chemicals and proteins. Chemicals are linked to other chemicals and proteins
      by evidence derived from experiments, databases and the literature.
    example: BQJCRHHNABKAKU
    homepage: http://stitch.embl.de/
    name: STITCH
    namespaceEmbeddedInLui: false
    pattern: ^\w{14}$
    prefix: stitch
    uri_format: http://stitch.embl.de/interactions/$1
  name: Search Tool for Interactions of Chemicals
  pathguide:
    abbreviation: STITCH
    homepage: http://stitch.embl.de/
    name: Chemical-Protein Interaction Networks
    prefix: '313'
  prefix: stitch
  prefixcommons:
    description: STITCH is a resource to explore known and predicted interactions
      of chemicals and proteins. Chemicals are linked to other chemicals and proteins
      by evidence derived from experiments, databases and the literature.
    example: ICXJVZHDZFXYQC
    homepage: http://stitch.embl.de
    keywords:
    - interaction
    - protein
    - small molecule
    name: 'STITCH: Chemical-Protein Interactions'
    pattern: ^\w{14}$
    prefix: stitch
    pubmed_ids:
    - '18084021'
  publications:
  - doi: 10.1093/nar/gkt1207
    pmc: PMC3964996
    pubmed: '24293645'
    title: 'STITCH 4: integration of protein-chemical interactions with user data'
    year: 2013
  - doi: 10.1093/nar/gkr1011
    pmc: PMC3245073
    pubmed: '22075997'
    title: 'STITCH 3: zooming in on protein-chemical interactions'
    year: 2011
  - doi: 10.1093/nar/gkp937
    pmc: PMC2808890
    pubmed: '19897548'
    title: 'STITCH 2: an interaction network database for small molecules and proteins'
    year: 2009
  - doi: 10.1093/nar/gkm795
    pmc: PMC2238848
    pubmed: '18084021'
    title: 'STITCH: interaction networks of chemicals and proteins'
    year: 2007
  re3data:
    description: The Database explores the interactions of chemicals and proteins.  It
      integrates information about interactions from metabolic pathways, crystal structures,
      binding experiments and drug-target relationships. Inferred information from
      phenotypic effects, text mining and chemical structure similarity is used to
      predict relations between chemicals. STITCH further allows exploring the network
      of chemical relations, also in the context of associated binding proteins.
    doi: 10.17616/R3606X
    homepage: http://stitch.embl.de/
    name: STITCH
    prefix: r3d100012165
    synonyms:
    - Search Tool for Interactions of Chemicals
    xrefs:
      nif: 0000-03499
stn:
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: The pre-IND tracking number for submissions to the FDA
  example: '125768'
  homepage: https://www.fda.gov/media/128698/download
  name: FDA Submission Tracking Number
  prefix: stn
storedb:
  banana: STOREDB
  biocontext:
    prefix: STOREDB
  example: STUDY1040
  fairsharing:
    abbreviation: STOREDB
    contact:
      email: PNS12@cam.ac.uk
      name: Dr Paul Schofield
      orcid: 0000-0002-5111-7263
    description: STOREDB provides infrastructure for sharing data and resources in
      radiation biology and epidemiology. It is a platform for the archiving and sharing
      of primary data and outputs of all kinds, including epidemiological and experimental
      data, from research on the effects of radiation. It also provides a directory
      of bioresources and databases containing information and materials that investigators
      are willing to share. STORE supports the creation of a radiation research commons.
    homepage: https://www.storedb.org
    license: https://creativecommons.org
    name: STOREDB
    prefix: FAIRsharing.6h8d2r
    publications: []
    subjects:
    - Ecology
    - Life Science
    - Biomedical Science
    - Epidemiology
    - Preclinical Studies
  integbio:
    description: STOREDB provides infrastructure for sharing data and resources in
      radiation biology and epidemiology. It is a platform for the archiving and sharing
      of primary data and outputs of all kinds, including epidemiological and experimental
      data, from research on the effects of radiation. It also provides a directory
      of bioresources and databases containing information and materials that investigators
      are willing to share. STORE supports the creation of a radiation research commons.
    fairsharing: FAIRsharing.6h8d2r
    homepage: https://www.storedb.org/store_v3/
    information_keywords:
    - Expression
    - Method
    - Bibliography/Documents
    - Repository
    maintainer: CONCERT-European Joint Programme for the Integration of Radiation
      Protection Research
    name: STOREDB
    prefix: nbdc02191
    status: Active
    target_keywords:
    - Genome/Gene
    - Genetic variation
    - Health/Disease
    - Organism
  mappings:
    biocontext: STOREDB
    fairsharing: FAIRsharing.6h8d2r
    integbio: nbdc02191
    miriam: storedb
    n2t: storedb
    re3data: r3d100011049
  miriam:
    deprecated: false
    description: STOREDB database is a repository for data used by the international
      radiobiology community, archiving and sharing primary data outputs from research
      on low dose radiation. It also provides a directory of bioresources and databases
      for radiobiology projects containing information and materials that investigators
      are willing to share. STORE supports the creation of a low dose radiation research
      commons.
    homepage: https://www.storedb.org/
    id: '00000577'
    name: STOREDB
    namespaceEmbeddedInLui: false
    pattern: ^STOREDB:(STUDY|FILE|DATASET)\d+$
    prefix: storedb
    sampleId: STOREDB:STUDY1040
    uri_format: https://www.storedb.org/?$1
  n2t:
    description: STOREDB database is a repository for data used by the international
      radiobiology community, archiving and sharing primary data outputs from research
      on low dose radiation. It also provides a directory of bioresources and databases
      for radiobiology projects containing information and materials that investigators
      are willing to share. STORE supports the creation of a low dose radiation research
      commons.
    example: STOREDB:STUDY1040
    homepage: https://www.storedb.org/
    name: STOREDB at University of Cambridge
    namespaceEmbeddedInLui: false
    pattern: ^STOREDB:(STUDY|FILE|DATASET)\d+$
    prefix: storedb
    uri_format: https://www.storedb.org/?$1
  name: Store DB
  namespace_in_lui: true
  pattern: ^(STUDY|FILE|DATASET)\d+$
  prefix: storedb
  re3data:
    description: STOREDB is a platform for the archiving and sharing of primary data
      and outputs of all kinds, including epidemiological and experimental data, from
      research on the effects of radiation. It also provides a directory of bioresources
      and databases containing information and materials that investigators are willing
      to share. STORE supports the creation of a radiation research commons.
    doi: 10.17616/R3732R
    homepage: https://www.storedb.org/store_v3/
    license: CC
    name: STOREDB
    prefix: r3d100011049
    synonyms:
    - STORE
    - Sustaining access to Tissues and data frOm Radiobiological Experiments
  uri_format: https://www.storedb.org/?$1
storedb.dataset:
  comment: Unfortunately, the resolver itself doesn't work since datasets are actually
    hierarchically assigned within studies.
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  deprecated: true
  description: Datasets inside StoreDB at University of Cambridge
  example: '1251'
  homepage: https://www.storedb.org/
  name: StoreDB Dataset
  part_of_database: storedb
  pattern: ^\d+$
  prefix: storedb.dataset
  uri_format: https://www.storedb.org/?STOREDB:DATASET$1
storedb.file:
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: File inside StoreDB at University of Cambridge
  example: '12929'
  homepage: https://www.storedb.org/
  name: StoreDB File
  part_of_database: storedb
  pattern: ^\d+$
  prefix: storedb.file
  uri_format: https://www.storedb.org/store_v3/download.jsp?fileId=$1
storedb.study:
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: Study inside StoreDB at University of Cambridge
  example: '1174'
  homepage: https://www.storedb.org/
  name: StoreDB Study
  part_of_database: storedb
  pattern: ^\d+$
  prefix: storedb.study
  providers:
  - code: doi
    description: DOIs for studies
    example: null
    first_party: null
    homepage: https://www.storedb.org/
    name: StoreDB DOI
    publications: null
    status: null
    uri_format: http://dx.doi.org/doi:10.20348/STOREDB/$1
  uri_format: https://www.storedb.org/store_v3/study.jsp?studyId=$1
streptomedb:
  contact:
    email: stefan.guenther@pharmazie.uni-freiburg.de
    github: null
    name: Stefan Günther
    orcid: 0000-0003-3744-189X
  contributor:
    email: m.naguthana@hotmail.com
    github: nagutm
    name: Mufaddal Naguthanawala
    orcid: 0009-0009-5240-7463
  description: Identifers for natural products isolated or mutasynthesized by bacteria
    of the genus Streptomyces.
  example: '15753'
  github_request_issue: 1287
  homepage: http://streptomedb.vm.uni-freiburg.de:8000/streptomedb
  name: StreptomeDB
  pattern: ^\d+$
  prefix: streptomedb
  publications:
  - doi: 10.1093/nar/gkae1030
    pmc: null
    pubmed: '39498494'
    title: 'StreptomeDB 4.0: a comprehensive database of streptomycetes natural products
      enriched with protein interactions and interactive spectral visualization'
    year: 2024
  - doi: 10.1093/nar/gkaa868
    pmc: PMC7779017
    pubmed: '33051671'
    title: 'StreptomeDB 3.0: an updated compendium of streptomycetes natural products'
    year: 2020
  - doi: 10.1093/nar/gkv1319
    pmc: PMC4702922
    pubmed: '26615197'
    title: StreptomeDB 2.0--an extended resource of natural products produced by streptomycetes
    year: 2015
  - doi: 10.1093/nar/gks1253
    pmc: PMC3531085
    pubmed: '23193280'
    title: 'StreptomeDB: a resource for natural compounds isolated from Streptomyces
      species'
    year: 2012
  reviewer:
    email: b.gyori@northeastern.edu
    github: bgyori
    name: Benjamin M. Gyori
    orcid: 0000-0001-9439-5346
  uri_format: http://streptomedb.vm.uni-freiburg.de:8000/streptomedb/get_drugcard/$1
string:
  biocontext:
    prefix: STRING
  edam:
    description: Unique identifier of an entry from the STRING database of protein-protein
      interactions.
    name: STRING
    obsolete: false
    prefix: '2302'
  fairsharing:
    abbreviation: STRING
    contact:
      email: bork@embl.de
      name: Peer Bork
      orcid: 0000-0002-2627-833X
    description: STRING is a database of known and predicted protein interactions.
      The interactions include direct (physical) and indirect (functional) associations.
    homepage: https://string-db.org/
    license: CC-BY-4.0
    name: STRING
    prefix: FAIRsharing.9b7wvk
    publications:
    - doi: 10.1093/bioinformatics/btv696
      pubmed_id: 26614125
      title: 'SVD-phy: improved prediction of protein functional associations through
        singular value decomposition of phylogenetic profiles.'
    - doi: 10.1093/nar/gks1094
      pubmed_id: 23203871
      title: 'STRING v9.1: protein-protein interaction networks, with increased coverage
        and integration.'
    - doi: 10.1093/nar/gku1003
      pubmed_id: 25352553
      title: 'STRING v10: protein-protein interaction networks, integrated over the
        tree of life.'
    - doi: 10.1093/nar/gky1131
      pubmed_id: 30476243
      title: 'STRING v11: protein-protein association networks with increased coverage,
        supporting functional discovery in genome-wide experimental datasets.'
    - doi: 10.1093/nar/gkw937
      pubmed_id: 27924014
      title: 'The STRING database in 2017: quality-controlled protein-protein association
        networks, made broadly accessible.'
    - doi: 10.1093/nar/gkn760
      pubmed_id: 18940858
      title: STRING 8--a global view on proteins and their functional interactions
        in 630 organisms.
    subjects:
    - Life Science
    - Biology
  integbio:
    alt_name: Search Tool for the Retrieval of Interacting Genes/Proteins
    description: 'STRING is a database of known and predicted protein interactions,
      including both physical and functional interactions. It contains data which
      derived from four sources: genomic context, high-throughput experiments, coexpression
      and previous knowledge. This database quantitatively integrates interaction
      data from these sources for a large number of organisms, and transfers information
      between these organisms where applicable. It performs iterative searches and
      visualizes the results in their genomic context. Many data including protein
      sequences, protein network, interaction types for protein links, orthologous
      groups or full database dumps (license required) are downloadable.'
    fairsharing: biodbcore-000340
    homepage: http://string-db.org/
    information_keywords:
    - Sequence
    - Interaction/Pathway
    - Classification
    maintainer: STRING Consortium
    name: STRING
    prefix: nbdc00690
    pubmeds:
    - '18940858'
    - '17098935'
    - '15608232'
    - '12519996'
    - '10982861'
    status: Active
    target_keywords:
    - Protein
  mappings:
    biocontext: STRING
    edam: '2302'
    fairsharing: FAIRsharing.9b7wvk
    integbio: nbdc00690
    miriam: string
    n2t: string
    pathguide: '93'
    prefixcommons: string
    re3data: r3d100010604
    uniprot: DB-0141
  miriam:
    deprecated: false
    description: "STRING (Search Tool for Retrieval of Interacting Genes/Proteins)\
      \ is a database of known and predicted protein interactions.\r\nThe interactions\
      \ include direct (physical) and indirect (functional) associations; they are\
      \ derived from four sources:Genomic Context, High-throughput Experiments,(Conserved)\
      \ Coexpression, Previous Knowledge. STRING quantitatively integrates interaction\
      \ data from these sources for a large number of organisms, and transfers information\
      \ between these organisms where applicable."
    homepage: http://string-db.org/
    id: '00000265'
    name: STRING
    namespaceEmbeddedInLui: false
    pattern: ^([A-N,R-Z][0-9][A-Z][A-Z, 0-9][A-Z, 0-9][0-9])|([O,P,Q][0-9][A-Z, 0-9][A-Z,
      0-9][A-Z, 0-9][0-9])|([0-9][A-Za-z0-9]{3})$
    prefix: string
    providers:
    - code: ''
      description: STRING at Heidelberg
      homepage: http://string.embl.de/
      name: STRING at Heidelberg
      uri_format: https://string.embl.de/cgi/network?identifier=$1
    sampleId: P53350
    uri_format: https://string-db.org/cgi/network?identifier=$1
  n2t:
    description: STRING (Search Tool for Retrieval of Interacting Genes/Proteins)
      is a database of known and predicted protein interactions. The interactions
      include direct (physical) and indirect (functional) associations; they are derived
      from four sources:Genomic Context, High-throughput Experiments,(Conserved) Coexpression,
      Previous Knowledge. STRING quantitatively integrates interaction data from these
      sources for a large number of organisms, and transfers information between these
      organisms where applicable.
    example: P53350
    homepage: http://string-db.org/
    name: STRING Mirror at Heidelberg
    namespaceEmbeddedInLui: false
    pattern: ^([A-N,R-Z][0-9][A-Z][A-Z, 0-9][A-Z, 0-9][0-9])|([O,P,Q][0-9][A-Z, 0-9][A-Z,
      0-9][A-Z, 0-9][0-9])|([0-9][A-Za-z0-9]{3})$
    prefix: string
    uri_format: http://string-db.org/interactions/$1
  name: Search Tool for Retrieval of Interacting Genes/Proteins
  pathguide:
    abbreviation: STRING
    homepage: http://string-db.org
    name: Search Tool for the Retrieval of Interacting Genes/Proteins
    prefix: '93'
  prefix: string
  prefixcommons:
    description: STRING is a database of known and predicted protein interactions.
      The interactions include direct (physical) and indirect (functional) associations
    example: P53350
    homepage: http://string-db.org
    keywords:
    - protein
    - interaction
    name: 'STRING: functional protein association networks'
    pattern: ^([A-N,R-Z][0-9][A-Z][A-Z, 0-9][A-Z, 0-9][0-9])|([O,P,Q][0-9][A-Z, 0-9][A-Z,
      0-9][A-Z, 0-9][0-9])|([0-9][A-Za-z0-9]{3})$
    prefix: string
    pubmed_ids:
    - '18940858'
  provides: uniprot
  publications:
  - doi: 10.1093/nar/gkae1113
    pmc: null
    pubmed: '39558183'
    title: 'The STRING database in 2025: protein networks with directionality of regulation'
    year: 2024
  - doi: 10.1093/nar/gky1131
    pmc: PMC6323986
    pubmed: '30476243'
    title: 'STRING v11: protein-protein association networks with increased coverage,
      supporting functional discovery in genome-wide experimental datasets'
    year: 2019
  - doi: 10.1093/nar/gkw937
    pmc: PMC5210637
    pubmed: '27924014'
    title: 'The STRING database in 2017: quality-controlled protein-protein association
      networks, made broadly accessible'
    year: 2016
  - doi: 10.1093/bioinformatics/btv696
    pmc: PMC4896368
    pubmed: '26614125'
    title: 'SVD-phy: improved prediction of protein functional associations through
      singular value decomposition of phylogenetic profiles'
    year: 2015
  - doi: 10.1093/nar/gku1003
    pmc: PMC4383874
    pubmed: '25352553'
    title: 'STRING v10: protein-protein interaction networks, integrated over the
      tree of life'
    year: 2014
  - doi: 10.1093/nar/gks1094
    pmc: PMC3531103
    pubmed: '23203871'
    title: 'STRING v9.1: protein-protein interaction networks, with increased coverage
      and integration'
    year: 2012
  - doi: 10.1093/nar/gkn760
    pmc: PMC2686466
    pubmed: '18940858'
    title: STRING 8--a global view on proteins and their functional interactions in
      630 organisms
    year: 2008
  - doi: 10.1093/bioinformatics/btv696
    pmc: null
    pubmed: null
    title: 'SVD-phy: improved prediction of protein functional associations through
      singular value decomposition of phylogenetic profiles.'
    year: null
  - doi: 10.1093/nar/gks1094
    pmc: null
    pubmed: null
    title: 'STRING v9.1: protein-protein interaction networks, with increased coverage
      and integration.'
    year: null
  - doi: 10.1093/nar/gku1003
    pmc: null
    pubmed: null
    title: 'STRING v10: protein-protein interaction networks, integrated over the
      tree of life.'
    year: null
  - doi: 10.1093/nar/gky1131
    pmc: null
    pubmed: null
    title: 'STRING v11: protein-protein association networks with increased coverage,
      supporting functional discovery in genome-wide experimental datasets.'
    year: null
  - doi: 10.1093/nar/gkw937
    pmc: null
    pubmed: null
    title: 'The STRING database in 2017: quality-controlled protein-protein association
      networks, made broadly accessible.'
    year: null
  - doi: 10.1093/nar/gkn760
    pmc: null
    pubmed: null
    title: STRING 8--a global view on proteins and their functional interactions in
      630 organisms.
    year: null
  - doi: null
    pmc: null
    pubmed: '18940858'
    title: null
    year: null
  - doi: 10.1093/nar/gkac1000
    pmc: null
    pubmed: '36370105'
    title: null
    year: null
  re3data:
    description: 'STRING is a database of known and predicted protein interactions.

      The interactions include direct (physical) and indirect (functional) associations;
      they are derived from four sources:

      - Genomic Context

      - High-throughput Experiments

      - (Conserved) Coexpression

      - Previous Knowledge

      STRING quantitatively integrates interaction data from these sources for a large
      number of organisms, and transfers information between these organisms where
      applicable.'
    doi: 10.17616/R3VS40
    homepage: https://string-db.org/
    name: STRING
    prefix: r3d100010604
    synonyms:
    - Known and Predicted Protein-Protein Interactions
    xrefs:
      nif: 0000-03503
      omics: '29032'
  uniprot:
    abbreviation: STRING
    category: Protein-protein interaction databases
    homepage: https://string-db.org/
    name: STRING
    prefix: DB-0141
    publications:
    - doi: 10.1093/nar/gkac1000
      pubmed: '36370105'
    uri_format: https://string-db.org/network/$1
sty:
  aberowl:
    description: UMLS Semantic Network The Semantic Network consists of (1) a set
      of broad subject categories, or Semantic Types, that provide a consistent categorization
      of all concepts represented in the UMLS Metathesaurus, and (2) a set of useful
      and important relationships, or Semantic Relations, that exist between Semantic
      Types. This section of the documentation provides an overview of the Semantic
      Network, and describes the files of the Semantic Network. Sample records illustrate
      structure and content of these files. The Semantic Network is distributed as
      one of the UMLS Knowledge Sources and as an open source resource available on
      the Semantic Network Web site, subject to these terms and conditions.
    homepage: https://semanticnetwork.nlm.nih.gov/
    name: Semantic Types Ontology
    prefix: STY
    version: 2016AB
  agroportal:
    contact:
      email: olivier@nlm.nih.gov
      name: Olivier Bodenreider
    description: The Semantic Network consists of (1) a set of broad subject categories,
      or Semantic Types, that provide a consistent categorization of all concepts
      represented in the UMLS Metathesaurus, and (2) a set of useful and important
      relationships, or Semantic Relations, that exist between Semantic Types. This
      section of the documentation provides an overview of the Semantic Network, and
      describes the files of the Semantic Network. Sample records illustrate structure
      and content of these files.
    example_uri: http://purl.bioontology.org/ontology/STY/T057
    homepage: https://lhncbc.nlm.nih.gov/semanticnetwork/
    license: CC0-1.0
    name: UMLS Semantic Network
    prefix: STY
    version: 12 (2022AA)
  biolink:
    is_identifiers: false
    is_obo: false
    prefix: UMLSSG
    uri_format: https://lhncbc.nlm.nih.gov/semanticnetwork/download/sg_archive/SemGroups-v04.txt$1
  bioportal:
    contact:
      email: support@bioontology.org
      name: bioportal
    description: UMLS Semantic Network The Semantic Network consists of (1) a set
      of broad subject categories, or Semantic Types, that provide a consistent categorization
      of all concepts represented in the UMLS Metathesaurus, and (2) a set of useful
      and important relationships, or Semantic Relations, that exist between Semantic
      Types. This section of the documentation provides an overview of the Semantic
      Network, and describes the files of the Semantic Network. Sample records illustrate
      structure and content of these files. The Semantic Network is distributed as
      one of the UMLS Knowledge Sources and as an open source resource available on
      the Semantic Network Web site, subject to these terms and conditions.
    homepage: https://semanticnetwork.nlm.nih.gov/
    name: Semantic Types Ontology
    prefix: STY
    version: 2024AB
  contact:
    email: olivier@nlm.nih.gov
    github: null
    name: Olivier Bodenreider
    orcid: 0000-0003-4769-4217
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  contributor_extras:
  - email: tiago.lubiana.alves@usp.br
    github: lubianat
    name: Tiago Lubiana
    orcid: 0000-0003-2473-2313
  description: UMLS Semantic Network The Semantic Network consists of (1) a set of
    broad subject categories, or Semantic Types, that provide a consistent categorization
    of all concepts represented in the UMLS Metathesaurus, and (2) a set of useful
    and important relationships, or Semantic Relations, that exist between Semantic
    Types.
  domain: classification
  ecoportal:
    contact:
      email: gs_bouazzoun@esi.dz
      name: Syphax  Bouazzouni
    description: The Semantic Network consists of (1) a set of broad subject categories,
      or Semantic Types, that provide a consistent categorization of all concepts
      represented in the UMLS Metathesaurus, and (2) a set of useful and important
      relationships, or Semantic Relations, that exist between Semantic Types. This
      section of the documentation provides an overview of the Semantic Network, and
      describes the files of the Semantic Network. Sample records illustrate structure
      and content of these files.
    example_uri: http://purl.bioontology.org/ontology/STY/T057
    homepage: https://lhncbc.nlm.nih.gov/semanticnetwork/
    license: CC0-1.0
    name: UMLS Semantic Network
    prefix: STY
    publications:
    - https://doi.org/10.1002/cfg.255
  example: T039
  homepage: https://lhncbc.nlm.nih.gov/semanticnetwork/
  license: https://www.nlm.nih.gov/research/umls/knowledge_sources/metathesaurus/release/license_agreement.html
  logo: https://www.nlm.nih.gov/research/umls/knowledge_sources/semantic_network/semantic-network.png
  mappings:
    aberowl: STY
    agroportal: STY
    biolink: UMLSSG
    bioportal: STY
    ecoportal: STY
    wikidata: P11955
  name: UMLS Semantic Types Ontology
  pattern: ^T\d{3}$
  prefix: sty
  providers:
  - code: bioportal.purl
    description: BioPortal PURL
    example: null
    first_party: null
    homepage: http://purl.bioontology.org/ontology/STY
    name: BioPortal PURL
    publications: null
    status: null
    uri_format: http://purl.bioontology.org/ontology/STY/$1
  publications:
  - doi: 10.1093/nar/gkh061
    pmc: PMC308795
    pubmed: '14681409'
    title: 'The Unified Medical Language System (UMLS): integrating biomedical terminology'
    year: 2004
  synonyms:
  - UMLSSG
  - umls.st
  - umls.sty
  uri_format: https://uts.nlm.nih.gov/uts/umls/semantic-network/$1
  wikidata:
    description: identifier for a concept in the Semantic Network vocabulary of the
      Unified Medical Language System
    example:
    - T005
    - T015
    homepage: https://uts.nlm.nih.gov/uts/umls/semantic-network/root
    name: UMLS Semantic Network ID
    prefix: P11955
    uri_format: https://uts.nlm.nih.gov/uts/umls/semantic-network/$1
subtilist:
  biocontext:
    prefix: SUBTILIST
  contact:
    email: antoine.danchin@normalesup.org
    github: null
    name: Antoine Danchin
    orcid: 0000-0002-6350-5001
  fairsharing:
    abbreviation: SubtiList
    description: Its purpose is to collate and integrate various aspects of the genomic
      information from B. subtilis, the paradigm of sporulating Gram-positive bacteria.
      SubtiList provides a complete dataset of DNA and protein sequences derived from
      the paradigm strain B. subtilis 168, linked to the relevant annotations and
      functional assignments
    homepage: http://genolist.pasteur.fr/SubtiList/
    name: Bacillus subtilis strain 168 genome
    prefix: FAIRsharing.40j2vd
    publications:
    - doi: 10.1093/nar/30.1.62
      pubmed_id: 11752255
      title: 'SubtiList: the reference database for the Bacillus subtilis genome.'
    subjects: []
  mappings:
    biocontext: SUBTILIST
    fairsharing: FAIRsharing.40j2vd
    miriam: subtilist
    n2t: subtilist
    ncbi: SubtiList
    prefixcommons: subtilist
  miriam:
    deprecated: true
    description: "SubtiList serves to collate and integrate various aspects of the\
      \ genomic information from B. subtilis, the paradigm of sporulating Gram-positive\
      \ bacteria.\r\nSubtiList provides a complete dataset of DNA and protein sequences\
      \ derived from the paradigm strain B. subtilis 168, linked to the relevant annotations\
      \ and functional assignments."
    homepage: http://genolist.pasteur.fr/SubtiList/
    id: '00000433'
    name: SubtiList
    namespaceEmbeddedInLui: false
    pattern: ^BG\d+$
    prefix: subtilist
    sampleId: BG11523
    uri_format: http://genolist.pasteur.fr/SubtiList/genome.cgi?external_query+$1
  n2t:
    description: SubtiList serves to collate and integrate various aspects of the
      genomic information from B. subtilis, the paradigm of sporulating Gram-positive
      bacteria. SubtiList provides a complete dataset of DNA and protein sequences
      derived from the paradigm strain B. subtilis 168, linked to the relevant annotations
      and functional assignments.
    example: BG11523
    homepage: http://genolist.pasteur.fr/SubtiList/
    name: SubtiList at Pasteur Institute
    namespaceEmbeddedInLui: false
    pattern: ^BG\d+$
    prefix: subtilist
    uri_format: http://genolist.pasteur.fr/SubtiList/genome.cgi?external_query+$1
  ncbi:
    example: BG10001
    homepage: http://genolist.pasteur.fr/SubtiList/
    name: Bacillus subtilis genome sequencing project
    prefix: SubtiList
  prefix: subtilist
  prefixcommons:
    description: Its purpose is to collate and integrate various aspects of the genomic
      information from B. subtilis, the paradigm of sporulating Gram-positive bacteria.
      SubtiList provides a complete dataset of DNA and protein sequences derived from
      the paradigm strain B. subtilis 168, linked to the relevant annotations and
      functional assignments
    example: BG11523
    homepage: http://genolist.pasteur.fr/SubtiList/
    keywords:
    - genome
    - DNA
    - protein
    name: Bacillus subtilis strain 168 genome database
    pattern: ^BG\d+$
    prefix: subtilist
  publications:
  - doi: 10.1093/nar/30.1.62
    pmc: PMC99059
    pubmed: '11752255'
    title: 'SubtiList: the reference database for the Bacillus subtilis genome'
    year: 2002
  - doi: 10.1093/nar/30.1.62
    pmc: null
    pubmed: null
    title: 'SubtiList: the reference database for the Bacillus subtilis genome.'
    year: null
subtiwiki:
  biocontext:
    prefix: SUBTIWIKI
  contact:
    email: jstuelk@gwdg.de
    github: null
    name: Jörg Stülke
    orcid: 0000-0001-5881-5390
  fairsharing:
    abbreviation: SubtiWiki
    description: Collaborative resource for the Bacillus community.
    homepage: http://subtiwiki.uni-goettingen.de
    name: SubtiWiki
    prefix: FAIRsharing.2ck3st
    publications:
    - doi: 10.1093/database/bap012
      pubmed_id: 20157485
      title: 'A community-curated consensual annotation that is continuously updated:
        the Bacillus subtilis centred wiki SubtiWiki.'
    - doi: 10.1099/mic.0.035790-0
      pubmed_id: 19959575
      title: 'Connecting parts with processes: SubtiWiki and SubtiPathways integrate
        gene and pathway annotation for Bacillus subtilis.'
    - doi: 10.1093/nar/gkv1006
      pubmed_id: 26433225
      title: SubtiWiki 2.0--an integrated database for the model organism Bacillus
        subtilis.
    subjects:
    - Life Science
  integbio:
    description: SubtiWiki is a collaborative user database for the bacterium Bacillus
      subtilis. The database contains user annotations of genes, annotations, pathways,
      and interactions. Users can contribute and download several different summary
      information tables.
    fairsharing: biodbcore-000146
    homepage: http://subtiwiki.uni-goettingen.de/
    information_keywords:
    - Bibliography/Documents
    - Method
    - Expression
    - Interaction/Pathway
    maintainer: Georg-August-Universitat Gottingen
    name: SubtiWiki
    prefix: nbdc00693
    pubmeds:
    - '26433225'
    - '20157485'
    - '19959575'
    - '22096228'
    status: Active
    target_keywords:
    - Genome/Gene
    - Protein
    - Metabolite
  mappings:
    biocontext: SUBTIWIKI
    fairsharing: FAIRsharing.2ck3st
    integbio: nbdc00693
    miriam: subtiwiki
    n2t: subtiwiki
    prefixcommons: subtiwiki
  miriam:
    deprecated: false
    description: "SubtiWiki is a scientific wiki for the model bacterium Bacillus\
      \ subtilis. It provides comprehensive information on all genes and their proteins\
      \ and RNA products, as well as information related to the current investigation\
      \ of the gene/protein. \r\nNote: Currently, direct access to RNA products is\
      \ restricted. This is expected to be rectified soon."
    homepage: http://www.subtiwiki.uni-goettingen.de/wiki/index.php/Main_Page
    id: '00000132'
    name: SubtiWiki
    namespaceEmbeddedInLui: false
    pattern: ^BSU\d{5}$
    prefix: subtiwiki
    sampleId: BSU29180
    uri_format: http://www.subtiwiki.uni-goettingen.de/wiki/index.php/$1
  n2t:
    description: 'SubtiWiki is a scientific wiki for the model bacterium Bacillus
      subtilis. It provides comprehensive information on all genes and their proteins
      and RNA products, as well as information related to the current investigation
      of the gene/protein.  Note: Currently, direct access to RNA products is restricted.
      This is expected to be rectified soon.'
    example: BSU29180
    homepage: http://www.subtiwiki.uni-goettingen.de/wiki/index.php/Main_Page
    name: SubtiWiki website
    namespaceEmbeddedInLui: false
    pattern: ^BSU\d{5}$
    prefix: subtiwiki
    uri_format: http://www.subtiwiki.uni-goettingen.de/wiki/index.php/$1
  prefix: subtiwiki
  prefixcommons:
    description: 'SubtiWiki is a scientific wiki for the model bacterium Bacillus
      subtilis. It provides comprehensive information on all genes and their proteins
      and RNA products, as well as information related to the current investigation
      of the gene/protein. Note: Currently, direct access to RNA products is restricted.
      This is expected to be rectified soon.'
    example: BSU29180
    homepage: http://www.subtiwiki.uni-goettingen.de/wiki/index.php/Main_Page
    keywords:
    - gene
    - protein
    - RNA
    - DNA
    name: SubtiWiki
    pattern: ^BSU\d{5}$
    prefix: subtiwiki
    pubmed_ids:
    - '19959575'
    - '20157485'
    uri_format: http://www.subtiwiki.uni-goettingen.de/wiki/index.php/$1
  publications:
  - doi: 10.1093/nar/gkv1006
    pmc: PMC4702770
    pubmed: '26433225'
    title: SubtiWiki 2.0--an integrated database for the model organism Bacillus subtilis
    year: 2015
  - doi: 10.1093/database/bap012
    pmc: PMC2790307
    pubmed: '20157485'
    title: 'A community-curated consensual annotation that is continuously updated:
      the Bacillus subtilis centred wiki SubtiWiki'
    year: 2009
  - doi: 10.1099/mic.0.035790-0
    pmc: null
    pubmed: '19959575'
    title: 'Connecting parts with processes: SubtiWiki and SubtiPathways integrate
      gene and pathway annotation for Bacillus subtilis'
    year: 2009
sugarbind:
  aberowl:
    description: Ontology for representing glycan and pathogen binding interaction
      data in RDF. Many of the terms are based on the data originally contained in
      the SugarBind database.
    download_owl: http://aber-owl.net/media/ontologies/SUGARBIND/1/sugarbind.owl
    name: SugarBind
    prefix: SUGARBIND
    version: 1.0.0
  biocontext:
    prefix: SUGARBIND
  bioportal:
    contact:
      email: bdkouiti5013@gmail.com
      name: Koichi Arakawa
    description: Ontology for representing glycan and pathogen binding interaction
      data in RDF. Many of the terms are based on the data originally contained in
      the SugarBind database.
    name: SugarBind
    prefix: SUGARBIND
    version: '2023-06-20'
  fairsharing:
    abbreviation: SugarBind
    contact:
      email: frederique.lisacek@isb-sib.ch
      name: Frederique Lisacek
      orcid: 0000-0002-0948-4537
    description: The SugarBind Database (SugarBindDB) was created in 2002 as part
      of an effort by the MITRE Corporation (http://www.mitre.org) to develop a pathogen-capture
      technology based on the binding of viral, bacterial and biotoxin lectins to
      specific glycans (aka, sugars, carbohydrates) displayed on glycoprotein films.
      The database content results from compiling publicly available information.
      In 2010, the 2008 version of the database was migrated from MITRE Corporation
      to the SIB Swiss Institute of Bioinformatics in Geneva, Switzerland. From then,
      substantial changes in the database design and usage were undertaken and previous
      content was significantly extended.
    homepage: http://sugarbind.expasy.org/
    license: https://creativecommons.org/licenses/by-nc-nd/3.0/us
    name: SugarBind
    prefix: FAIRsharing.d064y6
    publications:
    - doi: 10.1007/978-4-431-56454-6_13
      pubmed_id: null
      title: SugarBindDB
    - doi: 10.1093/nar/gkv1247
      pubmed_id: 26578555
      title: SugarBindDB, a resource of glycan-mediated host-pathogen interactions.
    subjects:
    - Glycomics
    - Biomedical Science
    twitter: ISBSIB
  integbio:
    description: The SugarBind Database (SugarBindDB) was created in 2002 as part
      of an effort by the MITRE Corporation (http://www.mitre.org) to develop a pathogen-capture
      technology based on the binding of viral, bacterial and biotoxin lectins to
      specific glycans (aka, sugars, carbohydrates) displayed on glycoprotein films.
      The database content results from compiling publicly available information.
      In 2010, the 2008 version of the database was migrated from MITRE Corporation
      to the SIB Swiss Institute of Bioinformatics in Geneva, Switzerland. From then,
      substantial changes in the database design and usage were undertaken and previous
      content was significantly extended.
    fairsharing: FAIRsharing.d064y6
    homepage: http://sugarbind.expasy.org/
    information_keywords:
    - Chemical structure
    - Interaction/Pathway
    - Bibliography/Documents
    maintainer: SIB (Swiss Institute of Bioinformatics)
    name: SugarBind
    prefix: nbdc02224
    pubmeds:
    - '26578555'
    status: Active
    target_keywords:
    - Carbohydrate
    - Health/Disease
  mappings:
    aberowl: SUGARBIND
    biocontext: SUGARBIND
    bioportal: SUGARBIND
    fairsharing: FAIRsharing.d064y6
    integbio: nbdc02224
    miriam: sugarbind
    n2t: sugarbind
  miriam:
    deprecated: false
    description: The SugarBind Database captures knowledge of glycan binding of human
      pathogen lectins and adhesins, where each glycan-protein binding pair is associated
      with at least one published reference. It provides information on the pathogen
      agent, the lectin/adhesin involved, and the human glycan ligand. This collection
      provides information on ligands.
    homepage: http://sugarbind.expasy.org/
    id: 00000629
    name: SugarBind
    namespaceEmbeddedInLui: false
    pattern: ^[A-Za-z]+\/[0-9]+$
    prefix: sugarbind
    sampleId: lectins/172
    uri_format: http://sugarbind.expasy.org/$1
  n2t:
    description: The SugarBind Database captures knowledge of glycan binding of human
      pathogen lectins and adhesins, where each glycan-protein binding pair is associated
      with at least one published reference. It provides information on the pathogen
      agent, the lectin/adhesin involved, and the human glycan ligand. This collection
      provides information on ligands.
    example: lectins/172
    homepage: http://sugarbind.expasy.org/
    name: SugarBind
    namespaceEmbeddedInLui: false
    pattern: ^[A-Za-z]+\/[0-9]+$
    prefix: sugarbind
    uri_format: http://sugarbind.expasy.org/$1
  prefix: sugarbind
  publications:
  - doi: 10.1007/978-4-431-56454-6_13
    pmc: null
    pubmed: null
    title: SugarBindDB
    year: 2016
  - doi: 10.1093/nar/gkv1247
    pmc: PMC4702881
    pubmed: '26578555'
    title: SugarBindDB, a resource of glycan-mediated host-pathogen interactions
    year: 2015
  - doi: 10.1007/978-4-431-56454-6_13
    pmc: null
    pubmed: null
    title: SugarBindDB
    year: null
  - doi: 10.1093/nar/gkv1247
    pmc: null
    pubmed: null
    title: SugarBindDB, a resource of glycan-mediated host-pathogen interactions.
    year: null
  - doi: 10.1007/978-4-431-56454-6_13
    pmc: null
    pubmed: null
    title: SugarBindDB
    year: null
  - doi: 10.1093/nar/gkv1247
    pmc: null
    pubmed: null
    title: SugarBindDB, a resource of glycan-mediated host-pathogen interactions.
    year: null
sulo:
  contact:
    email: michel.dumontier@gmail.com
    github: micheldumontier
    name: Michel Dumontier
    orcid: 0000-0003-4727-9435
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: The Simplified Upper Level Ontology (SULO) is ontology with a minimal
    set of classes and relations to guide the development of a personal health knowledge
    graph. [from homepage]
  download_rdf: https://w3id.org/sulo/sulo.ttl
  example: Capability
  github_request_issue: 1446
  homepage: https://aidava-dev.github.io/sulo/
  license: CC0-1.0
  lov:
    description: The Simplified Upper Level Ontology (SULO) is ontology with a minimal
      set of classes and relations to guide the development of a personal health knowledge
      graph.
    homepage: https://w3id.org/sulo/sulo/
    keywords:
    - Health
    modified: '2025-07-11'
    name: Simplified Upper Level Ontology
    prefix: sulo
    uri_prefix: https://w3id.org/sulo/$1
  mappings:
    lov: sulo
  name: Simplified Upper Level Ontology
  prefix: sulo
  rdf_uri_format: https://w3id.org/sulo/$1
  repository: https://github.com/aidava-dev/sulo
  uri_format: https://w3id.org/sulo/$1
supfam:
  biocontext:
    prefix: SUPFAM
  contact:
    email: pandura@mrc-lmb.cam.ac.uk
    github: null
    name: Arun Prasad Pandurangan
    orcid: 0000-0001-7168-7143
  mappings:
    biocontext: SUPFAM
    miriam: supfam
    n2t: supfam
    prefixcommons: superfamily
    uniprot: DB-0155
  miriam:
    deprecated: false
    description: SUPERFAMILY provides structural, functional and evolutionary information
      for proteins from all completely sequenced genomes, and large sequence collections
      such as UniProt.
    homepage: http://supfam.org/SUPERFAMILY/
    id: '00000357'
    name: SUPFAM
    namespaceEmbeddedInLui: false
    pattern: ^\w+$
    prefix: supfam
    sampleId: SSF57615
    uri_format: http://supfam.org/SUPERFAMILY/cgi-bin/scop.cgi?ipid=$1
  n2t:
    description: SUPERFAMILY provides structural, functional and evolutionary information
      for proteins from all completely sequenced genomes, and large sequence collections
      such as UniProt.
    example: SSF57615
    homepage: http://supfam.org/SUPERFAMILY/
    name: SUPFAM at MRC and University of Bristol
    namespaceEmbeddedInLui: false
    pattern: ^\w+$
    prefix: supfam
    uri_format: http://supfam.org/SUPERFAMILY/cgi-bin/scop.cgi?ipid=$1
  name: SUPERFAMILY
  prefix: supfam
  prefixcommons:
    description: SUPERFAMILY is a database of structural and functional annotation
      for all proteins and genomes.
    example: '46556'
    homepage: http://supfam.org
    keywords:
    - protein
    - genome
    - structure
    - classification
    name: SUPERFAMILY database of structural and functional annotation
    pattern: ^\d+$
    prefix: superfamily
    synonyms:
    - supfam
    uri_format: http://supfam.org/SUPERFAMILY/cgi-bin/scop.cgi?sunid=$1
  publications:
  - doi: 10.1006/jmbi.2001.5080
    pmc: null
    pubmed: '11697912'
    title: Assignment of homology to genome sequences using a library of hidden Markov
      models that represent all proteins of known structure
    year: 2001
  uniprot:
    abbreviation: SUPFAM
    category: Family and domain databases
    homepage: https://supfam.org
    name: Superfamily database of structural and functional annotation
    prefix: DB-0155
    publications:
    - doi: 10.1093/nar/gky1130
      pubmed: '30445555'
    uri_format: https://supfam.org/SUPERFAMILY/cgi-bin/scop.cgi?ipid=$1
suprabank.additive:
  contact:
    email: null
    github: StephanSinn
    name: Stephan Sinn
    orcid: 0000-0002-9676-9839
  contact_group_email: contact@suprabank.org
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: Identifiers for chemicals used as additives
  domain: chemical
  example: '10'
  github_request_issue: 1685
  homepage: https://suprabank.org/additives
  keywords:
  - chemical
  - molecule
  name: SupraBank Additive
  part_of_database: suprabank
  prefix: suprabank.additive
  uri_format: https://suprabank.org/additives/$1
suprabank.buffer:
  contact:
    email: null
    github: StephanSinn
    name: Stephan Sinn
    orcid: 0000-0002-9676-9839
  contact_group_email: contact@suprabank.org
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: Identifiers for chemicals used as buffers
  domain: chemical
  example: '189'
  github_request_issue: 1685
  homepage: https://suprabank.org/buffers
  keywords:
  - chemical
  - molecule
  name: SupraBank Buffer
  part_of_database: suprabank
  pattern: ^\d+$
  prefix: suprabank.buffer
  uri_format: https://suprabank.org/buffers/$1
suprabank.interaction:
  contact:
    email: null
    github: StephanSinn
    name: Stephan Sinn
    orcid: 0000-0002-9676-9839
  contact_group_email: contact@suprabank.org
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: Interactions are SupraBank's way to collect information about experiments
    that describe the binding interaction between molecules. The form for creating
    an interaction enables you to list all experimental conditions. An interaction
    is similar to an entry in a table in your scientific publication, but providing
    machine readable comprehensive information. (from homepage)
  domain: relationship
  example: '2329'
  github_request_issue: 1685
  homepage: https://suprabank.org/interactions
  keywords:
  - chemical
  - interaction
  - relationship
  name: SupraBank Interaction
  part_of_database: suprabank
  pattern: ^\d+$
  prefix: suprabank.interaction
  uri_format: https://suprabank.org/interactions/$1
suprabank.molecule:
  contact:
    email: null
    github: StephanSinn
    name: Stephan Sinn
    orcid: 0000-0002-9676-9839
  contact_group_email: contact@suprabank.org
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: Identifiers for molecules in SupraBank
  domain: chemical
  example: '2196'
  github_request_issue: 1685
  homepage: https://suprabank.org/molecules
  keywords:
  - chemical
  - molecule
  name: SupraBank Molecule
  part_of_database: suprabank
  pattern: ^\d+$
  prefix: suprabank.molecule
  uri_format: https://suprabank.org/molecules/$1
suprabank.solvent:
  contact:
    email: null
    github: StephanSinn
    name: Stephan Sinn
    orcid: 0000-0002-9676-9839
  contact_group_email: contact@suprabank.org
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: Identifiers for chemicals used as solvents in SupraBank
  domain: chemical
  example: '57'
  github_request_issue: 1685
  homepage: https://suprabank.org/solvents
  keywords:
  - chemical
  - molecule
  name: SupraBank Solvent
  part_of_database: suprabank
  pattern: ^\d+$
  prefix: suprabank.solvent
  uri_format: https://suprabank.org/solvents/$1
sustaingraph:
  example: 6T
  mappings:
    tib: sustaingraph
  prefix: sustaingraph
  tib:
    description: The SustainGraph ontology is developed to track the United Nations
      Sustainable Development Goals(SDGs) at national and regional level, their evolution
      accross time and inter-connectedness with existing and emerging policies and
      directives at European Union (EU) and global level. It is described using W3C
      RDF Schema and the Web Ontology Language.
    download_rdf: https://netmode.gitlab.io/sustaingraph-ontology/ontology.ttl
    homepage: https://netmode.gitlab.io/sustaingraph-ontology/
    keywords:
    - TIB
    name: SustainGraph Ontology
    prefix: sustaingraph
    uri_format: https://netmode.gitlab.io/sustaingraph/$1
swan:
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  deprecated: true
  description: SWAN ontology consists in a collection of ontologies used to create,
    manage and share scientific knowledge bases.
  download_owl: https://rawcdn.githack.com/pav-ontology/swan-ontology/2.0.1/swan.owl
  homepage: https://code.google.com/archive/p/swan-ontology
  license: CC-BY-3.0
  name: Semantic Web Applications in Neuromedicine
  prefix: swan
  publications:
  - doi: 10.1016/j.jbi.2008.04.010
    pmc: PMC4536833
    pubmed: '18583197'
    title: The SWAN biomedical discourse ontology
    year: 2008
  references:
  - https://www.hcklab.org/swan-project.html
  repository: https://github.com/pav-ontology/swan-ontology
sweet:
  aberowl:
    description: The Semantic Web for Earth and Environmental Terminology is a mature
      foundational ontology that contains over 6000 concepts organized in 200 ontologies
      represented in OWL. Top level concepts include Representation (math, space,
      science, time, data), Realm (Ocean, Land Surface, Terrestrial Hydroshere, Atmosphere,
      etc.), Phenomena (macro-scale ecological and physical), Processes (micro-scale
      physical, biological, chemical, and mathematical), Human Activities (Decision,
      Commerce, Jurisdiction, Environmental, Research). Originally developed by NASA
      Jet Propulsion Labs under Rob Raskin, SWEET is now officially under the governance
      of the ESIP foundation.
    download_owl: http://aber-owl.net/media/ontologies/SWEET/2/sweet.owl
    homepage: https://github.com/ESIPFed/sweet/blob/master/README.md
    name: Semantic Web for Earth and Environment Technology Ontology
    prefix: SWEET
    version: 3.1.0
  bartoc:
    abbreviation: SWEET
    description: The Semantic Web for Earth and Environmental Terminology is a mature
      foundational ontology that contains over 6000 concepts organized in 200 ontologies
      represented in OWL. Top level concepts include Representation (math, space,
      science, time, data), Realm (Ocean, Land Surface, Terrestrial Hydroshere, Atmosphere,
      etc.), Phenomena (macro-scale ecological and physical), Processes (micro-scale
      physical, biological, chemical, and mathematical), Human Activities (Decision,
      Commerce, Jurisdiction, Environmental, Research). Originally developed by NASA
      Jet Propulsion Labs under Rob Raskin, SWEET is now officially under the governance
      of the ESIP foundation.
    homepage: http://sweetontology.net/sweetAll
    license: CC_MARK
    name: Semantic Web for Earth and Environment Technology Ontology
    prefix: '20510'
  bioportal:
    description: The Semantic Web for Earth and Environmental Terminology is a mature
      foundational ontology that contains over 6000 concepts organized in 200 ontologies
      represented in OWL. Top level concepts include Representation (math, space,
      science, time, data), Realm (Ocean, Land Surface, Terrestrial Hydroshere, Atmosphere,
      etc.), Phenomena (macro-scale ecological and physical), Processes (micro-scale
      physical, biological, chemical, and mathematical), Human Activities (Decision,
      Commerce, Jurisdiction, Environmental, Research). Originally developed by NASA
      Jet Propulsion Labs under Rob Raskin, SWEET is now officially under the governance
      of the ESIP foundation.
    homepage: https://github.com/ESIPFed/sweet/blob/master/README.md
    name: Semantic Web for Earth and Environment Technology Ontology
    prefix: SWEET
    version: 3.6.0
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: The Semantic Web for Earth and Environmental Terminology is a mature
    foundational ontology that contains over 6000 concepts organized in 200 ontologies
    represented in OWL. Top level concepts include Representation (math, space, science,
    time, data), Realm (Ocean, Land Surface, Terrestrial Hydroshere, Atmosphere, etc.),
    Phenomena (macro-scale ecological and physical), Processes (micro-scale physical,
    biological, chemical, and mathematical), Human Activities (Decision, Commerce,
    Jurisdiction, Environmental, Research).
  download_obo: https://raw.githubusercontent.com/EnvironmentOntology/envo/master/src/envo/sources/sweetrealm.obo
  example: realmGeol/GeologicFeature
  fairsharing:
    abbreviation: SWEET
    description: The Semantic Web for Earth and Environmental Terminology is a mature
      foundation ontology originally developed at the NASA Jet Propulsion Laboratory.
      Containing over 11000 concepts organized into ~200 ontologies, its top-level
      concepts include Representation (math, space, science, time, data), Realm (Ocean,
      Land Surface, Terrestrial Hydroshere, Atmosphere, etc.), Phenomena (macro-scale
      ecological and physical), Processes (micro-scale physical, biological, chemical,
      and mathematical), and Human Activities (Decision, Commerce, Jurisdiction, Environmental,
      Research). Since 2017, SWEET has been under the governance of the ESIP foundation.
    homepage: http://sweetontology.net/
    license: CC0-1.0
    name: Semantic Web for Earth and Environmental Terminology Ontology
    prefix: FAIRsharing.jh4xht
    repository: https://github.com/ESIPFed/sweet/wiki/SWEET-IRI-Patterns-for-Ontologies-and-their-Terms
    subjects:
    - Environmental Science
    - Geography
    - Geology
    - Earth Science
  homepage: http://sweetontology.net/
  mappings:
    aberowl: SWEET
    bartoc: '20510'
    bioportal: SWEET
    fairsharing: FAIRsharing.jh4xht
    tib: sweet
  name: Semantic Web for Earth and Environment Technology Ontology
  prefix: sweet
  providers:
  - code: obo.incorrect
    description: Incorrectly encoded URL with an OBO PURL prefix
    example: null
    first_party: null
    homepage: http://purl.obolibrary.org
    name: OBO PURL (incorrect)
    publications: null
    status: null
    uri_format: http://purl.obolibrary.org/obo/http://sweet.jpl.nasa.gov/2.3/realm.owl#$1
  repository: https://github.com/ESIPFed/sweet
  tib:
    description: The Semantic Web for Earth and Environmental Terminology (SWEET)
      is a framework to enhance Earth science data discovery and usability by enabling
      software to understand the semantics of web resources. SWEET includes ontologies
      that define a knowledge space for Earth system science using OWL. It covers
      key concepts like space, time, and Earth systems, as well as scientific phenomena.
      SWEET is modularized into 224 files, each representing a namespace, with dependencies
      managed through OWL imports.
    download_rdf: https://raw.githubusercontent.com/ESIPFed/sweet/master/src/sweetAll.ttl
    homepage: http://sweetontology.net/sweetAll
    keywords:
    - ESS
    - NFDI4ING
    - earth sciences
    name: Semantic Web for Earth and Environmental Terminology (SWEET) Ontologies.
    prefix: sweet
    tracker: https://github.com/ESIPFed/sweet/issues
  uri_format: http://sweetontology.net/human/$1
sweet.hu:
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: The Semantic Web for Earth and Environmental Terminology (SWEET) ontology
    for Human
  download_rdf: https://github.com/ESIPFed/sweet/raw/refs/heads/master/src/human.ttl
  example: Behavior
  github_request_issue: 1772
  homepage: http://sweetontology.net/human/
  keywords:
  - human
  license: CC0-1.0
  name: SWEET Ontology Human
  part_of: sweet
  prefix: sweet.hu
  repository: https://github.com/ESIPFed/sweet
  synonyms:
  - sohu
  uri_format: http://sweetontology.net/human/$1
sweet.hua:
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: The Semantic Web for Earth and Environmental Terminology (SWEET) ontology
    for Human Agriculture
  download_rdf: https://github.com/ESIPFed/sweet/raw/refs/heads/master/src/humanAgriculture.ttl
  example: AnimalProduction
  github_request_issue: 1772
  homepage: http://sweetontology.net/humanAgriculture/
  keywords:
  - agriculture
  license: CC0-1.0
  name: SWEET Ontology Human Agriculture
  part_of: sweet
  prefix: sweet.hua
  repository: https://github.com/ESIPFed/sweet
  synonyms:
  - sohua
  uri_format: http://sweetontology.net/humanAgriculture/$1
sweet.huc:
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: The Semantic Web for Earth and Environmental Terminology (SWEET) ontology
    for Human Commerce
  download_rdf: https://github.com/ESIPFed/sweet/raw/refs/heads/master/src/humanCommerce.ttl
  example: Assembly
  github_request_issue: 1772
  homepage: http://sweetontology.net/humanCommerce/
  keywords:
  - commerce
  license: CC0-1.0
  name: SWEET Ontology Human Commerce
  part_of: sweet
  prefix: sweet.huc
  repository: https://github.com/ESIPFed/sweet
  synonyms:
  - sohuc
  uri_format: http://sweetontology.net/humanCommerce/$1
sweet.hud:
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: The Semantic Web for Earth and Environmental Terminology (SWEET) ontology
    for Human Decision
  download_rdf: https://github.com/ESIPFed/sweet/raw/refs/heads/master/src/humanDecision.ttl
  example: Allocation
  github_request_issue: 1772
  homepage: http://sweetontology.net/humanDecision/
  keywords:
  - decision
  license: CC0-1.0
  name: SWEET Ontology Human Decision
  part_of: sweet
  prefix: sweet.hud
  repository: https://github.com/ESIPFed/sweet
  synonyms:
  - sohud
  uri_format: http://sweetontology.net/humanDecision/$1
sweet.huea:
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: The Semantic Web for Earth and Environmental Terminology (SWEET) ontology
    for Human Environmental Assessment
  download_rdf: https://github.com/ESIPFed/sweet/raw/refs/heads/master/src/humanEnvirAssessment.ttl
  example: CEMS
  github_request_issue: 1772
  homepage: http://sweetontology.net/humanEnvirAssessment/
  keywords:
  - environmental assessment
  license: CC0-1.0
  name: SWEET Ontology Human Environmental Assessment
  part_of: sweet
  prefix: sweet.huea
  repository: https://github.com/ESIPFed/sweet
  synonyms:
  - sohuea
  uri_format: http://sweetontology.net/humanEnvirAssessment/$1
sweet.hueccont:
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: The Semantic Web for Earth and Environmental Terminology (SWEET) ontology
    for Human Environmental Control
  download_rdf: https://github.com/ESIPFed/sweet/raw/refs/heads/master/src/humanEnvirControl.ttl
  example: Abatement
  github_request_issue: 1772
  homepage: http://sweetontology.net/humanEnvirControl/
  keywords:
  - environmental control
  license: CC0-1.0
  name: SWEET Ontology Human Environmental Control
  part_of: sweet
  prefix: sweet.hueccont
  repository: https://github.com/ESIPFed/sweet
  synonyms:
  - sohueccont
  uri_format: http://sweetontology.net/humanEnvirControl/$1
sweet.huecons:
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: The Semantic Web for Earth and Environmental Terminology (SWEET) ontology
    for Human Environmental Conservation
  download_rdf: https://github.com/ESIPFed/sweet/raw/refs/heads/master/src/humanEnvirConservation.ttl
  example: Conservation
  github_request_issue: 1772
  homepage: http://sweetontology.net/humanEnvirConservation/
  keywords:
  - environmental conservation
  license: CC0-1.0
  name: SWEET Ontology Human Environmental Conservation
  part_of: sweet
  prefix: sweet.huecons
  repository: https://github.com/ESIPFed/sweet
  synonyms:
  - sohuecons
  uri_format: http://sweetontology.net/humanEnvirConservation/$1
sweet.hues:
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: The Semantic Web for Earth and Environmental Terminology (SWEET) ontology
    for Human Environmental Standards
  download_rdf: https://github.com/ESIPFed/sweet/raw/refs/heads/master/src/humanEnvirStandards.ttl
  example: AAQS
  github_request_issue: 1772
  homepage: http://sweetontology.net/humanEnvirStandards/
  keywords:
  - environmental standards
  license: CC0-1.0
  name: SWEET Ontology Human Environmental Standards
  part_of: sweet
  prefix: sweet.hues
  repository: https://github.com/ESIPFed/sweet
  synonyms:
  - sohues
  uri_format: http://sweetontology.net/humanEnvirStandards/$1
sweet.huj:
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: The Semantic Web for Earth and Environmental Terminology (SWEET) ontology
    for Human Jurisdiction
  download_rdf: https://github.com/ESIPFed/sweet/raw/refs/heads/master/src/humanJurisdiction.ttl
  example: AdministrativeRegion
  github_request_issue: 1772
  homepage: http://sweetontology.net/humanJurisdiction/
  keywords:
  - jurisdiction
  license: CC0-1.0
  name: SWEET Ontology Human Jurisdiction
  part_of: sweet
  prefix: sweet.huj
  repository: https://github.com/ESIPFed/sweet
  synonyms:
  - sohuj
  uri_format: http://sweetontology.net/humanJurisdiction/$1
sweet.hukd:
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: The Semantic Web for Earth and Environmental Terminology (SWEET) ontology
    for Human Knowledge Domain
  download_rdf: https://github.com/ESIPFed/sweet/raw/refs/heads/master/src/humanKnowledgeDomain.ttl
  example: Anatomy
  github_request_issue: 1772
  homepage: http://sweetontology.net/humanKnowledgeDomain/
  keywords:
  - knowledge domain
  license: CC0-1.0
  name: SWEET Ontology Human Knowledge Domain
  part_of: sweet
  prefix: sweet.hukd
  repository: https://github.com/ESIPFed/sweet
  synonyms:
  - sohukd
  uri_format: http://sweetontology.net/humanKnowledgeDomain/$1
sweet.hur:
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: The Semantic Web for Earth and Environmental Terminology (SWEET) ontology
    for Human Research
  download_rdf: https://github.com/ESIPFed/sweet/raw/refs/heads/master/src/humanResearch.ttl
  example: Analysis
  github_request_issue: 1772
  homepage: http://sweetontology.net/humanResearch/
  keywords:
  - research
  license: CC0-1.0
  name: SWEET Ontology Human Research
  part_of: sweet
  prefix: sweet.hur
  repository: https://github.com/ESIPFed/sweet
  synonyms:
  - sohur
  uri_format: http://sweetontology.net/humanResearch/$1
sweet.hut:
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: The Semantic Web for Earth and Environmental Terminology (SWEET) ontology
    for Human Transportation
  download_rdf: https://github.com/ESIPFed/sweet/raw/refs/heads/master/src/humanTransportation.ttl
  example: AirTraffic
  github_request_issue: 1772
  homepage: http://sweetontology.net/humanTransportation/
  keywords:
  - transportation
  license: CC0-1.0
  name: SWEET Ontology Human Transportation
  part_of: sweet
  prefix: sweet.hut
  repository: https://github.com/ESIPFed/sweet
  synonyms:
  - sohut
  uri_format: http://sweetontology.net/humanTransportation/$1
sweet.hutr:
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: The Semantic Web for Earth and Environmental Terminology (SWEET) ontology
    for Human Technology Readiness
  download_rdf: https://github.com/ESIPFed/sweet/raw/refs/heads/master/src/humanTechReadiness.ttl
  example: TRL
  github_request_issue: 1772
  homepage: http://sweetontology.net/humanTechReadiness/
  keywords:
  - technology readiness
  license: CC0-1.0
  name: SWEET Ontology Human Technology Readiness
  part_of: sweet
  prefix: sweet.hutr
  repository: https://github.com/ESIPFed/sweet
  synonyms:
  - sohutr
  uri_format: http://sweetontology.net/humanTechReadiness/$1
sweet.ma:
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: The Semantic Web for Earth and Environmental Terminology (SWEET) ontology
    for Materials
  download_rdf: https://github.com/ESIPFed/sweet/raw/refs/heads/master/src/matr.ttl
  example: Air
  github_request_issue: 1772
  homepage: http://sweetontology.net/matr/
  keywords:
  - materials
  license: CC0-1.0
  name: SWEET Ontology Materials
  part_of: sweet
  prefix: sweet.ma
  repository: https://github.com/ESIPFed/sweet
  synonyms:
  - soma
  uri_format: http://sweetontology.net/matr/$1
sweet.maae:
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: The Semantic Web for Earth and Environmental Terminology (SWEET) ontology
    for Material Aerosol
  download_rdf: https://github.com/ESIPFed/sweet/raw/refs/heads/master/src/matrAerosol.ttl
  example: Aerosol
  github_request_issue: 1772
  homepage: http://sweetontology.net/matrAerosol/
  keywords:
  - aerosol
  - materials
  license: CC0-1.0
  name: SWEET Ontology Material Aerosol
  part_of: sweet
  prefix: sweet.maae
  repository: https://github.com/ESIPFed/sweet
  synonyms:
  - somaae
  uri_format: http://sweetontology.net/matrAerosol/$1
sweet.mab:
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: The Semantic Web for Earth and Environmental Terminology (SWEET) ontology
    for Material Biomass
  download_rdf: https://github.com/ESIPFed/sweet/raw/refs/heads/master/src/matrBiomass.ttl
  example: AnimalWaste
  github_request_issue: 1772
  homepage: http://sweetontology.net/matrBiomass/
  keywords:
  - biomass
  - materials
  license: CC0-1.0
  name: SWEET Ontology Material Biomass
  part_of: sweet
  prefix: sweet.mab
  repository: https://github.com/ESIPFed/sweet
  synonyms:
  - somab
  uri_format: http://sweetontology.net/matrBiomass/$1
sweet.mac:
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: The Semantic Web for Earth and Environmental Terminology (SWEET) ontology
    for Material Compound
  download_rdf: https://github.com/ESIPFed/sweet/raw/refs/heads/master/src/matrCompound.ttl
  example: ChemicalCompound
  github_request_issue: 1772
  homepage: http://sweetontology.net/matrCompound/
  keywords:
  - compound
  - materials
  license: CC0-1.0
  name: SWEET Ontology Material Compound
  part_of: sweet
  prefix: sweet.mac
  repository: https://github.com/ESIPFed/sweet
  synonyms:
  - somac
  uri_format: http://sweetontology.net/matrCompound/$1
sweet.mael:
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: The Semantic Web for Earth and Environmental Terminology (SWEET) ontology
    for Material Element
  download_rdf: https://github.com/ESIPFed/sweet/raw/refs/heads/master/src/matrElement.ttl
  example: Actinoid
  github_request_issue: 1772
  homepage: http://sweetontology.net/matrElement/
  keywords:
  - element
  - materials
  license: CC0-1.0
  name: SWEET Ontology Material Element
  part_of: sweet
  prefix: sweet.mael
  repository: https://github.com/ESIPFed/sweet
  synonyms:
  - somael
  uri_format: http://sweetontology.net/matrElement/$1
sweet.maem:
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: The Semantic Web for Earth and Environmental Terminology (SWEET) ontology
    for Material Elemental Molecule
  download_rdf: https://github.com/ESIPFed/sweet/raw/refs/heads/master/src/matrElementalMolecule.ttl
  example: Allotrope
  github_request_issue: 1772
  homepage: http://sweetontology.net/matrElementalMolecule/
  keywords:
  - elemental molecule
  - materials
  license: CC0-1.0
  name: SWEET Ontology Material Elemental Molecule
  part_of: sweet
  prefix: sweet.maem
  repository: https://github.com/ESIPFed/sweet
  synonyms:
  - somaem
  uri_format: http://sweetontology.net/matrElementalMolecule/$1
sweet.maen:
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: The Semantic Web for Earth and Environmental Terminology (SWEET) ontology
    for Material Energy
  download_rdf: https://github.com/ESIPFed/sweet/raw/refs/heads/master/src/matrEnergy.ttl
  example: Battery
  github_request_issue: 1772
  homepage: http://sweetontology.net/matrEnergy/
  keywords:
  - energy
  - materials
  license: CC0-1.0
  name: SWEET Ontology Material Energy
  part_of: sweet
  prefix: sweet.maen
  repository: https://github.com/ESIPFed/sweet
  synonyms:
  - somaen
  uri_format: http://sweetontology.net/matrEnergy/$1
sweet.maeq:
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: The Semantic Web for Earth and Environmental Terminology (SWEET) ontology
    for Material Equipment
  download_rdf: https://github.com/ESIPFed/sweet/raw/refs/heads/master/src/matrEquipment.ttl
  example: Aircraft
  github_request_issue: 1772
  homepage: http://sweetontology.net/matrEquipment/
  keywords:
  - equipment
  - materials
  license: CC0-1.0
  name: SWEET Ontology Material Equipment
  part_of: sweet
  prefix: sweet.maeq
  repository: https://github.com/ESIPFed/sweet
  synonyms:
  - somaeq
  uri_format: http://sweetontology.net/matrEquipment/$1
sweet.maf:
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: The Semantic Web for Earth and Environmental Terminology (SWEET) ontology
    for Material Facility
  download_rdf: https://github.com/ESIPFed/sweet/raw/refs/heads/master/src/matrFacility.ttl
  example: AgriculturalProductionFacility
  github_request_issue: 1772
  homepage: http://sweetontology.net/matrFacility/
  keywords:
  - facility
  - materials
  license: CC0-1.0
  name: SWEET Ontology Material Facility
  part_of: sweet
  prefix: sweet.maf
  repository: https://github.com/ESIPFed/sweet
  synonyms:
  - somaf
  uri_format: http://sweetontology.net/matrFacility/$1
sweet.maind:
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: The Semantic Web for Earth and Environmental Terminology (SWEET) ontology
    for Material Industrial
  download_rdf: https://github.com/ESIPFed/sweet/raw/refs/heads/master/src/matrIndustrial.ttl
  example: Alloy
  github_request_issue: 1772
  homepage: http://sweetontology.net/matrIndustrial/
  keywords:
  - industrial
  - materials
  license: CC0-1.0
  name: SWEET Ontology Material Industrial
  part_of: sweet
  prefix: sweet.maind
  repository: https://github.com/ESIPFed/sweet
  synonyms:
  - somaind
  uri_format: http://sweetontology.net/matrIndustrial/$1
sweet.mains:
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: The Semantic Web for Earth and Environmental Terminology (SWEET) ontology
    for Material Instrument
  download_rdf: https://github.com/ESIPFed/sweet/raw/refs/heads/master/src/matrInstrument.ttl
  example: Anemometer
  github_request_issue: 1772
  homepage: http://sweetontology.net/matrInstrument/
  keywords:
  - instrument
  - materials
  license: CC0-1.0
  name: SWEET Ontology Material Instrument
  part_of: sweet
  prefix: sweet.mains
  repository: https://github.com/ESIPFed/sweet
  synonyms:
  - somains
  uri_format: http://sweetontology.net/matrInstrument/$1
sweet.maio:
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: The Semantic Web for Earth and Environmental Terminology (SWEET) ontology
    for Material Ion
  download_rdf: https://github.com/ESIPFed/sweet/raw/refs/heads/master/src/matrIon.ttl
  example: Anion
  github_request_issue: 1772
  homepage: http://sweetontology.net/matrIon/
  keywords:
  - ion
  - materials
  license: CC0-1.0
  name: SWEET Ontology Material Ion
  part_of: sweet
  prefix: sweet.maio
  repository: https://github.com/ESIPFed/sweet
  synonyms:
  - somaio
  uri_format: http://sweetontology.net/matrIon/$1
sweet.mais:
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: The Semantic Web for Earth and Environmental Terminology (SWEET) ontology
    for Material Isotope
  download_rdf: https://github.com/ESIPFed/sweet/raw/refs/heads/master/src/matrIsotope.ttl
  example: AlphaParticle
  github_request_issue: 1772
  homepage: http://sweetontology.net/matrIsotope/
  keywords:
  - isotope
  - materials
  license: CC0-1.0
  name: SWEET Ontology Material Isotope
  part_of: sweet
  prefix: sweet.mais
  repository: https://github.com/ESIPFed/sweet
  synonyms:
  - somais
  uri_format: http://sweetontology.net/matrIsotope/$1
sweet.mamic:
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: The Semantic Web for Earth and Environmental Terminology (SWEET) ontology
    for Material Microbiota
  download_rdf: https://github.com/ESIPFed/sweet/raw/refs/heads/master/src/matrMicrobiota.ttl
  example: Algae
  github_request_issue: 1772
  homepage: http://sweetontology.net/matrMicrobiota/
  keywords:
  - materials
  - microbiota
  license: CC0-1.0
  name: SWEET Ontology Material Microbiota
  part_of: sweet
  prefix: sweet.mamic
  repository: https://github.com/ESIPFed/sweet
  synonyms:
  - somamic
  uri_format: http://sweetontology.net/matrMicrobiota/$1
sweet.mamin:
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: The Semantic Web for Earth and Environmental Terminology (SWEET) ontology
    for Material Mineral
  download_rdf: https://github.com/ESIPFed/sweet/raw/refs/heads/master/src/matrMineral.ttl
  example: Calcite
  github_request_issue: 1772
  homepage: http://sweetontology.net/matrMineral/
  keywords:
  - materials
  - mineral
  license: CC0-1.0
  name: SWEET Ontology Material Mineral
  part_of: sweet
  prefix: sweet.mamin
  repository: https://github.com/ESIPFed/sweet
  synonyms:
  - somamin
  uri_format: http://sweetontology.net/matrMineral/$1
sweet.man:
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: The Semantic Web for Earth and Environmental Terminology (SWEET) ontology
    for Material Animal
  download_rdf: https://github.com/ESIPFed/sweet/raw/refs/heads/master/src/matrAnimal.ttl
  example: AcornWorm
  github_request_issue: 1772
  homepage: http://sweetontology.net/matrAnimal/
  keywords:
  - animal
  - materials
  license: CC0-1.0
  name: SWEET Ontology Material Animal
  part_of: sweet
  prefix: sweet.man
  repository: https://github.com/ESIPFed/sweet
  synonyms:
  - soman
  uri_format: http://sweetontology.net/matrAnimal/$1
sweet.manr:
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: The Semantic Web for Earth and Environmental Terminology (SWEET) ontology
    for Material Natural Resource
  download_rdf: https://github.com/ESIPFed/sweet/raw/refs/heads/master/src/matrNaturalResource.ttl
  example: Anthracite
  github_request_issue: 1772
  homepage: http://sweetontology.net/matrNaturalResource/
  keywords:
  - materials
  - natural resource
  license: CC0-1.0
  name: SWEET Ontology Material Natural Resource
  part_of: sweet
  prefix: sweet.manr
  repository: https://github.com/ESIPFed/sweet
  synonyms:
  - somanr
  uri_format: http://sweetontology.net/matrNaturalResource/$1
sweet.maoc:
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: The Semantic Web for Earth and Environmental Terminology (SWEET) ontology
    for Material Organic Compound
  download_rdf: https://github.com/ESIPFed/sweet/raw/refs/heads/master/src/matrOrganicCompound.ttl
  example: Alkane
  github_request_issue: 1772
  homepage: http://sweetontology.net/matrOrganicCompound/
  keywords:
  - materials
  - organic compound
  license: CC0-1.0
  name: SWEET Ontology Material Organic Compound
  part_of: sweet
  prefix: sweet.maoc
  repository: https://github.com/ESIPFed/sweet
  synonyms:
  - somaoc
  uri_format: http://sweetontology.net/matrOrganicCompound/$1
sweet.mapa:
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: The Semantic Web for Earth and Environmental Terminology (SWEET) ontology
    for Material Particle
  download_rdf: https://github.com/ESIPFed/sweet/raw/refs/heads/master/src/matrParticle.ttl
  example: AnomalousEnergeticParticle
  github_request_issue: 1772
  homepage: http://sweetontology.net/matrParticle/
  keywords:
  - materials
  - particle
  license: CC0-1.0
  name: SWEET Ontology Material Particle
  part_of: sweet
  prefix: sweet.mapa
  repository: https://github.com/ESIPFed/sweet
  synonyms:
  - somapa
  uri_format: http://sweetontology.net/matrParticle/$1
sweet.mapl:
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: The Semantic Web for Earth and Environmental Terminology (SWEET) ontology
    for Material Plant
  download_rdf: https://github.com/ESIPFed/sweet/raw/refs/heads/master/src/matrPlant.ttl
  example: Branch
  github_request_issue: 1772
  homepage: http://sweetontology.net/matrPlant/
  keywords:
  - materials
  - plant
  license: CC0-1.0
  name: SWEET Ontology Material Plant
  part_of: sweet
  prefix: sweet.mapl
  repository: https://github.com/ESIPFed/sweet
  synonyms:
  - somapl
  uri_format: http://sweetontology.net/matrPlant/$1
sweet.marock:
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: The Semantic Web for Earth and Environmental Terminology (SWEET) ontology
    for Material Rock
  download_rdf: https://github.com/ESIPFed/sweet/raw/refs/heads/master/src/matrRock.ttl
  example: Breccia
  github_request_issue: 1772
  homepage: http://sweetontology.net/matrRock/
  keywords:
  - materials
  - rock
  license: CC0-1.0
  name: SWEET Ontology Material Rock
  part_of: sweet
  prefix: sweet.marock
  repository: https://github.com/ESIPFed/sweet
  synonyms:
  - somarock
  uri_format: http://sweetontology.net/matrRock/$1
sweet.marocki:
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: The Semantic Web for Earth and Environmental Terminology (SWEET) ontology
    for Material Rock Igneous
  download_rdf: https://github.com/ESIPFed/sweet/raw/refs/heads/master/src/matrRockIgneous.ttl
  example: Aa
  github_request_issue: 1772
  homepage: http://sweetontology.net/matrRockIgneous/
  keywords:
  - materials
  - rock igneous
  license: CC0-1.0
  name: SWEET Ontology Material Rock Igneous
  part_of: sweet
  prefix: sweet.marocki
  repository: https://github.com/ESIPFed/sweet
  synonyms:
  - somarocki
  uri_format: http://sweetontology.net/matrRockIgneous/$1
sweet.mas:
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: The Semantic Web for Earth and Environmental Terminology (SWEET) ontology
    for Material Sediment
  download_rdf: https://github.com/ESIPFed/sweet/raw/refs/heads/master/src/matrSediment.ttl
  example: Alluvium
  github_request_issue: 1772
  homepage: http://sweetontology.net/matrSediment/
  keywords:
  - materials
  - sediment
  license: CC0-1.0
  name: SWEET Ontology Material Sediment
  part_of: sweet
  prefix: sweet.mas
  repository: https://github.com/ESIPFed/sweet
  synonyms:
  - somas
  uri_format: http://sweetontology.net/matrSediment/$1
sweet.maw:
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: The Semantic Web for Earth and Environmental Terminology (SWEET) ontology
    for Material Water
  download_rdf: https://github.com/ESIPFed/sweet/raw/refs/heads/master/src/matrWater.ttl
  example: BlackWater
  github_request_issue: 1772
  homepage: http://sweetontology.net/matrWater/
  keywords:
  - materials
  - water
  license: CC0-1.0
  name: SWEET Ontology Material Water
  part_of: sweet
  prefix: sweet.maw
  repository: https://github.com/ESIPFed/sweet
  synonyms:
  - somaw
  uri_format: http://sweetontology.net/matrWater/$1
sweet.ph:
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: The Semantic Web for Earth and Environmental Terminology (SWEET) ontology
    for Phenomena
  download_rdf: https://github.com/ESIPFed/sweet/raw/refs/heads/master/src/phen.ttl
  example: AirSeaExchange
  github_request_issue: 1772
  homepage: http://sweetontology.net/phen/
  keywords:
  - phenomena
  license: CC0-1.0
  name: SWEET Ontology Phenomena
  part_of: sweet
  prefix: sweet.ph
  repository: https://github.com/ESIPFed/sweet
  synonyms:
  - soph
  uri_format: http://sweetontology.net/phen/$1
sweet.phatmo:
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: The Semantic Web for Earth and Environmental Terminology (SWEET) ontology
    for Phenomena Atmosphere
  download_rdf: https://github.com/ESIPFed/sweet/raw/refs/heads/master/src/phenAtmo.ttl
  example: AirMass
  github_request_issue: 1772
  homepage: http://sweetontology.net/phenAtmo/
  keywords:
  - atmosphere
  - phenomena
  license: CC0-1.0
  name: SWEET Ontology Phenomena Atmosphere
  part_of: sweet
  prefix: sweet.phatmo
  repository: https://github.com/ESIPFed/sweet
  synonyms:
  - sophatmo
  uri_format: http://sweetontology.net/phenAtmo/$1
sweet.phatmoc:
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: The Semantic Web for Earth and Environmental Terminology (SWEET) ontology
    for Phenomena Atmosphere Cloud
  download_rdf: https://github.com/ESIPFed/sweet/raw/refs/heads/master/src/phenAtmoCloud.ttl
  example: Altostratus
  github_request_issue: 1772
  homepage: http://sweetontology.net/phenAtmoCloud/
  keywords:
  - atmosphere cloud
  - phenomena
  license: CC0-1.0
  name: SWEET Ontology Phenomena Atmosphere Cloud
  part_of: sweet
  prefix: sweet.phatmoc
  repository: https://github.com/ESIPFed/sweet
  synonyms:
  - sophatmoc
  uri_format: http://sweetontology.net/phenAtmoCloud/$1
sweet.phatmofo:
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: The Semantic Web for Earth and Environmental Terminology (SWEET) ontology
    for Phenomena Atmosphere Fog
  download_rdf: https://github.com/ESIPFed/sweet/raw/refs/heads/master/src/phenAtmoFog.ttl
  example: AdvectionFog
  github_request_issue: 1772
  homepage: http://sweetontology.net/phenAtmoFog/
  keywords:
  - atmosphere fog
  - phenomena
  license: CC0-1.0
  name: SWEET Ontology Phenomena Atmosphere Fog
  part_of: sweet
  prefix: sweet.phatmofo
  repository: https://github.com/ESIPFed/sweet
  synonyms:
  - sophatmofo
  uri_format: http://sweetontology.net/phenAtmoFog/$1
sweet.phatmofr:
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: The Semantic Web for Earth and Environmental Terminology (SWEET) ontology
    for Phenomena Atmosphere Front
  download_rdf: https://github.com/ESIPFed/sweet/raw/refs/heads/master/src/phenAtmoFront.ttl
  example: ColdFront
  github_request_issue: 1772
  homepage: http://sweetontology.net/phenAtmoFront/
  keywords:
  - atmosphere front
  - phenomena
  license: CC0-1.0
  name: SWEET Ontology Phenomena Atmosphere Front
  part_of: sweet
  prefix: sweet.phatmofr
  repository: https://github.com/ESIPFed/sweet
  synonyms:
  - sophatmofr
  uri_format: http://sweetontology.net/phenAtmoFront/$1
sweet.phatmol:
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: The Semantic Web for Earth and Environmental Terminology (SWEET) ontology
    for Phenomena Atmosphere Lightning
  download_rdf: https://github.com/ESIPFed/sweet/raw/refs/heads/master/src/phenAtmoLightning.ttl
  example: BallLightning
  github_request_issue: 1772
  homepage: http://sweetontology.net/phenAtmoLightning/
  keywords:
  - atmosphere lightning
  - phenomena
  license: CC0-1.0
  name: SWEET Ontology Phenomena Atmosphere Lightning
  part_of: sweet
  prefix: sweet.phatmol
  repository: https://github.com/ESIPFed/sweet
  synonyms:
  - sophatmol
  uri_format: http://sweetontology.net/phenAtmoLightning/$1
sweet.phatmopc:
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: The Semantic Web for Earth and Environmental Terminology (SWEET) ontology
    for Phenomena Atmosphere Precipitation
  download_rdf: https://github.com/ESIPFed/sweet/raw/refs/heads/master/src/phenAtmoPrecipitation.ttl
  example: AtmosphericPrecipitation
  github_request_issue: 1772
  homepage: http://sweetontology.net/phenAtmoPrecipitation/
  keywords:
  - atmosphere precipitation
  - phenomena
  license: CC0-1.0
  name: SWEET Ontology Phenomena Atmosphere Precipitation
  part_of: sweet
  prefix: sweet.phatmopc
  repository: https://github.com/ESIPFed/sweet
  synonyms:
  - sophatmopc
  uri_format: http://sweetontology.net/phenAtmoPrecipitation/$1
sweet.phatmops:
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: The Semantic Web for Earth and Environmental Terminology (SWEET) ontology
    for Phenomena Atmosphere Pressure
  download_rdf: https://github.com/ESIPFed/sweet/raw/refs/heads/master/src/phenAtmoPressure.ttl
  example: AtmosphericAnticyclone
  github_request_issue: 1772
  homepage: http://sweetontology.net/phenAtmoPressure/
  keywords:
  - atmosphere pressure
  - phenomena
  license: CC0-1.0
  name: SWEET Ontology Phenomena Atmosphere Pressure
  part_of: sweet
  prefix: sweet.phatmops
  repository: https://github.com/ESIPFed/sweet
  synonyms:
  - sophatmops
  uri_format: http://sweetontology.net/phenAtmoPressure/$1
sweet.phatmos:
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: The Semantic Web for Earth and Environmental Terminology (SWEET) ontology
    for Phenomena Atmosphere Sky
  download_rdf: https://github.com/ESIPFed/sweet/raw/refs/heads/master/src/phenAtmoSky.ttl
  example: AirPollution
  github_request_issue: 1772
  homepage: http://sweetontology.net/phenAtmoSky/
  keywords:
  - atmosphere sky
  - phenomena
  license: CC0-1.0
  name: SWEET Ontology Phenomena Atmosphere Sky
  part_of: sweet
  prefix: sweet.phatmos
  repository: https://github.com/ESIPFed/sweet
  synonyms:
  - sophatmos
  uri_format: http://sweetontology.net/phenAtmoSky/$1
sweet.phatmot:
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: The Semantic Web for Earth and Environmental Terminology (SWEET) ontology
    for Phenomena Atmosphere Transport
  download_rdf: https://github.com/ESIPFed/sweet/raw/refs/heads/master/src/phenAtmoTransport.ttl
  example: AcidFog
  github_request_issue: 1772
  homepage: http://sweetontology.net/phenAtmoTransport/
  keywords:
  - atmosphere transport
  - phenomena
  license: CC0-1.0
  name: SWEET Ontology Phenomena Atmosphere Transport
  part_of: sweet
  prefix: sweet.phatmot
  repository: https://github.com/ESIPFed/sweet
  synonyms:
  - sophatmot
  uri_format: http://sweetontology.net/phenAtmoTransport/$1
sweet.phatmow:
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: The Semantic Web for Earth and Environmental Terminology (SWEET) ontology
    for Phenomena Atmosphere Wind
  download_rdf: https://github.com/ESIPFed/sweet/raw/refs/heads/master/src/phenAtmoWind.ttl
  example: AgeostrophicWind
  github_request_issue: 1772
  homepage: http://sweetontology.net/phenAtmoWind/
  keywords:
  - atmosphere wind
  - phenomena
  license: CC0-1.0
  name: SWEET Ontology Phenomena Atmosphere Wind
  part_of: sweet
  prefix: sweet.phatmow
  repository: https://github.com/ESIPFed/sweet
  synonyms:
  - sophatmow
  uri_format: http://sweetontology.net/phenAtmoWind/$1
sweet.phatmowm:
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: The Semantic Web for Earth and Environmental Terminology (SWEET) ontology
    for Phenomena Atmosphere Wind Mesoscale
  download_rdf: https://github.com/ESIPFed/sweet/raw/refs/heads/master/src/phenAtmoWindMesoscale.ttl
  example: AnabaticWind
  github_request_issue: 1772
  homepage: http://sweetontology.net/phenAtmoWindMesoscale/
  keywords:
  - atmosphere wind mesoscale
  - phenomena
  license: CC0-1.0
  name: SWEET Ontology Phenomena Atmosphere Wind Mesoscale
  part_of: sweet
  prefix: sweet.phatmowm
  repository: https://github.com/ESIPFed/sweet
  synonyms:
  - sophatmowm
  uri_format: http://sweetontology.net/phenAtmoWindMesoscale/$1
sweet.phb:
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: The Semantic Web for Earth and Environmental Terminology (SWEET) ontology
    for Phenomena Biology
  download_rdf: https://github.com/ESIPFed/sweet/raw/refs/heads/master/src/phenBiol.ttl
  example: Assimilation
  github_request_issue: 1772
  homepage: http://sweetontology.net/phenBiol/
  keywords:
  - biology
  - phenomena
  license: CC0-1.0
  name: SWEET Ontology Phenomena Biology
  part_of: sweet
  prefix: sweet.phb
  repository: https://github.com/ESIPFed/sweet
  synonyms:
  - sophb
  uri_format: http://sweetontology.net/phenBiol/$1
sweet.phcm:
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: The Semantic Web for Earth and Environmental Terminology (SWEET) ontology
    for Phenomena Cycle Material
  download_rdf: https://github.com/ESIPFed/sweet/raw/refs/heads/master/src/phenCycleMaterial.ttl
  example: BiogeochemicalCycle
  github_request_issue: 1772
  homepage: http://sweetontology.net/phenCycleMaterial/
  keywords:
  - cycle material
  - phenomena
  license: CC0-1.0
  name: SWEET Ontology Phenomena Cycle Material
  part_of: sweet
  prefix: sweet.phcm
  repository: https://github.com/ESIPFed/sweet
  synonyms:
  - sophcm
  uri_format: http://sweetontology.net/phenCycleMaterial/$1
sweet.phcr:
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: The Semantic Web for Earth and Environmental Terminology (SWEET) ontology
    for Phenomena Cryosphere
  download_rdf: https://github.com/ESIPFed/sweet/raw/refs/heads/master/src/phenCryo.ttl
  example: Accumulation
  github_request_issue: 1772
  homepage: http://sweetontology.net/phenCryo/
  keywords:
  - cryosphere
  - phenomena
  license: CC0-1.0
  name: SWEET Ontology Phenomena Cryosphere
  part_of: sweet
  prefix: sweet.phcr
  repository: https://github.com/ESIPFed/sweet
  synonyms:
  - sophcr
  uri_format: http://sweetontology.net/phenCryo/$1
sweet.phcy:
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: The Semantic Web for Earth and Environmental Terminology (SWEET) ontology
    for Phenomena Cycle
  download_rdf: https://github.com/ESIPFed/sweet/raw/refs/heads/master/src/phenCycle.ttl
  example: AnnualCycle
  github_request_issue: 1772
  homepage: http://sweetontology.net/phenCycle/
  keywords:
  - cycle
  - phenomena
  license: CC0-1.0
  name: SWEET Ontology Phenomena Cycle
  part_of: sweet
  prefix: sweet.phcy
  repository: https://github.com/ESIPFed/sweet
  synonyms:
  - sophcy
  uri_format: http://sweetontology.net/phenCycle/$1
sweet.phec:
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: The Semantic Web for Earth and Environmental Terminology (SWEET) ontology
    for Phenomena Ecology
  download_rdf: https://github.com/ESIPFed/sweet/raw/refs/heads/master/src/phenEcology.ttl
  example: Adaptation
  github_request_issue: 1772
  homepage: http://sweetontology.net/phenEcology/
  keywords:
  - ecology
  - phenomena
  license: CC0-1.0
  name: SWEET Ontology Phenomena Ecology
  part_of: sweet
  prefix: sweet.phec
  repository: https://github.com/ESIPFed/sweet
  synonyms:
  - sophec
  uri_format: http://sweetontology.net/phenEcology/$1
sweet.phei:
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: The Semantic Web for Earth and Environmental Terminology (SWEET) ontology
    for Phenomena Environmental Impact
  download_rdf: https://github.com/ESIPFed/sweet/raw/refs/heads/master/src/phenEnvirImpact.ttl
  example: AirPollution
  github_request_issue: 1772
  homepage: http://sweetontology.net/phenEnvirImpact/
  keywords:
  - environmental impact
  - phenomena
  license: CC0-1.0
  name: SWEET Ontology Phenomena Environmental Impact
  part_of: sweet
  prefix: sweet.phei
  repository: https://github.com/ESIPFed/sweet
  synonyms:
  - sophei
  uri_format: http://sweetontology.net/phenEnvirImpact/$1
sweet.phel:
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: The Semantic Web for Earth and Environmental Terminology (SWEET) ontology
    for Phenomena ElectroMagnetic
  download_rdf: https://github.com/ESIPFed/sweet/raw/refs/heads/master/src/phenElecMag.ttl
  example: CurrentSheet
  github_request_issue: 1772
  homepage: http://sweetontology.net/phenElecMag/
  keywords:
  - electromagnetic
  - phenomena
  license: CC0-1.0
  name: SWEET Ontology Phenomena ElectroMagnetic
  part_of: sweet
  prefix: sweet.phel
  repository: https://github.com/ESIPFed/sweet
  synonyms:
  - sophel
  uri_format: http://sweetontology.net/phenElecMag/$1
sweet.phen:
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: The Semantic Web for Earth and Environmental Terminology (SWEET) ontology
    for Phenomena Energy
  download_rdf: https://github.com/ESIPFed/sweet/raw/refs/heads/master/src/phenEnergy.ttl
  example: ActiveSolarEnergy
  github_request_issue: 1772
  homepage: http://sweetontology.net/phenEnergy/
  keywords:
  - energy
  - phenomena
  license: CC0-1.0
  name: SWEET Ontology Phenomena Energy
  part_of: sweet
  prefix: sweet.phen
  repository: https://github.com/ESIPFed/sweet
  synonyms:
  - sophen
  uri_format: http://sweetontology.net/phenEnergy/$1
sweet.phfd:
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: The Semantic Web for Earth and Environmental Terminology (SWEET) ontology
    for Phenomena Fluid Dynamics
  download_rdf: https://github.com/ESIPFed/sweet/raw/refs/heads/master/src/phenFluidDynamics.ttl
  example: Anticyclone
  github_request_issue: 1772
  homepage: http://sweetontology.net/phenFluidDynamics/
  keywords:
  - fluid dynamics
  - phenomena
  license: CC0-1.0
  name: SWEET Ontology Phenomena Fluid Dynamics
  part_of: sweet
  prefix: sweet.phfd
  repository: https://github.com/ESIPFed/sweet
  synonyms:
  - sophfd
  uri_format: http://sweetontology.net/phenFluidDynamics/$1
sweet.phfi:
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: The Semantic Web for Earth and Environmental Terminology (SWEET) ontology
    for Phenomena Fluid Instability
  download_rdf: https://github.com/ESIPFed/sweet/raw/refs/heads/master/src/phenFluidInstability.ttl
  example: AbsoluteInstability
  github_request_issue: 1772
  homepage: http://sweetontology.net/phenFluidInstability/
  keywords:
  - fluid instability
  - phenomena
  license: CC0-1.0
  name: SWEET Ontology Phenomena Fluid Instability
  part_of: sweet
  prefix: sweet.phfi
  repository: https://github.com/ESIPFed/sweet
  synonyms:
  - sophfi
  uri_format: http://sweetontology.net/phenFluidInstability/$1
sweet.phft:
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: The Semantic Web for Earth and Environmental Terminology (SWEET) ontology
    for Phenomena Fluid Transport
  download_rdf: https://github.com/ESIPFed/sweet/raw/refs/heads/master/src/phenFluidTransport.ttl
  example: Advection
  github_request_issue: 1772
  homepage: http://sweetontology.net/phenFluidTransport/
  keywords:
  - fluid transport
  - phenomena
  license: CC0-1.0
  name: SWEET Ontology Phenomena Fluid Transport
  part_of: sweet
  prefix: sweet.phft
  repository: https://github.com/ESIPFed/sweet
  synonyms:
  - sophft
  uri_format: http://sweetontology.net/phenFluidTransport/$1
sweet.phg:
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: The Semantic Web for Earth and Environmental Terminology (SWEET) ontology
    for Phenomena Geologic
  download_rdf: https://github.com/ESIPFed/sweet/raw/refs/heads/master/src/phenGeol.ttl
  example: CompositeProcess
  github_request_issue: 1772
  homepage: http://sweetontology.net/phenGeol/
  keywords:
  - geologic
  - phenomena
  license: CC0-1.0
  name: SWEET Ontology Phenomena Geologic
  part_of: sweet
  prefix: sweet.phg
  repository: https://github.com/ESIPFed/sweet
  synonyms:
  - sophg
  uri_format: http://sweetontology.net/phenGeol/$1
sweet.phgf:
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: The Semantic Web for Earth and Environmental Terminology (SWEET) ontology
    for Phenomena Geologic Fault
  download_rdf: https://github.com/ESIPFed/sweet/raw/refs/heads/master/src/phenGeolFault.ttl
  example: Detachment
  github_request_issue: 1772
  homepage: http://sweetontology.net/phenGeolFault/
  keywords:
  - geologic fault
  - phenomena
  license: CC0-1.0
  name: SWEET Ontology Phenomena Geologic Fault
  part_of: sweet
  prefix: sweet.phgf
  repository: https://github.com/ESIPFed/sweet
  synonyms:
  - sophgf
  uri_format: http://sweetontology.net/phenGeolFault/$1
sweet.phgg:
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: The Semantic Web for Earth and Environmental Terminology (SWEET) ontology
    for Phenomena Geologic Geomorphology
  download_rdf: https://github.com/ESIPFed/sweet/raw/refs/heads/master/src/phenGeolGeomorphology.ttl
  example: Abrasion
  github_request_issue: 1772
  homepage: http://sweetontology.net/phenGeolGeomorphology/
  keywords:
  - geologic geomorphology
  - phenomena
  license: CC0-1.0
  name: SWEET Ontology Phenomena Geologic Geomorphology
  part_of: sweet
  prefix: sweet.phgg
  repository: https://github.com/ESIPFed/sweet
  synonyms:
  - sophgg
  uri_format: http://sweetontology.net/phenGeolGeomorphology/$1
sweet.phgs:
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: The Semantic Web for Earth and Environmental Terminology (SWEET) ontology
    for Phenomena Geologic Seismicity
  download_rdf: https://github.com/ESIPFed/sweet/raw/refs/heads/master/src/phenGeolSeismicity.ttl
  example: Aftershock
  github_request_issue: 1772
  homepage: http://sweetontology.net/phenGeolSeismicity/
  keywords:
  - geologic seismicity
  - phenomena
  license: CC0-1.0
  name: SWEET Ontology Phenomena Geologic Seismicity
  part_of: sweet
  prefix: sweet.phgs
  repository: https://github.com/ESIPFed/sweet
  synonyms:
  - sophgs
  uri_format: http://sweetontology.net/phenGeolSeismicity/$1
sweet.phgt:
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: The Semantic Web for Earth and Environmental Terminology (SWEET) ontology
    for Phenomena Geologic Tectonic
  download_rdf: https://github.com/ESIPFed/sweet/raw/refs/heads/master/src/phenGeolTectonic.ttl
  example: AsymmetricHeatFlow
  github_request_issue: 1772
  homepage: http://sweetontology.net/phenGeolTectonic/
  keywords:
  - geologic tectonic
  - phenomena
  license: CC0-1.0
  name: SWEET Ontology Phenomena Geologic Tectonic
  part_of: sweet
  prefix: sweet.phgt
  repository: https://github.com/ESIPFed/sweet
  synonyms:
  - sophgt
  uri_format: http://sweetontology.net/phenGeolTectonic/$1
sweet.phgv:
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: The Semantic Web for Earth and Environmental Terminology (SWEET) ontology
    for Phenomena Geologic Volcano
  download_rdf: https://github.com/ESIPFed/sweet/raw/refs/heads/master/src/phenGeolVolcano.ttl
  example: EruptionCloud
  github_request_issue: 1772
  homepage: http://sweetontology.net/phenGeolVolcano/
  keywords:
  - geologic volcano
  - phenomena
  license: CC0-1.0
  name: SWEET Ontology Phenomena Geologic Volcano
  part_of: sweet
  prefix: sweet.phgv
  repository: https://github.com/ESIPFed/sweet
  synonyms:
  - sophgv
  uri_format: http://sweetontology.net/phenGeolVolcano/$1
sweet.phhe:
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: The Semantic Web for Earth and Environmental Terminology (SWEET) ontology
    for Phenomena Heliosphere
  download_rdf: https://github.com/ESIPFed/sweet/raw/refs/heads/master/src/phenHelio.ttl
  example: Airglow
  github_request_issue: 1772
  homepage: http://sweetontology.net/phenHelio/
  keywords:
  - heliosphere
  - phenomena
  license: CC0-1.0
  name: SWEET Ontology Phenomena Heliosphere
  part_of: sweet
  prefix: sweet.phhe
  repository: https://github.com/ESIPFed/sweet
  synonyms:
  - sophhe
  uri_format: http://sweetontology.net/phenHelio/$1
sweet.phhy:
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: The Semantic Web for Earth and Environmental Terminology (SWEET) ontology
    for Phenomena Hydrosphere
  download_rdf: https://github.com/ESIPFed/sweet/raw/refs/heads/master/src/phenHydro.ttl
  example: BaseFlow
  github_request_issue: 1772
  homepage: http://sweetontology.net/phenHydro/
  keywords:
  - hydrosphere
  - phenomena
  license: CC0-1.0
  name: SWEET Ontology Phenomena Hydrosphere
  part_of: sweet
  prefix: sweet.phhy
  repository: https://github.com/ESIPFed/sweet
  synonyms:
  - sophhy
  uri_format: http://sweetontology.net/phenHydro/$1
sweet.phm:
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: The Semantic Web for Earth and Environmental Terminology (SWEET) ontology
    for Phenomena Mixing
  download_rdf: https://github.com/ESIPFed/sweet/raw/refs/heads/master/src/phenMixing.ttl
  example: Aeration
  github_request_issue: 1772
  homepage: http://sweetontology.net/phenMixing/
  keywords:
  - mixing
  - phenomena
  license: CC0-1.0
  name: SWEET Ontology Phenomena Mixing
  part_of: sweet
  prefix: sweet.phm
  repository: https://github.com/ESIPFed/sweet
  synonyms:
  - sophm
  uri_format: http://sweetontology.net/phenMixing/$1
sweet.pho:
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: The Semantic Web for Earth and Environmental Terminology (SWEET) ontology
    for Phenomena Ocean
  download_rdf: https://github.com/ESIPFed/sweet/raw/refs/heads/master/src/phenOcean.ttl
  example: OceanPhenomena
  github_request_issue: 1772
  homepage: http://sweetontology.net/phenOcean/
  keywords:
  - ocean
  - phenomena
  license: CC0-1.0
  name: SWEET Ontology Phenomena Ocean
  part_of: sweet
  prefix: sweet.pho
  repository: https://github.com/ESIPFed/sweet
  synonyms:
  - sopho
  uri_format: http://sweetontology.net/phenOcean/$1
sweet.phoc:
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: The Semantic Web for Earth and Environmental Terminology (SWEET) ontology
    for Phenomena Ocean Coastal
  download_rdf: https://github.com/ESIPFed/sweet/raw/refs/heads/master/src/phenOceanCoastal.ttl
  example: Attrition
  github_request_issue: 1772
  homepage: http://sweetontology.net/phenOceanCoastal/
  keywords:
  - ocean coastal
  - phenomena
  license: CC0-1.0
  name: SWEET Ontology Phenomena Ocean Coastal
  part_of: sweet
  prefix: sweet.phoc
  repository: https://github.com/ESIPFed/sweet
  synonyms:
  - sophoc
  uri_format: http://sweetontology.net/phenOceanCoastal/$1
sweet.phod:
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: The Semantic Web for Earth and Environmental Terminology (SWEET) ontology
    for Phenomena Ocean Dynamics
  download_rdf: https://github.com/ESIPFed/sweet/raw/refs/heads/master/src/phenOceanDynamics.ttl
  example: BoundaryCurrent
  github_request_issue: 1772
  homepage: http://sweetontology.net/phenOceanDynamics/
  keywords:
  - ocean dynamics
  - phenomena
  license: CC0-1.0
  name: SWEET Ontology Phenomena Ocean Dynamics
  part_of: sweet
  prefix: sweet.phod
  repository: https://github.com/ESIPFed/sweet
  synonyms:
  - sophod
  uri_format: http://sweetontology.net/phenOceanDynamics/$1
sweet.phpc:
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: The Semantic Web for Earth and Environmental Terminology (SWEET) ontology
    for Phenomena Planetary Climate
  download_rdf: https://github.com/ESIPFed/sweet/raw/refs/heads/master/src/phenPlanetClimate.ttl
  example: Climate
  github_request_issue: 1772
  homepage: http://sweetontology.net/phenPlanetClimate/
  keywords:
  - phenomena
  - planetary climate
  license: CC0-1.0
  name: SWEET Ontology Phenomena Planetary Climate
  part_of: sweet
  prefix: sweet.phpc
  repository: https://github.com/ESIPFed/sweet
  synonyms:
  - sophpc
  uri_format: http://sweetontology.net/phenPlanetClimate/$1
sweet.phr:
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: The Semantic Web for Earth and Environmental Terminology (SWEET) ontology
    for Phenomena Reaction
  download_rdf: https://github.com/ESIPFed/sweet/raw/refs/heads/master/src/phenReaction.ttl
  example: Activation
  github_request_issue: 1772
  homepage: http://sweetontology.net/phenReaction/
  keywords:
  - phenomena
  - reaction
  license: CC0-1.0
  name: SWEET Ontology Phenomena Reaction
  part_of: sweet
  prefix: sweet.phr
  repository: https://github.com/ESIPFed/sweet
  synonyms:
  - sophr
  uri_format: http://sweetontology.net/phenReaction/$1
sweet.phso:
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: The Semantic Web for Earth and Environmental Terminology (SWEET) ontology
    for Phenomena Solid
  download_rdf: https://github.com/ESIPFed/sweet/raw/refs/heads/master/src/phenSolid.ttl
  example: Ablation
  github_request_issue: 1772
  homepage: http://sweetontology.net/phenSolid/
  keywords:
  - phenomena
  - solid
  license: CC0-1.0
  name: SWEET Ontology Phenomena Solid
  part_of: sweet
  prefix: sweet.phso
  repository: https://github.com/ESIPFed/sweet
  synonyms:
  - sophso
  uri_format: http://sweetontology.net/phenSolid/$1
sweet.phst:
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: The Semantic Web for Earth and Environmental Terminology (SWEET) ontology
    for Phenomena Star
  download_rdf: https://github.com/ESIPFed/sweet/raw/refs/heads/master/src/phenStar.ttl
  example: Asteroseismology
  github_request_issue: 1772
  homepage: http://sweetontology.net/phenStar/
  keywords:
  - phenomena
  - star
  license: CC0-1.0
  name: SWEET Ontology Phenomena Star
  part_of: sweet
  prefix: sweet.phst
  repository: https://github.com/ESIPFed/sweet
  synonyms:
  - sophst
  uri_format: http://sweetontology.net/phenStar/$1
sweet.phsy:
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: The Semantic Web for Earth and Environmental Terminology (SWEET) ontology
    for Phenomena System
  download_rdf: https://github.com/ESIPFed/sweet/raw/refs/heads/master/src/phenSystem.ttl
  example: Accumulation
  github_request_issue: 1772
  homepage: http://sweetontology.net/phenSystem/
  keywords:
  - phenomena
  - system
  license: CC0-1.0
  name: SWEET Ontology Phenomena System
  part_of: sweet
  prefix: sweet.phsy
  repository: https://github.com/ESIPFed/sweet
  synonyms:
  - sophsy
  uri_format: http://sweetontology.net/phenSystem/$1
sweet.phsyc:
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: The Semantic Web for Earth and Environmental Terminology (SWEET) ontology
    for Phenomena System Complexity
  download_rdf: https://github.com/ESIPFed/sweet/raw/refs/heads/master/src/phenSystemComplexity.ttl
  example: Cascade
  github_request_issue: 1772
  homepage: http://sweetontology.net/phenSystemComplexity/
  keywords:
  - phenomena
  - system complexity
  license: CC0-1.0
  name: SWEET Ontology Phenomena System Complexity
  part_of: sweet
  prefix: sweet.phsyc
  repository: https://github.com/ESIPFed/sweet
  synonyms:
  - sophsyc
  uri_format: http://sweetontology.net/phenSystemComplexity/$1
sweet.phw:
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: The Semantic Web for Earth and Environmental Terminology (SWEET) ontology
    for Phenomena Wave
  download_rdf: https://github.com/ESIPFed/sweet/raw/refs/heads/master/src/phenWave.ttl
  example: Acoustic
  github_request_issue: 1772
  homepage: http://sweetontology.net/phenWave/
  keywords:
  - phenomena
  - wave
  license: CC0-1.0
  name: SWEET Ontology Phenomena Wave
  part_of: sweet
  prefix: sweet.phw
  repository: https://github.com/ESIPFed/sweet
  synonyms:
  - sophw
  uri_format: http://sweetontology.net/phenWave/$1
sweet.phwn:
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: The Semantic Web for Earth and Environmental Terminology (SWEET) ontology
    for Phenomena Wave Noise
  download_rdf: https://github.com/ESIPFed/sweet/raw/refs/heads/master/src/phenWaveNoise.ttl
  example: AmbientNoise
  github_request_issue: 1772
  homepage: http://sweetontology.net/phenWaveNoise/
  keywords:
  - phenomena
  - wave noise
  license: CC0-1.0
  name: SWEET Ontology Phenomena Wave Noise
  part_of: sweet
  prefix: sweet.phwn
  repository: https://github.com/ESIPFed/sweet
  synonyms:
  - sophwn
  uri_format: http://sweetontology.net/phenWaveNoise/$1
sweet.proc:
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: The Semantic Web for Earth and Environmental Terminology (SWEET) ontology
    for Process
  download_rdf: https://github.com/ESIPFed/sweet/raw/refs/heads/master/src/proc.ttl
  example: Force
  github_request_issue: 1772
  homepage: http://sweetontology.net/proc/
  keywords:
  - process
  license: CC0-1.0
  name: SWEET Ontology Process
  part_of: sweet
  prefix: sweet.proc
  repository: https://github.com/ESIPFed/sweet
  synonyms:
  - soproc
  uri_format: http://sweetontology.net/proc/$1
sweet.procc:
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: The Semantic Web for Earth and Environmental Terminology (SWEET) ontology
    for Process Chemical
  download_rdf: https://github.com/ESIPFed/sweet/raw/refs/heads/master/src/procChemical.ttl
  example: Absorption
  github_request_issue: 1772
  homepage: http://sweetontology.net/procChemical/
  keywords:
  - chemical
  license: CC0-1.0
  name: SWEET Ontology Process Chemical
  part_of: sweet
  prefix: sweet.procc
  repository: https://github.com/ESIPFed/sweet
  synonyms:
  - soprocc
  uri_format: http://sweetontology.net/procChemical/$1
sweet.procp:
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: The Semantic Web for Earth and Environmental Terminology (SWEET) ontology
    for Process Physical
  download_rdf: https://github.com/ESIPFed/sweet/raw/refs/heads/master/src/procPhysical.ttl
  example: Abrasion
  github_request_issue: 1772
  homepage: http://sweetontology.net/procPhysical/
  keywords:
  - physical
  license: CC0-1.0
  name: SWEET Ontology Process Physical
  part_of: sweet
  prefix: sweet.procp
  repository: https://github.com/ESIPFed/sweet
  synonyms:
  - soprocp
  uri_format: http://sweetontology.net/procPhysical/$1
sweet.procsc:
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: The Semantic Web for Earth and Environmental Terminology (SWEET) ontology
    for Process State Change
  download_rdf: https://github.com/ESIPFed/sweet/raw/refs/heads/master/src/procStateChange.ttl
  example: Boiling
  github_request_issue: 1772
  homepage: http://sweetontology.net/procStateChange/
  keywords:
  - state change
  license: CC0-1.0
  name: SWEET Ontology Process State Change
  part_of: sweet
  prefix: sweet.procsc
  repository: https://github.com/ESIPFed/sweet
  synonyms:
  - soprocsc
  uri_format: http://sweetontology.net/procStateChange/$1
sweet.procw:
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: The Semantic Web for Earth and Environmental Terminology (SWEET) ontology
    for Process Wave
  download_rdf: https://github.com/ESIPFed/sweet/raw/refs/heads/master/src/procWave.ttl
  example: Absorption
  github_request_issue: 1772
  homepage: http://sweetontology.net/procWave/
  keywords:
  - wave
  license: CC0-1.0
  name: SWEET Ontology Process Wave
  part_of: sweet
  prefix: sweet.procw
  repository: https://github.com/ESIPFed/sweet
  synonyms:
  - soprocw
  uri_format: http://sweetontology.net/procWave/$1
sweet.prop:
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: The Semantic Web for Earth and Environmental Terminology (SWEET) ontology
    for Property
  download_rdf: https://github.com/ESIPFed/sweet/raw/refs/heads/master/src/prop.ttl
  example: Accuracy
  github_request_issue: 1772
  homepage: http://sweetontology.net/prop/
  keywords:
  - property
  license: CC0-1.0
  name: SWEET Ontology Property
  part_of: sweet
  prefix: sweet.prop
  repository: https://github.com/ESIPFed/sweet
  synonyms:
  - soprop
  uri_format: http://sweetontology.net/prop/$1
sweet.propb:
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: The Semantic Web for Earth and Environmental Terminology (SWEET) ontology
    for Property Binary
  download_rdf: https://github.com/ESIPFed/sweet/raw/refs/heads/master/src/propBinary.ttl
  example: BinaryProperty
  github_request_issue: 1772
  homepage: http://sweetontology.net/propBinary/
  keywords:
  - binary
  license: CC0-1.0
  name: SWEET Ontology Property Binary
  part_of: sweet
  prefix: sweet.propb
  repository: https://github.com/ESIPFed/sweet
  synonyms:
  - sopropb
  uri_format: http://sweetontology.net/propBinary/$1
sweet.propcap:
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: The Semantic Web for Earth and Environmental Terminology (SWEET) ontology
    for Property Capacity
  download_rdf: https://github.com/ESIPFed/sweet/raw/refs/heads/master/src/propCapacity.ttl
  example: Capacity
  github_request_issue: 1772
  homepage: http://sweetontology.net/propCapacity/
  keywords:
  - capacity
  license: CC0-1.0
  name: SWEET Ontology Property Capacity
  part_of: sweet
  prefix: sweet.propcap
  repository: https://github.com/ESIPFed/sweet
  synonyms:
  - sopropcap
  uri_format: http://sweetontology.net/propCapacity/$1
sweet.propcat:
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: The Semantic Web for Earth and Environmental Terminology (SWEET) ontology
    for Property Categorical
  download_rdf: https://github.com/ESIPFed/sweet/raw/refs/heads/master/src/propCategorical.ttl
  example: CategoricalProperty
  github_request_issue: 1772
  homepage: http://sweetontology.net/propCategorical/
  keywords:
  - categorical
  license: CC0-1.0
  name: SWEET Ontology Property Categorical
  part_of: sweet
  prefix: sweet.propcat
  repository: https://github.com/ESIPFed/sweet
  synonyms:
  - sopropcat
  uri_format: http://sweetontology.net/propCategorical/$1
sweet.propcha:
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: The Semantic Web for Earth and Environmental Terminology (SWEET) ontology
    for Property Charge
  download_rdf: https://github.com/ESIPFed/sweet/raw/refs/heads/master/src/propCharge.ttl
  example: Capacitance
  github_request_issue: 1772
  homepage: http://sweetontology.net/propCharge/
  keywords:
  - charge
  license: CC0-1.0
  name: SWEET Ontology Property Charge
  part_of: sweet
  prefix: sweet.propcha
  repository: https://github.com/ESIPFed/sweet
  synonyms:
  - sopropcha
  uri_format: http://sweetontology.net/propCharge/$1
sweet.propche:
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: The Semantic Web for Earth and Environmental Terminology (SWEET) ontology
    for Property Chemical
  download_rdf: https://github.com/ESIPFed/sweet/raw/refs/heads/master/src/propChemical.ttl
  example: Abundance
  github_request_issue: 1772
  homepage: http://sweetontology.net/propChemical/
  keywords:
  - chemical
  license: CC0-1.0
  name: SWEET Ontology Property Chemical
  part_of: sweet
  prefix: sweet.propche
  repository: https://github.com/ESIPFed/sweet
  synonyms:
  - sopropche
  uri_format: http://sweetontology.net/propChemical/$1
sweet.propcon:
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: The Semantic Web for Earth and Environmental Terminology (SWEET) ontology
    for Property Conductivity
  download_rdf: https://github.com/ESIPFed/sweet/raw/refs/heads/master/src/propConductivity.ttl
  example: Conductance
  github_request_issue: 1772
  homepage: http://sweetontology.net/propConductivity/
  keywords:
  - conductivity
  license: CC0-1.0
  name: SWEET Ontology Property Conductivity
  part_of: sweet
  prefix: sweet.propcon
  repository: https://github.com/ESIPFed/sweet
  synonyms:
  - sopropcon
  uri_format: http://sweetontology.net/propConductivity/$1
sweet.propcou:
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: The Semantic Web for Earth and Environmental Terminology (SWEET) ontology
    for Property Count
  download_rdf: https://github.com/ESIPFed/sweet/raw/refs/heads/master/src/propCount.ttl
  example: AtomicNeutralNumberDensity
  github_request_issue: 1772
  homepage: http://sweetontology.net/propCount/
  keywords:
  - count
  license: CC0-1.0
  name: SWEET Ontology Property Count
  part_of: sweet
  prefix: sweet.propcou
  repository: https://github.com/ESIPFed/sweet
  synonyms:
  - sopropcou
  uri_format: http://sweetontology.net/propCount/$1
sweet.propdife:
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: The Semantic Web for Earth and Environmental Terminology (SWEET) ontology
    for Property Difference
  download_rdf: https://github.com/ESIPFed/sweet/raw/refs/heads/master/src/propDifference.ttl
  example: Amplitude
  github_request_issue: 1772
  homepage: http://sweetontology.net/propDifference/
  keywords:
  - difference
  license: CC0-1.0
  name: SWEET Ontology Property Difference
  part_of: sweet
  prefix: sweet.propdife
  repository: https://github.com/ESIPFed/sweet
  synonyms:
  - sopropdife
  uri_format: http://sweetontology.net/propDifference/$1
sweet.propdifu:
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: The Semantic Web for Earth and Environmental Terminology (SWEET) ontology
    for Property Diffusivity
  download_rdf: https://github.com/ESIPFed/sweet/raw/refs/heads/master/src/propDiffusivity.ttl
  example: Confluence
  github_request_issue: 1772
  homepage: http://sweetontology.net/propDiffusivity/
  keywords:
  - diffusivity
  license: CC0-1.0
  name: SWEET Ontology Property Diffusivity
  part_of: sweet
  prefix: sweet.propdifu
  repository: https://github.com/ESIPFed/sweet
  synonyms:
  - sopropdifu
  uri_format: http://sweetontology.net/propDiffusivity/$1
sweet.propdr:
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: The Semantic Web for Earth and Environmental Terminology (SWEET) ontology
    for Property Dimensionless Ratio
  download_rdf: https://github.com/ESIPFed/sweet/raw/refs/heads/master/src/propDimensionlessRatio.ttl
  example: BowenRatio
  github_request_issue: 1772
  homepage: http://sweetontology.net/propDimensionlessRatio/
  keywords:
  - dimensionless ratio
  license: CC0-1.0
  name: SWEET Ontology Property Dimensionless Ratio
  part_of: sweet
  prefix: sweet.propdr
  repository: https://github.com/ESIPFed/sweet
  synonyms:
  - sopropdr
  uri_format: http://sweetontology.net/propDimensionlessRatio/$1
sweet.prope:
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: The Semantic Web for Earth and Environmental Terminology (SWEET) ontology
    for Property Energy
  download_rdf: https://github.com/ESIPFed/sweet/raw/refs/heads/master/src/propEnergy.ttl
  example: AvailablePotentialEnergy
  github_request_issue: 1772
  homepage: http://sweetontology.net/propEnergy/
  keywords:
  - energy
  license: CC0-1.0
  name: SWEET Ontology Property Energy
  part_of: sweet
  prefix: sweet.prope
  repository: https://github.com/ESIPFed/sweet
  synonyms:
  - soprope
  uri_format: http://sweetontology.net/propEnergy/$1
sweet.propef:
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: The Semantic Web for Earth and Environmental Terminology (SWEET) ontology
    for Property Energy Flux
  download_rdf: https://github.com/ESIPFed/sweet/raw/refs/heads/master/src/propEnergyFlux.ttl
  example: AbsorbedSolarRadiation
  github_request_issue: 1772
  homepage: http://sweetontology.net/propEnergyFlux/
  keywords:
  - energy flux
  license: CC0-1.0
  name: SWEET Ontology Property Energy Flux
  part_of: sweet
  prefix: sweet.propef
  repository: https://github.com/ESIPFed/sweet
  synonyms:
  - sopropef
  uri_format: http://sweetontology.net/propEnergyFlux/$1
sweet.propfr:
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: The Semantic Web for Earth and Environmental Terminology (SWEET) ontology
    for Property Fraction
  download_rdf: https://github.com/ESIPFed/sweet/raw/refs/heads/master/src/propFraction.ttl
  example: Absorptance
  github_request_issue: 1772
  homepage: http://sweetontology.net/propFraction/
  keywords:
  - fraction
  license: CC0-1.0
  name: SWEET Ontology Property Fraction
  part_of: sweet
  prefix: sweet.propfr
  repository: https://github.com/ESIPFed/sweet
  synonyms:
  - sopropfr
  uri_format: http://sweetontology.net/propFraction/$1
sweet.propfu:
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: The Semantic Web for Earth and Environmental Terminology (SWEET) ontology
    for Property Function
  download_rdf: https://github.com/ESIPFed/sweet/raw/refs/heads/master/src/propFunction.ttl
  example: AnnualAverage
  github_request_issue: 1772
  homepage: http://sweetontology.net/propFunction/
  keywords:
  - function
  license: CC0-1.0
  name: SWEET Ontology Property Function
  part_of: sweet
  prefix: sweet.propfu
  repository: https://github.com/ESIPFed/sweet
  synonyms:
  - sopropfu
  uri_format: http://sweetontology.net/propFunction/$1
sweet.propi:
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: The Semantic Web for Earth and Environmental Terminology (SWEET) ontology
    for Property Index
  download_rdf: https://github.com/ESIPFed/sweet/raw/refs/heads/master/src/propIndex.ttl
  example: AdaptiveCapacity
  github_request_issue: 1772
  homepage: http://sweetontology.net/propIndex/
  keywords:
  - index
  license: CC0-1.0
  name: SWEET Ontology Property Index
  part_of: sweet
  prefix: sweet.propi
  repository: https://github.com/ESIPFed/sweet
  synonyms:
  - sopropi
  uri_format: http://sweetontology.net/propIndex/$1
sweet.propm:
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: The Semantic Web for Earth and Environmental Terminology (SWEET) ontology
    for Property Mass
  download_rdf: https://github.com/ESIPFed/sweet/raw/refs/heads/master/src/propMass.ttl
  example: BulkDensity
  github_request_issue: 1772
  homepage: http://sweetontology.net/propMass/
  keywords:
  - mass
  license: CC0-1.0
  name: SWEET Ontology Property Mass
  part_of: sweet
  prefix: sweet.propm
  repository: https://github.com/ESIPFed/sweet
  synonyms:
  - sopropm
  uri_format: http://sweetontology.net/propMass/$1
sweet.propmf:
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: The Semantic Web for Earth and Environmental Terminology (SWEET) ontology
    for Property Mass Flux
  download_rdf: https://github.com/ESIPFed/sweet/raw/refs/heads/master/src/propMassFlux.ttl
  example: DarcyFlux
  github_request_issue: 1772
  homepage: http://sweetontology.net/propMassFlux/
  keywords:
  - mass flux
  license: CC0-1.0
  name: SWEET Ontology Property Mass Flux
  part_of: sweet
  prefix: sweet.propmf
  repository: https://github.com/ESIPFed/sweet
  synonyms:
  - sopropmf
  uri_format: http://sweetontology.net/propMassFlux/$1
sweet.propo:
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: The Semantic Web for Earth and Environmental Terminology (SWEET) ontology
    for Property Ordinal
  download_rdf: https://github.com/ESIPFed/sweet/raw/refs/heads/master/src/propOrdinal.ttl
  example: ActivityLevel
  github_request_issue: 1772
  homepage: http://sweetontology.net/propOrdinal/
  keywords:
  - ordinal
  license: CC0-1.0
  name: SWEET Ontology Property Ordinal
  part_of: sweet
  prefix: sweet.propo
  repository: https://github.com/ESIPFed/sweet
  synonyms:
  - sopropo
  uri_format: http://sweetontology.net/propOrdinal/$1
sweet.propp:
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: The Semantic Web for Earth and Environmental Terminology (SWEET) ontology
    for Property Pressure
  download_rdf: https://github.com/ESIPFed/sweet/raw/refs/heads/master/src/propPressure.ttl
  example: AirPressure
  github_request_issue: 1772
  homepage: http://sweetontology.net/propPressure/
  keywords:
  - pressure
  license: CC0-1.0
  name: SWEET Ontology Property Pressure
  part_of: sweet
  prefix: sweet.propp
  repository: https://github.com/ESIPFed/sweet
  synonyms:
  - sopropp
  uri_format: http://sweetontology.net/propPressure/$1
sweet.propq:
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: The Semantic Web for Earth and Environmental Terminology (SWEET) ontology
    for Property Quantity
  download_rdf: https://github.com/ESIPFed/sweet/raw/refs/heads/master/src/propQuantity.ttl
  example: BalanceEquation
  github_request_issue: 1772
  homepage: http://sweetontology.net/propQuantity/
  keywords:
  - quantity
  license: CC0-1.0
  name: SWEET Ontology Property Quantity
  part_of: sweet
  prefix: sweet.propq
  repository: https://github.com/ESIPFed/sweet
  synonyms:
  - sopropq
  uri_format: http://sweetontology.net/propQuantity/$1
sweet.propr:
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: The Semantic Web for Earth and Environmental Terminology (SWEET) ontology
    for Property Rotation
  download_rdf: https://github.com/ESIPFed/sweet/raw/refs/heads/master/src/propRotation.ttl
  example: AbsoluteVorticity
  github_request_issue: 1772
  homepage: http://sweetontology.net/propRotation/
  keywords:
  - rotation
  license: CC0-1.0
  name: SWEET Ontology Property Rotation
  part_of: sweet
  prefix: sweet.propr
  repository: https://github.com/ESIPFed/sweet
  synonyms:
  - sopropr
  uri_format: http://sweetontology.net/propRotation/$1
sweet.props:
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: The Semantic Web for Earth and Environmental Terminology (SWEET) ontology
    for Property Space
  download_rdf: https://github.com/ESIPFed/sweet/raw/refs/heads/master/src/propSpace.ttl
  example: AngularDistribution
  github_request_issue: 1772
  homepage: http://sweetontology.net/propSpace/
  keywords:
  - space
  license: CC0-1.0
  name: SWEET Ontology Property Space
  part_of: sweet
  prefix: sweet.props
  repository: https://github.com/ESIPFed/sweet
  synonyms:
  - soprops
  uri_format: http://sweetontology.net/propSpace/$1
sweet.propsdir:
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: The Semantic Web for Earth and Environmental Terminology (SWEET) ontology
    for Property Space Direction
  download_rdf: https://github.com/ESIPFed/sweet/raw/refs/heads/master/src/propSpaceDirection.ttl
  example: Angle
  github_request_issue: 1772
  homepage: http://sweetontology.net/propSpaceDirection/
  keywords:
  - space direction
  license: CC0-1.0
  name: SWEET Ontology Property Space Direction
  part_of: sweet
  prefix: sweet.propsdir
  repository: https://github.com/ESIPFed/sweet
  synonyms:
  - sopropsdir
  uri_format: http://sweetontology.net/propSpaceDirection/$1
sweet.propsdis:
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: The Semantic Web for Earth and Environmental Terminology (SWEET) ontology
    for Property Space Distance
  download_rdf: https://github.com/ESIPFed/sweet/raw/refs/heads/master/src/propSpaceDistance.ttl
  example: AttenuationCoefficient
  github_request_issue: 1772
  homepage: http://sweetontology.net/propSpaceDistance/
  keywords:
  - space distance
  license: CC0-1.0
  name: SWEET Ontology Property Space Distance
  part_of: sweet
  prefix: sweet.propsdis
  repository: https://github.com/ESIPFed/sweet
  synonyms:
  - sopropsdis
  uri_format: http://sweetontology.net/propSpaceDistance/$1
sweet.propsh:
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: The Semantic Web for Earth and Environmental Terminology (SWEET) ontology
    for Property Space Height
  download_rdf: https://github.com/ESIPFed/sweet/raw/refs/heads/master/src/propSpaceHeight.ttl
  example: Altitude
  github_request_issue: 1772
  homepage: http://sweetontology.net/propSpaceHeight/
  keywords:
  - space height
  license: CC0-1.0
  name: SWEET Ontology Property Space Height
  part_of: sweet
  prefix: sweet.propsh
  repository: https://github.com/ESIPFed/sweet
  synonyms:
  - sopropsh
  uri_format: http://sweetontology.net/propSpaceHeight/$1
sweet.propsl:
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: The Semantic Web for Earth and Environmental Terminology (SWEET) ontology
    for Property Space Location
  download_rdf: https://github.com/ESIPFed/sweet/raw/refs/heads/master/src/propSpaceLocation.ttl
  example: Center
  github_request_issue: 1772
  homepage: http://sweetontology.net/propSpaceLocation/
  keywords:
  - space location
  license: CC0-1.0
  name: SWEET Ontology Property Space Location
  part_of: sweet
  prefix: sweet.propsl
  repository: https://github.com/ESIPFed/sweet
  synonyms:
  - sopropsl
  uri_format: http://sweetontology.net/propSpaceLocation/$1
sweet.propsm:
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: The Semantic Web for Earth and Environmental Terminology (SWEET) ontology
    for Property Space Multidimensional
  download_rdf: https://github.com/ESIPFed/sweet/raw/refs/heads/master/src/propSpaceMultidimensional.ttl
  example: AngularExtent
  github_request_issue: 1772
  homepage: http://sweetontology.net/propSpaceMultidimensional/
  keywords:
  - space multidimensional
  license: CC0-1.0
  name: SWEET Ontology Property Space Multidimensional
  part_of: sweet
  prefix: sweet.propsm
  repository: https://github.com/ESIPFed/sweet
  synonyms:
  - sopropsm
  uri_format: http://sweetontology.net/propSpaceMultidimensional/$1
sweet.propsp:
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: The Semantic Web for Earth and Environmental Terminology (SWEET) ontology
    for Property Speed
  download_rdf: https://github.com/ESIPFed/sweet/raw/refs/heads/master/src/propSpeed.ttl
  example: Acceleration
  github_request_issue: 1772
  homepage: http://sweetontology.net/propSpeed/
  keywords:
  - speed
  license: CC0-1.0
  name: SWEET Ontology Property Speed
  part_of: sweet
  prefix: sweet.propsp
  repository: https://github.com/ESIPFed/sweet
  synonyms:
  - sopropsp
  uri_format: http://sweetontology.net/propSpeed/$1
sweet.propst:
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: The Semantic Web for Earth and Environmental Terminology (SWEET) ontology
    for Property Space Thickness
  download_rdf: https://github.com/ESIPFed/sweet/raw/refs/heads/master/src/propSpaceThickness.ttl
  example: AverageAnnualPrecipitation
  github_request_issue: 1772
  homepage: http://sweetontology.net/propSpaceThickness/
  keywords:
  - space thickness
  license: CC0-1.0
  name: SWEET Ontology Property Space Thickness
  part_of: sweet
  prefix: sweet.propst
  repository: https://github.com/ESIPFed/sweet
  synonyms:
  - sopropst
  uri_format: http://sweetontology.net/propSpaceThickness/$1
sweet.propt:
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: The Semantic Web for Earth and Environmental Terminology (SWEET) ontology
    for Property Temperature
  download_rdf: https://github.com/ESIPFed/sweet/raw/refs/heads/master/src/propTemperature.ttl
  example: AntennaTemperature
  github_request_issue: 1772
  homepage: http://sweetontology.net/propTemperature/
  keywords:
  - temperature
  license: CC0-1.0
  name: SWEET Ontology Property Temperature
  part_of: sweet
  prefix: sweet.propt
  repository: https://github.com/ESIPFed/sweet
  synonyms:
  - sopropt
  uri_format: http://sweetontology.net/propTemperature/$1
sweet.proptf:
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: The Semantic Web for Earth and Environmental Terminology (SWEET) ontology
    for Property Time Frequency
  download_rdf: https://github.com/ESIPFed/sweet/raw/refs/heads/master/src/propTimeFrequency.ttl
  example: Bandwidth
  github_request_issue: 1772
  homepage: http://sweetontology.net/propTimeFrequency/
  keywords:
  - time frequency
  license: CC0-1.0
  name: SWEET Ontology Property Time Frequency
  part_of: sweet
  prefix: sweet.proptf
  repository: https://github.com/ESIPFed/sweet
  synonyms:
  - soproptf
  uri_format: http://sweetontology.net/propTimeFrequency/$1
sweet.proptg:
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: The Semantic Web for Earth and Environmental Terminology (SWEET) ontology
    for Property Temperature Gradient
  download_rdf: https://github.com/ESIPFed/sweet/raw/refs/heads/master/src/propTemperatureGradient.ttl
  example: AutoConvectiveLapseRate
  github_request_issue: 1772
  homepage: http://sweetontology.net/propTemperatureGradient/
  keywords:
  - temperature gradient
  license: CC0-1.0
  name: SWEET Ontology Property Temperature Gradient
  part_of: sweet
  prefix: sweet.proptg
  repository: https://github.com/ESIPFed/sweet
  synonyms:
  - soproptg
  uri_format: http://sweetontology.net/propTemperatureGradient/$1
sweet.propti:
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: The Semantic Web for Earth and Environmental Terminology (SWEET) ontology
    for Property Time
  download_rdf: https://github.com/ESIPFed/sweet/raw/refs/heads/master/src/propTime.ttl
  example: Age
  github_request_issue: 1772
  homepage: http://sweetontology.net/propTime/
  keywords:
  - time
  license: CC0-1.0
  name: SWEET Ontology Property Time
  part_of: sweet
  prefix: sweet.propti
  repository: https://github.com/ESIPFed/sweet
  synonyms:
  - sopropti
  uri_format: http://sweetontology.net/propTime/$1
sweet.rea:
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: The Semantic Web for Earth and Environmental Terminology (SWEET) ontology
    for Realm
  download_rdf: https://github.com/ESIPFed/sweet/raw/refs/heads/master/src/realm.ttl
  example: Atmosphere
  github_request_issue: 1772
  homepage: http://sweetontology.net/realm/
  keywords:
  - realm
  license: CC0-1.0
  name: SWEET Ontology Realm
  part_of: sweet
  prefix: sweet.rea
  repository: https://github.com/ESIPFed/sweet
  synonyms:
  - SWEETRealm
  - sorea
  uri_format: http://sweetontology.net/realm/$1
sweet.reaa:
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: The Semantic Web for Earth and Environmental Terminology (SWEET) ontology
    for Realm Atmospheric
  download_rdf: https://github.com/ESIPFed/sweet/raw/refs/heads/master/src/realmAtmo.ttl
  example: AtmosphereLayer
  github_request_issue: 1772
  homepage: http://sweetontology.net/realmAtmo/
  keywords:
  - atmospheric
  - realm
  license: CC0-1.0
  name: SWEET Ontology Realm Atmospheric
  part_of: sweet
  prefix: sweet.reaa
  repository: https://github.com/ESIPFed/sweet
  synonyms:
  - soreaa
  uri_format: http://sweetontology.net/realmAtmo/$1
sweet.reaab:
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: The Semantic Web for Earth and Environmental Terminology (SWEET) ontology
    for Realm Astrophysical Body
  download_rdf: https://github.com/ESIPFed/sweet/raw/refs/heads/master/src/realmAstroBody.ttl
  example: Asteroid
  github_request_issue: 1772
  homepage: http://sweetontology.net/realmAstroBody/
  keywords:
  - astrophysical body
  - realm
  license: CC0-1.0
  name: SWEET Ontology Realm Astrophysical Body
  part_of: sweet
  prefix: sweet.reaab
  repository: https://github.com/ESIPFed/sweet
  synonyms:
  - soreaab
  uri_format: http://sweetontology.net/realmAstroBody/$1
sweet.reaabl:
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: The Semantic Web for Earth and Environmental Terminology (SWEET) ontology
    for Realm Atmospheric Boundary Layer
  download_rdf: https://github.com/ESIPFed/sweet/raw/refs/heads/master/src/realmAtmoBoundaryLayer.ttl
  example: AtmosphericBoundaryLayer
  github_request_issue: 1772
  homepage: http://sweetontology.net/realmAtmoBoundaryLayer/
  keywords:
  - atmospheric boundary layer
  - realm
  license: CC0-1.0
  name: SWEET Ontology Realm Atmospheric Boundary Layer
  part_of: sweet
  prefix: sweet.reaabl
  repository: https://github.com/ESIPFed/sweet
  synonyms:
  - soreaabl
  uri_format: http://sweetontology.net/realmAtmoBoundaryLayer/$1
sweet.reaah:
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: The Semantic Web for Earth and Environmental Terminology (SWEET) ontology
    for Realm Astrophysical Heliosphere
  download_rdf: https://github.com/ESIPFed/sweet/raw/refs/heads/master/src/realmAstroHelio.ttl
  example: DLayer
  github_request_issue: 1772
  homepage: http://sweetontology.net/realmAstroHelio/
  keywords:
  - astrophysical heliosphere
  - realm
  license: CC0-1.0
  name: SWEET Ontology Realm Astrophysical Heliosphere
  part_of: sweet
  prefix: sweet.reaah
  repository: https://github.com/ESIPFed/sweet
  synonyms:
  - soreaah
  uri_format: http://sweetontology.net/realmAstroHelio/$1
sweet.reaas:
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: The Semantic Web for Earth and Environmental Terminology (SWEET) ontology
    for Realm Astrophysical
  download_rdf: https://github.com/ESIPFed/sweet/raw/refs/heads/master/src/realmAstroStar.ttl
  example: ActiveRegion
  github_request_issue: 1772
  homepage: http://sweetontology.net/realmAstroStar/
  keywords:
  - astrophysical
  - realm
  license: CC0-1.0
  name: SWEET Ontology Realm Astrophysical
  part_of: sweet
  prefix: sweet.reaas
  repository: https://github.com/ESIPFed/sweet
  synonyms:
  - soreaas
  uri_format: http://sweetontology.net/realmAstroStar/$1
sweet.reaaw:
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: The Semantic Web for Earth and Environmental Terminology (SWEET) ontology
    for Realm Atmospheric Weather
  download_rdf: https://github.com/ESIPFed/sweet/raw/refs/heads/master/src/realmAtmoWeather.ttl
  example: AdiabaticCondensationLevel
  github_request_issue: 1772
  homepage: http://sweetontology.net/realmAtmoWeather/
  keywords:
  - atmospheric weather
  - realm
  license: CC0-1.0
  name: SWEET Ontology Realm Atmospheric Weather
  part_of: sweet
  prefix: sweet.reaaw
  repository: https://github.com/ESIPFed/sweet
  synonyms:
  - soreaaw
  uri_format: http://sweetontology.net/realmAtmoWeather/$1
sweet.reabb:
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: The Semantic Web for Earth and Environmental Terminology (SWEET) ontology
    for Realm Biologic Biome
  download_rdf: https://github.com/ESIPFed/sweet/raw/refs/heads/master/src/realmBiolBiome.ttl
  example: Anthromes
  github_request_issue: 1772
  homepage: http://sweetontology.net/realmBiolBiome/
  keywords:
  - biologic biome
  - realm
  license: CC0-1.0
  name: SWEET Ontology Realm Biologic Biome
  part_of: sweet
  prefix: sweet.reabb
  repository: https://github.com/ESIPFed/sweet
  synonyms:
  - soreabb
  uri_format: http://sweetontology.net/realmBiolBiome/$1
sweet.reac:
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: The Semantic Web for Earth and Environmental Terminology (SWEET) ontology
    for Realm Cryosphere
  download_rdf: https://github.com/ESIPFed/sweet/raw/refs/heads/master/src/realmCryo.ttl
  example: AblationZone
  github_request_issue: 1772
  homepage: http://sweetontology.net/realmCryo/
  keywords:
  - cryosphere
  - realm
  license: CC0-1.0
  name: SWEET Ontology Realm Cryosphere
  part_of: sweet
  prefix: sweet.reac
  repository: https://github.com/ESIPFed/sweet
  synonyms:
  - soreac
  uri_format: http://sweetontology.net/realmCryo/$1
sweet.reacz:
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: The Semantic Web for Earth and Environmental Terminology (SWEET) ontology
    for Realm Climate Zone
  download_rdf: https://github.com/ESIPFed/sweet/raw/refs/heads/master/src/realmClimateZone.ttl
  example: A
  github_request_issue: 1772
  homepage: http://sweetontology.net/realmClimateZone/
  keywords:
  - climate zone
  - realm
  license: CC0-1.0
  name: SWEET Ontology Realm Climate Zone
  part_of: sweet
  prefix: sweet.reacz
  repository: https://github.com/ESIPFed/sweet
  synonyms:
  - soreacz
  uri_format: http://sweetontology.net/realmClimateZone/$1
sweet.reaer:
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: The Semantic Web for Earth and Environmental Terminology (SWEET) ontology
    for Realm Earth Reference
  download_rdf: https://github.com/ESIPFed/sweet/raw/refs/heads/master/src/realmEarthReference.ttl
  example: AbyssopelagicZone
  github_request_issue: 1772
  homepage: http://sweetontology.net/realmEarthReference/
  keywords:
  - earth reference
  - realm
  license: CC0-1.0
  name: SWEET Ontology Realm Earth Reference
  part_of: sweet
  prefix: sweet.reaer
  repository: https://github.com/ESIPFed/sweet
  synonyms:
  - soreaer
  uri_format: http://sweetontology.net/realmEarthReference/$1
sweet.reag:
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: The Semantic Web for Earth and Environmental Terminology (SWEET) ontology
    for Realm Geologic
  download_rdf: https://github.com/ESIPFed/sweet/raw/refs/heads/master/src/realmGeol.ttl
  example: Asthenosphere
  github_request_issue: 1772
  homepage: http://sweetontology.net/realmGeol/
  keywords:
  - geologic
  - realm
  license: CC0-1.0
  name: SWEET Ontology Realm Geologic
  part_of: sweet
  prefix: sweet.reag
  repository: https://github.com/ESIPFed/sweet
  synonyms:
  - soreag
  uri_format: http://sweetontology.net/realmGeol/$1
sweet.reagb:
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: The Semantic Web for Earth and Environmental Terminology (SWEET) ontology
    for Realm Geologic Basin
  download_rdf: https://github.com/ESIPFed/sweet/raw/refs/heads/master/src/realmGeolBasin.ttl
  example: BackArcBasin
  github_request_issue: 1772
  homepage: http://sweetontology.net/realmGeolBasin/
  keywords:
  - geologic basin
  - realm
  license: CC0-1.0
  name: SWEET Ontology Realm Geologic Basin
  part_of: sweet
  prefix: sweet.reagb
  repository: https://github.com/ESIPFed/sweet
  synonyms:
  - soreagb
  uri_format: http://sweetontology.net/realmGeolBasin/$1
sweet.reagcons:
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: The Semantic Web for Earth and Environmental Terminology (SWEET) ontology
    for Realm Geologic Constituent
  download_rdf: https://github.com/ESIPFed/sweet/raw/refs/heads/master/src/realmGeolConstituent.ttl
  example: ArmoredRelictInclusion
  github_request_issue: 1772
  homepage: http://sweetontology.net/realmGeolConstituent/
  keywords:
  - geologic constituent
  - realm
  license: CC0-1.0
  name: SWEET Ontology Realm Geologic Constituent
  part_of: sweet
  prefix: sweet.reagcons
  repository: https://github.com/ESIPFed/sweet
  synonyms:
  - soreagcons
  uri_format: http://sweetontology.net/realmGeolConstituent/$1
sweet.reagcont:
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: The Semantic Web for Earth and Environmental Terminology (SWEET) ontology
    for Realm Geologic Continental
  download_rdf: https://github.com/ESIPFed/sweet/raw/refs/heads/master/src/realmGeolContinental.ttl
  example: ActiveContinent
  github_request_issue: 1772
  homepage: http://sweetontology.net/realmGeolContinental/
  keywords:
  - geologic continental
  - realm
  license: CC0-1.0
  name: SWEET Ontology Realm Geologic Continental
  part_of: sweet
  prefix: sweet.reagcont
  repository: https://github.com/ESIPFed/sweet
  synonyms:
  - soreagcont
  uri_format: http://sweetontology.net/realmGeolContinental/$1
sweet.reagoc:
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: The Semantic Web for Earth and Environmental Terminology (SWEET) ontology
    for Realm Geologic Oceanic
  download_rdf: https://github.com/ESIPFed/sweet/raw/refs/heads/master/src/realmGeolOceanic.ttl
  example: AccretionaryPrism
  github_request_issue: 1772
  homepage: http://sweetontology.net/realmGeolOceanic/
  keywords:
  - geologic oceanic
  - realm
  license: CC0-1.0
  name: SWEET Ontology Realm Geologic Oceanic
  part_of: sweet
  prefix: sweet.reagoc
  repository: https://github.com/ESIPFed/sweet
  synonyms:
  - soreagoc
  uri_format: http://sweetontology.net/realmGeolOceanic/$1
sweet.reagor:
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: The Semantic Web for Earth and Environmental Terminology (SWEET) ontology
    for Realm Geologic Orogen
  download_rdf: https://github.com/ESIPFed/sweet/raw/refs/heads/master/src/realmGeolOrogen.ttl
  example: Arc
  github_request_issue: 1772
  homepage: http://sweetontology.net/realmGeolOrogen/
  keywords:
  - geologic orogen
  - realm
  license: CC0-1.0
  name: SWEET Ontology Realm Geologic Orogen
  part_of: sweet
  prefix: sweet.reagor
  repository: https://github.com/ESIPFed/sweet
  synonyms:
  - soreagor
  uri_format: http://sweetontology.net/realmGeolOrogen/$1
sweet.reah:
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: The Semantic Web for Earth and Environmental Terminology (SWEET) ontology
    for Realm Hydrosphere
  download_rdf: https://github.com/ESIPFed/sweet/raw/refs/heads/master/src/realmHydro.ttl
  example: Aquiclude
  github_request_issue: 1772
  homepage: http://sweetontology.net/realmHydro/
  keywords:
  - hydrosphere
  - realm
  license: CC0-1.0
  name: SWEET Ontology Realm Hydrosphere
  part_of: sweet
  prefix: sweet.reah
  repository: https://github.com/ESIPFed/sweet
  synonyms:
  - soreah
  uri_format: http://sweetontology.net/realmHydro/$1
sweet.reahb:
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: The Semantic Web for Earth and Environmental Terminology (SWEET) ontology
    for Realm Hydrosphere Body
  download_rdf: https://github.com/ESIPFed/sweet/raw/refs/heads/master/src/realmHydroBody.ttl
  example: Aqueduct
  github_request_issue: 1772
  homepage: http://sweetontology.net/realmHydroBody/
  keywords:
  - hydrosphere body
  - realm
  license: CC0-1.0
  name: SWEET Ontology Realm Hydrosphere Body
  part_of: sweet
  prefix: sweet.reahb
  repository: https://github.com/ESIPFed/sweet
  synonyms:
  - soreahb
  uri_format: http://sweetontology.net/realmHydroBody/$1
sweet.real:
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: The Semantic Web for Earth and Environmental Terminology (SWEET) ontology
    for Realm Landform
  download_rdf: https://github.com/ESIPFed/sweet/raw/refs/heads/master/src/realmLandform.ttl
  example: CentralCreekCrater
  github_request_issue: 1772
  homepage: http://sweetontology.net/realmLandform/
  keywords:
  - landform
  - realm
  license: CC0-1.0
  name: SWEET Ontology Realm Landform
  part_of: sweet
  prefix: sweet.real
  repository: https://github.com/ESIPFed/sweet
  synonyms:
  - soreal
  uri_format: http://sweetontology.net/realmLandform/$1
sweet.reala:
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: The Semantic Web for Earth and Environmental Terminology (SWEET) ontology
    for Realm Land Aeolian
  download_rdf: https://github.com/ESIPFed/sweet/raw/refs/heads/master/src/realmLandAeolian.ttl
  example: Aeolian
  github_request_issue: 1772
  homepage: http://sweetontology.net/realmLandAeolian/
  keywords:
  - ' aeolianland'
  license: CC0-1.0
  name: SWEET Ontology Realm Land Aeolian
  part_of: sweet
  prefix: sweet.reala
  repository: https://github.com/ESIPFed/sweet
  synonyms:
  - soreala
  uri_format: http://sweetontology.net/realmLandAeolian/$1
sweet.realc:
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: The Semantic Web for Earth and Environmental Terminology (SWEET) ontology
    for Realm Land Coastal
  download_rdf: https://github.com/ESIPFed/sweet/raw/refs/heads/master/src/realmLandCoastal.ttl
  example: Atoll
  github_request_issue: 1772
  homepage: http://sweetontology.net/realmLandCoastal/
  keywords:
  - ' coastalland'
  license: CC0-1.0
  name: SWEET Ontology Realm Land Coastal
  part_of: sweet
  prefix: sweet.realc
  repository: https://github.com/ESIPFed/sweet
  synonyms:
  - sorealc
  uri_format: http://sweetontology.net/realmLandCoastal/$1
sweet.realf:
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: The Semantic Web for Earth and Environmental Terminology (SWEET) ontology
    for Realm Land Fluvial
  download_rdf: https://github.com/ESIPFed/sweet/raw/refs/heads/master/src/realmLandFluvial.ttl
  example: Alluvial
  github_request_issue: 1772
  homepage: http://sweetontology.net/realmLandFluvial/
  keywords:
  - ' fluvialland'
  license: CC0-1.0
  name: SWEET Ontology Realm Land Fluvial
  part_of: sweet
  prefix: sweet.realf
  repository: https://github.com/ESIPFed/sweet
  synonyms:
  - sorealf
  uri_format: http://sweetontology.net/realmLandFluvial/$1
sweet.realg:
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: The Semantic Web for Earth and Environmental Terminology (SWEET) ontology
    for Realm Land Glacial
  download_rdf: https://github.com/ESIPFed/sweet/raw/refs/heads/master/src/realmLandGlacial.ttl
  example: Arete
  github_request_issue: 1772
  homepage: http://sweetontology.net/realmLandGlacial/
  keywords:
  - ' glacialland'
  license: CC0-1.0
  name: SWEET Ontology Realm Land Glacial
  part_of: sweet
  prefix: sweet.realg
  repository: https://github.com/ESIPFed/sweet
  synonyms:
  - sorealg
  uri_format: http://sweetontology.net/realmLandGlacial/$1
sweet.realo:
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: The Semantic Web for Earth and Environmental Terminology (SWEET) ontology
    for Realm Land Orographic
  download_rdf: https://github.com/ESIPFed/sweet/raw/refs/heads/master/src/realmLandOrographic.ttl
  example: Alpine
  github_request_issue: 1772
  homepage: http://sweetontology.net/realmLandOrographic/
  keywords:
  - ' orographicland'
  license: CC0-1.0
  name: SWEET Ontology Realm Land Orographic
  part_of: sweet
  prefix: sweet.realo
  repository: https://github.com/ESIPFed/sweet
  synonyms:
  - sorealo
  uri_format: http://sweetontology.net/realmLandOrographic/$1
sweet.realp:
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: The Semantic Web for Earth and Environmental Terminology (SWEET) ontology
    for Realm Land Protected
  download_rdf: https://github.com/ESIPFed/sweet/raw/refs/heads/master/src/realmLandProtected.ttl
  example: CityPark
  github_request_issue: 1772
  homepage: http://sweetontology.net/realmLandProtected/
  keywords:
  - ' protectedland'
  license: CC0-1.0
  name: SWEET Ontology Realm Land Protected
  part_of: sweet
  prefix: sweet.realp
  repository: https://github.com/ESIPFed/sweet
  synonyms:
  - sorealp
  uri_format: http://sweetontology.net/realmLandProtected/$1
sweet.realt:
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: The Semantic Web for Earth and Environmental Terminology (SWEET) ontology
    for Realm Land Tectonic
  download_rdf: https://github.com/ESIPFed/sweet/raw/refs/heads/master/src/realmLandTectonic.ttl
  example: AseismicRidge
  github_request_issue: 1772
  homepage: http://sweetontology.net/realmLandTectonic/
  keywords:
  - ' tectonicland'
  license: CC0-1.0
  name: SWEET Ontology Realm Land Tectonic
  part_of: sweet
  prefix: sweet.realt
  repository: https://github.com/ESIPFed/sweet
  synonyms:
  - sorealt
  uri_format: http://sweetontology.net/realmLandTectonic/$1
sweet.realv:
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: The Semantic Web for Earth and Environmental Terminology (SWEET) ontology
    for Realm Land Volcanic
  download_rdf: https://github.com/ESIPFed/sweet/raw/refs/heads/master/src/realmLandVolcanic.ttl
  example: Caldera
  github_request_issue: 1772
  homepage: http://sweetontology.net/realmLandVolcanic/
  keywords:
  - ' volcanicland'
  license: CC0-1.0
  name: SWEET Ontology Realm Land Volcanic
  part_of: sweet
  prefix: sweet.realv
  repository: https://github.com/ESIPFed/sweet
  synonyms:
  - sorealv
  uri_format: http://sweetontology.net/realmLandVolcanic/$1
sweet.reao:
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: The Semantic Web for Earth and Environmental Terminology (SWEET) ontology
    for Realm Ocean
  download_rdf: https://github.com/ESIPFed/sweet/raw/refs/heads/master/src/realmOcean.ttl
  example: Abyss
  github_request_issue: 1772
  homepage: http://sweetontology.net/realmOcean/
  keywords:
  - ocean
  - realm
  license: CC0-1.0
  name: SWEET Ontology Realm Ocean
  part_of: sweet
  prefix: sweet.reao
  repository: https://github.com/ESIPFed/sweet
  synonyms:
  - soreao
  uri_format: http://sweetontology.net/realmOcean/$1
sweet.reaofe:
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: The Semantic Web for Earth and Environmental Terminology (SWEET) ontology
    for Realm Ocean Feature
  download_rdf: https://github.com/ESIPFed/sweet/raw/refs/heads/master/src/realmOceanFeature.ttl
  example: EarthEasternBoundaryCurrent
  github_request_issue: 1772
  homepage: http://sweetontology.net/realmOceanFeature/
  keywords:
  - ocean feature
  - realm
  license: CC0-1.0
  name: SWEET Ontology Realm Ocean Feature
  part_of: sweet
  prefix: sweet.reaofe
  repository: https://github.com/ESIPFed/sweet
  synonyms:
  - soreaofe
  uri_format: http://sweetontology.net/realmOceanFeature/$1
sweet.reaofl:
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: The Semantic Web for Earth and Environmental Terminology (SWEET) ontology
    for Realm Ocean Floor
  download_rdf: https://github.com/ESIPFed/sweet/raw/refs/heads/master/src/realmOceanFloor.ttl
  example: AbyssalHill
  github_request_issue: 1772
  homepage: http://sweetontology.net/realmOceanFloor/
  keywords:
  - ocean floor
  - realm
  license: CC0-1.0
  name: SWEET Ontology Realm Ocean Floor
  part_of: sweet
  prefix: sweet.reaofl
  repository: https://github.com/ESIPFed/sweet
  synonyms:
  - soreaofl
  uri_format: http://sweetontology.net/realmOceanFloor/$1
sweet.rear:
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: The Semantic Web for Earth and Environmental Terminology (SWEET) ontology
    for Realm Region
  download_rdf: https://github.com/ESIPFed/sweet/raw/refs/heads/master/src/realmRegion.ttl
  example: Austral
  github_request_issue: 1772
  homepage: http://sweetontology.net/realmRegion/
  keywords:
  - realm
  - region
  license: CC0-1.0
  name: SWEET Ontology Realm Region
  part_of: sweet
  prefix: sweet.rear
  repository: https://github.com/ESIPFed/sweet
  synonyms:
  - sorear
  uri_format: http://sweetontology.net/realmRegion/$1
sweet.reas:
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: The Semantic Web for Earth and Environmental Terminology (SWEET) ontology
    for Realm Soil
  download_rdf: https://github.com/ESIPFed/sweet/raw/refs/heads/master/src/realmSoil.ttl
  example: A_Horizon
  github_request_issue: 1772
  homepage: http://sweetontology.net/realmSoil/
  keywords:
  - realm
  - soil
  license: CC0-1.0
  name: SWEET Ontology Realm Soil
  part_of: sweet
  prefix: sweet.reas
  repository: https://github.com/ESIPFed/sweet
  synonyms:
  - soreas
  uri_format: http://sweetontology.net/realmSoil/$1
sweet.rel:
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: The Semantic Web for Earth and Environmental Terminology (SWEET) ontology
    for Relationships
  download_rdf: https://github.com/ESIPFed/sweet/raw/refs/heads/master/src/rela.ttl
  example: hasPhenomena
  github_request_issue: 1772
  homepage: http://sweetontology.net/rela/
  keywords:
  - relationships
  license: CC0-1.0
  name: SWEET Ontology Relationships
  part_of: sweet
  prefix: sweet.rel
  repository: https://github.com/ESIPFed/sweet
  synonyms:
  - sorel
  uri_format: http://sweetontology.net/rela/$1
sweet.relch:
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: The Semantic Web for Earth and Environmental Terminology (SWEET) ontology
    for Relationships Chemical
  download_rdf: https://github.com/ESIPFed/sweet/raw/refs/heads/master/src/relaChemical.ttl
  example: atomicMass
  github_request_issue: 1772
  homepage: http://sweetontology.net/relaChemical/
  keywords:
  - chemical
  license: CC0-1.0
  name: SWEET Ontology Relationships Chemical
  part_of: sweet
  prefix: sweet.relch
  repository: https://github.com/ESIPFed/sweet
  synonyms:
  - sorelch
  uri_format: http://sweetontology.net/relaChemical/$1
sweet.relcl:
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: The Semantic Web for Earth and Environmental Terminology (SWEET) ontology
    for Relationships Climate
  download_rdf: https://github.com/ESIPFed/sweet/raw/refs/heads/master/src/relaClimate.ttl
  example: hasAverageAnnualPrecipitation
  github_request_issue: 1772
  homepage: http://sweetontology.net/relaClimate/
  keywords:
  - climate
  license: CC0-1.0
  name: SWEET Ontology Relationships Climate
  part_of: sweet
  prefix: sweet.relcl
  repository: https://github.com/ESIPFed/sweet
  synonyms:
  - sorelcl
  uri_format: http://sweetontology.net/relaClimate/$1
sweet.relh:
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: The Semantic Web for Earth and Environmental Terminology (SWEET) ontology
    for Relationships Human
  download_rdf: https://github.com/ESIPFed/sweet/raw/refs/heads/master/src/relaHuman.ttl
  example: hasAttribute
  github_request_issue: 1772
  homepage: http://sweetontology.net/relaHuman/
  keywords:
  - human
  license: CC0-1.0
  name: SWEET Ontology Relationships Human
  part_of: sweet
  prefix: sweet.relh
  repository: https://github.com/ESIPFed/sweet
  synonyms:
  - sorelh
  uri_format: http://sweetontology.net/relaHuman/$1
sweet.relm:
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: The Semantic Web for Earth and Environmental Terminology (SWEET) ontology
    for Relationships Mathematical
  download_rdf: https://github.com/ESIPFed/sweet/raw/refs/heads/master/src/relaMath.ttl
  example: averageOver
  github_request_issue: 1772
  homepage: http://sweetontology.net/relaMath/
  keywords:
  - mathematical
  license: CC0-1.0
  name: SWEET Ontology Relationships Mathematical
  part_of: sweet
  prefix: sweet.relm
  repository: https://github.com/ESIPFed/sweet
  synonyms:
  - sorelm
  uri_format: http://sweetontology.net/relaMath/$1
sweet.relph:
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: The Semantic Web for Earth and Environmental Terminology (SWEET) ontology
    for Relationships Physical
  download_rdf: https://github.com/ESIPFed/sweet/raw/refs/heads/master/src/relaPhysical.ttl
  example: colderThan
  github_request_issue: 1772
  homepage: http://sweetontology.net/relaPhysical/
  keywords:
  - physical
  license: CC0-1.0
  name: SWEET Ontology Relationships Physical
  part_of: sweet
  prefix: sweet.relph
  repository: https://github.com/ESIPFed/sweet
  synonyms:
  - sorelph
  uri_format: http://sweetontology.net/relaPhysical/$1
sweet.relpr:
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: The Semantic Web for Earth and Environmental Terminology (SWEET) ontology
    for Relationships Provenance
  download_rdf: https://github.com/ESIPFed/sweet/raw/refs/heads/master/src/relaProvenance.ttl
  example: fillValue
  github_request_issue: 1772
  homepage: http://sweetontology.net/relaProvenance/
  keywords:
  - provenance
  license: CC0-1.0
  name: SWEET Ontology Relationships Provenance
  part_of: sweet
  prefix: sweet.relpr
  repository: https://github.com/ESIPFed/sweet
  synonyms:
  - sorelpr
  uri_format: http://sweetontology.net/relaProvenance/$1
sweet.relsc:
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: The Semantic Web for Earth and Environmental Terminology (SWEET) ontology
    for Relationships Scientific
  download_rdf: https://github.com/ESIPFed/sweet/raw/refs/heads/master/src/relaSci.ttl
  example: causedBy
  github_request_issue: 1772
  homepage: http://sweetontology.net/relaSci/
  keywords:
  - scientific
  license: CC0-1.0
  name: SWEET Ontology Relationships Scientific
  part_of: sweet
  prefix: sweet.relsc
  repository: https://github.com/ESIPFed/sweet
  synonyms:
  - sorelsc
  uri_format: http://sweetontology.net/relaSci/$1
sweet.relsp:
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: The Semantic Web for Earth and Environmental Terminology (SWEET) ontology
    for Relationships Space
  download_rdf: https://github.com/ESIPFed/sweet/raw/refs/heads/master/src/relaSpace.ttl
  example: adjacentTo
  github_request_issue: 1772
  homepage: http://sweetontology.net/relaSpace/
  keywords:
  - space
  license: CC0-1.0
  name: SWEET Ontology Relationships Space
  part_of: sweet
  prefix: sweet.relsp
  repository: https://github.com/ESIPFed/sweet
  synonyms:
  - sorelsp
  uri_format: http://sweetontology.net/relaSpace/$1
sweet.relt:
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: The Semantic Web for Earth and Environmental Terminology (SWEET) ontology
    for Relationships Time
  download_rdf: https://github.com/ESIPFed/sweet/raw/refs/heads/master/src/relaTime.ttl
  example: dayOfYear
  github_request_issue: 1772
  homepage: http://sweetontology.net/relaTime/
  keywords:
  - time
  license: CC0-1.0
  name: SWEET Ontology Relationships Time
  part_of: sweet
  prefix: sweet.relt
  repository: https://github.com/ESIPFed/sweet
  synonyms:
  - sorelt
  uri_format: http://sweetontology.net/relaTime/$1
sweet.rep:
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: The Semantic Web for Earth and Environmental Terminology (SWEET) ontology
    for Representation
  download_rdf: https://github.com/ESIPFed/sweet/raw/refs/heads/master/src/repr.ttl
  example: CardinalScale
  github_request_issue: 1772
  homepage: http://sweetontology.net/repr/
  keywords:
  - representation
  license: CC0-1.0
  name: SWEET Ontology Representation
  part_of: sweet
  prefix: sweet.rep
  repository: https://github.com/ESIPFed/sweet
  synonyms:
  - sorep
  uri_format: http://sweetontology.net/repr/$1
sweet.repdf:
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: The Semantic Web for Earth and Environmental Terminology (SWEET) ontology
    for Representation Data Format
  download_rdf: https://github.com/ESIPFed/sweet/raw/refs/heads/master/src/reprDataFormat.ttl
  example: ByteOrder
  github_request_issue: 1772
  homepage: http://sweetontology.net/reprDataFormat/
  keywords:
  - representation data format
  license: CC0-1.0
  name: SWEET Ontology Representation Data Format
  part_of: sweet
  prefix: sweet.repdf
  repository: https://github.com/ESIPFed/sweet
  synonyms:
  - sorepdf
  uri_format: http://sweetontology.net/reprDataFormat/$1
sweet.repdm:
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: The Semantic Web for Earth and Environmental Terminology (SWEET) ontology
    for Representation Data Model
  download_rdf: https://github.com/ESIPFed/sweet/raw/refs/heads/master/src/reprDataModel.ttl
  example: Array
  github_request_issue: 1772
  homepage: http://sweetontology.net/reprDataModel/
  keywords:
  - representation data model
  license: CC0-1.0
  name: SWEET Ontology Representation Data Model
  part_of: sweet
  prefix: sweet.repdm
  repository: https://github.com/ESIPFed/sweet
  synonyms:
  - sorepdm
  uri_format: http://sweetontology.net/reprDataModel/$1
sweet.repdp:
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: The Semantic Web for Earth and Environmental Terminology (SWEET) ontology
    for Representation Data Product
  download_rdf: https://github.com/ESIPFed/sweet/raw/refs/heads/master/src/reprDataProduct.ttl
  example: Archive
  github_request_issue: 1772
  homepage: http://sweetontology.net/reprDataProduct/
  keywords:
  - representation data product
  license: CC0-1.0
  name: SWEET Ontology Representation Data Product
  part_of: sweet
  prefix: sweet.repdp
  repository: https://github.com/ESIPFed/sweet
  synonyms:
  - sorepdp
  uri_format: http://sweetontology.net/reprDataProduct/$1
sweet.repds:
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: The Semantic Web for Earth and Environmental Terminology (SWEET) ontology
    for Representation Data Service
  download_rdf: https://github.com/ESIPFed/sweet/raw/refs/heads/master/src/reprDataService.ttl
  example: Access
  github_request_issue: 1772
  homepage: http://sweetontology.net/reprDataService/
  keywords:
  - representation data service
  license: CC0-1.0
  name: SWEET Ontology Representation Data Service
  part_of: sweet
  prefix: sweet.repds
  repository: https://github.com/ESIPFed/sweet
  synonyms:
  - sorepds
  uri_format: http://sweetontology.net/reprDataService/$1
sweet.repdsa:
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: The Semantic Web for Earth and Environmental Terminology (SWEET) ontology
    for Representation Data Servcie Analysis
  download_rdf: https://github.com/ESIPFed/sweet/raw/refs/heads/master/src/reprDataServiceAnalysis.ttl
  example: Animate
  github_request_issue: 1772
  homepage: http://sweetontology.net/reprDataServiceAnalysis/
  keywords:
  - representation data servcie analysis
  license: CC0-1.0
  name: SWEET Ontology Representation Data Servcie Analysis
  part_of: sweet
  prefix: sweet.repdsa
  repository: https://github.com/ESIPFed/sweet
  synonyms:
  - sorepdsa
  uri_format: http://sweetontology.net/reprDataServiceAnalysis/$1
sweet.repdsg:
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: The Semantic Web for Earth and Environmental Terminology (SWEET) ontology
    for Representation Data Service Geospatial
  download_rdf: https://github.com/ESIPFed/sweet/raw/refs/heads/master/src/reprDataServiceGeospatial.ttl
  example: Buffer
  github_request_issue: 1772
  homepage: http://sweetontology.net/reprDataServiceGeospatial/
  keywords:
  - representation data service geospatial
  license: CC0-1.0
  name: SWEET Ontology Representation Data Service Geospatial
  part_of: sweet
  prefix: sweet.repdsg
  repository: https://github.com/ESIPFed/sweet
  synonyms:
  - sorepdsg
  uri_format: http://sweetontology.net/reprDataServiceGeospatial/$1
sweet.repdsr:
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: The Semantic Web for Earth and Environmental Terminology (SWEET) ontology
    for Representation Data Service Reduction
  download_rdf: https://github.com/ESIPFed/sweet/raw/refs/heads/master/src/reprDataServiceReduction.ttl
  example: Binning
  github_request_issue: 1772
  homepage: http://sweetontology.net/reprDataServiceReduction/
  keywords:
  - representation data service reduction
  license: CC0-1.0
  name: SWEET Ontology Representation Data Service Reduction
  part_of: sweet
  prefix: sweet.repdsr
  repository: https://github.com/ESIPFed/sweet
  synonyms:
  - sorepdsr
  uri_format: http://sweetontology.net/reprDataServiceReduction/$1
sweet.repdsv:
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: The Semantic Web for Earth and Environmental Terminology (SWEET) ontology
    for Representation Data Service Validation
  download_rdf: https://github.com/ESIPFed/sweet/raw/refs/heads/master/src/reprDataServiceValidation.ttl
  example: Acceptance
  github_request_issue: 1772
  homepage: http://sweetontology.net/reprDataServiceValidation/
  keywords:
  - representation data service validation
  license: CC0-1.0
  name: SWEET Ontology Representation Data Service Validation
  part_of: sweet
  prefix: sweet.repdsv
  repository: https://github.com/ESIPFed/sweet
  synonyms:
  - sorepdsv
  uri_format: http://sweetontology.net/reprDataServiceValidation/$1
sweet.repm:
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: The Semantic Web for Earth and Environmental Terminology (SWEET) ontology
    for Representation Mathematics
  download_rdf: https://github.com/ESIPFed/sweet/raw/refs/heads/master/src/reprMath.ttl
  example: Array
  github_request_issue: 1772
  homepage: http://sweetontology.net/reprMath/
  keywords:
  - representation mathematics
  license: CC0-1.0
  name: SWEET Ontology Representation Mathematics
  part_of: sweet
  prefix: sweet.repm
  repository: https://github.com/ESIPFed/sweet
  synonyms:
  - sorepm
  uri_format: http://sweetontology.net/reprMath/$1
sweet.repmf:
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: The Semantic Web for Earth and Environmental Terminology (SWEET) ontology
    for Representation Mathematics Function
  download_rdf: https://github.com/ESIPFed/sweet/raw/refs/heads/master/src/reprMathFunction.ttl
  example: Affine
  github_request_issue: 1772
  homepage: http://sweetontology.net/reprMathFunction/
  keywords:
  - representation mathematics function
  license: CC0-1.0
  name: SWEET Ontology Representation Mathematics Function
  part_of: sweet
  prefix: sweet.repmf
  repository: https://github.com/ESIPFed/sweet
  synonyms:
  - sorepmf
  uri_format: http://sweetontology.net/reprMathFunction/$1
sweet.repmfo:
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: The Semantic Web for Earth and Environmental Terminology (SWEET) ontology
    for Representation Mathematics Function Orthogonal
  download_rdf: https://github.com/ESIPFed/sweet/raw/refs/heads/master/src/reprMathFunctionOrthogonal.ttl
  example: Coefficient
  github_request_issue: 1772
  homepage: http://sweetontology.net/reprMathFunctionOrthogonal/
  keywords:
  - representation mathematics function orthogonal
  license: CC0-1.0
  name: SWEET Ontology Representation Mathematics Function Orthogonal
  part_of: sweet
  prefix: sweet.repmfo
  repository: https://github.com/ESIPFed/sweet
  synonyms:
  - sorepmfo
  uri_format: http://sweetontology.net/reprMathFunctionOrthogonal/$1
sweet.repmg:
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: The Semantic Web for Earth and Environmental Terminology (SWEET) ontology
    for Representation Mathematics Graph
  download_rdf: https://github.com/ESIPFed/sweet/raw/refs/heads/master/src/reprMathGraph.ttl
  example: Arc
  github_request_issue: 1772
  homepage: http://sweetontology.net/reprMathGraph/
  keywords:
  - representation mathematics graph
  license: CC0-1.0
  name: SWEET Ontology Representation Mathematics Graph
  part_of: sweet
  prefix: sweet.repmg
  repository: https://github.com/ESIPFed/sweet
  synonyms:
  - sorepmg
  uri_format: http://sweetontology.net/reprMathGraph/$1
sweet.repmo:
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: The Semantic Web for Earth and Environmental Terminology (SWEET) ontology
    for Representation Mathematics Operation
  download_rdf: https://github.com/ESIPFed/sweet/raw/refs/heads/master/src/reprMathOperation.ttl
  example: AreaIntegral
  github_request_issue: 1772
  homepage: http://sweetontology.net/reprMathOperation/
  keywords:
  - representation mathematics operation
  license: CC0-1.0
  name: SWEET Ontology Representation Mathematics Operation
  part_of: sweet
  prefix: sweet.repmo
  repository: https://github.com/ESIPFed/sweet
  synonyms:
  - sorepmo
  uri_format: http://sweetontology.net/reprMathOperation/$1
sweet.repmso:
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: The Semantic Web for Earth and Environmental Terminology (SWEET) ontology
    for Representation Mathematics Solution
  download_rdf: https://github.com/ESIPFed/sweet/raw/refs/heads/master/src/reprMathSolution.ttl
  example: AlgebraicSolution
  github_request_issue: 1772
  homepage: http://sweetontology.net/reprMathSolution/
  keywords:
  - representation mathematics solution
  license: CC0-1.0
  name: SWEET Ontology Representation Mathematics Solution
  part_of: sweet
  prefix: sweet.repmso
  repository: https://github.com/ESIPFed/sweet
  synonyms:
  - sorepmso
  uri_format: http://sweetontology.net/reprMathSolution/$1
sweet.repmst:
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: The Semantic Web for Earth and Environmental Terminology (SWEET) ontology
    for Representation Mathematics Statistics
  download_rdf: https://github.com/ESIPFed/sweet/raw/refs/heads/master/src/reprMathStatistics.ttl
  example: ANOVA
  github_request_issue: 1772
  homepage: http://sweetontology.net/reprMathStatistics/
  keywords:
  - representation mathematics statistics
  license: CC0-1.0
  name: SWEET Ontology Representation Mathematics Statistics
  part_of: sweet
  prefix: sweet.repmst
  repository: https://github.com/ESIPFed/sweet
  synonyms:
  - sorepmst
  uri_format: http://sweetontology.net/reprMathStatistics/$1
sweet.reps:
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: The Semantic Web for Earth and Environmental Terminology (SWEET) ontology
    for Representation Space
  download_rdf: https://github.com/ESIPFed/sweet/raw/refs/heads/master/src/reprSpace.ttl
  example: Space
  github_request_issue: 1772
  homepage: http://sweetontology.net/reprSpace/
  keywords:
  - representation space
  license: CC0-1.0
  name: SWEET Ontology Representation Space
  part_of: sweet
  prefix: sweet.reps
  repository: https://github.com/ESIPFed/sweet
  synonyms:
  - soreps
  uri_format: http://sweetontology.net/reprSpace/$1
sweet.repsc:
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: The Semantic Web for Earth and Environmental Terminology (SWEET) ontology
    for Representation Scientific Component
  download_rdf: https://github.com/ESIPFed/sweet/raw/refs/heads/master/src/reprSciComponent.ttl
  example: Component
  github_request_issue: 1772
  homepage: http://sweetontology.net/reprSciComponent/
  keywords:
  - representation scientific component
  license: CC0-1.0
  name: SWEET Ontology Representation Scientific Component
  part_of: sweet
  prefix: sweet.repsc
  repository: https://github.com/ESIPFed/sweet
  synonyms:
  - sorepsc
  uri_format: http://sweetontology.net/reprSciComponent/$1
sweet.repscd:
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: The Semantic Web for Earth and Environmental Terminology (SWEET) ontology
    for Representation Space Coordinate
  download_rdf: https://github.com/ESIPFed/sweet/raw/refs/heads/master/src/reprSpaceCoordinate.ttl
  example: AngularCoordinate
  github_request_issue: 1772
  homepage: http://sweetontology.net/reprSpaceCoordinate/
  keywords:
  - representation space coordinate
  license: CC0-1.0
  name: SWEET Ontology Representation Space Coordinate
  part_of: sweet
  prefix: sweet.repscd
  repository: https://github.com/ESIPFed/sweet
  synonyms:
  - sorepscd
  uri_format: http://sweetontology.net/reprSpaceCoordinate/$1
sweet.repsd:
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: The Semantic Web for Earth and Environmental Terminology (SWEET) ontology
    for Representation Space Direction
  download_rdf: https://github.com/ESIPFed/sweet/raw/refs/heads/master/src/reprSpaceDirection.ttl
  example: Counterclockwise
  github_request_issue: 1772
  homepage: http://sweetontology.net/reprSpaceDirection/
  keywords:
  - representation space direction
  license: CC0-1.0
  name: SWEET Ontology Representation Space Direction
  part_of: sweet
  prefix: sweet.repsd
  repository: https://github.com/ESIPFed/sweet
  synonyms:
  - sorepsd
  uri_format: http://sweetontology.net/reprSpaceDirection/$1
sweet.repsf:
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: The Semantic Web for Earth and Environmental Terminology (SWEET) ontology
    for Representation Scientific Function
  download_rdf: https://github.com/ESIPFed/sweet/raw/refs/heads/master/src/reprSciFunction.ttl
  example: AdiabaticInvariant
  github_request_issue: 1772
  homepage: http://sweetontology.net/reprSciFunction/
  keywords:
  - representation scientific function
  license: CC0-1.0
  name: SWEET Ontology Representation Scientific Function
  part_of: sweet
  prefix: sweet.repsf
  repository: https://github.com/ESIPFed/sweet
  synonyms:
  - sorepsf
  uri_format: http://sweetontology.net/reprSciFunction/$1
sweet.repsg:
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: The Semantic Web for Earth and Environmental Terminology (SWEET) ontology
    for Representation Space Geometry
  download_rdf: https://github.com/ESIPFed/sweet/raw/refs/heads/master/src/reprSpaceGeometry.ttl
  example: Arc
  github_request_issue: 1772
  homepage: http://sweetontology.net/reprSpaceGeometry/
  keywords:
  - representation space geometry
  license: CC0-1.0
  name: SWEET Ontology Representation Space Geometry
  part_of: sweet
  prefix: sweet.repsg
  repository: https://github.com/ESIPFed/sweet
  synonyms:
  - sorepsg
  uri_format: http://sweetontology.net/reprSpaceGeometry/$1
sweet.repsg3:
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: The Semantic Web for Earth and Environmental Terminology (SWEET) ontology
    for Representation Space Geometry 3D
  download_rdf: https://github.com/ESIPFed/sweet/raw/refs/heads/master/src/reprSpaceGeometry3D.ttl
  example: AirSpace
  github_request_issue: 1772
  homepage: http://sweetontology.net/reprSpaceGeometry3D/
  keywords:
  - representation space geometry 3d
  license: CC0-1.0
  name: SWEET Ontology Representation Space Geometry 3D
  part_of: sweet
  prefix: sweet.repsg3
  repository: https://github.com/ESIPFed/sweet
  synonyms:
  - sorepsg3
  uri_format: http://sweetontology.net/reprSpaceGeometry3D/$1
sweet.repsl:
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: The Semantic Web for Earth and Environmental Terminology (SWEET) ontology
    for Representation Scientific Law
  download_rdf: https://github.com/ESIPFed/sweet/raw/refs/heads/master/src/reprSciLaw.ttl
  example: BernoulliTheorem
  github_request_issue: 1772
  homepage: http://sweetontology.net/reprSciLaw/
  keywords:
  - representation scientific law
  license: CC0-1.0
  name: SWEET Ontology Representation Scientific Law
  part_of: sweet
  prefix: sweet.repsl
  repository: https://github.com/ESIPFed/sweet
  synonyms:
  - sorepsl
  uri_format: http://sweetontology.net/reprSciLaw/$1
sweet.repsme:
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: The Semantic Web for Earth and Environmental Terminology (SWEET) ontology
    for Representation Representation Scientific Methodology
  download_rdf: https://github.com/ESIPFed/sweet/raw/refs/heads/master/src/reprSciMethodology.ttl
  example: AerialPhotography
  github_request_issue: 1772
  homepage: http://sweetontology.net/reprSciMethodology/
  keywords:
  - representation representation scientific methodology
  license: CC0-1.0
  name: SWEET Ontology Representation Representation Scientific Methodology
  part_of: sweet
  prefix: sweet.repsme
  repository: https://github.com/ESIPFed/sweet
  synonyms:
  - sorepsme
  uri_format: http://sweetontology.net/reprSciMethodology/$1
sweet.repsmo:
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: The Semantic Web for Earth and Environmental Terminology (SWEET) ontology
    for Representation Scientific Model
  download_rdf: https://github.com/ESIPFed/sweet/raw/refs/heads/master/src/reprSciModel.ttl
  example: BoussinesqApproximation
  github_request_issue: 1772
  homepage: http://sweetontology.net/reprSciModel/
  keywords:
  - representation scientific model
  license: CC0-1.0
  name: SWEET Ontology Representation Scientific Model
  part_of: sweet
  prefix: sweet.repsmo
  repository: https://github.com/ESIPFed/sweet
  synonyms:
  - sorepsmo
  uri_format: http://sweetontology.net/reprSciModel/$1
sweet.repsp:
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: The Semantic Web for Earth and Environmental Terminology (SWEET) ontology
    for Representation Science Provenance
  download_rdf: https://github.com/ESIPFed/sweet/raw/refs/heads/master/src/reprSciProvenance.ttl
  example: Agent
  github_request_issue: 1772
  homepage: http://sweetontology.net/reprSciProvenance/
  keywords:
  - representation science provenance
  license: CC0-1.0
  name: SWEET Ontology Representation Science Provenance
  part_of: sweet
  prefix: sweet.repsp
  repository: https://github.com/ESIPFed/sweet
  synonyms:
  - sorepsp
  uri_format: http://sweetontology.net/reprSciProvenance/$1
sweet.repsrs:
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: The Semantic Web for Earth and Environmental Terminology (SWEET) ontology
    for Representation Space Reference System
  download_rdf: https://github.com/ESIPFed/sweet/raw/refs/heads/master/src/reprSpaceReferenceSystem.ttl
  example: HorizontalCoordinateSystem
  github_request_issue: 1772
  homepage: http://sweetontology.net/reprSpaceReferenceSystem/
  keywords:
  - representation space reference system
  license: CC0-1.0
  name: SWEET Ontology Representation Space Reference System
  part_of: sweet
  prefix: sweet.repsrs
  repository: https://github.com/ESIPFed/sweet
  synonyms:
  - sorepsrs
  uri_format: http://sweetontology.net/reprSpaceReferenceSystem/$1
sweet.repsu:
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: The Semantic Web for Earth and Environmental Terminology (SWEET) ontology
    for Representation Scientific Units
  download_rdf: https://github.com/ESIPFed/sweet/raw/refs/heads/master/src/reprSciUnits.ttl
  example: BaseUnit
  github_request_issue: 1772
  homepage: http://sweetontology.net/reprSciUnits/
  keywords:
  - representation scientific units
  license: CC0-1.0
  name: SWEET Ontology Representation Scientific Units
  part_of: sweet
  prefix: sweet.repsu
  repository: https://github.com/ESIPFed/sweet
  synonyms:
  - sorepsu
  uri_format: http://sweetontology.net/reprSciUnits/$1
sweet.rept:
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: The Semantic Web for Earth and Environmental Terminology (SWEET) ontology
    for Representation Time
  download_rdf: https://github.com/ESIPFed/sweet/raw/refs/heads/master/src/reprTime.ttl
  example: Duration
  github_request_issue: 1772
  homepage: http://sweetontology.net/reprTime/
  keywords:
  - representation time
  license: CC0-1.0
  name: SWEET Ontology Representation Time
  part_of: sweet
  prefix: sweet.rept
  repository: https://github.com/ESIPFed/sweet
  synonyms:
  - sorept
  uri_format: http://sweetontology.net/reprTime/$1
sweet.reptd:
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: The Semantic Web for Earth and Environmental Terminology (SWEET) ontology
    for Representation Time Day
  download_rdf: https://github.com/ESIPFed/sweet/raw/refs/heads/master/src/reprTimeDay.ttl
  example: Dawn
  github_request_issue: 1772
  homepage: http://sweetontology.net/reprTimeDay/
  keywords:
  - representation time day
  license: CC0-1.0
  name: SWEET Ontology Representation Time Day
  part_of: sweet
  prefix: sweet.reptd
  repository: https://github.com/ESIPFed/sweet
  synonyms:
  - soreptd
  uri_format: http://sweetontology.net/reprTimeDay/$1
sweet.repts:
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: The Semantic Web for Earth and Environmental Terminology (SWEET) ontology
    for Representation Time Season
  download_rdf: https://github.com/ESIPFed/sweet/raw/refs/heads/master/src/reprTimeSeason.ttl
  example: ColdestMonth
  github_request_issue: 1772
  homepage: http://sweetontology.net/reprTimeSeason/
  keywords:
  - representation time season
  license: CC0-1.0
  name: SWEET Ontology Representation Time Season
  part_of: sweet
  prefix: sweet.repts
  repository: https://github.com/ESIPFed/sweet
  synonyms:
  - sorepts
  uri_format: http://sweetontology.net/reprTimeSeason/$1
sweet.st:
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: The Semantic Web for Earth and Environmental Terminology (SWEET) ontology
    for State
  download_rdf: https://github.com/ESIPFed/sweet/raw/refs/heads/master/src/state.ttl
  example: BinaryState
  github_request_issue: 1772
  homepage: http://sweetontology.net/state/
  keywords:
  - state
  license: CC0-1.0
  name: SWEET Ontology State
  part_of: sweet
  prefix: sweet.st
  repository: https://github.com/ESIPFed/sweet
  synonyms:
  - sost
  uri_format: http://sweetontology.net/state/$1
sweet.stb:
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: The Semantic Web for Earth and Environmental Terminology (SWEET) ontology
    for State Biological
  download_rdf: https://github.com/ESIPFed/sweet/raw/refs/heads/master/src/stateBiological.ttl
  example: BiologicalState
  github_request_issue: 1772
  homepage: http://sweetontology.net/stateBiological/
  keywords:
  - state biological
  license: CC0-1.0
  name: SWEET Ontology State Biological
  part_of: sweet
  prefix: sweet.stb
  repository: https://github.com/ESIPFed/sweet
  synonyms:
  - sostb
  uri_format: http://sweetontology.net/stateBiological/$1
sweet.stc:
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: The Semantic Web for Earth and Environmental Terminology (SWEET) ontology
    for State Chemical
  download_rdf: https://github.com/ESIPFed/sweet/raw/refs/heads/master/src/stateChemical.ttl
  example: BiochemicalState
  github_request_issue: 1772
  homepage: http://sweetontology.net/stateChemical/
  keywords:
  - state chemical
  license: CC0-1.0
  name: SWEET Ontology State Chemical
  part_of: sweet
  prefix: sweet.stc
  repository: https://github.com/ESIPFed/sweet
  synonyms:
  - sostc
  uri_format: http://sweetontology.net/stateChemical/$1
sweet.stdp:
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: The Semantic Web for Earth and Environmental Terminology (SWEET) ontology
    for State Data Processing
  download_rdf: https://github.com/ESIPFed/sweet/raw/refs/heads/master/src/stateDataProcessing.ttl
  example: Archived
  github_request_issue: 1772
  homepage: http://sweetontology.net/stateDataProcessing/
  keywords:
  - state data processing
  license: CC0-1.0
  name: SWEET Ontology State Data Processing
  part_of: sweet
  prefix: sweet.stdp
  repository: https://github.com/ESIPFed/sweet
  synonyms:
  - sostdp
  uri_format: http://sweetontology.net/stateDataProcessing/$1
sweet.stef:
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: The Semantic Web for Earth and Environmental Terminology (SWEET) ontology
    for State Energy Flux
  download_rdf: https://github.com/ESIPFed/sweet/raw/refs/heads/master/src/stateEnergyFlux.ttl
  example: AClass
  github_request_issue: 1772
  homepage: http://sweetontology.net/stateEnergyFlux/
  keywords:
  - state energy flux
  license: CC0-1.0
  name: SWEET Ontology State Energy Flux
  part_of: sweet
  prefix: sweet.stef
  repository: https://github.com/ESIPFed/sweet
  synonyms:
  - sostef
  uri_format: http://sweetontology.net/stateEnergyFlux/$1
sweet.stf:
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: The Semantic Web for Earth and Environmental Terminology (SWEET) ontology
    for State Fluid
  download_rdf: https://github.com/ESIPFed/sweet/raw/refs/heads/master/src/stateFluid.ttl
  example: FluidEquilibriumState
  github_request_issue: 1772
  homepage: http://sweetontology.net/stateFluid/
  keywords:
  - state fluid
  license: CC0-1.0
  name: SWEET Ontology State Fluid
  part_of: sweet
  prefix: sweet.stf
  repository: https://github.com/ESIPFed/sweet
  synonyms:
  - sostf
  uri_format: http://sweetontology.net/stateFluid/$1
sweet.sto:
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: The Semantic Web for Earth and Environmental Terminology (SWEET) ontology
    for State Ordinal
  download_rdf: https://github.com/ESIPFed/sweet/raw/refs/heads/master/src/stateOrdinal.ttl
  example: Acute
  github_request_issue: 1772
  homepage: http://sweetontology.net/stateOrdinal/
  keywords:
  - state ordinal
  license: CC0-1.0
  name: SWEET Ontology State Ordinal
  part_of: sweet
  prefix: sweet.sto
  repository: https://github.com/ESIPFed/sweet
  synonyms:
  - sosto
  uri_format: http://sweetontology.net/stateOrdinal/$1
sweet.stp:
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: The Semantic Web for Earth and Environmental Terminology (SWEET) ontology
    for State Physical
  download_rdf: https://github.com/ESIPFed/sweet/raw/refs/heads/master/src/statePhysical.ttl
  example: MoistureState
  github_request_issue: 1772
  homepage: http://sweetontology.net/statePhysical/
  keywords:
  - state physical
  license: CC0-1.0
  name: SWEET Ontology State Physical
  part_of: sweet
  prefix: sweet.stp
  repository: https://github.com/ESIPFed/sweet
  synonyms:
  - sostp
  uri_format: http://sweetontology.net/statePhysical/$1
sweet.strb:
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: The Semantic Web for Earth and Environmental Terminology (SWEET) ontology
    for State Role Biological
  download_rdf: https://github.com/ESIPFed/sweet/raw/refs/heads/master/src/stateRoleBiological.ttl
  example: Autotroph
  github_request_issue: 1772
  homepage: http://sweetontology.net/stateRoleBiological/
  keywords:
  - state role biological
  license: CC0-1.0
  name: SWEET Ontology State Role Biological
  part_of: sweet
  prefix: sweet.strb
  repository: https://github.com/ESIPFed/sweet
  synonyms:
  - sostrb
  uri_format: http://sweetontology.net/stateRoleBiological/$1
sweet.strc:
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: The Semantic Web for Earth and Environmental Terminology (SWEET) ontology
    for State Role Chemical
  download_rdf: https://github.com/ESIPFed/sweet/raw/refs/heads/master/src/stateRoleChemical.ttl
  example: ChemicalRole
  github_request_issue: 1772
  homepage: http://sweetontology.net/stateRoleChemical/
  keywords:
  - state role chemical
  license: CC0-1.0
  name: SWEET Ontology State Role Chemical
  part_of: sweet
  prefix: sweet.strc
  repository: https://github.com/ESIPFed/sweet
  synonyms:
  - sostrc
  uri_format: http://sweetontology.net/stateRoleChemical/$1
sweet.stre:
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: The Semantic Web for Earth and Environmental Terminology (SWEET) ontology
    for State Realm
  download_rdf: https://github.com/ESIPFed/sweet/raw/refs/heads/master/src/stateRealm.ttl
  example: RealmConfiguration
  github_request_issue: 1772
  homepage: http://sweetontology.net/stateRealm/
  keywords:
  - state realm
  license: CC0-1.0
  name: SWEET Ontology State Realm
  part_of: sweet
  prefix: sweet.stre
  repository: https://github.com/ESIPFed/sweet
  synonyms:
  - sostre
  uri_format: http://sweetontology.net/stateRealm/$1
sweet.strg:
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: The Semantic Web for Earth and Environmental Terminology (SWEET) ontology
    for State Role Geographic
  download_rdf: https://github.com/ESIPFed/sweet/raw/refs/heads/master/src/stateRoleGeographic.ttl
  example: Barrier
  github_request_issue: 1772
  homepage: http://sweetontology.net/stateRoleGeographic/
  keywords:
  - state role geographic
  license: CC0-1.0
  name: SWEET Ontology State Role Geographic
  part_of: sweet
  prefix: sweet.strg
  repository: https://github.com/ESIPFed/sweet
  synonyms:
  - sostrg
  uri_format: http://sweetontology.net/stateRoleGeographic/$1
sweet.stri:
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: The Semantic Web for Earth and Environmental Terminology (SWEET) ontology
    for State Role Impact
  download_rdf: https://github.com/ESIPFed/sweet/raw/refs/heads/master/src/stateRoleImpact.ttl
  example: Catastrophic
  github_request_issue: 1772
  homepage: http://sweetontology.net/stateRoleImpact/
  keywords:
  - state role impact
  license: CC0-1.0
  name: SWEET Ontology State Role Impact
  part_of: sweet
  prefix: sweet.stri
  repository: https://github.com/ESIPFed/sweet
  synonyms:
  - sostri
  uri_format: http://sweetontology.net/stateRoleImpact/$1
sweet.stro:
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: The Semantic Web for Earth and Environmental Terminology (SWEET) ontology
    for State Role
  download_rdf: https://github.com/ESIPFed/sweet/raw/refs/heads/master/src/stateRole.ttl
  example: ConductionRole
  github_request_issue: 1772
  homepage: http://sweetontology.net/stateRole/
  keywords:
  - state role
  license: CC0-1.0
  name: SWEET Ontology State Role
  part_of: sweet
  prefix: sweet.stro
  repository: https://github.com/ESIPFed/sweet
  synonyms:
  - sostro
  uri_format: http://sweetontology.net/stateRole/$1
sweet.strr:
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: The Semantic Web for Earth and Environmental Terminology (SWEET) ontology
    for State Role Representative
  download_rdf: https://github.com/ESIPFed/sweet/raw/refs/heads/master/src/stateRoleRepresentative.ttl
  example: RepresentativeRole
  github_request_issue: 1772
  homepage: http://sweetontology.net/stateRoleRepresentative/
  keywords:
  - state role representative
  license: CC0-1.0
  name: SWEET Ontology State Role Representative
  part_of: sweet
  prefix: sweet.strr
  repository: https://github.com/ESIPFed/sweet
  synonyms:
  - sostrr
  uri_format: http://sweetontology.net/stateRoleRepresentative/$1
sweet.strt:
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: The Semantic Web for Earth and Environmental Terminology (SWEET) ontology
    for State Role Trust
  download_rdf: https://github.com/ESIPFed/sweet/raw/refs/heads/master/src/stateRoleTrust.ttl
  example: Accurate
  github_request_issue: 1772
  homepage: http://sweetontology.net/stateRoleTrust/
  keywords:
  - state role trust
  license: CC0-1.0
  name: SWEET Ontology State Role Trust
  part_of: sweet
  prefix: sweet.strt
  repository: https://github.com/ESIPFed/sweet
  synonyms:
  - sostrt
  uri_format: http://sweetontology.net/stateRoleTrust/$1
sweet.stsb:
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: The Semantic Web for Earth and Environmental Terminology (SWEET) ontology
    for State Spectral Band
  download_rdf: https://github.com/ESIPFed/sweet/raw/refs/heads/master/src/stateSpectralBand.ttl
  example: BandLimited
  github_request_issue: 1772
  homepage: http://sweetontology.net/stateSpectralBand/
  keywords:
  - state spectral band
  license: CC0-1.0
  name: SWEET Ontology State Spectral Band
  part_of: sweet
  prefix: sweet.stsb
  repository: https://github.com/ESIPFed/sweet
  synonyms:
  - sostsb
  uri_format: http://sweetontology.net/stateSpectralBand/$1
sweet.stsc:
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: The Semantic Web for Earth and Environmental Terminology (SWEET) ontology
    for State Space Configuration
  download_rdf: https://github.com/ESIPFed/sweet/raw/refs/heads/master/src/stateSpaceConfiguration.ttl
  example: Antumbra
  github_request_issue: 1772
  homepage: http://sweetontology.net/stateSpaceConfiguration/
  keywords:
  - state space configuration
  license: CC0-1.0
  name: SWEET Ontology State Space Configuration
  part_of: sweet
  prefix: sweet.stsc
  repository: https://github.com/ESIPFed/sweet
  synonyms:
  - sostsc
  uri_format: http://sweetontology.net/stateSpaceConfiguration/$1
sweet.stsl:
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: The Semantic Web for Earth and Environmental Terminology (SWEET) ontology
    for State Spectral Line
  download_rdf: https://github.com/ESIPFed/sweet/raw/refs/heads/master/src/stateSpectralLine.ttl
  example: CaK
  github_request_issue: 1772
  homepage: http://sweetontology.net/stateSpectralLine/
  keywords:
  - state spectral line
  license: CC0-1.0
  name: SWEET Ontology State Spectral Line
  part_of: sweet
  prefix: sweet.stsl
  repository: https://github.com/ESIPFed/sweet
  synonyms:
  - sostsl
  uri_format: http://sweetontology.net/stateSpectralLine/$1
sweet.stso:
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: The Semantic Web for Earth and Environmental Terminology (SWEET) ontology
    for State Solid
  download_rdf: https://github.com/ESIPFed/sweet/raw/refs/heads/master/src/stateSolid.ttl
  example: SolidState
  github_request_issue: 1772
  homepage: http://sweetontology.net/stateSolid/
  keywords:
  - state solid
  license: CC0-1.0
  name: SWEET Ontology State Solid
  part_of: sweet
  prefix: sweet.stso
  repository: https://github.com/ESIPFed/sweet
  synonyms:
  - sostso
  uri_format: http://sweetontology.net/stateSolid/$1
sweet.stsp:
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: The Semantic Web for Earth and Environmental Terminology (SWEET) ontology
    for State Space
  download_rdf: https://github.com/ESIPFed/sweet/raw/refs/heads/master/src/stateSpace.ttl
  example: Big
  github_request_issue: 1772
  homepage: http://sweetontology.net/stateSpace/
  keywords:
  - state space
  license: CC0-1.0
  name: SWEET Ontology State Space
  part_of: sweet
  prefix: sweet.stsp
  repository: https://github.com/ESIPFed/sweet
  synonyms:
  - sostsp
  uri_format: http://sweetontology.net/stateSpace/$1
sweet.stss:
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: The Semantic Web for Earth and Environmental Terminology (SWEET) ontology
    for State Space Scale
  download_rdf: https://github.com/ESIPFed/sweet/raw/refs/heads/master/src/stateSpaceScale.ttl
  example: Continental
  github_request_issue: 1772
  homepage: http://sweetontology.net/stateSpaceScale/
  keywords:
  - state space scale
  license: CC0-1.0
  name: SWEET Ontology State Space Scale
  part_of: sweet
  prefix: sweet.stss
  repository: https://github.com/ESIPFed/sweet
  synonyms:
  - sostss
  uri_format: http://sweetontology.net/stateSpaceScale/$1
sweet.stst:
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: The Semantic Web for Earth and Environmental Terminology (SWEET) ontology
    for State Storm
  download_rdf: https://github.com/ESIPFed/sweet/raw/refs/heads/master/src/stateStorm.ttl
  example: BeaufortScale
  github_request_issue: 1772
  homepage: http://sweetontology.net/stateStorm/
  keywords:
  - state storm
  license: CC0-1.0
  name: SWEET Ontology State Storm
  part_of: sweet
  prefix: sweet.stst
  repository: https://github.com/ESIPFed/sweet
  synonyms:
  - sostst
  uri_format: http://sweetontology.net/stateStorm/$1
sweet.stsy:
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: The Semantic Web for Earth and Environmental Terminology (SWEET) ontology
    for State System
  download_rdf: https://github.com/ESIPFed/sweet/raw/refs/heads/master/src/stateSystem.ttl
  example: Coherent
  github_request_issue: 1772
  homepage: http://sweetontology.net/stateSystem/
  keywords:
  - state system
  license: CC0-1.0
  name: SWEET Ontology State System
  part_of: sweet
  prefix: sweet.stsy
  repository: https://github.com/ESIPFed/sweet
  synonyms:
  - sostsy
  uri_format: http://sweetontology.net/stateSystem/$1
sweet.sttc:
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: The Semantic Web for Earth and Environmental Terminology (SWEET) ontology
    for State Time Cycle
  download_rdf: https://github.com/ESIPFed/sweet/raw/refs/heads/master/src/stateTimeCycle.ttl
  example: ElNino
  github_request_issue: 1772
  homepage: http://sweetontology.net/stateTimeCycle/
  keywords:
  - state time cycle
  license: CC0-1.0
  name: SWEET Ontology State Time Cycle
  part_of: sweet
  prefix: sweet.sttc
  repository: https://github.com/ESIPFed/sweet
  synonyms:
  - sosttc
  uri_format: http://sweetontology.net/stateTimeCycle/$1
sweet.sttf:
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: The Semantic Web for Earth and Environmental Terminology (SWEET) ontology
    for State Time Frequency
  download_rdf: https://github.com/ESIPFed/sweet/raw/refs/heads/master/src/stateTimeFrequency.ttl
  example: Annual
  github_request_issue: 1772
  homepage: http://sweetontology.net/stateTimeFrequency/
  keywords:
  - state time frequency
  license: CC0-1.0
  name: SWEET Ontology State Time Frequency
  part_of: sweet
  prefix: sweet.sttf
  repository: https://github.com/ESIPFed/sweet
  synonyms:
  - sosttf
  uri_format: http://sweetontology.net/stateTimeFrequency/$1
sweet.sttg:
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: The Semantic Web for Earth and Environmental Terminology (SWEET) ontology
    for State Time Geologic
  download_rdf: https://github.com/ESIPFed/sweet/raw/refs/heads/master/src/stateTimeGeologic.ttl
  example: 0MYA
  github_request_issue: 1772
  homepage: http://sweetontology.net/stateTimeGeologic/
  keywords:
  - state time geologic
  license: CC0-1.0
  name: SWEET Ontology State Time Geologic
  part_of: sweet
  prefix: sweet.sttg
  repository: https://github.com/ESIPFed/sweet
  synonyms:
  - sosttg
  uri_format: http://sweetontology.net/stateTimeGeologic/$1
sweet.stth:
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: The Semantic Web for Earth and Environmental Terminology (SWEET) ontology
    for State Thermodynamic
  download_rdf: https://github.com/ESIPFed/sweet/raw/refs/heads/master/src/stateThermodynamic.ttl
  example: ThermodynamicState
  github_request_issue: 1772
  homepage: http://sweetontology.net/stateThermodynamic/
  keywords:
  - state thermodynamic
  license: CC0-1.0
  name: SWEET Ontology State Thermodynamic
  part_of: sweet
  prefix: sweet.stth
  repository: https://github.com/ESIPFed/sweet
  synonyms:
  - sostth
  uri_format: http://sweetontology.net/stateThermodynamic/$1
sweet.stti:
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: The Semantic Web for Earth and Environmental Terminology (SWEET) ontology
    for State Time
  download_rdf: https://github.com/ESIPFed/sweet/raw/refs/heads/master/src/stateTime.ttl
  example: Age
  github_request_issue: 1772
  homepage: http://sweetontology.net/stateTime/
  keywords:
  - state time
  license: CC0-1.0
  name: SWEET Ontology State Time
  part_of: sweet
  prefix: sweet.stti
  repository: https://github.com/ESIPFed/sweet
  synonyms:
  - sostti
  uri_format: http://sweetontology.net/stateTime/$1
sweet.stv:
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: The Semantic Web for Earth and Environmental Terminology (SWEET) ontology
    for State Visibility
  download_rdf: https://github.com/ESIPFed/sweet/raw/refs/heads/master/src/stateVisibility.ttl
  example: Clear
  github_request_issue: 1772
  homepage: http://sweetontology.net/stateVisibility/
  keywords:
  - state visibility
  license: CC0-1.0
  name: SWEET Ontology State Visibility
  part_of: sweet
  prefix: sweet.stv
  repository: https://github.com/ESIPFed/sweet
  synonyms:
  - sostv
  uri_format: http://sweetontology.net/stateVisibility/$1
swh:
  banana: swh
  biocontext:
    prefix: SWH
  mappings:
    biocontext: SWH
    miriam: swh
    n2t: swh
  miriam:
    deprecated: false
    description: Software Heritage is the universal archive of software source code.
    homepage: https://archive.softwareheritage.org
    id: '00000655'
    name: Software Heritage
    namespaceEmbeddedInLui: true
    pattern: ^swh:[1-9]:(cnt|dir|rel|rev|snp):[0-9a-f]+(;(origin|visit|anchor|path|lines)=\S+)*$
    prefix: swh
    sampleId: 1:rev:309cf2674ee7a0749978cf8265ab91a60aea0f7d
    uri_format: https://archive.softwareheritage.org/browse/swh:$1
  n2t:
    description: Software Heritage is the universal archive of software source code.
    example: 1:rev:309cf2674ee7a0749978cf8265ab91a60aea0f7d
    homepage: https://archive.softwareheritage.org
    name: Software Heritage
    namespaceEmbeddedInLui: true
    pattern: ^swh:[1-9]:[a-z][a-z][a-z]:[a-f0-9]+$
    prefix: swh
    uri_format: https://archive.softwareheritage.org/browse/swh:$1
  pattern: ^[1-9]:(cnt|dir|rel|rev|snp):[0-9a-f]+(;(origin|visit|anchor|path|lines)=\S+)*$
  prefix: swh
swiss-model:
  biocontext:
    prefix: SWISS-MODEL
  contact:
    email: torsten.schwede@unibas.ch
    github: null
    name: Torsten Schwede
    orcid: 0000-0003-2715-335X
  contact_group_email: help-swissmodel@unibas.ch
  fairsharing:
    abbreviation: SWISS-MODEL
    contact:
      email: help-swissmodel@unibas.ch
      name: Torsten Schwede
      orcid: 0000-0003-2715-335X
    description: The SWISS-MODEL Repository is a database of annotated 3D protein
      structure models generated by the SWISS-MODEL homology-modelling pipeline for
      protein sequences of selected model organisms.
    homepage: https://swissmodel.expasy.org/repository/
    license: CC BY-SA 4.0
    name: SWISS-MODEL Repository of 3D protein structure models
    prefix: FAIRsharing.vxz9pn
    publications:
    - doi: 10.1093/nar/gkn750
      pubmed_id: 18931379
      title: The SWISS-MODEL Repository and associated resources.
    - doi: 10.1093/nar/gku340
      pubmed_id: 24782522
      title: 'SWISS-MODEL: modelling protein tertiary and quaternary structure using
        evolutionary information.'
    - doi: 10.1093/nar/gkw1132
      pubmed_id: 27899672
      title: The SWISS-MODEL Repository-new features and functionality.
    subjects:
    - Proteomics
    - Life Science
    twitter: SWISS_MODEL
  mappings:
    biocontext: SWISS-MODEL
    fairsharing: FAIRsharing.vxz9pn
    miriam: swiss-model
    n2t: swiss-model
    prefixcommons: swissmodel
    re3data: r3d100010605
  miriam:
    deprecated: false
    description: The SWISS-MODEL Repository is a database of 3D protein structure
      models generated by the SWISS-MODEL homology-modelling pipeline for UniProtKB
      protein sequences.
    homepage: https://swissmodel.expasy.org
    id: '00000231'
    name: SWISS-MODEL Repository
    namespaceEmbeddedInLui: false
    pattern: ^\w+$
    prefix: swiss-model
    sampleId: P23298
    uri_format: https://swissmodel.expasy.org/repository/uniprot/$1
  n2t:
    description: The SWISS-MODEL Repository is a database of 3D protein structure
      models generated by the SWISS-MODEL homology-modelling pipeline for UniProtKB
      protein sequences.
    example: P23298
    homepage: https://swissmodel.expasy.org
    name: SWISS-MODEL at SIB Swiss Institute of Bioinformatics
    namespaceEmbeddedInLui: false
    pattern: ^\w+$
    prefix: swiss-model
    uri_format: https://swissmodel.expasy.org/repository/uniprot/$1
  prefix: swiss-model
  prefixcommons:
    description: The SWISS-MODEL Repository is a database of 3D protein structure
      models generated by the SWISS-MODEL homology-modelling pipeline for sequences
      registered is SWISS-PROT.
    example: P23298
    homepage: http://swissmodel.expasy.org/
    keywords:
    - protein
    - structure
    name: SWISS-MODEL repository of 3D protein structure models
    pattern: ^\w+$
    prefix: swissmodel
    pubmed_ids:
    - '18931379'
    uri_format: http://swissmodel.expasy.org/repository/smr.php?sptr_ac=$1
  provides: uniprot
  publications:
  - doi: 10.1093/nar/gkw1132
    pmc: PMC5210589
    pubmed: '27899672'
    title: The SWISS-MODEL Repository-new features and functionality
    year: 2016
  - doi: 10.1093/nar/gku340
    pmc: PMC4086089
    pubmed: '24782522'
    title: 'SWISS-MODEL: modelling protein tertiary and quaternary structure using
      evolutionary information'
    year: 2014
  - doi: 10.1093/nar/gkn750
    pmc: PMC2686475
    pubmed: '18931379'
    title: The SWISS-MODEL Repository and associated resources
    year: 2008
  - doi: 10.1093/nar/gkn750
    pmc: null
    pubmed: null
    title: The SWISS-MODEL Repository and associated resources.
    year: null
  - doi: 10.1093/nar/gku340
    pmc: null
    pubmed: null
    title: 'SWISS-MODEL: modelling protein tertiary and quaternary structure using
      evolutionary information.'
    year: null
  - doi: 10.1093/nar/gkw1132
    pmc: null
    pubmed: null
    title: The SWISS-MODEL Repository-new features and functionality.
    year: null
  - doi: null
    pmc: null
    pubmed: '18931379'
    title: null
    year: null
  re3data:
    description: The SWISS-MODEL Repository is a database of annotated three-dimensional
      comparative protein structure models generated by the fully automated homology-modelling
      pipeline SWISS-MODEL.
    doi: 10.17616/R3R311
    homepage: https://swissmodel.expasy.org/repository/
    license: Copyrights
    name: SWISS-MODEL Repository
    prefix: r3d100010605
    synonyms:
    - SMR
    xrefs:
      nif: 0000-03522
swissregulon:
  biocontext:
    prefix: SWISSREGULON
  fairsharing:
    abbreviation: SwissRegulon
    contact:
      email: erik.vannimwegen@unibas.ch
      name: Erik van Nimwegen
      orcid: 0000-0001-6338-1312
    description: The Swissregulon Database contains genome-wide annotations of regulatory
      sites. The predictions are based on Bayesian probabilistic analysis of a combination
      of input information including i) Experimentally determined binding sites reported
      in the literature, ii) Known sequence-specificities of transcription factors,
      iii) ChIP-chip and ChIP-seq data, iiii) Alignments of orthologous non-coding
      regions.
    homepage: http://swissregulon.unibas.ch/sr/
    name: SwissRegulon
    prefix: FAIRsharing.7fnx38
    publications:
    - doi: 10.1093/nar/gkl857
      pubmed_id: 17130146
      title: 'SwissRegulon: a database of genome-wide annotations of regulatory sites.'
    - doi: 10.1093/nar/gks1145
      pubmed_id: 23180783
      title: 'SwissRegulon, a database of genome-wide annotations of regulatory sites:
        recent updates.'
    subjects:
    - Life Science
  integbio:
    description: The Swissregulon Database contains genome-wide annotations of regulatory
      sites. The predictions are based on Bayesian probabilistic analysis of a combination
      of input information including i) Experimentally determined binding sites reported
      in the literature, ii) Known sequence-specificities of transcription factors,
      iii) ChIP-chip and ChIP-seq data, iiii) Alignments of orthologous non-coding
      regions.
    fairsharing: biodbcore-000879
    homepage: http://swissregulon.unibas.ch/sr/
    information_keywords:
    - Sequence
    - Expression
    - Interaction/Pathway
    maintainer: SIB (Swiss Institute of Bioinformatics)
    name: SwissRegulon
    prefix: nbdc02225
    pubmeds:
    - '17130146'
    - '23180783'
    status: Active
    target_keywords:
    - Genome/Gene
    - Epigenetics
  mappings:
    biocontext: SWISSREGULON
    fairsharing: FAIRsharing.7fnx38
    integbio: nbdc02225
    miriam: swissregulon
    n2t: swissregulon
  miriam:
    deprecated: false
    description: A database of genome-wide annotations of regulatory sites. It contains
      annotations for 17 prokaryotes and 3 eukaryotes. The database frontend offers
      an intuitive interface showing genomic information in a graphical form.
    homepage: http://swissregulon.unibas.ch
    id: '00000632'
    name: SwissRegulon
    namespaceEmbeddedInLui: false
    pattern: ^[A-Za-z0-9]+$
    prefix: swissregulon
    sampleId: AHR
    uri_format: http://swissregulon.unibas.ch/query/$1
  n2t:
    description: A database of genome-wide annotations of regulatory sites. It contains
      annotations for 17 prokaryotes and 3 eukaryotes. The database frontend offers
      an intuitive interface showing genomic information in a graphical form.
    example: AHR
    homepage: http://swissregulon.unibas.ch
    name: SwissRegulon
    namespaceEmbeddedInLui: false
    pattern: ^[A-Za-z0-9]+$
    prefix: swissregulon
    uri_format: http://swissregulon.unibas.ch/query/$1
  prefix: swissregulon
  publications:
  - doi: 10.1093/nar/gks1145
    pmc: PMC3531101
    pubmed: '23180783'
    title: 'SwissRegulon, a database of genome-wide annotations of regulatory sites:
      recent updates'
    year: 2012
  - doi: 10.1093/nar/gkl857
    pmc: PMC1716717
    pubmed: '17130146'
    title: 'SwissRegulon: a database of genome-wide annotations of regulatory sites'
    year: 2006
  - doi: 10.1093/nar/gkl857
    pmc: null
    pubmed: null
    title: 'SwissRegulon: a database of genome-wide annotations of regulatory sites.'
    year: null
  - doi: 10.1093/nar/gks1145
    pmc: null
    pubmed: null
    title: 'SwissRegulon, a database of genome-wide annotations of regulatory sites:
      recent updates.'
    year: null
  - doi: 10.1093/nar/gkl857
    pmc: null
    pubmed: null
    title: 'SwissRegulon: a database of genome-wide annotations of regulatory sites.'
    year: null
  - doi: 10.1093/nar/gks1145
    pmc: null
    pubmed: null
    title: 'SwissRegulon, a database of genome-wide annotations of regulatory sites:
      recent updates.'
    year: null
  - doi: 10.1093/nar/gkl857
    pmc: null
    pubmed: null
    title: 'SwissRegulon: a database of genome-wide annotations of regulatory sites.'
    year: null
  - doi: 10.1093/nar/gks1145
    pmc: null
    pubmed: null
    title: 'SwissRegulon, a database of genome-wide annotations of regulatory sites:
      recent updates.'
    year: null
swo:
  aberowl:
    description: The Software Ontology (SWO) is a resource for describing software
      tools, their types, tasks, versions, provenance and associated data. It contains
      detailed information on licensing and formats as well as software applications
      themselves, mainly (but not limited) to the bioinformatics community.
    download_owl: http://aber-owl.net/media/ontologies/SWO/32/swo.owl
    homepage: https://github.com/allysonlister/swo
    name: Software ontology
    prefix: SWO
  biocontext:
    prefix: SWO
  bioportal:
    contact:
      email: james@scibite.com
      name: James Malone
    description: The Software Ontology (SWO) describes software used in research,
      primarily Bioinformatics. The SWO covers areas such as the software type, licence,
      manufacturer of the software, the input and output data types and the uses (i.e.
      objectives) to which the software can be put.
    homepage: https://github.com/allysonlister/swo
    name: Software Ontology
    prefix: SWO
    publications:
    - https://doi.org/10.1186/2041-1480-5-25
    version: '2023-03-05'
  contact:
    email: allyson.lister@oerc.ox.ac.uk
    github: allysonlister
    name: Allyson Lister
    orcid: 0000-0002-7702-4495
  download_json: https://raw.githubusercontent.com/allysonlister/swo/master/swo.json
  download_owl: https://raw.githubusercontent.com/allysonlister/swo/master/swo.owl
  example: '0000144'
  fairsharing:
    abbreviation: SWO
    contact:
      email: allyson.lister@oerc.ox.ac.uk
      name: Allyson Lister
      orcid: 0000-0002-7702-4495
    description: The Software Ontology (SWO) is a resource for describing software
      tools, their types, tasks, versions, provenance and associated data. SWO also
      covers software manufacturer, input and output data types and the uses (i.e.
      objectives) to which the software can be put.
    domains:
    - algorithm
    homepage: https://github.com/allysonlister/swo
    license: CC-BY-4.0
    name: SoftWare Ontology
    prefix: FAIRsharing.sp3szt
    publications:
    - doi: 10.1186/2041-1480-5-25
      pubmed: '25068035'
      title: 'The Software Ontology (SWO): a resource for reproducibility in biomedical
        data analysis, curation and digital preservation'
      year: 2014
    repository: https://github.com/allysonlister/swo/issues
    subjects:
    - Computer Science
    - Bioinformatics
  keywords:
  - license
  mappings:
    aberowl: SWO
    biocontext: SWO
    bioportal: SWO
    fairsharing: FAIRsharing.sp3szt
    obofoundry: swo
    ols: swo
    ontobee: SWO
    prefixcommons: swo
    tib: swo
    wikidata.entity: Q113014439
  obofoundry:
    appears_in:
    - mcro
    contact: allyson.lister@oerc.ox.ac.uk
    contact.github: allysonlister
    contact.label: Allyson Lister
    contact.orcid: 0000-0002-7702-4495
    deprecated: false
    description: The Software Ontology (SWO) is a resource for describing software
      tools, their types, tasks, versions, provenance and associated data. It contains
      detailed information on licensing and formats as well as software applications
      themselves, mainly (but not limited) to the bioinformatics community.
    domain: information technology
    download.json: http://purl.obolibrary.org/obo/swo.json
    download.owl: http://purl.obolibrary.org/obo/swo.owl
    homepage: https://github.com/allysonlister/swo
    license: CC BY 4.0
    license.url: https://creativecommons.org/licenses/by/4.0/
    name: Software ontology
    preferredPrefix: SWO
    prefix: swo
    publications:
    - id: https://www.ncbi.nlm.nih.gov/pubmed/25068035
      title: 'The Software Ontology (SWO): a resource for reproducibility in biomedical
        data analysis, curation and digital preservation'
    repository: https://github.com/allysonlister/swo
  ols:
    description: The Software Ontology (SWO) is a resource for describing software
      tools, their types, tasks, versions, provenance and associated data. It contains
      detailed information on licensing and formats as well as software applications
      themselves, mainly (but not limited) to the bioinformatics community.
    download_owl: http://purl.obolibrary.org/obo/swo.owl
    homepage: https://github.com/allysonlister/swo
    name: Software ontology
    prefix: swo
    tracker: https://github.com/allysonlister/swo/issues
    version: '2023-03-05'
    version.iri: http://www.ebi.ac.uk/swo/swo/releases/2023-03-05/swo.owl
  ontobee:
    library: Library
    name: Software ontology
    prefix: SWO
  pattern: ^\d{7,8}$
  prefix: swo
  prefixcommons:
    bioportal: '1413'
    description: 'The Software Ontology (SWO) has the scope of describing types of
      software used in Bioinformatics. The SWO covers areas such as the software type,
      the manufacturer of the software, the input and output data types and the uses
      (i.e. objectives) the software can be put to. The SWO intends to use BFO as
      an upper level ontolgoy and subclasses types from the Ontology of Biomedical
      Investigations. Contact James Malone for info: malone@ebi.ac.uk'
    example: SWO_0000396
    homepage: http://theswo.sourceforge.net
    name: Software Ontology
    pattern: ^SWO_\d{7}$
    prefix: swo
    rdf_uri_format: http://www.ebi.ac.uk/efo/swo/$1
  providers:
  - code: ebi
    description: The EBI's old SWO URIs before switching over to OBO PURLs
    example: null
    first_party: null
    homepage: http://www.ebi.ac.uk/swo/license
    name: Legacy EBI SWO
    publications: null
    status: null
    uri_format: http://www.ebi.ac.uk/swo/SWO_$1
  - code: ebi.efo
    description: The EBI's old SWO URIs before switching over to OBO PURLs
    example: null
    first_party: null
    homepage: http://www.ebi.ac.uk/efo/swo/
    name: Legacy EBI SWO
    publications: null
    status: null
    uri_format: http://www.ebi.ac.uk/efo/swo/SWO_$1
  - code: ebi.license
    description: The EBI's old SWO URIs before switching over to OBO PURLs
    example: null
    first_party: null
    homepage: http://www.ebi.ac.uk/swo/license
    name: Legacy EBI SWO
    publications: null
    status: null
    uri_format: http://www.ebi.ac.uk/swo/license/SWO_$1
  - code: ebi.objective
    description: The EBI's old SWO URIs before switching over to OBO PURLs
    example: null
    first_party: null
    homepage: http://www.ebi.ac.uk/swo/objective
    name: Legacy EBI SWO
    publications: null
    status: null
    uri_format: http://www.ebi.ac.uk/swo/objective/SWO_$1
  - code: ebi.version
    description: The EBI's old SWO URIs before switching over to OBO PURLs
    example: null
    first_party: null
    homepage: http://www.ebi.ac.uk/swo/version
    name: Legacy EBI SWO
    publications: null
    status: null
    uri_format: http://www.ebi.ac.uk/swo/version/SWO_$1
  - code: ebi.algorithm
    description: The EBI's old SWO URIs before switching over to OBO PURLs
    example: null
    first_party: null
    homepage: http://www.ebi.ac.uk/swo/algorithm
    name: Legacy EBI SWO
    publications: null
    status: null
    uri_format: http://www.ebi.ac.uk/swo/algorithm/SWO_$1
  - code: ebi.organization
    description: The EBI's old SWO URIs before switching over to OBO PURLs
    example: null
    first_party: null
    homepage: http://www.ebi.ac.uk/swo/organization
    name: Legacy EBI SWO
    publications: null
    status: null
    uri_format: http://www.ebi.ac.uk/swo/organization/SWO_$1
  - code: ebi.interface
    description: The EBI's old SWO URIs before switching over to OBO PURLs
    example: null
    first_party: null
    homepage: http://www.ebi.ac.uk/swo/interface
    name: Legacy EBI SWO
    publications: null
    status: null
    uri_format: http://www.ebi.ac.uk/swo/interface/SWO_$1
  - code: ebi.data
    description: The EBI's old SWO URIs before switching over to OBO PURLs
    example: null
    first_party: null
    homepage: http://www.ebi.ac.uk/swo/data
    name: Legacy EBI SWO
    publications: null
    status: null
    uri_format: http://www.ebi.ac.uk/swo/data/SWO_$1
  - code: ebi.maturity
    description: The EBI's old SWO URIs before switching over to OBO PURLs
    example: null
    first_party: null
    homepage: http://www.ebi.ac.uk/swo/maturity
    name: Legacy EBI SWO
    publications: null
    status: null
    uri_format: http://www.ebi.ac.uk/swo/maturity/SWO_$1
  publications:
  - doi: 10.1186/2041-1480-5-25
    pmc: PMC4098953
    pubmed: '25068035'
    title: 'The Software Ontology (SWO): a resource for reproducibility in biomedical
      data analysis, curation and digital preservation'
    year: 2014
  - doi: null
    pmc: null
    pubmed: '25068035'
    title: 'The Software Ontology (SWO): a resource for reproducibility in biomedical
      data analysis, curation and digital preservation'
    year: null
  - doi: 10.1186/2041-1480-5-25
    pmc: null
    pubmed: '25068035'
    title: 'The Software Ontology (SWO): a resource for reproducibility in biomedical
      data analysis, curation and digital preservation'
    year: 2014
  tib:
    description: The Software Ontology (SWO) is a resource for describing software
      tools, their types, tasks, versions, licenses, provenance and associated data.
    download_owl: http://purl.obolibrary.org/obo/swo.owl
    homepage: https://github.com/allysonlister/swo
    keywords:
    - NFDI4ING
    - NFDI4CHEM
    - DataPLANT
    - computer science
    name: The Software Ontology (SWO)
    prefix: swo
    tracker: https://github.com/allysonlister/swo/issues
    version.iri: http://www.ebi.ac.uk/swo/swo/releases/2023-03-05/swo.owl
swrl:
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: SWRL enables Horn-like rules to be combined with an OWL knowledge base.
  example: Variable
  homepage: https://www.w3.org/2003/11/swrl#
  lov:
    description: OWL definition of the RDF Concrete Syntax for the Semantic Web Rule
      Language
    homepage: http://www.w3.org/2003/11/swrl
    keywords:
    - Vocabularies
    modified: '2004-05-21'
    name: Semantic Web Rule Language
    prefix: swrl
    uri_prefix: http://www.w3.org/2003/11/swrl#$1
  mappings:
    lov: swrl
  name: A Semantic Web Rule Language Combining OWL and RuleML
  preferred_prefix: swrl
  prefix: swrl
  uri_format: http://www.w3.org/2003/11/swrl#$1
symp:
  aberowl:
    description: An ontology of disease symptoms, with symptoms encompasing perceived
      changes in function, sensations or appearance reported by a patient indicative
      of a disease.
    download_owl: http://aber-owl.net/media/ontologies/SYMP/42/symp.owl
    homepage: http://symptomontologywiki.igs.umaryland.edu/mediawiki/index.php/Main_Page
    name: Symptom Ontology
    prefix: SYMP
  biocontext:
    prefix: SYMP
  bioportal:
    contact:
      email: lynn.schriml@gmail.com
      name: Lynn Schriml
    description: 'The symptom ontology was designed around the guiding concept of
      a symptom being: "A perceived change in function, sensation or appearance reported
      by a patient indicative of a disease". Understanding the close relationship
      of Signs and Symptoms, where Signs are the objective observation of an illness,
      the Symptom Ontology will work to broaden it''s scope to capture and document
      in a more robust manor these two sets of terms. Understanding that at times,
      the same term may be both a Sign and a Symptom'
    homepage: https://disease-ontology.org
    name: Symptom Ontology
    prefix: SYMP
    version: '2024-05-17'
  download_json: http://purl.obolibrary.org/obo/symp.json
  example: 0019171
  fairsharing:
    abbreviation: SYMP
    contact:
      email: lynn.schriml@gmail.com
      name: Lynn Schriml
      orcid: 0000-0001-8910-9851
    description: 'The symptom ontology was designed around the guiding concept of
      a symptom being: "A perceived change in function, sensation or appearance reported
      by a patient indicative of a disease". There is a close relationship between
      Signs and Symptoms, where Signs are the objective observation of an illness.
      The Symptom Ontology will work to broaden its scope to capture and document
      in a more robust manor these two sets of terms. At times, the same term may
      be both a Sign and a Symptom.'
    domains:
    - Patient Care
    - disease
    - diagnosis
    homepage: https://disease-ontology.org/resources/symptom-ontology
    license: CC0-1.0
    name: Symptom Ontology
    prefix: FAIRsharing.ay74mj
    publications:
    - doi: 10.1093/nar/gkp832
      pubmed: '19850722'
      title: GeMInA, Genomic Metadata for Infectious Agents, a geospatial surveillance
        pathogen database
      year: 2010
    - doi: 10.1093/nar/gkad1051
      pubmed: '37953304'
      title: 'The DO-KB Knowledgebase: a 20-year journey developing the disease open
        science ecosystem'
      year: 2023
    repository: https://github.com/DiseaseOntology/SymptomOntology/issues
    subjects:
    - Life Science
    - Pain Medicine
    - Biomedical Science
  mappings:
    aberowl: SYMP
    biocontext: SYMP
    bioportal: SYMP
    fairsharing: FAIRsharing.ay74mj
    obofoundry: symp
    ols: symp
    ontobee: SYMP
    prefixcommons: symptom
    wikidata: P8656
    wikidata.entity: Q81661810
  obofoundry:
    appears_in:
    - scdo
    contact: lynn.schriml@gmail.com
    contact.github: lschriml
    contact.label: Lynn Schriml
    contact.orcid: 0000-0001-8910-9851
    deprecated: false
    description: An ontology of disease symptoms, with symptoms encompasing perceived
      changes in function, sensations or appearance reported by a patient indicative
      of a disease.
    domain: health
    download.obo: http://purl.obolibrary.org/obo/symp.obo
    download.owl: http://purl.obolibrary.org/obo/symp.owl
    homepage: https://github.com/DiseaseOntology/SymptomOntology
    license: CC0 1.0
    license.url: https://creativecommons.org/publicdomain/zero/1.0/
    name: Symptom Ontology
    preferredPrefix: SYMP
    prefix: symp
    publications:
    - id: https://www.ncbi.nlm.nih.gov/pubmed/19850722
      title: GeMInA, Genomic Metadata for Infectious Agents, a geospatial surveillance
        pathogen database
    - id: https://www.ncbi.nlm.nih.gov/pubmed/34755882
      title: The Human Disease Ontology 2022 update
    repository: https://github.com/DiseaseOntology/SymptomOntology
  ols:
    description: The Symptom Ontology has been developed as a standardized ontology
      for symptoms of human diseases.
    download_owl: http://purl.obolibrary.org/obo/symp.owl
    homepage: https://github.com/DiseaseOntology/SymptomOntology
    name: Symptom Ontology
    prefix: symp
    tracker: https://github.com/DiseaseOntology/SymptomOntology/issues
    version: '2024-05-17'
    version.iri: http://purl.obolibrary.org/obo/symp/releases/2024-05-17/symp.owl
  ontobee:
    library: Library
    name: Symptom Ontology
    prefix: SYMP
  pattern: ^\d{7}$
  prefix: symp
  prefixcommons:
    bioportal: '1224'
    description: 'The symptom ontology was designed around the guiding concept of
      a symptom being: "A perceived change in function, sensation or appearance reported
      by a patient indicative of a disease"'
    example: SYMP_0000461
    homepage: http://symptomontologywiki.igs.umaryland.edu/wiki/index.php/Main_Page
    keywords:
    - obo
    - ontology
    name: Symptom Ontology
    pattern: ^SYMP_\d{7}$
    prefix: symptom
    synonyms:
    - symptomontology
    - symp
  publications:
  - doi: 10.1093/nar/gkab1063
    pmc: PMC8728220
    pubmed: '34755882'
    title: The Human Disease Ontology 2022 update
    year: 2022
  - doi: 10.1093/nar/gkp832
    pmc: PMC2808878
    pubmed: '19850722'
    title: GeMInA, Genomic Metadata for Infectious Agents, a geospatial surveillance
      pathogen database
    year: 2009
  synonyms:
  - SYMP
  uri_format: http://purl.obolibrary.org/obo/SYMP_$1
  wikidata:
    database: Q81661810
    description: identifier in the Symptom Ontology
    example:
    - '0000007'
    - 0000099
    homepage: https://github.com/DiseaseOntology/SymptomOntology
    name: Symptom Ontology ID
    prefix: P8656
    uri_format: https://www.ebi.ac.uk/ols/ontologies/symp/terms?iri=http://purl.obolibrary.org/obo/SYMP_$1
synapse:
  contact:
    email: kevin.boske@sagebase.org
    github: kevinboske
    name: Kevin Boske
    orcid: 0000-0002-3278-5207
  integbio:
    description: Synapse is a collaborative research platform that allows individuals
      and teams to share, track, and discuss their data and analysis in projects.
      Synapse allows researchers to share and describe data, analyses, and other content.
      Data and analyses can be stored in many types of locations, including private
      servers, local hard drives, or cloud storage. Synapse provides a common interface
      to describe these data or analyses, where they come from, and how to use them.
      Synapse also provides mechanisms for adding and retrieving data, analyses, and
      their respective descriptions.
    fairsharing: FAIRsharing.dnxzmk
    homepage: https://www.synapse.org/
    information_keywords:
    - Method
    - Bibliography/Documents
    - Repository
    maintainer: Sage Bionetworks
    name: Synapse
    prefix: nbdc02162
    pubmeds:
    - '24071850'
    status: Active
  mappings:
    integbio: nbdc02162
    miriam: synapse
    re3data: r3d100011894
    wikidata.entity: Q56328412
  miriam:
    deprecated: false
    description: Synapse is a collaborative, open-source research platform that allows
      teams to share data, track analyses, and collaborate.
    homepage: https://sagebionetworks.org
    id: '00001043'
    name: Synapse Data Repository
    namespaceEmbeddedInLui: false
    pattern: ^[0-9]*\.*[0-9]*$
    prefix: synapse
    sampleId: '41455251.1'
    uri_format: https://repo-prod.prod.sagebase.org/ga4gh/drs/v1/objects/syn$1
  prefix: synapse
  re3data:
    description: Synapse is an open source software platform that clinical and biological  data
      scientists can use to carry out, track, and communicate their research in real
      time. Synapse enables co-location of scientific content (data, code, results)
      and narrative descriptions of that work.
    doi: 10.17616/R3B934
    homepage: https://www.synapse.org
    name: Synapse
    prefix: r3d100011894
  synonyms:
  - syn
  uri_format: https://www.synapse.org/Synapse:syn$1
synbip.bts:
  contact:
    email: lifengcheng@zju.edu.cn
    github: null
    name: Fengcheng Li
    orcid: 0000-0002-1846-639X
  contributor:
    email: m.naguthana@hotmail.com
    github: nagutm
    name: Mufaddal Naguthanawala
    orcid: 0009-0009-5240-7463
  description: Identifiers for the binding targets of synthetic binding proteins (SBP),
    describing the specific molecules or complexes that SBPs interact with for their
    intended applications
  example: st00576
  github_request_issue: 1268
  homepage: http://synbip.idrblab.net
  name: Synthetic Binding Proteins Binding Target
  pattern: ^st\d+$
  prefix: synbip.bts
  publications:
  - doi: 10.1093/nar/gkae893
    pmc: null
    pubmed: '39413165'
    title: 'SYNBIP 2.0: epitopes mapping, sequence expansion and scaffolds discovery
      for synthetic binding protein innovation'
    year: 2024
  reviewer:
    email: b.gyori@northeastern.edu
    github: bgyori
    name: Benjamin M. Gyori
    orcid: 0000-0001-9439-5346
  uri_format: http://synbip.idrblab.net/data/bts/details/$1
synbip.epitope:
  contact:
    email: lifengcheng@zju.edu.cn
    github: null
    name: Fengcheng Li
    orcid: 0000-0002-1846-639X
  contributor:
    email: m.naguthana@hotmail.com
    github: nagutm
    name: Mufaddal Naguthanawala
    orcid: 0009-0009-5240-7463
  description: Identifiers for synthetic binding protein-target complexes, detailing
    their components, 3D structures and docking statistics
  example: mt002305
  github_request_issue: 1268
  homepage: http://synbip.idrblab.net
  name: Synthetic Binding Protein Epitope
  pattern: ^mt\d+$
  prefix: synbip.epitope
  publications:
  - doi: 10.1093/nar/gkae893
    pmc: null
    pubmed: '39413165'
    title: 'SYNBIP 2.0: epitopes mapping, sequence expansion and scaffolds discovery
      for synthetic binding protein innovation'
    year: 2024
  reviewer:
    email: b.gyori@northeastern.edu
    github: bgyori
    name: Benjamin M. Gyori
    orcid: 0000-0001-9439-5346
  uri_format: http://synbip.idrblab.net/data/sbp-target-complex/details/$1
synbip.pss:
  contact:
    email: lifengcheng@zju.edu.cn
    github: null
    name: Fengcheng Li
    orcid: 0000-0002-1846-639X
  contributor:
    email: m.naguthana@hotmail.com
    github: nagutm
    name: Mufaddal Naguthanawala
    orcid: 0009-0009-5240-7463
  description: Identifiers for the protein scaffolds of synthetic binding proteins
    (SBP), detailing their structural frameworks and roles in facilitating SBP function.
  example: ps048
  github_request_issue: 1268
  homepage: http://synbip.idrblab.net
  name: Synthetic Binding Protein Protein Scaffold
  pattern: ^ps\d+$
  prefix: synbip.pss
  publications:
  - doi: 10.1093/nar/gkae893
    pmc: null
    pubmed: '39413165'
    title: 'SYNBIP 2.0: epitopes mapping, sequence expansion and scaffolds discovery
      for synthetic binding protein innovation'
    year: 2024
  reviewer:
    email: b.gyori@northeastern.edu
    github: bgyori
    name: Benjamin M. Gyori
    orcid: 0000-0001-9439-5346
  uri_format: http://synbip.idrblab.net/data/scaffold/details/$1
synbip.sbp:
  contact:
    email: lifengcheng@zju.edu.cn
    github: null
    name: Fengcheng Li
    orcid: 0000-0002-1846-639X
  contributor:
    email: m.naguthana@hotmail.com
    github: nagutm
    name: Mufaddal Naguthanawala
    orcid: 0009-0009-5240-7463
  description: Identifiers for synthetic binding proteins, providing detailed information
    on their sequences, structures, targets, and functional properties for research,
    diagnostic, and therapeutic applications.
  example: sbp000002
  github_request_issue: 1268
  homepage: http://synbip.idrblab.net
  name: Synthetic Binding Protein
  pattern: ^sbp\d+$
  prefix: synbip.sbp
  publications:
  - doi: 10.1093/nar/gkae893
    pmc: null
    pubmed: '39413165'
    title: 'SYNBIP 2.0: epitopes mapping, sequence expansion and scaffolds discovery
      for synthetic binding protein innovation'
    year: 2024
  reviewer:
    email: b.gyori@northeastern.edu
    github: bgyori
    name: Benjamin M. Gyori
    orcid: 0000-0001-9439-5346
  uri_format: http://synbip.idrblab.net/data/sbp/details/$1
syoid:
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  deprecated: true
  name: Gemina Symptom Ontology
  prefix: syoid
  references:
  - https://github.com/DiseaseOntology/SymptomOntology/issues/7#event-4223716562
t3db:
  biocontext:
    prefix: T3DB
  edam:
    description: Unique identifier of a toxin from the Toxin and Toxin Target Database
      (T3DB) database.
    name: T3DB
    obsolete: false
    prefix: '2662'
  fairsharing:
    abbreviation: T3DB
    contact:
      email: david.wishart@ualberta.ca
      name: David Wishart
      orcid: 0000-0002-3207-2434
    description: Toxin and Toxin Target Database (T3DB) is a bioinformatics resource
      that combines detailed toxin data with comprehensive toxin target information.
    homepage: http://www.t3db.ca/
    name: Toxin and Toxin Target Database
    prefix: FAIRsharing.psn0h2
    publications:
    - doi: 10.1093/nar/gkp934
      pubmed_id: 19897546
      title: 'T3DB: a comprehensively annotated database of common toxins and their
        targets.'
    - doi: 10.1093/nar/gku1004
      pubmed_id: 25378312
      title: 'T3DB: the toxic exposome database.'
    subjects:
    - Life Science
    - Biomedical Science
  mappings:
    biocontext: T3DB
    edam: '2662'
    fairsharing: FAIRsharing.psn0h2
    miriam: t3db
    n2t: t3db
    pathguide: '326'
    prefixcommons: t3db
    re3data: r3d100012189
  miriam:
    deprecated: false
    description: Toxin and Toxin Target Database (T3DB) is a bioinformatics resource
      that combines detailed toxin data with comprehensive toxin target information.
    homepage: http://www.t3db.org/
    id: '00000103'
    name: T3DB
    namespaceEmbeddedInLui: false
    pattern: ^T3D\d+$
    prefix: t3db
    sampleId: T3D0001
    uri_format: http://www.t3db.org/toxins/$1
  n2t:
    description: Toxin and Toxin Target Database (T3DB) is a bioinformatics resource
      that combines detailed toxin data with comprehensive toxin target information.
    example: T3D0001
    homepage: http://www.t3db.org/
    name: Toxin and Toxin Target Database
    namespaceEmbeddedInLui: false
    pattern: ^T3D\d+$
    prefix: t3db
    uri_format: http://www.t3db.org/toxins/$1
  name: Toxin and Toxin Target Database
  pathguide:
    abbreviation: T3DB
    homepage: http://www.t3db.ca/
    name: Toxin and Toxin-Target Database
    prefix: '326'
  prefix: t3db
  prefixcommons:
    description: Toxin and Toxin Target Database (T3DB) is a bioinformatics resource
      that combines detailed toxin data with comprehensive toxin target information.
    example: T3D0001
    homepage: http://www.t3db.org/
    keywords:
    - protein
    - molecule
    license: http://www.t3db.org/about#cite
    name: Toxin and Toxin Target Database
    pattern: ^T3D\d+$
    prefix: t3db
    uri_format: http://www.t3db.org/toxins/$1
  publications:
  - doi: 10.1093/nar/gku1004
    pmc: PMC4383875
    pubmed: '25378312'
    title: 'T3DB: the toxic exposome database'
    year: 2014
  - doi: 10.1093/nar/gkp934
    pmc: PMC2808899
    pubmed: '19897546'
    title: 'T3DB: a comprehensively annotated database of common toxins and their
      targets'
    year: 2009
  re3data:
    description: The Toxin and Toxin Target Database is a unique bioinformatics resource
      that combines detailed toxin data with comprehensive toxin target information.
      The focus of the T3DB is on providing mechanisms of toxicity and target proteins
      for each toxin. This dual nature of the T3DB, in which toxin and toxin target
      records are interactively linked in both directions, makes it unique from existing
      databases.
    doi: 10.17616/R3VM0R
    homepage: http://www.t3db.ca/
    name: T3DB
    prefix: r3d100012189
    synonyms:
    - Toxic Exposome Database
    - Toxin and Toxin Target Database
    xrefs:
      nif: 0000-22933
      omics: 01592
t4fs:
  aberowl:
    description: A terminology for the skills necessary to make data FAIR and to keep
      it FAIR.
    download_owl: http://aber-owl.net/media/ontologies/T4FS/4/t4fs.owl
    homepage: https://github.com/terms4fairskills/FAIRterminology
    name: terms4FAIRskills
    prefix: T4FS
  bioportal:
    contact:
      email: allyson.lister@oerc.ox.ac.uk
      name: Allyson Lister
    description: A terminology for the skills necessary to make data FAIR and to keep
      it FAIR
    homepage: https://github.com/terms4fairskills/FAIRterminology
    name: terms4FAIRskills
    prefix: T4FS
    version: '2025-02-09'
  contact:
    email: allyson.lister@oerc.ox.ac.uk
    github: allysonlister
    name: Allyson Lister
    orcid: 0000-0002-7702-4495
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: A terminology for the skills necessary to make data FAIR and to keep
    it FAIR.
  example: '0000127'
  fairsharing:
    abbreviation: T4FS
    contact:
      email: allyson.lister@oerc.ox.ac.uk
      name: Allyson Lister
      orcid: 0000-0002-7702-4495
    description: terms4FAIRskills terminology is designed to capture the necessary
      competencies, skills and knowledge associated with how to make data FAIR and
      to keep it FAIR. terms4FAIRskills terms can be implemented to serve a variety
      of use-case applications such as 1) creation and assessment of stewardship curricula,
      2) annotation for the discovery and evaluation of various FAIR-enabling materials/resources
      (e.g.training, etc.), and 3) formalisation of job descriptions and CVs for recognising
      structured FAIR competencies for hire. User integrations include implementations
      from the FAIR Cookbook, FAIRsFAIR Competency Centre, FAIRassist, and Semaphora.
      terms4FAIRskills provides user flexibility for terms by FAIR trainers for FAIR
      data skills, researchers and/or data managers working to identify FAIR gaps
      for teams requiring support, managers recruiting specific FAIR implementation
      competencies, and developments leveraging FAIR competency-based reward structures
      and training plans.
    domains:
    - curated information
    - digital curation
    - FAIR
    homepage: https://github.com/terms4fairskills/FAIRterminology
    license: CC-BY-4.0
    logo: https://api.fairsharing.org/rails/active_storage/blobs/redirect/eyJfcmFpbHMiOnsibWVzc2FnZSI6IkJBaHBBZ1VDIiwiZXhwIjpudWxsLCJwdXIiOiJibG9iX2lkIn19--692c3b4cc5ea2f7aa8cc80267dad833f16dcccbb/terms4FAIRskills.png?disposition=inline
    name: terms4FAIRskills
    prefix: FAIRsharing.fb99fa
    publications:
    - doi: 10.5281/zenodo.4772741
      title: 'EOSC Co-creation funded project 074: Delivery of a proof of concept
        for terms4FAIRskills: Technical report'
      year: 2021
    repository: https://github.com/terms4fairskills
    subjects:
    - Subject Agnostic
  homepage: https://github.com/terms4fairskills/FAIRterminology
  keywords:
  - competence
  - skills
  mappings:
    aberowl: T4FS
    bioportal: T4FS
    fairsharing: FAIRsharing.fb99fa
    obofoundry: t4fs
    ols: t4fs
    ontobee: T4FS
    tib: t4fs
  name: terms4FAIRskills
  obofoundry:
    contact: allyson.lister@oerc.ox.ac.uk
    contact.github: allysonlister
    contact.label: Allyson Lister
    contact.orcid: 0000-0002-7702-4495
    deprecated: false
    description: A terminology for the skills necessary to make data FAIR and to keep
      it FAIR.
    domain: information
    download.json: http://purl.obolibrary.org/obo/t4fs.json
    download.obo: http://purl.obolibrary.org/obo/t4fs.obo
    download.owl: http://purl.obolibrary.org/obo/t4fs.owl
    homepage: https://github.com/terms4fairskills/FAIRterminology
    license: CC BY 4.0
    license.url: https://creativecommons.org/licenses/by/4.0/
    name: terms4FAIRskills
    preferredPrefix: T4FS
    prefix: t4fs
    publications:
    - id: https://doi.org/10.5281/zenodo.4705219
      title: 'EOSC Co-creation funded project 074: Delivery of a proof of concept
        for terms4FAIRskills: Technical report'
    repository: https://github.com/terms4fairskills/FAIRterminology
  ols:
    description: A terminology for the skills necessary to make data FAIR and to keep
      it FAIR.
    download_owl: http://purl.obolibrary.org/obo/t4fs.owl
    homepage: https://github.com/terms4fairskills/FAIRterminology
    name: terms4FAIRskills
    prefix: t4fs
    tracker: https://github.com/terms4fairskills/FAIRterminology/issues
    version: '2025-02-09'
    version.iri: http://purl.obolibrary.org/obo/t4fs/releases/2025-02-09/t4fs.owl
  ontobee:
    library: Library
    name: terms4FAIRskills
    prefix: T4FS
  pattern: ^\d{7}$
  prefix: t4fs
  publications:
  - doi: 10.5281/zenodo.4705219
    pmc: null
    pubmed: null
    title: 'EOSC Co-creation funded project 074: Delivery of a proof of concept for
      terms4FAIRskills: Technical report'
    year: 2021
  - doi: 10.5281/zenodo.4772741
    pmc: null
    pubmed: null
    title: 'EOSC Co-creation funded project 074: Delivery of a proof of concept for
      terms4FAIRskills: Technical report'
    year: 2021
  - doi: 10.5281/zenodo.4705219
    pmc: null
    pubmed: null
    title: 'EOSC Co-creation funded project 074: Delivery of a proof of concept for
      terms4FAIRskills: Technical report'
    year: null
  - doi: 10.5281/zenodo.4772741
    pmc: null
    pubmed: null
    title: 'EOSC Co-creation funded project 074: Delivery of a proof of concept for
      terms4FAIRskills: Technical report'
    year: 2021
  repository: https://github.com/terms4fairskills/FAIRterminology
  tib:
    description: 'terms4FAIRskills describes the competencies, skills and knowledge
      associated with making and keeping data FAIR. This terminology applies to a
      variety of use cases, including: assisting with the creation and assessment
      of stewardship curricula; facilitating the annotation, discovery and evaluation
      of FAIR-enabling materials (e.g. training) and resources; enabling the formalisation
      of job descriptions and CVs with recognised, structured competencies.It is intended
      to be of use to trainers who teach FAIR data skills, researchers who wish to
      identify skill gaps in their teams and managers who need to recruit individuals
      to relevant roles.'
    download_owl: http://purl.obolibrary.org/obo/t4fs.owl
    homepage: https://github.com/terms4fairskills/FAIRterminology
    keywords:
    - NFDI4ING
    - ESS
    name: terms4FAIRskills (T4FS)
    prefix: t4fs
    tracker: https://github.com/terms4fairskills/FAIRterminology/issues
    version.iri: http://purl.obolibrary.org/obo/t4fs/releases/2025-02-09/t4fs.owl
  uri_format: http://purl.obolibrary.org/obo/T4FS_$1
tads:
  aberowl:
    description: 'The anatomy of the Tick, <i>Families: Ixodidae, Argassidae</i>'
    download_owl: http://aber-owl.net/media/ontologies/TADS/18/tads.owl
    homepage: https://www.vectorbase.org/ontology-browser
    name: Tick Anatomy Ontology
    prefix: TADS
  biocontext:
    prefix: TADS
  bioportal:
    contact:
      email: dsonensh@odu.edu
      name: Daniel Sonenshine
    description: 'The anatomy of the Tick, <i>Families: Ixodidae, Argassidae</i>'
    homepage: http://www.anobase.org
    name: Tick Gross Anatomy Ontology
    prefix: TADS
    version: '1.21'
  download_obo: http://purl.obolibrary.org/obo/tads.obo
  example: '0000547'
  fairsharing:
    abbreviation: TADS
    contact:
      email: dsonensh@odu.edu
      name: Daniel Sonenshine
      orcid: 0000-0001-9370-918X
    description: This ontology covers all the terms relevant for the gross anatomy
      of the tick (family Ixodida).
    homepage: https://www.vectorbase.org/ontology-types/tick-anatomy
    name: Tick Gross Anatomy
    prefix: FAIRsharing.8wm364
    publications:
    - doi: 10.1111/j.1365-2583.2008.00781.x
      pubmed: '18237287'
      title: Anatomical ontologies of mosquitoes and ticks, and their web browsers
        in VectorBase
      year: 2008
    subjects:
    - Life Science
    - Anatomy
  mappings:
    aberowl: TADS
    biocontext: TADS
    bioportal: TADS
    fairsharing: FAIRsharing.8wm364
    obofoundry: tads
    ols: tads
    ontobee: TADS
  obofoundry:
    contact: dsonensh@odu.edu
    contact.label: Daniel Sonenshine
    deprecated: true
    description: 'The anatomy of the Tick, <i>Families: Ixodidae, Argassidae</i>'
    domain: anatomy and development
    download.obo: http://purl.obolibrary.org/obo/tads.obo
    download.owl: http://purl.obolibrary.org/obo/tads.owl
    homepage: https://www.vectorbase.org/ontology-browser
    license: CC BY 4.0
    license.url: https://creativecommons.org/licenses/by/4.0/
    name: Tick Anatomy Ontology
    prefix: tads
    repository: https://github.com/VEuPathDB-ontology/TADS
  ols:
    description: 'The anatomy of the Tick, <i>Families: Ixodidae, Argassidae</i>'
    download_owl: http://purl.obolibrary.org/obo/tads.owl
    homepage: https://www.vectorbase.org/ontology-browser
    name: Tick Anatomy Ontology
    prefix: tads
    version: '2015-08-20'
    version.iri: http://purl.obolibrary.org/obo/tads/2015-08-20/tads.owl
  ontobee:
    library: Library
    name: Tick Anatomy Ontology
    prefix: TADS
  pattern: ^\d{7}$
  prefix: tads
  publications:
  - doi: 10.1111/j.1365-2583.2008.00781.x
    pmc: null
    pubmed: '18237287'
    title: Anatomical ontologies of mosquitoes and ticks, and their web browsers in
      VectorBase
    year: 2008
  - doi: 10.1111/j.1365-2583.2008.00781.x
    pmc: null
    pubmed: '18237287'
    title: Anatomical ontologies of mosquitoes and ticks, and their web browsers in
      VectorBase
    year: 2008
  - doi: 10.1111/j.1365-2583.2008.00781.x
    pmc: null
    pubmed: '18237287'
    title: Anatomical ontologies of mosquitoes and ticks, and their web browsers in
      VectorBase
    year: 2008
tahe:
  biocontext:
    prefix: TAHE
  mappings:
    biocontext: TAHE
    obofoundry: tahe
    wikidata.entity: Q114677914
  obofoundry:
    contact: pierre.sprumont@unifr.ch
    contact.label: Pierre Sprumont
    deprecated: true
    domain: anatomy and development
    name: Terminology of Anatomy of Human Embryology
    prefix: tahe
  prefix: tahe
tahh:
  biocontext:
    prefix: TAHH
  mappings:
    biocontext: TAHH
    obofoundry: tahh
    wikidata.entity: Q114677915
  obofoundry:
    contact: pierre.sprumont@unifr.ch
    contact.label: Pierre Sprumont
    deprecated: true
    domain: health
    name: Terminology of Anatomy of Human Histology
    prefix: tahh
  prefix: tahh
tair.gene:
  banana: Gene
  banana_peel: ':'
  biocontext:
    prefix: TAIR.GENE
  contact:
    email: aisling.doyle9@gmail.com
    github: null
    name: Aisling Doyle
    orcid: 0000-0003-3871-858X
  example: '2200934'
  mappings:
    biocontext: TAIR.GENE
    miriam: tair.gene
    n2t: tair.gene
    prefixcommons: tair.gene
  miriam:
    deprecated: false
    description: The Arabidopsis Information Resource (TAIR) maintains a database
      of genetic and molecular biology data for the model higher plant Arabidopsis
      thaliana. This is the reference gene model for a given locus.
    homepage: http://arabidopsis.org/index.jsp
    id: 00000049
    name: TAIR Gene
    namespaceEmbeddedInLui: false
    pattern: ^Gene:\d{7}$
    prefix: tair.gene
    sampleId: Gene:2200934
  n2t:
    description: The Arabidopsis Information Resource (TAIR) maintains a database
      of genetic and molecular biology data for the model higher plant Arabidopsis
      thaliana. This is the reference gene model for a given locus.
    example: Gene:2200934
    homepage: http://arabidopsis.org/index.jsp
    name: The Arabidopsis Information Resource (TAIR) Gene
    namespaceEmbeddedInLui: false
    pattern: ^Gene:\d{7}$
    prefix: tair.gene
  pattern: ^\d{7}$
  prefix: tair.gene
  prefixcommons:
    description: The reference gene model for a given locus
    example: Gene:2200934
    keywords:
    - gene
    name: TAIR-Gene
    pattern: ^Gene:\d{7}$
    prefix: tair.gene
    pubmed_ids:
    - '12444417'
  publications:
  - doi: 10.1007/s10142-002-0077-z
    pmc: null
    pubmed: '12444417'
    title: 'TAIR: a resource for integrated Arabidopsis data'
    year: 2002
  - doi: null
    pmc: null
    pubmed: '12444417'
    title: null
    year: null
  uri_format: http://arabidopsis.org/servlets/TairObject?accession=Gene:$1
tair.locus:
  biocontext:
    prefix: TAIR.LOCUS
  contact:
    email: aisling.doyle9@gmail.com
    github: null
    name: Aisling Doyle
    orcid: 0000-0003-3871-858X
  contributor_extras:
  - email: b.gyori@northeastern.edu
    github: bgyori
    name: Benjamin M. Gyori
    orcid: 0000-0001-9439-5346
  go:
    homepage: http://www.arabidopsis.org/
    name: The Arabidopsis Information Resource
    prefix: TAIR
  mappings:
    biocontext: TAIR.LOCUS
    go: TAIR
    miriam: tair.locus
    n2t: tair.locus
    ncbi: TAIR
    prefixcommons: tair.locus
  miriam:
    deprecated: false
    description: The Arabidopsis Information Resource (TAIR) maintains a database
      of genetic and molecular biology data for the model higher plant Arabidopsis
      thaliana. The name of a Locus is unique and used by TAIR, TIGR, and MIPS.
    homepage: http://arabidopsis.org/
    id: '00000050'
    name: TAIR Locus
    namespaceEmbeddedInLui: false
    pattern: ^\d{7}$
    prefix: tair.locus
    sampleId: '2200950'
    uri_format: https://www.arabidopsis.org/locus?accession=$1
  n2t:
    description: The Arabidopsis Information Resource (TAIR) maintains a database
      of genetic and molecular biology data for the model higher plant Arabidopsis
      thaliana. The name of a Locus is unique and used by TAIR, TIGR, and MIPS.
    example: '2200950'
    homepage: http://arabidopsis.org/index.jsp
    name: The Arabidopsis Information Resource (TAIR) Locus
    namespaceEmbeddedInLui: false
    pattern: ^\d{7}$
    prefix: tair.locus
    uri_format: http://www.arabidopsis.org/servlets/TairObject?accession=Locus:$1
  ncbi:
    example: AT1F51370
    homepage: http://www.arabidopsis.org/servlets/Search?type=gene&action=new_search
    name: Arabidopsis IR
    prefix: TAIR
  pattern: ^\d+$
  prefix: tair.locus
  prefixcommons:
    description: The locus name
    example: AT1G01030
    keywords:
    - genome
    name: TAIR-Locus
    pattern: ^AT[1-5]G\d{5}$
    prefix: tair.locus
    pubmed_ids:
    - '12444417'
    uri_format: http://arabidopsis.org/servlets/TairObject?type=locus&name=$1
  providers:
  - code: thalemine
    description: Data mining on aradopsis
    example: null
    first_party: null
    homepage: https://bar.utoronto.ca/thalemine
    name: ThaleMine
    publications: null
    status: null
    uri_format: https://bar.utoronto.ca/thalemine/portal.do?externalids=$1
  publications:
  - doi: 10.1007/s10142-002-0077-z
    pmc: null
    pubmed: '12444417'
    title: 'TAIR: a resource for integrated Arabidopsis data'
    year: 2002
  uri_format: https://www.arabidopsis.org/locus?accession=$1
tair.protein:
  banana: AASequence
  banana_peel: ':'
  biocontext:
    prefix: TAIR.PROTEIN
  contact:
    email: aisling.doyle9@gmail.com
    github: null
    name: Aisling Doyle
    orcid: 0000-0003-3871-858X
  contributor_extras:
  - email: b.gyori@northeastern.edu
    github: bgyori
    name: Benjamin M. Gyori
    orcid: 0000-0001-9439-5346
  example: '1009107926'
  mappings:
    biocontext: TAIR.PROTEIN
    miriam: tair.protein
    n2t: tair.protein
    prefixcommons: tair.protein
  miriam:
    deprecated: false
    description: The Arabidopsis Information Resource (TAIR) maintains a database
      of genetic and molecular biology data for the model higher plant Arabidopsis
      thaliana. This provides protein information for a given gene model and provides
      links to other sources such as UniProtKB and GenPept
    homepage: http://arabidopsis.org/index.jsp
    id: 00000048
    name: TAIR Protein
    namespaceEmbeddedInLui: false
    pattern: ^AASequence:\d{10}$
    prefix: tair.protein
    sampleId: AASequence:1009107926
  n2t:
    description: The Arabidopsis Information Resource (TAIR) maintains a database
      of genetic and molecular biology data for the model higher plant Arabidopsis
      thaliana. This provides protein information for a given gene model and provides
      links to other sources such as UniProtKB and GenPept
    example: AASequence:1009107926
    homepage: http://arabidopsis.org/index.jsp
    name: The Arabidopsis Information Resource (TAIR) Protein
    namespaceEmbeddedInLui: false
    pattern: ^AASequence:\d{10}$
    prefix: tair.protein
  pattern: ^\d{10}$
  prefix: tair.protein
  prefixcommons:
    description: The protein entry
    example: AASequence:1009107926
    keywords:
    - protein
    name: TAIR-Protein
    pattern: ^AASequence:\d{10}$
    prefix: tair.protein
    pubmed_ids:
    - '12444417'
  providers:
  - code: legacy
    description: This was the old URI for TAIR proteins
    example: null
    first_party: null
    homepage: https://www.arabidopsis.org
    name: Legacy
    publications: null
    status: null
    uri_format: http://arabidopsis.org/servlets/TairObject?accession=AASequence:$1
  publications:
  - doi: 10.1007/s10142-002-0077-z
    pmc: null
    pubmed: '12444417'
    title: 'TAIR: a resource for integrated Arabidopsis data'
    year: 2002
  - doi: null
    pmc: null
    pubmed: '12444417'
    title: null
    year: null
  uri_format: https://www.arabidopsis.org/protein?key=$1
tao:
  aberowl:
    description: TAO is a multispecies anatomy ontology for teleost fishes. Originally
      seeded from ZFA, but intended to cover terms relevant to other taxa.
    download_obo: http://aber-owl.net/media/ontologies/TAO/135/tao.obo
    homepage: https://www.nescent.org/phenoscape/Main_Page
    name: Teleost Anatomy Ontology
    prefix: TAO
    version: '2012-08-10'
  biocontext:
    prefix: TAO
  bioportal:
    contact:
      email: wasila.dahdul@usd.edu
      name: Wasila Dahdul
    description: TAO is a multispecies anatomy ontology for teleost fishes. Originally
      seeded from ZFA, but intended to cover terms relevant to other taxa.
    homepage: https://www.nescent.org/phenoscape/Main_Page
    name: Teleost Anatomy Ontology
    prefix: TAO
    publications:
    - http://dx.doi.org/10.1093/sysbio/syq013
    version: '2012-08-10'
  example: 0000086
  mappings:
    aberowl: TAO
    biocontext: TAO
    bioportal: TAO
    obofoundry: tao
    ols: tao
    prefixcommons: tao
  name: Teleost Anatomy Ontology
  obofoundry:
    contact: wasila.dahdul@usd.edu
    contact.label: Wasila Dahdul
    contact.orcid: 0000-0003-3162-7490
    deprecated: true
    description: Multispecies fish anatomy ontology. Originally seeded from ZFA, but
      intended to cover terms relevant to other taxa
    domain: anatomy and development
    download.owl: http://purl.obolibrary.org/obo/tao.owl
    homepage: http://wiki.phenoscape.org/wiki/Teleost_Anatomy_Ontology
    license: CC0 1.0
    license.url: http://creativecommons.org/publicdomain/zero/1.0/
    name: Teleost Anatomy Ontology
    prefix: tao
    publications:
    - id: https://www.ncbi.nlm.nih.gov/pubmed/20547776
      title: 'The teleost anatomy ontology: anatomical representation for the genomics
        age'
  ols:
    description: Multispecies fish anatomy ontology. Originally seeded from ZFA, but
      intended to cover terms relevant to other taxa
    homepage: http://wiki.phenoscape.org/wiki/Teleost_Anatomy_Ontology
    name: Teleost Anatomy Ontology
    prefix: tao
    version: '2012-08-10'
    version.iri: http://purl.obolibrary.org/obo/tao/2012-08-10/tao.owl
  pattern: ^\d{7}$
  prefix: tao
  prefixcommons:
    bioportal: '1110'
    description: Multispecies fish anatomy ontology. Originally seeded from ZFA, but
      intended to cover terms relevant to other taxa
    example: TAO_0000297
    homepage: https://www.nescent.org/phenoscape/Main_Page
    keywords:
    - obo
    - classification
    - anatomy
    name: Teleost Anatomy Ontology
    pattern: ^TAO_\d{7}$
    prefix: tao
    synonyms:
    - teleost_anatomy
  publications:
  - doi: 10.1093/sysbio/syq013
    pmc: PMC2885267
    pubmed: '20547776'
    title: 'The teleost anatomy ontology: anatomical representation for the genomics
      age'
    year: 2010
  - doi: null
    pmc: null
    pubmed: '20547776'
    title: 'The teleost anatomy ontology: anatomical representation for the genomics
      age'
    year: null
  - doi: null
    pmc: null
    pubmed: '20547776'
    title: 'The teleost anatomy ontology: anatomical representation for the genomics
      age'
    year: null
  synonyms:
  - TAO_RETIRED
tarbase:
  biocontext:
    prefix: TARBASE
  fairsharing:
    abbreviation: TarBase
    description: DIANA-TarBase is a reference database that indexes experimentally-supported
      microRNA (miRNA) targets. It integrates information on cell-type specific miRNA–gene
      regulation and includes miRNA-binding locations. The target data provided by
      DIANA-TarBase is supported by information on methodologies, cell types/tissues
      and experimental conditions.
    homepage: http://www.microrna.gr/tarbase
    name: TarBase
    prefix: FAIRsharing.a0k4cd
    publications:
    - doi: 10.1093/nar/gkx1141
      pubmed_id: 29156006
      title: 'DIANA-TarBase v8: a decade-long collection of experimentally supported
        miRNA-gene interactions.'
    - doi: 10.1093/nar/gkn809
      pubmed_id: 18957447
      title: 'The database of experimentally supported targets: a functional update
        of TarBase.'
    - doi: 10.1261/rna.2239606
      pubmed_id: 16373484
      title: 'TarBase: A comprehensive database of experimentally supported animal
        microRNA targets.'
    - doi: 10.1093/nar/gku1215
      pubmed_id: 25416803
      title: 'DIANA-TarBase v7.0: indexing more than half a million experimentally
        supported miRNA:mRNA interactions.'
    subjects:
    - Life Science
    - Biomedical Science
  integbio:
    description: DIANA-TarBase is a reference database that indexes experimentally-supported
      microRNA (miRNA) targets. It integrates information on cell-type specific miRNA-gene
      regulation and includes miRNA-binding locations. The target data provided by
      DIANA-TarBase is supported by information on methodologies, cell types/tissues
      and experimental conditions.
    fairsharing: FAIRsharing.a0k4cd
    homepage: http://www.microrna.gr/tarbase
    information_keywords:
    - Bibliography/Documents
    - Method
    - Interaction/Pathway
    maintainer: IBI (Institute for Biomedical Informatics, University of Pennsylvania)||Diana
      Lab Group||BSRC (Biomedical Sciences Research Center Alexander Fleming)
    name: TarBase
    prefix: nbdc02102
    pubmeds:
    - '18957447'
    - '16373484'
    - '25416803'
    status: Active
    target_keywords:
    - Genome/Gene
    - RNA
  mappings:
    biocontext: TARBASE
    fairsharing: FAIRsharing.a0k4cd
    integbio: nbdc02102
    miriam: tarbase
    n2t: tarbase
    pathguide: '283'
  miriam:
    deprecated: false
    description: TarBase stores microRNA (miRNA) information for miRNA–gene interactions,
      as well as miRNA- and gene-related facts to information specific to the interaction
      and the experimental validation methodologies used.
    homepage: http://diana.imis.athena-innovation.gr/DianaTools/index.php?r=tarbase/index
    id: '00000340'
    name: TarBase
    namespaceEmbeddedInLui: false
    pattern: ^[a-z]{3}\-(mir|let|lin)\-\w+(\-\w+\-\w+)?$
    prefix: tarbase
    sampleId: hsa-let-7a-2-3p
    uri_format: http://diana.imis.athena-innovation.gr/DianaTools/index.php?r=tarbase/index&mirnas=$1
  n2t:
    description: TarBase stores microRNA (miRNA) information for miRNA&#x2013;gene
      interactions, as well as miRNA- and gene-related facts to information specific
      to the interaction and the experimental validation methodologies used.
    example: hsa-let-7a-2-3p
    homepage: http://diana.imis.athena-innovation.gr/DianaTools/index.php?r=tarbase/index
    name: TarBase v7 at University of Thessaly
    namespaceEmbeddedInLui: false
    pattern: ^[a-z]{3}\-(mir|let|lin)\-\w+(\-\w+\-\w+)?
    prefix: tarbase
    uri_format: http://diana.imis.athena-innovation.gr/DianaTools/index.php?r=tarbase/index&mirnas=$1
  pathguide:
    abbreviation: TarBase
    homepage: http://diana.imis.athena-innovation.gr/DianaTools/index.php?r=tarbase/index
    name: TarBase
    prefix: '283'
  prefix: tarbase
  publications:
  - doi: 10.1093/nar/gkx1141
    pmc: PMC5753203
    pubmed: '29156006'
    title: 'DIANA-TarBase v8: a decade-long collection of experimentally supported
      miRNA-gene interactions'
    year: 2018
  - doi: 10.1093/nar/gku1215
    pmc: PMC4383989
    pubmed: '25416803'
    title: 'DIANA-TarBase v7.0: indexing more than half a million experimentally supported
      miRNA:mRNA interactions'
    year: 2014
  - doi: 10.1093/nar/gkn809
    pmc: PMC2686456
    pubmed: '18957447'
    title: 'The database of experimentally supported targets: a functional update
      of TarBase'
    year: 2008
  - doi: 10.1261/rna.2239606
    pmc: PMC1370898
    pubmed: '16373484'
    title: 'TarBase: A comprehensive database of experimentally supported animal microRNA
      targets'
    year: 2005
  - doi: 10.1093/nar/gkx1141
    pmc: null
    pubmed: null
    title: 'DIANA-TarBase v8: a decade-long collection of experimentally supported
      miRNA-gene interactions.'
    year: null
  - doi: 10.1093/nar/gkn809
    pmc: null
    pubmed: null
    title: 'The database of experimentally supported targets: a functional update
      of TarBase.'
    year: null
  - doi: 10.1261/rna.2239606
    pmc: null
    pubmed: null
    title: 'TarBase: A comprehensive database of experimentally supported animal microRNA
      targets.'
    year: null
  - doi: 10.1093/nar/gku1215
    pmc: null
    pubmed: null
    title: 'DIANA-TarBase v7.0: indexing more than half a million experimentally supported
      miRNA:mRNA interactions.'
    year: null
  - doi: 10.1093/nar/gkx1141
    pmc: null
    pubmed: null
    title: 'DIANA-TarBase v8: a decade-long collection of experimentally supported
      miRNA-gene interactions.'
    year: null
  - doi: 10.1093/nar/gkn809
    pmc: null
    pubmed: null
    title: 'The database of experimentally supported targets: a functional update
      of TarBase.'
    year: null
  - doi: 10.1261/rna.2239606
    pmc: null
    pubmed: null
    title: 'TarBase: A comprehensive database of experimentally supported animal microRNA
      targets.'
    year: null
  - doi: 10.1093/nar/gku1215
    pmc: null
    pubmed: null
    title: 'DIANA-TarBase v7.0: indexing more than half a million experimentally supported
      miRNA:mRNA interactions.'
    year: null
  - doi: 10.1093/nar/gkx1141
    pmc: null
    pubmed: null
    title: 'DIANA-TarBase v8: a decade-long collection of experimentally supported
      miRNA-gene interactions.'
    year: null
  - doi: 10.1093/nar/gkn809
    pmc: null
    pubmed: null
    title: 'The database of experimentally supported targets: a functional update
      of TarBase.'
    year: null
  - doi: 10.1261/rna.2239606
    pmc: null
    pubmed: null
    title: 'TarBase: A comprehensive database of experimentally supported animal microRNA
      targets.'
    year: null
  - doi: 10.1093/nar/gku1215
    pmc: null
    pubmed: null
    title: 'DIANA-TarBase v7.0: indexing more than half a million experimentally supported
      miRNA:mRNA interactions.'
    year: null
  - doi: 10.1093/nar/gkx1141
    pmc: null
    pubmed: null
    title: 'DIANA-TarBase v8: a decade-long collection of experimentally supported
      miRNA-gene interactions.'
    year: null
  - doi: 10.1093/nar/gkn809
    pmc: null
    pubmed: null
    title: 'The database of experimentally supported targets: a functional update
      of TarBase.'
    year: null
  - doi: 10.1261/rna.2239606
    pmc: null
    pubmed: null
    title: 'TarBase: A comprehensive database of experimentally supported animal microRNA
      targets.'
    year: null
  - doi: 10.1093/nar/gku1215
    pmc: null
    pubmed: null
    title: 'DIANA-TarBase v7.0: indexing more than half a million experimentally supported
      miRNA:mRNA interactions.'
    year: null
  - doi: 10.1093/nar/gkx1141
    pmc: null
    pubmed: null
    title: 'DIANA-TarBase v8: a decade-long collection of experimentally supported
      miRNA-gene interactions.'
    year: null
  - doi: 10.1093/nar/gkn809
    pmc: null
    pubmed: null
    title: 'The database of experimentally supported targets: a functional update
      of TarBase.'
    year: null
  - doi: 10.1261/rna.2239606
    pmc: null
    pubmed: null
    title: 'TarBase: A comprehensive database of experimentally supported animal microRNA
      targets.'
    year: null
  - doi: 10.1093/nar/gku1215
    pmc: null
    pubmed: null
    title: 'DIANA-TarBase v7.0: indexing more than half a million experimentally supported
      miRNA:mRNA interactions.'
    year: null
taxrank:
  aberowl:
    description: A vocabulary of taxonomic ranks (species, family, phylum, etc)
    download_owl: http://aber-owl.net/media/ontologies/TAXRANK/13/taxrank.owl
    homepage: https://github.com/phenoscape/taxrank
    name: Taxonomic rank vocabulary
    prefix: TAXRANK
  agroportal:
    contact:
      email: peter.midford@gmail.com
      name: Peter Midford
    description: A vocabulary of taxonomic ranks developed as part of Phenoscape's
      Vertebrate Taxonomy Ontology. It provides terms for taxonomic ranks drawn from
      both the NCBI taxonomy database and from a rank vocabulary developed for the
      TDWG biodiversity information standards group. Cross references to appearances
      of each term in each source are provided. Consistent with its intended use as
      a vocabulary of labels, there is no relation specifying an ordering of the rank
      terms.
    license: CC0-1.0
    name: Taxonomic Rank Ontology
    prefix: TAXRANK
  biocontext:
    prefix: TAXRANK
  bioportal:
    contact:
      email: peteremidford@yahoo.com
      name: Peter Midford
    description: A vocabulary of taxonomic ranks intended to replace the sets of rank
      terms found in the Teleost Taxonomy Ontology, the OBO translation of the NCBI
      taxonomy and similar OBO taxonomy ontologies. It provides terms for taxonomic
      ranks drawn from both the NCBI taxonomy database and from a rank vocabulary
      developed for the TDWG biodiversity information standards group. Cross references
      to appearances of each term in each source are provided. Consistent with its
      intended use as a vocabulary of labels, there is no relation specifying an ordering
      of the rank terms.
    homepage: https://www.phenoscape.org/wiki/Taxonomic_Rank_Vocabulary
    license: CC0-1.0
    name: Taxonomic Rank Vocabulary
    prefix: TAXRANK
    version: unknown
  example: '0000001'
  fairsharing:
    abbreviation: TAXRANK
    contact:
      email: peteremidford@yahoo.com
      name: Peter E. Midford
      orcid: 0000-0001-6512-3296
    description: This is a vocabulary of taxonomic ranks intended to replace the sets
      of rank terms found in the Teleost Taxonomy Ontology, the OBO translation of
      the NCBI taxonomy and similar OBO taxonomy ontologies. It provides terms for
      taxonomic ranks drawn from both the NCBI taxonomy database and from a rank vocabulary
      developed for the TDWG biodiversity information standards group. Each term contains
      cross reference links to the resources that use the terms. Consistent with its
      intended use as a vocabulary, there is no relation specifying an ordering of
      the rank terms. Likewise, all terms are directly descended from the term 'taxonomic
      rank' (TAXRANK:0000000).
    domains:
    - Taxonomic classification
    homepage: https://github.com/phenoscape/taxrank
    license: CC0-1.0
    name: Taxonomic Rank Vocabulary
    prefix: FAIRsharing.p1sejz
    subjects:
    - Life Science
    - Taxonomy
  mappings:
    aberowl: TAXRANK
    agroportal: TAXRANK
    biocontext: TAXRANK
    bioportal: TAXRANK
    fairsharing: FAIRsharing.p1sejz
    obofoundry: taxrank
    ols: taxrank
    ontobee: TAXRANK
    prefixcommons: taxrank
    wikidata.entity: Q81661813
  obofoundry:
    contact: balhoff@renci.org
    contact.github: balhoff
    contact.label: Jim Balhoff
    contact.orcid: 0000-0002-8688-6599
    deprecated: false
    description: A vocabulary of taxonomic ranks (species, family, phylum, etc)
    domain: organisms
    download.obo: http://purl.obolibrary.org/obo/taxrank.obo
    download.owl: http://purl.obolibrary.org/obo/taxrank.owl
    homepage: https://github.com/phenoscape/taxrank
    license: CC0 1.0
    license.url: http://creativecommons.org/publicdomain/zero/1.0/
    name: Taxonomic rank vocabulary
    preferredPrefix: TAXRANK
    prefix: taxrank
    publications:
    - id: https://doi.org/10.1186/2041-1480-4-34
      title: 'The vertebrate taxonomy ontology: a framework for reasoning across model
        organism and species phenotypes'
    repository: https://github.com/phenoscape/taxrank
  ols:
    description: A vocabulary of taxonomic ranks (species, family, phylum, etc)
    download_owl: http://purl.obolibrary.org/obo/taxrank.owl
    homepage: https://github.com/phenoscape/taxrank
    name: Taxonomic rank vocabulary
    prefix: taxrank
    tracker: https://github.com/phenoscape/taxrank/issues
    version: '2025-09-24'
    version.iri: http://purl.obolibrary.org/obo/taxrank/releases/2025-09-24/taxrank.owl
  ontobee:
    library: Library
    name: Taxonomic rank vocabulary
    prefix: TAXRANK
  pattern: ^\d{7}$
  prefix: taxrank
  prefixcommons:
    bioportal: '1419'
    description: Taxonomic ranks drawn from both the NCBI taxonomy database and from
      a rank vocabulary developed for the TDWG biodiversity information standards
      group.
    example: TAXRANK:0000001
    homepage: https://www.phenoscape.org/wiki/Taxonomic_Rank_Vocabulary
    keywords:
    - obo
    name: Taxonomic rank vocabulary
    pattern: ^TAXRANK:\d+$
    prefix: taxrank
    synonyms:
    - taxonomic_rank
  publications:
  - doi: 10.1186/2041-1480-4-34
    pmc: PMC4177199
    pubmed: '24267744'
    title: 'The vertebrate taxonomy ontology: a framework for reasoning across model
      organism and species phenotypes'
    year: 2013
  - doi: 10.1186/2041-1480-4-34
    pmc: null
    pubmed: null
    title: 'The vertebrate taxonomy ontology: a framework for reasoning across model
      organism and species phenotypes'
    year: null
  - doi: 10.1186/2041-1480-4-34
    pmc: null
    pubmed: null
    title: 'The vertebrate taxonomy ontology: a framework for reasoning across model
      organism and species phenotypes'
    year: null
  uri_format: http://purl.obolibrary.org/obo/TAXRANK_$1
tcb:
  cellosaurus:
    category: Cell line collections
    homepage: https://www.pirbright.ac.uk/tick-cell-lines-views-page
    name: Tick Cell Biobank
    prefix: TCB
    uri_format: https://www.pirbright.ac.uk/node/$1
  example: '2966'
  mappings:
    cellosaurus: TCB
  pattern: ^\d+$
  prefix: tcb
tccd:
  comment: This resource doesn't exist on the web anymore
  deprecated: true
  mappings:
    prefixcommons: tccd
  prefix: tccd
  prefixcommons:
    description: Cell Cycle Database is a collection of genes and proteins involved
      in human and yeast cell cycle
    example: TP53
    homepage: http://www.itb.cnr.it/cellcycle
    keywords:
    - gene
    - protein
    - pathway
    name: The Cell Cycle DB
    pattern: ^[A-Z,0-9]+$
    prefix: tccd
    uri_format: http://www.itb.cnr.it/cellcycle/gene_rep.php?gene_name=$1
  reviewer:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
tcdb:
  biocontext:
    prefix: TCDB
  edam:
    description: Identifier of a membrane transport proteins from the transport classification
      database (TCDB).
    name: TC
    obsolete: false
    prefix: '2756'
  fairsharing:
    abbreviation: TCDB
    contact:
      email: msaier@ucsd.edu
      name: Milton H. Saier, Jr.
      orcid: 0000-0001-5530-0017
    description: This freely accessible database details a comprehensive IUBMB approved
      classification system for membrane transport proteins known as the Transporter
      Classification (TC) system. The TC system is analogous to the Enzyme Commission
      (EC) system for classification of enzymes, except that it incorporates both
      functional and phylogenetic information for organisms of all types. As of August
      1, 2021, TCDB consists of 22,132 proteins classified in 17,390 transport systems
      with 1,604 tabulated 3D structures, 21,174 reference citations describing 1,708
      transporter families, of which 25% are members of 94 recognized superfamilies.
      Overall, this is an increase of over 50% since the last published update of
      the database in 2016. The most recent update of the database contents and features
      include (1) adoption of a chemical ontology for substrates of transporters,
      (2) inclusion of new superfamilies, (3) a domain-based characterization of transporter
      families (tcDoms) for the identification of new members as well as functional
      and evolutionary relationships between families, (4) development of novel software
      to facilitate curation and use of the database, (5) addition of new subclasses
      of transport systems including 11 novel types of channels and 3 types of group
      translocators, and (6) the inclusion of many man-made (artificial) transmembrane
      pores/channels and carriers.
    homepage: https://tcdb.org/
    license: CC BY-SA 3.0
    name: Transporter Classification Database
    prefix: FAIRsharing.p3bzqb
    publications:
    - doi: 10.1093/nar/gkt1097
      pubmed_id: 24225317
      title: The transporter classification database
    - doi: 10.1093/nar/gkaa1004
      pubmed_id: 33170213
      title: 'The Transporter Classification Database (TCDB): 2021 update'
    - doi: 10.1093/nar/gkj001
      pubmed_id: 16381841
      title: 'TCDB: the Transporter Classification Database for membrane transport
        protein analyses and information.'
    - doi: 10.1093/nar/gkn862
      pubmed_id: 19022853
      title: 'The Transporter Classification Database: recent advances.'
    - doi: 10.1093/nar/gkv1103
      pubmed_id: 26546518
      title: 'The Transporter Classification Database (TCDB): recent advances'
    subjects:
    - Knowledge and Information Systems
    - Phylogenetics
    - Computational Biology
    - Life Science
    - Cell Biology
  go:
    homepage: http://www.tcdb.org/
    name: Transport Protein Database
    prefix: TC
    uri_format: http://www.tcdb.org/tcdb/index.php?tc=$1
  homepage: https://www.tcdb.org
  mappings:
    biocontext: TCDB
    edam: '2756'
    fairsharing: FAIRsharing.p3bzqb
    go: TC
    miriam: tcdb
    n2t: tcdb
    pathguide: '104'
    prefixcommons: tcdb
    uniprot: DB-0135
    wikidata: P7260
  miriam:
    deprecated: false
    description: The database details a comprehensive  IUBMB approved classification
      system for membrane transport proteins known as the Transporter Classification
      (TC) system. The TC system is analogous to the Enzyme Commission (EC) system
      for classification of enzymes, but incorporates phylogenetic information additionally.
    homepage: http://www.tcdb.org/
    id: '00000040'
    name: Transport Classification Database
    namespaceEmbeddedInLui: false
    pattern: ^\d+(\.[A-Z])?(\.\d+)?(\.\d+)?(\.\d+)?$
    prefix: tcdb
    sampleId: 5.A.1.1.1
    uri_format: http://www.tcdb.org/search/result.php?tc=$1
  n2t:
    description: The database details a comprehensive  IUBMB approved classification
      system for membrane transport proteins known as the Transporter Classification
      (TC) system. The TC system is analogous to the Enzyme Commission (EC) system
      for classification of enzymes, but incorporates phylogenetic information additionally.
    example: 5.A.1.1.1
    homepage: http://www.tcdb.org/
    name: TCDB
    namespaceEmbeddedInLui: false
    pattern: ^\d+(\.[A-Z])?(\.\d+)?(\.\d+)?(\.\d+)?$
    prefix: tcdb
    uri_format: http://www.tcdb.org/search/result.php?tc=$1
  name: Transporter Classification Database
  pathguide:
    abbreviation: TCDB
    homepage: http://www.tcdb.org/
    name: Transporter Classification Database
    prefix: '104'
  prefix: tcdb
  prefixcommons:
    description: TCDB is a curated database of factual information from over 10,000
      published references; it contains about 5,600 unique protein sequences that
      are classified into over 600 transporter families based on the TC-system.
    example: 5.A.1.1.1
    homepage: http://www.tcdb.org/
    keywords:
    - protein
    - structure
    name: Transport Classification Database
    pattern: ^\d+\.[A-Z]\.\d+\.\d+\.\d+$
    prefix: tcdb
    pubmed_ids:
    - '16381841'
    synonyms:
    - tc
    uri_format: http://www.tcdb.org/search/result.php?tc=$1
  publications:
  - doi: 10.1093/nar/gkaa1004
    pmc: PMC7778945
    pubmed: '33170213'
    title: 'The Transporter Classification Database (TCDB): 2021 update'
    year: 2021
  - doi: 10.1093/nar/gkv1103
    pmc: PMC4702804
    pubmed: '26546518'
    title: 'The Transporter Classification Database (TCDB): recent advances'
    year: 2015
  - doi: 10.1093/nar/gkt1097
    pmc: PMC3964967
    pubmed: '24225317'
    title: The transporter classification database
    year: 2013
  - doi: 10.1093/nar/gkn862
    pmc: PMC2686586
    pubmed: '19022853'
    title: 'The Transporter Classification Database: recent advances'
    year: 2008
  - doi: 10.1093/nar/gkj001
    pmc: PMC1334385
    pubmed: '16381841'
    title: 'TCDB: the Transporter Classification Database for membrane transport protein
      analyses and information'
    year: 2006
  - doi: 10.1093/nar/gkt1097
    pmc: null
    pubmed: null
    title: The transporter classification database
    year: null
  - doi: 10.1093/nar/gkaa1004
    pmc: null
    pubmed: null
    title: 'The Transporter Classification Database (TCDB): 2021 update'
    year: null
  - doi: 10.1093/nar/gkj001
    pmc: null
    pubmed: null
    title: 'TCDB: the Transporter Classification Database for membrane transport protein
      analyses and information.'
    year: null
  - doi: 10.1093/nar/gkn862
    pmc: null
    pubmed: null
    title: 'The Transporter Classification Database: recent advances.'
    year: null
  - doi: 10.1093/nar/gkv1103
    pmc: null
    pubmed: null
    title: 'The Transporter Classification Database (TCDB): recent advances'
    year: null
  - doi: null
    pmc: null
    pubmed: '16381841'
    title: null
    year: null
  - doi: 10.1093/nar/gkaa1004
    pmc: null
    pubmed: '33170213'
    title: null
    year: null
  - doi: 10.1093/nar/gkt1097
    pmc: null
    pubmed: null
    title: The transporter classification database
    year: null
  - doi: 10.1093/nar/gkaa1004
    pmc: null
    pubmed: null
    title: 'The Transporter Classification Database (TCDB): 2021 update'
    year: null
  - doi: 10.1093/nar/gkj001
    pmc: null
    pubmed: null
    title: 'TCDB: the Transporter Classification Database for membrane transport protein
      analyses and information.'
    year: null
  - doi: 10.1093/nar/gkn862
    pmc: null
    pubmed: null
    title: 'The Transporter Classification Database: recent advances.'
    year: null
  - doi: 10.1093/nar/gkv1103
    pmc: null
    pubmed: null
    title: 'The Transporter Classification Database (TCDB): recent advances'
    year: null
  - doi: null
    pmc: null
    pubmed: '16381841'
    title: null
    year: null
  - doi: 10.1093/nar/gkaa1004
    pmc: null
    pubmed: '33170213'
    title: null
    year: null
  - doi: 10.1093/nar/gkt1097
    pmc: null
    pubmed: null
    title: The transporter classification database
    year: null
  - doi: 10.1093/nar/gkaa1004
    pmc: null
    pubmed: null
    title: 'The Transporter Classification Database (TCDB): 2021 update'
    year: null
  - doi: 10.1093/nar/gkj001
    pmc: null
    pubmed: null
    title: 'TCDB: the Transporter Classification Database for membrane transport protein
      analyses and information.'
    year: null
  - doi: 10.1093/nar/gkn862
    pmc: null
    pubmed: null
    title: 'The Transporter Classification Database: recent advances.'
    year: null
  - doi: 10.1093/nar/gkv1103
    pmc: null
    pubmed: null
    title: 'The Transporter Classification Database (TCDB): recent advances'
    year: null
  - doi: null
    pmc: null
    pubmed: '16381841'
    title: null
    year: null
  - doi: 10.1093/nar/gkaa1004
    pmc: null
    pubmed: '33170213'
    title: null
    year: null
  - doi: 10.1093/nar/gkt1097
    pmc: null
    pubmed: null
    title: The transporter classification database
    year: null
  - doi: 10.1093/nar/gkaa1004
    pmc: null
    pubmed: null
    title: 'The Transporter Classification Database (TCDB): 2021 update'
    year: null
  - doi: 10.1093/nar/gkj001
    pmc: null
    pubmed: null
    title: 'TCDB: the Transporter Classification Database for membrane transport protein
      analyses and information.'
    year: null
  - doi: 10.1093/nar/gkn862
    pmc: null
    pubmed: null
    title: 'The Transporter Classification Database: recent advances.'
    year: null
  - doi: 10.1093/nar/gkv1103
    pmc: null
    pubmed: null
    title: 'The Transporter Classification Database (TCDB): recent advances'
    year: null
  - doi: null
    pmc: null
    pubmed: '16381841'
    title: null
    year: null
  - doi: 10.1093/nar/gkaa1004
    pmc: null
    pubmed: '33170213'
    title: null
    year: null
  synonyms:
  - TC
  uniprot:
    abbreviation: TCDB
    category: Protein family/group databases
    homepage: https://www.tcdb.org/
    name: Transport Classification Database
    prefix: DB-0135
    publications:
    - doi: 10.1093/nar/gkaa1004
      pubmed: '33170213'
    uri_format: https://www.tcdb.org/search/result.php?tc=$1
  wikidata:
    description: classifies transport proteins similar to how EC classifies enzymes
    example:
    - 1.A.1
    - 2.A.1.1.28
    - 3.A.3
    homepage: https://www.tcdb.org
    name: Transporter Classification Database ID
    pattern: ^\d|(\d\.[A-Z](\.(\d{1,3}){0,3}))$
    prefix: P7260
    uri_format: http://www.tcdb.org/search/result.php?tc=$1
tctr:
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: The TCTR was estabished in 2009 and has been operated by Clinical Research
    Collaboration Network (CRCN), an organization under the Medical Research Foundation,
    which is a non-profit organization, and financially supported by Thailand Center
    of Excellence for Life Sciences (TCELS). CRCN has been retitled the Medical Research
    Network (MedResNet) since June 15, 2012. (from homepage)
  example: TCTR20230429001
  homepage: https://www.thaiclinicaltrials.org
  name: Thai Clinical Trials Registry
  pattern: ^TCTR\d+$
  prefix: tctr
  uri_format: https://www.thaiclinicaltrials.org/show/$1
tdwg.abcd:
  example: Accession
  mappings:
    tib: abcd
  name: Access to Biological Collection Data Schema
  part_of_database: tdwg
  prefix: tdwg.abcd
  tib:
    description: The base ontology of the ABCD Standard.
    download_owl: https://raw.githubusercontent.com/tdwg/abcd/master/ontology/abcd_concepts.owl
    homepage: https://www.tdwg.org/standards/abcd/
    keywords:
    - FAIR Data Spaces
    - ESS
    - life sciences, biology
    name: ABCD Base Ontology
    prefix: abcd
    tracker: https://github.com/tdwg/abcd/issues
tdwg.format:
  example: e001
  mappings:
    tib: format
  prefix: tdwg.format
  tib:
    description: Controlled vocabulary for the Dublin Core term format
    download_rdf: http://rs.tdwg.org/format.ttl
    homepage: http://rs.tdwg.org/format.htm
    keywords:
    - FAIR Data Spaces
    - life sciences, biology
    name: format controlled vocabulary
    prefix: format
    uri_format: http://rs.tdwg.org/format/$1
tdwg.taxonrank:
  contact:
    email: rhyam@rbge.org.uk
    github: null
    name: Roger Hyam
    orcid: 0000-0003-4581-1379
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: Ontology describing a controlled vocabulary for taxon ranks.
  download_owl: https://tdwg.github.io/ontology/ontology/voc/TaxonRank.rdf
  example: InfragenericTaxon
  github_request_issue: 1321
  homepage: https://github.com/tdwg/ontology
  name: TDWG Taxon Rank LSID Ontology
  part_of_database: tdwg
  prefix: tdwg.taxonrank
  repository: https://github.com/tdwg/ontology
  uri_format: http://rs.tdwg.org/ontology/voc/TaxonRank#$1
tdwg.vms:
  mappings:
    tib: vms
  no_own_terms: true
  prefix: tdwg.vms
  tib:
    description: 'The TDWG Vocabulary Maintenance Standard consists of a single document:
      the Vocabulary Maintenance Specification.'
    download_rdf: https://raw.githubusercontent.com/tdwg/vocab/master/vms/maintenance-specification.ttl
    homepage: https://www.tdwg.org/standards/vms/
    keywords:
    - FAIR Data Spaces
    - life sciences, biology
    name: Vocabulary Maintenance Standard
    prefix: vms
    tracker: https://github.com/tdwg/vocab/tree/master/vms
    uri_format: http://www.tdwg.org/standards/642$1
te:
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: The Terminologia Embryologica (TE) is a standardized list of words
    used in the description of human embryologic and fetal structures. It was produced
    by the Federative International Committee on Anatomical Terminology on behalf
    of the International Federation of Associations of Anatomists and posted on the
    Internet since 2010. [wikipedia]
  example: E5.11.2.0.0.0.4
  homepage: https://ifaa.unifr.ch/
  mappings:
    wikidata: P1693
  name: Terminologia Embryologica
  prefix: te
  references:
  - https://en.wikipedia.org/wiki/Terminologia_Embryologica
  wikidata:
    description: standardized list of words used in the description of human embryologic
      and fetal structures
    name: Terminologia Embryologica
    prefix: P1693
tfclass:
  contact:
    email: edgar.wingender@edgar-wingender.de
    github: null
    name: Edgar Wingender
    orcid: 0000-0002-7729-8453
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: TFClass is a classification of eukaryotic transcription factors based
    on the characteristics of their DNA-binding domains. It comprises four general
    levels (superclass, class, family, subfamily) and two levels of instantiation
    (genus and molecular species). Two of them (subfamily and factor species) are
    optional. More detailed explanations about the classification scheme and its criteria
    are given here..
  example: 2.1.1
  fairsharing:
    abbreviation: TFClass
    description: TFClass is a resource that classifies eukaryotic transcription factors
      (TFs) according to their DNA-binding domains. Combining information from different
      resources, manually checking the retrieved mammalian TF sequences and applying
      extensive phylogenetic analyses, >39,000 TFs from up to 41 mammalian species
      were assigned to the Superclasses, Classes, Families and Subfamilies of TFClass.
      TFClass provides corresponding sequence collections in FASTA format; sequence
      logos and phylogenetic trees at different classification levels; predicted TF
      binding sites for human, mouse, dog and cow genomes; and links to several external
      databases.
    domains:
    - Expression data
    - Transcription factor binding site prediction
    - binding
    - Transcription Factor
    - binding site
    homepage: http://tfclass.bioinf.med.uni-goettingen.de/
    name: Transcription Factor Class
    prefix: FAIRsharing.XykycZ
    publications:
    - doi: 10.1093/nar/gkx987
      pubmed: '29087517'
      title: 'TFClass: expanding the classification of human transcription factors
        to their mammalian orthologs'
      year: 2017
    subjects:
    - Phylogenetics
    - Transcriptomics
    - Bioinformatics
  go:
    homepage: http://tfclass.bioinf.med.uni-goettingen.de/
    name: TFClass is a resource for the classification of eukaryotic transcription
      factors based on the characteristics of their DNA-binding domains
    prefix: TFClass
    synonyms:
    - TFCLASS_FAMILY
    - tfclass
    uri_format: http://tfclass.bioinf.med.uni-goettingen.de/?tfclass=$1
  homepage: http://tfclass.bioinf.med.uni-goettingen.de
  mappings:
    fairsharing: FAIRsharing.XykycZ
    go: TFClass
    pathguide: '666'
  name: Classification of Transcription Factors in Mammalia
  pathguide:
    abbreviation: TFClass
    homepage: http://tfclass.bioinf.med.uni-goettingen.de/tfclass
    name: Classification of Human Transcription Factors and Mouse Orthologs
    prefix: '666'
  prefix: tfclass
  publications:
  - doi: 10.1093/nar/gkx987
    pmc: PMC5753292
    pubmed: '29087517'
    title: 'TFClass: expanding the classification of human transcription factors to
      their mammalian orthologs'
    year: 2018
  - doi: 10.1093/nar/gkx987
    pmc: null
    pubmed: '29087517'
    title: 'TFClass: expanding the classification of human transcription factors to
      their mammalian orthologs'
    year: 2017
  uri_format: http://tfclass.bioinf.med.uni-goettingen.de/?tfclass=$1
tfsco:
  example: '00000001'
  homepage: https://github.com/nomad-hzb/autoperosol
  mappings:
    tib: tfsco
  name: Thin-film Solar Cells Ontology
  prefix: tfsco
  repository: https://github.com/nomad-hzb/autoperosol
  tib:
    description: Domain ontology for thin-film solar cells and related tandem solar
      cells. Contains relevant terms and concepts from BFO, IAO, UO, PATO, OBI, CHMO.
    keywords:
    - FAIRmat
    - material science
    - physics
    - mechanical engineering, energy technology
    name: Ontology for thin-film solar cells (TFSCO)
    prefix: tfsco
    tracker: https://github.com/nomad-hzb/autoperosol/issues
    uri_format: https://purl.archive.org/tfsco/TFSCO_$1
    version.iri: https://purl.archive.org/tfsco/release/v_1_2
tgd:
  biocontext:
    prefix: TGD
  go:
    homepage: http://www.ciliate.org/
    name: Tetrahymena Genome Database
    prefix: TGD
  mappings:
    biocontext: TGD
    go: TGD
    miriam: tgd
    n2t: tgd
    prefixcommons: tgd
  miriam:
    deprecated: false
    description: The Tetrahymena Genome Database (TGD) Wiki is a database of information
      about the Tetrahymena thermophila genome sequence. It provides information curated
      from the literature about each published gene, including a standardized gene
      name, a link to the genomic locus, gene product annotations utilizing the Gene
      Ontology, and links to published literature.
    homepage: http://ciliate.org/index.php/
    id: '00000313'
    name: Tetrahymena Genome Database
    namespaceEmbeddedInLui: false
    pattern: ^TTHERM\_\d+$
    prefix: tgd
    sampleId: TTHERM_00648910
    uri_format: http://ciliate.org/index.php/feature/details/$1
  n2t:
    description: The Tetrahymena Genome Database (TGD) Wiki is a database of information
      about the Tetrahymena thermophila genome sequence. It provides information curated
      from the literature about each published gene, including a standardized gene
      name, a link to the genomic locus, gene product annotations utilizing the Gene
      Ontology, and links to published literature.
    example: TTHERM_00648910
    homepage: http://ciliate.org/index.php/
    name: TGD at Stanford University
    namespaceEmbeddedInLui: false
    pattern: ^TTHERM\_\d+$
    prefix: tgd
    uri_format: http://ciliate.org/index.php/feature/details/$1
  prefix: tgd
  prefixcommons:
    description: Pages with links to phage information are also available, including
      a T4 genetic map reference figure, RB69, RB49, and Aeh1 Map figures, electron
      micrographs, annotation tables, sequence files, and links to NCBI T4 and Integrated
      Genomics RB69 annotation sites are available.
    example: RB51
    homepage: http://phage.bioc.tulane.edu
    keywords:
    - genome
    name: T4-like genome database
    pattern: ^[A-Z,0-9]+$
    prefix: tgd
    uri_format: http://phage.bioc.tulane.edu/cgi-bin/gbrowse/$1?name=$1
tgma:
  aberowl:
    description: A structured controlled vocabulary of the anatomy of mosquitoes.
    download_owl: http://aber-owl.net/media/ontologies/TGMA/18/tgma.owl
    homepage: https://www.vectorbase.org/ontology-browser
    name: Mosquito gross anatomy ontology
    prefix: TGMA
  biocontext:
    prefix: TGMA
  bioportal:
    contact:
      email: louis@imbb.forth.gr
      name: C. Louis
    description: A structured controlled vocabulary of the anatomy of mosquitoes.
    homepage: http://www.anobase.org
    name: Mosquito Gross Anatomy Ontology
    prefix: TGMA
    version: releases/2013-06-03
  contact:
    email: topalis@imbb.forth.gr
    github: null
    name: Pantelis Topalis
    orcid: 0000-0002-1635-4810
  download_obo: http://purl.obolibrary.org/obo/tgma.obo
  example: 0000984
  fairsharing:
    abbreviation: TGMA
    description: A structured controlled vocabulary of the anatomy of mosquitoes.
    homepage: https://www.vectorbase.org/ontology-browser
    name: Mosquito gross anatomy
    prefix: FAIRsharing.dqnfkg
    publications:
    - doi: 10.1111/j.1365-2583.2008.00781.x
      pubmed: '18237287'
      title: Anatomical ontologies of mosquitoes and ticks, and their web browsers
        in VectorBase
      year: 2008
    repository: https://github.com/VEuPathDB-ontology/TGMA
    subjects:
    - Life Science
    - Anatomy
  mappings:
    aberowl: TGMA
    biocontext: TGMA
    bioportal: TGMA
    fairsharing: FAIRsharing.dqnfkg
    obofoundry: tgma
    ols: tgma
    ontobee: TGMA
    prefixcommons: tgma
  obofoundry:
    contact: topalis@imbb.forth.gr
    contact.label: Pantelis Topalis
    deprecated: true
    description: A structured controlled vocabulary of the anatomy of mosquitoes.
    domain: anatomy and development
    download.obo: http://purl.obolibrary.org/obo/tgma.obo
    download.owl: http://purl.obolibrary.org/obo/tgma.owl
    homepage: https://www.vectorbase.org/ontology-browser
    license: CC0 1.0
    license.url: https://creativecommons.org/publicdomain/zero/1.0/
    name: Mosquito gross anatomy ontology
    prefix: tgma
    repository: https://github.com/VEuPathDB-ontology/TGMA
  ols:
    description: A structured controlled vocabulary of the anatomy of mosquitoes.
    download_owl: http://purl.obolibrary.org/obo/tgma.owl
    homepage: https://www.vectorbase.org/ontology-browser
    name: Mosquito gross anatomy ontology
    prefix: tgma
    version: '2013-06-03'
    version.iri: http://purl.obolibrary.org/obo/tgma/releases/2013-06-03/tgma.owl
  ontobee:
    library: Library
    name: Mosquito gross anatomy ontology
    prefix: TGMA
  pattern: ^\d{7}$
  prefix: tgma
  prefixcommons:
    bioportal: '1030'
    description: A structured controlled vocabulary of the anatomy of mosquitoes.
    example: TGMA_0001525
    homepage: http://www.anobase.org
    keywords:
    - obo
    - anatomy
    - mosquito
    name: Mosquito gross anatomy
    pattern: ^TGMA_\d{7}$
    prefix: tgma
  publications:
  - doi: 10.1111/j.1365-2583.2008.00781.x
    pmc: null
    pubmed: '18237287'
    title: Anatomical ontologies of mosquitoes and ticks, and their web browsers in
      VectorBase
    year: 2008
th:
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: The Terminologia Histologica (TH) is the controlled vocabulary for
    use in cytology and histology. It was intended to replace Nomina Histologica.
    [wikipedia]
  example: H3.03.00.0.00007
  homepage: https://ifaa.unifr.ch/
  keywords:
  - biology
  - cytology
  - histology
  - life sciences
  mappings:
    wikidata: P1694
  name: Terminologia Histologica
  prefix: th
  references:
  - https://en.wikipedia.org/wiki/Terminologia_Histologica
  wikidata:
    description: controlled vocabulary for use in cytology and histology
    example:
    - H2.00.06.1.00001
    - H2.00.06.2.00001
    - H3.09.02.0.02001
    name: Terminologia Histologica
    pattern: ^H\d\.\d{2}\.\d{2}\.\d\.\d{5}$
    prefix: P1694
theiler:
  appears_in:
  - emaps
  - mmusdv
  contact:
    email: Terry.Hayamizu@jax.org
    github: tfhayamizu
    name: Terry Hayamizu
    orcid: 0000-0002-0956-8634
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: Theiler stages (TS) define mouse development by a set of morphological
    criteria ([Theiler, 1989](https://doi.org/10.1007/978-3-642-88418-4)). This staging
    scheme is used because embryos at the same gestational age can have developed
    at different rates and therefore exhibit different morphological characteristics.
    Theiler stages may in some cases correspond to a single gestation age, but more
    often cover a range of ages. (from [https://www.informatics.jax.org/glossary/theiler](https://www.informatics.jax.org/glossary/theiler))
  example: '23'
  example_decoys:
  - 10e
  example_extras:
  - 10b
  github_request_issue: 747
  homepage: https://embryology.med.unsw.edu.au/embryology/index.php?title=Mouse_Stages
  name: Theiler Stage
  pattern: ^\d+[a-d]?$
  prefix: theiler
  providers:
  - code: legacy
    description: Legacy URL at UNSW
    example: null
    first_party: null
    homepage: https://embryology.med.unsw.edu.au/embryology/index.php?title=Mouse_Stages
    name: Legacy URL at UNSW
    publications: null
    status: null
    uri_format: https://embryology.med.unsw.edu.au/embryology/index.php?title=Mouse_Stages#Theiler_Stage_$1
  - code: legacy2
    description: Legacy URL at UNSW
    example: null
    first_party: null
    homepage: http://php.med.unsw.edu.au/embryology/index.php?title=Mouse_Stages
    name: Legacy URL at UNSW
    publications: null
    status: null
    uri_format: http://php.med.unsw.edu.au/embryology/index.php?title=Mouse_Stages#Theiler_Stage_$1
  references:
  - https://www.emouseatlas.org/emap/ema/theiler_stages/StageDefinition/stagedefinition.html
  reviewer:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  synonyms:
  - thielerstage
  uri_format: https://www.emouseatlas.org/emap/ema/DAOAnatomyJSP/anatomy.html?stage=TS$1
thermofisher:
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: ThermoFisher is a life sciences supply vendor.
  example: OSR00185W
  homepage: https://www.thermofisher.com
  keywords:
  - biology
  - chemistry
  - life sciences
  - vendor
  name: Thermo Fisher Scientific
  pattern: ^\w+$
  prefix: thermofisher
  uri_format: https://www.thermofisher.com/antibody/product/$1
tib.bk:
  example: '0'
  mappings:
    tib: bk
  prefix: tib.bk
  tib:
    description: The (Dutch) Basic Classification  (nl Nederlandse basisclassificatie),
      BK or NBC  is a hierarchical classification system developed by Dutch libraries
      specifically for scientific works. The classification system was introduced
      at the end of the 1980s under the direction of the Royal Library of the Netherlands
      and has been in use since 1990. Since then it has been continually revised.
      The BK is mainly used in the Netherlands and in the Common Library Network (GBV).
    homepage: http://bartoc.org/en/node/18785
    keywords:
    - Digital Planning and Construction
    - FID BAUdigital
    - FID move
    - NFDI4ING
    - ESS
    - earth sciences
    name: Basisklassifikation
    prefix: bk
    uri_format: http://uri.gbv.de/terminology/bk/$1
tib.bo:
  example: AreaNetwork
  mappings:
    tib: bo
  prefix: tib.bo
  tib:
    description: This file contains the Base Ontology of oneM2M as specified in TS-0012
    download_owl: https://git.onem2m.org/MAS/BaseOntology/-/raw/master/base_ontology.owl
    homepage: https://git.onem2m.org/MAS/BaseOntology
    keywords:
    - NFDI4ING
    - engineering
    name: Base Ontology
    prefix: bo
    uri_format: https://git.onem2m.org/MAS/BaseOntology/raw/master/base_ontology.owl#$1
    version.iri: https://git.onem2m.org/MAS/BaseOntology/raw/3_6_0/base_ontology.owl
tib.cgo:
  example: AbioticStressTrait
  mappings:
    tib: cgo
  prefix: tib.cgo
  tib:
    description: This ontology describes concepts related to greenhouses. It mainly
      describes Dutch greenhouses, but can also be applied to greenhouses outside
      of The Netherlands. The ontology describes multiple aspects of the domain of
      greenhouses.
    download_rdf: https://ontology.tno.nl/ddings/Greenhouse_ontology_v1.3.ttl
    homepage: https://gitlab.com/ddings/common-greenhouse-ontology
    keywords:
    - TIB
    - chemical and environmental engineering
    - horticulture
    - earth sciences
    name: Common Greenhouse Ontology
    prefix: cgo
    uri_format: https://www.tno.nl/agrifood/ontology/common-greenhouse-ontology#$1
    version.iri: https://www.tno.nl/agrifood/ontology/common-greenhouse-ontology#1.3
tib.dot:
  example: Causation
  mappings:
    tib: dot
  prefix: tib.dot
  tib:
    description: The Damage Topology Ontology (DOT) allows the definition of damage
      representations and their relations with other damages and affected construction
      components. The ontology supports a generic damage modeling approach and therefore
      could be applied for any type of degradation as well as for any construction
      type (e.g. buildings or bridges). Damage representations can be modeled either
      as damaged areas (dot:DamageArea) or elementary damage elements (dot:DamageElement).
      Thereby, instances of dot:DamageElement should be aggregated in a dot:DamageArea,
      however significant damages e.g. large cracks could be modelled as dot:DamageElement
      without dot:DamageArea. For grouping multiple coherent damages, a damage pattern
      could be defined by using dot:DamagePattern as third type for damage representation.
      Besides the topological damage classes, damage can also be categorized acording
      to a certain damage type using subclasses of dot:ClassifiedDamage as defined
      in extensions of DOT. A division between structural and non-structural damage
      is made by using the dot:StructuralDamage or dot:Defect classes. In addition
      to the topology, damage documentation that is commonly created during inspections
      and damage assessment can be linked to the damages as well as to the damaged
      components.
    download_rdf: https://alhakam.github.io/dot/ontology.ttl
    homepage: https://alhakam.github.io/dot
    keywords:
    - NFDI4ING
    - engineering
    name: Damage Topology Ontology
    prefix: dot
    uri_format: https://w3id.org/dot#$1
    version.iri: https://w3id.org/dot/0.8
tib.dr:
  example: Application
  mappings:
    tib: dr
  prefix: tib.dr
  tib:
    description: Holistic Ontology for semiconductor manufacturing and development,
      products and systems containing semiconductors and connected supply chains.
    download_rdf: https://raw.githubusercontent.com/tibonto/dr/master/DigitalReference.ttl
    homepage: https://github.com/tibonto/dr
    keywords:
    - NFDI4ING
    - CoyPu
    - electrical engineering
    - economics
    name: Digital Reference
    prefix: dr
    tracker: https://github.com/tibonto/dr/issues
    uri_format: http://www.w3id.org/ecsel-dr-SO#$1
tib.fto:
  example: Agent
  mappings:
    tib: fto
  prefix: tib.fto
  tib:
    description: Modular Ontology Modeling for Food Supply Chains.
    download_rdf: https://raw.githubusercontent.com/Data-Semantics-Laboratory/Modular-Ontology-Modeling-for-Food-Supply-Chains/master/food-traceability-schema.ttl
    homepage: https://github.com/Data-Semantics-Laboratory/Modular-Ontology-Modeling-for-Food-Supply-Chains
    keywords:
    - CoyPu
    - economics
    name: Modular Ontology Modeling for Food Supply Chains
    prefix: fto
    tracker: https://github.com/Data-Semantics-Laboratory/Modular-Ontology-Modeling-for-Food-Supply-Chains/issues
    uri_format: http://dase.cs.ksu.edu/ontology/food-traceability#$1
tib.gpo:
  example: 01cd2578_8730_4ac9_a555_9112728ea939
  license: CC-BY-4.0
  mappings:
    tib: gpo
  name: General Process Ontology
  prefix: tib.gpo
  repository: https://github.com/General-Process-Ontology/ontology
  tib:
    description: Ontology to model processes
    download_rdf: https://raw.githubusercontent.com/General-Process-Ontology/ontology/master/GPO.ttl
    homepage: https://github.com/General-Process-Ontology/ontology
    keywords:
    - NFDI4ING
    - engineering
    name: General Process Ontology (GPO)
    prefix: gpo
    uri_format: https://gpo.ontology.link/GPO_$1
tib.hpont:
  example: HeatPumpOperatingMode
  mappings:
    tib: hpont
  name: Heat Pump Ontology
  prefix: tib.hpont
  repository: https://github.com/react2020/REACT-ONTOLOGY
  tib:
    description: The Heat Pump Ontology (HPOnt) aims to formalize and represent all
      the relevant information of Heat Pumps. The HPOnt has been developed as part
      of the REACT project which has received funding from the European Union’s Horizon
      2020 research and innovation programme under grant agreement no. 824395.
    download_rdf: https://react2020.github.io/REACT-ONTOLOGY/HPOnt/ontology/ontology.ttl
    homepage: https://react2020.github.io/REACT-ONTOLOGY/HPOnt/index-en.html
    keywords:
    - NFDI4ING
    - engineering
    name: The Heat Pump Ontology (HPOnt).
    prefix: hpont
    uri_format: https://w3id.org/hpont#$1
tib.ifc:
  download_rdf: https://standards.buildingsmart.org/IFC/DEV/IFC4/ADD2_TC1/OWL/ontology.ttl
  example: IfcAbsorbedDoseMeasure
  mappings:
    tib: ifc
  name: Industrial Foundational Classes
  prefix: tib.ifc
  tib:
    description: OWL ontology for the IFC conceptual data schema and exchange file
      format for Building Information Model (BIM) data
    homepage: https://standards.buildingsmart.org/IFC/DEV/IFC4/ADD2_TC1/OWL/index.html
    keywords:
    - Digital Planning and Construction
    - FID BAUdigital
    - NFDI4ING
    - civil engineering
    - architecture
    - computer science
    name: IFC4_ADD2_TC1
    prefix: ifc
    uri_format: https://standards.buildingsmart.org/IFC/DEV/IFC4/ADD2_TC1/OWL#$1
tib.io:
  example: InformationObject
  mappings:
    tib: io
  prefix: tib.io
  tib:
    description: An ontology for the description of information objects.
    homepage: https://bimerr.iot.linkeddata.es/def/information-objects/
    keywords:
    - Digital Planning and Construction
    - FID BAUdigital
    - NFDI4ING
    - computer science
    name: Information Objects Ontology
    prefix: io
    uri_format: http://bimerr.iot.linkeddata.es/def/information-objects#$1
tib.ioc:
  example: Actor
  mappings:
    tib: ioc
  prefix: tib.ioc
  tib:
    description: The Internet of Construction Ontology (IoC) construction process
      ontology is intended to represent a comprehensive solution of how processes
      in the construction industry can be modelled. Due to the iterative nature of
      creating an ontology, the construction process ontology presented here can at
      best be considered a working state at the time of publication. Our approach
      emphasizes the simplest and most comprehensive mapping possible, which is only
      extended based on insights from practical use when otherwise compelling limitations
      in usability and applicability arise. Thus, the extension and refinement of
      the developed construction process ontology strongly depends on the integration
      of further areas of the construction value chain and the connection of further
      domain ontologies.
    download_rdf: https://internet-of-construction.github.io/IoC-Process-Ontology/ontology.ttl
    homepage: https://ip.pages.rwth-aachen.de/ioc/core/
    keywords:
    - NFDI4ING
    - Digital Planning and Construction
    - FID BAUdigital
    - civil engineering
    name: 'IOC: Internet of Construction Ontology'
    prefix: ioc
    uri_format: http://w3id.org/ioc#$1
tib.linsearch:
  example: arc
  homepage: https://github.com/TIBHannover/annif_automated_indexing_at_tib
  mappings:
    tib: linsearch
  prefix: tib.linsearch
  repository: https://github.com/TIBHannover/annif_automated_indexing_at_tib
  tib:
    description: Fächer für die LinSearch-Fachzuordnung
    download_rdf: https://raw.githubusercontent.com/TIBHannover/annif_automated_indexing_at_tib/main/vocab/LinSearch/linsearch20230105.ttl
    keywords:
    - TIB
    - computer science
    name: Fachsystematik LinSearch
    prefix: linsearch
    tracker: https://github.com/TIBHannover/annif_automated_indexing_at_tib/issues
    uri_format: https://purl.org/linsearch/$1
    version.iri: https://purl.org/linsearch/version/20230105
tib.lis:
  example: Activity
  mappings:
    tib: lis
  prefix: tib.lis
  tib:
    description: The Industrial Data Ontology is an upper ontology for industrial
      data, inspired by the ISO 15926-2 data model and Basic Formal Ontology.
    homepage: https://rds.posccaesar.org/ontology/lis14/ont/core/
    keywords:
    - NFDI4ING
    - engineering
    name: Industrial Data Ontology
    prefix: lis
    uri_format: http://rds.posccaesar.org/ontology/lis14/rdl/$1
    version.iri: http://rds.posccaesar.org/ontology/lis14/ont/core/4.0
tib.mat:
  example: Accesories
  mappings:
    tib: mat
  prefix: tib.mat
  tib:
    description: The material properties ontology provides the vocabulary to describe
      the composition of building elements.
    download_rdf: https://bimerr.iot.linkeddata.es/def/material-properties/ontology.ttl
    homepage: https://bimerr.iot.linkeddata.es/def/material-properties/
    keywords:
    - FID BAUdigital
    - Digital Planning and Construction
    - NFDI4ING
    - engineering
    name: Material properties ontology
    prefix: mat
    tracker: https://github.com/oeg-upm/bimerr-material-properties/issues
    uri_format: http://bimerr.iot.linkeddata.es/def/material-properties#$1
tib.mdo:
  mappings:
    tib: mdo
  no_own_terms: true
  prefix: tib.mdo
  repository: https://github.com/LiUSemWeb/Materials-Design-Ontology
  tib:
    description: The Materials Design Ontology is designed to enable semantic query
      and integrated query over multiple databases. By generating mappings between
      MDO and the schemas of materials databases, we can create MDO-enabled query
      interfaces. The querying can occur, for instance, via MDO-based query expansion,
      MDO-based mediation or through MDO-enabled data warehouses.
    download_owl: https://liusemweb.github.io/mdo/full/1.0/mdo-full.owl
    homepage: https://liusemweb.github.io/mdo/full/1.0/index.html#namespaces
    keywords:
    - NFDI4ING
    - material science
    name: Materials Design Ontology - Full
    prefix: mdo
    tracker: https://github.com/LiUSemWeb/Materials-Design-Ontology/issues
    uri_format: https://w3id.org/mdo/$1
    version.iri: https://w3id.org/mdo/full/1.0/
tib.mdv:
  download_skos: https://data.nist.gov/od/ds/67C783D4BA814C8EE05324570681708A1899/NMRRVocab20210726.rdf
  example: '953'
  mappings:
    tib: mdv
  prefix: tib.mdv
  tib:
    description: 'A version of the Materials Data Vocabulary structured as Simple
      Knowledge Organization System (SKOS). The XML was originally created by the
      TemaTres software. This vocabulary describes the applicability to material science
      of records in the NIST Materials Resource Registry (NMRR - https://materials.registry.nist.gov/).
      The NMRR allows for the registration of materials resources, bridging the gap
      between existing resources and the end users. The NMRR functions as a node in
      a federated system, making the registered information available for research
      to the materials community. This is being developed at the National Institute
      of Standards and Technology and is made available to solicit comments from the
      Material Science community. (An Excel version of the file is also included in
      the distributions for ease of use.) Please cite this resource as: Medina-Smith,
      Andrea; Becker, Chandler (2017), Simple Knowledge Organization System (SKOS)
      version of Materials Data Vocabulary , National Institute of Standards and Technology,
      https://doi.org/10.18434/T4/1435037'
    homepage: https://data.nist.gov/od/id/67C783D4BA814C8EE05324570681708A1899
    keywords:
    - NFDI4ING
    - material science
    name: Simple Knowledge Organization System (SKOS) version of Materials Data Vocabulary
    prefix: mdv
    uri_format: https://data.nist.gov/od/dm/nmrr/vocab$1
  uri_format: https://data.nist.gov/od/dm/nmrr/vocab/?tema=$1
tib.meth:
  example: acceleratormassspectrometry
  mappings:
    tib: meth
  prefix: tib.meth
  tib:
    description: This concept scheme contains skos concepts for analysis methods used
      to produce observation results with information about the physical properties,
      chemical or isotopic composition, crystallography, or molecular structure of
      material samples. Based on spreadsheet compilation of method vocabularies from
      Geo.X, GEOROC, PetDB and OSIRIS-REx. Definitions added and updated based on
      web research, and SKOS serialization by S.M. Richard. Note that although there
      are high-level method categories for 'Physical property measurements' and the
      'Bioanalytical method', these are placeholders and only include a few examples
      that are relevant to analytical methods in geo- or cosmochemistry.
    download_rdf: https://raw.githubusercontent.com/SArndt-TIB/Vocabulary/refs/heads/master/geochemistry/GeochemAnalyticalMethod.ttl
    homepage: https://amds-ldeo.github.io/Vocabulary/geochemistry/html/GeochemAnalyticalMethod.html
    keywords:
    - ESS
    - earth sciences
    name: Analytical methods for geochemistry
    prefix: meth
    tracker: https://github.com/amds-ldeo/Vocabulary/issues
    uri_format: https://w3id.org/geochem/1.0/analyticalmethod/$1
tib.mt:
  example: accesibility-information-for-vehicles
  mappings:
    tib: mt
  prefix: tib.mt
  tib:
    description: Controlled vocabulary for the classification of the theme for a mobility
      dataset.
    homepage: https://w3id.org/mobilitydcat-ap/mobility-theme
    keywords:
    - FID move
    - NFDI4ING
    - traffic engineering
    name: Mobility Theme
    prefix: mt
    tracker: https://github.com/mobilityDCAT-AP/controlled-vocabularies/issues
    uri_format: https://w3id.org/mobilitydcat-ap/mobility-theme/$1
    version.iri: https://w3id.org/mobilitydcat-ap/mobility-theme/1.1.1
tib.n0:
  example: AnalogSignal
  mappings:
    tib: n0
  prefix: tib.n0
  tib:
    description: "The Audio Commons Ontology has been created in the context of the\
      \ European project [Audio Commons](https://www.audiocommons.org/), which were\
      \ aimed at favouring sharing and reuse of audio content (both of musical and\
      \ non-musical nature), specially using [Creative Commons](https://creativecommons.org/)\
      \ licenses.\n\nIt is designed specifically to integrate access to multiple heterogeneously\
      \ structured audio content providers. In particular the following ones have\
      \ been considered in the project:\n- [Freesound](https://freesound.org/), a\
      \ collaborative database of Creative Commons Licensed sounds;\n- [Jamendo](https://www.jamendo.com/),\
      \ a music website for independent artists;\n- [Europeana Sounds](https://www.eusounds.eu/),\
      \ a European project collecting and sharing data from several archives of sounds\
      \ and sound-related media;\n- [Internet Archive](https://archive.org/), a non-profit\
      \ library of millions of freely accessible media contents.\n\n### The base model\n\
      <center> ![A diagram showing the entities Work, Expression, Manifestation, Item](./img/FRBR-Group-1-entities-and-basic-relations.svg.png)\
      \ </center>\nThe Audio Commons ontology is based on [Functional Requirements\
      \ for Bibliographic Records (FRBR)](https://en.wikipedia.org/wiki/Functional_Requirements_for_Bibliographic_Records),\
      \ a bibliographic model designed for user tasks of retrieval and access in online\
      \ library catalogues and bibliographic databases. FRBR distinguish the products\
      \ of intellectual or artistic endeavor in four main classes: work, expression,\
      \ manifestation, item. It is available as RDF vocabulary at https://vocab.org/frbr/core.\
      \ For further information on FRBR, check the [standard](https://repository.ifla.org/handle/123456789/811).\n\
      \nAnother important model related to audio is the [Music Ontology](http://musicontology.com/),\
      \ which is also based on the FRBR model. Our ontology is more generic than the\
      \ Music Ontology but is interoperable with it to support the specificities of\
      \ music-related audio content.\n\nThe Audio Commons ontology works also in conjunction\
      \ with\n- [Dublin Core](https://www.dublincore.org/specifications/dublin-core/dcmi-terms/)\
      \ for basic metadata,\n- [EBU Core](https://www.ebu.ch/metadata/ontologies/ebucore/)\
      \ for technical properties of audio files,\n- [SKOS](https://www.w3.org/TR/skos-primer/)\
      \ to support taxonomic classifications,\n- [Creative Commons Licensing schema](https://creativecommons.org/ns)\
      \ to represent media licensing,\n- [Event ontology](http://motools.sf.net/event/event.html)\
      \ for the formalisation of events,\n- [Audio Features Ontology](https://w3id.org/afo/onto/)\
      \ for the characterisation of audio features.\n\n### Ontology overview\n\n![A\
      \ diagram showing the main classes of the Audio Commons ontology](./img/AC-Ontology-Skeleton.png)\n\
      \nThe figure above shows the most general classes and properties of the Audio\
      \ Commons ontology and their relationship with classes of the FRBR and the Music\
      \ Ontology:\n- **`ac:AudioExpression`**, the specific intellectual or artistic\
      \ form that a work takes each time it is _realised_, in the audio domain, e.g.,\
      \ the recording or synthesis of music or sounds;\n- **`ac:AudioManifestation`**,\
      \ the physical embodiment of an audio expression, e.g., a musical track, a sound,\
      \ an album; \n- **`ac:AudioItem`**, a single exemplar of an audio manifestation,\
      \ e.g., a copy of a CD or a specific media file.\n\nThe FRBR class Work, representing\
      \ a distinct intellectual or artistic creation on a more conceptual level, has\
      \ not been specialised in Audio Commons.\n\nThe Audio Commons ontology provides\
      \ a generic schema for audio classification through the property **`ac:audioCategory`**\
      \ that associates any audio expression, manifestation, or item to some generic\
      \ **`ac:AudioCategory`**. These two terms can be specialised to provide spefic\
      \ categorisations.\n\n### Manifestations: audio clips and collections\n\n![A\
      \ diagram showing the main classes of the Audio Commons ontology](./img/AC-Ontology-Manifestation.png)\n\
      \nThe figure above shows classes and properties related to audio manifestations.\
      \ An instance of **`ac:AudioClip`**, a subclass of `ac:AudioManifestation`,\
      \ is any audio segment that has been published in some form or uploaded for\
      \ consumption, for example, a track in a music label's repository or a sound\
      \ in an audio repository, library or archive.\n\nThe class **`ac:AudioCollection`**,\
      \ another subclass of `ac:AudioManifestation`, is used to represent collections\
      \ of audio clips. The class **`ac:AudioCollectionNode`** is used to represent\
      \ single nodes of a collection, offering local information like the index in\
      \ the collection and pointers to previous and next nodes. The separation between\
      \ the collection node and its actual content (e.g., an `ac:AudioClip`) permits\
      \ the same content to be shared in multiple collections.\n\nThe content of each\
      \ node of a collection is not limited to an `ac:AudioClip`, but may contain\
      \ any `ac:AudioManifestation`. Collections can thus contain other collections\
      \ to support specific cases, e.g. a mapping to the Music Ontology model where\
      \ an `mo:Release` can contain multiple `mo:Record`(s) that can in turn contain\
      \ multiple `mo:Track`(s).\n### Items: audio files\n![A diagram showing ac:Item\
      \ class and related class and properties](./img/AC-Ontology-Item.png)\n\nAn\
      \ `ac:AudioItem` is a concrete exemplar of an audio manifestation. In our domain,\
      \ the main exemplars are the actual audio files. \n\nThe corresponding class\
      \ **`ac:AudioFile`** is a subclass of `ac:AudioItem`. It is subclass of `ebu:MediaResource`\
      \ too and the corresponging properties of EBU Core can be used to describe the\
      \ file (e.g., `ebu:hasEncodingFormat`, `ebu:fileSize`).\n\n### Expressions:\
      \ audio signals\n![A diagram showing ac:Expression class and related class and\
      \ properties](./img/AC-Ontology-Expression.png)\n\nWhile `ac:AudioFile` represents\
      \ a concrete file encoded in a certain format, **`ac:DigitalSignal`** is the\
      \ representation of the corresponding digital signal. `ac:DigitalSignal` is\
      \ a subclass of `ac:MusicalExpression`. \n\nThe data properties `ac:sampleRate`,\
      \ `ac:bitsPerSample`, and `ac:channels`, associate a signal with its basic features\
      \ specific to digital representations.\n\nThe property `ac:publicationOf` can\
      \ be used to associate an `ac:AudioClip` with the corresponding digital signal.\
      \ The property `ac:encodes` instead, associates an `ac:AudioFile` with the encoded\
      \ digital signal.\n\n### Events: recording/syntesis\n![A diagram showing ac:SignalProduction\
      \ class and related class and properties!](./img/AC-Ontology-SignalProduction.png)\n\
      \nThe description of temporal events is crucial to formalise and document transitions\
      \ in the workflow of audio production and publication. The class `event:Event`\
      \ of the Event Ontology is thus specialised for specific actions that are interesting\
      \ for the audio domain.\n\nUsing the `event:Event` class, details of an event\
      \ such as its location in time and space, its factor and its products may be\
      \ explicitly described. Moreover, events can be composed using the property\
      \ `event:sub_event`, to build complex events.\n\nThe class `ac:SignalProduction`\
      \ represents the act of producing a `ac:Signal`, which could be either an `ac:AnalogSignal`\
      \ or a `ac:DigitalSignal`. This is complemented by **`ac:Recording`**, representing\
      \ the process of recording a sound (`ac:Sound`) or the product of **`ac:Synthesis`**,\
      \ in case of artificially generated sounds. \n\n### Events (continued): publication\n\
      ![A diagram showing ac:Publication class and related class and properties!](./img/AC-Ontology-Publication.png)\n\
      \nThe event **`ac:AudioPublication`** represents the public release of a piece\
      \ of work, e.g., the release of a new album by a band.\n\n### Usage Example\n\
      ![A diagram showing an example of ontology usage!](./img/AC_Example-AudioClip.png)\n\
      \nThe figure above shows an example of use of the Audio Commons ontology to\
      \ represent a sound from the Freesound database. For simplicity only the classes\
      \ `ac:AudioClip`, `ac:AudioFile`, and `ac:AudioCategory` are used in this case."
    download_rdf: https://raw.githubusercontent.com/AudioCommons/ac-ontology/master/aco.ttl
    homepage: http://www.audiocommons.org/ac-ontology/aco.html
    keywords:
    - NFDI4ING
    - engineering
    name: The Audio Commons Ontology
    prefix: n0
    uri_format: https://w3id.org/ac-ontology/aco#$1
tib.ofm:
  example: Anthropomorphic_Robot
  mappings:
    tib: ofm
  prefix: tib.ofm
  repository: https://github.com/enegri/OFM
  tib:
    description: Ontology for manufacturing and logistics
    download_owl: https://raw.githubusercontent.com/enegri/OFM/master/OFM.owl
    homepage: https://github.com/enegri/OFM
    keywords:
    - NFDI4ING
    - engineering
    name: Ontology for manufacturing and logistics
    prefix: ofm
    tracker: https://github.com/enegri/OFM/issues
    uri_format: http://www.ontologies.com/Ontology3197.owl#$1
tib.re:
  example: Advanced_Meter
  homepage: https://github.com/DataCreater/GBEnergy
  mappings:
    tib: re
  prefix: tib.re
  repository: https://github.com/DataCreater/GBEnergy
  tib:
    description: An ontology of the Retail Energy Market of Great Britain created
      by Lidcast Data Limited.
    download_owl: https://raw.githubusercontent.com/DataCreater/GBEnergy/refs/heads/main/RetailEnergy0.0.1.owl
    keywords:
    - NFDI4Energy
    license: https://creativecommons.org/licenses/by-sa/3.0/
    name: Retail Energy Market of Great Britain
    prefix: re
    tracker: https://github.com/DataCreater/GBEnergy/issues
    uri_format: https://www.lidcast.co.uk/ontologies/RE#$1
    version.iri: https://www.lidcast.co.uk/ontologies/RE0.0.1
tib.sto:
  example: AiiClassification
  mappings:
    tib: sto
  prefix: tib.sto
  tib:
    description: An ontology to describe standards related to Industry 4.0 and Smart
      Manufacturing
    download_rdf: https://i40-tools.github.io/I40KG/docs/serializations/ontology.ttl
    homepage: https://i40-tools.github.io/I40KG/docs/index.html
    keywords:
    - NFDI4ING
    - engineering
    name: Standards Ontology
    prefix: sto
    uri_format: https://w3id.org/i40/sto#$1
    version.iri: https://w3id.org/i40/sto/iot/0.1/concerns/
tib.ts:
  contact:
    email: baum@zbmed.de
    github: rombaum
    name: Roman Baum
    orcid: 0000-0001-5246-9351
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: An instance of the EBI Lookup Service deployed by TIB
  example: abcd
  homepage: https://terminology.tib.eu
  name: TIB Terminology Service
  prefix: tib.ts
  uri_format: https://terminology.tib.eu/ts/ontologies/$1
tib.tso:
  example: AutomationSystem
  mappings:
    tib: tso
  prefix: tib.tso
  tib:
    description: The scope of the TUBES ontology is to explicitly define the topology
      of interconnected building service system and their relationship to the spatial
      structure. It has a strong alignment to other ontologies within the W3C community
      and aims to provide the means to link information at data level within the AEC
      industry.
    download_rdf: https://raw.githubusercontent.com/RWTH-E3D/tso/master/tubes.ttl
    homepage: https://rwth-e3d.github.io/tso/index.html
    keywords:
    - NFDI4ING
    - engineering
    name: TUBES system ontology
    prefix: tso
    uri_format: https://w3id.org/tso#$1
    version.iri: https://w3id.org/v0.3/tubes
tigrfam:
  biocontext:
    prefix: TIGRFAM
  contributor_extras:
  - email: cjmungall@lbl.gov
    github: cmungall
    name: Chris Mungall
    orcid: 0000-0002-6601-2165
  edam:
    description: Accession number of an entry (family) from the TIGRFam database.
    name: TIGRFam
    obsolete: false
    prefix: '1141'
  mappings:
    biocontext: TIGRFAM
    edam: '1141'
    miriam: tigrfam
    n2t: tigrfam
    ncbi: TIGRFAM
    prefixcommons: tigrfams
  miriam:
    deprecated: false
    description: TIGRFAMs is a resource consisting of curated multiple sequence alignments,
      Hidden Markov Models (HMMs) for protein sequence classification, and associated
      information designed to support automated annotation of (mostly prokaryotic)
      proteins.
    homepage: http://www.jcvi.org/cgi-bin/tigrfams/Listing.cgi
    id: '00000315'
    name: TIGRFAMS
    namespaceEmbeddedInLui: false
    pattern: ^TIGR\d+$
    prefix: tigrfam
    sampleId: TIGR00010
    uri_format: http://www.jcvi.org/cgi-bin/tigrfams/HmmReportPage.cgi?acc=$1
  n2t:
    description: TIGRFAMs is a resource consisting of curated multiple sequence alignments,
      Hidden Markov Models (HMMs) for protein sequence classification, and associated
      information designed to support automated annotation of (mostly prokaryotic)
      proteins.
    example: TIGR00010
    homepage: http://www.jcvi.org/cgi-bin/tigrfams/Listing.cgi
    name: TIGRFAM at JCVI
    namespaceEmbeddedInLui: false
    pattern: ^TIGR\d+$
    prefix: tigrfam
    uri_format: http://www.jcvi.org/cgi-bin/tigrfams/HmmReportPage.cgi?acc=$1
  ncbi:
    example: TIGR00094
    homepage: http://www.tigr.org/TIGRFAMs/index.shtml
    name: TIGR protein families
    prefix: TIGRFAM
  prefix: tigrfam
  prefixcommons:
    description: TIGRFAMs are protein families based on Hidden Markov Models or HMMs.
      This collection is used to see the curated seed alignmet for each TIGRFam, the
      full alignment of all family members and the cutoff scores for inclusion in
      each of the TIGRFAMs.
    example: TIGR00254
    homepage: http://www.jcvi.org/cms/research/projects/tigrfams/
    keywords:
    - protein
    name: TIGRFAMs HMM collection at the J. Craig Venter Institute
    pattern: ^TIGR\d+$
    prefix: tigrfams
    synonyms:
    - jcvi.tigrfams
    uri_format: http://cmr.jcvi.org/cgi-bin/CMR/HmmReport.cgi?hmm_acc=$1
  references:
  - https://ftp.ncbi.nlm.nih.gov/hmm/TIGRFAMs/license_and_availability.txt
  - https://github.com/biopragmatics/bioregistry/issues/366
  uri_format: https://www.ncbi.nlm.nih.gov/cdd?term=$1
time:
  aberowl:
    description: OWL-Time is an OWL-2 DL ontology of temporal concepts, for describing
      the temporal properties of resources in the world or described in Web pages.
      The ontology provides a vocabulary for expressing facts about topological (ordering)
      relations among instants and intervals, together with information about durations,
      and about temporal position including date-time information. Time positions
      and durations may be expressed using either the conventional (Gregorian) calendar
      and clock, or using another temporal reference system such as Unix-time, geologic
      time, or different calendars.
    download_owl: http://aber-owl.net/media/ontologies/TIME/2/time.owl
    homepage: https://www.w3.org/TR/owl-time/
    name: OWL-Time
    prefix: TIME
    version: '2017'
  bartoc:
    abbreviation: time
    description: OWL-Time is an OWL-2 DL ontology of temporal concepts, for describing
      the temporal properties of resources in the world or described in Web pages.
      The ontology provides a vocabulary for expressing facts about topological (ordering)
      relations among instants and intervals, together with information about durations,
      and about temporal position including date-time information. Time positions
      and durations may be expressed using either the conventional (Gregorian) calendar
      and clock, or using another temporal reference system such as Unix-time, geologic
      time, or different calendars.
    homepage: https://www.w3.org/TR/owl-time/
    license: CC-BY-4.0
    name: Time Ontology
    prefix: '18311'
  bioportal:
    contact:
      email: chris.little@metoffice.gov.uk
      name: Chris Little
    description: OWL-Time is an OWL-2 DL ontology of temporal concepts, for describing
      the temporal properties of resources in the world or described in Web pages.
      The ontology provides a vocabulary for expressing facts about topological (ordering)
      relations among instants and intervals, together with information about durations,
      and about temporal position including date-time information. Time positions
      and durations may be expressed using either the conventional (Gregorian) calendar
      and clock, or using another temporal reference system such as Unix-time, geologic
      time, or different calendars.
    homepage: https://www.w3.org/TR/owl-time/
    name: OWL-Time
    prefix: TIME
    version: '2017'
  contact:
    email: dr.shorthair@pm.me
    github: dr-shorthair
    name: Simon Cox
    orcid: 0000-0002-3884-3420
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: Owl-time is an owl-2 dl ontology of temporal concepts, for describing
    the temporal properties of resources in the world or described in web pages. the
    ontology provides a vocabulary for expressing facts about topological (ordering)
    relations among instants and intervals, together with information about durations,
    and about temporal position including date-time information. time positions and
    durations may be expressed using either the conventional (gregorian) calendar
    and clock, or using another temporal reference system such as unix-time, geologic
    time, or different calendars.
  example: DateTimeDescription
  fairsharing:
    abbreviation: TIME
    contact:
      email: simon.cox@csiro.au
      name: Simon Cox, Chris Little
      orcid: 0000-0002-3884-3420
    description: OWL-Time is an OWL-2 DL ontology of temporal concepts, for describing
      the temporal properties of resources in the world or described in Web pages.
      The ontology provides a vocabulary for expressing facts about topological (ordering)
      relations among instants and intervals, together with information about durations,
      and about temporal position including date-time information. Time positions
      and durations may be expressed using either the conventional (Gregorian) calendar
      and clock, or using another temporal reference system such as Unix-time, geologic
      time, or different calendars.
    domains:
    - Resource metadata
    homepage: https://www.w3.org/TR/owl-time/
    license: CC-BY-4.0
    name: OWL-Time
    prefix: FAIRsharing.hw3bh2
    subjects:
    - Subject Agnostic
    user_defined_tags:
    - Data coordination
    - Metadata standardization
  github_request_issue: 505
  homepage: https://www.w3.org/TR/owl-time/
  lov:
    description: This vocabulary defines temporal entities such as time intervals,
      their properties and relationships.
    homepage: http://www.w3.org/TR/owl-time
    keywords:
    - Time
    modified: '2017-04-06'
    name: Time Ontology
    prefix: time
    uri_prefix: http://www.w3.org/2006/time#$1
  mappings:
    aberowl: TIME
    bartoc: '18311'
    bioportal: TIME
    fairsharing: FAIRsharing.hw3bh2
    lov: time
    tib: time
    zazuko: time
  name: Time Ontology in OWL
  prefix: time
  repository: https://github.com/w3c/sdw
  tib:
    description: Description of date and time structured with separate values for
      the various elements of a calendar-clock system. The temporal reference system
      is fixed to Gregorian Calendar, and the range of year, month, day properties
      restricted to corresponding XML Schema types xsd:gYear, xsd:gMonth and xsd:gDay,
      respectively.
    download_rdf: https://raw.githubusercontent.com/w3c/sdw/gh-pages/time/rdf/time.ttl
    homepage: https://www.w3.org/TR/owl-time/
    keywords:
    - FAIR Data Spaces
    - NFDI4CHEM
    - ESS
    name: Time Ontology in OWL
    prefix: time
    tracker: https://github.com/w3c/sdw/issues
    uri_format: http://www.w3.org/2006/time#$1
    version.iri: http://www.w3.org/2006/time#2016
  uri_format: http://www.w3.org/2006/time#$1
  zazuko:
    prefix: time
    uri_format: http://www.w3.org/2006/time#$1
tkg:
  cellosaurus:
    category: Cell line collections (Providers)
    homepage: http://www2.idac.tohoku.ac.jp/dep/ccr/
    name: Tohoku University cell line catalog
    prefix: TKG
    uri_format: http://www2.idac.tohoku.ac.jp/dep/ccr/TKGdate/TKGvo10%n/$1.html
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: Collection of cell lines by Tohoku University. This includes transplantable
    animal cell lines, such as Yoshida sarcoma and rat ascites hepatoma (AH series)
    cell lines as well as human, murine cell lines and hybridoma cells.
  example: '0221'
  homepage: http://www2.idac.tohoku.ac.jp/dep/ccr/
  mappings:
    cellosaurus: TKG
  name: Tohoku University cell line catalog
  pattern: ^\d+$
  prefix: tkg
  uri_format: http://www2.idac.tohoku.ac.jp/dep/ccr/TKGdate/TKGvol08/$1.html
tngb:
  cellosaurus:
    category: Cell line collections (Providers)
    homepage: https://biobanknetwork.telethon.it/
    name: Telethon Network of Genetic Biobanks
    prefix: TNGB
    uri_format: https://biobanknetwork.telethon.it/Sample/View?sampleId=$1
  example: '67035'
  mappings:
    cellosaurus: TNGB
  pattern: ^\d+$
  prefix: tngb
to:
  aberowl:
    description: A controlled vocabulary to describe phenotypic traits in plants.
    download_owl: http://aber-owl.net/media/ontologies/TO/13/to.owl
    homepage: http://browser.planteome.org/amigo
    name: Plant Trait Ontology
    prefix: TO
  agroportal:
    contact:
      email: cooperl@oregonstate.edu
      name: Laurel Cooper
    description: An ontology that describes phenotypic traits in plants. Each trait
      is a distinguishable feature, characteristic, quality or phenotypic feature
      of a developing or mature plant.
    example_uri: http://purl.obolibrary.org/obo/TO_0000064
    homepage: https://planteome.org/
    license: CC-BY-4.0
    name: Plant Trait Ontology
    prefix: TO
    publications:
    - https://planteome.org/references
    repository: https://github.com/Planteome/plant-trait-ontology
    version: November 2025
  biocontext:
    prefix: TO
  bioportal:
    contact:
      email: jaiswalp@oregonstate.edu
      name: Pankaj Jaiswal
    description: A controlled vocabulary to describe phenotypic traits in plants.
      Each trait is a distinguishable feature, characteristic, quality or phenotypic
      feature of a developing or mature plant, or a plant part.
    homepage: http://www.planteome.org
    name: Plant Trait Ontology
    prefix: PTO
    version: May 2025
  example: '0000630'
  fairsharing:
    abbreviation: TO
    contact:
      email: cooperl@science.oregonstate.edu
      name: Laurel Cooper
      orcid: 0000-0002-6379-8932
    description: A controlled vocabulary to describe phenotypic traits in plants.
      Each trait is a distinguishable feature, characteristic, quality or phenotypic
      feature of a developing or mature plant, or a plant part. The TO is part of
      the Planteome Project.
    domains:
    - phenotype
    - structure
    - life cycle
    homepage: http://browser.planteome.org/amigo/term/TO:0000387#display-lineage-tab
    license: CC-BY-4.0
    name: Plant Trait Ontology
    prefix: FAIRsharing.w69t6r
    publications:
    - doi: 10.1093/nar/gkx1152
      pubmed: '29186578'
      title: 'The Planteome database: an integrated resource for reference ontologies,
        plant genomics and phenomics'
      year: 2017
    repository: https://github.com/Planteome/plant-trait-ontology
    subjects:
    - Botany
  mappings:
    aberowl: TO
    agroportal: TO
    biocontext: TO
    bioportal: PTO
    fairsharing: FAIRsharing.w69t6r
    obofoundry: to
    ols: to
    ontobee: TO
    prefixcommons: pto
    tib: to
    wikidata.entity: Q81661818
  obofoundry:
    appears_in:
    - agro
    contact: jaiswalp@science.oregonstate.edu
    contact.github: jaiswalp
    contact.label: Pankaj Jaiswal
    contact.orcid: 0000-0002-1005-8383
    deprecated: false
    description: A controlled vocabulary to describe phenotypic traits in plants.
    domain: phenotype
    download.obo: http://purl.obolibrary.org/obo/to.obo
    download.owl: http://purl.obolibrary.org/obo/to.owl
    homepage: http://browser.planteome.org/amigo
    license: CC BY 4.0
    license.url: https://creativecommons.org/licenses/by/4.0/
    logo: http://planteome.org/sites/default/files/garland_logo.PNG
    name: Plant Trait Ontology
    preferredPrefix: TO
    prefix: to
    publications:
    - id: https://www.ncbi.nlm.nih.gov/pubmed/29186578
      title: 'The Planteome database: an integrated resource for reference ontologies,
        plant genomics and phenomics.'
    repository: https://github.com/Planteome/plant-trait-ontology
  ols:
    description: A controlled vocabulary to describe phenotypic traits in plants.
    download_owl: http://purl.obolibrary.org/obo/to.owl
    homepage: http://browser.planteome.org/amigo
    name: Plant Trait Ontology
    prefix: to
    tracker: https://github.com/Planteome/plant-trait-ontology/issues
    version: '2025-11-07'
    version.iri: http://purl.obolibrary.org/obo/to/releases/2025-11-07/to.owl
  ontobee:
    library: Library
    name: Plant Trait Ontology
    prefix: TO
  pattern: ^\d{7}$
  prefix: to
  prefixcommons:
    bioportal: '1037'
    description: A controlled vocabulary to describe phenotypic traits in plants.
      Each trait is a distinguishable feature, characteristic, quality or phenotypic
      feature of a developing or mature plant, or a plant part.
    example: TO_0000017
    homepage: http://www.gramene.org/plant_ontology/
    keywords:
    - obo
    - plant
    - trait
    name: Plant Trait Ontology
    pattern: ^TO_\d{7}$
    prefix: pto
    synonyms:
    - to
    - gramene.po
  publications:
  - doi: 10.1093/nar/gkx1152
    pmc: PMC5753347
    pubmed: '29186578'
    title: 'The Planteome database: an integrated resource for reference ontologies,
      plant genomics and phenomics'
    year: 2018
  tib:
    description: An ontology that describes phenotypic traits in plants. Each trait
      is a distinguishable feature, characteristic, quality or phenotypic feature
      of a developing or mature plant.
    download_owl: http://purl.obolibrary.org/obo/to.owl
    homepage: https://obofoundry.org/ontology/to.html
    keywords:
    - ESS
    - DataPLANT
    - earth sciences
    name: Plant Trait Ontology
    prefix: to
    version.iri: http://purl.obolibrary.org/obo/to/releases/2025-11-07/to.owl
  uri_format: http://purl.obolibrary.org/obo/TO_$1
togoid:
  contact:
    email: ktym@dbcls.jp
    github: ktym
    name: Toshiaki Katayama
    orcid: 0000-0003-2391-0384
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: TogoID is an ID conversion service implementing unique features with
    an intuitive web interface and an API for programmatic access. TogoID supports
    datasets from various biological categories such as gene, protein, chemical compound,
    pathway, disease, etc. TogoID users can perform exploratory multistep conversions
    to find a path among IDs. To guide the interpretation of biological meanings in
    the conversions, we crafted an ontology that defines the semantics of the dataset
    relations. (from https://togoid.dbcls.jp/)
  download_owl: https://raw.githubusercontent.com/togoid/togoid-config/main/ontology/togoid-ontology.ttl
  example: AffyProbeset
  homepage: https://togoid.dbcls.jp/ontology
  name: TogoID Ontology
  prefix: togoid
  publications:
  - doi: 10.1093/bioinformatics/btac491
    pmc: PMC9438948
    pubmed: '35801937'
    title: 'TogoID: an exploratory ID converter to bridge biological datasets'
    year: 2022
  rdf_uri_format: https://togoid.dbcls.jp/ontology#$1
  repository: https://github.com/dbcls/togoid/togoid-config
  uri_format: https://togoid.dbcls.jp/#$1
togovar:
  integbio:
    alt_name: Integrated database of Japanese genomic variation
    description: 'TogoVar (NBDC''s integrated database of Japanese genomic variation)
      is a database that has collected and organized genome sequence differences between
      individuals (variants) in the Japanese population and disease information associated
      with them. TogoVar provides variant frequencies in the Japanese population that
      have been aggregated across research projects. Two available datasets, JGA-NGS
      and JGA-SNP, are obtained by aggregating individual genomic data that have been
      registered in the NBDC Human Database / Japanese Genotype-phenotype Archive
      (JGA). In addition, TogoVar integrates information related to genotypes or phenotypes
      that has been compiled independently in a variety of different databases and
      provides information for interpreting variants in a one-stop, easy-to-understand
      manner.

      Users can learn how to use it by a movie: https://togotv.dbcls.jp/en/20181012.html'
    fairsharing: biodbcore-001182/
    homepage: https://togovar.org/
    information_keywords:
    - Sequence
    maintainer: NBDC (Japan Science and Technology Agency Department of NBDC Program)||DBCLS
      (Database Center for Life Science, Research Organization of Information and
      Systems)
    name: TogoVar
    prefix: nbdc02359
    pubmeds: []
    status: Active
    target_keywords:
    - Genome/Gene
    - Genetic variation
    - Health/Disease
  mappings:
    integbio: nbdc02359
    miriam: togovar
    togoid: Togovar
  miriam:
    deprecated: false
    description: TogoVar (A comprehensive Japanese genetic variation database) is
      a database that has collected and organized genome sequence differences between
      individuals (variants) in the Japanese population and disease information associated
      with them.
    homepage: https://grch38.togovar.org/
    id: '00001006'
    name: TogoVar
    namespaceEmbeddedInLui: false
    pattern: ^tgv[0-9]+$
    prefix: togovar
    sampleId: tgv139393198
    uri_format: https://grch38.togovar.org/variant/$1
  prefix: togovar
  togoid:
    catalog: nbdc02359
    description: 'TogoVar (NBDC''s integrated database of Japanese genomic variation)
      is a database that has collected and organized genome sequence differences between
      individuals (variants) in the Japanese population and disease information associated
      with them. TogoVar provides variant frequencies in the Japanese population that
      have been aggregated across research projects. Two available datasets, JGA-NGS
      and JGA-SNP, are obtained by aggregating individual genomic data that have been
      registered in the NBDC Human Database / Japanese Genotype-phenotype Archive
      (JGA). In addition, TogoVar integrates information related to genotypes or phenotypes
      that has been compiled independently in a variety of different databases and
      provides information for interpreting variants in a one-stop, easy-to-understand
      manner. Users can learn how to use it by a movie: https://togotv.dbcls.jp/en/20181012.html'
    examples:
    - tgv100005930
    - tgv100000890
    - tgv16331
    - tgv10000341
    - tgv21330879
    - tgv15847
    - tgv1354996
    - tgv100002132
    - tgv16568524
    - tgv62035164
    keywords:
    - Variant
    name: TogoVar variant
    pattern: ^(?tgv\d+)$
    prefix: Togovar
    uri_format: http://identifiers.org/togovar/$1
tokue:
  cellosaurus:
    category: Cell line databases/resources
    homepage: http://cell-lines.toku-e.com
    name: TOKU-E Cell-culture Database
    prefix: TOKU-E
    uri_format: http://cell-lines.toku-e.com/Cell-Lines_$1.html
  deprecated: true
  mappings:
    cellosaurus: TOKU-E
  prefix: tokue
tol:
  bartoc:
    description: The Tree of Life Web Project is a collection of information about
      biodiversity compiled collaboratively by hundreds of expert and amateur contributors.
      Its goal is to contain a page with pictures, text, and other information for
      every species and for each group of organisms, living or extinct. Connections
      between Tree of Life web pages follow phylogenetic branching patterns between
      groups of organisms, so visitors can browse the hierarchy of life and learn
      about phylogeny and evolution as well as the characteristics of individual groups.
    homepage: http://tolweb.org/tree/phylogeny.html
    prefix: '400'
    wikidata_database: Q2300489
  biocontext:
    prefix: TOL
  contributor_extras:
  - email: meghan.balk@gmail.com
    github: megbalk
    name: Meghan Balk
    orcid: 0000-0003-2699-3066
  mappings:
    bartoc: '400'
    biocontext: TOL
    miriam: tol
    n2t: tol
    wikidata: P5221
    wikidata.entity: Q2300489
  miriam:
    deprecated: false
    description: "The Tree of Life Web Project (ToL) is a collaborative effort of\
      \ biologists and nature enthusiasts from around the world. On more than 10,000\
      \ World Wide Web pages, the project provides information about biodiversity,\
      \ the characteristics of different groups of organisms, and their evolutionary\
      \ history (phylogeny). \r\n\r\nEach page contains information about a particular\
      \ group, with pages linked one to another hierarchically, in the form of the\
      \ evolutionary tree of life. Starting with the root of all Life on Earth and\
      \ moving out along diverging branches to individual species, the structure of\
      \ the ToL project thus illustrates the genetic connections between all living\
      \ things."
    homepage: http://tolweb.org/tree/
    id: '00000405'
    name: Tree of Life
    namespaceEmbeddedInLui: false
    pattern: ^\d+$
    prefix: tol
    sampleId: '98034'
    uri_format: http://tolweb.org/$1
  n2t:
    description: The Tree of Life Web Project (ToL) is a collaborative effort of biologists
      and nature enthusiasts from around the world. On more than 10,000 World Wide
      Web pages, the project provides information about biodiversity, the characteristics
      of different groups of organisms, and their evolutionary history (phylogeny).   Each
      page contains information about a particular group, with pages linked one to
      another hierarchically, in the form of the evolutionary tree of life. Starting
      with the root of all Life on Earth and moving out along diverging branches to
      individual species, the structure of the ToL project thus illustrates the genetic
      connections between all living things.
    example: '98034'
    homepage: http://tolweb.org/tree/
    name: Tree of Life Web
    namespaceEmbeddedInLui: false
    pattern: ^\d+$
    prefix: tol
    uri_format: http://tolweb.org/$1
  name: Tree of Life Web Project
  prefix: tol
  synonyms:
  - tol.webproj
  wikidata:
    description: identifier in the Tree of Life Web Project
    example:
    - '16952'
    - '5838'
    homepage: http://tolweb.org/tree/
    name: Tree of Life Web Project ID
    pattern: ^[1-9]\d*$
    prefix: P5221
    uri_format: http://tolweb.org/$1
topdb:
  biocontext:
    prefix: TOPDB
  edam:
    description: Unique identifier for a membrane protein from the TopDB database.
    name: Protein ID (TopDB)
    obsolete: false
    prefix: '2789'
  mappings:
    biocontext: TOPDB
    edam: '2789'
    miriam: topdb
    n2t: topdb
    prefixcommons: topdb
  miriam:
    deprecated: false
    description: The Topology Data Bank of Transmembrane Proteins (TOPDB) is a collection
      of transmembrane protein datasets containing experimentally derived topology
      information. It contains information gathered from the literature and from public
      databases availableon transmembrane proteins. Each record in TOPDB also contains
      information on the given protein sequence, name, organism and cross references
      to various other databases.
    homepage: http://topdb.enzim.hu/
    id: '00000503'
    name: TOPDB
    namespaceEmbeddedInLui: false
    pattern: ^[A-Z0-9]+$
    prefix: topdb
    sampleId: AP00378
    uri_format: http://topdb.enzim.hu/?m=show&id=$1
  n2t:
    description: The Topology Data Bank of Transmembrane Proteins (TOPDB) is a collection
      of transmembrane protein datasets containing experimentally derived topology
      information. It contains information gathered from the literature and from public
      databases availableon transmembrane proteins. Each record in TOPDB also contains
      information on the given protein sequence, name, organism and cross references
      to various other databases.
    example: AP00378
    homepage: http://topdb.enzim.hu/
    name: TOPDB at Hungarian Academy of Sciences
    namespaceEmbeddedInLui: false
    pattern: ^[A-Z0-9]+$
    prefix: topdb
    uri_format: http://topdb.enzim.hu/?m=show&id=$1
  name: Topology Data Bank of Transmembrane Proteins
  prefix: topdb
  prefixcommons:
    description: The Topology Data Bank of Transmembrane Proteins (TOPDB) is currently
      the most complete and comprehensive collection of transmembrane protein datasets
      containing experimentally derived topology information.
    example: AB00979
    homepage: http://topdb.enzim.hu
    keywords:
    - protein
    name: The Topology Databank
    pattern: ^[A-Z]+\d+$
    prefix: topdb
    uri_format: http://topdb.enzim.hu/?m=show&id=$1
topfind:
  biocontext:
    prefix: TOPFIND
  contact:
    email: chris.overall@ubc.ca
    github: null
    name: Christopher M. Overall
    orcid: 0000-0001-5844-2731
  fairsharing:
    abbreviation: TopFIND
    description: The Termini-Oriented Protein Function INferred Database (TopFIND)
      is an integrated knowledgebase focused on protein termini, their formation by
      proteases and functional implications. It contains information about the processing
      and the processing state of proteins and functional implications thereof derived
      from research literature, contributions by the scientific community and biological
      databases.
    homepage: https://topfind.clip.msl.ubc.ca/
    license: CC BY-ND 3.0
    name: Termini-Oriented Protein Function INferred Database
    prefix: FAIRsharing.rkpmhn
    publications:
    - doi: 10.1093/nar/gku1012
      pubmed_id: 25332401
      title: 'Proteome TopFIND 3.0 with TopFINDer and PathFINDer: database and analysis
        tools for the association of protein termini to pre- and post-translational
        events.'
    - doi: 10.1038/nmeth.1669
      pubmed_id: 21822272
      title: TopFIND, a knowledgebase linking protein termini with function.
    - doi: 10.1093/nar/gkr1025
      pubmed_id: 22102574
      title: TopFIND 2.0—linking protein termini with proteolytic processing and modifications
        altering protein function
    subjects:
    - Life Science
  homepage: https://topfind.clip.msl.ubc.ca
  mappings:
    biocontext: TOPFIND
    fairsharing: FAIRsharing.rkpmhn
    miriam: topfind
    n2t: topfind
    re3data: r3d100012721
  miriam:
    deprecated: false
    description: 'TopFIND is a database of protein termini, terminus modifications
      and their proteolytic processing in the species: Homo sapiens, Mus musculus,
      Arabidopsis thaliana, Saccharomyces cerevisiae and Escherichia coli.'
    homepage: http://clipserve.clip.ubc.ca/topfind
    id: '00000255'
    name: TopFind
    namespaceEmbeddedInLui: false
    pattern: ^([A-N,R-Z][0-9][A-Z][A-Z, 0-9][A-Z, 0-9][0-9])|([O,P,Q][0-9][A-Z, 0-9][A-Z,
      0-9][A-Z, 0-9][0-9])$
    prefix: topfind
    sampleId: Q9UKQ2
    uri_format: http://clipserve.clip.ubc.ca/topfind/proteins/$1
  n2t:
    description: 'TopFIND is a database of protein termini, terminus modifications
      and their proteolytic processing in the species: Homo sapiens, Mus musculus,
      Arabidopsis thaliana, Saccharomyces cerevisiae and Escherichia coli.'
    example: Q9UKQ2
    homepage: http://clipserve.clip.ubc.ca/topfind
    name: TopFind at University of British Columbia
    namespaceEmbeddedInLui: false
    pattern: ^([A-N,R-Z][0-9][A-Z][A-Z, 0-9][A-Z, 0-9][0-9])|([O,P,Q][0-9][A-Z, 0-9][A-Z,
      0-9][A-Z, 0-9][0-9])$
    prefix: topfind
    uri_format: http://clipserve.clip.ubc.ca/topfind/proteins/$1
  prefix: topfind
  provides: uniprot
  publications:
  - doi: 10.1093/nar/gku1012
    pmc: PMC4383881
    pubmed: '25332401'
    title: 'Proteome TopFIND 3.0 with TopFINDer and PathFINDer: database and analysis
      tools for the association of protein termini to pre- and post-translational
      events'
    year: 2014
  - doi: 10.1093/nar/gkr1025
    pmc: PMC3244998
    pubmed: '22102574'
    title: TopFIND 2.0--linking protein termini with proteolytic processing and modifications
      altering protein function
    year: 2011
  - doi: 10.1038/nmeth.1669
    pmc: null
    pubmed: '21822272'
    title: TopFIND, a knowledgebase linking protein termini with function
    year: 2011
  - doi: 10.1093/nar/gku1012
    pmc: null
    pubmed: null
    title: 'Proteome TopFIND 3.0 with TopFINDer and PathFINDer: database and analysis
      tools for the association of protein termini to pre- and post-translational
      events.'
    year: null
  - doi: 10.1038/nmeth.1669
    pmc: null
    pubmed: null
    title: TopFIND, a knowledgebase linking protein termini with function.
    year: null
  - doi: 10.1093/nar/gkr1025
    pmc: null
    pubmed: null
    title: TopFIND 2.0—linking protein termini with proteolytic processing and modifications
      altering protein function
    year: null
  re3data:
    description: TopFIND is a protein-centric database for the annotation of protein
      termini currently in its third version. Non-canonical protein termini can be
      the result of multiple different biological processes, including pre-translational
      processes such as alternative splicing and alternative translation initiation
      or post-translational protein processing by proteases that cleave proteases
      as part of protein maturation or as a regulatory modification. Accordingly,
      protein termini evidence in TopFIND is inferred from other databases such as
      ENSEMBL transcripts, TISdb for alternative translation initiation, MEROPS for
      protein cleavage by proteases, and UniProt for canonical and protein isoform
      start sites.
    doi: 10.17616/R3KB8J
    homepage: https://topfind.clip.msl.ubc.ca/
    name: TopFIND
    prefix: r3d100012721
    synonyms:
    - The public knowledgebase for protein termini and protease processing
    xrefs:
      omics: '10578'
toxoplasma:
  biocontext:
    prefix: TOXOPLASMA
  mappings:
    biocontext: TOXOPLASMA
    miriam: toxoplasma
    n2t: toxoplasma
  miriam:
    deprecated: false
    description: ToxoDB is one of the databases that can be accessed through the EuPathDB
      (http://EuPathDB.org; formerly ApiDB) portal, covering eukaryotic pathogens
      of the genera Cryptosporidium, Giardia, Leishmania, Neospora, Plasmodium, Toxoplasma,
      Trichomonas and Trypanosoma. While each of these groups is supported by a taxon-specific
      database built upon the same infrastructure, the EuPathDB portal offers an entry
      point to all these resources, and the opportunity to leverage orthology for
      searches across genera.
    homepage: http://toxodb.org/toxo/
    id: '00000153'
    name: ToxoDB
    namespaceEmbeddedInLui: false
    pattern: ^\w+$
    prefix: toxoplasma
    sampleId: TGME49_053730
    uri_format: http://toxodb.org/toxo/showRecord.do?name=GeneRecordClasses.GeneRecordClass&source_id=$1
  n2t:
    description: ToxoDB is one of the databases that can be accessed through the EuPathDB
      (http://EuPathDB.org; formerly ApiDB) portal, covering eukaryotic pathogens
      of the genera Cryptosporidium, Giardia, Leishmania, Neospora, Plasmodium, Toxoplasma,
      Trichomonas and Trypanosoma. While each of these groups is supported by a taxon-specific
      database built upon the same infrastructure, the EuPathDB portal offers an entry
      point to all these resources, and the opportunity to leverage orthology for
      searches across genera.
    example: TGME49_053730
    homepage: http://toxodb.org/toxo/
    name: ToxoDB at EuPathDB
    namespaceEmbeddedInLui: false
    pattern: ^\w+$
    prefix: toxoplasma
    uri_format: http://toxodb.org/toxo/showRecord.do?name=GeneRecordClasses.GeneRecordClass&source_id=$1
  prefix: toxoplasma
trans:
  aberowl:
    description: An ontology representing the disease transmission process during
      which the pathogen is transmitted directly or indirectly from its natural reservoir,
      a susceptible host or source to a new host.
    download_owl: http://aber-owl.net/media/ontologies/TRANS/5/trans.owl
    homepage: https://github.com/DiseaseOntology/PathogenTransmissionOntology
    name: Pathogen Transmission Ontology
    prefix: TRANS
  biocontext:
    prefix: TRANS
  bioportal:
    contact:
      email: philip.shields@live.vu.edu.au
      name: Philip Shields
    description: This is an ontology of a transitional care nurse's process domain
    name: Nurse Transitional
    prefix: TRANS
  example: '0000024'
  fairsharing:
    abbreviation: TRANS
    description: This resource is no longer available because its underlying source
      material is not in scope for FAIRsharing.
    homepage: http://bioportal.bioontology.org/ontologies/TRANS
    name: Nurse Transitional
    prefix: FAIRsharing.nygmp7
    subjects:
    - Health Science
  mappings:
    aberowl: TRANS
    biocontext: TRANS
    bioportal: TRANS
    fairsharing: FAIRsharing.nygmp7
    obofoundry: trans
    ols: trans
    ontobee: TRANS
    prefixcommons: pt
    wikidata.entity: Q15304508
  obofoundry:
    contact: lynn.schriml@gmail.com
    contact.github: lschriml
    contact.label: Lynn Schriml
    contact.orcid: 0000-0001-8910-9851
    deprecated: false
    description: An ontology representing the disease transmission process during
      which the pathogen is transmitted directly or indirectly from its natural reservoir,
      a susceptible host or source to a new host.
    domain: health
    download.obo: http://purl.obolibrary.org/obo/trans.obo
    download.owl: http://purl.obolibrary.org/obo/trans.owl
    homepage: https://github.com/DiseaseOntology/PathogenTransmissionOntology
    license: CC0 1.0
    license.url: https://creativecommons.org/publicdomain/zero/1.0/
    name: Pathogen Transmission Ontology
    preferredPrefix: TRANS
    prefix: trans
    publications:
    - id: https://www.ncbi.nlm.nih.gov/pubmed/19850722
      title: GeMInA, Genomic Metadata for Infectious Agents, a geospatial surveillance
        pathogen database
    - id: https://www.ncbi.nlm.nih.gov/pubmed/34755882
      title: The Human Disease Ontology 2022 update
    repository: https://github.com/DiseaseOntology/PathogenTransmissionOntology
  ols:
    description: The Pathogen Transmission Ontology describes the tranmission methods
      of human disease pathogens describing how a pathogen is transmitted from one
      host, reservoir, or source to another host. The pathogen transmission may occur
      either directly or indirectly and may involve animate vectors or inanimate vehicles.
    download_owl: http://purl.obolibrary.org/obo/trans.owl
    homepage: https://github.com/DiseaseOntology/PathogenTransmissionOntology
    name: Pathogen Transmission Ontology
    prefix: trans
    tracker: https://github.com/DiseaseOntology/PathogenTransmissionOntology/issues
    version: '2022-10-10'
    version.iri: http://purl.obolibrary.org/obo/trans/releases/2022-10-10/trans.owl
  ontobee:
    library: Library
    name: Pathogen Transmission Ontology
    prefix: TRANS
  pattern: ^\d{7}$
  prefix: trans
  prefixcommons:
    bioportal: '1094'
    description: This vocabulary describes a process that is the means of how a pathogen
      is transmitted from one host, reservoir, or source to another host. This transmission
      may occur either directly or indirectly and may involve animate vectors or inanimate
      vehicles.
    example: TRANS_0000001
    homepage: http://diseaseontology.sourceforge.net/
    keywords:
    - obo
    - pathogen
    name: Pathogen transmission
    pattern: ^TRANS_\d{7}$
    prefix: pt
    synonyms:
    - trans
  publications:
  - doi: 10.1093/nar/gkab1063
    pmc: PMC8728220
    pubmed: '34755882'
    title: The Human Disease Ontology 2022 update
    year: 2022
  - doi: 10.1093/nar/gkp832
    pmc: PMC2808878
    pubmed: '19850722'
    title: GeMInA, Genomic Metadata for Infectious Agents, a geospatial surveillance
      pathogen database
    year: 2009
  - doi: null
    pmc: null
    pubmed: '19850722'
    title: GeMInA, Genomic Metadata for Infectious Agents, a geospatial surveillance
      pathogen database
    year: null
  - doi: null
    pmc: null
    pubmed: '34755882'
    title: The Human Disease Ontology 2022 update
    year: null
  uri_format: http://purl.obolibrary.org/obo/TRANS_$1
transportdb:
  mappings:
    pathguide: '105'
    prefixcommons: transportdb
  pathguide:
    abbreviation: TransportDB
    homepage: http://www.membranetransport.org/transportDB2/index.html
    name: TransportDB
    prefix: '105'
  prefix: transportdb
  prefixcommons:
    description: TransportDB is a relational database describing the predicted cytoplasmic
      membrane transport protein complement for organisms whose complete genome sequence
      are available.
    example: MMP0523
    homepage: http://www.membranetransport.org
    keywords:
    - protein
    name: TransportDB
    pattern: ^MMP\d+$
    prefix: transportdb
    uri_format: http://www.membranetransport.org/protein.php?pOID=mmar1&pSynonym=$1
  reviewer:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
transyt:
  mappings:
    miriam: transyt
  miriam:
    deprecated: false
    description: The Transport Systems Tracker (TranSyT) is a tool to identify transport
      systems and the compounds carried across membranes.
    homepage: https://www.bio.di.uminho.pt/
    id: '00000736'
    name: TranSyT
    namespaceEmbeddedInLui: false
    pattern: ^T[A-Z]\d{7}$
    prefix: transyt
    sampleId: TR0000001
    uri_format: https://transyt.bio.di.uminho.pt/reactions/$1
  name: Transport Systems Tracker
  prefix: transyt
tred:
  comment: This resource doesn't exist on the web anymore
  deprecated: true
  mappings:
    pathguide: '167'
    prefixcommons: tred
  pathguide:
    abbreviation: TRED
    homepage: https://cb.utdallas.edu/cgi-bin/TRED/tred.cgi?process=home
    name: Transcriptional Regulatory Element Database
    prefix: '167'
  prefix: tred
  prefixcommons:
    description: Transcriptional Regulatory Element Database (TRED) has been built
      in response to increasing needs of an integrated repository for both cis- and
      trans- regulatory elements in mammals, and the lack of such resources at present.
    example: '21552'
    homepage: http://rulai.cshl.edu/TRED
    keywords:
    - DNA
    - regulation
    name: Transcriptional Regulatory Element Database
    pattern: ^\d+$
    prefix: tred
    uri_format: http://rulai.cshl.edu/cgi-bin/TRED/tred.cgi?process=geneInfo&gid=$1
  reviewer:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
treebase:
  biocontext:
    prefix: TREEBASE
  contact:
    email: rutgeraldo@gmail.com
    github: rvosa
    name: Rutger Vos
    orcid: 0000-0001-9254-7318
  fairsharing:
    abbreviation: TreeBase
    description: TreeBASE is a repository of phylogenetic information, specifically
      user-submitted phylogenetic trees and the data used to generate them. TreeBASE
      accepts all types of phylogenetic data (e.g., trees of species, trees of populations,
      trees of genes) representing all biotic taxa. TreeBASE is temporarily offline
      except to provide access to editors/curators, as security updates are required
      before re-publishing the site.
    homepage: https://www.treebase.org
    name: TreeBase
    prefix: FAIRsharing.zcn4w4
    publications:
    - doi: 10.1186/1471-2148-9-93
      pubmed_id: 19426482
      title: Improved data retrieval from TreeBASE via taxonomic and linguistic data
        enrichment.
    repository: https://github.com/TreeBASE/treebase/issues
    subjects:
    - Phylogenetics
    - Phylogenomics
    twitter: treebase
  integbio:
    description: TreeBASE is a repository of phylogenetic information, specifically
      user-submitted phylogenetic trees and the data used to generate them. TreeBASE
      accepts all types of phylogenetic data (e.g., trees of species, trees of populations,
      trees of genes) representing all biotic taxa. TreeBASE is temporarily offline
      except to provide access to editors/curators, as security updates are required
      before re-publishing the site.
    fairsharing: FAIRsharing.zcn4w4
    homepage: https://www.treebase.org
    information_keywords:
    - Taxonomy
    - Sequence
    maintainer: Naturalis Biodiversity Center
    name: TreeBase
    prefix: nbdc01882
    pubmeds:
    - '19426482'
    status: Inactive
    target_keywords:
    - Organism
  mappings:
    biocontext: TREEBASE
    fairsharing: FAIRsharing.zcn4w4
    integbio: nbdc01882
    miriam: treebase
    n2t: treebase
    prefixcommons: treebase
    re3data: r3d100010170
  miriam:
    deprecated: true
    description: TreeBASE is a relational database designed to manage and explore
      information on phylogenetic relationships. It includes phylogenetic trees and
      data matrices, together with information about the relevant publication, taxa,
      morphological and sequence-based characters, and published analyses. Data in
      TreeBASE are exposed to the public if they are used in a publication that is
      in press or published in a peer-reviewed scientific journal, etc.
    homepage: http://treebase.org/
    id: '00000312'
    name: TreeBASE
    namespaceEmbeddedInLui: false
    pattern: ^TB[1,2]?:[A-Z][a-z]?\d+$
    prefix: treebase
    sampleId: TB2:S1000
    uri_format: http://purl.org/phylo/treebase/phylows/study/$1?format=html
  n2t:
    description: TreeBASE is a relational database designed to manage and explore
      information on phylogenetic relationships. It includes phylogenetic trees and
      data matrices, together with information about the relevant publication, taxa,
      morphological and sequence-based characters, and published analyses. Data in
      TreeBASE are exposed to the public if they are used in a publication that is
      in press or published in a peer-reviewed scientific journal, etc.
    example: TB2:S1000
    homepage: http://treebase.org/
    name: TreeBASE (hosted at National Evolutionary Synthesis Center)
    namespaceEmbeddedInLui: false
    pattern: ^TB[1,2]?:[A-Z][a-z]?\d+$
    prefix: treebase
    uri_format: http://purl.org/phylo/treebase/phylows/study/$1?format=html
  prefix: treebase
  prefixcommons:
    description: TreeBASE is a repository of phylogenetic information, specifically
      user-submitted phylogenetic trees and the data used to generate them. TreeBASE
      accepts all types of phylogenetic data (e.g., trees of species, trees of populations,
      trees of genes) representing all biotic taxa.
    example: '1245'
    homepage: http://www.treebase.org/
    keywords:
    - classification
    name: TreeBase
    pattern: ^\d+$
    prefix: treebase
    uri_format: http://www.treebase.org/treebase-web/search/study/summary.html?id=$1
  publications:
  - doi: 10.1186/1471-2148-9-93
    pmc: PMC2685121
    pubmed: '19426482'
    title: Improved data retrieval from TreeBASE via taxonomic and linguistic data
      enrichment
    year: 2009
  - doi: 10.1186/1471-2148-9-93
    pmc: null
    pubmed: null
    title: Improved data retrieval from TreeBASE via taxonomic and linguistic data
      enrichment.
    year: null
  re3data:
    description: TreeBASE is a repository of phylogenetic information, specifically
      user-submitted phylogenetic trees and the data used to generate them. TreeBASE
      accepts all types of phylogenetic data (e.g., trees of species, trees of populations,
      trees of genes) representing all biotic taxa. Data in TreeBASE are exposed to
      the public if they are used in a publication that is in press or published in
      a peer-reviewed scientific journal, book, conference proceedings, or thesis.
      Data used in publications that are in preparation or in review can be submitted
      to TreeBASE but are only available to the authors, publication editors, or reviewers
      using a special access code.
    doi: 10.17616/R3DK58
    homepage: https://www.treebase.org/treebase-web/home.html
    license: BSD
    name: TreeBASE
    prefix: r3d100010170
    synonyms:
    - a database of phylogenetic knowledge
    xrefs:
      nif: 0000-03587
treefam:
  biocontext:
    prefix: TREEFAM
  contact:
    email: Fab.Schreiber@gmail.com
    github: fabsta
    name: Fabian Schreiber
    orcid: 0000-0001-9150-5706
  integbio:
    description: "TreeFam is a database of phylogenetic trees inferred from animal\
      \ genomes. It provides the following information about the TreeFam gene family:\n\
      1) Summary page\nTextual background information on the TreeFam gene family\n\
      2) Trees\nReconciled gene tree \n3) Alignment\nAn alignment of all homologous\
      \ sequences in the TreeFam family\n4) Sequences\nInformation about sequences\
      \ in the TreeFam family, including e-values, Pfam domains, sequence description,\
      \ and the species name\n5) Species\nInteractive tree graphic displaying species\
      \ distribution for the full alignment."
    homepage: http://www.treefam.org
    information_keywords:
    - Sequence
    - Taxonomy
    - Classification
    maintainer: EMBL-EBI (European Bioinformatics Institute)
    name: TreeFam
    prefix: nbdc01596
    pubmeds:
    - '16381935'
    - '18056084'
    status: Active
    target_keywords:
    - Genome/Gene
    - Organism
  mappings:
    biocontext: TREEFAM
    integbio: nbdc01596
    miriam: treefam
    n2t: treefam
    prefixcommons: treefam
    uniprot: DB-0185
  miriam:
    deprecated: false
    description: TreeFam is a database of phylogenetic trees of gene families found
      in animals. Automatically generated trees are curated, to create a curated resource
      that presents the accurate evolutionary history of all animal gene families,
      as well as reliable ortholog and paralog assignments.
    homepage: http://www.treefam.org/
    id: 00000395
    name: TreeFam
    namespaceEmbeddedInLui: false
    pattern: ^\w{1,2}\d+$
    prefix: treefam
    sampleId: TF101014
    uri_format: http://www.treefam.org/family/$1
  n2t:
    description: TreeFam is a database of phylogenetic trees of gene families found
      in animals. Automatically generated trees are curated, to create a curated resource
      that presents the accurate evolutionary history of all animal gene families,
      as well as reliable ortholog and paralog assignments.
    example: TF101014
    homepage: http://www.treefam.org/
    name: TreeFam database
    namespaceEmbeddedInLui: false
    pattern: ^\w{1,2}\d+$
    prefix: treefam
    uri_format: http://www.treefam.org/family/$1
  prefix: treefam
  prefixcommons:
    description: TreeFam (Tree families database) is a database of phylogenetic trees
      of animal genes. It aims at developing a curated resource that gives reliable
      information about ortholog and paralog assignments, and evolutionary history
      of various gene families.
    example: TF101142
    homepage: http://www.treefam.org
    keywords:
    - gene
    - classification
    name: TreeFam
    pattern: ^TF\d+$
    prefix: treefam
    uri_format: http://www.treefam.org/cgi-bin/TFinfo.pl?ac=$1
  publications:
  - doi: 10.1093/nar/gkt1055
    pmc: PMC3965059
    pubmed: '24194607'
    title: 'TreeFam v9: a new website, more species and orthology-on-the-fly'
    year: 2013
  uniprot:
    abbreviation: TreeFam
    category: Phylogenomic databases
    homepage: http://www.treefam.org
    name: TreeFam database of animal gene trees
    prefix: DB-0185
    publications:
    - doi: 10.1093/nar/gkt1055
      pubmed: '24194607'
    uri_format: http://www.treefam.org/family/$1
treehub:
  contact:
    email: wuhui@ibcas.ac.cn
    github: null
    name: Hui Wu
    orcid: 0000-0003-2430-9689
  contributor:
    email: maaya.m466@gmail.com
    github: maayamanoj466
    name: Maaya Manoj
    orcid: 0009-0000-6974-6386
  description: TreeHub is a taxonomical database for trees. TreeHub contains extracted
    phylogenetic data and integrates relevant species information for each identifier.
  example: T00232742
  github_request_issue: 1619
  homepage: https://www.plantplus.cn/treehub
  keywords:
  - dendrology
  - taxonomy
  - tree
  name: TreeHub
  pattern: ^T\d{8}$
  prefix: treehub
  publications:
  - doi: 10.1038/s41597-025-05282-4
    pmc: PMC12130454
    pubmed: '40456766'
    title: 'TreeHub: a comprehensive dataset of phylogenetic trees'
    year: 2025
  reviewer:
    email: b.gyori@northeastern.edu
    github: bgyori
    name: Benjamin M. Gyori
    orcid: 0000-0001-9439-5346
  uri_format: https://www.plantplus.cn/treehub/tree/$1
tribain:
  example: 100Cr6
  mappings:
    tib: tai
  name: Tribology Ontology for Artificial Intelligence
  prefix: tribain
  repository: https://github.com/snow0815/tribAIn
  tib:
    description: The tribAIn1 ontology aims to formalize knowledge gained from tribological
      experiments for reuse, comparison and documentation. Therefore, the tribAin
      ontology provides concepts for the specification of methodological background
      knowledge of experimental design, the documentation of the experimental setup
      and the representation of different kinds of results (e.g. measurements series,
      analysis, interpretation in natural-language). Using the EXPO2 (ontology of
      scientific experiments) as basis, gives tribAIn a generic background about scientific
      experimental design, methodology and results representation.
    download_rdf: https://raw.githubusercontent.com/snow0815/tribAIn/refs/heads/master/tribAin.ttl
    homepage: https://github.com/snow0815/tribAIn
    keywords:
    - NFDI4ING
    - engineering
    name: tribAIn - Derived from the ancient Greek word “tribein” (= rubbing) and
      the acronym “AI” (= Artificial Intelligence)
    prefix: tai
    tracker: https://github.com/snow0815/tribAIn/issues
    uri_format: http://ktmfk.de/ontology/tribAIn/$1
    version.iri: http://ktmfk.de/ontology/tribAIn
tricdb:
  mappings:
    miriam: tricdb
  miriam:
    deprecated: false
    description: Tri©DB is a newly developed integrated platform functioning as a
      knowledge base and reporting system for cancer precision medicine. This platform
      harmonizes and mines cancer-related data from various aspects, presenting them
      on a centralized platform with enhanced accessibility, rich annotations, and
      robust analysis capabilities. The development of Tri©DB is aimed at meeting
      the needs of a broad range of researchers, thereby propelling both foundational
      and translational research in cancer precision medicine.
    homepage: http://www.biomeddb.org/
    id: '00001036'
    name: tricdb
    namespaceEmbeddedInLui: false
    pattern: ^[0-9a-f]{8}-[0-9a-f]{4}-[0-9a-f]{4}-[0-9a-f]{4}-[0-9a-f]{12}$
    prefix: tricdb
    sampleId: 1eec8393-e598-41ed-9d8b-6d5b0db94470
    uri_format: http://biomeddb.org/Disease/Details?DISEASEID=$1
  prefix: tricdb
trichdb:
  biocontext:
    prefix: TRICHDB
  fairsharing:
    abbreviation: TrichDB
    contact:
      email: oharb@pcbi.upenn.edu
      name: Omar Harb
      orcid: 0000-0003-4446-6200
    description: TrichDB is one of the databases that can be accessed through the
      EuPathDB (http://EuPathDB.org; formerly ApiDB) portal, covering eukaryotic pathogens
      of the genera Cryptosporidium, Giardia, Leishmania, Neospora, Plasmodium, Toxoplasma,
      Trichomonas and Trypanosoma. While each of these groups is supported by a taxon-specific
      database built upon the same infrastructure, the EuPathDB portal offers an entry
      point to all these resources, and the opportunity to leverage orthology for
      searches across genera.
    homepage: http://trichdb.org/trichdb/
    license: http://opendatacommons.org/licenses/pddl/1.0
    name: TrichDB
    prefix: FAIRsharing.pv0ezt
    publications:
    - doi: 10.1093/nar/gkn631
      pubmed_id: 18824479
      title: 'GiardiaDB and TrichDB: integrated genomic resources for the eukaryotic
        protist pathogens Giardia lamblia and Trichomonas vaginalis.'
    subjects:
    - Genomics
    twitter: eupathdb
  integbio:
    description: TrichDB is one of the databases that can be accessed through the
      EuPathDB (http://EuPathDB.org; formerly ApiDB) portal, covering eukaryotic pathogens
      of the genera Cryptosporidium, Giardia, Leishmania, Neospora, Plasmodium, Toxoplasma,
      Trichomonas and Trypanosoma. While each of these groups is supported by a taxon-specific
      database built upon the same infrastructure, the EuPathDB portal offers an entry
      point to all these resources, and the opportunity to leverage orthology for
      searches across genera.
    fairsharing: FAIRsharing.pv0ezt
    homepage: http://trichdb.org/trichdb/
    information_keywords:
    - Sequence
    - Expression
    - Ontology/Terminology/Nomenclature
    maintainer: CBIL (Computational Biology and Informatics Laboratory, University
      of Pennsylvania)||Center for Tropical & Emerging Global Diseases, University
      of Georgia
    name: TrichDB
    prefix: nbdc01785
    pubmeds:
    - '18824479'
    status: Active
    target_keywords:
    - Genome/Gene
    - Health/Disease
    - Organism
    - cDNA/EST
  mappings:
    biocontext: TRICHDB
    fairsharing: FAIRsharing.pv0ezt
    integbio: nbdc01785
    miriam: trichdb
    n2t: trichdb
    re3data: r3d100012461
  miriam:
    deprecated: false
    description: TrichDB is one of the databases that can be accessed through the
      EuPathDB (http://EuPathDB.org; formerly ApiDB) portal, covering eukaryotic pathogens
      of the genera Cryptosporidium, Giardia, Leishmania, Neospora, Plasmodium, Toxoplasma,
      Trichomonas and Trypanosoma. While each of these groups is supported by a taxon-specific
      database built upon the same infrastructure, the EuPathDB portal offers an entry
      point to all these resources, and the opportunity to leverage orthology for
      searches across genera.
    homepage: http://trichdb.org/trichdb/
    id: '00000154'
    name: TrichDB
    namespaceEmbeddedInLui: false
    pattern: ^\w+$
    prefix: trichdb
    sampleId: TVAG_386080
    uri_format: http://trichdb.org/trichdb/showRecord.do?name=GeneRecordClasses.GeneRecordClass&source_id=$1
  n2t:
    description: TrichDB is one of the databases that can be accessed through the
      EuPathDB (http://EuPathDB.org; formerly ApiDB) portal, covering eukaryotic pathogens
      of the genera Cryptosporidium, Giardia, Leishmania, Neospora, Plasmodium, Toxoplasma,
      Trichomonas and Trypanosoma. While each of these groups is supported by a taxon-specific
      database built upon the same infrastructure, the EuPathDB portal offers an entry
      point to all these resources, and the opportunity to leverage orthology for
      searches across genera.
    example: TVAG_386080
    homepage: http://trichdb.org/trichdb/
    name: TrichDB at EuPathDB
    namespaceEmbeddedInLui: false
    pattern: ^\w+$
    prefix: trichdb
    uri_format: http://trichdb.org/trichdb/showRecord.do?name=GeneRecordClasses.GeneRecordClass&source_id=$1
  prefix: trichdb
  publications:
  - doi: 10.1093/nar/gkn631
    pmc: PMC2686445
    pubmed: '18824479'
    title: 'GiardiaDB and TrichDB: integrated genomic resources for the eukaryotic
      protist pathogens Giardia lamblia and Trichomonas vaginalis'
    year: 2008
  - doi: 10.1093/nar/gkn631
    pmc: null
    pubmed: null
    title: 'GiardiaDB and TrichDB: integrated genomic resources for the eukaryotic
      protist pathogens Giardia lamblia and Trichomonas vaginalis.'
    year: null
  re3data:
    description: TrichDB integrated genomic resources for the eukaryotic protist pathogens
      Trichomonas vaginalis.
    doi: 10.17616/R3ZB66
    homepage: https://trichdb.org/trichdb/app
    name: TrichDB
    prefix: r3d100012461
    synonyms:
    - Trichomonas vaginalis Sequence Database
    xrefs:
      omics: '03162'
tritrypdb:
  biocontext:
    prefix: TRITRYPDB
  fairsharing:
    abbreviation: TriTrypDB
    contact:
      email: oharb@pcbi.upenn.edu
      name: Omar Harb
      orcid: 0000-0003-4446-6200
    description: TriTrypDB is one of the databases that can be accessed through the
      VEuPathDB portal, covering eukaryotic pathogens of the genera Cryptosporidium,
      Giardia, Leishmania, Neospora, Plasmodium, Toxoplasma, Trichomonas and Trypanosoma.
      While each of these groups is supported by a taxon-specific database built upon
      the same infrastructure, the VEuPathDB portal offers an entry point to all these
      resources, and the opportunity to leverage orthology for searches across genera.
    homepage: http://tritrypdb.org/tritrypdb/
    name: TriTrypDB
    prefix: FAIRsharing.fs1z27
    publications:
    - doi: 10.1093/nar/gkp851
      pubmed_id: 19843604
      title: 'TriTrypDB: a functional genomic resource for the Trypanosomatidae.'
    subjects:
    - Genomics
    - Infectious Disease Medicine
    - Comparative Genomics
    twitter: VEuPathDB
  go:
    homepage: https://tritrypdb.org/
    name: TriTrypDB
    prefix: TriTrypDB
    uri_format: https://tritrypdb.org/tritrypdb/app/record/gene/$1
  integbio:
    description: TriTrypDB is one of the databases that can be accessed through the
      VEuPathDB portal, covering eukaryotic pathogens of the genera Cryptosporidium,
      Giardia, Leishmania, Neospora, Plasmodium, Toxoplasma, Trichomonas and Trypanosoma.
      While each of these groups is supported by a taxon-specific database built upon
      the same infrastructure, the VEuPathDB portal offers an entry point to all these
      resources, and the opportunity to leverage orthology for searches across genera.
    fairsharing: FAIRsharing.fs1z27
    homepage: http://tritrypdb.org/tritrypdb/
    information_keywords:
    - Sequence
    - Expression
    - Ontology/Terminology/Nomenclature
    maintainer: CBIL (Computational Biology and Informatics Laboratory, University
      of Pennsylvania)||Center for Tropical & Emerging Global Diseases, University
      of Georgia||Wellcome Sanger Institute
    name: TriTrypDB
    prefix: nbdc01786
    pubmeds:
    - '19843604'
    status: Active
    target_keywords:
    - Genome/Gene
    - Health/Disease
    - Organism
    - cDNA/EST
  mappings:
    biocontext: TRITRYPDB
    fairsharing: FAIRsharing.fs1z27
    go: TriTrypDB
    integbio: nbdc01786
    miriam: tritrypdb
    n2t: tritrypdb
    re3data: r3d100011479
  miriam:
    deprecated: false
    description: TriTrypDB is one of the databases that can be accessed through the
      EuPathDB (http://EuPathDB.org; formerly ApiDB) portal, covering eukaryotic pathogens
      of the genera Cryptosporidium, Giardia, Leishmania, Neospora, Plasmodium, Toxoplasma,
      Trichomonas and Trypanosoma. While each of these groups is supported by a taxon-specific
      database built upon the same infrastructure, the EuPathDB portal offers an entry
      point to all these resources, and the opportunity to leverage orthology for
      searches across genera.
    homepage: http://tritrypdb.org/tritrypdb/
    id: '00000155'
    name: TriTrypDB
    namespaceEmbeddedInLui: false
    pattern: ^\w+(\.)?\w+(\.)?\w+$
    prefix: tritrypdb
    sampleId: Tb927.8.620
    uri_format: http://tritrypdb.org/tritrypdb/showRecord.do?name=GeneRecordClasses.GeneRecordClass&source_id=$1
  n2t:
    description: TriTrypDB is one of the databases that can be accessed through the
      EuPathDB (http://EuPathDB.org; formerly ApiDB) portal, covering eukaryotic pathogens
      of the genera Cryptosporidium, Giardia, Leishmania, Neospora, Plasmodium, Toxoplasma,
      Trichomonas and Trypanosoma. While each of these groups is supported by a taxon-specific
      database built upon the same infrastructure, the EuPathDB portal offers an entry
      point to all these resources, and the opportunity to leverage orthology for
      searches across genera.
    example: Tb927.8.620
    homepage: http://tritrypdb.org/tritrypdb/
    name: TriTrypDB at EuPathDB
    namespaceEmbeddedInLui: false
    pattern: ^\w+(\.)?\w+(\.)?\w+
    prefix: tritrypdb
    uri_format: http://tritrypdb.org/tritrypdb/showRecord.do?name=GeneRecordClasses.GeneRecordClass&source_id=$1
  prefix: tritrypdb
  publications:
  - doi: 10.1093/nar/gkp851
    pmc: PMC2808979
    pubmed: '19843604'
    title: 'TriTrypDB: a functional genomic resource for the Trypanosomatidae'
    year: 2009
  re3data:
    description: TriTrypDB is an integrated genomic and functional genomic database
      for pathogens of the family Trypanosomatidae, including organisms in both Leishmania
      and Trypanosoma genera. TriTrypDB and its continued development are possible
      through the collaborative efforts between EuPathDB, GeneDB and colleagues at
      the Seattle Biomedical Research Institute (SBRI).
    doi: 10.17616/R3J05N
    homepage: https://tritrypdb.org/tritrypdb/app
    name: TriTrypDB
    prefix: r3d100011479
    synonyms:
    - kinetoplastid genomics resource
    xrefs:
      omics: '03144'
trnadbce:
  comment: requires authentication to access
  integbio:
    alt_name: tRNA gene database curated manually by experts
    description: tRNADB-CE is a database of manually curated tRNA gene information.
      It contains tRNA sequences that have been evaluated experimentally after initial
      identification by computational algorithms. Entries can be searched by keyword,
      and a BLAST search tool is available. Bulk download is also available.
    homepage: http://trna.ie.niigata-u.ac.jp
    information_keywords:
    - Sequence
    maintainer: Niigata University Faculty of Engineering Department of Information
      Engineering
    name: tRNADB-CE
    prefix: nbdc00720
    pubmeds:
    - '21071414'
    - '18842632'
    status: Active
    target_keywords:
    - Genome/Gene
    - RNA
  mappings:
    integbio: nbdc00720
    prefixcommons: trnadbce
  prefix: trnadbce
  prefixcommons:
    description: The tRNA Gene DataBase Curated by Experts "tRNADB-CE" was constructed
      by analyzing 927 complete and 1301 draft genomes of Bacteria and Archaea, 171
      complete virus genomes, 121 complete chloroplast genomes, 12 complete eukaryote
      (Plant and Fungi) genomes and approximately 230 million DNA sequence entries
      that originated from environmental metagenomic clones.
    example: '265912'
    homepage: http://trna.nagahama-i-bio.ac.jp
    keywords:
    - RNA
    - gene
    - genome
    - DNA
    name: tRNA Gene Database
    pattern: ^\d+$
    prefix: trnadbce
    uri_format: http://trna.nagahama-i-bio.ac.jp/cgi-bin/trnadb/whole_detail.cgi?SID=$1
  proprietary: true
  reviewer:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
tsc:
  description: Centralized repository and distribution site for variety of Tetrahymena
    strains and species. Maintains diverse array of wild type, mutant, and genetically
    engineered strains of T. thermophila, the most commonly used laboratory species,
    and variety of other species derived from both laboratory maintained stocks and
    wild isolates. All stocks are stored in liquid nitrogen to maintain genetic integrity
    and prevent senescence. In addition to providing worldwide access to strains currently
    in collection, TSC continually upgrades collection by accepting deposition of
    newly developed laboratory strains and well characterized wild isolates collected
    from clearly defined natural sites. [from RRID]
  example: SD00043
  mappings:
    rrid: TSC
  pattern: ^SD\d+$
  prefix: tsc
  rrid:
    homepage: https://tetrahymena.vet.cornell.edu/
    keywords:
    - biology
    - cell
    - cellular
    - culture
    - eukaryota
    - genetics
    - model
    - molecular
    - protozoan
    - repository
    - research
    - tetrahymena thermophila
    name: Tetrahymena Stock Center
    prefix: TSC
    scr: 008362
  uri_format: https://tetrahymena.vet.cornell.edu/display.php?stockid=$1
tsrnadisease:
  contact:
    email: zhenyang@fudan.edu.cn
    github: null
    name: Zhen Yang
    orcid: 0000-0002-6782-0316
  contributor:
    email: ji.kang@northeastern.edu
    github: kanghosaeyo
    name: Kangho Ji
    orcid: 0009-0009-3402-8013
  description: Identifiers correspond to curated associations between diseases and
    tRNA-derived small RNAs (tsRNAs) in the tsRNADisease database.
  example: TRD00001
  github_request_issue: 1700
  homepage: http://compgenelab.info/tsRNADisease
  keywords:
  - cancer
  - disease
  - tsrna
  name: tsRNADisease
  pattern: ^TRD\d{5}$
  prefix: tsrnadisease
  publications:
  - doi: 10.1016/j.jgg.2025.08.001
    pmc: null
    pubmed: '40812678'
    title: 'tsRNADisease: a manually curated database of tsRNAs associated with human
      disease'
    year: 2025
  reviewer:
    email: b.gyori@northeastern.edu
    github: bgyori
    name: Benjamin M. Gyori
    orcid: 0000-0001-9439-5346
  uri_format: http://118.178.132.53/tsRNADisease/detail.php?entry_ID=$1
ttd.drug:
  biocontext:
    prefix: TTD.DRUG
  edam:
    description: Identifier of a drug from the Therapeutic Target Database (TTD).
    name: Drug ID (TTD)
    obsolete: false
    prefix: '2653'
  mappings:
    biocontext: TTD.DRUG
    edam: '2653'
    miriam: ttd.drug
    n2t: ttd.drug
  miriam:
    deprecated: false
    description: The Therapeutic Target Database (TTD) is designed to provide information
      about the known therapeutic protein and nucleic acid targets described in the
      literature, the targeted disease conditions, the pathway information and the
      corresponding drugs/ligands directed at each of these targets. Cross-links to
      other databases allow the access to information about the sequence, 3D structure,
      function, nomenclature, drug/ligand binding properties, drug usage and effects,
      and related literature for each target.
    homepage: https://db.idrblab.net/ttd
    id: 00000092
    name: TTD Drug
    namespaceEmbeddedInLui: false
    pattern: ^\w+$
    prefix: ttd.drug
    sampleId: D0N5OV
    uri_format: https://db.idrblab.net/ttd/data/drug/details/$1
  n2t:
    description: The Therapeutic Target Database (TTD) is designed to provide information
      about the known therapeutic protein and nucleic acid targets described in the
      literature, the targeted disease conditions, the pathway information and the
      corresponding drugs/ligands directed at each of these targets. Cross-links to
      other databases allow the access to information about the sequence, 3D structure,
      function, nomenclature, drug/ligand binding properties, drug usage and effects,
      and related literature for each target.
    example: DAP000773
    homepage: http://bidd.nus.edu.sg/group/ttd/ttd.asp
    name: Therapeutic Target Database Drug
    namespaceEmbeddedInLui: false
    pattern: ^DAP\d+$
    prefix: ttd.drug
    uri_format: http://bidd.nus.edu.sg/group/TTD/ZFTTDDRUG.asp?ID=$1
  prefix: ttd.drug
ttd.target:
  biocontext:
    prefix: TTD.TARGET
  edam:
    description: Identifier of a target protein from the Therapeutic Target Database
      (TTD).
    name: Target ID (TTD)
    obsolete: false
    prefix: '2654'
  mappings:
    biocontext: TTD.TARGET
    edam: '2654'
    miriam: ttd.target
    n2t: ttd.target
  miriam:
    deprecated: false
    description: The Therapeutic Target Database (TTD) is designed to provide information
      about the known therapeutic protein and nucleic acid targets described in the
      literature, the targeted disease conditions, the pathway information and the
      corresponding drugs/ligands directed at each of these targets. Cross-links to
      other databases are also introduced to facilitate the access of information
      about the sequence, 3D structure, function, nomenclature, drug/ligand binding
      properties, drug usage and effects, and related literature for each target.
    homepage: https://db.idrblab.net/ttd
    id: 00000093
    name: TTD Target
    namespaceEmbeddedInLui: false
    pattern: ^t\d+$
    prefix: ttd.target
    sampleId: t59328
    uri_format: https://db.idrblab.net/ttd/data/target/details/$1
  n2t:
    description: The Therapeutic Target Database (TTD) is designed to provide information
      about the known therapeutic protein and nucleic acid targets described in the
      literature, the targeted disease conditions, the pathway information and the
      corresponding drugs/ligands directed at each of these targets. Cross-links to
      other databases are also introduced to facilitate the access of information
      about the sequence, 3D structure, function, nomenclature, drug/ligand binding
      properties, drug usage and effects, and related literature for each target.
    example: TTDS00056
    homepage: http://bidd.nus.edu.sg/group/ttd/ttd.asp
    name: Therapeutic Target Database Target
    namespaceEmbeddedInLui: false
    pattern: ^TTDS\d+$
    prefix: ttd.target
    uri_format: http://bidd.nus.edu.sg/group/TTD/ZFTTDDetail.asp?ID=$1
  prefix: ttd.target
tto:
  aberowl:
    description: An ontology covering the taxonomy of teleosts (bony fish)
    download_owl: http://aber-owl.net/media/ontologies/TTO/44/tto.owl
    homepage: https://www.nescent.org/phenoscape/Main_Page
    name: Teleost taxonomy ontology
    prefix: TTO
  biocontext:
    prefix: TTO
  bioportal:
    contact:
      email: peteremidford@yahoo.com
      name: Peter Midford
    description: The Teleost taxonomy ontology is being used to facilitate annotation
      of phenotypes, particularly for taxa that are not covered by NCBI because no
      submissions of molecular data have been made. Taxonomy ontologies can also be
      valuable in annotating legacy data, where authors make phenotype or ecological
      assertions (e.g., host-parasite associations) that refer to groups that are
      reorganized or no longer recognized. The taxonomy ontology serves as the source
      of taxa for our project's use for identifying evolutionary changes that match
      the phenotype of a zebrafish mutant.
    homepage: http://obofoundry.org/ontology/tto.html
    name: Teleost Taxonomy Ontology
    prefix: TTO
    version: unknown
  example: '1058367'
  fairsharing:
    abbreviation: TTO
    contact:
      email: pmabee@usd.edu
      name: Paula Mabee
      orcid: 0000-0002-8455-3213
    description: This is an ontology of taxonomic terms (names of taxonomic groups)
      used in the systematics of fish, including non-teleost groups such as Chondrichthys
      (sharks and rays), Sarcopterygii (lungfish and coelacanths), lampreys, and hagfish.
    domains:
    - Taxonomic classification
    homepage: https://github.com/phenoscape/teleost-taxonomy-ontology
    license: CC0-1.0
    name: Teleost Taxonomy Ontology
    prefix: FAIRsharing.1rj558
    subjects:
    - Life Science
  mappings:
    aberowl: TTO
    biocontext: TTO
    bioportal: TTO
    fairsharing: FAIRsharing.1rj558
    obofoundry: tto
    ols: tto
    ontobee: TTO
    prefixcommons: tto
    wikidata.entity: Q81661821
  obofoundry:
    contact: balhoff@renci.org
    contact.github: balhoff
    contact.label: Jim Balhoff
    contact.orcid: 0000-0002-8688-6599
    deprecated: false
    description: An ontology covering the taxonomy of teleosts (bony fish)
    domain: organisms
    download.obo: http://purl.obolibrary.org/obo/tto.obo
    download.owl: http://purl.obolibrary.org/obo/tto.owl
    homepage: https://github.com/phenoscape/teleost-taxonomy-ontology
    license: CC0 1.0
    license.url: http://creativecommons.org/publicdomain/zero/1.0/
    name: Teleost taxonomy ontology
    preferredPrefix: TTO
    prefix: tto
    publications:
    - id: https://doi.org/10.1038/npre.2010.4629.1
      title: The Teleost Taxonomy Ontology
    repository: https://github.com/phenoscape/teleost-taxonomy-ontology
  ols:
    description: An ontology covering the taxonomy of teleosts (bony fish)
    download_owl: http://purl.obolibrary.org/obo/tto.owl
    homepage: https://github.com/phenoscape/teleost-taxonomy-ontology
    name: Teleost taxonomy ontology
    prefix: tto
    tracker: https://github.com/phenoscape/teleost-taxonomy-ontology/issues
  ontobee:
    library: Library
    name: Teleost taxonomy ontology
    prefix: TTO
  pattern: ^\d+$
  prefix: tto
  prefixcommons:
    bioportal: '1081'
    description: The Teleost taxonomy ontology is being used to facilitate annotation
      of phenotypes, particularly for taxa that are not covered by NCBI because no
      submissions of molecular data have been made.
    example: TTO_2
    homepage: https://www.nescent.org/phenoscape/Main_Page
    keywords:
    - obo
    - phenotype
    - fish
    name: Teleost taxonomy Ontology
    pattern: ^TTO_\d$
    prefix: tto
    synonyms:
    - teleost_taxonomy
  publications:
  - doi: 10.1038/npre.2010.4629.1
    pmc: null
    pubmed: null
    title: The Teleost Taxonomy Ontology
    year: 2010
  - doi: 10.1038/npre.2010.4629.1
    pmc: null
    pubmed: null
    title: The Teleost Taxonomy Ontology
    year: null
  - doi: 10.1038/npre.2010.4629.1
    pmc: null
    pubmed: null
    title: The Teleost Taxonomy Ontology
    year: null
  - doi: 10.1038/npre.2010.4629.1
    pmc: null
    pubmed: null
    title: The Teleost Taxonomy Ontology
    year: null
  uri_format: http://purl.obolibrary.org/obo/TTO_$1
  wikidata:
    database: Q81661821
txpo:
  aberowl:
    description: TOXic Process Ontology (TXPO) systematizes a wide variety of terms
      involving toxicity courses and processes. The first version of TXPO focuses
      on liver toxicity.
    download_owl: http://aber-owl.net/media/ontologies/TXPO/28/txpo.owl
    homepage: https://toxpilot.nibiohn.go.jp/
    name: Toxic Process Ontology
    prefix: TXPO
  bioportal:
    contact:
      email: yuki.yamagata@riken.jp
      name: Yuki Yamagata
    description: 'TOXic Process Ontology (TXPO) includes entities related to toxic
      mechanisms (toxic courses) and processes, mainly focusing on hepatotoxicity.
      Application system TOXPILOT: https://toxpilot.nibiohn.go.jp'
    homepage: https://toxpilot.nibiohn.go.jp
    name: Toxic Process Ontology
    prefix: TXPO
    publications:
    - https://pubmed.ncbi.nlm.nih.gov/32883995/
    version: 2022/12/07
  example: '0002066'
  mappings:
    aberowl: TXPO
    bioportal: TXPO
    obofoundry: txpo
    ols: txpo
    ontobee: TXPO
    wikidata.entity: Q113014440
  obofoundry:
    contact: yuki.yamagata@riken.jp
    contact.github: yuki-yamagata
    contact.label: Yuki Yamagata
    contact.orcid: 0000-0002-9673-1283
    deprecated: false
    description: TOXic Process Ontology (TXPO) systematizes a wide variety of terms
      involving toxicity courses and processes. The first version of TXPO focuses
      on liver toxicity.
    domain: chemistry and biochemistry
    download.owl: http://purl.obolibrary.org/obo/txpo.owl
    homepage: https://toxpilot.nibiohn.go.jp/
    license: CC BY 3.0
    license.url: https://creativecommons.org/licenses/by/3.0/
    name: Toxic Process Ontology
    preferredPrefix: TXPO
    prefix: txpo
    publications:
    - id: https://www.ncbi.nlm.nih.gov/pubmed/32883995
      title: Ontological approach to the knowledge systematization of a toxic process
        and toxic course representation framework for early drug risk management
    repository: https://github.com/txpo-ontology/TXPO
  ols:
    description: 'Elucidating the mechanism of toxicity is crucial in drug safety
      evaluations. TOXic Process Ontology (TXPO) systematizes a wide variety of terms
      involving toxicity courses and processes. The first version of TXPO focuses
      on liver toxicity.


      The TXPO contains an is-a hierarchy that is organized into three layers: the
      top layer contains general terms, mostly derived from the Basic Formal Ontology.
      The intermediate layer contains biomedical terms in OBO foundry from UBERON,
      Cell Ontology, NCBI Taxon, ChEBI, Gene Ontology, PATO, OGG, INOH, HINO, NCIT,
      DOID and Relational ontology (RO). The lower layer contains toxicological terms.


      In applied work, we have developed a prototype of TOXPILOT, a TOXic Process
      InterpretabLe knOwledge sysTem. TOXPILOT provides visualization maps of the
      toxic course, which facilitates capturing the comprehensive picture for understanding
      toxicity mechanisms. A prototype of TOXPILOT is available: https://toxpilot.nibiohn.go.jp'
    download_owl: http://purl.obolibrary.org/obo/txpo.owl
    homepage: https://toxpilot.nibiohn.go.jp/
    name: TOXic Process Ontology (TXPO)
    prefix: txpo
    tracker: https://github.com/txpo-ontology/TXPO/issues
    version: '2022-12-07'
    version.iri: http://purl.obolibrary.org/obo/txpo/releases/2022-12-07/txpo.owl
  ontobee:
    library: Library
    name: Toxic Process Ontology
    prefix: TXPO
  pattern: ^\d{7}$
  prefix: txpo
  publications:
  - doi: 10.1038/s41598-020-71370-7
    pmc: PMC7471325
    pubmed: '32883995'
    title: Ontological approach to the knowledge systematization of a toxic process
      and toxic course representation framework for early drug risk management
    year: 2020
  uri_format: http://purl.obolibrary.org/obo/TXPO_$1
uat:
  bartoc:
    abbreviation: UAT
    description: 'The Unified Astronomy Thesaurus (UAT) is an open, interoperable
      and community-supported thesaurus which unifies the existing divergent and isolated
      Astronomy & Astrophysics thesauri into a single high-quality, freely-available
      open thesaurus formalizing astronomical concepts and their inter-relationships.  The
      UAT builds upon the existing IAU Thesaurus with major contributions from the
      Astronomy portions of the thesauri developed by the Institute of Physics Publishing
      and the American Institute of Physics.  We expect that the Unified Astronomy
      Thesaurus will be further enhanced and updated through a collaborative effort
      involving broad community participation.


      While the AAS has assumed formal ownership of the UAT, the work will be available
      under a Creative Commons License, ensuring its widest use while protecting the
      intellectual property of the contributors. We envision that development and
      maintenance will be stewarded by a broad group of parties having a direct stake
      in it.  This includes professional associations (IVOA, IAU), learned societies
      (AAS, RAS), publishers (IOP, AIP), librarians and other curators working for
      major astronomy institutes and data archives.


      The main impetus behind the creation of a single thesaurus has been the wish
      to support semantic enrichment of the literature, but we expect that use of
      the UAT (along with other vocabularies and ontologies currently being developed
      in our community) will be much broader and will have a positive impact on the
      discovery of a wide range of astronomy resources, including data products and
      services.'
    homepage: http://astrothesaurus.org/
    license: CC BY-SA 3.0
    name: Unified Astronomy Thesaurus
    prefix: '820'
    wikidata_database: Q24254757
  example: '0'
  fairsharing:
    abbreviation: UAT
    description: The Unified Astronomy Thesaurus (UAT) is an open, interoperable and
      community-supported thesaurus being developed to unify the existing divergent
      and isolated Astronomy & Astrophysics thesauri into a single high-quality, freely-available
      open-source thesaurus which will be of immediate value to both research and
      research support, and provide a mechanism for reviewing, discussing and evaluating
      the continuous evolution of terminology in these fields.
    homepage: https://astrothesaurus.org
    license: CC BY-SA 3.0
    logo: https://api.fairsharing.org/rails/active_storage/blobs/redirect/eyJfcmFpbHMiOnsibWVzc2FnZSI6IkJBaHBBbXNGIiwiZXhwIjpudWxsLCJwdXIiOiJibG9iX2lkIn19--c891d240862cdbcf96ccc7422197c97d663d82c9/Screenshot%20From%202024-11-20%2013-15-32.png?disposition=inline
    name: Unified Astronomy Thesaurus
    prefix: FAIRsharing.998c4c
    publications:
    - doi: 10.3847/1538-4365/aab760
      title: 'The Unified Astronomy Thesaurus: Semantic Metadata for Astronomy and
        Astrophysics'
      year: 2018
    repository: https://github.com/astrothesaurus/UAT
    subjects:
    - Astronomy and Astrophysics
  mappings:
    bartoc: '820'
    fairsharing: FAIRsharing.998c4c
    tib: uat
  name: Unified Astronomy Thesaurus
  prefix: uat
  tib:
    contact: sio-ontology@googlegroups.com
    description: The Unified Astronomy Thesaurus (UAT) is an open, interoperable and
      community-supported thesaurus which unifies existing, divergent, and isolated
      controlled vocabularies in astronomy and astrophysics into a single high-quality,
      freely-available open thesaurus formalizing astronomical concepts and their
      inter-relationships. The UAT builds upon the IAU Thesaurus with major contributions
      from the Astronomy portions of the thesauri developed by the Institute of Physics
      Publishing and the American Institute of Physics. The Unified Astronomy Thesaurus
      will be further enhanced and updated through a collaborative effort involving
      broad community participation.
    download_rdf: https://raw.githubusercontent.com/astrothesaurus/UAT/master/UAT.rdf
    homepage: http://astrothesaurus.org
    keywords:
    - NFDI4ING
    - ESS
    - physics
    name: Unified Astronomy Thesaurus (UAT)
    prefix: uat
    tracker: https://github.com/astrothesaurus/UAT/issues
    uri_format: http://astrothesaurus.org/uat/$1
uberon:
  aberowl:
    description: An integrated cross-species anatomy ontology covering animals and
      bridging multiple species-specific ontologies
    download_owl: http://aber-owl.net/media/ontologies/UBERON/310/uberon.owl
    homepage: http://uberon.org
    name: Uberon multi-species anatomy ontology
    prefix: UBERON
  biocontext:
    prefix: UBERON
  bioportal:
    contact:
      email: cjmungall@lbl.gov
      name: Chris Mungall
    description: Uberon is an integrated cross-species anatomy ontology representing
      a variety of entities classified according to traditional anatomical criteria
      such as structure, function and developmental lineage. The ontology includes
      comprehensive relationships to taxon-specific anatomical ontologies, allowing
      integration of functional, phenotype and expression data.
    homepage: http://uberon.org
    license: CC-BY-3.0
    name: Uber Anatomy Ontology
    prefix: UBERON
    publications:
    - http://genomebiology.com/content/13/1/R5
    version: '2023-07-25'
  cellosaurus:
    category: Anatomy/cell type resources
    homepage: https://uberon.github.io/
    name: Uber-anatomy ontology
    prefix: UBERON
  download_json: http://purl.obolibrary.org/obo/uberon.json
  download_obo: http://purl.obolibrary.org/obo/uberon/basic.obo
  example: '2005080'
  fairsharing:
    abbreviation: UBERON
    description: Uberon is an integrated cross-species anatomy ontology covering animals
      and bridging multiple species-specific ontologies. It represents a variety of
      entities classified according to traditional anatomical criteria such as structure,
      function and developmental lineage. The ontology includes comprehensive relationships
      to taxon-specific anatomical ontologies, allowing integration of functional,
      phenotype and expression data.
    homepage: http://uberon.org/
    license: CC-BY-3.0
    name: UBER anatomy ONtology
    prefix: FAIRsharing.4c0b6b
    publications:
    - doi: 10.1186/2041-1480-5-21
      pubmed: '25009735'
      title: Unification of multi-species vertebrate anatomy ontologies for comparative
        biology in Uberon
      year: 2014
    - doi: 10.1186/gb-2012-13-1-r5
      pubmed: '22293552'
      title: Uberon, an integrative multi-species anatomy ontology
      year: 2012
    repository: https://github.com/obophenotype/uberon/wiki/Manual
    subjects:
    - Life Science
    - Taxonomy
    - Anatomy
    - Developmental Biology
    twitter: uberanat
  go:
    description: A multi-species anatomy ontology
    homepage: http://uberon.org
    name: Uber-anatomy ontology
    prefix: UBERON
  mappings:
    aberowl: UBERON
    biocontext: UBERON
    bioportal: UBERON
    cellosaurus: UBERON
    fairsharing: FAIRsharing.4c0b6b
    go: UBERON
    miriam: uberon
    n2t: uberon
    obofoundry: uberon
    ols: uberon
    ontobee: UBERON
    tib: uberon
    togoid: Uberon
    wikidata: P1554
    wikidata.entity: Q7876491
  miriam:
    deprecated: false
    description: Uberon is an integrated cross-species anatomy ontology representing
      a variety of entities classified according to traditional anatomical criteria
      such as structure, function and developmental lineage. The ontology includes
      comprehensive relationships to taxon-specific anatomical ontologies, allowing
      integration of functional, phenotype and expression data.
    homepage: https://www.ebi.ac.uk/ols4/ontologies/uberon
    id: '00000446'
    name: UBERON
    namespaceEmbeddedInLui: true
    pattern: ^UBERON:\d+$
    prefix: uberon
    sampleId: 0008203
    uri_format: https://www.ebi.ac.uk/ols4/ontologies/uberon/terms?obo_id=UBERON:$1
  n2t:
    description: Uberon is an integrated cross-species anatomy ontology representing
      a variety of entities classified according to traditional anatomical criteria
      such as structure, function and developmental lineage. The ontology includes
      comprehensive relationships to taxon-specific anatomical ontologies, allowing
      integration of functional, phenotype and expression data.
    example: 0008203
    homepage: http://bioportal.bioontology.org/ontologies/UBERON
    name: UBERON through bioPortal
    namespaceEmbeddedInLui: true
    pattern: ^UBERON\:\d+$
    prefix: uberon
    uri_format: http://purl.bioontology.org/ontology/UBERON/UBERON:$1
  name: Uber Anatomy Ontology
  obofoundry:
    appears_in:
    - aism
    - amphx
    - chiro
    - cl
    - clo
    - clyh
    - colao
    - cteno
    - ecao
    - ecocore
    - ecto
    - envo
    - foodon
    - fovt
    - genepio
    - go
    - hso
    - lepao
    - maxo
    - mco
    - ons
    - pcl
    - plana
    - poro
    - zp
    - mfmo
    contact: cjmungall@lbl.gov
    contact.github: cmungall
    contact.label: Chris Mungall
    contact.orcid: 0000-0002-6601-2165
    depends_on:
    - bfo
    - bspo
    - chebi
    - cl
    - envo
    - go
    - nbo
    - ncbitaxon
    - omo
    - pato
    - pr
    - ro
    deprecated: false
    description: An integrated cross-species anatomy ontology covering animals and
      bridging multiple species-specific ontologies
    domain: anatomy and development
    download.owl: http://purl.obolibrary.org/obo/uberon.owl
    homepage: http://uberon.org
    license: CC BY 3.0
    license.url: http://creativecommons.org/licenses/by/3.0/
    logo: https://raw.githubusercontent.com/jmcmurry/closed-illustrations/master/logos/uberon-logos/uberon_logo_black-banner.png
    name: Uberon multi-species anatomy ontology
    preferredPrefix: UBERON
    prefix: uberon
    publications:
    - id: https://www.ncbi.nlm.nih.gov/pubmed/22293552
      title: Uberon, an integrative multi-species anatomy ontology
    - id: https://www.ncbi.nlm.nih.gov/pubmed/25009735
      title: Unification of multi-species vertebrate anatomy ontologies for comparative
        biology in Uberon
    repository: https://github.com/obophenotype/uberon
    twitter: uberanat
  ols:
    description: Uberon is an integrated cross-species anatomy ontology representing
      a variety of entities classified according to traditional anatomical criteria
      such as structure, function and developmental lineage. The ontology includes
      comprehensive relationships to taxon-specific anatomical ontologies, allowing
      integration of functional, phenotype and expression data.
    download_owl: http://purl.obolibrary.org/obo/uberon.owl
    homepage: http://uberon.org
    name: Uber-anatomy ontology
    prefix: uberon
    tracker: https://github.com/obophenotype/uberon/issues
    version: '2025-12-04'
    version.iri: http://purl.obolibrary.org/obo/uberon/releases/2025-12-04/uberon.owl
  ontobee:
    library: Library
    name: Uberon multi-species anatomy ontology
    prefix: UBERON
  pattern: ^\d+$
  prefix: uberon
  providers:
  - code: cellguide
    description: CellGuide is a comprehensive resource for knowledge about cell types.
    example: null
    first_party: null
    homepage: https://cellxgene.cziscience.com/cellguide
    name: Cell Guide
    publications: null
    status: null
    uri_format: https://cellxgene.cziscience.com/cellguide/tissues/UBERON_$1
  publications:
  - doi: 10.1186/2041-1480-5-21
    pmc: PMC4089931
    pubmed: '25009735'
    title: Unification of multi-species vertebrate anatomy ontologies for comparative
      biology in Uberon
    year: 2014
  - doi: 10.1186/gb-2012-13-1-r5
    pmc: PMC3334586
    pubmed: '22293552'
    title: Uberon, an integrative multi-species anatomy ontology
    year: 2012
  synonyms:
  - UBERON
  - Uber-anatomy ontology
  - Uberon
  tib:
    description: Uberon is an integrated cross-species anatomy ontology representing
      a variety of entities classified according to traditional anatomical criteria
      such as structure, function and developmental lineage. The ontology includes
      comprehensive relationships to taxon-specific anatomical ontologies, allowing
      integration of functional, phenotype and expression data.
    download_owl: http://purl.obolibrary.org/obo/uberon.owl
    homepage: http://obophenotype.github.io/uberon/
    keywords:
    - DataPLANT
    - life sciences, biology
    name: Uber-anatomy ontology
    prefix: uberon
    tracker: https://github.com/obophenotype/uberon/issues/
    version.iri: http://purl.obolibrary.org/obo/uberon/releases/2025-08-15/uberon.owl
  togoid:
    examples:
    - UBERON:0002115
    - UBERON:0001004
    - UBERON:0000007
    - UBERON:0001044
    - UBERON:0001825
    - UBERON:0001361
    - UBERON:0002186
    - UBERON:0000945
    - UBERON:0036068
    - UBERON:0001017
    keywords:
    - Anatomy
    name: UBERON
    pattern: ^UBERON[:_](?\d{7})$
    prefix: Uberon
    uri_format: http://purl.obolibrary.org/obo/UBERON_$1
  uri_format: http://purl.obolibrary.org/obo/UBERON_$1
  wikidata:
    description: identifier from UBERON ontology (without prefix)
    example:
    - '0000033'
    - '0000057'
    homepage: http://uberon.github.io
    miriam: UBERON
    name: UBERON ID
    pattern: ^\d{7}$
    prefix: P1554
    uri_format: http://purl.obolibrary.org/obo/UBERON_$1
    uri_format_rdf: http://purl.obolibrary.org/obo/UBERON_$1
uberon.issue:
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: An issue on the UBERON GitHub Issue tracker
  example: '530'
  github_request_issue: 1553
  homepage: https://github.com/obophenotype/uberon/issues
  name: UBERON Issue Tracker
  pattern: ^\d+$
  prefix: uberon.issue
  uri_format: https://github.com/obophenotype/uberon/issues/$1
ubio.namebank:
  biocontext:
    prefix: UBIO.NAMEBANK
  mappings:
    biocontext: UBIO.NAMEBANK
    miriam: ubio.namebank
    n2t: ubio.namebank
  miriam:
    deprecated: true
    description: NameBank is a "biological name server" focused on storing names and
      objectively-derived nomenclatural attributes. NameBank is a repository for all
      recorded names including scientific names, vernacular (or common names), misspelled
      names, as well as ad-hoc nomenclatural labels that may have limited context.
    homepage: http://www.ubio.org
    id: 00000338
    name: uBio NameBank
    namespaceEmbeddedInLui: false
    pattern: ^\d+$
    prefix: ubio.namebank
    sampleId: '2555646'
    uri_format: http://www.ubio.org/browser/details.php?namebankID=$1
  n2t:
    description: NameBank is a "biological name server" focused on storing names and
      objectively-derived nomenclatural attributes. NameBank is a repository for all
      recorded names including scientific names, vernacular (or common names), misspelled
      names, as well as ad-hoc nomenclatural labels that may have limited context.
    example: '2555646'
    homepage: http://www.ubio.org
    name: uBio NameBank at The Marine Biological Laboratory
    namespaceEmbeddedInLui: false
    pattern: ^\d+$
    prefix: ubio.namebank
    uri_format: http://www.ubio.org/browser/details.php?namebankID=$1
  prefix: ubio.namebank
ubprop:
  comment: All of these are typedefs in uberon now
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  deprecated: true
  name: Uberon Property
  prefix: ubprop
  synonyms:
  - UBPROP
  - UBREL
ucas:
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: An identifier for institutions in the United Kingdom, used in GRID
    and ROR.
  example: N21
  homepage: https://www.ucas.com
  keywords:
  - bibliometrics
  - institution
  name: UK Universities and Colleges Admissions Service
  pattern: ^\w\d+$
  prefix: ucas
ucsc:
  biocontext:
    prefix: UCSC
    uri_format: ftp://hgdownload.cse.ucsc.edu/goldenPath/$1
  contact:
    email: max@soe.ucsc.edu
    github: maximilianh
    name: Maximilian Haeussler
    orcid: 0000-0001-8721-8253
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: The UCSC Genome Browser is an on-line, and downloadable, genome browser
    hosted by the University of California, Santa Cruz (UCSC).[2][3][4] It is an interactive
    website offering access to genome sequence data from a variety of vertebrate and
    invertebrate species and major model organisms, integrated with a large collection
    of aligned annotations.
  example: uc001rvw.5
  homepage: https://genome.ucsc.edu/
  mappings:
    biocontext: UCSC
    uniprot: DB-0139
    wikidata: P2576
  name: UCSC Genome Browser
  prefix: ucsc
  publications:
  - doi: 10.1093/nar/gky1095
    pmc: PMC6323953
    pubmed: '30407534'
    title: 'The UCSC Genome Browser database: 2019 update'
    year: 2019
  uniprot:
    abbreviation: UCSC
    category: Genome annotation databases
    homepage: https://genome.ucsc.edu/
    name: UCSC genome browser
    prefix: DB-0139
    publications:
    - doi: 10.1093/nar/gkae974
      pubmed: '39460617'
    uri_format: https://genome.ucsc.edu/cgi-bin/hgLinkIn?resource=uniprot&id=$1
  wikidata:
    description: identifier of a UCSC's release of a genome
    example:
    - 'Chr 19: 34.85 – 34.89 Mb'
    - hg38
    - uc002xza.4
    homepage: https://genome.ucsc.edu
    name: UCSC Genome Browser assembly ID
    prefix: P2576
    uri_format: https://genome.ucsc.edu/cgi-bin/hgTracks?db=$1
ucum:
  bartoc:
    abbreviation: UCUM
    description: 'The Unified Code for Units of Measure is a code system intended
      to include all units of measures being contemporarily used in international
      science, engineering, and business. The purpose is to facilitate unambiguous
      electronic communication of quantities together with their units. The focus
      is on electronic communication, as opposed to communication between humans.
      A typical application of The Unified Code for Units of Measure are electronic
      data interchange (EDI) protocols, but there is nothing that prevents it from
      being used in other types of machine communication. How does it relate?


      The Unified Code for Units of Measure is inspired by and heavily based on ISO
      2955-1983, ANSI X3.50-1986, and HL7''s extensions called ISO+. The respective
      ISO and ANSI standards are both entitled Representation of [...] units in systems
      with limited character sets where ISO 2955 refers to SI and other units provided
      by ISO 1000-1981, while ANSI X3.50 extends ISO 2955 to include U.S. customary
      units. Because these standards carry the restriction of limited character sets
      in their names they seem to be of less value today where graphical user interface
      and laser printers are in wide-spread use, which is why the european standard
      ENV 12435 in its clause 7.3 declares ISO 2955 obsolete.


      ENV 12435 is dedicated exclusively to the communication of measurements between
      humans in display and print, and does not provide codes that can be used in
      communication between systems. It does not even provide a specification that
      would allow communication of units from one system to the screen or printer
      of another system. The issue about displaying units in the common style defined
      by the 9th Conférence Générale des Poids et Mesures (CGPM) in 1947 is not just
      the character set. Although The Unicode Standard and its predecessor ISO/IEC
      10646 is the richest character set ever it is still not enough to specify the
      presentation of units because there are important typographical details such
      as superscripts, subscripts, roman and italics."


      Several URI namespaces and encoding methods have been proposed to map UCUM codes
      to URIs.'
    homepage: http://unitsofmeasure.org/
    name: Unified Code for Units of Measure
    prefix: '1895'
    wikidata_database: Q2494286
  contact:
    email: dr.shorthair@pm.me
    github: dr-shorthair
    name: Simon Cox
    orcid: 0000-0002-3884-3420
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: Unified Code for Units of Measure (UCUM) is a code system intended
    to include all units of measures being contemporarily used in international science,
    engineering, and business.
  example: aBq
  example_extras:
  - /A/s3/cg3/T3
  - /g
  - /m3
  - '%'
  - Cel.d-1
  - dL/g
  - dlm
  - dlx
  - Em.s-2
  - g.cm-3
  - K2
  - kW/h
  - m/s
  - m.s-2
  - m/s/d
  - mmol.mL-1
  - mol.L-1
  - mol.um
  - ng-1
  - pA
  - ug.mL-1
  - umol.L-1
  - us
  - Wb
  fairsharing:
    abbreviation: UCUM
    description: The Unified Code for Units of Measure is a code system intended to
      include all units of measures being contemporarily used in international science,
      engineering, and business. The purpose is to facilitate unambiguous electronic
      communication of quantities together with their units. The focus is on electronic
      communication, as opposed to communication between humans. A typical application
      of The Unified Code for Units of Measure are electronic data interchange (EDI)
      protocols, but there is nothing that prevents it from being used in other types
      of machine communication.
    domains:
    - Data identity and mapping
    - unit
    - measurement
    homepage: https://ucum.org/trac
    name: The Unified Code for Units of Measure
    prefix: FAIRsharing.27w8k0
    publications:
    - doi: 10.1136/jamia.1999.0060151
      pubmed: '10094068'
      title: Units of measure in clinical information systems
      year: 1999
    subjects:
    - Subject Agnostic
  hl7:
    description: Unified Code for Units of Measure.  The Unified Code for Units of
      Measure is a code system intended to include all units of measures being contemporarily
      used in international science, engineering, and business. The purpose is to
      facilitate unambiguous electronic communication of quantities together with
      their units. The focus is on electronic communication, as opposed to communication
      between humans. A typical application of The Unified Code for Units of Measure
      are electronic data interchange (EDI) protocols, but there is nothing that prevents
      it from being used in other types of machine communication.http://unitsofmeasure.org/
    homepage: http://www.regenstrief.org
    name: Unified Code for Units of Measure
    organization: Regenstrief Institute
    preferred_prefix: ucum
    prefix: 2.16.840.1.113883.6.8
    status: Complete
  homepage: https://ucum.org
  lov:
    description: "The instances of this ontology have been automatically\n       \
      \  generated from the UCUM (The Unified Code for Units of Measure).\n      \
      \   See http://aurora.rg.iupui.edu/UCUM/ for more details\n         on UCUM.\
      \ The members of the MyMobileWeb consortium\n         explicitly acknowledge\
      \ the copyright of the data from\n         the UCUM ontology."
    homepage: http://purl.oclc.org/NET/muo/ucum/
    keywords:
    - General & Upper
    modified: '2008-01-01'
    name: Units of measurement ontology
    prefix: ucum
    uri_prefix: http://purl.oclc.org/NET/muo/ucum/$1
  mappings:
    bartoc: '1895'
    fairsharing: FAIRsharing.27w8k0
    hl7: 2.16.840.1.113883.6.8
    lov: ucum
    wikidata.entity: Q2494286
  name: Unified Code for Units of Measure
  prefix: ucum
  publications:
  - doi: 10.1136/jamia.1999.0060151
    pmc: PMC61354
    pubmed: '10094068'
    title: Units of measure in clinical information systems
    year: 1999
  references:
  - https://units-of-measurement.org/
  repository: https://github.com/ucum-org/ucum
  uri_format: https://units-of-measurement.org/$1
udsaes.fmi:
  description: An ontology transcription of definitions in the Functional Mock-up
    Interface (FMI) standard document from https://fmi-standard.org/ that enables
    representing Functional Mock-up Units (FMUs) in RDF
  example: FMU
  mappings:
    tib: fmi
  name: Functional Mock-up Interface Ontology
  prefix: udsaes.fmi
  repository: https://github.com/UdSAES/fmi2rdf
  tib:
    description: Ontology for representing FMUs in RDF
    homepage: https://github.com/UdSAES/fmi2rdf
    keywords:
    - NFDI4Energy
    - mechanical engineering, energy technology
    name: FMI-Ontology
    prefix: fmi
    tracker: https://github.com/UdSAES/fmi2rdf/issues
    uri_format: https://purl.org/fmi-ontology#$1
udsaes.sms:
  example: CanBeApproximated
  mappings:
    tib: sms
  prefix: udsaes.sms
  repository: https://github.com/UdSAES/sms-ontology
  tib:
    description: Ontology for representing systems, models and simulations in RDF.
    homepage: https://github.com/UdSAES/sms-ontology
    keywords:
    - NFDI4Energy
    - mechanical engineering, energy technology
    name: SMS-Ontology
    prefix: sms
    tracker: https://github.com/UdSAES/sms-ontology/issues
    uri_format: https://purl.org/sms-ontology#$1
ukprn:
  comment: Added because of appearance in ROR
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: identifier for an educational organization issued by the UK Register
    of Learning Providers
  example: '10007835'
  homepage: https://www.ukrlp.co.uk
  mappings:
    wikidata: P4971
  name: UK Provider Reference Number
  pattern: ^[1-9]\d*$
  prefix: ukprn
  synonyms:
  - ukprns
  uri_format: https://www.ukrlp.co.uk/ukrlp/ukrlp_provider.page_pls_provDetails?x=&pn_p_id=$1&pv_status=VERIFIED&pv_vis_code=L
  wikidata:
    description: identifier for an educational organization issued by the UK Register
      of Learning Providers
    example:
    - '10007835'
    - '10008408'
    homepage: https://www.ukrlp.co.uk/
    name: UK Provider Reference Number
    pattern: ^[1-9][0-9]{7}$
    prefix: P4971
    uri_format: https://www.ukrlp.co.uk/ukrlp/ukrlp_provider.page_pls_provDetails?x=&pn_p_id=$1&pv_status=VERIFIED&pv_vis_code=L
umbbd.compound:
  biocontext:
    prefix: UMBBD.COMPOUND
  mappings:
    biocontext: UMBBD.COMPOUND
    miriam: umbbd.compound
    n2t: umbbd.compound
    wikidata: P8121
  miriam:
    deprecated: false
    description: The University of Minnesota Biocatalysis/Biodegradation Database
      (UM-BBD) contains information on microbial biocatalytic reactions and biodegradation
      pathways for primarily xenobiotic, chemical compounds. The goal of the UM-BBD
      is to provide information on microbial enzyme-catalyzed reactions that are important
      for biotechnology. This collection refers to compound information.
    homepage: http://umbbd.ethz.ch/
    id: '00000276'
    name: UM-BBD Compound
    namespaceEmbeddedInLui: false
    pattern: ^c\d+$
    prefix: umbbd.compound
    sampleId: c0001
    uri_format: http://umbbd.ethz.ch/servlets/pageservlet?ptype=c&compID=$1
  n2t:
    description: The University of Minnesota Biocatalysis/Biodegradation Database
      (UM-BBD) contains information on microbial biocatalytic reactions and biodegradation
      pathways for primarily xenobiotic, chemical compounds. The goal of the UM-BBD
      is to provide information on microbial enzyme-catalyzed reactions that are important
      for biotechnology. This collection refers to compound information.
    example: c0001
    homepage: http://umbbd.ethz.ch/
    name: Biocatalysis/Biodegradation Database Mirror (Compound) at ETH Zurich
    namespaceEmbeddedInLui: false
    pattern: ^c\d+$
    prefix: umbbd.compound
    uri_format: http://umbbd.ethz.ch/servlets/pageservlet?ptype=c&compID=$1
  name: UM-BBD compound
  part_of_database: umbbd
  prefix: umbbd.compound
  synonyms:
  - UM-BBD_compID
  uri_format: http://eawag-bbd.ethz.ch/servlets/pageservlet?ptype=c&compID=$1
  wikidata:
    description: ID for chemical compound in The University of Minnesota Biocatalysis/Biodegradation
      Database
    example:
    - c0001
    - c0002
    - c0003
    homepage: http://eawag-bbd.ethz.ch/servlets/pageservlet?ptype=allcomps
    name: UM-BBD compound ID
    prefix: P8121
    uri_format: https://eawag-bbd.ethz.ch/servlets/pageservlet?ptype=c&compID=$1
umbbd.enzyme:
  biocontext:
    prefix: UMBBD.ENZYME
  go:
    homepage: http://eawag-bbd.ethz.ch/
    name: EAWAG Biocatalysis/Biodegradation Database
    prefix: UM-BBD_enzymeID
    uri_format: http://eawag-bbd.ethz.ch/servlets/pageservlet?ptype=ep&enzymeID=$1
  mappings:
    biocontext: UMBBD.ENZYME
    go: UM-BBD_enzymeID
    miriam: umbbd.enzyme
    n2t: umbbd.enzyme
  miriam:
    deprecated: false
    description: The University of Minnesota Biocatalysis/Biodegradation Database
      (UM-BBD) contains information on microbial biocatalytic reactions and biodegradation
      pathways for primarily xenobiotic, chemical compounds. The goal of the UM-BBD
      is to provide information on microbial enzyme-catalyzed reactions that are important
      for biotechnology. This collection refers to enzyme information.
    homepage: http://umbbd.ethz.ch/
    id: '00000326'
    name: UM-BBD Enzyme
    namespaceEmbeddedInLui: false
    pattern: ^e\d+$
    prefix: umbbd.enzyme
    sampleId: e0333
    uri_format: http://umbbd.ethz.ch/servlets/pageservlet?ptype=ep&enzymeID=$1
  n2t:
    description: The University of Minnesota Biocatalysis/Biodegradation Database
      (UM-BBD) contains information on microbial biocatalytic reactions and biodegradation
      pathways for primarily xenobiotic, chemical compounds. The goal of the UM-BBD
      is to provide information on microbial enzyme-catalyzed reactions that are important
      for biotechnology. This collection refers to enzyme information.
    example: e0333
    homepage: http://umbbd.ethz.ch/
    name: Biocatalysis/Biodegradation Database Mirror (Enzyme) at ETH Zurich
    namespaceEmbeddedInLui: false
    pattern: ^e\d+$
    prefix: umbbd.enzyme
    uri_format: http://umbbd.ethz.ch/servlets/pageservlet?ptype=ep&enzymeID=$1
  name: EAWAG Biocatalysis/Biodegradation Database enzyme
  part_of_database: umbbd
  prefix: umbbd.enzyme
  synonyms:
  - UM-BBD_enzymeID
  uri_format: http://eawag-bbd.ethz.ch/servlets/pageservlet?ptype=ep&enzymeID=$1
umbbd.pathway:
  biocontext:
    prefix: UMBBD.PATHWAY
  go:
    homepage: http://eawag-bbd.ethz.ch/
    name: EAWAG Biocatalysis/Biodegradation Database
    prefix: UM-BBD_pathwayID
    uri_format: http://eawag-bbd.ethz.ch/$1/$1_map.html
  mappings:
    biocontext: UMBBD.PATHWAY
    go: UM-BBD_pathwayID
    miriam: umbbd.pathway
    n2t: umbbd.pathway
  miriam:
    deprecated: false
    description: The University of Minnesota Biocatalysis/Biodegradation Database
      (UM-BBD) contains information on microbial biocatalytic reactions and biodegradation
      pathways for primarily xenobiotic, chemical compounds. The goal of the UM-BBD
      is to provide information on microbial enzyme-catalyzed reactions that are important
      for biotechnology. This collection refers to pathway information.
    homepage: http://umbbd.ethz.ch/
    id: '00000327'
    name: UM-BBD Pathway
    namespaceEmbeddedInLui: false
    pattern: ^\w+$
    prefix: umbbd.pathway
    sampleId: ala
    uri_format: http://umbbd.ethz.ch/servlets/pageservlet?ptype=p&pathway_abbr=$1
  n2t:
    description: The University of Minnesota Biocatalysis/Biodegradation Database
      (UM-BBD) contains information on microbial biocatalytic reactions and biodegradation
      pathways for primarily xenobiotic, chemical compounds. The goal of the UM-BBD
      is to provide information on microbial enzyme-catalyzed reactions that are important
      for biotechnology. This collection refers to pathway information.
    example: ala
    homepage: http://umbbd.ethz.ch/
    name: Biocatalysis/Biodegradation Database Mirror (Pathway) at ETH Zurich
    namespaceEmbeddedInLui: false
    pattern: ^\w+$
    prefix: umbbd.pathway
    uri_format: http://umbbd.ethz.ch/servlets/pageservlet?ptype=p&pathway_abbr=$1
  name: EAWAG Biocatalysis/Biodegradation Database pathway
  part_of_database: umbbd
  prefix: umbbd.pathway
  providers:
  - code: eawag
    description: Graphical depiction of pathway
    example: null
    first_party: null
    homepage: http://eawag-bbd.ethz.ch
    name: Pathway map diagram
    publications: null
    status: null
    uri_format: http://eawag-bbd.ethz.ch/$1/$1_map.html
  synonyms:
  - UM-BBD_pathwayID
  uri_format: http://umbbd.ethz.ch/servlets/pageservlet?ptype=p&pathway_abbr=$1
umbbd.reaction:
  biocontext:
    prefix: UMBBD.REACTION
  go:
    homepage: http://eawag-bbd.ethz.ch/
    name: EAWAG Biocatalysis/Biodegradation Database
    prefix: UM-BBD_reactionID
    uri_format: http://eawag-bbd.ethz.ch/servlets/pageservlet?ptype=r&reacID=$1
  mappings:
    biocontext: UMBBD.REACTION
    go: UM-BBD_reactionID
    miriam: umbbd.reaction
    n2t: umbbd.reaction
    wikidata.entity: Q24188985
  miriam:
    deprecated: false
    description: The University of Minnesota Biocatalysis/Biodegradation Database
      (UM-BBD) contains information on microbial biocatalytic reactions and biodegradation
      pathways for primarily xenobiotic, chemical compounds. The goal of the UM-BBD
      is to provide information on microbial enzyme-catalyzed reactions that are important
      for biotechnology. This collection refers to reaction information.
    homepage: http://umbbd.ethz.ch/
    id: '00000325'
    name: UM-BBD Reaction
    namespaceEmbeddedInLui: false
    pattern: ^r\d+$
    prefix: umbbd.reaction
    sampleId: r0001
    uri_format: http://umbbd.ethz.ch/servlets/pageservlet?ptype=r&reacID=$1
  n2t:
    description: The University of Minnesota Biocatalysis/Biodegradation Database
      (UM-BBD) contains information on microbial biocatalytic reactions and biodegradation
      pathways for primarily xenobiotic, chemical compounds. The goal of the UM-BBD
      is to provide information on microbial enzyme-catalyzed reactions that are important
      for biotechnology. This collection refers to reaction information.
    example: r0001
    homepage: http://umbbd.ethz.ch/
    name: Biocatalysis/Biodegradation Database Mirror (Reaction) at ETH Zurich
    namespaceEmbeddedInLui: false
    pattern: ^r\d+$
    prefix: umbbd.reaction
    uri_format: http://umbbd.ethz.ch/servlets/pageservlet?ptype=r&reacID=$1
  name: EAWAG Biocatalysis/Biodegradation Database reaction
  part_of_database: umbbd
  prefix: umbbd.reaction
  synonyms:
  - UM-BBD_reactionID
  uri_format: http://eawag-bbd.ethz.ch/servlets/pageservlet?ptype=r&reacID=$1
  wikidata:
    database: Q24188985
umbbd.rule:
  biocontext:
    prefix: UMBBD.RULE
  go:
    homepage: http://eawag-bbd.ethz.ch/
    name: EAWAG Biocatalysis/Biodegradation Database
    prefix: UM-BBD_ruleID
    uri_format: http://eawag-bbd.ethz.ch/servlets/rule.jsp?rule=$1
  mappings:
    biocontext: UMBBD.RULE
    go: UM-BBD_ruleID
    miriam: umbbd.rule
    n2t: umbbd.rule
  miriam:
    deprecated: false
    description: The University of Minnesota Biocatalysis/Biodegradation Database
      (UM-BBD) contains information on microbial biocatalytic reactions and biodegradation
      pathways for primarily xenobiotic, chemical compounds. The UM-BBD Pathway Prediction
      System (PPS) predicts microbial catabolic reactions using substructure searching,
      a rule-base, and atom-to-atom mapping. The PPS recognizes organic functional
      groups found in a compound and predicts transformations based on biotransformation
      rules. These rules are based on reactions found in the UM-BBD database. This
      collection references those rules.
    homepage: http://umbbd.ethz.ch/servlets/pageservlet?ptype=allrules
    id: 00000328
    name: UM-BBD Biotransformation Rule
    namespaceEmbeddedInLui: false
    pattern: ^bt\d+$
    prefix: umbbd.rule
    sampleId: bt0001
    uri_format: http://www.umbbd.ethz.ch/servlets/rule.jsp?rule=$1
  n2t:
    description: The University of Minnesota Biocatalysis/Biodegradation Database
      (UM-BBD) contains information on microbial biocatalytic reactions and biodegradation
      pathways for primarily xenobiotic, chemical compounds. The UM-BBD Pathway Prediction
      System (PPS) predicts microbial catabolic reactions using substructure searching,
      a rule-base, and atom-to-atom mapping. The PPS recognizes organic functional
      groups found in a compound and predicts transformations based on biotransformation
      rules. These rules are based on reactions found in the UM-BBD database. This
      collection references those rules.
    example: bt0001
    homepage: http://umbbd.ethz.ch/servlets/pageservlet?ptype=allrules
    name: Biocatalysis/Biodegradation Database Mirror (Biotransformation Rule) at
      ETH Zurich
    namespaceEmbeddedInLui: false
    pattern: ^bt\d+$
    prefix: umbbd.rule
    uri_format: http://www.umbbd.ethz.ch/servlets/rule.jsp?rule=$1
  name: EAWAG Biocatalysis/Biodegradation Database rule
  part_of_database: umbbd
  prefix: umbbd.rule
  synonyms:
  - UM-BBD_ruleID
uminctr:
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: An additional Japanese clinical trial registry
  domain: clinical trial
  example: UMIN000049383
  homepage: https://www.umin.ac.jp/ctr/index.htm
  integbio:
    alt_name: UMIN Clinical Trials Registry
    description: UMIN-CTR is a registration database for clinical trials. Each entry
      contains title of the study, condition, objectives, assessment, study design,
      intervention, public contact, etc. It requires a UMIN ID and password in order
      to register clinical trials, but not to browse and search data.
    homepage: http://www.umin.ac.jp/ctr/index.htm
    information_keywords:
    - Bibliography/Documents
    maintainer: UMIN (University Hospital Medical Information Network Center)
    name: UMIN-CTR
    prefix: nbdc01470
    status: Active
    target_keywords:
    - Health/Disease
  mappings:
    integbio: nbdc01470
  name: University hospital Medical Information Network Clinical Trial Registry
  pattern: ^UMIN\d+$|^C\d+$
  prefix: uminctr
  references:
  - https://center6.umin.ac.jp/cgi-open-bin/ctr_e/ctr_view.cgi?recptno=R000056224
umls:
  bartoc:
    abbreviation: UMLS
    description: The Unified Medical Language System (UMLS) is a compendium of many
      controlled vocabularies in the biomedical sciences.
    homepage: https://www.nlm.nih.gov/research/umls/index.html
    name: Unified Medical Language System
    prefix: '20052'
    wikidata_database: Q455338
  biocontext:
    prefix: UMLS
    uri_format: http://linkedlifedata.com/resource/umls/id/$1
  contact:
    email: olivier@nlm.nih.gov
    github: null
    name: Olivier Bodenreider
    orcid: 0000-0003-4769-4217
  domain: multiple
  edam:
    description: An identifier of a concept from the UMLS vocabulary.
    name: UMLS concept
    obsolete: false
    prefix: '1181'
  example: C2584994
  hl7:
    description: UMLS codes as CUIs making up the values in a coding system.  More
      information may be found at http://www.nlm.nih.gov/research/umls/
    homepage: http://www.nlm.nih.gov
    name: Unified Medical Language System
    organization: National Library of Medicine
    preferred_prefix: umls
    prefix: 2.16.840.1.113883.6.86
    status: Complete
  homepage: https://www.nlm.nih.gov/research/umls
  keywords:
  - biomedicine
  license: https://www.nlm.nih.gov/research/umls/knowledge_sources/metathesaurus/release/license_agreement.html
  logo: https://uts.nlm.nih.gov/uts/assets/images/umls_tree_sm.jpg
  mappings:
    bartoc: '20052'
    biocontext: UMLS
    edam: '1181'
    hl7: 2.16.840.1.113883.6.86
    miriam: umls
    n2t: umls
    wikidata: P2892
    wikidata.entity: Q455338
  miriam:
    deprecated: false
    description: The Unified Medical Language System is a repository of biomedical
      vocabularies. Vocabularies integrated in the UMLS Metathesaurus include the
      NCBI taxonomy, Gene Ontology, the Medical Subject Headings (MeSH), OMIM and
      the Digital Anatomist Symbolic Knowledge Base. UMLS concepts are not only inter-related,
      but may also be linked to external resources such as GenBank.
    homepage: https://www.nlm.nih.gov/
    id: 00000559
    name: UMLS
    namespaceEmbeddedInLui: false
    pattern: ^C\d+$
    prefix: umls
    sampleId: C0021390
    uri_format: https://uts.nlm.nih.gov/uts/umls/concept/$1
  n2t:
    description: The Unified Medical Language System is a repository of biomedical
      vocabularies. Vocabularies integrated in the UMLS Metathesaurus include the
      NCBI taxonomy, Gene Ontology, the Medical Subject Headings (MeSH), OMIM and
      the Digital Anatomist Symbolic Knowledge Base. UMLS concepts are not only inter-related,
      but may also be linked to external resources such as GenBank.
    example: C0021390
    homepage: http://linkedlifedata.com/
    name: Unified Medical Language System at LinkedLifeData
    namespaceEmbeddedInLui: false
    pattern: ^C\d+$
    prefix: umls
    uri_format: http://linkedlifedata.com/resource/umls/id/$1
  name: Unified Medical Language System Concept Unique Identifier
  part_of_database: umls
  prefix: umls
  publications:
  - doi: 10.1093/nar/gkh061
    pmc: PMC308795
    pubmed: '14681409'
    title: 'The Unified Medical Language System (UMLS): integrating biomedical terminology'
    year: 2004
  synonyms:
  - UMLS
  - UMLS CUI
  - UMLS_CUI
  - umls.cui
  uri_format: https://uts.nlm.nih.gov/uts/umls/concept/$1
  wikidata:
    database: Q455338
    description: NLM Unified Medical Language System (UMLS) controlled biomedical
      vocabulary unique identifier
    example:
    - C0011551
    - C0037379
    - C1274928
    homepage: https://www.nlm.nih.gov/research/umls/rxnorm/
    miriam: umls
    name: UMLS CUI
    pattern: ^C\w\d{6}$
    prefix: P2892
    uri_format: https://evsexplore.semantics.cancer.gov/evsexplore/concept/ncim/$1
umls.aui:
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: An identifier for an atom; the smallest unit of naming in a source,
    viz, a specific string with specific code values and identifiers from a specific
    source. As such, they can be thought of as representing a single meaning with
    a source Atoms are the units of terminology that come from sources and form the
    building blocks of the concepts in the Metathesaurus.
  example: A0118748
  homepage: https://www.nlm.nih.gov/research/umls
  name: Unified Medical Language System Atomic Unique Identifier
  part_of_database: umls
  pattern: ^A\d+$
  prefix: umls.aui
  synonyms:
  - UMLS_ICD9CM_2005_AUI
unesco.thesaurus:
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: The UNESCO Thesaurus is a controlled and structured list of terms used
    in subject analysis and retrieval of documents and publications in the fields
    of education, culture, natural sciences, social and human sciences, communication
    and information. Continuously enriched and updated, its multidisciplinary terminology
    reflects the evolution of UNESCO's programmes and activities. [from homepage]
  example: '585'
  fairsharing:
    abbreviation: UNESCO Thesaurus
    description: The UNESCO Thesaurus is a controlled and structured list of concepts
      used in subject analysis and retrieval of documents and publications in the
      fields of education, culture, natural sciences, social and human sciences, communication
      and information. Continuously enriched and updated, its multidisciplinary terminology
      reflects the evolution of UNESCO's programmes and activities. It is available
      in English, French, Spanish, Russian, and Arabic.
    homepage: http://vocabularies.unesco.org
    license: https://creativecommons.org/licenses/by-sa/3.0/igo
    name: UNESCO Thesaurus
    prefix: FAIRsharing.81dc5f
    subjects:
    - Culture
    - Education Science
    - Communication Science
    - Political Science
    - Subject Agnostic
  homepage: http://vocabularies.unesco.org/thesaurus
  license: CC-BY-3.0-IGO
  mappings:
    fairsharing: FAIRsharing.81dc5f
  name: UNESCO Thesaurus
  pattern: ^\d+$
  prefix: unesco.thesaurus
  uri_format: http://vocabularies.unesco.org/thesaurus/concept$1
unicarbdb:
  contact:
    email: niclas.karlsson@medkem.gu.se
    github: null
    name: Niclas Karlsson
    orcid: 0000-0002-3045-2628
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: UniCarb-DB stores structural and mass spectrometry (MS) glycomic data,
    and has now grown to be one of the largest experimental glycomic MS databases.
    Identifiers correspond to individual glycan structures and corresponding MS spectra.
  example: '91'
  github_request_issue: 1509
  homepage: https://unicarb-db.expasy.org
  license: CC-BY-4.0
  name: UniCarb-DB
  pattern: ^\d+$
  prefix: unicarbdb
  publications:
  - doi: 10.1016/j.bbapap.2013.04.018
    pmc: null
    pubmed: '23624262'
    title: 'Validation of the curation pipeline of UniCarb-DB: building a global glycan
      reference MS/MS repository'
    year: 2014
  reviewer:
    email: b.gyori@northeastern.edu
    github: bgyori
    name: Benjamin M. Gyori
    orcid: 0000-0001-9439-5346
  uri_format: https://unicarb-db.expasy.org/msData/$1
unichem:
  mappings:
    wikidata: P11089
  name: UniChem compound
  prefix: unichem
  wikidata:
    description: identifier of a compound in the UniChem database
    example:
    - '161671'
    - '289153'
    - '39562'
    homepage: https://chembl.gitbook.io/unichem/downloads
    name: UniChem compound ID
    pattern: ^\d+$
    prefix: P11089
    uri_format: https://www.ebi.ac.uk/unichem/compoundsources?type=uci&compound=$1
unigene:
  biocontext:
    prefix: UNIGENE
  deprecated: true
  fairsharing:
    abbreviation: UniGene
    description: Each UniGene entry is a set of transcript sequences that appear to
      come from the same transcription locus (gene or expressed pseudogene), together
      with information on protein similarities, gene expression, cDNA clone reagents,
      and genomic location.
    homepage: http://www.ncbi.nlm.nih.gov/unigene
    license: http://opendatacommons.org/licenses/pddl/1.0
    name: UniGene gene-oriented nucleotide sequence clusters
    prefix: FAIRsharing.ge1c3p
    publications:
    - doi: 10.1093/nar/gkg033
      pubmed_id: 12519941
      title: Database resources of the National Center for Biotechnology.
    subjects:
    - Life Science
  integbio:
    description: This database contains sets of transcriptional sequences obtained
      from the same locus. It includes information such as the homology between transcripts
      and the reference protein, expression pattern, cDNA clones, and genomic position.
    fairsharing: biodbcore-000459
    homepage: http://www.ncbi.nlm.nih.gov/unigene
    information_keywords:
    - Sequence
    - Expression
    maintainer: NCBI (National Center for Biotechnology Information)
    name: UniGene
    prefix: nbdc00220
    pubmeds:
    - '8849440'
    - '7670480'
    target_keywords:
    - cDNA/EST
    - Protein
  mappings:
    biocontext: UNIGENE
    fairsharing: FAIRsharing.ge1c3p
    integbio: nbdc00220
    miriam: unigene
    n2t: unigene
    prefixcommons: unigene
    re3data: r3d100010774
  miriam:
    deprecated: true
    description: A UniGene entry is a set of transcript sequences that appear to come
      from the same transcription locus (gene or expressed pseudogene), together with
      information on protein similarities, gene expression, cDNA clone reagents, and
      genomic location.
    homepage: http://www.ncbi.nlm.nih.gov/unigene
    id: '00000346'
    name: UniGene
    namespaceEmbeddedInLui: false
    pattern: ^\d+$
    prefix: unigene
    sampleId: '4900'
    uri_format: http://www.ncbi.nlm.nih.gov/UniGene/clust.cgi?UGID=$1
  n2t:
    description: A UniGene entry is a set of transcript sequences that appear to come
      from the same transcription locus (gene or expressed pseudogene), together with
      information on protein similarities, gene expression, cDNA clone reagents, and
      genomic location.
    example: '4900'
    homepage: http://www.ncbi.nlm.nih.gov/unigene
    name: UniGene at NCBI
    namespaceEmbeddedInLui: false
    pattern: ^\d+$
    prefix: unigene
    uri_format: http://www.ncbi.nlm.nih.gov/UniGene/clust.cgi?UGID=$1
  prefix: unigene
  prefixcommons:
    description: Each UniGene entry is a set of transcript sequences that appear to
      come from the same transcription locus (gene or expressed pseudogene), together
      with information on protein similarities, gene expression, cDNA clone reagents,
      and genomic location.
    example: '4900'
    homepage: http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=unigene
    keywords:
    - DNA
    - gene
    - gene expression
    - protein
    name: UniGene gene-oriented nucleotide sequence clusters
    pattern: ^\d+$
    prefix: unigene
    uri_format: http://www.ncbi.nlm.nih.gov/UniGene/clust.cgi?UGID=$1
  publications:
  - doi: 10.1093/nar/gkg033
    pmc: PMC165480
    pubmed: '12519941'
    title: Database resources of the National Center for Biotechnology
    year: 2003
  - doi: 10.1093/nar/gkg033
    pmc: null
    pubmed: null
    title: Database resources of the National Center for Biotechnology.
    year: null
  - doi: 10.1093/nar/gkg033
    pmc: null
    pubmed: null
    title: Database resources of the National Center for Biotechnology.
    year: null
  re3data:
    description: <<<!!!<<< This repository is no longer available>>>!!!>>>.  Although
      the web pages are no longer available, you will still be able to download the
      final UniGene builds as static content from the FTP site https://ftp.ncbi.nlm.nih.gov/repository/UniGene/.  You
      will also be able to match UniGene cluster numbers to Gene records by searching
      Gene with UniGene cluster numbers. For best results, restrict to the “UniGene
      Cluster Number” field rather than all fields in Gene.  For example, a search
      with Mm.2108[UniGene Cluster Number] finds the mouse  transthyretin Gene record
      (Ttr).  You can use the advanced search page https://www.ncbi.nlm.nih.gov/gene/advanced
      to help construct these searches. Keep in mind that the Gene record contains
      selected Reference Sequences and GenBank mRNA sequences rather than the larger
      set of expressed sequences in the UniGene cluster.
    doi: 10.17616/R35G7T
    homepage: https://www.ncbi.nlm.nih.gov/unigene
    name: UniGene
    prefix: r3d100010774
unii:
  biocontext:
    prefix: UNII
    uri_format: http://fdasis.nlm.nih.gov/srs/unii/$1
  cheminf:
    description: Identifier used by the USA Food and Drug Administration.
    name: Unique Ingredient Identifier
    obsolete: false
    prefix: '000563'
  mappings:
    biocontext: UNII
    cheminf: '000563'
    miriam: unii
    n2t: unii
    wikidata: P652
  miriam:
    deprecated: false
    description: The purpose of the joint FDA/USP Substance Registration System (SRS)
      is to support health information technology initiatives by generating unique
      ingredient identifiers (UNIIs) for substances in drugs, biologics, foods, and
      devices. The UNII is a non- proprietary, free, unique, unambiguous, non semantic,
      alphanumeric identifier based on a substance’s molecular structure and/or descriptive
      information.
    homepage: https://precision.fda.gov/uniisearch
    id: '00000531'
    name: UNII
    namespaceEmbeddedInLui: false
    pattern: ^[A-Z0-9]+$
    prefix: unii
    sampleId: 3G6A5W338E
    uri_format: https://precision.fda.gov/uniisearch/srs/unii/$1
  n2t:
    description: The purpose of the joint FDA/USP Substance Registration System (SRS)
      is to support health information technology initiatives by generating unique
      ingredient identifiers (UNIIs) for substances in drugs, biologics, foods, and
      devices. The UNII is a non- proprietary, free, unique, unambiguous, non semantic,
      alphanumeric identifier based on a substance&#x2019;s molecular structure and/or
      descriptive information.
    example: 3G6A5W338E
    homepage: http://fdasis.nlm.nih.gov/srs/
    name: UNII at U.S. Food and Drug Administration
    namespaceEmbeddedInLui: false
    pattern: ^[A-Z0-9]+$
    prefix: unii
    uri_format: http://fdasis.nlm.nih.gov/srs/srsdirect.jsp?regno=$1
  name: Unique Ingredient Identifier
  prefix: unii
  wikidata:
    description: identifier issued by the FDA / Unique Ingredient Identifier
    example:
    - 3XMK78S47O
    - 97C5T2UQ7J
    - YKH834O4BH
    miriam: unii
    name: UNII
    pattern: ^[0-9A-Za-z]{10}$
    prefix: P652
    uri_format: https://gsrs.ncats.nih.gov/ginas/app/beta/substances/$1
unimod:
  biocontext:
    prefix: UNIMOD
  contact:
    email: jcottrell@matrixscience.com
    github: null
    name: John Cottrell
    orcid: 0000-0003-3843-0818
  domain: ptm
  edam:
    description: Identifier of a protein modification catalogued in the Unimod database.
    name: Unimod
    obsolete: false
    prefix: '3757'
  fairsharing:
    abbreviation: Unimod
    description: Unimod is a community-supported, comprehensive database of protein
      modifications for mass spectrometry applications. The aim is to provide accurate
      and verifiable values, derived from elemental compositions, for the mass differences
      introduced by all types of natural and artificial modifications. Other important
      information includes any mass change, (neutral loss), that occurs during MS/MS
      analysis, and site specificity, (which residues are susceptible to modification
      and any constraints on the position of the modification within the protein or
      peptide).
    homepage: http://www.unimod.org
    name: Unimod
    prefix: FAIRsharing.zZHCUQ
    publications:
    - doi: 10.1002/pmic.200300744
      pubmed_id: 15174123
      title: 'Unimod: Protein modifications for mass spectrometry.'
    subjects:
    - Bioinformatics
  logo: https://www.unimod.org/images/logo.gif
  mappings:
    biocontext: UNIMOD
    edam: '3757'
    fairsharing: FAIRsharing.zZHCUQ
    miriam: unimod
    n2t: unimod
    ols: unimod
  miriam:
    deprecated: false
    description: Unimod is a public domain database created to provide a community
      supported, comprehensive database of protein modifications for mass spectrometry
      applications. That is, accurate and verifiable values, derived from elemental
      compositions, for the mass differences introduced by all types of natural and
      artificial modifications. Other important information includes any mass change,
      (neutral loss), that occurs during MS/MS analysis, and site specificity, (which
      residues are susceptible to modification and any constraints on the position
      of the modification within the protein or peptide).
    homepage: http://www.unimod.org/
    id: '00000447'
    name: Unimod
    namespaceEmbeddedInLui: false
    pattern: ^\d+$
    prefix: unimod
    sampleId: '1200'
    uri_format: http://www.unimod.org/modifications_view.php?editid1=$1
  n2t:
    description: Unimod is a public domain database created to provide a community
      supported, comprehensive database of protein modifications for mass spectrometry
      applications. That is, accurate and verifiable values, derived from elemental
      compositions, for the mass differences introduced by all types of natural and
      artificial modifications. Other important information includes any mass change,
      (neutral loss), that occurs during MS/MS analysis, and site specificity, (which
      residues are susceptible to modification and any constraints on the position
      of the modification within the protein or peptide).
    example: '1200'
    homepage: http://www.unimod.org/
    name: Unimod at Matrix Sciences Ltd.
    namespaceEmbeddedInLui: false
    pattern: ^\d+$
    prefix: unimod
    uri_format: http://www.unimod.org/modifications_view.php?editid1=$1
  ols:
    contact: psidev-ms-vocab@lists.sourceforge.net
    description: Unimod is a community supported, comprehensive database of protein
      modifications for mass spectrometry applications. That is, accurate and verifiable
      values, derived from elemental compositions, for the mass differences introduced
      by all types of natural and artificial modifications. Other important information
      includes any mass change, (neutral loss), that occurs during MS/MS analysis,
      an d site specificity, (which residues are susceptible to modification and any
      constraints on the position of the modification within the protein or peptide).
    download_owl: https://raw.githubusercontent.com/PRIDE-Utilities/pride-ontology/master/unimod.owl
    homepage: http://www.unimod.org/
    name: Unimod protein modification database for mass spectrometry
    prefix: unimod
    uri_format: http://purl.obolibrary.org/obo/UNIMOD_$1
  prefix: unimod
  publications:
  - doi: 10.1002/pmic.200300744
    pmc: null
    pubmed: '15174123'
    title: 'Unimod: Protein modifications for mass spectrometry'
    year: 2004
uniparc:
  biocontext:
    prefix: UNIPARC
  contact:
    email: agb@ebi.ac.uk
    github: bateman-research
    name: Alex Bateman
    orcid: 0000-0002-6982-4660
  contact_group_email: help@uniprot.org
  edam:
    description: Accession number of a UniParc (protein sequence) database entry.
    name: UniParc
    obsolete: false
    prefix: '2392'
  go:
    description: A non-redundant archive of protein sequences extracted from Swiss-Prot,
      TrEMBL, PIR-PSD, EMBL, Ensembl, IPI, PDB, RefSeq, FlyBase, WormBase, European
      Patent Office, United States Patent and Trademark Office, and Japanese Patent
      Office
    homepage: https://www.uniprot.org/uniparc/
    name: UniProt Archive
    prefix: UniParc
    uri_format: https://www.uniprot.org/uniparc/$1
  mappings:
    biocontext: UNIPARC
    edam: '2392'
    go: UniParc
    miriam: uniparc
    n2t: uniparc
    prefixcommons: uniparc
    re3data: r3d100011519
  miriam:
    deprecated: false
    description: The UniProt Archive (UniParc) is a  database containing non-redundant
      protein sequence information from many sources. Each unique sequence is given
      a stable and unique identifier (UPI) making it possible to identify the same
      protein from different source databases.
    homepage: http://www.uniprot.org/uniparc/
    id: '00000041'
    name: UniParc
    namespaceEmbeddedInLui: false
    pattern: ^UPI[A-F0-9]{10}$
    prefix: uniparc
    sampleId: UPI000000000A
    uri_format: https://www.uniprot.org/uniparc/$1
  n2t:
    description: The UniProt Archive (UniParc) is a  database containing non-redundant
      protein sequence information from many sources. Each unique sequence is given
      a stable and unique identifier (UPI) making it possible to identify the same
      protein from different source databases.
    example: UPI000000000A
    homepage: http://www.uniprot.org/uniparc/
    name: UniParc through UniProt
    namespaceEmbeddedInLui: false
    pattern: ^UPI[A-F0-9]{10}$
    prefix: uniparc
    uri_format: http://www.uniprot.org/uniparc/$1
  prefix: uniparc
  prefixcommons:
    description: The UniProt Archive (UniParc) is a  database containing non-redundant
      protein sequence information from many sources. Each unique sequence is given
      a stable and unique identifier (UPI) making it possible to identify the same
      protein from different source databases.
    example: UPI000000000A
    homepage: http://www.ebi.ac.uk/uniparc/
    keywords:
    - protein
    - structure
    name: UniProt Archive
    pattern: ^UPI[A-F0-9]{10}$
    prefix: uniparc
    pubmed_ids:
    - '14681372'
    uri_format: http://www.ebi.ac.uk/cgi-bin/dbfetch?db=uniparc&id=$1
  publications:
  - doi: 10.1093/nar/gkh131
    pmc: PMC308865
    pubmed: '14681372'
    title: 'UniProt: the Universal Protein knowledgebase'
    year: 2004
  - doi: null
    pmc: null
    pubmed: '14681372'
    title: null
    year: null
  re3data:
    description: The UniProt Archive (UniParc) is a comprehensive and non-redundant
      database that contains most of the publicly available protein sequences in the
      world.
    doi: 10.17616/R3X33B
    homepage: https://www.uniprot.org/help/uniparc
    name: UniParc
    prefix: r3d100011519
    synonyms:
    - UniProt Archive
unipathway.compound:
  biocontext:
    prefix: UNIPATHWAY.COMPOUND
  mappings:
    biocontext: UNIPATHWAY.COMPOUND
    miriam: unipathway.compound
    n2t: unipathway.compound
  miriam:
    deprecated: false
    description: UniPathway is a manually curated resource of enzyme-catalyzed and
      spontaneous chemical reactions. It provides a hierarchical representation of
      metabolic pathways and a controlled vocabulary for pathway annotation in UniProtKB.
      UniPathway data are cross-linked to existing metabolic resources such as ChEBI/Rhea,
      KEGG and MetaCyc. This collection references compounds.
    id: '00000551'
    name: UniPathway Compound
    namespaceEmbeddedInLui: false
    pattern: ^UPC\d{5}$
    prefix: unipathway.compound
    sampleId: UPC04349
  n2t:
    description: UniPathway is a manually curated resource of enzyme-catalyzed and
      spontaneous chemical reactions. It provides a hierarchical representation of
      metabolic pathways and a controlled vocabulary for pathway annotation in UniProtKB.
      UniPathway data are cross-linked to existing metabolic resources such as ChEBI/Rhea,
      KEGG and MetaCyc. This collection references compounds.
    example: UPC04349
    homepage: http://www.grenoble.prabi.fr/obiwarehouse/unipathway
    name: UniPathway Compound at Swiss Institute of Bioinformatics (SIB)
    namespaceEmbeddedInLui: false
    pattern: ^UPC\d{5}$
    prefix: unipathway.compound
    uri_format: http://www.grenoble.prabi.fr/obiwarehouse/unipathway/upc?upid=$1
  prefix: unipathway.compound
unipathway.reaction:
  biocontext:
    prefix: UNIPATHWAY.REACTION
  mappings:
    biocontext: UNIPATHWAY.REACTION
    miriam: unipathway.reaction
    n2t: unipathway.reaction
  miriam:
    deprecated: false
    description: UniPathway is a manually curated resource of enzyme-catalyzed and
      spontaneous chemical reactions. It provides a hierarchical representation of
      metabolic pathways and a controlled vocabulary for pathway annotation in UniProtKB.
      UniPathway data are cross-linked to existing metabolic resources such as ChEBI/Rhea,
      KEGG and MetaCyc. This collection references individual reactions.
    id: '00000570'
    name: UniPathway Reaction
    namespaceEmbeddedInLui: false
    pattern: ^UCR\d{5}$
    prefix: unipathway.reaction
    sampleId: UCR00226
  n2t:
    description: UniPathway is a manually curated resource of enzyme-catalyzed and
      spontaneous chemical reactions. It provides a hierarchical representation of
      metabolic pathways and a controlled vocabulary for pathway annotation in UniProtKB.
      UniPathway data are cross-linked to existing metabolic resources such as ChEBI/Rhea,
      KEGG and MetaCyc. This collection references individual reactions.
    example: UCR00226
    homepage: http://www.grenoble.prabi.fr/obiwarehouse/unipathway
    name: UniPathway Reaction at Swiss Institute of Bioinformatics (SIB)
    namespaceEmbeddedInLui: false
    pattern: ^UCR\d{5}$
    prefix: unipathway.reaction
    uri_format: http://www.grenoble.prabi.fr/obiwarehouse/unipathway/ucr?upid=$1
  prefix: unipathway.reaction
uniprot:
  aberowl:
    name: UP Board Exam Date Sheet 2019
    prefix: UP
  biocontext:
    prefix: UniProtKB
  biolink:
    is_identifiers: false
    is_obo: false
    prefix: UniProtKB
    uri_format: http://purl.uniprot.org/uniprot/$1
  cellosaurus:
    category: Sequence databases
    name: UniProt knowledgebase
    prefix: UniProtKB
    uri_format: https://www.uniprot.org/uniprotkb/$1/entry
  contact:
    email: agb@ebi.ac.uk
    github: bateman-research
    name: Alex Bateman
    orcid: 0000-0002-6982-4660
  contact_extras:
  - email: alan.bridge@sib.swiss
    github: null
    name: Alan Bridge
    orcid: 0000-0003-2148-9135
  - email: wuc@udel.edu
    github: null
    name: Cathy Wu
    orcid: 0000-0001-6379-8601
  contact_page: https://www.uniprot.org/contact
  contributor_extras:
  - email: m.naguthana@hotmail.com
    github: nagutm
    name: Mufaddal Naguthanawala
    orcid: 0009-0009-5240-7463
  domain: protein
  edam:
    description: Accession number of a UniProt (protein sequence) database entry.
    name: UniProt
    obsolete: false
    prefix: '3021'
  fairsharing:
    abbreviation: UP
    description: The taxonomy database that is maintained by the UniProt group is
      based on the NCBI taxonomy database, which is supplemented with data specific
      to the UniProt Knowledgebase (UniProtKB). While the NCBI taxonomy is updated
      daily to be in sync with GenBank/EMBL-Bank/DDBJ, the UniProt taxonomy is updated
      only at UniProt releases to be in sync with UniProtKB. It may therefore happen
      that for the time period of a UniProt release, you can find new taxa at the
      NCBI that are not yet in UniProt (and vice versa for deleted taxa). Species
      with manually annotated and reviewed protein sequences in the Swiss-Prot section
      of UniProtKB are named according to UniProt nomenclature. In particular, we
      have adopted a systematic convention for naming viral and bacterial strains
      and isolates.
    domains:
    - Taxonomic classification
    homepage: http://www.uniprot.org/taxonomy/
    license: CC-BY-4.0
    name: UniProt Taxonomy
    prefix: FAIRsharing.wf28wm
    subjects:
    - Biology
  go:
    description: A central repository of protein sequence and function created by
      joining the information contained in Swiss-Prot, TrEMBL, and PIR database
    homepage: http://www.uniprot.org
    name: Universal Protein Knowledgebase
    prefix: UniProtKB
    uri_format: https://www.uniprot.org/uniprot/$1
  homepage: http://www.uniprot.org
  integbio:
    alt_name: The Universal Protein Resource
    description: "This database contains information on amino acid sequences and their\
      \ functions. It is composed of four core databases, UniProtKB, UniRef, UniParc,\
      \ and Proteomes. UniProtKB contains two types of data, which are manually curated\
      \ high quality SwissProt annotations based on literature information, and automatically\
      \ annotated TrEMBL. \nUniRef provides results of sequence similarity searches.\
      \ \nUniParc integrates information such as ID for other databases per sequence\
      \ ID.\nProteomes provides proteome data of each organism with completely sequenced\
      \ genomes."
    homepage: http://www.uniprot.org/
    information_keywords:
    - Sequence
    - Repository
    maintainer: UniProt Consortium
    name: UniProt
    prefix: nbdc00221
    status: Active
    target_keywords:
    - Protein
  license: CC-BY-4.0
  logo: https://www.uniprot.org/uniprot-logo.img.0df091.svg
  mappings:
    aberowl: UP
    biocontext: UniProtKB
    biolink: UniProtKB
    cellosaurus: UniProtKB
    edam: '3021'
    fairsharing: FAIRsharing.wf28wm
    go: UniProtKB
    integbio: nbdc00221
    miriam: uniprot
    n2t: uniprot
    ncbi: UniProt
    prefixcommons: uniprot
    re3data: r3d100011521
    togoid: Uniprot
    wikidata: P352
  miriam:
    deprecated: false
    description: The UniProt Knowledgebase (UniProtKB) is a comprehensive resource
      for protein sequence and functional information with extensive cross-references
      to more than 120 external databases. Besides amino acid sequence and a description,
      it also provides taxonomic data and citation information.
    homepage: https://www.uniprot.org/
    id: '00000005'
    name: UniProt Knowledgebase
    namespaceEmbeddedInLui: false
    pattern: ^([A-N,R-Z][0-9]([A-Z][A-Z, 0-9][A-Z, 0-9][0-9]){1,2})|([O,P,Q][0-9][A-Z,
      0-9][A-Z, 0-9][A-Z, 0-9][0-9])(\.\d+)?(-\d+)?(#PRO_\d+)?$
    prefix: uniprot
    providers:
    - code: ncbi
      description: UniProt through NCBI
      homepage: https://www.ncbi.nlm.nih.gov/protein/
      name: UniProt through NCBI
      uri_format: https://www.ncbi.nlm.nih.gov/protein/$1
    sampleId: P0DP23
    uri_format: http://purl.uniprot.org/uniprot/$1
  n2t:
    description: The UniProt Knowledgebase (UniProtKB) is a comprehensive resource
      for protein sequence and functional information with extensive cross-references
      to more than 120 external databases. Besides amino acid sequence and a description,
      it also provides taxonomic data and citation information.
    example: P0DP23
    homepage: https://www.uniprot.org/
    name: Universal Protein Resource using Persistent URL system
    namespaceEmbeddedInLui: false
    pattern: ^([A-N,R-Z][0-9]([A-Z][A-Z, 0-9][A-Z, 0-9][0-9]){1,2})|([O,P,Q][0-9][A-Z,
      0-9][A-Z, 0-9][A-Z, 0-9][0-9])(\.\d+)?$
    prefix: uniprot
    uri_format: https://purl.uniprot.org/uniprot/$1
  name: UniProt Protein
  ncbi:
    example: P12345
    homepage: http://www.uniprot.org
    name: section of the UniProt Knowledgebase, containing annotated records, which
      include curator-evaluated computational analysis, as well as, information extracted
      from the literature
    prefix: UniProt
  prefix: uniprot
  prefixcommons:
    description: UniProtKB consists of the manually annotated and reviewed Swiss-Prot,
      the automatically annotated TrEMBL, and the PIR protein databases.
    example: P62158
    homepage: http://www.uniprot.org/
    keywords:
    - protein
    name: UniProt Knowledgebase
    pattern: ^([A-N,R-Z][0-9][A-Z][A-Z, 0-9][A-Z, 0-9][0-9])|([O,P,Q][0-9][A-Z, 0-9][A-Z,
      0-9][A-Z, 0-9][0-9])(\.\d+)?$
    prefix: uniprot
    pubmed_ids:
    - '16381842'
    rdf_uri_format: http://purl.uniprot.org/uniprot/$1
    synonyms:
    - uniprotkb
    - uniprotkb/trembl
    - swiss-prot
    - sp
    - UNIPROTKB/SWISSPROT
    uri_format: http://www.uniprot.org/uniprot/$1
  providers:
  - code: bfvd
    description: Predicted protein structures for viral sequences
    example: null
    first_party: null
    homepage: https://bfvd.foldseek.com
    name: Big Fantastic Virus Database
    publications:
    - doi: 10.1093/nar/gkae1119
      pmc: null
      pubmed: '39574394'
      title: BFVD-a large repository of predicted viral protein structures
      year: 2024
    status: null
    uri_format: https://bfvd.foldseek.com/cluster/$1
  - code: proteinsplus
    description: Database of protein-ligand interactions.
    example: null
    first_party: null
    homepage: https://proteins.plus/
    name: ProteinsPlus
    publications:
    - doi: 10.1093/nar/gkaf377
      pmc: null
      pubmed: '40326518'
      title: 'ProteinsPlus: a publicly available resource for protein structure mining'
      year: 2025
    status: null
    uri_format: https://proteins.plus/$1
  - code: describeprot
    description: Structural and functional descriptors for proteins at the amino acid
      level
    example: null
    first_party: null
    homepage: http://biomine.cs.vcu.edu/servers/DESCRIBEPROT
    name: DescribePROT
    publications:
    - doi: 10.1007/978-1-0716-4196-5_10
      pmc: null
      pubmed: '39576581'
      title: DescribePROT Database of Residue-Level Protein Structure and Function
        Annotations
      year: 2024
    status: null
    uri_format: http://biomine.cs.vcu.edu/servers/DESCRIBEPROT/result_v2.php?uniprot=$1
  - code: oglcnac
    description: A comprehensive catalog of O-GlcNAcylated proteins
    example: null
    first_party: null
    homepage: https://www.oglcnac.mcw.edu
    name: The O-GlcNAc Database
    publications:
    - doi: 10.1007/s00216-024-05571-8
      pmc: null
      pubmed: '39379619'
      title: 'The O-GlcNAc database: introducing new features and tools developed
        from community feedback'
      year: 2024
    status: null
    uri_format: https://www.oglcnac.mcw.edu/search/?query_protein=$1
  - code: iedb.antigen
    description: A comprehensive collection of data on immune epitopes, covering experimental
      data and resources, including antigens
    example: null
    first_party: null
    homepage: https://www.iedb.org/
    name: Immune Epitope Database
    publications: null
    status: null
    uri_format: https://www.iedb.org/antigen/UNIPROT:$1
  - code: omnipath
    description: Molecular interations endpoint from OmniPathDB
    example: null
    first_party: null
    homepage: https://omnipathdb.org/
    name: OmniPathDB
    publications: null
    status: null
    uri_format: https://omnipathdb.org/interactions/?fields=sources,references&partners=$1
  - code: pharos
    description: Part of the Illuminating the Druggable Genome project
    example: null
    first_party: null
    homepage: https://pharos.nih.gov/idg
    name: Pharos
    publications: null
    status: null
    uri_format: https://pharos.nih.gov/idg/targets/$1
  - code: iptmnet
    description: Protein post translational modification information
    example: null
    first_party: null
    homepage: https://research.bioinformatics.udel.edu/iptmnet
    name: iPTMnet
    publications: null
    status: null
    uri_format: https://research.bioinformatics.udel.edu/iptmnet/entry/$1
  - code: indra
    description: A large scale database of biomedical statements.
    example: null
    first_party: null
    homepage: https://db.indra.bio
    name: INDRA Database
    publications: null
    status: null
    uri_format: https://db.indra.bio/statements/from_agents?&format=html&agent0=$1@UP
  - code: scholia
    description: Scholia is a service that creates visual scholarly profiles for topic,
      people, organizations, species, chemicals, etc using bibliographic and other
      information in Wikidata.
    example: null
    first_party: null
    homepage: https://scholia.toolforge.org/
    name: Scholia
    publications: null
    status: null
    uri_format: https://scholia.toolforge.org/uniprot/$1
  - code: oma
    description: The OMA project is a method and database for the inference of orthologs
      among complete genomes.
    example: null
    first_party: null
    homepage: https://omabrowser.org/oma/home/
    name: Orthologous Matrix Browser
    publications: null
    status: null
    uri_format: http://omabrowser.org/cgi-bin/gateway.pl?f=DisplayEntry&p2=orthologs&p1=$1
  - code: drugbank
    description: DrugBank PolyPeptide.
    example: null
    first_party: null
    homepage: https://go.drugbank.com
    name: DrugBank Polypeptide
    publications: null
    status: null
    uri_format: https://go.drugbank.com/polypeptides/$1
  - code: aipd
    description: A curated database standardizing information on autoinhibited proteins.
    example: null
    first_party: null
    homepage: http://ssbio.cau.ac.kr/databases/AiPD/
    name: Autoinhibited Protein Database
    publications:
    - doi: 10.1093/database/baae085
      pmc: PMC11349611
      pubmed: '39192607'
      title: 'Autoinhibited Protein Database: a curated database of autoinhibitory
        domains and their autoinhibition mechanisms'
      year: 2024
    status: null
    uri_format: http://165.194.60.211:9006/detail/$1
  publications:
  - doi: 10.1093/nar/gkae1010
    pmc: null
    pubmed: '39552041'
    title: 'UniProt: the Universal Protein Knowledgebase in 2025'
    year: 2024
  - doi: 10.1093/nar/gkj161
    pmc: PMC1347523
    pubmed: '16381842'
    title: 'The Universal Protein Resource (UniProt): an expanding universe of protein
      information'
    year: 2006
  - doi: null
    pmc: null
    pubmed: '16381842'
    title: null
    year: null
  - doi: 10.1093/nar/gkae1119
    pmc: null
    pubmed: '39574394'
    title: BFVD-a large repository of predicted viral protein structures
    year: 2024
  - doi: 10.1093/nar/gkaf377
    pmc: null
    pubmed: '40326518'
    title: 'ProteinsPlus: a publicly available resource for protein structure mining'
    year: 2025
  - doi: 10.1007/978-1-0716-4196-5_10
    pmc: null
    pubmed: '39576581'
    title: DescribePROT Database of Residue-Level Protein Structure and Function Annotations
    year: 2024
  - doi: 10.1007/s00216-024-05571-8
    pmc: null
    pubmed: '39379619'
    title: 'The O-GlcNAc database: introducing new features and tools developed from
      community feedback'
    year: 2024
  - doi: 10.1093/database/baae085
    pmc: PMC11349611
    pubmed: '39192607'
    title: 'Autoinhibited Protein Database: a curated database of autoinhibitory domains
      and their autoinhibition mechanisms'
    year: 2024
  - doi: null
    pmc: null
    pubmed: '16381842'
    title: null
    year: null
  - doi: 10.1093/nar/gkae1119
    pmc: null
    pubmed: '39574394'
    title: BFVD-a large repository of predicted viral protein structures
    year: 2024
  - doi: 10.1093/nar/gkaf377
    pmc: null
    pubmed: '40326518'
    title: 'ProteinsPlus: a publicly available resource for protein structure mining'
    year: 2025
  - doi: 10.1007/978-1-0716-4196-5_10
    pmc: null
    pubmed: '39576581'
    title: DescribePROT Database of Residue-Level Protein Structure and Function Annotations
    year: 2024
  - doi: 10.1007/s00216-024-05571-8
    pmc: null
    pubmed: '39379619'
    title: 'The O-GlcNAc database: introducing new features and tools developed from
      community feedback'
    year: 2024
  - doi: 10.1093/database/baae085
    pmc: PMC11349611
    pubmed: '39192607'
    title: 'Autoinhibited Protein Database: a curated database of autoinhibitory domains
      and their autoinhibition mechanisms'
    year: 2024
  - doi: null
    pmc: null
    pubmed: '16381842'
    title: null
    year: null
  - doi: 10.1093/nar/gkae1119
    pmc: null
    pubmed: '39574394'
    title: BFVD-a large repository of predicted viral protein structures
    year: 2024
  - doi: 10.1093/nar/gkaf377
    pmc: null
    pubmed: '40326518'
    title: 'ProteinsPlus: a publicly available resource for protein structure mining'
    year: 2025
  - doi: 10.1007/978-1-0716-4196-5_10
    pmc: null
    pubmed: '39576581'
    title: DescribePROT Database of Residue-Level Protein Structure and Function Annotations
    year: 2024
  - doi: 10.1007/s00216-024-05571-8
    pmc: null
    pubmed: '39379619'
    title: 'The O-GlcNAc database: introducing new features and tools developed from
      community feedback'
    year: 2024
  - doi: 10.1093/database/baae085
    pmc: PMC11349611
    pubmed: '39192607'
    title: 'Autoinhibited Protein Database: a curated database of autoinhibitory domains
      and their autoinhibition mechanisms'
    year: 2024
  - doi: null
    pmc: null
    pubmed: '16381842'
    title: null
    year: null
  - doi: 10.1093/nar/gkae1119
    pmc: null
    pubmed: '39574394'
    title: BFVD-a large repository of predicted viral protein structures
    year: 2024
  - doi: 10.1093/nar/gkaf377
    pmc: null
    pubmed: '40326518'
    title: 'ProteinsPlus: a publicly available resource for protein structure mining'
    year: 2025
  - doi: 10.1007/978-1-0716-4196-5_10
    pmc: null
    pubmed: '39576581'
    title: DescribePROT Database of Residue-Level Protein Structure and Function Annotations
    year: 2024
  - doi: 10.1007/s00216-024-05571-8
    pmc: null
    pubmed: '39379619'
    title: 'The O-GlcNAc database: introducing new features and tools developed from
      community feedback'
    year: 2024
  - doi: 10.1093/database/baae085
    pmc: PMC11349611
    pubmed: '39192607'
    title: 'Autoinhibited Protein Database: a curated database of autoinhibitory domains
      and their autoinhibition mechanisms'
    year: 2024
  - doi: null
    pmc: null
    pubmed: '16381842'
    title: null
    year: null
  - doi: 10.1093/nar/gkae1119
    pmc: null
    pubmed: '39574394'
    title: BFVD-a large repository of predicted viral protein structures
    year: 2024
  - doi: 10.1093/nar/gkaf377
    pmc: null
    pubmed: '40326518'
    title: 'ProteinsPlus: a publicly available resource for protein structure mining'
    year: 2025
  - doi: 10.1007/978-1-0716-4196-5_10
    pmc: null
    pubmed: '39576581'
    title: DescribePROT Database of Residue-Level Protein Structure and Function Annotations
    year: 2024
  - doi: 10.1007/s00216-024-05571-8
    pmc: null
    pubmed: '39379619'
    title: 'The O-GlcNAc database: introducing new features and tools developed from
      community feedback'
    year: 2024
  - doi: 10.1093/database/baae085
    pmc: PMC11349611
    pubmed: '39192607'
    title: 'Autoinhibited Protein Database: a curated database of autoinhibitory domains
      and their autoinhibition mechanisms'
    year: 2024
  - doi: null
    pmc: null
    pubmed: '16381842'
    title: null
    year: null
  - doi: 10.1093/nar/gkae1119
    pmc: null
    pubmed: '39574394'
    title: BFVD-a large repository of predicted viral protein structures
    year: 2024
  - doi: 10.1093/nar/gkaf377
    pmc: null
    pubmed: '40326518'
    title: 'ProteinsPlus: a publicly available resource for protein structure mining'
    year: 2025
  - doi: 10.1007/978-1-0716-4196-5_10
    pmc: null
    pubmed: '39576581'
    title: DescribePROT Database of Residue-Level Protein Structure and Function Annotations
    year: 2024
  - doi: 10.1007/s00216-024-05571-8
    pmc: null
    pubmed: '39379619'
    title: 'The O-GlcNAc database: introducing new features and tools developed from
      community feedback'
    year: 2024
  - doi: 10.1093/database/baae085
    pmc: PMC11349611
    pubmed: '39192607'
    title: 'Autoinhibited Protein Database: a curated database of autoinhibitory domains
      and their autoinhibition mechanisms'
    year: 2024
  re3data:
    description: The UniProt Knowledgebase (UniProtKB) is the central hub for the
      collection of functional information on proteins, with accurate, consistent
      and rich annotation. In addition to capturing the core data mandatory for each
      UniProtKB entry (mainly, the amino acid sequence, protein name or description,
      taxonomic data and citation information), as much annotation information as
      possible is added. This includes widely accepted biological ontologies, classifications
      and cross-references, and clear indications of the quality of annotation in
      the form of evidence attribution of experimental and computational data. The
      Universal Protein Resource (UniProt) is a comprehensive resource for protein
      sequence and annotation data. The UniProt databases are the UniProt Knowledgebase
      (UniProtKB), the UniProt Reference Clusters (UniRef), and the UniProt Archive
      (UniParc). The UniProt Metagenomic and Environmental Sequences (UniMES) database
      is a repository specifically developed for metagenomic and environmental data.
      The UniProt Knowledgebase,is an expertly and richly curated protein database,
      consisting of two sections called UniProtKB/Swiss-Prot and UniProtKB/TrEMBL.
    doi: 10.17616/R3NK9Z
    homepage: https://www.uniprot.org/uniprotkb/
    license: Apache License 2.0
    name: UniProtKB
    prefix: r3d100011521
    synonyms:
    - UniProtKnowledgebase
    - Universal Protein Knowledgebase
  synonyms:
  - SwissProt
  - UP
  - UniProt
  - UniProtKB
  - Uniprot ID
  - uniprot/swiss-prot
  togoid:
    catalog: nbdc00221
    description: This database contains information on amino acid sequences and their
      functions. It is composed of four core databases, UniProtKB, UniRef, UniParc,
      and Proteomes. UniProtKB contains two types of data, which are manually curated
      high quality SwissProt annotations based on literature information, and automatically
      annotated TrEMBL.  UniRef provides results of sequence similarity searches.  UniParc
      integrates information such as ID for other databases per sequence ID. Proteomes
      provides proteome data of each organism with completely sequenced genomes.
    examples:
    - A0A174V9D2
    - A0A1V4U2Y9
    - Q7NXD4
    - P0AAM3
    - O43423
    - D4IJI4
    - Q66SS1
    - B5IDU9
    - D3TBR4
    - D4ILS5
    keywords:
    - Protein
    name: UniProt
    pattern: ^(?:(?<id1>[A-NR-Z][0-9](?:[A-Z][A-Z0-9][A-Z0-9][0-9]){1,2}(?:-\d+)?)|(?<id2>[OPQ][0-9][A-Z0-9][A-Z0-9][A-Z0-9][0-9](?:-\d+)?)(?:\.\d+)?)$
    prefix: Uniprot
    uri_format: http://purl.uniprot.org/uniprot/$1
  uri_format: http://purl.uniprot.org/uniprot/$1
  wikidata:
    database: Q905695
    description: identifier for a protein per the UniProt database
    example:
    - P78509
    - Q8WZ42
    homepage: http://mygene.info
    miriam: uniprot
    name: UniProt protein ID
    pattern: ^([OPQ][0-9][A-Z0-9]|[A-NR-Z][0-9][A-Z])[A-Z0-9][A-Z0-9][0-9]([A-Z][A-Z0-9][A-Z0-9][0-9])?$
    prefix: P352
    uri_format: https://www.uniprot.org/uniprot/$1
    uri_format_rdf: http://purl.uniprot.org/uniprot/$1
uniprot.arba:
  contact:
    email: agb@ebi.ac.uk
    github: bateman-research
    name: Alex Bateman
    orcid: 0000-0002-6982-4660
  contact_group_email: help@uniprot.org
  contributor:
    email: cjmungall@lbl.gov
    github: cmungall
    name: Chris Mungall
    orcid: 0000-0002-6601-2165
  description: Association-Rule-Based Annotator (ARBA), a multiclass, self-training
    annotation system for automatic classification and annotation of UniProtKB proteins.
    This replaces the previous rule-based SAAS system.
  example: ARBA00000001
  github_request_issue: 620
  go:
    homepage: https://www.uniprot.org/arba/
    name: ARBA machine learning models for automatic annotation of UniProtKB unreviewed
      entries
    prefix: ARBA
    uri_format: https://www.uniprot.org/arba/$1
  homepage: https://www.uniprot.org/arba
  logo: https://www.uniprot.org/uniprot-logo.img.0df091.svg
  mappings:
    go: ARBA
  name: Association-Rule-Based Annotator
  part_of_database: uniprot
  pattern: ^ARBA\d+$
  prefix: uniprot.arba
  reviewer:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  synonyms:
  - arba
  uri_format: https://www.uniprot.org/arba/$1
uniprot.chain:
  contact:
    email: agb@ebi.ac.uk
    github: bateman-research
    name: Alex Bateman
    orcid: 0000-0002-6982-4660
  contact_group_email: help@uniprot.org
  logo: https://www.uniprot.org/uniprot-logo.img.0df091.svg
  mappings:
    miriam: uniprot.chain
  miriam:
    deprecated: false
    description: This collection is a subset of UniProtKB that provides a means to
      reference the proteolytic cleavage products of a precursor protein.
    homepage: https://www.uniprot.org
    id: 00000739
    name: UniProt Chain
    namespaceEmbeddedInLui: false
    pattern: ^PRO_[0-9]{10}$
    prefix: uniprot.chain
    sampleId: PRO_0000016681
    uri_format: http://purl.uniprot.org/annotation/$1
  part_of_database: uniprot
  prefix: uniprot.chain
  synonyms:
  - UPPRO
uniprot.core:
  contact:
    email: agb@ebi.ac.uk
    github: bateman-research
    name: Alex Bateman
    orcid: 0000-0002-6982-4660
  contact_group_email: help@uniprot.org
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  download_owl: https://ftp.uniprot.org/pub/databases/uniprot/current_release/rdf/core.owl
  example: certain
  lov:
    description: Properties and classes used for protein annotation
    homepage: http://purl.uniprot.org/core/
    keywords:
    - Biology
    modified: '2012-10-03'
    name: Uniprot Core Ontology
    prefix: uniprot
    uri_prefix: http://purl.uniprot.org/core/$1
  mappings:
    lov: uniprot
    ols: uniprotrdfs
  ols:
    download_owl: https://ftp.uniprot.org/pub/databases/uniprot/current_release/rdf/core.owl
    prefix: uniprotrdfs
    version: '2025_03'
  part_of_database: uniprot
  prefix: uniprot.core
  uri_format: http://purl.uniprot.org/core/$1
uniprot.disease:
  biolink:
    is_identifiers: false
    is_obo: false
    prefix: SPDI
    uri_format: https://api.ncbi.nlm.nih.gov/variation/v0/spdi/$1
  contact:
    email: agb@ebi.ac.uk
    github: bateman-research
    name: Alex Bateman
    orcid: 0000-0002-6982-4660
  contact_group_email: help@uniprot.org
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: The human diseases in which proteins are involved are described in
    UniProtKB entries with a controlled vocabulary.
  download_obo: https://rest.uniprot.org/diseases/stream?compressed=false&format=obo&query=%28%2A%29
  example: DI-04240
  homepage: https://www.uniprot.org/diseases/
  logo: https://www.uniprot.org/uniprot-logo.img.0df091.svg
  mappings:
    biolink: SPDI
    wikidata: P11430
  name: UniProt Diseases
  part_of_database: uniprot
  pattern: ^DI-\d{5}$
  prefix: uniprot.disease
  synonyms:
  - DI
  - SP_DI
  uri_format: https://www.uniprot.org/diseases/$1
  wikidata:
    database: Q905695
    description: identifier for a disease in the UniProt database
    example:
    - DI-00005
    - DI-00012
    name: UniProt disease ID
    pattern: ^DI-\d{5}$
    prefix: P11430
    uri_format: https://www.uniprot.org/diseases/$1
uniprot.isoform:
  biocontext:
    prefix: UNIPROT.ISOFORM
  biolink:
    is_identifiers: false
    is_obo: false
    prefix: UNIPROT.ISOFORM
    uri_format: http://purl.uniprot.org/isoforms/$1
  contact:
    email: agb@ebi.ac.uk
    github: bateman-research
    name: Alex Bateman
    orcid: 0000-0002-6982-4660
  contact_group_email: help@uniprot.org
  logo: https://www.uniprot.org/uniprot-logo.img.0df091.svg
  mappings:
    biocontext: UNIPROT.ISOFORM
    biolink: UNIPROT.ISOFORM
    miriam: uniprot.isoform
    n2t: uniprot.isoform
  miriam:
    deprecated: false
    description: The UniProt Knowledgebase (UniProtKB) is a comprehensive resource
      for protein sequence and functional information with extensive cross-references
      to more than 120 external databases. This collection is a subset of UniProtKB,
      and provides a means to reference isoform information.
    homepage: http://www.uniprot.org/
    id: 00000388
    name: UniProt Isoform
    namespaceEmbeddedInLui: false
    pattern: ^([A-N,R-Z][0-9][A-Z][A-Z, 0-9][A-Z, 0-9][0-9])|([O,P,Q][0-9][A-Z, 0-9][A-Z,
      0-9][A-Z, 0-9][0-9])(\-\d+)$
    prefix: uniprot.isoform
    providers:
    - code: ''
      description: UniProt Isoform through Universal Protein Resource using Persistent
        URL system
      homepage: http://purl.uniprot.org/
      name: UniProt Isoform through Universal Protein Resource using Persistent URL
        system
      uri_format: http://purl.uniprot.org/uniprot/$1
    - code: ''
      description: UniProt Isoform through UniParc
      homepage: http://www.uniprot.org/uniparc/
      name: UniProt Isoform through UniParc
      uri_format: http://www.uniprot.org/uniparc/?query=$1
    sampleId: Q5BJF6-3
    uri_format: http://www.uniprot.org/uniprot/$1
  n2t:
    description: The UniProt Knowledgebase (UniProtKB) is a comprehensive resource
      for protein sequence and functional information with extensive cross-references
      to more than 120 external databases. This collection is a subset of UniProtKB,
      and provides a means to reference isoform information.
    example: Q5BJF6-3
    homepage: http://www.uniprot.org/uniparc/
    name: UniProt Isoform through UniParc
    namespaceEmbeddedInLui: false
    pattern: ^([A-N,R-Z][0-9][A-Z][A-Z, 0-9][A-Z, 0-9][0-9])|([O,P,Q][0-9][A-Z, 0-9][A-Z,
      0-9][A-Z, 0-9][0-9])(\-\d+)$
    prefix: uniprot.isoform
    uri_format: http://www.uniprot.org/uniparc/?query=$1
  part_of_database: uniprot
  prefix: uniprot.isoform
  providers:
  - code: obo.1
    description: This incorrect encoding was found inside IDO-COVID-19
    example: null
    first_party: null
    homepage: http://purl.obolibrary.org
    name: Nonstandard OBO PURL
    publications: null
    status: null
    uri_format: http://purl.obolibrary.org/obo/UniProtKB_$1
  synonyms:
  - UPISO
  uri_format: http://purl.uniprot.org/isoforms/$1
uniprot.journal:
  contact:
    email: agb@ebi.ac.uk
    github: bateman-research
    name: Alex Bateman
    orcid: 0000-0002-6982-4660
  contact_group_email: help@uniprot.org
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: identifier for a scientific journal, in the UniProt database
  example: '3546'
  keywords:
  - journal
  - publication
  logo: https://www.uniprot.org/uniprot-logo.img.0df091.svg
  mappings:
    wikidata: P4616
  name: UniProt journal
  part_of_database: uniprot
  prefix: uniprot.journal
  wikidata:
    database: Q905695
    description: identifier for a scientific journal, in the UniProt database
    example:
    - '0341'
    - '3546'
    homepage: https://www.uniprot.org/journals
    name: UniProt journal ID
    pattern: ^\d{4}$
    prefix: P4616
    uri_format: https://www.uniprot.org/journals/$1
    uri_format_rdf: http://purl.uniprot.org/journals/$1
uniprot.keyword:
  contact:
    email: agb@ebi.ac.uk
    github: bateman-research
    name: Alex Bateman
    orcid: 0000-0002-6982-4660
  contact_group_email: help@uniprot.org
  description: UniProtKB entries are tagged with keywords that can be used to retrieve
    particular subsets of entries.
  download_obo: https://rest.uniprot.org/keywords/stream?compressed=false&fields=id%2Cname%2Ccategory%2Cgene_ontologies&format=tsv&query=%28%2A%29
  example: KW-1273
  go:
    homepage: http://www.uniprot.org/keywords/
    name: UniProt Knowledgebase keywords
    prefix: UniProtKB-KW
    synonyms:
    - SP_KW
    uri_format: https://www.uniprot.org/keywords/$1
  logo: https://www.uniprot.org/uniprot-logo.img.0df091.svg
  mappings:
    go: UniProtKB-KW
    prefixcommons: uniprot.kw
  name: UniProt Keywords
  part_of_database: uniprot
  pattern: ^KW-\d{4}$
  prefix: uniprot.keyword
  prefixcommons:
    description: UniProtKB entries are tagged with keywords that can be used to retrieve
      particular subsets of entries. There are 10 categories of keywords.
    example: KW-9998
    homepage: http://www.uniprot.org/keywords/
    keywords:
    - classification
    name: UniProt Knowledgebase keywords
    pattern: ^KW-\d+$
    prefix: uniprot.kw
    synonyms:
    - spkw
    - uniprotkb-kw
    uri_format: http://www.uniprot.org/keywords/$1
  synonyms:
  - SP_KW
  - UniProtKB-KW
  - uniprot.keyword
  - uniprot.kw
  uri_format: https://www.uniprot.org/keywords/$1
uniprot.location:
  contact:
    email: agb@ebi.ac.uk
    github: bateman-research
    name: Alex Bateman
    orcid: 0000-0002-6982-4660
  contact_group_email: help@uniprot.org
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: The subcellular locations in which a protein is found are described
    in UniProtKB entries with a controlled vocabulary, which includes also membrane
    topology and orientation terms.
  download_obo: https://rest.uniprot.org/locations/stream?compressed=false&format=obo&query=%28%2A%29
  example: SL-0002
  go:
    homepage: https://www.uniprot.org/locations/
    name: UniProt Knowledgebase Subcellular Location vocabulary
    prefix: UniProtKB-SubCell
    synonyms:
    - SP_SL
    uri_format: http://www.uniprot.org/locations/$1
  homepage: https://www.uniprot.org/locations/
  logo: https://www.uniprot.org/uniprot-logo.img.0df091.svg
  mappings:
    go: UniProtKB-SubCell
  name: UniProt Subcellular Locations
  part_of_database: uniprot
  pattern: ^SL-\d+$
  prefix: uniprot.location
  synonyms:
  - SP_SL
  - UPLOC
  - UniProtKB-SubCell
  uri_format: https://www.uniprot.org/locations/$1
uniprot.mnemonic:
  contact:
    email: agb@ebi.ac.uk
    github: bateman-research
    name: Alex Bateman
    orcid: 0000-0002-6982-4660
  contact_group_email: help@uniprot.org
  contributor:
    email: b.gyori@northeastern.edu
    github: bgyori
    name: Benjamin M. Gyori
    orcid: 0000-0001-9439-5346
  description: The UniProt Knowledgebase (UniProtKB) is a comprehensive resource for
    protein sequence and functional information with extensive cross-references to
    more than 120 external databases. Besides amino acid sequence and a description,
    it also provides taxonomic data and citation information. This entry represents
    UniProt mnemonics which combine an alphanumeric representation the protein name
    and a species identification code representing the biological source of the protein.
  example: BRAF_HUMAN
  github_request_issue: 1110
  homepage: https://www.uniprot.org/
  logo: https://www.uniprot.org/uniprot-logo.img.0df091.svg
  mappings:
    togoid: UniprotMnemonic
  name: UniProt
  part_of_database: uniprot
  pattern: ^[A-Z0-9]{1,10}_[A-Z0-9]{1,5}$
  prefix: uniprot.mnemonic
  publications:
  - doi: 10.1093/nar/gkj161
    pmc: PMC1347523
    pubmed: '16381842'
    title: 'The Universal Protein Resource (UniProt): an expanding universe of protein
      information'
    year: 2006
  reviewer:
    email: tiago.lubiana.alves@usp.br
    github: lubianat
    name: Tiago Lubiana
    orcid: 0000-0003-2473-2313
  togoid:
    catalog: nbdc00221
    description: This database contains information on amino acid sequences and their
      functions. It is composed of four core databases, UniProtKB, UniRef, UniParc,
      and Proteomes. UniProtKB contains two types of data, which are manually curated
      high quality SwissProt annotations based on literature information, and automatically
      annotated TrEMBL.  UniRef provides results of sequence similarity searches.  UniParc
      integrates information such as ID for other databases per sequence ID. Proteomes
      provides proteome data of each organism with completely sequenced genomes.
    examples:
    - 2ABA_ORYSJ
    - 33K_ADES1
    - 1003L_ASFK5
    - 1A1D_VARPS
    - 1B02_GORGO
    - 1003L_ASFP4
    - 1433B_MACFA
    - 1107L_ASFWA
    - 3BHS1_MOUSE
    - 14331_SCHMA
    keywords:
    - Protein
    name: UniProt mnemonic
    pattern: ^(?[A-Z0-9]+_[A-Z0-9]{0,5})$
    prefix: UniprotMnemonic
    uri_format: http://purl.uniprot.org/uniprot/$1
  uri_format: https://www.uniprot.org/uniprotkb/$1
uniprot.proteome:
  contributor:
    email: benjamin_gyori@hms.harvard.edu
    github: bgyori
    name: Benjamin M. Gyori
    orcid: 0000-0001-9439-5346
  contributor_extras:
  - email: null
    github: JervenBolleman
    name: JervenBolleman
    orcid: 0000-0002-7449-1266
  - email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: UniProt provides proteome sets of proteins whose genomes have been
    completely sequenced.
  example: UP000005640
  github_request_issue: 604
  homepage: https://www.uniprot.org/proteomes
  logo: https://www.uniprot.org/uniprot-logo.img.0df091.svg
  mappings:
    togoid: UniprotProteome
  name: UniProt Proteomes
  part_of_database: uniprot
  pattern: ^UP\d{9}$
  prefix: uniprot.proteome
  rdf_uri_format: http://purl.uniprot.org/proteomes/$1
  reviewer:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  togoid:
    catalog: nbdc00221
    description: This database contains information on amino acid sequences and their
      functions. It is composed of four core databases, UniProtKB, UniRef, UniParc,
      and Proteomes. UniProtKB contains two types of data, which are manually curated
      high quality SwissProt annotations based on literature information, and automatically
      annotated TrEMBL.  UniRef provides results of sequence similarity searches.  UniParc
      integrates information such as ID for other databases per sequence ID. Proteomes
      provides proteome data of each organism with completely sequenced genomes.
    examples:
    - UP000005640
    - UP000002311
    - UP000000589
    - UP000000803
    - UP000000437
    - UP000001819
    - UP000008028
    - UP000008143
    - UP000079169
    keywords:
    - Proteome
    name: UniProt proteome
    pattern: ^(?UP\d{0,9})$
    prefix: UniprotProteome
    uri_format: http://purl.uniprot.org/proteomes/$1
  uri_format: https://www.uniprot.org/proteomes/$1
uniprot.ptm:
  contact:
    email: agb@ebi.ac.uk
    github: bateman-research
    name: Alex Bateman
    orcid: 0000-0002-6982-4660
  contact_group_email: help@uniprot.org
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  contributor_extras:
  - email: benjamin_gyori@hms.harvard.edu
    github: bgyori
    name: Benjamin M. Gyori
    orcid: 0000-0001-9439-5346
  description: The post-translational modifications used in the UniProt knowledgebase
    (Swiss-Prot and TrEMBL). The definition of the post-translational modifications
    usage as well as other information is provided in the following format
  domain: ptm
  example: PTM-0450
  homepage: https://ftp.uniprot.org/pub/databases/uniprot/current_release/knowledgebase/complete/docs/ptmlist
  keywords:
  - biochemistry
  - post-translational modification
  - structural biology
  license: CC-BY-4.0
  logo: https://www.uniprot.org/uniprot-logo.img.0df091.svg
  name: UniProt Post-Translational Modification
  part_of_database: uniprot
  pattern: ^PTM-\d{4}$
  prefix: uniprot.ptm
  references:
  - https://twitter.com/cthoyt/status/1510570256619778053
  - https://www.uniprot.org/docs/ptmlist.txt
  synonyms:
  - PTM
  uri_format: https://biopragmatics.github.io/providers/uniprot.ptm/$1
uniprot.resource:
  contact:
    email: agb@ebi.ac.uk
    github: bateman-research
    name: Alex Bateman
    orcid: 0000-0002-6982-4660
  contact_group_email: help@uniprot.org
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: The cross-references section of UniProtKB entries displays explicit
    and implicit links to databases such as nucleotide sequence databases, model organism
    databases and genomics and proteomics resources.
  example: DB-0174
  homepage: https://www.uniprot.org/database/
  logo: https://www.uniprot.org/og-uniprot-wide-logo-1200x630.png
  name: UniProt Resource
  part_of_database: uniprot
  pattern: ^DB-\d{4}$
  prefix: uniprot.resource
  synonyms:
  - uniprot.database
  - uniprot.db
  uri_format: https://www.uniprot.org/database/$1
uniprot.tissue:
  biocontext:
    prefix: TISSUELIST
  contact:
    email: agb@ebi.ac.uk
    github: bateman-research
    name: Alex Bateman
    orcid: 0000-0002-6982-4660
  contact_group_email: help@uniprot.org
  example: TS-0285
  logo: https://www.uniprot.org/uniprot-logo.img.0df091.svg
  mappings:
    biocontext: TISSUELIST
    miriam: tissuelist
    n2t: tissuelist
  miriam:
    deprecated: false
    description: The UniProt Tissue List is a controlled vocabulary of terms used
      to annotate biological tissues. It also contains cross-references to other ontologies
      where tissue types are specified.
    homepage: https://www.uniprot.org/docs/tisslist.txt
    id: '00000360'
    name: Tissue List
    namespaceEmbeddedInLui: false
    pattern: ^TS-\d{4}$
    prefix: tissuelist
    sampleId: TS-0285
    uri_format: https://www.uniprot.org/tissues/$1
  n2t:
    description: The UniProt Tissue List is a controlled vocabulary of terms used
      to annotate biological tissues. It also contains cross-references to other ontologies
      where tissue types are specified.
    example: TS-0285
    homepage: https://www.uniprot.org/docs/tisslist.txt
    name: Tissue List at Swiss Institute of Bioinformatics
    namespaceEmbeddedInLui: false
    pattern: ^TS-\d{4}$
    prefix: tissuelist
    uri_format: https://www.uniprot.org/tissues/$1
  part_of_database: uniprot
  pattern: ^TS-\d{4}$
  prefix: uniprot.tissue
  uri_format: https://www.uniprot.org/tissues/$1
uniprot.var:
  contact:
    email: agb@ebi.ac.uk
    github: bateman-research
    name: Alex Bateman
    orcid: 0000-0002-6982-4660
  contact_group_email: help@uniprot.org
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: 'The purpose of the UniProtKB/Swiss-Prot variant pages is: to display
    the variant related information extracted from UniProtKB/Swiss-Prot, and to provide
    useful additional information such as the conservation of the modified residues
    across orthologous species.'
  example: 068078
  homepage: https://web.expasy.org/variant_pages
  logo: https://www.uniprot.org/og-uniprot-wide-logo-1200x630.png
  name: UniProt Variants
  part_of_database: uniprot
  pattern: ^\d+$
  prefix: uniprot.var
  providers:
  - code: expasy
    description: Expasy external page for protein variant
    example: null
    first_party: null
    homepage: https://web.expasy.org/variant_pages
    name: ExPaSy
    publications: null
    status: null
    uri_format: https://web.expasy.org/variant_pages/VAR_$1.html
  synonyms:
  - SP_VAR
  - UPVAR
  - UniProtKB_VAR
  uri_format: http://purl.uniprot.org/annotation/VAR_$1
uniref:
  contact:
    email: agb@ebi.ac.uk
    github: bateman-research
    name: Alex Bateman
    orcid: 0000-0002-6982-4660
  contact_group_email: help@uniprot.org
  edam:
    description: Unique identifier of an entry from the UniRef database.
    name: Sequence cluster ID (UniRef)
    obsolete: false
    prefix: '2346'
  logo: https://www.uniprot.org/uniprot-logo.img.0df091.svg
  mappings:
    edam: '2346'
    miriam: uniref
    re3data: r3d100011518
  miriam:
    deprecated: false
    description: The UniProt Reference Clusters (UniRef) provide clustered sets of
      sequences from the UniProt Knowledgebase (including isoforms) and selected UniParc
      records in order to obtain complete coverage of the sequence space at several
      resolutions while hiding redundant sequences (but not their descriptions) from
      view.
    homepage: https://www.uniprot.org/
    id: 00000878
    name: UniRef
    namespaceEmbeddedInLui: false
    pattern: ^UniRef(100|90|50)_([OPQ][0-9][A-Z0-9]{3}[0-9]|[A-NR-Z][0-9]([A-Z][A-Z0-9]{2}[0-9]){1,2}|UPI[A-F0-9]{10})$
    prefix: uniref
    sampleId: UniRef90_P00750
    uri_format: https://www.uniprot.org/uniref/$1
  part_of_database: uniprot
  prefix: uniref
  re3data:
    description: The UniProt Reference Clusters (UniRef) provide clustered sets of
      sequences from the UniProt Knowledgebase (including isoforms) and selected UniParc
      records in order to obtain complete coverage of the sequence space at several
      resolutions while hiding redundant sequences (but not their descriptions) from
      view.
    doi: 10.17616/R31W6B
    homepage: https://www.uniprot.org/help/uniref
    name: UniRef
    prefix: r3d100011518
    synonyms:
    - UniProt Reference Clusters
    xrefs:
      omics: 03879
unirule:
  contact:
    email: agb@ebi.ac.uk
    github: bateman-research
    name: Alex Bateman
    orcid: 0000-0002-6982-4660
  contact_group_email: help@uniprot.org
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: Rules are devised and tested by experienced curators using experimental
    data from manually annotated entries as templates. UniRule rules can annotate
    protein properties such as the protein name, function, catalytic activity, pathway
    membership, and subcellular location, along with sequence specific information,
    such as the positions of post-translational modifications and active sites.
  example: UR000124451
  go:
    homepage: https://www.uniprot.org/unirule/
    name: Manually curated rules for automatic annotation of UniProtKB unreviewed
      entries
    prefix: UniRule
    uri_format: https://www.uniprot.org/unirule/$1
  homepage: https://www.uniprot.org/unirule/
  logo: https://www.uniprot.org/uniprot-logo.img.0df091.svg
  mappings:
    go: UniRule
  name: UniRule
  part_of_database: uniprot
  prefix: unirule
  uri_format: https://www.uniprot.org/unirule/$1
unists:
  biocontext:
    prefix: UNISTS
  edam:
    description: Identifier of an entry from the UniSTS database.
    name: UniSTS
    obsolete: false
    prefix: '2389'
  mappings:
    biocontext: UNISTS
    edam: '2389'
    miriam: unists
    n2t: unists
    ncbi: UniSTS
    prefixcommons: unists
  miriam:
    deprecated: true
    description: UniSTS is a comprehensive database of sequence tagged sites (STSs)
      derived from STS-based maps and other experiments. STSs are defined by PCR primer
      pairs and are associated with additional information such as genomic position,
      genes, and sequences.
    homepage: https://www.ncbi.nlm.nih.gov/sites/entrez?db=unists
    id: '00000162'
    name: UniSTS
    namespaceEmbeddedInLui: false
    pattern: ^\d+$
    prefix: unists
    sampleId: '456789'
    uri_format: https://www.ncbi.nlm.nih.gov/genome/sts/sts.cgi?uid=$1
  n2t:
    description: UniSTS is a comprehensive database of sequence tagged sites (STSs)
      derived from STS-based maps and other experiments. STSs are defined by PCR primer
      pairs and are associated with additional information such as genomic position,
      genes, and sequences.
    example: '456789'
    homepage: https://www.ncbi.nlm.nih.gov/sites/entrez?db=unists
    name: UniSTS at NCBI
    namespaceEmbeddedInLui: false
    pattern: ^\d+$
    prefix: unists
    uri_format: https://www.ncbi.nlm.nih.gov/genome/sts/sts.cgi?uid=$1
  ncbi:
    example: '486599'
    name: Database of Sequence Tagged Sites
    prefix: UniSTS
  prefix: unists
  prefixcommons:
    description: UniSTS is a comprehensive database of sequence tagged sites (STSs)
      derived from STS-based maps and other experiments. STSs are defined by PCR primer
      pairs and are associated with additional information such as genomic position,
      genes, and sequences.
    example: '456789'
    homepage: http://www.ncbi.nlm.nih.gov/unists
    keywords:
    - gene
    - protein
    name: NCBI UniSTS
    pattern: ^\d+$
    prefix: unists
    uri_format: http://www.ncbi.nlm.nih.gov/genome/sts/sts.cgi?uid=$1
unite:
  biocontext:
    prefix: UNITE
  edam:
    description: Identifier of an entry from the UNITE database.
    name: UNITE
    obsolete: false
    prefix: '2390'
  fairsharing:
    abbreviation: null
    contact:
      email: urmas.koljalg@ut.ee
      name: Urmas Kõljalg
      orcid: 0000-0002-5171-1668
    description: 'UNITE is a database and sequence management environment centered
      on the eukaryotic nuclear ribosomal ITS region. All eukaryotic ITS sequences
      from the International Nucleotide Sequence Database Collaboration are clustered
      to approximately the species level (distance between species in steps of 0.5%),
      and all such species hypotheses are given a DOI to facilitate unambiguous scientific
      communication and data assembly. The user can interact with these species hypotheses
      (e.g., SH1566366.08FU) in various ways, and third-party sequence and metadata
      annotation are supported. Registration is needed to access the more powerful
      features of the accompanying PlutoF workbench. A range of search and query options
      are available, and precompiled reference datasets for local sequence similarity
      searches and HTS pipelines are available for download. Owing to the mycological
      roots of UNITE, two versions of the release files are available: all eukaryotes
      (including fungi), and fungi only. UNITE is a community effort that relies on
      the scientific expertise of its users – please consider contributing by, e.g.,
      annotating sequences of your taxa of expertise.'
    homepage: https://unite.ut.ee/index.php
    license: https://creativecommons.org/licenses/by-nc-nd/2.5
    name: UNITE
    prefix: FAIRsharing.cnwx8c
    publications:
    - doi: 10.1111/j.1469-8137.2009.03160.x
      pubmed_id: 20409185
      title: The UNITE database for molecular identification of fungi--recent updates
        and future perspectives.
    subjects:
    - Metagenomics
    - Genomics
    - Bioinformatics
    - Taxonomy
    - Ecology
    - Biodiversity
  integbio:
    description: 'UNITE is a database and sequence management environment centered
      on the eukaryotic nuclear ribosomal ITS region. All eukaryotic ITS sequences
      from the International Nucleotide Sequence Database Collaboration are clustered
      to approximately the species level (distance between species in steps of 0.5%),
      and all such species hypotheses are given a DOI to facilitate unambiguous scientific
      communication and data assembly. The user can interact with these species hypotheses
      (e.g., SH1566366.08FU) in various ways, and third-party sequence and metadata
      annotation are supported. Registration is needed to access the more powerful
      features of the accompanying PlutoF workbench. A range of search and query options
      are available, and precompiled reference datasets for local sequence similarity
      searches and HTS pipelines are available for download. Owing to the mycological
      roots of UNITE, two versions of the release files are available: all eukaryotes
      (including fungi), and fungi only. UNITE is a community effort that relies on
      the scientific expertise of its users - please consider contributing by, e.g.,
      annotating sequences of your taxa of expertise.'
    fairsharing: FAIRsharing.cnwx8c
    homepage: https://unite.ut.ee/index.php
    information_keywords:
    - Sequence
    - Taxonomy
    maintainer: University of Tartu
    name: UNITE
    prefix: nbdc01905
    pubmeds:
    - '30371820'
    status: Active
    target_keywords:
    - Genome/Gene
    - Organism
  mappings:
    biocontext: UNITE
    edam: '2390'
    fairsharing: FAIRsharing.cnwx8c
    integbio: nbdc01905
    miriam: unite
    n2t: unite
    ncbi: UNITE
    prefixcommons: unite
    re3data: r3d100011316
  miriam:
    deprecated: false
    description: UNITE is a fungal rDNA internal transcribed spacer (ITS) sequence
      database. It focuses on high-quality ITS sequences generated from fruiting bodies
      collected and identified by experts and deposited in public herbaria. Entries
      may be supplemented with metadata on describing locality, habitat, soil, climate,
      and interacting taxa.
    homepage: http://unite.ut.ee/
    id: '00000352'
    name: Unite
    namespaceEmbeddedInLui: false
    pattern: ^UDB\d{6}$
    prefix: unite
    sampleId: UDB000691
    uri_format: http://unite.ut.ee/bl_forw.php?nimi=$1
  n2t:
    description: UNITE is a fungal rDNA internal transcribed spacer (ITS) sequence
      database. It focuses on high-quality ITS sequences generated from fruiting bodies
      collected and identified by experts and deposited in public herbaria. Entries
      may be supplemented with metadata on describing locality, habitat, soil, climate,
      and interacting taxa.
    example: UDB000691
    homepage: http://unite.ut.ee/
    name: Unite at University of Tartu
    namespaceEmbeddedInLui: false
    pattern: ^UDB\d{6}$
    prefix: unite
    uri_format: http://unite.ut.ee/bl_forw.php?nimi=$1
  ncbi:
    example: UDB000157
    homepage: http://unite.ut.ee/index.php
    name: Molecular database for the identification of fungi
    prefix: UNITE
  prefix: unite
  prefixcommons:
    description: The UNITE is primarily a fungal rDNA ITS sequence database, although
      we also welcome additional genes and genetic markers. UNITE focuses on high-quality
      ITS sequences generated from fruiting bodies collected and identified by experts
      and deposited in public herbaria.
    example: UDB000691
    homepage: http://unite.ut.ee/index.php
    keywords:
    - DNA
    name: Molecular database for the identification of fungi
    pattern: ^UDB\d{6}$
    prefix: unite
    pubmed_ids:
    - '20409185'
    uri_format: http://unite.ut.ee/bl_forw.php?nimi=$1
  publications:
  - doi: 10.1111/j.1469-8137.2009.03160.x
    pmc: null
    pubmed: '20409185'
    title: The UNITE database for molecular identification of fungi--recent updates
      and future perspectives
    year: 2010
  - doi: 10.1111/j.1469-8137.2009.03160.x
    pmc: null
    pubmed: null
    title: The UNITE database for molecular identification of fungi--recent updates
      and future perspectives.
    year: null
  - doi: null
    pmc: null
    pubmed: '20409185'
    title: null
    year: null
  re3data:
    description: UNITE provides unified way how you delimit, identify, communicate
      and work with DNA based Species Hypotheses (SH).
    doi: 10.17616/R37635
    homepage: https://unite.ut.ee
    license: CC
    name: UNITE
    prefix: r3d100011316
    synonyms:
    - UNITE database for molecular identification and taxonomic communication of fungi
      and other eukaryotes
    - Unified system for the DNA based fungal species linked to the classification
    xrefs:
      omics: '23522'
unpd:
  comment: The website is dead, there are no places to get the source information
    except inside https://oolonek.github.io/ISDB/.
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  deprecated: true
  homepage: http://pkuxxj.pku.edu.cn/UNPD/
  keywords:
  - compound
  - natural product
  - small molecule
  name: Universal Natural Products Database
  prefix: unpd
  publications:
  - doi: 10.1021/acs.jnatprod.6b01093
    pmc: null
    pubmed: '28616931'
    title: Database for Rapid Dereplication of Known Natural Products Using Data from
      MS and Fast NMR Experiments
    year: 2017
  - doi: 10.1371/journal.pone.0062839
    pmc: PMC3636197
    pubmed: '23638153'
    title: Use of natural products as chemical library for drug discovery and network
      pharmacology
    year: 2013
  references:
  - http://bioinf-applied.charite.de/supernatural_new/index.php?site=vendor_info&id=Universal%20Natural%20Products%20Database
  - https://pharmacognosy.in/the-universal-natural-products-database-unpd/
  - https://oolonek.github.io/ISDB/
uo:
  aberowl:
    description: Metrical units for use in conjunction with PATO
    download_owl: http://aber-owl.net/media/ontologies/UO/61/uo.owl
    homepage: https://github.com/bio-ontology-research-group/unit-ontology
    name: Units of measurement ontology
    prefix: UO
  agroportal:
    contact:
      email: g.gkoutos@gmail.com
      name: George Gkoutos
    description: Units Ontology (UO) is an ontology currently being used in many scientific
      resources for the standardized description of units of measurements. Metrical
      units for use in conjunction with PATO
    example_uri: http://purl.obolibrary.org/obo/UO_0000294
    homepage: https://github.com/bio-ontology-research-group/unit-ontology
    license: CC-BY-3.0
    name: Units of Measurement Ontology
    prefix: UO
    publications:
    - https://doi.org/10.1093/database/bas033
    repository: https://github.com/bio-ontology-research-group/unit-ontology
    version: '2023-05-25'
  biocontext:
    prefix: UO
  bioportal:
    contact:
      email: g.gkoutos@gmail.com
      name: George Gkoutos
    description: Metrical units for use in conjunction with PATO
    homepage: https://github.com/bio-ontology-research-group/unit-ontology
    name: Units of Measurement Ontology
    prefix: UO
    version: '2023-05-25'
  fairsharing:
    abbreviation: UO
    contact:
      email: geg18@aber.ac.uk
      name: George Gkoutos
      orcid: 0000-0002-2061-091X
    description: The Units Ontology (UO) models metrical units for use in conjunction
      with PATO. Units are basic scientific tools that render meaning to numerical
      data. Their standardization and formalization caters for the report, exchange,
      process, reproducibility and integration of quantitative measurements. The Units
      Ontology is an ontology currently being used for the standardized description
      of units of measurements.
    domains:
    - unit
    - measurement
    homepage: https://github.com/bio-ontology-research-group/unit-ontology
    license: CC-BY-3.0
    name: Units Ontology
    prefix: FAIRsharing.mjnypw
    publications:
    - doi: 10.1093/database/bas033
      pubmed: '23060432'
      title: 'The Units Ontology: a tool for integrating units of measurement in science'
      year: 2012
    repository: https://github.com/bio-ontology-research-group/unit-ontology/issues
    subjects:
    - Life Science
    - Mathematics
  keywords:
  - ontology
  - unit
  - units
  mappings:
    aberowl: UO
    agroportal: UO
    biocontext: UO
    bioportal: UO
    fairsharing: FAIRsharing.mjnypw
    miriam: uo
    n2t: uo
    obofoundry: uo
    ols: uo
    ontobee: UO
    prefixcommons: uo
    tib: uo
    wikidata.entity: Q81661826
  miriam:
    deprecated: false
    description: Ontology of standardized units
    homepage: https://www.ebi.ac.uk/ols4/ontologies/uo
    id: '00000136'
    name: Unit Ontology
    namespaceEmbeddedInLui: true
    pattern: ^UO:\d{7}?$
    prefix: uo
    sampleId: 0000080
    uri_format: https://www.ebi.ac.uk/ols4/ontologies/uo/terms?obo_id=UO:$1
  n2t:
    description: Ontology of standardized units
    example: 0000080
    homepage: http://bioportal.bioontology.org/ontologies/UO
    name: Unit Ontology through BioPortal
    namespaceEmbeddedInLui: true
    pattern: ^UO:\d{7}?
    prefix: uo
    uri_format: http://purl.bioontology.org/ontology/UO/UO:$1
  obofoundry:
    appears_in:
    - agro
    - ms
    - rbo
    - scdo
    contact: g.gkoutos@gmail.com
    contact.github: gkoutos
    contact.label: George Gkoutos
    contact.orcid: 0000-0002-2061-091X
    deprecated: false
    description: Metrical units for use in conjunction with PATO
    domain: phenotype
    download.obo: http://purl.obolibrary.org/obo/uo.obo
    download.owl: http://purl.obolibrary.org/obo/uo.owl
    homepage: https://github.com/bio-ontology-research-group/unit-ontology
    license: CC BY 3.0
    license.url: http://creativecommons.org/licenses/by/3.0/
    name: Units of measurement ontology
    preferredPrefix: UO
    prefix: uo
    publications:
    - id: https://www.ncbi.nlm.nih.gov/pubmed/23060432
      title: 'The Units Ontology: a tool for integrating units of measurement in science'
    repository: https://github.com/bio-ontology-research-group/unit-ontology
  ols:
    description: Metrical units for use in conjunction with PATO
    download_owl: http://purl.obolibrary.org/obo/uo.owl
    homepage: https://github.com/bio-ontology-research-group/unit-ontology
    name: Units of measurement ontology
    prefix: uo
    tracker: https://github.com/bio-ontology-research-group/unit-ontology/issues
    version: '2023-05-25'
    version.iri: http://purl.obolibrary.org/obo/uo/releases/2023-05-25/uo.owl
  ontobee:
    library: Library
    name: Units of measurement ontology
    prefix: UO
  pattern: ^\d{7}$
  prefix: uo
  prefixcommons:
    alt_uri_formats:
    - http://purl.org/obo/owl/UO#$1
    - http://mimi.case.edu/ontologies/2009/1/UnitsOntology#$1
    bioportal: '1112'
    description: Ontology of standardized units in conjunction with PATO
    example: UO:0000080
    homepage: http://code.google.com/p/unit-ontology/
    keywords:
    - obo
    - ontology
    license: CC-BY-3.0
    name: Unit Ontology
    pattern: ^UO:\d{7}?$
    prefix: uo
    synonyms:
    - obo.unit
    - unit
  publications:
  - doi: 10.1093/database/bas033
    pmc: PMC3468815
    pubmed: '23060432'
    title: 'The Units Ontology: a tool for integrating units of measurement in science'
    year: 2012
  tib:
    description: The Ontology of Units of Measure models concepts and relations for
      defining and using measures and units in scientific research. It includes common
      units like SI units (meter, kilogram) and others like the mile. OM supports
      the following application areas- Geometry; Mechanics; Thermodynamics; Electromagnetism;
      Fluid mechanics; Chemical physics; Photometry; Radiometry and Radiobiology;
      Nuclear physics; Astronomy and Astrophysics; Cosmology; Earth science; Meteorology;
      Material science; Microbiology; Economics; Information technology and Typography.
    download_owl: http://purl.obolibrary.org/obo/uo.owl
    homepage: https://github.com/bio-ontology-research-group/unit-ontology
    keywords:
    - NFDI4ING
    - NFDI4CHEM
    - ESS
    - DataPLANT
    - physics
    - life sciences, biology
    - earth sciences
    name: Units of measurement ontology
    prefix: uo
    tracker: https://github.com/bio-ontology-research-group/unit-ontology/issues
    version.iri: http://purl.obolibrary.org/obo/uo/releases/2023-05-25/uo.owl
  uri_format: http://purl.obolibrary.org/obo/UO_$1
upa:
  aberowl:
    description: A manually curated resource for the representation and annotation
      of metabolic pathways
    download_owl: http://aber-owl.net/media/ontologies/UPA/2/upa.owl
    homepage: https://github.com/geneontology/unipathway
    name: Unipathway
    prefix: UPA
  biocontext:
    prefix: UNIPATHWAY
  bioportal:
    contact:
      email: Anne.Morgat@sib.swiss
      name: Anne Morgat
    description: UniPathway (http://www.unipathway.org) is a fully manually curated
      resource for the representation and annotation of metabolic pathways. UniPathway
      provides explicit representations of enzyme-catalyzed and spontaneous chemical
      reactions, as well as a hierarchical representation of metabolic pathways. This
      hierarchy uses linear subpathways as the basic building block for the assembly
      of larger and more complex pathways, including species-specific pathway variants.
      All of the pathway data in UniPathway has been extensively cross-linked to existing
      pathway resources such as KEGG and MetaCyc, as well as sequence resources such
      as the UniProt KnowledgeBase (UniProtKB), for which UniPathway provides a controlled
      vocabulary for pathway annotation. We introduce here the basic concepts underlying
      the UniPathway resource, with the aim of allowing users to fully exploit the
      information provided by UniPathway.
    homepage: https://github.com/geneontology/unipathway
    name: Unipathway
    prefix: UPA
    publications:
    - https://www.ncbi.nlm.nih.gov/pubmed/22102589
    version: UniPathway Release 2015_03
  deprecated: true
  download_obo: https://raw.githubusercontent.com/geneontology/unipathway/master/upa.obo
  edam:
    description: Identifier of a biological pathway from the Unipathway database.
    name: Pathway ID (Unipathway)
    obsolete: false
    prefix: '2645'
  example: UCR00513
  go:
    description: UniPathway is a a metabolic door to UniProtKB/Swiss-Prot, a curated
      resource of metabolic pathways for the UniProtKB/Swiss-Prot knowledgebase.
    homepage: http://www.grenoble.prabi.fr/obiwarehouse/unipathway
    name: UniPathway
    prefix: UniPathway
    uri_format: http://www.grenoble.prabi.fr/obiwarehouse/unipathway/upa?upid=$1
  mappings:
    aberowl: UPA
    biocontext: UNIPATHWAY
    bioportal: UPA
    edam: '2645'
    go: UniPathway
    obofoundry: upa
    ols: upa
    ontobee: UPA
    pathguide: '414'
    prefixcommons: unipathway
    wikidata.entity: Q85719315
  obofoundry:
    contact: Anne.Morgat@sib.swiss
    contact.github: amorgat
    contact.label: Anne Morgat
    contact.orcid: 0000-0002-1216-2969
    depends_on:
    - ro
    deprecated: true
    description: A manually curated resource for the representation and annotation
      of metabolic pathways
    domain: biological systems
    download.obo: http://purl.obolibrary.org/obo/upa.obo
    download.owl: http://purl.obolibrary.org/obo/upa.owl
    homepage: https://github.com/geneontology/unipathway
    license: CC BY 3.0
    license.url: http://creativecommons.org/licenses/by/3.0/
    name: Unipathway
    prefix: upa
    publications:
    - id: https://www.ncbi.nlm.nih.gov/pubmed/22102589
      title: 'UniPathway: a resource for the exploration and annotation of metabolic
        pathways'
    repository: https://github.com/geneontology/unipathway
  ols:
    description: A manually curated resource for the representation and annotation
      of metabolic pathways
    download_owl: http://purl.obolibrary.org/obo/upa.owl
    homepage: https://github.com/geneontology/unipathway
    name: Unipathway
    prefix: upa
    tracker: https://github.com/geneontology/unipathway/issues
    version: '2024-03-06'
    version.iri: http://purl.obolibrary.org/obo/upa/releases/2024-03-06/upa.owl
  ontobee:
    library: Library
    name: Unipathway
    prefix: UPA
  pathguide:
    abbreviation: UniPathway
    homepage: http://www.grenoble.prabi.fr/obiwarehouse/unipathway
    name: 'UniPathway: a resource for the exploration of metabolic pathways'
    prefix: '414'
  pattern: ^(UCR|UCY|UER|ULS|UPA|UPC|UPX)\d{5}$
  prefix: upa
  prefixcommons:
    description: UniPathway is a manually curated resource of metabolic pathways for
      the UniProtKB/Swiss-Prot knowledgebase. It provides a structured controlled
      vocabulary to describe the role of a protein in a metabolic pathway.
    example: UPA00206
    homepage: http://www.grenoble.prabi.fr/obiwarehouse/unipathway
    keywords:
    - pathway
    name: UniPathway, a metabolic door to UniProtKB/Swiss-Prot
    pattern: ^UPA\d{5}$
    prefix: unipathway
    uri_format: http://www.grenoble.prabi.fr/obiwarehouse/unipathway/upa?upid=$1
  publications:
  - doi: 10.1093/nar/gkr1023
    pmc: PMC3245108
    pubmed: '22102589'
    title: 'UniPathway: a resource for the exploration and annotation of metabolic
      pathways'
    year: 2011
  - doi: null
    pmc: null
    pubmed: '22102589'
    title: 'UniPathway: a resource for the exploration and annotation of metabolic
      pathways'
    year: null
  synonyms:
  - UPa
  - unipathway
  - unipathway.pathway
  wikidata:
    database: Q85719315
upheno:
  aberowl:
    description: The uPheno ontology integrates multiple phenotype ontologies into
      a unified cross-species phenotype ontology.
    download_owl: http://aber-owl.net/media/ontologies/UPHENO/10/upheno.owl
    homepage: https://github.com/obophenotype/upheno
    name: Unified Phenotype Ontology (uPheno)
    prefix: UPHENO
  biocontext:
    prefix: UPHENO
  bioportal:
    contact:
      email: cjmungall@lbl.gov
      name: Chris Mungall
    description: Combined phenotype ontology, The Unified Phenotype Ontology (uPheno)
      is an ontology that integrates other species-specific phenotype ontologies.
    license: CC0-1.0
    name: Combined Phenotype Ontology
    prefix: UPHENO
    version: '2025-10-12'
  fairsharing:
    abbreviation: uPheno
    description: The Unified Phenotype Ontology (uPheno) framework is a community
      effort providing unified integration layers over domain-specific phenotype ontologies.
      uPheno is comprised of (1) computational definitions of phenotype terms using
      ontology design patterns, (2) hierarchical species-neutral phenotype vocabulary
      terms grouped with species-specific counterparts, and (3) a mapping between
      species-specific ontologies.
    domains:
    - Expression data
    - Data analysis
    - phenotype
    homepage: https://github.com/obophenotype/upheno
    license: CC0-1.0
    logo: https://api.fairsharing.org/rails/active_storage/blobs/redirect/eyJfcmFpbHMiOnsibWVzc2FnZSI6IkJBaHBBa01CIiwiZXhwIjpudWxsLCJwdXIiOiJibG9iX2lkIn19--3f5258d2bcf30a7e127b5a9fe209b27e25e88883/up.png?disposition=inline
    name: The Unified Phenotype Ontology
    prefix: FAIRsharing.r41qhx
    publications:
    - doi: 10.1093/genetics/iyaf027
      pubmed: '40048704'
      title: 'The Unified Phenotype Ontology : a framework for cross-species integrative
        phenomics'
      year: 2025
    repository: https://github.com/obophenotype/upheno/issues
    subjects:
    - Phenomics
    - Evolutionary Biology
    - Omics
  mappings:
    aberowl: UPHENO
    biocontext: UPHENO
    bioportal: UPHENO
    fairsharing: FAIRsharing.r41qhx
    obofoundry: upheno
    ols: upheno
    ontobee: UPHENO
    wikidata.entity: Q81661827
  name: Unified Phenotype Ontology
  no_own_terms: true
  obofoundry:
    contact: jmcl@ebi.ac.uk
    contact.github: jamesamcl
    contact.label: James McLaughlin
    contact.orcid: 0000-0002-8361-2795
    deprecated: false
    description: The uPheno ontology integrates multiple phenotype ontologies into
      a unified cross-species phenotype ontology.
    domain: phenotype
    download.owl: http://purl.obolibrary.org/obo/upheno.owl
    homepage: https://github.com/obophenotype/upheno
    license: CC0 1.0
    license.url: https://creativecommons.org/publicdomain/zero/1.0/
    name: Unified Phenotype Ontology (uPheno)
    preferredPrefix: UPHENO
    prefix: upheno
    publications:
    - id: https://doi.org/10.1101/2024.09.18.613276
      title: 'The Unified Phenotype Ontology (uPheno): A framework for cross-species
        integrative phenomics'
    - id: https://zenodo.org/record/2382757
      title: Phenotype Ontologies Traversing All The Organisms (POTATO) workshop aims
        to reconcile logical definitions across species
    - id: https://zenodo.org/record/3352149
      title: 'Phenotype Ontologies Traversing All The Organisms (POTATO) workshop:
        2nd edition'
    repository: https://github.com/obophenotype/upheno
  ols:
    description: The uPheno ontology integrates multiple phenotype ontologies into
      a unified cross-species phenotype ontology.
    download_owl: http://purl.obolibrary.org/obo/upheno.owl
    homepage: https://github.com/obophenotype/upheno
    name: Unified Phenotype Ontology (uPheno)
    prefix: upheno
    tracker: https://github.com/obophenotype/upheno/issues
    version: '2025-10-12'
    version.iri: http://purl.obolibrary.org/obo/upheno/releases/2025-10-12/upheno.owl
  ontobee:
    library: Library
    name: Unified Phenotype Ontology (uPheno)
    prefix: UPHENO
  prefix: upheno
urdbms.syndromefinder:
  appears_in:
  - nando
  contact:
    email: naritomi@med.u-ryukyu.ac.jp
    github: null
    name: Kenji Naritomi
    orcid: null
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  deprecated: true
  example: '3567'
  github_request_issue: 1320
  mappings:
    integbio: nbdc00728
  name: UR-DBMS Syndrome Finder
  pattern: ^\d+$
  prefix: urdbms.syndromefinder
  publications:
  - doi: 10.1038/s10038-024-01277-y
    pmc: null
    pubmed: '39085458'
    title: An application supporting diagnosis for rare genetic diseases - UR-DBMS
      and Syndrome Finder
    year: 2024
  uri_format: http://syndromefinder.ncchd.go.jp/UR-DBMS/SyndromeDetail.php?winid=1&recid=$1
usda.cvb.pcn:
  appears_in:
  - vo
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: "A Product Code Number (PCN) assigned by the Animal and Plant Health\
    \ Inspection Service (APHIS)'s Center for Veterinary Biologics (CVB) to veterinary\
    \ biological products such as vaccines, bacterins, antibodies, diagnostic products,\
    \ antitoxins, bacterin-toxoids, and toxioids approved for veterinary use by the\
    \ United States Department of Agriculture Veterinary (USDA). A quarterly release,\
    \ as PDF, can be found [here](https://www.aphis.usda.gov/sites/default/files/currentprodcodebook.pdf).\n\
    \n The PDF document states (verbatim): The alphanumeric system used for product\
    \ codes provides for a six-digit number of number-letter combination to be assigned\
    \ to each product, i.e., the first digit denotes product types; second and third,\
    \ group by agents; fourth, the viability of vaccine, (live, killed, modified live,\
    \ etc.); fifth, substrates; and sixth, miscellaneous variables"
  example: '1011.00'
  example_extras:
  - 1K11.00
  - 10T1.40
  - 19O5.D0
  - GA94.00
  homepage: https://www.aphis.usda.gov/veterinary-biologics/licensed-products
  keywords:
  - antitoxin
  - bacterin
  - bacterin-toxoid
  - diagnostic product
  - toxoid
  - vaccine
  name: United States Department of Agriculture Veterinary Biological Product Code
    Number
  owners:
  - name: Animal and Plant Health Inspection Service
    partnered: false
    ror: 0599wfz09
    wikidata: null
  pattern: ^[A-Z0-9]{4}\.[A-Z0-9]{2}$
  prefix: usda.cvb.pcn
  references:
  - https://www.aphis.usda.gov/sites/default/files/currentprodcodebook.pdf
  - https://www.aphis.usda.gov/veterinary-biologics
uspto:
  biocontext:
    prefix: USPTO
  comment: Information about the regular expression was derived from examples at https://patft.uspto.gov/netahtml/PTO/srchnum.htm.
    TODO, make the regular expression work for '100000000'
  contributor_extras:
  - email: null
    github: dhimmel
    name: Daniel Himmelstein
    orcid: 0000-0002-3012-7446
  example_extras:
  - 10,000,000
  - '6923014'
  - '0000001'
  - D000152
  - PP07514
  - RE12345
  - T855019
  - H001234
  - AI00007
  - X000001
  - RX00001
  mappings:
    biocontext: USPTO
    miriam: uspto
    n2t: uspto
  miriam:
    deprecated: false
    description: The United States Patent and Trademark Office (USPTO) is the federal
      agency for granting U.S. patents and registering trademarks. As a mechanism
      that protects new ideas and investments in innovation and creativity, the USPTO
      is at the cutting edge of the nation's technological progress and achievement.
    homepage: http://patft.uspto.gov/netahtml/PTO/index.html
    id: 00000538
    name: USPTO
    namespaceEmbeddedInLui: false
    pattern: ^(D|PP|R|T|H|X|AI)?\d+$
    prefix: uspto
    sampleId: '4145692'
    uri_format: http://patft.uspto.gov/netacgi/nph-Parser?Sect2=PTO1&Sect2=HITOFF&p=1&u=/netahtml/PTO/search-bool.html&r=1&f=G&l=50&d=PALL&RefSrch=yes&Query=PN/$1
  n2t:
    description: The United States Patent and Trademark Office (USPTO) is the federal
      agency for granting U.S. patents and registering trademarks. As a mechanism
      that protects new ideas and investments in innovation and creativity, the USPTO
      is at the cutting edge of the nation's technological progress and achievement.
    example: '4145692'
    homepage: http://patft.uspto.gov/netahtml/PTO/index.html
    name: USPTO patents at USPTO
    namespaceEmbeddedInLui: false
    pattern: ^(D|PP|R|T|H|X|AI)?\d+$
    prefix: uspto
    uri_format: http://patft.uspto.gov/netacgi/nph-Parser?Sect2=PTO1&Sect2=HITOFF&p=1&u=/netahtml/PTO/search-bool.html&r=1&f=G&l=50&d=PALL&RefSrch=yes&Query=PN/$1
  name: United States Patent and Trademark Office
  pattern: ^(\d{1,2},?\d{3},?\d{3}|(PP|RE|AI|RX)\d{2},?\d{3}|(D|T|H|X)\d{3},?\d{3})$
  prefix: uspto
  references:
  - https://github.com/biopragmatics/bioregistry/issues/253
utrdb:
  integbio:
    description: UTRdb is a database of untranslated region sequences and other information
      related to the regulation of genes by way of 5' and 3' UTRs. The database contains
      sequence information for hundreds of thousands of genes in dozens of species,
      and a second, more comprehensive resource specifically dedicated to human UTRs.
      Tools for analyzing UTRs and bulk data downloads are available.
    homepage: http://utrdb.ba.itb.cnr.it/
    information_keywords:
    - Sequence
    maintainer: Institute for Biomedical Technologies
    name: UTRdb
    prefix: nbdc00730
    pubmeds:
    - '19880380'
    - '15608165'
    - '11752330'
    - '11897027'
    - '11591473'
    - '10592223'
    status: Active
    target_keywords:
    - RNA
  mappings:
    integbio: nbdc00730
    miriam: utrdb
  miriam:
    deprecated: false
    description: 'A curated database of 5'' and 3'' untranslated sequences of eukaryotic
      mRNAs. In the current update, the UTR entries are organized in a gene-centric
      structure to better visualize and retrieve 5'' and 3''UTR variants generated
      by alternative initiation and termination of transcription and alternative splicing.
      Experimentally validated miRNA targets and conserved sequence elements are also
      annotated. The integration of UTRdb with genomic data has allowed the implementation
      of an efficient annotation system and a powerful retrieval resource for the
      selection and extraction of specific UTR subsets. '
    homepage: https://utrdb.cloud.ba.infn.it/utrdb/index_107.html
    id: 00000993
    name: UTRdb
    namespaceEmbeddedInLui: false
    pattern: ^([3-5][A-Z])\w+[^A-Z][0-9]$
    prefix: utrdb
    sampleId: 5UTR_107_ENST00000517291.2
    uri_format: https://utrdb.cloud.ba.infn.it/cgi-bin/utrdb/utrdb?e=$1
  prefix: utrdb
vac:
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: The Vaccine Adjuvant Compendium (VAC) was established in 2020 by the
    NIAID Division of Allergy, Immunology, and Transplantation to foster collaborations
    between NIAID-supported adjuvant researchers and the broader scientific community.
    The VAC displays adjuvant characteristics or metadata defined through NIAID-supported
    adjuvant studies to help vaccine developers identify suitable adjuvants for various
    vaccine indications, including immune-mediated and infectious diseases. In addition,
    the VAC welcomes the inclusion of adjuvant metadata generated by other research
    programs.
  example: '15'
  homepage: https://vac.niaid.nih.gov
  keywords:
  - biology
  - immunology
  - vaccines
  name: Vaccine Adjuvant Compendium
  pattern: ^\d+$
  prefix: vac
  uri_format: https://vac.niaid.nih.gov/view?id=$1
validatordb:
  biocontext:
    prefix: VALIDATORDB
  example: 2h6o
  fairsharing:
    abbreviation: ValidatorDB
    contact:
      email: david.sehnal@gmail.com
      name: David Sehnal
      orcid: 0000-0002-0682-3089
    description: ValidatorDB is a collection of validation results for the entire
      Protein Data Bank. Annotation (3-letter code) of HET residues larger than 6
      heavy atoms is inspected, i.e. if the residue has the same topology and stereochemistry
      as the model ligand or residue stored in the wwCCD. Validation reports for the
      entire database can be inspected as well as for the arbitrary set of PDB entries
      or PDB annotations (3-letter residue code). Results are available in graphical
      form via Web UI and can be downloaded in the form of CSV files for further inspection.
    homepage: http://webchem.ncbr.muni.cz/Platform/ValidatorDB
    name: ValidatorDB
    prefix: FAIRsharing.c9psgb
    publications:
    - doi: 10.1093/nar/gku1118
      pubmed_id: 25392418
      title: 'ValidatorDB: database of up-to-date validation results for ligands and
        non-standard residues from the Protein Data Bank.'
    subjects:
    - Life Science
  integbio:
    description: ValidatorDB is a collection of validation results for the entire
      Protein Data Bank. Annotation (3-letter code) of HET residues larger than 6
      heavy atoms is inspected, i.e. if the residue has the same topology and stereochemistry
      as the model ligand or residue stored in the wwCCD. Validation reports for the
      entire database can be inspected as well as for the arbitrary set of PDB entries
      or PDB annotations (3-letter residue code). Results are available in graphical
      form via Web UI and can be downloaded in the form of CSV files for further inspection.
    fairsharing: FAIRsharing.c9psgb
    homepage: http://webchem.ncbr.muni.cz/Platform/ValidatorDB
    information_keywords:
    - 3D structure
    maintainer: Central European Institute of Technology
    name: ValidatorDB
    prefix: nbdc02174
    pubmeds:
    - '25392418'
    status: Active
    target_keywords:
    - Protein
  mappings:
    biocontext: VALIDATORDB
    fairsharing: FAIRsharing.c9psgb
    integbio: nbdc02174
    miriam: validatordb
    n2t: validatordb
  miriam:
    deprecated: false
    description: Database of validation results for ligands and non-standard residues
      in the Protein Data Bank.
    homepage: https://webchem.ncbr.muni.cz/Platform/ValidatorDb/
    id: '00000633'
    name: ValidatorDB
    namespaceEmbeddedInLui: false
    pattern: ^[A-Za-z0-9\/]+$
    prefix: validatordb
    sampleId: ByStructure/2h6o
    uri_format: https://webchem.ncbr.muni.cz/Platform/ValidatorDb/$1
  n2t:
    description: Database of validation results for ligands and non-standard residues
      in the Protein Data Bank.
    example: ByStructure/2h6o
    homepage: https://webchem.ncbr.muni.cz/Platform/ValidatorDb/
    name: ValidatorDB
    namespaceEmbeddedInLui: false
    pattern: ^[A-Za-z0-9\/]+$
    prefix: validatordb
    uri_format: https://webchem.ncbr.muni.cz/Platform/ValidatorDb/$1
  prefix: validatordb
  provides: pdb
  publications:
  - doi: 10.1093/nar/gku1118
    pmc: PMC4383933
    pubmed: '25392418'
    title: 'ValidatorDB: database of up-to-date validation results for ligands and
      non-standard residues from the Protein Data Bank'
    year: 2014
  - doi: 10.1093/nar/gku1118
    pmc: null
    pubmed: null
    title: 'ValidatorDB: database of up-to-date validation results for ligands and
      non-standard residues from the Protein Data Bank.'
    year: null
  uri_format: https://webchem.ncbr.muni.cz/Platform/ValidatorDb/ByStructure/$1
vandf:
  aberowl:
    description: NDF includes information on clinical drugs, drug classes, ingredients
      and National Drug Code (NDC) Directory codes.
    homepage: http://www.pbm.va.gov/NationalFormulary.aspx
    name: Veterans Health Administration National Drug File
    prefix: VANDF
    version: 2016AB
  biolink:
    is_identifiers: false
    is_obo: false
    prefix: VANDF
    uri_format: https://www.nlm.nih.gov/research/umls/sourcereleasedocs/current/VANDF/$1
  bioportal:
    contact:
      email: michael.lincoln@med.va.gov
      name: Michael Lincoln
    description: NDF includes information on clinical drugs, drug classes, ingredients
      and National Drug Code (NDC) Directory codes.
    homepage: http://www.pbm.va.gov/NationalFormulary.aspx
    name: Veterans Health Administration National Drug File
    prefix: VANDF
    version: VANDF_2024_07_31
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: The National Drug File (NDF) is produced by the U.S. Department of
    Veterans Affairs, Veterans Health Administration (VHA). NDF is a centrally maintained
    electronic drug list used by the VHA hospitals and clinics. Facilities use the
    NDF to check drug interactions, to manage orders, and to send outpatient prescriptions
    to regional automated mail-out pharmacies. NDF includes information on clinical
    drugs, drug classes, ingredients and National Drug Code (NDC) Directory codes.
  example: '4019477'
  fairsharing:
    abbreviation: VANDF
    description: Veterans Health Administration National Drug File is a centrally
      maintained electronic drug list used by the VHA hospitals and clinics. Facilities
      use the NDF to check drug interactions, to manage orders, and to send outpatient
      prescriptions to regional automated mail-out pharmacies.
    domains:
    - drug
    - drug interaction
    homepage: https://www.nlm.nih.gov/research/umls/sourcereleasedocs/current/VANDF/
    name: Veterans Health Administration National Drug File
    prefix: FAIRsharing.xn3pb3
    publications:
    - pubmed: '12463886'
      title: 'A semantic normal form for clinical drugs in the UMLS: early experiences
        with the VANDF'
      year: 2002
    subjects:
    - Biomedical Science
    - Pharmacology
  hl7:
    description: 'U.S. Department of Veterns Affairs, Veterans Health Administration
      National Drug File. Department of Veterans Affairs, Washington, DC. URL: http://www.vapbm.org/PBM/natform.htm'
    name: National Drug File
    preferred_prefix: VANDF
    prefix: 2.16.840.1.113883.6.229
    status: Pending
  homepage: https://www.nlm.nih.gov/research/umls/sourcereleasedocs/current/VANDF
  mappings:
    aberowl: VANDF
    biolink: VANDF
    bioportal: VANDF
    fairsharing: FAIRsharing.xn3pb3
    hl7: 2.16.840.1.113883.6.229
  name: Veterans Administration National Drug File
  pattern: ^\d+$
  prefix: vandf
  publications:
  - doi: null
    pmc: PMC2244318
    pubmed: '12463886'
    title: 'A semantic normal form for clinical drugs in the UMLS: early experiences
      with the VANDF'
    year: 2002
  uri_format: http://purl.bioontology.org/ontology/VANDF/$1
vann:
  contact:
    email: nospam@iandavis.com
    github: iand
    name: Ian Davis
    orcid: null
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: This document describes a vocabulary for annotating descriptions of
    vocabularies with examples and usage notes.
  example: usageNote
  homepage: https://vocab.org/vann/
  lov:
    description: A vocabulary for annotating descriptions of vocabularies with examples
      and usage notes.
    homepage: http://purl.org/vocab/vann/
    keywords:
    - Metadata
    modified: '2010-06-07'
    name: 'VANN: A vocabulary for annotating vocabulary descriptions'
    prefix: vann
    uri_prefix: http://purl.org/vocab/vann/$1
  mappings:
    lov: vann
    tib: vann
    zazuko: vann
  name: A vocabulary for annotating vocabulary descriptions
  preferred_prefix: vann
  prefix: vann
  rdf_uri_format: http://purl.org/vocab/vann/$1
  tib:
    description: This document describes a vocabulary for annotating descriptions
      of vocabularies with examples and usage notes.
    download_rdf: https://vocab.org/vann/vann-vocab-20100607.rdf
    homepage: https://vocab.org/vann/
    keywords:
    - TIB
    - computer science
    name: 'VANN: A vocabulary for annotating vocabulary descriptions'
    prefix: vann
    uri_format: http://purl.org/vocab/vann/$1
  uri_format: https://vocab.org/vann/#$1
  zazuko:
    prefix: vann
    uri_format: http://purl.org/vocab/vann/$1
vario:
  aberowl:
    description: Variation Ontology, VariO, is an ontology for standardized, systematic
      description of effects, consequences and mechanisms of variations.
    download_owl: http://aber-owl.net/media/ontologies/VARIO/19/vario.owl
    homepage: http://variationontology.org
    name: Variation Ontology
    prefix: VARIO
  agroportal:
    contact:
      email: mauno.vihinen@med.lu.se
      name: Mauno Vihinen
    description: Variation Ontology, VariO, is an ontology for standardized, systematic
      description of effects, consequences and mechanisms of variations. VariO allows
      unambiguous description of variation effects as well as computerized analyses
      over databases utilizing the ontology for annotation. VariO is a position specific
      ontology that can be used to describe effects of variations on DNA, RNA and/or
      protein level, whatever is appropriate.
    example_uri: http://purl.obolibrary.org/obo/VariO_0117
    homepage: http://variationontology.org/
    name: Variation Ontology
    prefix: VARIO
    publications:
    - http://genome.cshlp.org/content/early/2013/10/25/gr.157495.113.abstract
    version: '2017-02-06'
  banana: VariO
  biocontext:
    prefix: VARIO
  bioportal:
    contact:
      email: mauno.vihinen@med.lu.se
      name: Mauno Vihinen
    description: Variation Ontology, VariO, is an ontology for standardized, systematic
      description of effects, consequences and mechanisms of variations. Ontology
      is unreachable as of 2024, but continues to be available on BioPortal as a retired
      ontology.
    homepage: http://variationontology.org
    name: Variation Ontology
    prefix: VARIO
    publications:
    - https://obofoundry.org/ontology/vario
    version: '2018-11-09'
  contact:
    email: mauno.vihinen@med.lu.se
    github: maunov
    name: Mauno Vihinen
    orcid: 0000-0002-9614-7976
  example: '0376'
  fairsharing:
    abbreviation: VariO
    description: Variation Ontology, VariO, is an ontology for standardized, systematic
      description of effects, consequences and mechanisms of variations. VariO allows
      unambiguous description of variation effects as well as computerized analyses
      over databases utilizing the ontology for annotation. VariO is a position specific
      ontology that can be used to describe effects of variations on DNA, RNA and/or
      proteins.
    domains:
    - deoxyribonucleic acid
    - ribonucleic acid
    - protein
    - sequence variant
    - chromosome structure variation
    homepage: http://variationontology.org
    name: Variation Ontology
    prefix: FAIRsharing.65xkbs
    publications:
    - doi: 10.1101/gr.157495.113
      pubmed: '24162187'
      title: Variation Ontology for annotation of variation effects and mechanisms
      year: 2013
    - doi: 10.1007/s00439-015-1529-6
      pubmed: '25616435'
      title: Types and effects of protein variations
      year: 2015
    - doi: 10.1186/2041-1480-5-9
      pubmed: '24533660'
      title: 'Variation ontology: annotator guide'
      year: 2014
    - doi: 10.1002/humu.22954
      pubmed: '26773573'
      title: VariOtator, a Software Tool for Variation Annotation with the Variation
        Ontology
      year: 2016
    - doi: 10.1186/s12864-018-5262-0
      pubmed: '30591019'
      title: Systematics for types and effects of DNA variations
      year: 2018
    subjects:
    - Genetics
  mappings:
    aberowl: VARIO
    agroportal: VARIO
    biocontext: VARIO
    bioportal: VARIO
    fairsharing: FAIRsharing.65xkbs
    miriam: vario
    n2t: vario
    obofoundry: vario
    ols: vario
    ontobee: VariO
    wikidata.entity: Q114677953
  miriam:
    deprecated: false
    description: The Variation Ontology (VariO) is an ontology for the standardized,
      systematic description of effects, consequences and mechanisms of variations.
      It describes the effects of variations at the DNA, RNA and/or protein level.
    homepage: http://bioportal.bioontology.org/ontologies/VARIO
    id: '00000406'
    name: VariO
    namespaceEmbeddedInLui: true
    pattern: ^VariO:\d+$
    prefix: vario
    sampleId: 0294
    uri_format: https://purl.bioontology.org/ontology/VARIO?conceptid=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FVariO_$1
  n2t:
    description: The Variation Ontology (VariO) is an ontology for the standardized,
      systematic description of effects, consequences and mechanisms of variations.
      It describes the effects of variations at the DNA, RNA and/or protein level.
    example: 0294
    homepage: http://bioportal.bioontology.org/ontologies/VARIO
    name: VariO through BioPortal
    namespaceEmbeddedInLui: true
    pattern: ^VariO:\d+$
    prefix: vario
    uri_format: http://purl.bioontology.org/ontology/VARIO/VariO:$1
  name: Variation Ontology
  obofoundry:
    contact: mauno.vihinen@med.lu.se
    contact.github: maunov
    contact.label: Mauno Vihinen
    contact.orcid: 0000-0002-9614-7976
    deprecated: true
    description: Variation Ontology, VariO, is an ontology for standardized, systematic
      description of effects, consequences and mechanisms of variations.
    domain: biological systems
    download.obo: http://purl.obolibrary.org/obo/vario.obo
    download.owl: http://purl.obolibrary.org/obo/vario.owl
    homepage: http://variationontology.org
    license: CC BY 4.0
    license.url: https://creativecommons.org/licenses/by/4.0/
    name: Variation Ontology
    preferredPrefix: VariO
    prefix: vario
    publications:
    - id: https://www.ncbi.nlm.nih.gov/pubmed/24162187
      title: Variation Ontology for annotation of variation effects and mechanisms
    - id: https://www.ncbi.nlm.nih.gov/pubmed/24533660
      title: 'Variation ontology: annotator guide'
    - id: https://www.ncbi.nlm.nih.gov/pubmed/25616435
      title: Types and effects of protein variations
  ols:
    description: Variation Ontology, VariO, is an ontology for standardized, systematic
      description of effects, consequences and mechanisms of variations.
    download: http://purl.obolibrary.org/obo/vario.owl
    homepage: http://variationontology.org
    name: Variation Ontology
    prefix: vario
    version: '2018-11-09'
    version.iri: http://purl.obolibrary.org/obo/vario/2018-11-09/vario.owl
  ontobee:
    library: Library
    name: Variation Ontology
    prefix: VariO
  pattern: ^\d+$
  preferred_prefix: VariO
  prefix: vario
  publications:
  - doi: 10.1186/s12864-018-5262-0
    pmc: PMC6309100
    pubmed: '30591019'
    title: Systematics for types and effects of DNA variations
    year: 2018
  - doi: 10.1002/humu.22954
    pmc: null
    pubmed: '26773573'
    title: VariOtator, a Software Tool for Variation Annotation with the Variation
      Ontology
    year: 2016
  - doi: 10.1007/s00439-015-1529-6
    pmc: null
    pubmed: '25616435'
    title: Types and effects of protein variations
    year: 2015
  - doi: 10.1186/2041-1480-5-9
    pmc: PMC3931275
    pubmed: '24533660'
    title: 'Variation ontology: annotator guide'
    year: 2014
  - doi: 10.1101/gr.157495.113
    pmc: PMC3912426
    pubmed: '24162187'
    title: Variation Ontology for annotation of variation effects and mechanisms
    year: 2013
  - doi: null
    pmc: null
    pubmed: '24162187'
    title: Variation Ontology for annotation of variation effects and mechanisms
    year: null
  - doi: null
    pmc: null
    pubmed: '24533660'
    title: 'Variation ontology: annotator guide'
    year: null
  - doi: null
    pmc: null
    pubmed: '25616435'
    title: Types and effects of protein variations
    year: null
  - doi: 10.1101/gr.157495.113
    pmc: null
    pubmed: '24162187'
    title: Variation Ontology for annotation of variation effects and mechanisms
    year: 2013
  - doi: 10.1007/s00439-015-1529-6
    pmc: null
    pubmed: '25616435'
    title: Types and effects of protein variations
    year: 2015
  - doi: 10.1186/2041-1480-5-9
    pmc: null
    pubmed: '24533660'
    title: 'Variation ontology: annotator guide'
    year: 2014
  - doi: 10.1002/humu.22954
    pmc: null
    pubmed: '26773573'
    title: VariOtator, a Software Tool for Variation Annotation with the Variation
      Ontology
    year: 2016
  - doi: 10.1186/s12864-018-5262-0
    pmc: null
    pubmed: '30591019'
    title: Systematics for types and effects of DNA variations
    year: 2018
vbase2:
  biocontext:
    prefix: VBASE2
  fairsharing:
    abbreviation: VBASE2
    contact:
      email: wmueller@gbf.de
      name: Werner Müller
      orcid: 0000-0002-1297-9725
    description: VBASE2 is an integrative database of germ-line variable genes from
      the immunoglobulin loci of human and mouse. All variable gene sequences are
      extracted from the EMBL-Bank.
    homepage: http://www.vbase2.org
    license: http://opendatacommons.org/licenses/pddl/1.0
    name: VBASE2
    prefix: FAIRsharing.qvxhb1
    publications:
    - doi: 10.1093/nar/gki088
      pubmed_id: 15608286
      title: VBASE2, an integrative V gene database.
    subjects:
    - Life Science
  integbio:
    description: VBASE2 is an integrative database of germ-line variable genes from
      the immunoglobulin loci of human and mouse. All variable gene sequences are
      extracted from the EMBL-Bank.
    fairsharing: FAIRsharing.qvxhb1
    homepage: http://www.vbase2.org
    information_keywords:
    - Sequence
    maintainer: University of Cologne
    name: VBASE2
    prefix: nbdc01897
    pubmeds:
    - '15608286'
    status: Active
    target_keywords:
    - Genome/Gene
    - Genetic variation
    - Protein
  mappings:
    biocontext: VBASE2
    fairsharing: FAIRsharing.qvxhb1
    integbio: nbdc01897
    miriam: vbase2
    n2t: vbase2
    ncbi: VBASE2
    prefixcommons: vbase2
  miriam:
    deprecated: false
    description: The database VBASE2 provides germ-line sequences of human and mouse
      immunoglobulin variable (V) genes.
    homepage: http://www.vbase2.org/vbase2.php
    id: '00000320'
    name: Vbase2
    namespaceEmbeddedInLui: false
    pattern: ^\w+$
    prefix: vbase2
    sampleId: humIGHV025
    uri_format: http://www.vbase2.org/vgene.php?id=$1
  n2t:
    description: The database VBASE2 provides germ-line sequences of human and mouse
      immunoglobulin variable (V) genes.
    example: humIGHV025
    homepage: http://www.vbase2.org/vbase2.php
    name: Vbase2 at German Research Centre for Biotechnology
    namespaceEmbeddedInLui: false
    pattern: ^\w+$
    prefix: vbase2
    uri_format: http://www.vbase2.org/vgene.php?id=$1
  ncbi:
    example: humIGKV165
    homepage: http://www.vbase2.org/
    name: Integrative database of germ-line V genes from the immunoglobulin loci of
      human and mouse
    prefix: VBASE2
  prefix: vbase2
  prefixcommons:
    description: VBASE2 is an integrative database of germ-line variable genes from
      the immunoglobulin loci of human and mouse. All variable gene sequences are
      extracted from the EMBL-Bank.
    example: humIGHV025
    homepage: http://www.vbase2.org
    keywords:
    - gene
    name: VBASE2
    pattern: ^\w+$
    prefix: vbase2
    pubmed_ids:
    - '15608286'
    uri_format: http://www.vbase2.org/vgene.php?id=$1
  publications:
  - doi: 10.1093/nar/gki088
    pmc: PMC540042
    pubmed: '15608286'
    title: VBASE2, an integrative V gene database
    year: 2005
  - doi: 10.1093/nar/gki088
    pmc: null
    pubmed: null
    title: VBASE2, an integrative V gene database.
    year: null
  - doi: null
    pmc: null
    pubmed: '15608286'
    title: null
    year: null
  - doi: 10.1093/nar/gki088
    pmc: null
    pubmed: null
    title: VBASE2, an integrative V gene database.
    year: null
  - doi: null
    pmc: null
    pubmed: '15608286'
    title: null
    year: null
  - doi: 10.1093/nar/gki088
    pmc: null
    pubmed: null
    title: VBASE2, an integrative V gene database.
    year: null
  - doi: null
    pmc: null
    pubmed: '15608286'
    title: null
    year: null
vbo:
  aberowl:
    description: Vertebrate Breed Ontology is an ontology created to serve as a single
      computable resource for vertebrate breed names.
    download_owl: http://aber-owl.net/media/ontologies/VBO/14/vbo.owl
    homepage: https://github.com/monarch-initiative/vertebrate-breed-ontology
    name: Vertebrate Breed Ontology
    prefix: VBO
  agroportal:
    contact:
      email: Sabrina@tislab.org
      name: Sabrina Toro
    description: VBO is used in the Online Mendelian Inheritance in Animals (OMIA)
      for breed annotations., None, Vertebrate Breed Ontology is an ontology created
      to serve as a single computable resource for vertebrate breed names.
    example_uri: http://purl.obolibrary.org/obo/VBO_0016224
    homepage: https://monarch-initiative.github.io/vertebrate-breed-ontology/
    license: CC-BY-4.0
    name: Vertebrate Breed Ontology
    prefix: VBO
    publications:
    - https://doi.org/10.48550/arXiv.2406.02623
    repository: https://github.com/monarch-initiative/vertebrate-breed-ontology
    version: '2025-02-12'
  bioportal:
    contact:
      email: Sabrina@tislab.org
      name: Sabrina Toro
    description: Vertebrate Breed Ontology is an ontology created to serve as a single
      computable resource for vertebrate breed names.
    homepage: https://github.com/monarch-initiative/vertebrate-breed-ontology
    license: CC-BY-4.0
    name: Vertebrate Breed Ontology
    prefix: VBO
    version: '2025-11-07'
  cellosaurus:
    category: Taxonomy
    homepage: https://monarch-initiative.github.io/vertebrate-breed-ontology/
    name: Vertebrate Breed Ontology
    prefix: VBO
  example: 0000038
  mappings:
    aberowl: VBO
    agroportal: VBO
    bioportal: VBO
    cellosaurus: VBO
    obofoundry: vbo
    ols: vbo
    ontobee: VBO
    wikidata.entity: Q114296193
  obofoundry:
    contact: Sabrina@tislab.org
    contact.github: sabrinatoro
    contact.label: Sabrina Toro
    contact.orcid: 0000-0002-4142-7153
    depends_on:
    - ncbitaxon
    deprecated: false
    description: Vertebrate Breed Ontology is an ontology created to serve as a single
      computable resource for vertebrate breed names.
    domain: organisms
    download.json: http://purl.obolibrary.org/obo/vbo.json
    download.obo: http://purl.obolibrary.org/obo/vbo.obo
    download.owl: http://purl.obolibrary.org/obo/vbo.owl
    homepage: https://github.com/monarch-initiative/vertebrate-breed-ontology
    license: CC BY 4.0
    license.url: https://creativecommons.org/licenses/by/4.0/
    logo: https://raw.githubusercontent.com/tis-lab/closed-illustrations/master/logos/vbo-logo/VBO-black-logo-stackedv2.png
    name: Vertebrate Breed Ontology
    preferredPrefix: VBO
    prefix: vbo
    publications:
    - id: https://doi.org/10.1111/jvim.70133
      title: 'The Vertebrate Breed Ontology: Toward Effective Breed Data Standardization'
    repository: https://github.com/monarch-initiative/vertebrate-breed-ontology
  ols:
    description: Vertebrate Breed Ontology is an ontology created to serve as a single
      computable resource for vertebrate breed names.
    download_owl: http://purl.obolibrary.org/obo/vbo.owl
    homepage: https://github.com/monarch-initiative/vertebrate-breed-ontology
    name: Vertebrate Breed Ontology
    prefix: vbo
    tracker: https://github.com/monarch-initiative/vertebrate-breed-ontology/issues
    version: '2025-11-07'
    version.iri: http://purl.obolibrary.org/obo/vbo/releases/2025-11-07/vbo.owl
  ontobee:
    library: Library
    name: Vertebrate Breed Ontology
    prefix: VBO
  pattern: ^\d{7}$
  prefix: vbo
  uri_format: http://purl.obolibrary.org/obo/VBO_$1
vbo.issue:
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: An issue on the Vertebrate Breed Ontology GitHub issue tracker
  example: '126'
  github_request_issue: 1553
  homepage: https://github.com/monarch-initiative/vertebrate-breed-ontology/issues
  name: Vertebrate Breed Ontology Issue Tracker
  pattern: ^\d+$
  prefix: vbo.issue
  uri_format: https://github.com/monarch-initiative/vertebrate-breed-ontology/issues/$1
vbrc:
  biocontext:
    prefix: VBRC
  mappings:
    biocontext: VBRC
    miriam: vbrc
    n2t: vbrc
    prefixcommons: vbrc
  miriam:
    deprecated: true
    description: The VBRC provides bioinformatics resources to support scientific
      research directed at viruses belonging to the Arenaviridae, Bunyaviridae, Filoviridae,
      Flaviviridae, Paramyxoviridae, Poxviridae, and Togaviridae families. The Center
      consists of a relational database and web application that support the data
      storage, annotation, analysis, and information exchange goals of this work.
      Each data release contains the complete genomic sequences for all viral pathogens
      and related strains that are available for species in the above-named families.
      In addition to sequence data, the VBRC provides a curation for each virus species,
      resulting in a searchable, comprehensive mini-review of gene function relating
      genotype to biological phenotype, with special emphasis on pathogenesis.
    homepage: http://vbrc.org/
    id: 00000448
    name: VBRC
    namespaceEmbeddedInLui: false
    pattern: ^\d+$
    prefix: vbrc
    sampleId: '35742'
    uri_format: http://vbrc.org/gene_detail.asp?gene_id=$1
  n2t:
    description: The VBRC provides bioinformatics resources to support scientific
      research directed at viruses belonging to the Arenaviridae, Bunyaviridae, Filoviridae,
      Flaviviridae, Paramyxoviridae, Poxviridae, and Togaviridae families. The Center
      consists of a relational database and web application that support the data
      storage, annotation, analysis, and information exchange goals of this work.
      Each data release contains the complete genomic sequences for all viral pathogens
      and related strains that are available for species in the above-named families.
      In addition to sequence data, the VBRC provides a curation for each virus species,
      resulting in a searchable, comprehensive mini-review of gene function relating
      genotype to biological phenotype, with special emphasis on pathogenesis.
    example: '35742'
    homepage: http://vbrc.org/
    name: VBRC at University of Alabama
    namespaceEmbeddedInLui: false
    pattern: ^\d+$
    prefix: vbrc
    uri_format: http://vbrc.org/gene_detail.asp?gene_id=$1
  name: Viral Bioinformatics Resource Center
  prefix: vbrc
  prefixcommons:
    description: The VBRC is one of eight NIH/NIAID-funded Bioinformatics Resource
      Centers nationwide providing a comprehensive web-based battery of informational
      and analytical tools and resources.
    example: VP0033331
    homepage: http://vbrc.org
    name: Viral Bioinformatics Resource Center
    pattern: ^VP\d+$
    prefix: vbrc
vcard:
  contact:
    email: r@iannel.la
    github: riannella
    name: Renato Iannella
    orcid: 0000-0001-5547-3508
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: vCard is a specification developed by the Internet Engineering Task
    Force (IETF) for the description of people and organisations
  download_owl: https://www.w3.org/2006/vcard/ns
  example: Agent
  github_request_issue: 1317
  homepage: https://www.w3.org/TR/vcard-rdf/
  lov:
    description: This ontology models and represents vCards in RDF using current best
      practices
    homepage: http://www.w3.org/TR/vcard-rdf/
    keywords:
    - People
    modified: '2014-05-22'
    name: An Ontology for vCards
    prefix: vcard
    uri_prefix: http://www.w3.org/2006/vcard/ns#$1
  mappings:
    lov: vcard
    zazuko: vcard
  name: Virtual Contact File
  prefix: vcard
  uri_format: http://www.w3.org/2006/vcard/ns#$1
  zazuko:
    prefix: vcard
    uri_format: http://www.w3.org/2006/vcard/ns#$1
vcell:
  mappings:
    miriam: vcell
  miriam:
    deprecated: false
    description: Models developed with the Virtual Cell (VCell) software prorgam.
    homepage: https://health.uconn.edu/
    id: 00000893
    name: VCell Published Models
    namespaceEmbeddedInLui: false
    pattern: ^\d{5,}$
    prefix: vcell
    sampleId: '201022999'
    uri_format: https://vcell.org/biomodel-$1
  prefix: vcell
vdrc:
  description: Biomaterial supply resource which collects, maintains, and distributes
    independent transgenic fly lines. Most of the 38,000 fly lines are RNAi lines,
    but VDRC also maintains a collection of enhancer-GAL4 driver lines. Nearly all
    lines are in duplicate. Users can search for the stocks or DNA constructs for
    the gene of interest by entering CG number, synonym, or Transformant ID. [from
    RRID]
  example: '100291'
  mappings:
    rrid: VDRC
  pattern: ^\d+$
  prefix: vdrc
  rrid:
    homepage: http://stockcenter.vdrc.at/control/main
    keywords:
    - biomaterial supply resource
    - drosophila
    - fly lines
    name: Vienna Drosophila Resource Center
    prefix: VDRC
    scr: 013805
  uri_format: https://shop.vbc.ac.at/vdrc_store/$1.html
vectorbase:
  biocontext:
    prefix: VECTORBASE
  contact:
    email: d.e.starns@liv.ac.uk
    github: obsidian83
    name: David Starns
    orcid: 0000-0001-6583-9067
  fairsharing:
    abbreviation: VectorBase
    description: VectorBase is a web-accessible data repository for information about
      invertebrate vectors of human pathogens. VectorBase annotates and maintains
      vector genomes (as well as a number of non-vector genomes for comparative analysis)
      providing an integrated resource for the research community. VectorBase contains
      genome information for organisms such as Anopheles gambiae, a vector for the
      Plasmodium protozoan agent causing malaria, and Aedes aegypti, a vector for
      the flaviviral agents causing Yellow fever and Dengue fever. Hosted data range
      from genome assemblies with annotated gene features, transcript and protein
      expression data to population genetics including variation and insecticide-resistance
      phenotypes.
    homepage: https://vectorbase.org/vectorbase/app
    name: VectorBase
    prefix: FAIRsharing.3etvdn
    publications:
    - doi: 10.1093/nar/gkn857
      pubmed_id: 19028744
      title: 'VectorBase: a data resource for invertebrate vector genomics.'
    - doi: 10.1093/nar/gku1117
      pubmed_id: 25510499
      title: 'VectorBase: an updated bioinformatics resource for invertebrate vectors
        and other organisms related with human diseases.'
    subjects:
    - Functional Genomics
    - Population Dynamics
    - Genomics
    - Comparative Genomics
    - Population Genetics
    twitter: VectorBase
  integbio:
    description: VectorBase is a web-accessible data repository for information about
      invertebrate vectors of human pathogens. VectorBase annotates and maintains
      vector genomes (as well as a number of non-vector genomes for comparative analysis)
      providing an integrated resource for the research community. VectorBase contains
      genome information for organisms such as Anopheles gambiae, a vector for the
      Plasmodium protozoan agent causing malaria, and Aedes aegypti, a vector for
      the flaviviral agents causing Yellow fever and Dengue fever. Hosted data range
      from genome assemblies with annotated gene features, transcript and protein
      expression data to population genetics including variation and insecticide-resistance
      phenotypes.
    fairsharing: FAIRsharing.3etvdn
    homepage: https://vectorbase.org/vectorbase/app
    information_keywords:
    - Sequence
    - Expression
    - Localization
    - Environment
    maintainer: United States Department of Health and Human Services||VectorBase
    name: VectorBase
    prefix: nbdc01909
    pubmeds:
    - '19028744'
    status: Active
    target_keywords:
    - Genome/Gene
    - Protein
    - Organism
  mappings:
    biocontext: VECTORBASE
    fairsharing: FAIRsharing.3etvdn
    integbio: nbdc01909
    miriam: vectorbase
    n2t: vectorbase
    ncbi: VectorBase
    prefixcommons: vectorbase
    re3data: r3d100010880
  miriam:
    deprecated: false
    description: 'VectorBase is part of the VEuPathDB, a NIAID-funded Bioinformatic
      Resource Center focused on invertebrate vectors of human pathogens and related
      species of interest. Currently, VectorBase contains genome information for approximately
      80 organisms: mosquitoes, bed bugs, biting midges, ticks, tsetse flies, mites,
      sand flies, house flies, body lice, stable flies, kissing bugs, and a snail
      which is an intermediate host.'
    homepage: https://www.vectorbase.org/
    id: '00000232'
    name: VectorBase
    namespaceEmbeddedInLui: false
    pattern: ^\D{4}\d{6}(\-\D{2})?$
    prefix: vectorbase
    sampleId: ISCW007415
    uri_format: https://vectorbase.org/gene/$1
  n2t:
    description: 'VectorBase is an NIAID-funded Bioinformatic Resource Center focused
      on invertebrate vectors of human pathogens. VectorBase annotates and curates
      vector genomes providing a web accessible integrated resource for the research
      community. Currently, VectorBase contains genome information for three mosquito
      species: Aedes aegypti, Anopheles gambiae and Culex quinquefasciatus, a body
      louse Pediculus humanus and a tick species Ixodes scapularis.'
    example: ISCW007415
    homepage: https://www.vectorbase.org/
    name: Vectorbase at EMBL-EBI
    namespaceEmbeddedInLui: false
    pattern: ^\D{4}\d{6}(\-\D{2})?$
    prefix: vectorbase
    uri_format: https://www.vectorbase.org/search/site/$1?&site="Genome"
  ncbi:
    example: ENSANGG00000007825
    homepage: http://www.vectorbase.org/index.php
    name: Bioinformatics Resource Center for Invertebrate Vectors of Human Pathogens
    prefix: VectorBase
  prefix: vectorbase
  prefixcommons:
    description: 'VectorBase is a web-accessible data repository for information about
      invertebrate vectors of human pathogens. VectorBase annotates and maintains
      vector genomes providing an integrated resource for the research community.
      Currently, VectorBase contains genome information for two organisms: Anopheles
      gambiae, a vector for the Plasmodium protozoan agent causing malaria, and Aedes
      aegypti, a vector for the flaviviral agents causing Yellow fever and Dengue
      fever.'
    example: ISCW007415
    homepage: http://www.vectorbase.org/index.php
    keywords:
    - gene
    - genome
    - protein
    name: Invertebrate Vectors of Human Pathogens
    pattern: ^\D{4}\d{6}(\-\D{2})?$
    prefix: vectorbase
    pubmed_ids:
    - '19028744'
    uri_format: http://www.vectorbase.org/[?species_name]/Gene/Summary?db=core;g=$1
  providers:
  - code: vectorbase.alt1
    description: An alternate provider based on the search functionality
    example: null
    first_party: null
    homepage: https://www.vectorbase.org
    name: Vectorbase Alt. 1
    publications: null
    status: null
    uri_format: https://www.vectorbase.org/search/site/$1?&site="Genome"
  - code: vectorbase.alt2
    description: An alternate provider based on the app structure
    example: null
    first_party: null
    homepage: https://www.vectorbase.org
    name: Vectorbase Alt. 2
    publications: null
    status: null
    uri_format: https://vectorbase.org/vectorbase/app/record/gene/$1
  publications:
  - doi: 10.1093/nar/gku1117
    pmc: PMC4383932
    pubmed: '25510499'
    title: 'VectorBase: an updated bioinformatics resource for invertebrate vectors
      and other organisms related with human diseases'
    year: 2014
  - doi: 10.1093/nar/gkn857
    pmc: PMC2686483
    pubmed: '19028744'
    title: 'VectorBase: a data resource for invertebrate vector genomics'
    year: 2008
  re3data:
    description: VectorBase provides data on arthropod vectors of human pathogens.
      Sequence data, gene expression data, images, population data, and insecticide
      resistance data for arthropod vectors are available for download.  VectorBase
      also offers genome browser, gene expression and microarray repository,  and
      BLAST searches for all VectorBase genomes.  VectorBase Genomes include Aedes
      aegypti, Anopheles gambiae, Culex quinquefasciatus, Ixodes scapularis, Pediculus
      humanus, Rhodnius prolixus.  VectorBase is one the Bioinformatics Resource Centers
      (BRC) projects which is funded by National Institute of Allergy and Infectious
      Diseases (NAID).
    doi: 10.17616/R3CK6B
    homepage: https://vectorbase.org/vectorbase/app
    name: VectorBase
    prefix: r3d100010880
    synonyms:
    - Bioinformatics Resource for Invertebrate Vectors of Human Pathogens
    xrefs:
      nif: 0000-03624
      omics: '03146'
vega:
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: A repository for high-quality gene models produced by the manual annotation
    of vertebrate genomes.
  example: OTTHUMG00000169812
  fairsharing:
    abbreviation: VEGA
    contact:
      email: jla1@sanger.ac.uk
      name: Jennifer L Harrow
      orcid: 0000-0003-0338-3070
    description: The Vertebrate Genome Annotation (VEGA) database is a central repository
      for high quality manual annotation of vertebrate finished genome sequence.
    homepage: https://vega.archive.ensembl.org/index.html
    name: The Vertebrate Genome Annotation Database
    prefix: FAIRsharing.mr293q
    publications:
    - doi: 10.1093/nar/gkm987
      pubmed_id: 18003653
      title: The vertebrate genome annotation (Vega) database.
    - doi: 10.1093/nar/gkt1241
      pubmed_id: 24316575
      title: The Vertebrate Genome Annotation browser 10 years on.
    subjects:
    - Life Science
  homepage: https://vega.archive.ensembl.org/index.html
  mappings:
    fairsharing: FAIRsharing.mr293q
    prefixcommons: vega
    re3data: r3d100012575
  name: Vertebrate Genome Annotation Database
  prefix: vega
  prefixcommons:
    description: The Vertebrate Genome Annotation (VEGA) database is a central repository
      for high quality manual annotation of vertebrate finished genome sequence.
    example: OTTHUMG00000017411
    homepage: http://vega.sanger.ac.uk/
    keywords:
    - genome
    name: The Vertebrate Genome Annotation Database
    pattern: ^[A-Z]+\d+$
    prefix: vega
    uri_format: http://vega.sanger.ac.uk/[?species_name]/Gene/Summary?g=$1
  publications:
  - doi: 10.1093/nar/gkt1241
    pmc: PMC3964964
    pubmed: '24316575'
    title: The Vertebrate Genome Annotation browser 10 years on
    year: 2013
  - doi: 10.1093/nar/gkm987
    pmc: PMC2238886
    pubmed: '18003653'
    title: The vertebrate genome annotation (Vega) database
    year: 2007
  re3data:
    description: A repository for high-quality gene models produced by the manual
      annotation of vertebrate genomes. The final update of Vega, version 68, was
      released in February 2017 and is now archived at vega.archive.ensembl.org. We
      plan to maintain this resource until Feb 2020.
    doi: 10.17616/R3W77X
    homepage: http://vega.archive.ensembl.org/index.html
    name: Vega
    prefix: r3d100012575
    synonyms:
    - Vertebrate Genome Annotation database
    xrefs:
      nif: 0000-03626
  synonyms:
  - VEGA
vegbank:
  mappings:
    miriam: vegbank
    re3data: r3d100010153
  miriam:
    deprecated: false
    description: 'VegBank is the vegetation plot database of the Ecological Society
      of America''s Panel on Vegetation Classification. VegBank consists of three
      linked databases that contain (1) vegetation plot records, (2) vegetation types
      recognized in the U.S. National Vegetation Classification and other vegetation
      types submitted by users, and (3) all plant taxa recognized by ITIS/USDA as
      well as all other plant taxa recorded in plot records. Vegetation records, community
      types and plant taxa may be submitted to VegBank and may be subsequently searched,
      viewed, annotated, revised, interpreted, downloaded, and cited. '
    homepage: http://vegbank.org/
    id: '00000723'
    name: VegBank
    namespaceEmbeddedInLui: false
    pattern: ^VB\.[A-Za-z][A-Za-z]\..*$
    prefix: vegbank
    sampleId: VB.Ob.3736.GRSM125
    uri_format: http://vegbank.org/cite/$1
  prefix: vegbank
  re3data:
    description: VegBank is the vegetation plot database of the Ecological Society
      of America's Panel on Vegetation Classification. VegBank consists of three linked
      databases that contain  the actual plot records,  vegetation types recognized
      in the U.S. National Vegetation Classification and other vegetation types submitted
      by users, and  all plant taxa recognized by ITIS/USDA as well as all other plant
      taxa recorded in plot records. Vegetation records, community types and plant
      taxa may be submitted to VegBank and may be subsequently searched, viewed, annotated,
      revised, interpreted, downloaded, and cited. VegBank receives its data from
      the VegBank community of users.
    doi: 10.17616/R3GK5W
    homepage: http://vegbank.org/vegbank/index.jsp
    name: VegBank
    prefix: r3d100010153
    synonyms:
    - The Vegetation Plot Archive Project
venom:
  appears_in:
  - vbo
  contact:
    email: DBrodbelt@RVC.AC.UK
    github: null
    name: David Brodbelt
    orcid: 0000-0001-5628-4194
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: The Veterinary Nomenclature (VeNom) is a standard set of clinical veterinary
    terms for use in referral veterinary hospital electronic patient records and first
    opinion veterinary practice management systems.
  example: '12969'
  homepage: https://venomcoding.org/
  name: Veterinary Nomenclature
  pattern: ^\d+$
  preferred_prefix: VeNom
  prefix: venom
  proprietary: true
  references:
  - https://github.com/biopragmatics/bioregistry/pull/724
vfb:
  fairsharing:
    abbreviation: VFB
    contact:
      email: r.court@ed.ac.uk
      name: Robert Court
      orcid: 0000-0002-0173-9080
    description: VFB is an interactive tool for neurobiologists to explore the detailed
      neuroanatomy, neuron connectivity and gene expression of Drosophila melanogaster.
      Our goal is to make it easier for researchers to find relevant anatomical information
      and reagents. We integrate the neuroanatomical and expression data from the
      published literature, as well as image datasets onto the same brain template,
      making it possible to run cross searches, find similar neurons and compare image
      data on our 3D Viewer.
    homepage: https://virtualflybrain.org
    license: CC BY-SA 4.0
    name: Virtual Fly Brain
    prefix: FAIRsharing.nzaz6z
    publications:
    - doi: 10.1093/bioinformatics/bts113
      pubmed_id: 22402613
      title: A strategy for building neuro-anatomy ontologies
    - doi: 10.1093/bioinformatics/btr677
      pubmed_id: 22180411
      title: The Virtual Fly Brain Browser and Query Interface
    - doi: doi:10.1186/1471-2105-13-122
      pubmed_id: 22676296
      title: Web tools for large-scale 3D biological images and atlases
    subjects:
    - Neurobiology
    - Life Science
  mappings:
    fairsharing: FAIRsharing.nzaz6z
    miriam: vfb
    n2t: vfb
    re3data: r3d100011373
  miriam:
    deprecated: false
    description: An interactive tool for neurobiologists to explore the detailed neuroanatomy,
      neuron connectivity and gene expression of the Drosophila melanogaster.
    homepage: https://VirtualFlyBrain.org
    id: 00000680
    name: Virtual Fly Brain
    namespaceEmbeddedInLui: false
    pattern: ^[0-9a-zA-Z]{8}$
    prefix: vfb
    sampleId: '00000001'
    uri_format: http://virtualflybrain.org/reports/$1
  n2t:
    description: An interactive tool for neurobiologists to explore the detailed neuroanatomy,
      neuron connectivity and gene expression of the Drosophila melanogaster.
    example: '00000001'
    homepage: https://VirtualFlyBrain.org
    name: Virtual Fly Brain
    namespaceEmbeddedInLui: false
    pattern: ^[0-9a-zA-Z]{8}$
    prefix: vfb
    uri_format: http://virtualflybrain.org/reports/$1
  prefix: vfb
  publications:
  - doi: 10.1093/bioinformatics/bts113
    pmc: null
    pubmed: '22402613'
    title: A strategy for building neuroanatomy ontologies
    year: 2012
  - doi: 10.1186/1471-2105-13-122
    pmc: PMC3412715
    pubmed: '22676296'
    title: Web tools for large-scale 3D biological images and atlases
    year: 2012
  - doi: 10.1093/bioinformatics/btr677
    pmc: null
    pubmed: '22180411'
    title: The Virtual Fly Brain browser and query interface
    year: 2011
  - doi: 10.1093/bioinformatics/bts113
    pmc: null
    pubmed: null
    title: A strategy for building neuro-anatomy ontologies
    year: null
  - doi: 10.1093/bioinformatics/btr677
    pmc: null
    pubmed: null
    title: The Virtual Fly Brain Browser and Query Interface
    year: null
  - doi: doi:10.1186/1471-2105-13-122
    pmc: null
    pubmed: null
    title: Web tools for large-scale 3D biological images and atlases
    year: null
  re3data:
    description: Virtual Fly Brain (VFB) - an interactive tool for neurobiologists
      to explore the detailed neuroanatomy, neuron connectivity and gene expression
      of the Drosophila melanogaster CNS.
    doi: 10.17616/R3XK9F
    homepage: https://virtualflybrain.org/
    name: Virtual Fly Brain
    prefix: r3d100011373
    synonyms:
    - VFB
    - VFB Drosophila melanogaster fly brain atlas
vfdb.gene:
  biocontext:
    prefix: VFDB.GENE
  mappings:
    biocontext: VFDB.GENE
    miriam: vfdb.gene
    n2t: vfdb.gene
  miriam:
    deprecated: false
    description: VFDB is a repository of virulence factors (VFs) of pathogenic bacteria.This
      collection references VF genes.
    homepage: http://www.mgc.ac.cn/VFs/
    id: '00000472'
    name: VFDB Gene
    namespaceEmbeddedInLui: false
    pattern: ^\w+$
    prefix: vfdb.gene
    sampleId: VFG2154
    uri_format: http://www.mgc.ac.cn/cgi-bin/VFs/gene.cgi?GeneID=$1
  n2t:
    description: VFDB is a repository of virulence factors (VFs) of pathogenic bacteria.This
      collection references VF genes.
    example: VFG2154
    homepage: http://www.mgc.ac.cn/VFs/
    name: VFDB Gene at Institute of Pathogen Biology
    namespaceEmbeddedInLui: false
    pattern: ^\w+$
    prefix: vfdb.gene
    uri_format: http://www.mgc.ac.cn/cgi-bin/VFs/gene.cgi?GeneID=$1
  prefix: vfdb.gene
vfdb.genus:
  biocontext:
    prefix: VFDB.GENUS
  mappings:
    biocontext: VFDB.GENUS
    miriam: vfdb.genus
    n2t: vfdb.genus
  miriam:
    deprecated: false
    description: VFDB is a repository of virulence factors (VFs) of pathogenic bacteria.This
      collection references VF information by Genus.
    homepage: http://www.mgc.ac.cn/VFs/
    id: '00000471'
    name: VFDB Genus
    namespaceEmbeddedInLui: false
    pattern: ^\w+$
    prefix: vfdb.genus
    sampleId: Chlamydia
    uri_format: http://www.mgc.ac.cn/cgi-bin/VFs/genus.cgi?Genus=$1
  n2t:
    description: VFDB is a repository of virulence factors (VFs) of pathogenic bacteria.This
      collection references VF information by Genus.
    example: Chlamydia
    homepage: http://www.mgc.ac.cn/VFs/
    name: VFDB Genus at Institute of Pathogen Biology
    namespaceEmbeddedInLui: false
    pattern: ^\w+$
    prefix: vfdb.genus
    uri_format: http://www.mgc.ac.cn/cgi-bin/VFs/genus.cgi?Genus=$1
  prefix: vfdb.genus
vgnc:
  cellosaurus:
    category: Organism-specific databases
    homepage: https://vertebrate.genenames.org/
    name: Vertebrate Gene Nomenclature Committee Database
    prefix: VGNC
    uri_format: https://vertebrate.genenames.org/data/gene-symbol-report/#!/vgnc_id/$1
  contact:
    email: stweedie@ebi.ac.uk
    github: null
    name: Susan Tweedie
    orcid: 0000-0003-1818-8243
  example: '3792'
  fairsharing:
    abbreviation: VGNC
    description: The VGNC approves both a short-form abbreviation known as a gene
      symbol, and also a longer and more descriptive name. Each symbol is unique and
      the committee ensures that each gene is only given one approved gene symbol.
      This allows for clear and unambiguous reference to genes in scientific communications,
      and facilitates electronic data retrieval from databases and publications.
    homepage: https://vertebrate.genenames.org/download/statistics-and-files/
    name: VGNC Gene Symbols, Gene Names and IDs
    prefix: FAIRsharing.5NhJFK
    subjects:
    - Life Science
  integbio:
    alt_name: Vertebrate Gene Nomenclature Committee
    description: The Vertebrate Gene Nomenclature Committee (VGNC) is an extension
      of the established HGNC (HUGO Gene Nomenclature Committee) project that names
      human genes. VGNC is responsible for assigning standardized names to genes in
      selected vertebrate species that lack a nomenclature authority; currently these
      are chimpanzee, macaque, dog, cat, cattle, pig and horse. The VGNC also coordinates
      with the existing vertebrate nomenclature committees, MGNC (mouse), RGNC (rat),
      CGNC (chicken), XNC (Xenopus frog) and ZNC (zebrafish), to ensure genes are
      named in line with their human homologs.
    fairsharing: FAIRsharing.eBP3tb
    homepage: https://vertebrate.genenames.org/
    information_keywords:
    - Ontology/Terminology/Nomenclature
    maintainer: Vertebrate Gene Nomenclature Committee
    name: VGNC
    prefix: nbdc02624
    pubmeds:
    - '33152070'
    status: Active
    target_keywords:
    - Genome/Gene
    - Protein
  mappings:
    cellosaurus: VGNC
    fairsharing: FAIRsharing.5NhJFK
    integbio: nbdc02624
    miriam: vgnc
    ncbi: VGNC
    togoid: Vgnc
    uniprot: DB-0226
  miriam:
    deprecated: false
    description: The Vertebrate Gene Nomenclature Committee (VGNC) is an extension
      of the established HGNC (HUGO Gene Nomenclature Committee) project that names
      human genes. VGNC is responsible for assigning standardized names to genes in
      vertebrate species that currently lack a nomenclature committee.
    homepage: https://vertebrate.genenames.org
    id: '00000765'
    name: VGNC
    namespaceEmbeddedInLui: false
    pattern: ^((VGNC|vgnc):)?\d{1,9}$
    prefix: vgnc
    sampleId: VGNC:3792
    uri_format: https://vertebrate.genenames.org/data/gene-symbol-report/#!/vgnc_id/$1
  ncbi:
    example: VGNC:4927
    homepage: http://vertebrate.genenames.org/data/gene-symbol-report/#!/
    name: Vertebrate Gene Nomenclature Committee
    prefix: VGNC
  pattern: ^\d{1,9}$
  prefix: vgnc
  publications:
  - doi: 10.1093/nar/gkaa980
    pmc: PMC7779007
    pubmed: '33152070'
    title: 'Genenames.org: the HGNC and VGNC resources in 2021'
    year: 2021
  - doi: 10.1093/nar/gkaa980
    pmc: null
    pubmed: '33152070'
    title: null
    year: null
  togoid:
    catalog: nbdc02624
    examples:
    - '39230'
    - '49608'
    - '85188'
    - '76040'
    - '72808'
    - '73601'
    - '9436'
    - '78821'
    - '74596'
    - '5304'
    keywords:
    - Gene
    name: VGNC
    pattern: ^((VGNC|vgnc):)?(?\d{1,9})$
    prefix: Vgnc
    uri_format: http://identifiers.org/vgnc/$1
  uniprot:
    abbreviation: VGNC
    category: Organism-specific databases
    homepage: https://vertebrate.genenames.org/
    name: Vertebrate Gene Nomenclature Database
    prefix: DB-0226
    publications:
    - doi: 10.1093/nar/gkaa980
      pubmed: '33152070'
    uri_format: https://vertebrate.genenames.org/data/gene-symbol-report/#!/vgnc_id/$1
vhog:
  aberowl:
    description: 'vHOG is a multi-species anatomical ontology for the vertebrate lineage,
      developed as part of the Bgee project. The mapping to species-specific anatomical
      ontologies is provided as a separated file: http://bgee.unil.ch/download/organ_association_vHOG.txt
      This mapping represents homology-strict relationships, in the sense of HOM:0000007
      "historical homology". Each mapping has been manually reviewed, and we provide
      confidence codes and references when available.'
    download_obo: http://aber-owl.net/media/ontologies/VHOG/12/vhog.obo
    homepage: http://bgee.unil.ch
    name: Vertebrate Homologous Organ Group Ontology
    prefix: VHOG
    version: unknown
  biocontext:
    prefix: VHOG
  bioportal:
    contact:
      email: bgee@isb-sib.ch
      name: Bgee team
    description: 'vHOG is a multi-species anatomical ontology for the vertebrate lineage,
      developed as part of the Bgee project. The mapping to species-specific anatomical
      ontologies is provided as a separated file: http://bgee.unil.ch/download/organ_association_vHOG.txt
      This mapping represents homology-strict relationships, in the sense of HOM:0000007
      "historical homology". Each mapping has been manually reviewed, and we provide
      confidence codes and references when available.'
    homepage: http://bgee.unil.ch
    name: Vertebrate Homologous Organ Group Ontology
    prefix: VHOG
    publications:
    - http://www.unil.ch/dee/page31219_en.html
    version: unknown
  download_obo: ftp://ftp.bgee.org/general/ontologies/vHOG.obo
  example: '0000411'
  mappings:
    aberowl: VHOG
    biocontext: VHOG
    bioportal: VHOG
    obofoundry: vhog
    prefixcommons: vhog
  name: Vertebrate Homologous Organ Group Ontology
  obofoundry:
    deprecated: true
    domain: anatomy and development
    download.owl: http://purl.obolibrary.org/obo/vhog.owl
    logo: http://bgee.org/img/logo/bgee13_logo.png
    name: Vertebrate Homologous Ontology Group Ontology
    prefix: vhog
  pattern: ^\d{7}$
  prefix: vhog
  prefixcommons:
    bioportal: '1574'
    description: 'vHOG is a multi-species anatomical ontology for the vertebrate lineage,
      developed as part of the Bgee project. The mapping to species-specific anatomical
      ontologies is provided as a separated file: http://bgee.unil.ch/download/organ_association_vHOG.txt
      This mapping represents homology-strict relationships, in the sense of HOM:0000007
      "historical homology". Each mapping has been manually reviewed, and we provide
      confidence codes and references when available.'
    example: VHOG_0000555
    homepage: http://bgee.unil.ch
    keywords:
    - obo
    - anatomy
    - development
    name: vertebrate Homologous Organ Groups
    pattern: ^VHOG_\d{7}$
    prefix: vhog
  synonyms:
  - VHOG_RETIRED
viaf:
  bartoc:
    abbreviation: VIAF
    description: 'The Virtual International Authority File (VIAF) is an international
      service designed to provide convenient access to the world''s major name authority
      files. Its creators envision the VIAF as a building block for the Semantic Web
      to enable switching of the displayed form of names for persons to the preferred
      language and script of the Web user. VIAF began as a joint project with the
      Library of Congress (LC), the Deutsche Nationalbibliothek (DNB), the Bibliothèque
      nationale de France (BNF) and OCLC. It has, over the past decade, become a cooperative
      effort involving an expanding number of other national libraries and other agencies.
      (...)


      VIAF helps to make library authority files less expensive to maintain and more
      generally useful to the library domain and beyond. To achieve this, VIAF matches
      and links the authority files of national libraries and groups all authority
      records for a given entity into a merged ''super'' authority record that brings
      together the different names for that entity. By linking disparate names for
      the same person or organization, VIAF provides a convenient means for a wider
      community of libraries and other agencies to repurpose bibliographic data produced
      by libraries serving different language communities.'
    homepage: http://viaf.org/
    license: http://www.opendatacommons.org/licenses/by/1.0
    name: Virtual International Authority File
    pattern: ^[1-9]\d(\d{0,7}|\d{17,20})]$
    prefix: '2053'
    wikidata_database: Q54919
  fairsharing:
    abbreviation: VIAF
    description: The VIAF® (Virtual International Authority File) combines multiple
      name authority files into a single OCLC-hosted name authority service. The goal
      of the service is to lower the cost and increase the utility of library authority
      files by matching and linking widely-used authority files and making that information
      available on the Web.
    domains:
    - centrally registered identifier
    homepage: https://viaf.org/
    name: Virtual International Authority File
    prefix: FAIRsharing.a15ac6
    subjects:
    - Subject Agnostic
  mappings:
    bartoc: '2053'
    fairsharing: FAIRsharing.a15ac6
    miriam: viaf
    n2t: viaf
    wikidata: P214
    wikidata.entity: Q19832964
  miriam:
    deprecated: false
    description: The VIAF® (Virtual International Authority File) combines multiple
      name authority files into a single OCLC-hosted name authority service. The goal
      of the service is to lower the cost and increase the utility of library authority
      files by matching and linking widely-used authority files and making that information
      available on the Web.
    homepage: http://viaf.org
    id: 00000685
    name: Virtual International Authority File
    namespaceEmbeddedInLui: false
    pattern: ^\d+$
    prefix: viaf
    sampleId: '75121530'
    uri_format: http://viaf.org/viaf/$1
  n2t:
    description: The VIAF&#xAE; (Virtual International Authority File) combines multiple
      name authority files into a single OCLC-hosted name authority service. The goal
      of the service is to lower the cost and increase the utility of library authority
      files by matching and linking widely-used authority files and making that information
      available on the Web.
    example: '75121530'
    homepage: http://viaf.org
    name: Virtual International Authority File
    namespaceEmbeddedInLui: false
    pattern: ^\d+$
    prefix: viaf
    uri_format: http://viaf.org/viaf/$1
  prefix: viaf
  providers:
  - code: viaf.https
    description: A duplicate endpoint over HTTPS
    example: null
    first_party: true
    homepage: http://viaf.org
    name: VIAF (https)
    publications: null
    status: null
    uri_format: https://viaf.org/$1
  - code: scholia
    description: Scholia is a service that creates visual scholarly profiles for topic,
      people, organizations, species, chemicals, etc using bibliographic and other
      information in Wikidata.
    example: null
    first_party: null
    homepage: https://scholia.toolforge.org/
    name: Scholia
    publications: null
    status: null
    uri_format: https://scholia.toolforge.org/viaf/$1
  wikidata:
    database: Q19832964
    description: 'identifier for the Virtual International Authority File database
      [format: up to 22 digits]; please note: VIAF is a cluster, the ID can include
      multiple items'
    example:
    - '120062731'
    - '141940265'
    - '15'
    - '150088538'
    - '198592695'
    - '214796741'
    - '240782041'
    - '44298806'
    - '9972147907520779210008'
    homepage: https://viaf.org
    name: VIAF cluster ID
    pattern: ^[1-9]\d(\d{0,7}|\d{17,20})$
    prefix: P214
    short_name:
    - VIAF
    uri_format: https://viaf.org/viaf/$1
    uri_format_rdf: http://viaf.org/viaf/$1
vibso:
  contact:
    email: philip.stroemert@tib.eu
    github: StroemPhi
    name: Philip Strömert
    orcid: 0000-0002-1595-3213
  contributor:
    email: philip.stroemert@tib.eu
    github: StroemPhi
    name: Philip Strömert
    orcid: 0000-0002-1595-3213
  description: The Vibration Spectroscopy Ontology defines technical terms with which
    research data produced in vibrational spectroscopy experiments can be semantically
    enriched, made machine readable and FAIR.
  example: 0000008
  github_request_issue: 1278
  homepage: https://nfdi4chem.github.io/VibrationalSpectroscopyOntology/
  license: CC-BY-4.0
  mappings:
    tib: vibso
  name: Vibrational Spectroscopy Ontology
  pattern: ^\d{7}$
  prefix: vibso
  repository: https://github.com/NFDI4Chem/VibrationalSpectroscopyOntology
  reviewer:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  tib:
    description: WIP - NOT READY FOR PRODUCTION - The Vibration Spectroscopy Ontology
      defines technical terms with which research data produced in vibrational spectroscopy
      experiments can be semantically enriched, made machine readable and FAIR.
    download_owl: https://raw.githubusercontent.com/NFDI4Chem/VibrationalSpectroscopyOntology/main/vibso.owl
    homepage: https://nfdi4chem.github.io/VibrationalSpectroscopyOntology/
    keywords:
    - NFDI4CHEM
    - chemistry
    name: Vibrational Spectroscopy Ontology (VIBSO)
    prefix: vibso
    tracker: https://github.com/NFDI4Chem/VibrationalSpectroscopyOntology/issues
    version.iri: http://purl.obolibrary.org/obo/vibso/releases/2024-09-23/vibso.owl
  uri_format: http://purl.obolibrary.org/obo/VIBSO_$1
vido:
  aberowl:
    description: The Virus Infectious Disease Ontology (IDO Virus) is an extension
      of the Infectious Disease Ontology (IDO). IDO Virus follows OBO Foundry guidelines,
      employs the Basic Formal Ontology as its starting point, and covers epidemiology,
      classification, pathogenesis, and treatment of terms used by Virologists, i.e.
      virus, prion, satellite, viroid, etc.
    download_owl: http://aber-owl.net/media/ontologies/VIDO/3/vido.owl
    homepage: https://github.com/infectious-disease-ontology-extensions/ido-virus
    name: Virus Infectious Disease Ontology
    prefix: VIDO
    version: 10-27-2022
  bioportal:
    contact:
      email: johnbeve@buffalo.edu
      name: John Beverley
    description: The Virus Infectious Disease Ontology (IDO Virus) is an extension
      of the Infectious Disease Ontology (IDO). IDO Virus follows OBO Foundry guidelines,
      employs the Basic Formal Ontology as its starting point, and covers epidemiology,
      classification, pathogenesis, and treatment of terms used by Virologists, i.e.
      virus, prion, satellite, viroid, etc.
    homepage: https://github.com/infectious-disease-ontology-extensions/ido-virus
    name: Virus Infectious Disease Ontology
    prefix: VIDO
    publications:
    - https://osf.io/5bx8c
    version: 10-27-2022
  contact:
    email: johnbeverley2021@u.northwestern.edu
    github: johnbeve
    name: John Beverly
    orcid: 0000-0002-1118-1738
  download_owl: https://raw.githubusercontent.com/infectious-disease-ontology-extensions/ido-virus/master/ontology/vido.owl
  example: '0001114'
  homepage: https://github.com/infectious-disease-ontology-extensions/ido-virus
  mappings:
    aberowl: VIDO
    bioportal: VIDO
    ols: vido
    ontobee: VIDO
  ols:
    contact: johnbeverley2021@u.northwestern.edu
    description: The Virus Infectious Disease Ontology (IDO Virus) is an extension
      of the Infectious Disease Ontology (IDO). IDO Virus follows OBO Foundry guidelines,
      employs the Basic Formal Ontology as its starting point, and covers epidemiology,
      classification, pathogenesis, and treatment of terms used by Virologists, i.e.
      virus, prion, satellite, viroid, etc.
    download: https://raw.githubusercontent.com/infectious-disease-ontology-extensions/ido-virus/master/ontology/vido.owl
    homepage: https://github.com/infectious-disease-ontology-extensions/ido-virus
    name: The Virus Infectious Disease Ontology
    prefix: vido
    version: '2020-08-25'
    version.iri: http://purl.obolibrary.org/obo/2020-25-08/vido.owl
  ontobee:
    library: Not Specified/No
    name: Virus Infectious Disease Ontology
    prefix: VIDO
  pattern: ^\d{7}$
  prefix: vido
  providers:
  - code: obo.1
    description: This incorrect encoding was found inside IDO-COVID-19
    example: null
    first_party: null
    homepage: http://purl.obolibrary.org
    name: Nonstandard OBO PURL
    publications: null
    status: null
    uri_format: http://purl.obolibrary.org/VIDO_$1
  repository: https://github.com/infectious-disease-ontology-extensions/ido-virus
  uri_format: http://purl.obolibrary.org/obo/VIDO_$1
violinnet:
  appears_in:
  - oae
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  deprecated: true
  description: Defunct vaccine information source from the He Lab
  example: '4140'
  mappings:
    wikidata: P1925
  name: ViolinNet
  pattern: ^\d+$
  prefix: violinnet
  synonyms:
  - violinID
  - violinId
  uri_format: http://www.violinet.org/vaxquery/vaccine_detail.php?c_vaccine_id=$1
  wikidata:
    description: identifier in the VIOLIN database for vaccines and related subjects
    example:
    - '597'
    - '740'
    name: VIOLIN ID
    prefix: P1925
    uri_format: https://violinet.org/vaxquery/vaccine_detail.php?c_vaccine_id=$1
viperdb:
  integbio:
    description: VIPERdb is a database of viral capsid structures. The database contains
      structural x-ray crystallographic and cryo-EM data on the structures of 350
      icosahedral viruses. Structures are interactive and available for download,
      and can be searched by PDB ID or virus name.
    homepage: https://viperdb.org/
    information_keywords:
    - Sequence
    - Image/Movie
    - 3D structure
    maintainer: The Scripps Research Institute
    name: VIPERdb
    prefix: nbdc00835
    pubmeds:
    - '18981051'
    status: Inactive
    target_keywords:
    - RNA
    - Protein
  mappings:
    integbio: nbdc00835
    prefixcommons: viperdb
    re3data: r3d100012362
  prefix: viperdb
  prefixcommons:
    description: VIPERdb is a database for icosahedral virus capsid structures . The
      emphasis of the resource is on providing data from structural and computational
      analyses on these systems, as well as high quality renderings for visual exploration.
    example: 2c6s
    homepage: http://viperdb.scripps.edu/
    keywords:
    - structure
    - small molecule
    name: VIPERdb
    pattern: ^[A-Z,0-9]+$
    prefix: viperdb
    uri_format: http://viperdb.scripps.edu/info_page.php?VDB=$1
  provides: pdb
  re3data:
    description: VIPERdb is a database for icosahedral virus capsid structures . The
      emphasis of the resource is on providing data from structural and computational
      analyses on these systems, as well as high quality renderings for visual exploration.
      In addition, all virus capsids are placed in a single icosahedral orientation
      convention, facilitating comparison between different structures. The web site
      includes powerful search utilities , links to other relevant databases, background
      information on virus capsid structure, and useful database interface tools.
    doi: 10.17616/R3HT0Q
    homepage: https://viperdb.org/
    name: VIPERdb
    prefix: r3d100012362
    synonyms:
    - Virus Particle Explorer database
    xrefs:
      nif: 0000-03630
  uri_format: https://viperdb.org/Info_Page.php?VDB=$1
vipr:
  biocontext:
    prefix: VIPR
  fairsharing:
    abbreviation: ViPR
    contact:
      email: rscheuermann@jcvi.org
      name: Richard Scheuermann
      orcid: 0000-0003-1355-892X
    description: The Virus Pathogen Database and Analysis Resource (ViPR) is an integrated
      repository of data and analysis tools for multiple virus families, supported
      by the National Institute of Allergy and Infectious Diseases (NIAID) Bioinformatics
      Resource Centers (BRC) program. ViPR captures various types of information,
      including sequence records, gene and protein annotations, 3D protein structures,
      immune epitope locations, clinical and surveillance metadata and novel data
      derived from comparative genomics analysis. The database is available without
      charge as a service to the virology research community to help facilitate the
      development of diagnostics, prophylactics and therapeutics for priority pathogens
      and other viruses.
    homepage: http://www.viprbrc.org
    name: Virus Pathogen Database and Analysis Resource
    prefix: FAIRsharing.2qx8n8
    publications:
    - doi: 10.1093/nar/gkr859
      pubmed_id: 22006842
      title: 'ViPR: an open bioinformatics database and analysis resource for virology
        research.'
    - doi: 10.3390/v4113209
      pubmed_id: null
      title: 'Virus Pathogen Database and Analysis Resource (ViPR): A Comprehensive
        Bioinformatics Database and Analysis Resource for the Coronavirus Research
        Community'
    - doi: 10.1016/b978-0-12-801238-3.95728-3
      pubmed_id: null
      title: Virus Databases ☆
    - doi: 10.1016/b978-0-12-809633-8.20995-3
      pubmed_id: null
      title: Database and Analytical Resources for Viral Research Community
    repository: https://github.com/VirusBRC
    subjects:
    - Genomics
    - Proteomics
    - Virology
    - Life Science
    - Biomedical Science
    - Epidemiology
  keywords:
  - immunology
  mappings:
    biocontext: VIPR
    fairsharing: FAIRsharing.2qx8n8
    miriam: vipr
    n2t: vipr
    ncbi: ViPR
    re3data: r3d100011931
  miriam:
    deprecated: false
    description: The Virus Pathogen Database and Analysis Resource (ViPR) supports
      bioinformatics workflows for a broad range of human virus pathogens and other
      related viruses. It provides access to sequence records, gene and protein annotations,
      immune epitopes, 3D structures,  and host factor data. This collection references
      viral strain information.
    homepage: http://www.viprbrc.org/brc/home.do?decorator=vipr
    id: '00000407'
    name: ViPR Strain
    namespaceEmbeddedInLui: false
    pattern: ^[A-Za-z 0-9]+$
    prefix: vipr
    sampleId: BeAn 70563
    uri_format: http://www.viprbrc.org/brc/viprStrainDetails.do?strainName=$1&decorator=arena
  n2t:
    description: The Virus Pathogen Database and Analysis Resource (ViPR) supports
      bioinformatics workflows for a broad range of human virus pathogens and other
      related viruses. It provides access to sequence records, gene and protein annotations,
      immune epitopes, 3D structures,  and host factor data. This collection references
      viral strain information.
    example: BeAn 70563
    homepage: http://www.viprbrc.org/brc/home.do?decorator=vipr
    name: ViPR Strain at J. Craig Venter Institute
    namespaceEmbeddedInLui: false
    pattern: ^[A-Za-z 0-9]+$
    prefix: vipr
    uri_format: http://www.viprbrc.org/brc/viprStrainDetails.do?strainName=$1&decorator=arena
  ncbi:
    example: HRV-A34_p1058_sR263_2008
    homepage: http://www.viprbrc.org/brc/home.do?decorator=vipr
    name: Virus Pathogen Resource
    prefix: ViPR
  prefix: vipr
  publications:
  - doi: 10.1016/b978-0-12-809633-8.20995-3
    pmc: PMC7173540
    pubmed: null
    title: Database and Analytical Resources for Viral Research Community
    year: 2021
  - doi: 10.1016/b978-0-12-801238-3.95728-3
    pmc: PMC7157461
    pubmed: null
    title: Virus Databases ☆
    year: 2017
  - doi: 10.3390/v4113209
    pmc: PMC3509690
    pubmed: '23202522'
    title: 'Virus pathogen database and analysis resource (ViPR): a comprehensive
      bioinformatics database and analysis resource for the coronavirus research community'
    year: 2012
  - doi: 10.1093/nar/gkr859
    pmc: PMC3245011
    pubmed: '22006842'
    title: 'ViPR: an open bioinformatics database and analysis resource for virology
      research'
    year: 2011
  - doi: 10.1093/nar/gkr859
    pmc: null
    pubmed: null
    title: 'ViPR: an open bioinformatics database and analysis resource for virology
      research.'
    year: null
  - doi: 10.3390/v4113209
    pmc: null
    pubmed: null
    title: 'Virus Pathogen Database and Analysis Resource (ViPR): A Comprehensive
      Bioinformatics Database and Analysis Resource for the Coronavirus Research Community'
    year: null
  - doi: 10.1016/b978-0-12-801238-3.95728-3
    pmc: null
    pubmed: null
    title: Virus Databases ☆
    year: null
  - doi: 10.1016/b978-0-12-809633-8.20995-3
    pmc: null
    pubmed: null
    title: Database and Analytical Resources for Viral Research Community
    year: null
  - doi: 10.1093/nar/gkr859
    pmc: null
    pubmed: null
    title: 'ViPR: an open bioinformatics database and analysis resource for virology
      research.'
    year: null
  - doi: 10.3390/v4113209
    pmc: null
    pubmed: null
    title: 'Virus Pathogen Database and Analysis Resource (ViPR): A Comprehensive
      Bioinformatics Database and Analysis Resource for the Coronavirus Research Community'
    year: null
  - doi: 10.1016/b978-0-12-801238-3.95728-3
    pmc: null
    pubmed: null
    title: Virus Databases ☆
    year: null
  - doi: 10.1016/b978-0-12-809633-8.20995-3
    pmc: null
    pubmed: null
    title: Database and Analytical Resources for Viral Research Community
    year: null
  - doi: 10.1093/nar/gkr859
    pmc: null
    pubmed: null
    title: 'ViPR: an open bioinformatics database and analysis resource for virology
      research.'
    year: null
  - doi: 10.3390/v4113209
    pmc: null
    pubmed: null
    title: 'Virus Pathogen Database and Analysis Resource (ViPR): A Comprehensive
      Bioinformatics Database and Analysis Resource for the Coronavirus Research Community'
    year: null
  - doi: 10.1016/b978-0-12-801238-3.95728-3
    pmc: null
    pubmed: null
    title: Virus Databases ☆
    year: null
  - doi: 10.1016/b978-0-12-809633-8.20995-3
    pmc: null
    pubmed: null
    title: Database and Analytical Resources for Viral Research Community
    year: null
  - doi: 10.1093/nar/gkr859
    pmc: null
    pubmed: null
    title: 'ViPR: an open bioinformatics database and analysis resource for virology
      research.'
    year: null
  - doi: 10.3390/v4113209
    pmc: null
    pubmed: null
    title: 'Virus Pathogen Database and Analysis Resource (ViPR): A Comprehensive
      Bioinformatics Database and Analysis Resource for the Coronavirus Research Community'
    year: null
  - doi: 10.1016/b978-0-12-801238-3.95728-3
    pmc: null
    pubmed: null
    title: Virus Databases ☆
    year: null
  - doi: 10.1016/b978-0-12-809633-8.20995-3
    pmc: null
    pubmed: null
    title: Database and Analytical Resources for Viral Research Community
    year: null
  re3data:
    description: '<<<!!!<<< This repository is no longer available. >>>!!!>>>

      Migration of the data, tools, and services from IRD and ViPR to BV-BRC is complete!
      We are now in the sunsetting phase of the transition. Starting on October 31,
      2022, launching the IRD or ViPR home pages will redirect you to the new BV-BRC
      home page. The current plan is to completely shut down IRD and ViPR by the end
      of this calendar year. Although it will still be possible to use those sites
      until shutdown, we strongly encourage you to start using BV-BRC now.'
    doi: 10.17616/R30P93
    homepage: https://www.viprbrc.org/brc/home.spg?decorator=vipr
    license: other
    name: Virus Pathogen Resource
    prefix: r3d100011931
    synonyms:
    - ViPR
    xrefs:
      nif: 0000-25312
viralzone:
  biocontext:
    prefix: VIRALZONE
  fairsharing:
    abbreviation: ViralZone
    contact:
      email: Philippe.Lemercier@sib.swiss
      name: Philippe Le Mercier
      orcid: 0000-0001-8528-090X
    description: ViralZone is a web resource for viral genes and families, providing
      detailed molecular and epidemiological information, along with virion and genome
      figures. Each virus or family page gives easy access to UniProtKB/Swiss-Prot
      viral protein entries.
    homepage: http://viralzone.expasy.org/
    license: CC BY-NC 4.0
    name: ViralZone
    prefix: FAIRsharing.tppk10
    publications:
    - doi: 10.1093/nar/gks1220
      pubmed_id: 23193299
      title: 'ViralZone: recent updates to the virus knowledge resource.'
    - doi: 10.1093/nar/gkq901
      pubmed_id: 20947564
      title: 'ViralZone: a knowledge resource to understand virus diversity.'
    subjects:
    - Molecular biology
    - Virology
    - Life Science
    - Epidemiology
  go:
    homepage: http://viralzone.expasy.org/
    name: ViralZone
    prefix: VZ
    uri_format: http://viralzone.expasy.org/all_by_protein/$1.html
  integbio:
    description: ViralZone is a web resource for viral genes and families, providing
      detailed molecular and epidemiological information, along with virion and genome
      figures. Each virus or family page gives easy access to UniProtKB/Swiss-Prot
      viral protein entries.
    fairsharing: FAIRsharing.tppk10
    homepage: http://viralzone.expasy.org/
    information_keywords:
    - Sequence
    - Expression
    - Taxonomy
    maintainer: SIB (Swiss Institute of Bioinformatics)
    name: ViralZone
    prefix: nbdc02226
    pubmeds:
    - '20947564'
    - '23193299'
    status: Active
    target_keywords:
    - Genome/Gene
    - Organism
    - Health/Disease
  mappings:
    biocontext: VIRALZONE
    fairsharing: FAIRsharing.tppk10
    go: VZ
    integbio: nbdc02226
    miriam: viralzone
    n2t: viralzone
    prefixcommons: vz
    re3data: r3d100013314
    wikidata.entity: Q15674507
  miriam:
    deprecated: false
    description: ViralZone is a resource bridging textbook knowledge with genomic
      and proteomic sequences. It provides fact sheets on all known virus families/genera
      with easy access to sequence data. A selection of reference strains (RefStrain)
      provides annotated standards to circumvent the exponential increase of virus
      sequences. Moreover ViralZone offers a complete set of detailed and accurate
      virion pictures.
    homepage: http://www.expasy.org/viralzone/
    id: 00000449
    name: ViralZone
    namespaceEmbeddedInLui: false
    pattern: ^\d+$
    prefix: viralzone
    sampleId: '992'
    uri_format: http://viralzone.expasy.org/all_by_protein/$1.html
  n2t:
    description: ViralZone is a resource bridging textbook knowledge with genomic
      and proteomic sequences. It provides fact sheets on all known virus families/genera
      with easy access to sequence data. A selection of reference strains (RefStrain)
      provides annotated standards to circumvent the exponential increase of virus
      sequences. Moreover ViralZone offers a complete set of detailed and accurate
      virion pictures.
    example: '992'
    homepage: http://www.expasy.org/viralzone/
    name: ViralZone at SIB
    namespaceEmbeddedInLui: false
    pattern: ^\d+$
    prefix: viralzone
    uri_format: http://viralzone.expasy.org/all_by_protein/$1.html
  prefix: viralzone
  prefixcommons:
    description: ViralZone is a SIB Swiss Institute of Bioinformatics web-resource
      for all viral genus and families, providing general molecular and epidemiological
      information, along with virion and genome figures
    example: '886'
    homepage: http://viralzone.expasy.org/
    keywords:
    - virus
    name: ViralZone
    pattern: ^\d+$
    prefix: vz
    uri_format: http://viralzone.expasy.org/all_by_protein/$1.html
  providers:
  - code: viralzone.alt1
    description: Alternate view
    example: null
    first_party: null
    homepage: http://viralzone.expasy.org
    name: Viralzone Alt 1.
    publications: null
    status: null
    uri_format: http://viralzone.expasy.org/all_by_protein/$1
  publications:
  - doi: 10.1093/nar/gks1220
    pmc: PMC3531065
    pubmed: '23193299'
    title: 'ViralZone: recent updates to the virus knowledge resource'
    year: 2012
  - doi: 10.1093/nar/gkq901
    pmc: PMC3013774
    pubmed: '20947564'
    title: 'ViralZone: a knowledge resource to understand virus diversity'
    year: 2010
  - doi: 10.1093/nar/gks1220
    pmc: null
    pubmed: null
    title: 'ViralZone: recent updates to the virus knowledge resource.'
    year: null
  - doi: 10.1093/nar/gkq901
    pmc: null
    pubmed: null
    title: 'ViralZone: a knowledge resource to understand virus diversity.'
    year: null
  - doi: 10.1093/nar/gks1220
    pmc: null
    pubmed: null
    title: 'ViralZone: recent updates to the virus knowledge resource.'
    year: null
  - doi: 10.1093/nar/gkq901
    pmc: null
    pubmed: null
    title: 'ViralZone: a knowledge resource to understand virus diversity.'
    year: null
  re3data:
    description: ViralZone is a SIB Swiss Institute of Bioinformatics web-resource
      for all viral genus and families, providing general molecular and epidemiological
      information, along with virion and genome figures. Each virus or family page
      gives an easy access to UniProtKB/Swiss-Prot viral protein entries.
    doi: 10.17616/R31NJMRM
    homepage: https://viralzone.expasy.org/
    name: ViralZone
    prefix: r3d100013314
  synonyms:
  - vz
  uri_format: https://viralzone.expasy.org/$1
  wikidata:
    database: Q15674507
virgen:
  mappings:
    prefixcommons: virgen
  prefix: virgen
  prefixcommons:
    description: VirGen a comprehensive viral genome resource, which organizes the
      ‘sequence space’ of viral genomes in a structured fashion. It has been developed
      with an objective to serve as an annotated and curated database for complete
      viral genome sequences.
    example: AY321118
    homepage: http://bioinfo.ernet.in/virgen/virgen.html
    keywords:
    - genome
    name: VirGen
    pattern: ^A[A-Z]\d+$
    prefix: virgen
virmirdb:
  mappings:
    prefixcommons: virmirdb
  prefix: virmirdb
  prefixcommons:
    description: A database containing predicted viral miRNA candidate hairpins.
    example: '11002'
    homepage: http://alk.ibms.sinica.edu.tw
    keywords:
    - RNA
    - structure
    name: Vir-Mir db
    pattern: ^\d+$
    prefix: virmirdb
    uri_format: http://alk.ibms.sinica.edu.tw/cgi-bin/miRNA/virus.cgi?tax_id=$1
  provides: ncbitaxon
  reviewer:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
viroligo:
  mappings:
    prefixcommons: viroligo
  prefix: viroligo
  prefixcommons:
    description: The VirOligo database (1) is part of an effort to provide methods
      suitable for assessing what viruses are present in samples. Such methods should
      faciliate studies of the spatial and temporal distribution of viruses and their
      diversity at any one time and place.
    example: BM0456
    homepage: http://viroligo.okstate.edu
    keywords:
    - small molecule
    name: VirOligo
    pattern: ^[A-Z]+\d+$
    prefix: viroligo
    uri_format: http://viroligo.okstate.edu/main.php?vid=$1
virsirna:
  biocontext:
    prefix: VIRSIRNA
  mappings:
    biocontext: VIRSIRNA
    miriam: virsirna
    n2t: virsirna
  miriam:
    deprecated: false
    description: The VIRsiRNA database contains details of siRNA/shRNA which target
      viral genome regions. It provides efficacy information where available, as well
      as the siRNA sequence, viral target and subtype, as well as the target genomic
      region.
    homepage: http://crdd.osdd.net/servers/virsirnadb
    id: 00000249
    name: VIRsiRNA
    namespaceEmbeddedInLui: false
    pattern: ^virsi\d+$
    prefix: virsirna
    sampleId: virsi1909
    uri_format: http://crdd.osdd.net/servers/virsirnadb/record.php?details=$1
  n2t:
    description: The VIRsiRNA database contains details of siRNA/shRNA which target
      viral genome regions. It provides efficacy information where available, as well
      as the siRNA sequence, viral target and subtype, as well as the target genomic
      region.
    example: virsi1909
    homepage: http://crdd.osdd.net/servers/virsirnadb
    name: VIRsiRNA at Institute of Microbial Technology
    namespaceEmbeddedInLui: false
    pattern: ^virsi\d+$
    prefix: virsirna
    uri_format: http://crdd.osdd.net/servers/virsirnadb/record.php?details=$1
  prefix: virsirna
virushostdb:
  contact:
    email: ogata@kuicr.kyoto-u.ac.jp
    github: null
    name: Hiroyuki Ogata
    orcid: 0000-0001-6594-377X
  integbio:
    description: Virus-Host DB is a database about the relationships between viruses
      and their hosts. It provides information of the relationships represented in
      the form of pairs of NCBI taxonomy IDs for viruses and their hosts. This database
      covers viruses with complete genomes stored in 1) NCBI/RefSeq and 2) GenBank
      whose accession numbers are listed in EBI Genomes. The host information is collected
      from RefSeq, GenBank (in free text format), UniProt, ViralZone, and manually
      curated with additional information obtained from literatures.
    homepage: http://www.genome.jp/virushostdb
    information_keywords:
    - Interaction/Pathway
    maintainer: Kyoto University Institute for Chemical Research Bioinformatics Center
    name: Virus-Host DB
    prefix: nbdc02395
    pubmeds:
    - '26938550'
    status: Active
    target_keywords:
    - Organism
  mappings:
    integbio: nbdc02395
    prefixcommons: virushostdb
  prefix: virushostdb
  prefixcommons:
    description: Virus-Host DB organizes data about the relationships between viruses
      and their hosts, represented in the form of pairs of NCBI taxonomy IDs for viruses
      and their hosts.  Virus-Host DB covers viruses with complete genomes stored
      in 1) NCBI/RefSeq and 2) GenBank whose accession numbers are listed in EBI Genomes.
      The host information is collected from RefSeq, GenBank (in free text format),
      UniProt, ViralZone, and manually curated with additional information obtained
      by literature surveys.
    example: '438782'
    homepage: https://www.genome.jp/virushostdb/
    keywords:
    - virus
    license: CC BY-NC-SA 4.0
    name: Virus-HostDB
    pattern: ^\d+$
    prefix: virushostdb
    pubmed_ids:
    - '26938550'
    synonyms:
    - virus-hostdb
    uri_format: https://www.genome.jp/virushostdb/$1
  provides: ncbitaxon
  publications:
  - doi: 10.3390/v8030066
    pmc: PMC4810256
    pubmed: '26938550'
    title: Linking Virus Genomes with Host Taxonomy
    year: 2016
  reviewer:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
vita:
  mappings:
    prefixcommons: vita
  name: Virus' miRNA target
  prefix: vita
  prefixcommons:
    description: ViTa is a database which collects virus data from miRBase and ICTV,
      VirGne, VBRC.., etc, including known miRNAs on virus and supporting predicted
      host miRNA targets by miRanda and TargetScan. ViTa also rovide effective annotations,
      including human miRNA expression, virus infected tissues, annotation of virus
      and comparisons.
    example: AB016785
    homepage: http://vita.mbc.nctu.edu.tw/
    keywords:
    - RNA
    - structure
    - gene expression
    name: 'ViTa: virus'' miRNA target'
    pattern: ^[A-Z]+\d+$
    prefix: vita
    uri_format: http://vita.mbc.nctu.edu.tw/search.php?acc=$1
vitro:
  appears_in:
  - fabio
  - foaf
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: Vitro is a full stack framework for building semantic web applications.
    It is not domain specific.
  download_owl: https://raw.githubusercontent.com/vivo-archive/Linked-Data-Indexer/refs/heads/master/src/main/resources/vitro-0.7.owl
  example: descriptionAnnot
  github_request_issue: 1317
  homepage: https://github.com/vivo-project/Vitro
  name: Vitro Application Ontology
  prefix: vitro
  repository: https://github.com/vivo-project/Vitro
  uri_format: http://vitro.mannlib.cornell.edu/ns/vitro/0.7#$1
vivo:
  aberowl:
    description: The VIVO ontology represents researchers in the context of their
      experience, outputs, interests, accomplishments, and associated institutions.
    download_owl: http://aber-owl.net/media/ontologies/VIVO/2/vivo.owl
    homepage: http://sourceforge.net/apps/mediawiki/vivo/index.php?title=Ontology
    name: VIVO Ontology for Researcher Discovery
    prefix: VIVO
    version: version 1.1
  biocontext:
    prefix: VIVO
    uri_format: http://vivoweb.org/ontology/core#$1
  bioportal:
    contact:
      email: sjm222@cornell.edu
      name: Stella Mitchell
    description: The VIVO ontology represents researchers in the context of their
      experience, outputs, interests, accomplishments, and associated institutions.
    homepage: http://vivoweb.org/ontology/core
    name: VIVO Ontology for Researcher Discovery
    prefix: VIVO
    version: version 1.7
  contact:
    email: christian.hauschke@tib.eu
    github: hauschke
    name: Christian Hauschke
    orcid: 0000-0003-2499-7741
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: An ontology about scholarship
  download_owl: https://raw.githubusercontent.com/vivo-ontologies/vivo-ontology/master/vivo.owl
  example: Laboratory
  fairsharing:
    abbreviation: VIVO
    description: The VIVO Ontology provides a set of concepts to represent researchers
      and the full context in which they work. It is used as part of the VIVO project,
      which uses a collection of ontologies to represent scholarship.
    domains:
    - Resource metadata
    - study design
    homepage: https://wiki.lyrasis.org/display/VIVODOC111x/Ontology+Reference
    license: CC-BY-4.0
    name: VIVO Ontology
    prefix: FAIRsharing.6xfgaq
    subjects:
    - Natural Science
  github_request_issue: 1317
  homepage: https://vivoweb.org
  license: unlicense
  lov:
    description: An ontology of academic and research domain, developed in the framework
      of the VIVO project
    homepage: http://www.vivoweb.org/download
    keywords:
    - Academy
    modified: '2014-07-12'
    name: VIVO Core Ontology
    prefix: vivo
    uri_prefix: http://vivoweb.org/ontology/core#$1
  mappings:
    aberowl: VIVO
    biocontext: VIVO
    bioportal: VIVO
    fairsharing: FAIRsharing.6xfgaq
    lov: vivo
    tib: vivo
  name: VIVO Ontology
  prefix: vivo
  repository: https://github.com/vivo-ontologies/vivo-ontology
  tib:
    description: The VIVO Ontology is used to represent the expertise of people engaged
      in the creation, transmission, and preservation of knowledge and creative works.
      The VIVO ontology (hereafter referred to as “the ontology”) represents expertise
      by describing the activities and accomplishments of people in terms of their
      relationships to particular artifacts of the work, resources they use, institutions
      that employ them, and other indicators. The ontology is independent of knowledge
      or creative domain. The ontology supports the identification, evaluation, and
      impact assessment of individual people and groups of people, as well as identification
      and reuse of the works of the people.
    download_owl: https://raw.githubusercontent.com/vivo-ontologies/vivo-ontology/refs/tags/vivo-ontology-1.8.0/vivo.owl
    keywords:
    - TIB
    name: VIVO Core Ontology
    prefix: vivo
    tracker: https://github.com/vivo-ontologies/vivo-ontology/issues
  uri_format: http://vivoweb.org/ontology/core#$1
vmc:
  biolink:
    is_identifiers: false
    is_obo: false
    prefix: VMC
    uri_format: https://github.com/ga4gh/vr-spec/$1
  deprecated: true
  mappings:
    biolink: VMC
  name: Variation Modelling Collaboration
  prefix: vmc
  references:
  - https://docs.google.com/document/d/12E8WbQlvfZWk5NrxwLytmympPby6vsv60RxCeD5wc1E/edit#heading=h.67hbe76b6a4z
  - https://github.com/ga4gh/vr-spec
vmhgene:
  mappings:
    miriam: vmhgene
  miriam:
    deprecated: false
    description: The Virtual Metabolic Human (VMH) is a resource that combines human
      and gut microbiota metabolism with nutrition and disease.
    homepage: https://www.vmh.life/
    id: '00000774'
    name: VMH Gene
    namespaceEmbeddedInLui: false
    pattern: ^[0-9]+\.[0-9]+$
    prefix: vmhgene
    sampleId: '8639.1'
    uri_format: https://www.vmh.life/#gene/$1
  prefix: vmhgene
vmhmetabolite:
  biocontext:
    prefix: VMHMETABOLITE
  mappings:
    biocontext: VMHMETABOLITE
    miriam: vmhmetabolite
    n2t: vmhmetabolite
  miriam:
    deprecated: false
    description: The Virtual Metabolic Human (VMH) is a resource that combines human
      and gut microbiota metabolism with nutrition and disease.
    homepage: https://www.vmh.life/
    id: '00000636'
    name: VMH metabolite
    namespaceEmbeddedInLui: false
    pattern: ^[a-zA-Z0-9_\(\_\)\[\]]+$
    prefix: vmhmetabolite
    sampleId: h2o
    uri_format: https://www.vmh.life/#metabolite/$1
  n2t:
    description: The Virtual Metabolic Human (VMH) is a resource that combines human
      and gut microbiota metabolism with nutrition and disease.
    example: h2o
    homepage: http://vmh.uni.lu
    name: VMH metabolite
    namespaceEmbeddedInLui: false
    pattern: '[a-zA-Z0-9_\(\_\)\[\]]+'
    prefix: vmhmetabolite
    uri_format: http://vmh.uni.lu/#metabolite/$1
  prefix: vmhmetabolite
vmhreaction:
  biocontext:
    prefix: VMHREACTION
  mappings:
    biocontext: VMHREACTION
    miriam: vmhreaction
    n2t: vmhreaction
  miriam:
    deprecated: false
    description: The Virtual Metabolic Human (VMH) is a resource that combines human
      and gut microbiota metabolism with nutrition and disease.
    homepage: https://www.vmh.life/
    id: '00000640'
    name: VMH reaction
    namespaceEmbeddedInLui: false
    pattern: ^[a-zA-Z0-9_\(\_\)\[\]]+$
    prefix: vmhreaction
    sampleId: HEX1
    uri_format: https://www.vmh.life/#reaction/$1
  n2t:
    description: The Virtual Metabolic Human (VMH) is a resource that combines human
      and gut microbiota metabolism with nutrition and disease.
    example: HEX1
    homepage: https://vmh.uni.lu
    name: VMH reaction
    namespaceEmbeddedInLui: false
    pattern: '[a-zA-Z0-9_\(\_\)\[\]]+'
    prefix: vmhreaction
    uri_format: https://vmh.uni.lu/#reaction/$1
  prefix: vmhreaction
vo:
  aberowl:
    description: VO is a biomedical ontology in the domain of vaccine and vaccination.
    download_owl: http://aber-owl.net/media/ontologies/VO/311/vo.owl
    homepage: https://violinet.org/vaccineontology
    name: Vaccine Ontology
    prefix: VO
  biocontext:
    prefix: VO
  bioportal:
    contact:
      email: yongqunh@med.umich.edu
      name: Yongqunh He
    description: A biomedical ontology in the vaccine domain, The Vaccine Ontology
      (VO) is a community-based biomedical ontology in the domain of vaccine and vaccination.
      VO aims to standardize vaccine types and annotations, integrate various vaccine
      data, and support computer-assisted reasoning. The VO supports basic vaccine
      R&D and clinical vaccine usage. VO is being developed as a community-based ontology
      with support and collaborations from the vaccine and bio-ontology communities.
    homepage: https://github.com/vaccineontology/VO
    license: CC-BY-4.0
    name: Vaccine Ontology
    prefix: VO
    version: '2025-11-01'
  example: 0000093
  fairsharing:
    abbreviation: VO
    contact:
      email: yongqunh@med.umich.edu
      name: Yongqunh He
      orcid: 0000-0001-9189-9661
    description: The Vaccine Ontology (VO) was created as part of an international
      community-based effort to represent vaccine knowledge and to support automated
      reasoning. VO describes the detailed classification and definitions of vaccine
      components and vaccine administration processes. To ensure consistent representation
      of vaccine knowledge and to support automated reasoning, a community-based effort
      to develop the Vaccine Ontology (VO) has been initiated. This international
      collaborative VO development effort has been joined by many institutes and disciplines
      around the world. The Vaccine Ontology is also being used in a variety of applications
      by many user groups in academia and industry.
    domains:
    - biological_process
    - infection process
    - vaccine
    - pathogen
    - vaccination
    homepage: https://github.com/vaccineontology/VO
    license: CC-BY-3.0
    logo: https://api.fairsharing.org/rails/active_storage/blobs/redirect/eyJfcmFpbHMiOnsibWVzc2FnZSI6IkJBaHBBaUFDIiwiZXhwIjpudWxsLCJwdXIiOiJibG9iX2lkIn19--0d3898a5618b34c0bc948bb0d101e906f212f05f/vo_banner.png?disposition=inline
    name: The Vaccine Ontology
    prefix: FAIRsharing.zwtww5
    publications:
    - doi: 10.1186/1745-7580-6-s1-s5
      pubmed: '20875156'
      title: Bioinformatics analysis of Brucella vaccines and vaccine targets using
        VIOLIN
      year: 2010
    - doi: 10.1186/2041-1480-3-17
      pubmed: '23256535'
      title: Ontology representation and analysis of vaccine formulation and administration
        and their effects on vaccine immune responses
      year: 2012
    - doi: 10.1186/2041-1480-2-s2-s8
      pubmed: '21624163'
      title: Mining of vaccine-associated IFN-gamma gene interaction networks using
        the Vaccine Ontology
      year: 2011
    - doi: 10.1038/npre.2009.3553
      pubmed: '21871085'
      title: 'VO: Vaccine Ontology'
      year: 2010
    - doi: 10.1186/2041-1480-4-33
      pubmed: '24209834'
      title: Network-based analysis of vaccine-related associations reveals consistent
        knowledge with the vaccine ontology
      year: 2013
    repository: https://github.com/vaccineontology
    subjects:
    - Preclinical Studies
    - Biomedical Science
    - Clinical Studies
    - Immunology
    - Infectious Disease Medicine
    - Pathobiochemistry
  keywords:
  - immunology
  mappings:
    aberowl: VO
    biocontext: VO
    bioportal: VO
    fairsharing: FAIRsharing.zwtww5
    obofoundry: vo
    ols: vo
    ontobee: VO
    prefixcommons: vo
    wikidata: P1928
    wikidata.entity: Q55118646
  obofoundry:
    appears_in:
    - scdo
    contact: yongqunh@med.umich.edu
    contact.github: yongqunh
    contact.label: Yongqunh He
    contact.orcid: 0000-0001-9189-9661
    deprecated: false
    description: VO is a biomedical ontology in the domain of vaccine and vaccination.
    domain: health
    download.owl: http://purl.obolibrary.org/obo/vo.owl
    homepage: https://violinet.org/vaccineontology
    license: CC BY 4.0
    license.url: http://creativecommons.org/licenses/by/4.0/
    name: Vaccine Ontology
    preferredPrefix: VO
    prefix: vo
    publications:
    - id: https://www.ncbi.nlm.nih.gov/pubmed/23256535
      title: Ontology representation and analysis of vaccine formulation and administration
        and their effects on vaccine immune responses
    - id: https://www.ncbi.nlm.nih.gov/pubmed/21624163
      title: Mining of vaccine-associated IFN-γ gene interaction networks using the
        Vaccine Ontology
    repository: https://github.com/vaccineontology/VO
  ols:
    description: The Vaccine Ontology (VO) is a community-based biomedical ontology
      in the domain of vaccine and vaccination. VO aims to standardize vaccine types
      and annotations, integrate various vaccine data, and support computer-assisted
      reasoning. The VO supports basic vaccine R&D and clinical vaccine usage. VO
      is being developed as a community-based ontology with support and collaborations
      from the vaccine and bio-ontology communities.
    download_owl: http://purl.obolibrary.org/obo/vo.owl
    homepage: https://violinet.org/vaccineontology
    name: Vaccine Ontology
    prefix: vo
    tracker: https://github.com/vaccineontology/VO/issues
    version: '2025-12-03'
    version.iri: http://purl.obolibrary.org/obo/vo/releases/2025-12-03/vo.owl
  ontobee:
    library: Library
    name: Vaccine Ontology
    prefix: VO
  pattern: ^\d{7}$
  prefix: vo
  prefixcommons:
    bioportal: '1172'
    description: A biomedical ontology in the vaccine domain
    example: VO_0000811
    homepage: http://www.violinet.org/vaccineontology
    keywords:
    - obo
    - ontology
    - small molecule
    - vaccine
    name: Vaccine ontology
    pattern: ^VO_\d{7}$
    prefix: vo
  publications:
  - doi: 10.2174/1381612826666201125112131
    pmc: null
    pubmed: '33238868'
    title: Ontology-based Precision Vaccinology for Deep Mechanism Understanding and
      Precision Vaccine Development
    year: 2021
  - doi: 10.1186/2041-1480-3-17
    pmc: PMC3639077
    pubmed: '23256535'
    title: Ontology representation and analysis of vaccine formulation and administration
      and their effects on vaccine immune responses
    year: 2012
  - doi: 10.1186/2041-1480-2-s2-s8
    pmc: PMC3102897
    pubmed: '21624163'
    title: Mining of vaccine-associated IFN-γ gene interaction networks using the
      Vaccine Ontology
    year: 2011
  - doi: 10.1186/1745-7580-6-s1-s5
    pmc: PMC2946783
    pubmed: '20875156'
    title: Bioinformatics analysis of Brucella vaccines and vaccine targets using
      VIOLIN
    year: 2010
  - doi: null
    pmc: null
    pubmed: '23256535'
    title: Ontology representation and analysis of vaccine formulation and administration
      and their effects on vaccine immune responses
    year: null
  - doi: null
    pmc: null
    pubmed: '21624163'
    title: Mining of vaccine-associated IFN-γ gene interaction networks using the
      Vaccine Ontology
    year: null
  - doi: 10.1186/1745-7580-6-s1-s5
    pmc: null
    pubmed: '20875156'
    title: Bioinformatics analysis of Brucella vaccines and vaccine targets using
      VIOLIN
    year: 2010
  - doi: 10.1186/2041-1480-3-17
    pmc: null
    pubmed: '23256535'
    title: Ontology representation and analysis of vaccine formulation and administration
      and their effects on vaccine immune responses
    year: 2012
  - doi: 10.1186/2041-1480-2-s2-s8
    pmc: null
    pubmed: '21624163'
    title: Mining of vaccine-associated IFN-gamma gene interaction networks using
      the Vaccine Ontology
    year: 2011
  - doi: 10.1038/npre.2009.3553
    pmc: null
    pubmed: '21871085'
    title: 'VO: Vaccine Ontology'
    year: 2010
  - doi: 10.1186/2041-1480-4-33
    pmc: null
    pubmed: '24209834'
    title: Network-based analysis of vaccine-related associations reveals consistent
      knowledge with the vaccine ontology
    year: 2013
  - doi: null
    pmc: null
    pubmed: '23256535'
    title: Ontology representation and analysis of vaccine formulation and administration
      and their effects on vaccine immune responses
    year: null
  - doi: null
    pmc: null
    pubmed: '21624163'
    title: Mining of vaccine-associated IFN-γ gene interaction networks using the
      Vaccine Ontology
    year: null
  - doi: 10.1186/1745-7580-6-s1-s5
    pmc: null
    pubmed: '20875156'
    title: Bioinformatics analysis of Brucella vaccines and vaccine targets using
      VIOLIN
    year: 2010
  - doi: 10.1186/2041-1480-3-17
    pmc: null
    pubmed: '23256535'
    title: Ontology representation and analysis of vaccine formulation and administration
      and their effects on vaccine immune responses
    year: 2012
  - doi: 10.1186/2041-1480-2-s2-s8
    pmc: null
    pubmed: '21624163'
    title: Mining of vaccine-associated IFN-gamma gene interaction networks using
      the Vaccine Ontology
    year: 2011
  - doi: 10.1038/npre.2009.3553
    pmc: null
    pubmed: '21871085'
    title: 'VO: Vaccine Ontology'
    year: 2010
  - doi: 10.1186/2041-1480-4-33
    pmc: null
    pubmed: '24209834'
    title: Network-based analysis of vaccine-related associations reveals consistent
      knowledge with the vaccine ontology
    year: 2013
  uri_format: http://purl.obolibrary.org/obo/VO_$1
  wikidata:
    description: identifier in the Vaccine Ontology database
    example:
    - VO_0000455
    - VO_0000867
    - VO_0011559
    name: Vaccine Ontology ID
    pattern: ^VO_[0-9]{7}$
    prefix: P1928
voc4cat:
  bartoc:
    description: A vocabulary for all areas of catalysis initiated in NFDI4Cat. Starting
      with photocatalysis we add more and more terms from other areas of catalysis
      and related disciplines like chemical engineering or materials science.
    homepage: https://nfdi4cat.github.io/voc4cat/
    license: CC_MARK
    name: voc4cat
    prefix: '20501'
  comment: The most current version of a concept can be accessed so * https://w3id.org/nfdi4cat/voc4cat_0000123
    other/older versions from releases like so * https://w3id.org/nfdi4cat/voc4cat/v2023-08-17/voc4cat_0000123.
    This is pretty unique and isn't tracked by the Bioregistry currently.
  contact:
    email: nikolaos.moustakas@catalysis.de
    github: nmoust
    name: Nikolaos Moustakas
    orcid: 0000-0002-6242-2167
  contributor:
    email: David.Linke@catalysis.de
    github: dalito
    name: David Linke
    orcid: 0000-0002-5898-1820
  description: Voc4Cat is a [SKOS](https://www.w3.org/TR/2009/REC-skos-reference-20090818/)
    vocabulary for the catalysis disciplines. The vocabulary was created in the [NFDI4Cat](http://www.nfdi4cat.org/)
    initiative. The first collection of terms was published in June 2023 with a focus
    on photo catalysis. Our goal is to continuously extend the vocabulary to other
    areas of catalysis and related disciplines like chemical engineering or materials
    science.
  example: '0000123'
  github_request_issue: 957
  homepage: https://nfdi4cat.github.io/voc4cat/
  license: CC0-1.0
  mappings:
    bartoc: '20501'
    tib: voc4cat
  name: A vocabulary for the catalysis disciplines
  pattern: ^\d{7,}$
  prefix: voc4cat
  repository: https://github.com/nfdi4cat/voc4cat
  reviewer:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  tib:
    description: A vocabulary for all areas of catalysis initiated in NFDI4Cat. Starting
      with photocatalysis we add more and more terms from other areas of catalysis
      and related disciplines like chemical enineering or material science.
    homepage: https://nfdi4cat.github.io/voc4cat/latest/voc4cat/index.html
    keywords:
    - NFDI4CAT
    - NFDI4CHEM
    - FAIRmat
    - chemistry
    name: Voc4Cat - A SKOS vocabulary for Catalysis
    prefix: voc4cat
    tracker: https://github.com/nfdi4cat/voc4cat/issues
    uri_format: https://w3id.org/nfdi4cat/voc4cat_$1
  uri_format: https://w3id.org/nfdi4cat/voc4cat_$1
void:
  biocontext:
    prefix: void
    uri_format: http://rdfs.org/ns/void#$1
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: The Vocabulary of Interlinked Datasets (VoID) is an RDF Schema vocabulary
    for expressing metadata about RDF datasets. It is intended as a bridge between
    the publishers and users of RDF data, with applications ranging from data discovery
    to cataloging and archiving of datasets. This document provides a formal definition
    of the new RDF classes and properties introduced for VoID. It is a companion to
    the main specification document for VoID, Describing Linked Datasets with the
    VoID Vocabulary.
  example: feature
  homepage: http://vocab.deri.ie/void
  lov:
    description: The Vocabulary of Interlinked Datasets (VoID) is an RDF Schema vocabulary
      for expressing metadata about RDF datasets.
    homepage: http://www.w3.org/TR/void/
    keywords:
    - Metadata
    modified: '2011-03-06'
    name: Vocabulary of Interlinked Datasets
    prefix: void
    uri_prefix: http://rdfs.org/ns/void#$1
  mappings:
    biocontext: void
    lov: void
    zazuko: void
  name: Vocabulary of Interlinked Datasets
  preferred_prefix: void
  prefix: void
  uri_format: http://rdfs.org/ns/void#$1
  zazuko:
    prefix: void
    uri_format: http://rdfs.org/ns/void#$1
vs:
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: This vocabulary was created in the FOAF project, based on experience
    with FOAF, Dublin Core and other early RDF vocabularies. Deployment experience
    shows that changing namespace URIs is expensive and unrewarding, so this vocabulary
    provides terms to support in-place evolution of structured data vocabularies.
    By indicating status at the level of terms rather than vocabularies, dictionary-style,
    fine grained improvements become easier. Different organizations and parties can
    agree or disagree on the status of a vocabulary term; however the status published
    alongside the term may deserve special attention. Future work could include patterns
    for citing announcements and decisions, or using SKOS to decentralise the extension
    of the basic status levels. (from artifact)
  download_owl: https://www.w3.org/2003/06/sw-vocab-status/ns
  example: term_status
  github_request_issue: 1677
  homepage: https://www.w3.org/2003/06/sw-vocab-status/ns
  keywords:
  - semantic web
  lov:
    description: An RDF vocabulary for relating SW vocabulary terms to their status.
    homepage: http://www.w3.org/2003/06/sw-vocab-status/ns
    keywords:
    - Metadata
    modified: '2011-12-12'
    name: SemWeb Vocab Status ontology
    prefix: vs
    uri_prefix: http://www.w3.org/2003/06/sw-vocab-status/ns#$1
  mappings:
    lov: vs
    zazuko: vs
  name: SemWeb Vocab Status ontology
  prefix: vs
  rdf_uri_format: http://www.w3.org/2003/06/sw-vocab-status/ns#$1
  uri_format: http://www.w3.org/2003/06/sw-vocab-status/ns#$1
  zazuko:
    prefix: vs
    uri_format: http://www.w3.org/2003/06/sw-vocab-status/ns#$1
vsao:
  aberowl:
    description: VSAO is an anatomy ontology covering the vertebrate skeletal system.
      VSAO integrates terms for skeletal cells, tissues, biological processes, organs
      (skeletal elements such as bones and cartilages), and subdivisions of the skeletal
      system.
    download_obo: http://aber-owl.net/media/ontologies/VSAO/20/vsao.obo
    homepage: http://phenoscape.org/wiki/Main_Page
    name: Vertebrate Skeletal Anatomy Ontology
    prefix: VSAO
    version: '2012-11-06'
  biocontext:
    prefix: VSAO
  bioportal:
    contact:
      email: wasila.dahdul@usd.edu
      name: Wasila Dahdul
    description: VSAO is an anatomy ontology covering the vertebrate skeletal system.
      VSAO integrates terms for skeletal cells, tissues, biological processes, organs
      (skeletal elements such as bones and cartilages), and subdivisions of the skeletal
      system.
    homepage: http://phenoscape.org/wiki/Main_Page
    name: Vertebrate Skeletal Anatomy Ontology
    prefix: VSAO
    publications:
    - http://dx.plos.org/10.1371/journal.pone.0051070
    version: '2012-11-06'
  example: 0000183
  mappings:
    aberowl: VSAO
    biocontext: VSAO
    bioportal: VSAO
    obofoundry: vsao
    ols: vsao
    prefixcommons: vao
    wikidata.entity: Q114677916
  name: Vertebrate Skeletal Anatomy Ontology
  obofoundry:
    contact: wasila.dahdul@usd.edu
    contact.label: Wasila Dahdul
    contact.orcid: 0000-0003-3162-7490
    deprecated: true
    description: Vertebrate skeletal anatomy ontology.
    domain: anatomy and development
    download.owl: http://purl.obolibrary.org/obo/vsao.owl
    homepage: https://www.nescent.org/phenoscape/Main_Page
    name: Vertebrate Skeletal Anatomy Ontology-
    prefix: vsao
  ols:
    description: Vertebrate skeletal anatomy ontology.
    homepage: https://www.nescent.org/phenoscape/Main_Page
    name: Vertebrate Skeletal Anatomy Ontology-
    prefix: vsao
    version: '2012-11-06'
    version.iri: http://purl.obolibrary.org/obo/vsao/2012-11-06/vsao.owl
  pattern: ^\d{7}$
  prefix: vsao
  prefixcommons:
    bioportal: '1555'
    description: Vertebrate anatomy ontology. Currently covers the skeletal system
    example: VSAO_0000183
    homepage: https://www.nescent.org/phenoscape/Main_Page
    keywords:
    - obo
    - anatomy
    - vertebrate
    name: Vertebrate Anatomy Ontology
    pattern: ^VSA_\d{7}$
    prefix: vao
    synonyms:
    - vsao
  synonyms:
  - VSAO_RETIRED
vsdb:
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: Veterinary pharmaceuticals are biologically active and potentially
    persistent substances which are recognised as a continuing threat to environmental
    quality. Whilst the environmental risk of agricultural pesticides has had considerable
    attention in recent decades, risks assessments for veterinary pharmaceuticals
    have only relatively recently began to be addressed. Risk assessments and risk
    modelling tend to be inherently data hungry processes and one of the main obstacles
    to consistent, accurate and efficient assessments is the need for a reliable,
    quality and comprehensive data source.
  example: '1868'
  homepage: https://sitem.herts.ac.uk/aeru/vsdb
  name: Veterinary Substances DataBase
  pattern: ^\d+$
  prefix: vsdb
  uri_format: https://sitem.herts.ac.uk/aeru/vsdb/Reports/$1.htm
vsmo:
  contact:
    email: lars.eisen@colostate.edu
    github: null
    name: Lars Eisen
    orcid: 0000-0002-0094-3186
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: an ontology for vector surveillance and management, focusing on arthropod
    vectors and vector-borne pathogens with relevance to humans or domestic animals,
    and with special emphasis on content to support operational activities through
    inclusion in databases, data management systems, or decision support systems.
  download_json: https://raw.githubusercontent.com/cthoyt/vsmo/main/vsmo.json
  download_obo: https://raw.githubusercontent.com/cthoyt/vsmo/main/vsmo.obo
  download_owl: https://raw.githubusercontent.com/cthoyt/vsmo/main/vsmo.owl
  example: '0000000'
  homepage: https://code.google.com/archive/p/vector-surveillance-and-management-ontology/
  license: New BSD License
  name: Ontology for vector surveillance and management
  prefix: vsmo
  publications:
  - doi: 10.1603/me12169
    pmc: PMC3695545
    pubmed: '23427646'
    title: Ontology for vector surveillance and management
    year: 2013
  uri_format: http://purl.obolibrary.org/obo/VSMO_$1
vso:
  aberowl:
    description: 'The Vital Sign Ontology (VSO) is an extension of the Ontology for
      General Medical Science (OGMS). VSO covers the four consensus human vital signs:
      blood pressure, body temperature, respiration rate, pulse rate. VSO provides
      also a controlled structured vocabulary for describing vital signs measurement
      data, the various processes of measuring vital signs, and the various devices
      and anatomical entities participating in such measurements.'
    download_owl: http://aber-owl.net/media/ontologies/VSO/1/vso.owl
    homepage: http://code.google.com/p/vital-sign-ontology/
    name: Vital Sign Ontology
    prefix: VSO
    version: '2012-04-25'
  bartoc:
    abbreviation: vso
    description: The Vehicle Sales Ontology is a Web vocabulary for describings cars,
      boats, bikes, and other vehicles for e-commerce. The vocabulary is designed
      to be used in combination with GoodRelations, a standard vocabulary for the
      commercial aspects of offers for sale, rental, repair, or disposal. GoodRelations
      is a language (also known as "schema", "data dictionary", or "ontology") for
      product, price, and company data that can (1) be embedded into existing static
      and dynamic Web pages and that (2) can be processed by other computers. This
      increases the visibility of your products and services in the latest generation
      of search engines, recommender systems, and other novel applications.
    homepage: http://purl.org/vso/ns
    license: CC-BY-3.0
    name: Vehicle Sales Ontology
    prefix: '18355'
  bioportal:
    contact:
      email: albertgoldfain@gmail.com
      name: Albert Goldfain
    description: 'The Vital Sign Ontology (VSO) is an extension of the Ontology for
      General Medical Science (OGMS). VSO covers the four consensus human vital signs:
      blood pressure, body temperature, respiration rate, pulse rate. VSO provides
      also a controlled structured vocabulary for describing vital signs measurement
      data, the various processes of measuring vital signs, and the various devices
      and anatomical entities participating in such measurements.'
    homepage: http://code.google.com/p/vital-sign-ontology/
    name: Vital Sign Ontology
    prefix: VSO
    publications:
    - http://ontology.buffalo.edu/smith/articles/Vital_Sign_Ontology.pdf
    version: '2012-04-25'
  description: 'The Vital Sign Ontology (VSO) is an extension of the Ontology for
    General Medical Science (OGMS). VSO covers the four consensus human vital signs:
    blood pressure, body temperature, respiration rate, pulse rate. VSO provides also
    a controlled structured vocabulary for describing vital signs measurement data,
    the various processes of measuring vital signs, and the various devices and anatomical
    entities participating in such measurements.'
  example: '0000041'
  fairsharing:
    abbreviation: VSO
    description: 'The Vital Sign Ontology (VSO) is an extension of the Ontology for
      General Medical Science (OGMS). VSO covers the four consensus human vital signs:
      blood pressure, body temperature, respiration rate, pulse rate. VSO provides
      also a controlled structured vocabulary for describing vital signs measurement
      data, the various processes of measuring vital signs, and the various devices
      and anatomical entities participating in such measurements.'
    domains:
    - Experimental measurement
    - blood
    homepage: https://code.google.com/p/vital-sign-ontology/
    name: Vital Sign Ontology
    prefix: FAIRsharing.jjb2p2
    subjects:
    - Biomedical Science
    - Health Science
  homepage: https://bioportal.bioontology.org/ontologies/VSO
  mappings:
    aberowl: VSO
    bartoc: '18355'
    bioportal: VSO
    fairsharing: FAIRsharing.jjb2p2
    prefixcommons: vso
    zazuko: vso
  pattern: ^\d{7}$
  prefix: vso
  prefixcommons:
    bioportal: '3124'
    description: 'The Vital Sign Ontology (VSO) covers the four consensus human vital
      signs: blood pressure, body temperature, respiration rate, pulse rate.  VSO
      provides also a controlled structured vocabulary for describing vital signs
      measurement data, the various processes of measuring vital signs, and the various
      devices and anatomical entities participating in such measurements.'
    example: VSO_0000015
    homepage: http://code.google.com/p/vital-sign-ontology/
    keywords:
    - owl
    - health
    name: Vital Sign Ontology
    pattern: ^VSO_\d{7}$
    prefix: vso
  uri_format: https://bioportal.bioontology.org/ontologies/VSO/?p=classes&conceptid=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FVSO_$1
  zazuko:
    prefix: vso
    uri_format: http://purl.org/vso/ns#$1
vssocore:
  example: VehicleProperty
  mappings:
    tib: vssocore
  name: Vehicle Signal Specification Core Ontology
  prefix: vssocore
  tib:
    description: This ontology describes the car's attributes, branches and signals
      defined in the Vehicle Signal Specification.
    download_rdf: https://raw.githubusercontent.com/w3c/vsso/gh-pages/spec/vsso-core.ttl
    homepage: https://www.w3.org/TR/2022/WD-vsso-core-20220303/
    keywords:
    - NFDI4ING
    - FID move
    - traffic engineering
    name: 'VSSo Core: Vehicle Signal Specification Core Ontology. W3C First Public
      Working Draft 03 March 2022'
    prefix: vssocore
    tracker: https://github.com/w3c/vsso/issues
    uri_format: https://github.com/w3c/vsso-core#$1
vt:
  aberowl:
    description: An ontology of traits covering vertebrates
    download_owl: http://aber-owl.net/media/ontologies/VT/141/vt.owl
    homepage: https://github.com/AnimalGenome/vertebrate-trait-ontology
    name: Vertebrate trait ontology
    prefix: VT
  agroportal:
    contact:
      email: jreecy@iastate.edu
      name: Jim Reecy
    description: The Vertebrate Trait Ontology is a controlled vocabulary for the
      description of traits (measurable or observable characteristics) pertaining
      to the morphology, physiology, or development of vertebrate organisms.
    example_uri: http://purl.obolibrary.org/obo/VT_1000047
    homepage: https://www.animalgenome.org/bioinfo/projects/vt/
    license: CC-BY-4.0
    name: Vertebrate Trait Ontology
    prefix: VT
    repository: https://github.com/AnimalGenome/vertebrate-trait-ontology
    version: '2025-02-11'
  biocontext:
    prefix: VT
  bioportal:
    contact:
      email: caripark@iastate.edu
      name: Cari Park
    description: The Vertebrate Trait Ontology is a controlled vocabulary for the
      description of traits (measurable or observable characteristics) pertaining
      to the morphology, physiology, or development of vertebrate organisms.
    license: CC-BY-4.0
    name: Vertebrate Trait Ontology
    prefix: VT
    publications:
    - https://www.animalgenome.org/bioinfo/projects/vt/
    version: '2025-11-25'
  download_obo: https://github.com/AnimalGenome/vertebrate-trait-ontology/raw/master/current_release/vt.obo
  example: 0000685
  fairsharing:
    abbreviation: VT
    description: The Vertebrate Trait Ontology is a controlled vocabulary for the
      description of traits (measurable or observable characteristics) pertaining
      to the morphology, physiology, or development of vertebrate organisms.
    domains:
    - phenotype
    - morphology
    homepage: https://github.com/AnimalGenome/vertebrate-trait-ontology
    license: CC-BY-4.0
    name: Vertebrate Trait Ontology
    prefix: FAIRsharing.10gr18
    publications:
    - doi: 10.1186/2041-1480-4-13
      pubmed: '23937709'
      title: 'The Vertebrate Trait Ontology: a controlled vocabulary for the annotation
        of trait data across species'
      year: 2013
    repository: https://github.com/AnimalGenome/vertebrate-trait-ontology/issues
    subjects:
    - Animal Physiology
    - Physiology
    - Biology
    - Developmental Biology
  mappings:
    aberowl: VT
    agroportal: VT
    biocontext: VT
    bioportal: VT
    fairsharing: FAIRsharing.10gr18
    obofoundry: vt
    ols: vt
    ontobee: VT
    prefixcommons: vt
    wikidata.entity: Q81661831
  obofoundry:
    appears_in:
    - scdo
    contact: caripark@iastate.edu
    contact.github: caripark
    contact.label: Carissa Park
    contact.orcid: 0000-0002-2346-5201
    deprecated: false
    description: An ontology of traits covering vertebrates
    domain: phenotype
    download.owl: http://purl.obolibrary.org/obo/vt.owl
    homepage: https://github.com/AnimalGenome/vertebrate-trait-ontology
    license: CC BY 4.0
    license.url: https://creativecommons.org/licenses/by/4.0/
    name: Vertebrate trait ontology
    preferredPrefix: VT
    prefix: vt
    repository: https://github.com/AnimalGenome/vertebrate-trait-ontology
  ols:
    description: The Vertebrate Trait Ontology is a controlled vocabulary for the
      description of traits (measurable or observable characteristics) pertaining
      to the morphology, physiology, or development of vertebrate organisms.
    download_owl: http://purl.obolibrary.org/obo/vt.owl
    homepage: https://github.com/AnimalGenome/vertebrate-trait-ontology
    name: The Vertebrate Trait Ontology
    prefix: vt
    tracker: https://github.com/AnimalGenome/vertebrate-trait-ontology/issues
    version: '2025-12-02'
    version.iri: http://purl.obolibrary.org/obo/vt/releases/2025-12-02/vt.owl
  ontobee:
    library: Library
    name: Vertebrate trait ontology
    prefix: VT
  pattern: ^\d{7}$
  prefix: vt
  prefixcommons:
    bioportal: '1659'
    description: The Vertebrate Trait Ontology is a controlled vocabulary for the
      description of traits (measurable or observable characteristics) pertaining
      to the morphology, physiology, or development of vertebrate organisms.
    example: VT_0015074
    keywords:
    - obo
    - vertebrate
    - trait
    name: Vertebrate Trait Ontology
    pattern: ^VT_\d{7}$
    prefix: vt
  publications:
  - doi: 10.1186/2041-1480-4-13
    pmc: PMC3851175
    pubmed: '23937709'
    title: 'The Vertebrate Trait Ontology: a controlled vocabulary for the annotation
      of trait data across species'
    year: 2013
  - doi: 10.1186/2041-1480-4-13
    pmc: null
    pubmed: '23937709'
    title: 'The Vertebrate Trait Ontology: a controlled vocabulary for the annotation
      of trait data across species'
    year: 2013
  - doi: 10.1186/2041-1480-4-13
    pmc: null
    pubmed: '23937709'
    title: 'The Vertebrate Trait Ontology: a controlled vocabulary for the annotation
      of trait data across species'
    year: 2013
  uri_format: http://purl.obolibrary.org/obo/VT_$1
vto:
  aberowl:
    description: Comprehensive hierarchy of extinct and extant vertebrate taxa.
    download_owl: http://aber-owl.net/media/ontologies/VTO/15/vto.owl
    homepage: https://github.com/phenoscape/vertebrate-taxonomy-ontology
    name: Vertebrate Taxonomy Ontology
    prefix: VTO
  biocontext:
    prefix: VTO
  bioportal:
    contact:
      email: balhoff@renci.org
      name: James Balhoff
    description: The Vertebrate Taxonomy Ontology includes both extinct and extant
      vertebrates, aiming to provide one comprehensive hierarchy. The hierarchy backbone
      for extant taxa is based on the NCBI taxonomy. Since the NCBI taxonomy only
      includes species associated with archived genetic data, to complement this,
      we also incorporate taxonomic information across the vertebrates from the Paleobiology
      Database (PaleoDB). The Teleost Taxonomy Ontology (TTO) and AmphibiaWeb (AWeb)
      are incorporated to provide a more authoritative hierarchy and a richer set
      of names for specific taxonomic groups.
    homepage: http://code.google.com/p/vertebrate-taxonomy-ontology/
    name: Vertebrate Taxonomy Ontology
    prefix: VTO
    version: unknown
  example: '9008500'
  fairsharing:
    abbreviation: VTO
    description: The Vertebrate Taxonomy Ontology includes both extinct and extant
      vertebrates, aiming to provide one comprehensive hierarchy. The hierarchy backbone
      for extant taxa is based on the NCBI taxonomy. Since the NCBI taxonomy only
      includes species associated with archived genetic data, to complement this,
      we also incorporate taxonomic information across the vertebrates from the Paleobiology
      Database (PaleoDB). The Teleost Taxonomy Ontology (TTO) and AmphibiaWeb (AWeb)
      are incorporated to provide a more authoritative hierarchy and a richer set
      of names for specific taxonomic groups.
    domains:
    - bone element
    homepage: https://gitlab.com/phenoscape/vto
    name: Vertebrate Taxonomy Ontology
    prefix: FAIRsharing.akmeb9
    publications:
    - doi: 10.1186/2041-1480-4-34
      pubmed: '24267744'
      title: 'The vertebrate taxonomy ontology: a framework for reasoning across model
        organism and species phenotypes'
      year: 2013
    repository: https://github.com/phenoscape/vertebrate-taxonomy-ontology
    subjects:
    - Taxonomy
  mappings:
    aberowl: VTO
    biocontext: VTO
    bioportal: VTO
    fairsharing: FAIRsharing.akmeb9
    obofoundry: vto
    ols: vto
    ontobee: VTO
    wikidata.entity: Q81661832
  obofoundry:
    contact: balhoff@renci.org
    contact.github: balhoff
    contact.label: Jim Balhoff
    contact.orcid: 0000-0002-8688-6599
    deprecated: false
    description: Comprehensive hierarchy of extinct and extant vertebrate taxa.
    domain: organisms
    download.obo: http://purl.obolibrary.org/obo/vto.obo
    download.owl: http://purl.obolibrary.org/obo/vto.owl
    homepage: https://github.com/phenoscape/vertebrate-taxonomy-ontology
    license: CC0 1.0
    license.url: http://creativecommons.org/publicdomain/zero/1.0/
    name: Vertebrate Taxonomy Ontology
    preferredPrefix: VTO
    prefix: vto
    publications:
    - id: https://doi.org/10.1186/2041-1480-4-34
      title: 'The vertebrate taxonomy ontology: a framework for reasoning across model
        organism and species phenotypes'
    repository: https://github.com/phenoscape/vertebrate-taxonomy-ontology
  ols:
    description: Comprehensive hierarchy of extinct and extant vertebrate taxa.
    download_owl: http://purl.obolibrary.org/obo/vto.owl
    homepage: https://github.com/phenoscape/vertebrate-taxonomy-ontology
    name: Vertebrate Taxonomy Ontology
    prefix: vto
    tracker: https://github.com/phenoscape/vertebrate-taxonomy-ontology/issues
    version: '2020-11-13'
    version.iri: http://purl.obolibrary.org/obo/vto/2020-11-13/vto.owl
  ontobee:
    library: Library
    name: Vertebrate Taxonomy Ontology
    prefix: VTO
  pattern: ^\d{7}$
  prefix: vto
  publications:
  - doi: 10.1186/2041-1480-4-34
    pmc: PMC4177199
    pubmed: '24267744'
    title: 'The vertebrate taxonomy ontology: a framework for reasoning across model
      organism and species phenotypes'
    year: 2013
  - doi: 10.1186/2041-1480-4-34
    pmc: null
    pubmed: null
    title: 'The vertebrate taxonomy ontology: a framework for reasoning across model
      organism and species phenotypes'
    year: null
  - doi: 10.1186/2041-1480-4-34
    pmc: null
    pubmed: '24267744'
    title: 'The vertebrate taxonomy ontology: a framework for reasoning across model
      organism and species phenotypes'
    year: 2013
  uri_format: http://purl.obolibrary.org/obo/VTO_$1
vuid:
  comment: The example corresponds to acetaminophen
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: The Veterans Health Administration is America’s largest integrated
    health care system, providing care at 1,293 health care facilities, including
    171 medical centers and 1,112 outpatient sites of care of varying complexity (VHA
    outpatient clinics), serving 9 million enrolled Veterans each year.
  example: '4007166'
  homepage: https://www.va.gov/health
  name: Veterans Health Administration (VHA) unique identifier
  pattern: ^\d+$
  prefix: vuid
  references:
  - https://academic.oup.com/jamia/article/17/4/432/866953
wb.rnai:
  biocontext:
    prefix: WB.RNAI
  mappings:
    biocontext: WB.RNAI
    miriam: wb.rnai
    n2t: wb.rnai
  miriam:
    deprecated: false
    description: WormBase is an online bioinformatics database of the biology and
      genome of the model organism Caenorhabditis elegans and related nematodes. It
      is used by the C. elegans research community both as an information resource
      and as a mode to publish and distribute their results. This collection references
      RNAi experiments, detailing target and phenotypes.
    homepage: https://www.wormbase.org/
    id: '00000466'
    name: WormBase RNAi
    namespaceEmbeddedInLui: false
    pattern: ^WBRNAi\d{8}$
    prefix: wb.rnai
    sampleId: WBRNAi00086878
    uri_format: https://www.wormbase.org/species/c_elegans/rnai/$1
  n2t:
    description: WormBase is an online bioinformatics database of the biology and
      genome of the model organism Caenorhabditis elegans and related nematodes. It
      is used by the C. elegans research community both as an information resource
      and as a mode to publish and distribute their results. This collection references
      RNAi experiments, detailing target and phenotypes.
    example: WBRNAi00086878
    homepage: https://www.wormbase.org/
    name: WormBase RNAi
    namespaceEmbeddedInLui: false
    pattern: ^WBRNAi\d{8}$
    prefix: wb.rnai
    uri_format: https://www.wormbase.org/species/c_elegans/rnai/$1
  prefix: wb.rnai
wbbt:
  aberowl:
    description: A structured controlled vocabulary of the anatomy of <i>Caenorhabditis
      elegans</i>.
    download_owl: http://aber-owl.net/media/ontologies/WBBT/32/wbbt.owl
    homepage: https://github.com/obophenotype/c-elegans-gross-anatomy-ontology
    name: C. elegans Gross Anatomy Ontology
    prefix: WBBT
  biocontext:
    prefix: WBbt
  biolink:
    is_identifiers: false
    is_obo: true
    prefix: WBbt
    uri_format: http://purl.obolibrary.org/obo/WBbt_$1
  bioportal:
    contact:
      email: raymond@caltech.edu
      name: Raymond Lee
    description: A structured controlled vocabulary of the anatomy of <i>Caenorhabditis
      elegans</i>.
    homepage: http://www.wormbase.org/
    name: C. elegans Gross Anatomy Vocabulary
    prefix: WB-BT
    version: releases/2025-03-26
  example: 0001290
  fairsharing:
    abbreviation: WB-BT
    contact:
      email: raymond@caltech.edu
      name: Raymond Lee
      orcid: 0000-0002-8151-7479
    description: A structured controlled vocabulary of the anatomy of Caenorhabditis
      elegans.
    domains:
    - cell
    homepage: https://www.wormbase.org/tools/ontology_browser
    name: C. elegans gross anatomy
    prefix: FAIRsharing.phk7dd
    publications:
    - doi: 10.1002/cfg.248
      pubmed: '18629098'
      title: Building a cell and anatomy ontology of Caenorhabditis elegans
      year: 2008
    subjects:
    - Life Science
    - Anatomy
  go:
    homepage: http://www.wormbase.org/
    name: C. elegans gross anatomy
    prefix: WBbt
  mappings:
    aberowl: WBBT
    biocontext: WBbt
    biolink: WBbt
    bioportal: WB-BT
    fairsharing: FAIRsharing.phk7dd
    go: WBbt
    obofoundry: wbbt
    ols: wbbt
    ontobee: WBbt
    prefixcommons: wbbt
    wikidata.entity: Q81661834
  obofoundry:
    contact: raymond@caltech.edu
    contact.github: raymond91125
    contact.label: Raymond Lee
    contact.orcid: 0000-0002-8151-7479
    deprecated: false
    description: A structured controlled vocabulary of the anatomy of <i>Caenorhabditis
      elegans</i>.
    domain: anatomy and development
    download.obo: http://purl.obolibrary.org/obo/wbbt.obo
    download.owl: http://purl.obolibrary.org/obo/wbbt.owl
    homepage: https://github.com/obophenotype/c-elegans-gross-anatomy-ontology
    license: CC BY 4.0
    license.url: https://creativecommons.org/licenses/by/4.0/
    name: C. elegans Gross Anatomy Ontology
    preferredPrefix: WBbt
    prefix: wbbt
    publications:
    - id: https://www.ncbi.nlm.nih.gov/pubmed/18629098
      title: Building a cell and anatomy ontology of Caenorhabditis elegans
    repository: https://github.com/obophenotype/c-elegans-gross-anatomy-ontology
  ols:
    description: Ontology about the gross anatomy of the C. elegans
    download_owl: http://purl.obolibrary.org/obo/wbbt.owl
    homepage: https://github.com/obophenotype/c-elegans-gross-anatomy-ontology
    name: C. elegans Gross Anatomy Ontology
    prefix: wbbt
    tracker: https://github.com/obophenotype/c-elegans-gross-anatomy-ontology/issues
    version: '2025-08-19'
    version.iri: http://purl.obolibrary.org/obo/wbbt/releases/2025-08-19/wbbt.owl
  ontobee:
    library: Library
    name: C. elegans Gross Anatomy Ontology
    prefix: WBbt
  pattern: ^\d{7}$
  prefix: wbbt
  prefixcommons:
    bioportal: '1048'
    description: A structured controlled vocabulary of the anatomy of <i>Caenorhabditis
      elegans</i>.
    example: WBbt_0005733
    homepage: http://www.wormbase.org/
    keywords:
    - obo
    - anatomy
    - worm
    name: C. elegans gross anatomy
    pattern: ^WBbt_\d{7}$
    prefix: wbbt
    synonyms:
    - worm_anatomy
    uri_format: http://wormbase.org/db/ontology/anatomy?name=$1
  publications:
  - doi: 10.1002/cfg.248
    pmc: PMC2447384
    pubmed: '18629098'
    title: Building a cell and anatomy ontology of Caenorhabditis elegans
    year: 2003
  synonyms:
  - WBbt
  uri_format: http://purl.obolibrary.org/obo/WBbt_$1
wbls:
  aberowl:
    description: A structured controlled vocabulary of the development of <i>Caenorhabditis
      elegans</i>.
    download_owl: http://aber-owl.net/media/ontologies/WBLS/37/wbls.owl
    homepage: https://github.com/obophenotype/c-elegans-development-ontology
    name: C. elegans development ontology
    prefix: WBLS
  biocontext:
    prefix: WBLS
  biolink:
    is_identifiers: false
    is_obo: true
    prefix: WBls
    uri_format: http://purl.obolibrary.org/obo/WBls_$1
  bioportal:
    contact:
      email: wchen@its.caltech.edu
      name: Worm_development Administrators
    description: A structured controlled vocabulary of the development of <i>Caenorhabditis
      elegans</i>.
    homepage: http://www.wormbase.org/
    name: C. elegans Development Vocabulary
    prefix: WB-LS
    version: unknown
  example: 0000690
  fairsharing:
    abbreviation: WBLS
    description: A structured controlled vocabulary of the development of Caenorhabditis
      elegans. This resource is also referred to as the Life Stage ontology on the
      wormbase database.
    domains:
    - life cycle
    - life cycle stage
    homepage: https://www.wormbase.org/tools/ontology_browser
    name: WormBase Life Stage ontology
    prefix: FAIRsharing.sm90nh
    repository: https://github.com/obophenotype/c-elegans-development-ontology
    subjects:
    - Life Science
    - Developmental Biology
  go:
    homepage: http://www.wormbase.org/
    name: C. elegans development
    prefix: WBls
  mappings:
    aberowl: WBLS
    biocontext: WBLS
    biolink: WBls
    bioportal: WB-LS
    fairsharing: FAIRsharing.sm90nh
    go: WBls
    obofoundry: wbls
    ols: wbls
    ontobee: WBls
    prefixcommons: wbls
    wikidata.entity: Q81661837
  obofoundry:
    contact: cgrove@caltech.edu
    contact.github: chris-grove
    contact.label: Chris Grove
    contact.orcid: 0000-0001-9076-6015
    deprecated: false
    description: A structured controlled vocabulary of the development of <i>Caenorhabditis
      elegans</i>.
    domain: anatomy and development
    download.obo: http://purl.obolibrary.org/obo/wbls.obo
    download.owl: http://purl.obolibrary.org/obo/wbls.owl
    homepage: https://github.com/obophenotype/c-elegans-development-ontology
    license: CC BY 4.0
    license.url: https://creativecommons.org/licenses/by/4.0/
    name: C. elegans development ontology
    preferredPrefix: WBls
    prefix: wbls
    publications:
    - id: https://www.ncbi.nlm.nih.gov/pubmed/31642470
      title: 'WormBase: a modern Model Organism Information Resource'
    repository: https://github.com/obophenotype/c-elegans-development-ontology
  ols:
    description: Ontology about the development and life stages of the C. elegans
    download_owl: http://purl.obolibrary.org/obo/wbls.owl
    homepage: https://github.com/obophenotype/c-elegans-development-ontology
    name: C. elegans Development Ontology
    prefix: wbls
    tracker: https://github.com/obophenotype/c-elegans-development-ontology/issues
    version: '2025-08-12'
    version.iri: http://purl.obolibrary.org/obo/wbls/releases/2025-08-12/wbls.owl
  ontobee:
    library: Library
    name: C. elegans development ontology
    prefix: WBls
  pattern: ^\d{7}$
  prefix: wbls
  prefixcommons:
    bioportal: '1049'
    description: A structured controlled vocabulary of the development of <i>Caenorhabditis
      elegans</i>.
    example: WBls_0000003
    homepage: http://www.wormbase.org/
    keywords:
    - obo
    - development
    - worm
    name: C. elegans development
    pattern: ^WBIs_\d{7}$
    prefix: wbls
    synonyms:
    - worm_development
  publications:
  - doi: 10.1093/nar/gkz920
    pmc: PMC7145598
    pubmed: '31642470'
    title: 'WormBase: a modern Model Organism Information Resource'
    year: 2020
  synonyms:
  - WBls
  uri_format: http://purl.obolibrary.org/obo/WBls_$1
wbphenotype:
  aberowl:
    description: A structured controlled vocabulary of <i>Caenorhabditis elegans</i>
      phenotypes
    download_owl: http://aber-owl.net/media/ontologies/WBPHENOTYPE/84/wbphenotype.owl
    homepage: https://github.com/obophenotype/c-elegans-phenotype-ontology
    name: C. elegans phenotype
    prefix: WBPHENOTYPE
  biocontext:
    prefix: WBPhenotype
  bioportal:
    contact:
      email: cgrove@caltech.edu
      name: Chris Grove
    description: A structured controlled vocabulary of <i>Caenorhabditis elegans</i>
      phenotypes
    homepage: http://www.wormbase.org/
    name: C. elegans Phenotype Vocabulary
    prefix: WB-PHENOTYPE
    version: '2025-08-12'
  example: 0000983
  fairsharing:
    abbreviation: WBPHENOTYPE
    contact:
      email: garys@caltech.edu
      name: Gary Schindelman
      orcid: 0000-0001-7883-4388
    description: An ontology for phenotypes pertaining to the nematode Caenorhabditis
      elegans (C. elegans) and related nematodes used by the nematode genome database
      WormBase.
    domains:
    - Data analysis
    - phenotype
    homepage: https://github.com/obophenotype/c-elegans-phenotype-ontology
    license: CC-BY-4.0
    name: C. elegans phenotype
    prefix: FAIRsharing.agvc7y
    publications:
    - doi: 10.1186/1471-2105-12-32
      pubmed: '21261995'
      title: 'Worm Phenotype Ontology: integrating phenotype data within and beyond
        the C. elegans community'
      year: 2011
    repository: https://github.com/obophenotype/c-elegans-phenotype-ontology/issues
    subjects:
    - Life Science
    - Anatomy
    - Phenomics
    - Omics
  go:
    homepage: http://www.wormbase.org/
    name: WormBase phenotype ontology
    prefix: WBPhenotype
  mappings:
    aberowl: WBPHENOTYPE
    biocontext: WBPhenotype
    bioportal: WB-PHENOTYPE
    fairsharing: FAIRsharing.agvc7y
    go: WBPhenotype
    obofoundry: wbphenotype
    ols: wbphenotype
    ontobee: WBPhenotype
    prefixcommons: wbphenotype
    wikidata.entity: Q81660503
  obofoundry:
    contact: cgrove@caltech.edu
    contact.github: chris-grove
    contact.label: Chris Grove
    contact.orcid: 0000-0001-9076-6015
    deprecated: false
    description: A structured controlled vocabulary of <i>Caenorhabditis elegans</i>
      phenotypes
    domain: phenotype
    download.obo: http://purl.obolibrary.org/obo/wbphenotype.obo
    download.owl: http://purl.obolibrary.org/obo/wbphenotype.owl
    homepage: https://github.com/obophenotype/c-elegans-phenotype-ontology
    license: CC BY 4.0
    license.url: http://creativecommons.org/licenses/by/4.0/
    name: C. elegans phenotype
    preferredPrefix: WBPhenotype
    prefix: wbphenotype
    publications:
    - id: https://www.ncbi.nlm.nih.gov/pubmed/21261995
      title: 'Worm Phenotype Ontology: integrating phenotype data within and beyond
        the C. elegans community.'
    repository: https://github.com/obophenotype/c-elegans-phenotype-ontology
  ols:
    description: Ontology about C. elegans and other nematode phenotypes
    download_owl: http://purl.obolibrary.org/obo/wbphenotype.owl
    homepage: https://github.com/obophenotype/c-elegans-phenotype-ontology
    name: C elegans Phenotype Ontology
    prefix: wbphenotype
    tracker: https://github.com/obophenotype/c-elegans-phenotype-ontology/issues
    version: '2025-08-12'
    version.iri: http://purl.obolibrary.org/obo/wbphenotype/releases/2025-08-12/wbphenotype.owl
  ontobee:
    library: Library
    name: C. elegans phenotype
    prefix: WBPhenotype
  pattern: ^\d{7}$
  prefix: wbphenotype
  prefixcommons:
    bioportal: '1067'
    description: A structured controlled vocabulary of <i>Caenorhabditis elegans</i>
      phenotypes
    example: WBPhenotype_0000517
    homepage: http://www.wormbase.org/
    keywords:
    - obo
    - phenotype
    - worm
    name: C. elegans phenotype
    pattern: ^WBPhenotype_\d{7}$
    prefix: wbphenotype
    synonyms:
    - worm_phenotype
  publications:
  - doi: 10.1186/1471-2105-12-32
    pmc: PMC3039574
    pubmed: '21261995'
    title: 'Worm Phenotype Ontology: integrating phenotype data within and beyond
      the C. elegans community'
    year: 2011
  - doi: null
    pmc: null
    pubmed: '21261995'
    title: 'Worm Phenotype Ontology: integrating phenotype data within and beyond
      the C. elegans community'
    year: null
  - doi: 10.1186/1471-2105-12-32
    pmc: null
    pubmed: '21261995'
    title: 'Worm Phenotype Ontology: integrating phenotype data within and beyond
      the C. elegans community'
    year: 2011
  synonyms:
  - WBPhenotype
  uri_format: http://purl.obolibrary.org/obo/WBPhenotype_$1
wdr:
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: Underlying schema for POWDER
  example: tag
  homepage: https://www.w3.org/TR/powder-formal/
  name: Protocol for Web Description Resources (POWDER) Schema
  prefix: wdr
  uri_format: http://www.w3.org/2007/05/powder#$1
wdrs:
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: The Protocol for Web Description Resources (POWDER) allows metadata
    to be associated with groups of resources such as those found on a Web site. Its
    main 'unit of information' is the Description Resource (DR), one or more of which
    are contained in a POWDER document. Processing such a document yields RDF triples
    describing the resources that are within the scope of the DRs. POWDER documents
    are written in XML and have relatively loose semantics, however, a GRDDL transform,
    associated with the root namespace, renders the data in RDF/OWL with more formal
    semantics. [from homepage]
  example: structure
  homepage: https://www.w3.org/2007/05/powder-s
  lov:
    description: The Protocol for Web Description Resources (POWDER) allows metadata
      to be associated with groups of resources such as those found on a Web site.
    homepage: http://www.w3.org/2007/05/powder-s
    keywords:
    - API
    modified: '2010-11-08'
    name: Protocol for Web Description Resources
    prefix: wdrs
    uri_prefix: http://www.w3.org/2007/05/powder-s#$1
  mappings:
    lov: wdrs
    zazuko: wdrs
  name: 'Protocol for Web Description Resources (POWDER): POWDER-S Vocabulary'
  prefix: wdrs
  uri_format: http://www.w3.org/2007/05/powder-s#$1
  zazuko:
    prefix: wdrs
    uri_format: http://www.w3.org/2007/05/powder-s#$1
webelements:
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: Browser for the periodic table of the elements
  example: chromium
  homepage: https://www.webelements.com/
  keywords:
  - chemistry
  name: Web Elements
  pattern: ^\w+$
  prefix: webelements
  uri_format: https://www.webelements.com/$1
wgs84:
  biolink:
    is_identifiers: false
    is_obo: false
    prefix: wgs
    uri_format: http://www.w3.org/2003/01/geo/wgs84_pos$1
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: A vocabulary for representing latitude, longitude and altitude information
    in the WGS84 geodetic reference datum
  example: latitude
  homepage: https://www.w3.org/2003/01/geo/wgs84_pos
  lov:
    description: A vocabulary for representing latitude, longitude and   altitude
      information in the WGS84 geodetic reference datum.
    homepage: http://www.w3.org/2003/01/geo/
    keywords:
    - Geography
    modified: '2009-04-20'
    name: WGS84 Geo Positioning
    prefix: geo
    uri_prefix: http://www.w3.org/2003/01/geo/wgs84_pos#$1
  mappings:
    biolink: wgs
    lov: geo
    zazuko: wgs
  name: WGS84 Geo Positioning
  prefix: wgs84
  uri_format: http://www.w3.org/2003/01/geo/wgs84_pos#$1
  zazuko:
    prefix: wgs
    uri_format: http://www.w3.org/2003/01/geo/wgs84_pos#$1
who.va:
  contributor:
    email: b.gyori@northeastern.edu
    github: bgyori
    name: Benjamin M. Gyori
    orcid: 0000-0001-9439-5346
  description: Identifiers assigned by the World Health Organization for coding causes
    of death from verbal autopsy (VA) reports. These codes are produced as outputs
    in standard VA analysis software.
  example: VAs-09.01
  example_extras:
  - VAs-09
  github_request_issue: 1739
  homepage: https://www.who.int/publications/m/item/verbal-autopsy-standards-the-2016-who-verbal-autopsy-instrument
  keywords:
  - cause of death
  - verbal autopsy
  name: World Health Organization Verbal Autopsy Code
  pattern: ^VAs-\d{2}(?:\.\d{2})?$
  prefix: who.va
  publications:
  - doi: 10.1371/journal.pmed.1002486
    pmc: PMC5761828
    pubmed: '29320495'
    title: 'The WHO 2016 verbal autopsy instrument: An international standard suitable
      for automated analysis by InterVA, InSilicoVA, and Tariff 2.0'
    year: 2018
  reviewer:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
wicell:
  cellosaurus:
    category: Cell line collections (Providers)
    homepage: https://www.wicell.org
    name: WiCell Research Institute Cell Collection
    prefix: WiCell
    uri_format: https://www.wicell.org/home/stem-cells/catalog-of-stem-cell-lines/$1.cmsx?closable=true
  example: ai10e-kctd13b
  mappings:
    cellosaurus: WiCell
  prefix: wicell
wikidata:
  bartoc:
    abbreviation: WD
    description: Wikidata is a free linked database that can be read and edited by
      both humans and machines. Wikidata acts as central storage for the structured
      data of its Wikimedia sister projects including Wikipedia, Wikivoyage, Wikisource,
      and others. Wikidata also provides support to many other sites and services
      beyond just Wikimedia projects! The content of Wikidata is available under a
      free license, exported using standard formats, and can be interlinked to other
      open data sets on the linked data web.
    homepage: https://www.wikidata.org/wiki/Wikidata:Main_Page
    license: CC0-1.0
    name: Wikidata
    pattern: ^Q[0-9]+$
    prefix: '1940'
    wikidata_database: Q2013
  biocontext:
    prefix: WIKIDATA
  biolink:
    is_identifiers: false
    is_obo: false
    prefix: WIKIDATA
    uri_format: https://www.wikidata.org/entity/$1
  cellosaurus:
    category: Encyclopedic resources
    homepage: https://www.wikidata.org/wiki/Wikidata:Main_Page
    name: Wikidata
    prefix: Wikidata
    uri_format: https://www.wikidata.org/wiki/$1
  contact:
    email: vrandecic@gmail.com
    github: vrandezo
    name: Denny Vrandečić
    orcid: 0000-0002-9593-2294
  example: Q47475003
  example_extras:
  - L704278
  - P675
  fairsharing:
    abbreviation: Wikidata
    description: Free knowledge database project hosted by Wikimedia and edited by
      volunteers.
    homepage: http://wikidata.org/
    license: CC0-1.0
    name: Wikidata
    prefix: FAIRsharing.6s749p
    publications:
    - doi: 10.1145/2187980.2188242
      pubmed_id: null
      title: 'Wikidata: a new platform for collaborative data collection'
    subjects:
    - Genomics
    - Proteomics
    - Chemistry
    - Metabolomics
    - Subject Agnostic
    twitter: wikidata
  license: CC0-1.0
  mappings:
    bartoc: '1940'
    biocontext: WIKIDATA
    biolink: WIKIDATA
    cellosaurus: Wikidata
    cheminf: '000567'
    fairsharing: FAIRsharing.6s749p
    miriam: wikidata
    n2t: wikidata
    wikidata.entity: Q2013
  miriam:
    deprecated: false
    description: Wikidata is a collaboratively edited knowledge base operated by the
      Wikimedia Foundation. It is intended to provide a common source of certain types
      of data which can be used by Wikimedia projects such as Wikipedia. Wikidata
      functions as a document-oriented database, centred on individual items. Items
      represent topics, for which basic information is stored that identifies each
      topic.
    homepage: https://www.wikidata.org/
    id: 00000549
    name: Wikidata
    namespaceEmbeddedInLui: false
    pattern: ^(Q|P)\d+$
    prefix: wikidata
    sampleId: Q2207226
    uri_format: http://www.wikidata.org/entity/$1
  n2t:
    description: Wikidata is a collaboratively edited knowledge base operated by the
      Wikimedia Foundation. It is intended to provide a common source of certain types
      of data which can be used by Wikimedia projects such as Wikipedia. Wikidata
      functions as a document-oriented database, centred on individual items. Items
      represent topics, for which basic information is stored that identifies each
      topic.
    example: Q2207226
    homepage: https://www.wikidata.org/
    name: Wikidata at Wikimedia Foundation
    namespaceEmbeddedInLui: false
    pattern: ^Q\d+$
    prefix: wikidata
    uri_format: https://www.wikidata.org/wiki/$1
  pattern: ^(Q|P|E|L)\d+$
  prefix: wikidata
  providers:
  - code: scholia
    description: Scholia can generally resolve many Wikidata entries in the biomedical
      and bibliometric domains
    example: null
    first_party: null
    homepage: https://scholia.toolforge.org
    name: Scholia
    publications: null
    status: null
    uri_format: https://scholia.toolforge.org/$1
  publications:
  - doi: 10.1145/2187980.2188242
    pmc: null
    pubmed: null
    title: Wikidata
    year: 2012
  - doi: 10.1145/2187980.2188242
    pmc: null
    pubmed: null
    title: 'Wikidata: a new platform for collaborative data collection'
    year: null
  rdf_uri_format: http://www.wikidata.org/entity/$1
  synonyms:
  - WD_Entity
  - wd
  - wdeschema
  uri_format: http://www.wikidata.org/entity/$1
wikidata.entity:
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: Entity in Wikidata
  example: Q42
  homepage: https://www.wikidata.org
  license: CC0-1.0
  name: Wikidata Entity
  part_of: wikidata
  pattern: ^Q\d+$
  prefix: wikidata.entity
  providers:
  - code: scholia
    description: Scholia can generally resolve many Wikidata entries in the biomedical
      and bibliometric domains
    example: null
    first_party: null
    homepage: https://scholia.toolforge.org
    name: Scholia
    publications: null
    status: null
    uri_format: https://scholia.toolforge.org/$1
  rdf_uri_format: http://www.wikidata.org/entity/$1
  uri_format: http://www.wikidata.org/entity/$1
wikidata.property:
  biocontext:
    prefix: WD_Prop
    uri_format: https://www.wikidata.org/wiki/Property:$1
  biolink:
    is_identifiers: false
    is_obo: false
    prefix: WIKIDATA_PROPERTY
    uri_format: https://www.wikidata.org/prop/$1
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: 'Wikidata is a free and open knowledge base that can be read and edited
    by both humans and machines.

    Wikidata acts as central storage for the structured data of its Wikimedia sister
    projects including Wikipedia, Wikivoyage, Wiktionary, Wikisource, and others.'
  example: P4355
  homepage: https://www.wikidata.org
  license: CC0-1.0
  mappings:
    biocontext: WD_Prop
    biolink: WIKIDATA_PROPERTY
  name: Wikidata Property
  part_of: wikidata
  pattern: ^P\d+$
  prefix: wikidata.property
  providers:
  - code: scholia
    description: Scholia can generally resolve many Wikidata entries in the biomedical
      and bibliometric domains
    example: null
    first_party: null
    homepage: https://scholia.toolforge.org
    name: Scholia
    publications: null
    status: null
    uri_format: https://scholia.toolforge.org/$1
  rdf_uri_format: http://www.wikidata.org/entity/$1
  uri_format: http://www.wikidata.org/entity/$1
wikigenes:
  biocontext:
    prefix: WIKIGENES
  mappings:
    biocontext: WIKIGENES
    miriam: wikigenes
    n2t: wikigenes
  miriam:
    deprecated: false
    description: WikiGenes is a collaborative knowledge resource for the life sciences,
      which is based on the general wiki idea but employs specifically developed technology
      to serve as a rigorous scientific tool. The rationale behind WikiGenes is to
      provide a platform for the scientific community to collect, communicate and
      evaluate knowledge about genes, chemicals, diseases and other biomedical concepts
      in a bottom-up process.
    homepage: http://www.wikigenes.org/
    id: '00000437'
    name: WikiGenes
    namespaceEmbeddedInLui: false
    pattern: ^\d+$
    prefix: wikigenes
    sampleId: '3771877'
    uri_format: http://www.wikigenes.org/e/gene/e/$1.html
  n2t:
    description: WikiGenes is a collaborative knowledge resource for the life sciences,
      which is based on the general wiki idea but employs specifically developed technology
      to serve as a rigorous scientific tool. The rationale behind WikiGenes is to
      provide a platform for the scientific community to collect, communicate and
      evaluate knowledge about genes, chemicals, diseases and other biomedical concepts
      in a bottom-up process.
    example: '3771877'
    homepage: http://www.wikigenes.org/
    name: WikiGenes at Massachusetts Institute of Technology
    namespaceEmbeddedInLui: false
    pattern: ^\d+$
    prefix: wikigenes
    uri_format: http://www.wikigenes.org/e/gene/e/$1.html
  prefix: wikigenes
  provides: ncbigene
wikipathways:
  biocontext:
    prefix: WIKIPATHWAYS
  contact:
    email: egon.willighagen@gmail.com
    github: egonw
    name: Egon Willighagen
    orcid: 0000-0001-7542-0286
  contributor_extras:
  - email: egon.willighagen@gmail.com
    github: egonw
    name: Egon Willighagen
    orcid: 0000-0001-7542-0286
  description: WikiPathways is a database of biological pathways maintained by and
    for the scientific community.
  domain: pathway
  edam:
    description: Identifier of a pathway from the WikiPathways pathway database.
    name: Pathway ID (WikiPathways)
    obsolete: false
    prefix: '3952'
  example: WP732
  fairsharing:
    abbreviation: WIKIPATHWAYS
    description: WikiPathways simplifies the contribution and maintenance of biological
      pathway information. It is an open and collaborative platform that curates pathways,
      complementing existing databases like KEGG, Reactome, and Pathway Commons. The
      web-based format makes it easy for anyone to participate, from students to experts.
      The community takes on peer review, editorial curation, and maintenance tasks.
    domains:
    - Reaction data
    - Protein interactions
    - signaling
    - biological regulation
    - molecular interaction
    - genetic interaction (sensu unexpected)
    - pathway
    - drug interaction
    homepage: http://www.wikipathways.org/
    name: WikiPathways
    prefix: FAIRsharing.g7b4rj
    subjects:
    - Virology
    - Epidemiology
  integbio:
    description: WikiPathways is an open, collaborative platform dedicated to the
      curation of biological pathways. WikiPathways was established to facilitate
      the contribution and maintenance of pathway information by the biology community.
    fairsharing: FAIRsharing.1x53qk
    homepage: https://wikipathways.org
    information_keywords:
    - Image/Movie
    - Interaction/Pathway
    maintainer: Universiteit Maastricht||Gladstone Institutes
    name: WikiPathways
    prefix: nbdc02116
    pubmeds:
    - '18651794'
    - '19649250'
    - '26481357'
    - '22096230'
    status: Active
    target_keywords:
    - Protein
  license: CC0-1.0
  logo: https://www.wikipathways.org/assets/img/wikipathways-logo-horizontal.svg
  mappings:
    biocontext: WIKIPATHWAYS
    edam: '3952'
    fairsharing: FAIRsharing.g7b4rj
    integbio: nbdc02116
    miriam: wikipathways
    n2t: wikipathways
    ols: wikipathways
    pathguide: '237'
    prefixcommons: wikipathways
    re3data: r3d100013316
    togoid: Wikipathways
    wikidata: P2410
    wikidata.entity: Q7999828
  mastodon: wikipathways@fosstodon.org
  miriam:
    deprecated: false
    description: WikiPathways is a resource providing an open and public collection
      of pathway maps created and curated by the community in a Wiki-like style.
    homepage: http://www.wikipathways.org/
    id: '00000076'
    name: WikiPathways
    namespaceEmbeddedInLui: false
    pattern: ^WP\d{1,5}(\_r\d+)?$
    prefix: wikipathways
    providers:
    - code: scholia
      description: 'Scholia is a service that creates visual scholarly profiles for
        topic, people, organizations, species, chemicals, etc using bibliographic
        and other information in Wikidata.

        '
      homepage: https://scholia.toolforge.org/
      name: Scholia
      uri_format: https://scholia.toolforge.org/wikipathways/$1
    sampleId: WP100
    uri_format: http://www.wikipathways.org/instance/$1
  n2t:
    description: WikiPathways is a resource providing an open and public collection
      of  pathway maps created and curated by the community in a Wiki like style.
      All content is under the Creative Commons Attribution 3.0 Unported license.
    example: WP100
    homepage: http://www.wikipathways.org/
    name: Wikipathways
    namespaceEmbeddedInLui: false
    pattern: WP\d{1,5}(\_r\d+)?$
    prefix: wikipathways
    uri_format: http://www.wikipathways.org/instance/$1
  name: WikiPathways
  ols:
    contact: egon.willighagen@gmail.com
    description: WikiPathways is a database of biological pathways maintained by and
      for the scientific community.
    download_owl: https://w3id.org/biopragmatics/resources/wikipathways/wikipathways.owl
    homepage: http://www.wikipathways.org/
    name: WikiPathways
    prefix: wikipathways
    uri_format: http://identifiers.org/wikipathways/$1
    version.iri: https://w3id.org/biopragmatics/resources/wikipathways/20251010/wikipathways.ofn
  part_of_database: wikipathways
  pathguide:
    abbreviation: WikiPathways
    homepage: http://wikipathways.org/index.php/WikiPathways
    keywords:
    - BioPAX
    name: WikiPathways
    prefix: '237'
  prefix: wikipathways
  prefixcommons:
    description: WikiPathways is a resource providing an open and public collection
      of  pathway maps created and curated by the community in a Wiki like style.
    example: WP100
    homepage: http://wikipathways.org/
    keywords:
    - pathway
    license: CC0-1.0
    name: WikiPathways
    pattern: ^P\d{1,5}(\_r\d+)?$
    prefix: wikipathways
    pubmed_ids:
    - '18651794'
    uri_format: http://www.wikipathways.org/index.php/Pathway:$1
  publications:
  - doi: 10.1093/nar/gkad960
    pmc: PMC10767877
    pubmed: '37941138'
    title: 'WikiPathways 2024: next generation pathway database'
    year: 2024
  - doi: 10.1093/nar/gkaa1024
    pmc: PMC7779061
    pubmed: '33211851'
    title: 'WikiPathways: connecting communities'
    year: 2021
  - doi: 10.1093/nar/gkx1064
    pmc: PMC5753270
    pubmed: '29136241'
    title: 'WikiPathways: a multifaceted pathway database bridging metabolomics to
      other omics research'
    year: 2018
  - doi: 10.1093/nar/gkv1024
    pmc: PMC4702772
    pubmed: '26481357'
    title: 'WikiPathways: capturing the full diversity of pathway knowledge'
    year: 2015
  - doi: 10.1093/nar/gkr1074
    pmc: PMC3245032
    pubmed: '22096230'
    title: 'WikiPathways: building research communities on biological pathways'
    year: 2011
  - doi: 10.1371/journal.pbio.0060184
    pmc: PMC2475545
    pubmed: '18651794'
    title: 'WikiPathways: pathway editing for the people'
    year: 2008
  - doi: null
    pmc: null
    pubmed: '18651794'
    title: null
    year: null
  re3data:
    description: WikiPathways was established to facilitate the contribution and maintenance
      of pathway information by the biology community. WikiPathways is an open, collaborative
      platform dedicated to the curation of biological pathways. WikiPathways thus
      presents a new model for pathway databases that enhances and complements ongoing
      efforts, such as KEGG, Reactome and Pathway Commons. Building on the same MediaWiki
      software that powers Wikipedia, we added a custom graphical pathway editing
      tool and integrated databases covering major gene, protein, and small-molecule
      systems. The familiar web-based format of WikiPathways greatly reduces the barrier
      to participate in pathway curation. More importantly, the open, public approach
      of WikiPathways allows for broader participation by the entire community, ranging
      from students to senior experts in each field. This approach also shifts the
      bulk of peer review, editorial curation, and maintenance to the community.
    doi: 10.17616/R31NJMRO
    homepage: https://www.wikipathways.org/
    name: WikiPathways
    prefix: r3d100013316
    xrefs:
      nif: 0000-20925
  togoid:
    catalog: nbdc02116
    examples:
    - WP1531
    - WP4312
    - WP4877
    - WP5020
    - WP4400
    - WP4474
    - WP4183
    - WP3650
    - WP4545
    - WP4462
    keywords:
    - Pathway
    name: WikiPathways
    pattern: ^(?WP\d{1,5})(?:\_r\d+)?$
    prefix: Wikipathways
    uri_format: http://identifiers.org/wikipathways/$1
  twitter: WikiPathways
  wikidata:
    description: describes in which biological pathways a biological entity occurs
    example:
    - WP2253
    - WP2533
    - WP4921
    homepage: http://www.wikipathways.org
    miriam: wikipathways
    name: WikiPathways ID
    pattern: ^WP\d{1,4}$
    prefix: P2410
    uri_format: https://new.wikipathways.org/pathways/$1
    uri_format_rdf: http://identifiers.org/wikipathways/$1
wikipathways.type:
  contact:
    email: egon.willighagen@gmail.com
    github: egonw
    name: Egon Willighagen
    orcid: 0000-0001-7542-0286
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: Types used in WikiPathways RDF
  download_owl: https://github.com/wikipathways/WpVocabularies/raw/refs/heads/master/docs/wpTypes.owl
  example: Arrow
  github_request_issue: 1754
  homepage: https://vocabularies.wikipathways.org/wpTypes
  mastodon: wikipathways@fosstodon.org
  name: WikiPathways Types
  part_of_database: wikipathways
  prefix: wikipathways.type
  rdf_uri_format: http://vocabularies.wikipathways.org/wpTypes#$1
  repository: https://github.com/wikipathways/WpVocabularies
  synonyms:
  - wikipathways.types
  - wptypes
  uri_format: http://vocabularies.wikipathways.org/wpTypes#$1
wikipathways.vocab:
  aberowl:
    description: The WP ontology for WikiPathways.
    download_owl: http://aber-owl.net/media/ontologies/WIKIPATHWAYS/225/wikipathways.owl
    homepage: http://www.wikipathways.org/
    name: WikiPathways
    prefix: WIKIPATHWAYS
  bioportal:
    contact:
      email: egon.willighagen@gmail.com
      name: Egon Willighagen
    description: The WP ontology for WikiPathways.
    homepage: https://vocabularies.wikipathways.org/wp
    name: WikiPathways
    prefix: WIKIPATHWAYS
    publications:
    - https://scholia.toolforge.org/topic/Q7999828
    version: 2013a
  contact:
    email: egon.willighagen@gmail.com
    github: egonw
    name: Egon Willighagen
    orcid: 0000-0001-7542-0286
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: An ontology supporting data modeling in WikiPathways
  download_owl: https://github.com/wikipathways/WpVocabularies/raw/refs/heads/master/docs/wp.owl
  example: DataNode
  homepage: http://www.wikipathways.org
  mappings:
    aberowl: WIKIPATHWAYS
    bioportal: WIKIPATHWAYS
  mastodon: wikipathways@fosstodon.org
  name: WikiPathways Ontology
  part_of_database: wikipathways
  prefix: wikipathways.vocab
  references:
  - https://github.com/biopragmatics/bioregistry/issues/818
  repository: https://github.com/wikipathways/WpVocabularies
  uri_format: https://bioportal.bioontology.org/ontologies/WIKIPATHWAYS/?p=classes&conceptid=http%3A%2F%2Fvocabularies.wikipathways.org%2Fwp%23$1
wikipedia.en:
  biocontext:
    prefix: WIKIPEDIA.EN
  contributor_extras:
  - email: cjmungall@lbl.gov
    github: cmungall
    name: Chris Mungall
    orcid: 0000-0002-6601-2165
  example_extras:
  - Pharyngeal_pouch_(embryology)
  go:
    homepage: http://en.wikipedia.org/
    name: Wikipedia
    prefix: Wikipedia
    uri_format: http://en.wikipedia.org/wiki/$1
  mappings:
    biocontext: WIKIPEDIA.EN
    go: Wikipedia
    miriam: wikipedia.en
    n2t: wikipedia.en
    prefixcommons: wikipedia
  miriam:
    deprecated: false
    description: Wikipedia is a multilingual, web-based, free-content encyclopedia
      project based on an openly editable model. It is written collaboratively by
      largely anonymous Internet volunteers who write without pay.
    homepage: http://en.wikipedia.org/wiki/Main_Page
    id: 00000384
    name: Wikipedia (En)
    namespaceEmbeddedInLui: false
    pattern: ^[A-Za-z-0-9_]+$
    prefix: wikipedia.en
    providers:
    - code: ''
      description: Wikipedia structured content through DBpedia
      homepage: http://wiki.dbpedia.org/
      name: Wikipedia structured content through DBpedia
      uri_format: http://dbpedia.org/page/$1
    sampleId: SM_UB-81
    uri_format: http://en.wikipedia.org/wiki/$1
  n2t:
    description: Wikipedia is a multilingual, web-based, free-content encyclopedia
      project based on an openly editable model. It is written collaboratively by
      largely anonymous Internet volunteers who write without pay.
    example: SM_UB-81
    homepage: http://wiki.dbpedia.org/
    name: Wikipedia structured content through DBpedia
    namespaceEmbeddedInLui: false
    pattern: ^[A-Za-z-0-9_]+$
    prefix: wikipedia.en
    uri_format: http://dbpedia.org/page/$1
  name: Wikipedia
  pattern: ^\S+$
  prefix: wikipedia.en
  prefixcommons:
    description: Encyclopedia of Everything.
    example: SM_UB-81
    homepage: http://en.wikipedia.org/
    name: Wikipedia
    pattern: ^[A-Za-z0-9_]+$
    prefix: wikipedia
    synonyms:
    - wikipedia.en
    uri_format: http://en.wikipedia.org/wiki/$1
  providers:
  - code: volupedia
    description: A mix of wikipedia and 3d
    example: null
    first_party: null
    homepage: http://en.volupedia.org
    name: Volupedia
    publications: null
    status: null
    uri_format: http://en.volupedia.org/wiki/$1
  references:
  - https://github.com/biopragmatics/bioregistry/issues/794
  synonyms:
  - Wikipedia
  - wikipedia
wiktionary:
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: A free dictionary
  example: pharmacist
  github_request_issue: 1310
  homepage: https://wiktionary.org
  license: CC BY SA 4.0
  name: Wiktionary
  prefix: wiktionary
  uri_format: https://en.wiktionary.org/wiki/$1
wlmo:
  example: Annotation
  mappings:
    tib: wlmo
  name: Wildlife Monitoring Ontology
  prefix: wlmo
  tib:
    description: The ontology developed for representing wildlife monitoring capture
      events, the setup within which they were observed and their results.
    download_owl: https://wildlive.senckenberg.de/wlmo/current/ontology.owl
    homepage: https://wildlive.senckenberg.de/wlmo/current/
    keywords:
    - ESS
    - earth sciences
    name: Wildlife Monitoring Ontology (WLMO)
    prefix: wlmo
    uri_format: https://wildlive.senckenberg.de/wlmo/$1
woc.ontology:
  example: AccessModifier
  mappings:
    tib: co
  name: Code Ontology
  prefix: woc.ontology
  repository: https://github.com/codeontology/parser
  tib:
    description: An ontology that represents object-oriented programming languages
    download_owl: https://raw.githubusercontent.com/codeontology/parser/master/ontology/CodeOntology.owl
    homepage: http://codeontology.org/
    keywords:
    - NFDI4ING
    - engineering
    name: CodeOntology
    prefix: co
    uri_format: http://rdf.webofcode.org/woc/$1
worfdb:
  biocontext:
    prefix: WORFDB
  integbio:
    alt_name: Worm ORFeome Database
    description: WORFDB is a database of C. elegans open reading frame information.
      The database contains data from ORF projects, which can be searched by keyword
      or BLAST, as well as data from RACE experiments to verify predicted genes. A
      database of promoters is also available.
    homepage: http://worfdb.dfci.harvard.edu/html/
    information_keywords:
    - Sequence
    maintainer: Harvard Medical School
    name: WORFDB
    prefix: nbdc00738
    pubmeds:
    - '15489327'
    - '12679813'
    - '12519990'
    - '11242119'
    status: Active
    target_keywords:
    - cDNA/EST
  mappings:
    biocontext: WORFDB
    integbio: nbdc00738
    miriam: worfdb
    n2t: worfdb
    ncbi: WorfDB
    prefixcommons: worfdb
  miriam:
    deprecated: false
    description: WOrfDB (Worm ORFeome DataBase) contains data from the cloning of
      complete set of predicted protein-encoding Open Reading Frames (ORFs) of Caenorhabditis
      elegans. This collection describes experimentally defined transcript structures
      of unverified genes through RACE (Rapid Amplification of cDNA Ends).
    homepage: http://worfdb.dfci.harvard.edu/
    id: 00000288
    name: Worfdb
    namespaceEmbeddedInLui: false
    pattern: ^\w+(\.\d+)?$
    prefix: worfdb
    sampleId: T01B6.1
    uri_format: http://worfdb.dfci.harvard.edu/html/index.php?search_type=name&page=showresultrc&race_query=$1
  n2t:
    description: WOrfDB (Worm ORFeome DataBase) contains data from the cloning of
      complete set of predicted protein-encoding Open Reading Frames (ORFs) of Caenorhabditis
      elegans. This collection describes experimentally defined transcript structures
      of unverified genes through RACE (Rapid Amplification of cDNA Ends).
    example: T01B6.1
    homepage: http://worfdb.dfci.harvard.edu/
    name: Worm Orf DB at Harvard
    namespaceEmbeddedInLui: false
    pattern: ^\w+(\.\d+)?
    prefix: worfdb
    uri_format: http://worfdb.dfci.harvard.edu/index.php?search_type=name&page=showresultrc&race_query=$1
  ncbi:
    example: pos-1
    homepage: http://worfdb.dfci.harvard.edu/
    name: C. elegans ORFeome cloning project
    prefix: WorfDB
  prefix: worfdb
  prefixcommons:
    description: In total, approximately 12,500 C. elegans ORFs are now available
      as Gateway Entry clones for various reverse proteomics (ORFeome v3.1). This
      work illustrates why the cloning of a complete C. elegans ORFeome, and likely
      the ORFeomes of other multicellular organisms, needs to be an iterative process
      that requires multiple rounds of experimental validation together with gradually
      improving gene predictions.
    example: R10E9.1
    homepage: http://worfdb.dfci.harvard.edu/
    keywords:
    - DNA
    name: The C.elegans ORFeome cloning project
    pattern: ^[A-Z,0-9]+$
    prefix: worfdb
    uri_format: http://worfdb.dfci.harvard.edu/searchallwormorfs.pl?sid=$1
world2dpage:
  comment: This resource doesn't exist on the web anymore
  deprecated: true
  mappings:
    prefixcommons: world2dpage
    uniprot: DB-0121
  prefix: world2dpage
  prefixcommons:
    description: A public repository, standards compliant, for proteomics image data
      published in the literature. This repository currently contains data from 16
      published articles, putting together 22 reference maps for 15 species, totalizing
      nearly 4'400 identified spots.
    example: '0020'
    homepage: http://world-2dpage.expasy.org/repository/
    keywords:
    - protein
    - structure
    - 2d-page
    name: The World-2DPAGE database
    pattern: ^\d+$
    prefix: world2dpage
    uri_format: http://world-2dpage.expasy.org/repository/database=$1
  publications:
  - doi: 10.1016/j.jprot.2008.02.005
    pmc: null
    pubmed: '18617148'
    title: The World-2DPAGE Constellation to promote and publish gel-based proteomics
      data through the ExPASy server
    year: 2008
  - doi: 10.1016/j.jprot.2008.02.005
    pmc: null
    pubmed: '18617148'
    title: null
    year: null
  reviewer:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  uniprot:
    abbreviation: World-2DPAGE
    category: 2D gel databases
    homepage: https://world-2dpage.expasy.org/repository/
    name: The World-2DPAGE database
    prefix: DB-0121
    publications:
    - doi: 10.1016/j.jprot.2008.02.005
      pubmed: '18617148'
    uri_format: https://world-2dpage.expasy.org/repository/$1
worldavatar.compchem:
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: Linked-data framework for connecting species in chemical kinetic reaction
    mechanisms with quantum calculations. A mechanism can be constructed from thermodynamic,
    reaction rate, and transport data that has been obtained either experimentally,
    computationally, or by a combination of both. In order to implement this approach,
    two existing ontologies, namely OntoKin, for representing chemical kinetic reaction
    mechanisms, and OntoCompChem, for representing quantum chemistry calculations,
    are extended. (from https://nfdi4cat.org/services/ontologie-sammlung/)
  download_owl: http://www.theworldavatar.com/ontology/ontocompchem/ontocompchem.owl
  homepage: https://como.ceb.cam.ac.uk/preprints/223/
  mappings:
    tib: ontocompchem
  name: Computational Chemistry Ontology
  no_own_terms: true
  prefix: worldavatar.compchem
  tib:
    description: Linked-data framework for connecting species in chemical kinetic
      reaction mechanisms with quantum calculations. A mechanism can be constructed
      from thermodynamic, reaction rate, and transport data that has been obtained
      either experimentally, computationally, or by a combination of both. In order
      to implement this approach, two existing ontologies, namely OntoKin, for representing
      chemical kinetic reaction mechanisms, and OntoCompChem, for representing quantum
      chemistry calculations, are extended.
    download_owl: https://raw.githubusercontent.com/TheWorldAvatar/ontology/refs/heads/main/ontology/ontocompchem/ontocompchem.owl
    keywords:
    - NFDI4CAT
    - NFDI4CHEM
    - chemistry
    - chemical and environmental engineering
    name: Computational Chemistry Ontology
    prefix: ontocompchem
    tracker: https://github.com/TheWorldAvatar/ontology/issues
    uri_format: http://theworldavatar.com/ontology/ontocompchem/ontocompchem.owl#$1
worldavatar.kin:
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: Represents chemical kinetic reaction mechanisms.
  download_owl: http://www.theworldavatar.com/ontology/ontokin/OntoKin.owl
  example: ElementNumber
  homepage: http://www.theworldavatar.com/ontokin/
  mappings:
    tib: ontokin
  name: Ontology for Chemical Kinetic Reaction Mechanisms
  prefix: worldavatar.kin
  tib:
    description: OntoKin is an ontology developed for representing chemical kinetic
      reaction mechanisms.
    download_owl: https://raw.githubusercontent.com/TheWorldAvatar/ontology/refs/heads/main/ontology/ontokin/OntoKin.owl
    homepage: http://www.theworldavatar.com/ontokin/
    keywords:
    - NFDI4CAT
    - NFDI4CHEM
    - chemistry
    - chemical and environmental engineering
    name: Ontology for Chemical Kinetic Reaction Mechanisms
    prefix: ontokin
    tracker: https://github.com/TheWorldAvatar/ontology/issues
    uri_format: http://www.theworldavatar.com/ontology/ontokin/OntoKin.owl#$1
  uri_format: http://www.theworldavatar.com/ontology/ontokin/OntoKin.owl#$1
worldavatar.os:
  example: Charge
  mappings:
    tib: os
  prefix: worldavatar.os
  tib:
    description: OntoSpecies is an ontology developed for representing chemical species.
    download_owl: https://raw.githubusercontent.com/TheWorldAvatar/ontology/refs/heads/main/ontology/ontospecies/OntoSpecies.owl
    homepage: https://doi.org/10.17863/CAM.97235.2
    keywords:
    - NFDI4CHEM
    - chemistry
    name: OntoSpecies - Chemical Species Ontology for Data Integration and Knowledge
      Discovery
    prefix: os
    tracker: https://github.com/TheWorldAvatar/ontology/issues
    uri_format: http://www.theworldavatar.com/ontology/ontospecies/OntoSpecies.owl#$1
wormbase:
  biocontext:
    prefix: WormBase
    uri_format: https://www.wormbase.org/get?name=$1
  biolink:
    is_identifiers: false
    is_obo: false
    prefix: WBVocab
    uri_format: http://bio2rdf.org/wormbase_vocabulary$1
  contact:
    email: todd@wormbase.org
    github: tharris
    name: Todd W Harris
    orcid: 0000-0003-3406-163X
  contributor_extras:
  - email: cjmungall@lbl.gov
    github: cmungall
    name: Chris Mungall
    orcid: 0000-0002-6601-2165
  edam:
    description: Gene identifier used by WormBase database.
    name: Gene ID (WormBase)
    obsolete: false
    prefix: '1805'
  fairsharing:
    abbreviation: WormBase
    description: WormBase is an international consortium of biologists and computer
      scientists dedicated to providing the research community with accurate, current,
      accessible information concerning the genetics, genomics and biology of C. elegans
      and related nematodes.
    homepage: http://www.wormbase.org/
    name: WormBase
    prefix: FAIRsharing.zx1td8
    publications:
    - doi: 10.1186/1471-2105-12-175
      pubmed_id: 21595960
      title: 'Toward an interactive article: integrating journals and biological databases.'
    - doi: 10.1093/nar/gkq1116
      pubmed_id: 21071413
      title: 'The BioGRID Interaction Database: 2011 update.'
    - doi: 10.1186/1471-2105-11-550
      pubmed_id: 21059240
      title: Localizing triplet periodicity in DNA and cDNA sequences.
    - doi: 10.1002/mrd.21130
      pubmed_id: 19921742
      title: 'Representing ontogeny through ontology: a developmental biologist''s
        guide to the gene ontology.'
    - doi: 10.1093/nar/gkp1018
      pubmed_id: 19920128
      title: 'The Gene Ontology in 2010: extensions and refinements.'
    - doi: 10.1093/nar/gkp952
      pubmed_id: 19910365
      title: 'WormBase: a comprehensive resource for nematode research.'
    - doi: 10.1186/1471-2105-10-228
      pubmed_id: 19622167
      title: 'Semi-automated curation of protein subcellular localization: a text
        mining-based approach to Gene Ontology (GO) Cellular Component curation.'
    - doi: 10.1371/journal.pcbi.1000431
      pubmed_id: 19578431
      title: 'The Gene Ontology''s Reference Genome Project: a unified framework for
        functional annotation across species.'
    - doi: 10.1186/1471-2105-9-549
      pubmed_id: 19099578
      title: nGASP--the nematode genome annotation assessment project.
    - doi: 10.1093/nar/gkz920
      pubmed_id: 31642470
      title: 'WormBase: a modern Model Organism Information Resource.'
    - doi: 10.1093/nar/gkx998
      pubmed_id: 29069413
      title: 'WormBase 2017: molting into a new stage.'
    subjects:
    - Anatomy
    - Life Science
    twitter: wormbase
  go:
    homepage: http://www.wormbase.org/
    name: WormBase database of nematode biology
    prefix: WB_REF
  integbio:
    description: WormBase is a database of information on nematodes and other worms.
      The database contains extensive information on a number of species including
      genome sequences, genes, gene expression, proteins, and phenotypes. Users can
      search by keyword, BLAST, or BLAT, and create user accounts to save searches
      and other useful information.
    fairsharing: biodbcore-000156
    homepage: http://www.wormbase.org
    information_keywords:
    - Bioresource
    - Ontology/Terminology/Nomenclature
    - Sequence
    - Expression
    - Image/Movie
    - Bibliography/Documents
    - Repository
    maintainer: Ontario Institute For Cancer Research
    name: WormBase
    prefix: nbdc00740
    pubmeds:
    - '29069413'
    - '27899279'
    - '26578572'
    - '24194605'
    - '23160413'
    - '24058818'
    - '22067452'
    - '21543339'
    - '19910365'
    - '17991679'
    - '17099234'
    - '16988424'
    - '16381915'
    - '15608221'
    - '15489338'
    - '14681445'
    - '12519966'
    - '11125056'
    status: Active
    target_keywords:
    - Genome/Gene
    - cDNA/EST
    - Genetic variation
    - Protein
    - Organism
    - Health/Disease
  license: CC0-1.0
  logo: https://wormbase.org/img/logo/logo_wormbase_gradient.svg
  mappings:
    biocontext: WormBase
    biolink: WBVocab
    edam: '1805'
    fairsharing: FAIRsharing.zx1td8
    go: WB_REF
    integbio: nbdc00740
    miriam: wb
    n2t: wb
    ncbi: WormBase
    pathguide: '426'
    prefixcommons: wormbase
    re3data: r3d100010424
    rrid: WB-STRAIN:WBStrain
    uniprot: DB-0110
    wikidata: P3860
  miriam:
    deprecated: false
    description: WormBase is an online bioinformatics database of the biology and
      genome of the model organism Caenorhabditis elegans and other nematodes. It
      is used by the C. elegans research community both as an information resource
      and as a mode to publish and distribute their results. This collection references
      WormBase-accessioned entities.
    homepage: https://www.wormbase.org/
    id: '00000027'
    name: WormBase
    namespaceEmbeddedInLui: false
    pattern: ^WB[A-Z][a-z]+\d+$
    prefix: wb
    providers:
    - code: agr
      description: WormBase through the Alliance of Genome Resources
      homepage: https://www.alliancegenome.org
      name: WormBase through the Alliance of Genome Resources
      uri_format: https://www.alliancegenome.org/gene/WB:$1
    sampleId: WBGene00000001
    uri_format: https://www.wormbase.org/get?name=$1
  n2t:
    description: WormBase is an online bioinformatics database of the biology and
      genome of the model organism Caenorhabditis elegans and other nematodes. It
      is used by the C. elegans research community both as an information resource
      and as a mode to publish and distribute their results. This collection references
      WormBase-accessioned entities.
    example: WBGene00000001
    homepage: https://www.wormbase.org/
    name: WormBase
    namespaceEmbeddedInLui: false
    pattern: ^WB[A-Z][a-z]+\d+$
    prefix: wb
    uri_format: https://www.wormbase.org/get?name=$1
  name: WormBase
  ncbi:
    example: R13H7
    homepage: http://www.wormbase.org/
    name: Caenorhabditis elegans Genome Database
    prefix: WormBase
  pathguide:
    abbreviation: WormBase
    homepage: http://www.wormbase.org/
    name: Worm Base
    prefix: '426'
  pattern: ^(CE[0-9]{5}|WB[A-Z][a-z]+\d+)$
  preferred_prefix: WormBase
  prefix: wormbase
  prefixcommons:
    description: WormBase is an online bioinformatics database of the biology and
      genome of the model organism Caenorhabditis elegans and related nematodes. It
      is used by the C. elegans research community both as an information resource
      and as a mode to publish and distribute their results.
    example: WBGene00000001
    homepage: http://www.wormbase.org/
    keywords:
    - genome
    - gene
    - anatomy
    license: http://wiki.wormbase.org/index.php/WormBaseWiki:Copyrights
    name: WormBase
    pattern: ^WBGene\d{8}$
    prefix: wormbase
    pubmed_ids:
    - '11125056'
    synonyms:
    - wb
  providers:
  - code: wormbase.c_elegans
    description: Pages describing C. Elegans genes.
    example: null
    first_party: null
    homepage: http://www.wormbase.org
    name: WormBase C. Elegans Gene Portal
    publications: null
    status: null
    uri_format: http://www.wormbase.org/species/c_elegans/gene/$1
  publications:
  - doi: 10.1093/nar/gkz920
    pmc: PMC7145598
    pubmed: '31642470'
    title: 'WormBase: a modern Model Organism Information Resource'
    year: 2020
  - doi: 10.1093/nar/gkx998
    pmc: PMC5753391
    pubmed: '29069413'
    title: 'WormBase 2017: molting into a new stage'
    year: 2018
  - doi: 10.1186/1471-2105-12-175
    pmc: PMC3213741
    pubmed: '21595960'
    title: 'Toward an interactive article: integrating journals and biological databases'
    year: 2011
  - doi: 10.1186/1471-2105-11-550
    pmc: PMC2992068
    pubmed: '21059240'
    title: Localizing triplet periodicity in DNA and cDNA sequences
    year: 2010
  - doi: 10.1002/mrd.21130
    pmc: PMC2830379
    pubmed: '19921742'
    title: 'Representing ontogeny through ontology: a developmental biologist''s guide
      to the gene ontology'
    year: 2010
  - doi: 10.1093/nar/gkq1116
    pmc: PMC3013707
    pubmed: '21071413'
    title: 'The BioGRID Interaction Database: 2011 update'
    year: 2010
  - doi: 10.1186/1471-2105-10-228
    pmc: PMC2719631
    pubmed: '19622167'
    title: 'Semi-automated curation of protein subcellular localization: a text mining-based
      approach to Gene Ontology (GO) Cellular Component curation'
    year: 2009
  - doi: 10.1093/nar/gkp1018
    pmc: PMC2808930
    pubmed: '19920128'
    title: 'The Gene Ontology in 2010: extensions and refinements'
    year: 2009
  - doi: 10.1371/journal.pcbi.1000431
    pmc: PMC2699109
    pubmed: '19578431'
    title: 'The Gene Ontology''s Reference Genome Project: a unified framework for
      functional annotation across species'
    year: 2009
  - doi: 10.1093/nar/gkp952
    pmc: PMC2808986
    pubmed: '19910365'
    title: 'WormBase: a comprehensive resource for nematode research'
    year: 2009
  - doi: 10.1186/1471-2105-9-549
    pmc: PMC2651883
    pubmed: '19099578'
    title: nGASP--the nematode genome annotation assessment project
    year: 2008
  - doi: 10.1093/nar/29.1.82
    pmc: PMC29781
    pubmed: '11125056'
    title: 'WormBase: network access to the genome and biology of Caenorhabditis elegans'
    year: 2001
  - doi: 10.1186/1471-2105-12-175
    pmc: null
    pubmed: null
    title: 'Toward an interactive article: integrating journals and biological databases.'
    year: null
  - doi: 10.1093/nar/gkq1116
    pmc: null
    pubmed: null
    title: 'The BioGRID Interaction Database: 2011 update.'
    year: null
  - doi: 10.1186/1471-2105-11-550
    pmc: null
    pubmed: null
    title: Localizing triplet periodicity in DNA and cDNA sequences.
    year: null
  - doi: 10.1002/mrd.21130
    pmc: null
    pubmed: null
    title: 'Representing ontogeny through ontology: a developmental biologist''s guide
      to the gene ontology.'
    year: null
  - doi: 10.1093/nar/gkp1018
    pmc: null
    pubmed: null
    title: 'The Gene Ontology in 2010: extensions and refinements.'
    year: null
  - doi: 10.1093/nar/gkp952
    pmc: null
    pubmed: null
    title: 'WormBase: a comprehensive resource for nematode research.'
    year: null
  - doi: 10.1186/1471-2105-10-228
    pmc: null
    pubmed: null
    title: 'Semi-automated curation of protein subcellular localization: a text mining-based
      approach to Gene Ontology (GO) Cellular Component curation.'
    year: null
  - doi: 10.1371/journal.pcbi.1000431
    pmc: null
    pubmed: null
    title: 'The Gene Ontology''s Reference Genome Project: a unified framework for
      functional annotation across species.'
    year: null
  - doi: 10.1186/1471-2105-9-549
    pmc: null
    pubmed: null
    title: nGASP--the nematode genome annotation assessment project.
    year: null
  - doi: 10.1093/nar/gkz920
    pmc: null
    pubmed: null
    title: 'WormBase: a modern Model Organism Information Resource.'
    year: null
  - doi: 10.1093/nar/gkx998
    pmc: null
    pubmed: null
    title: 'WormBase 2017: molting into a new stage.'
    year: null
  - doi: null
    pmc: null
    pubmed: '11125056'
    title: null
    year: null
  - doi: null
    pmc: null
    pubmed: '24194605'
    title: null
    year: null
  - doi: null
    pmc: null
    pubmed: '19910365'
    title: null
    year: null
  - doi: null
    pmc: null
    pubmed: '17991679'
    title: null
    year: null
  - doi: null
    pmc: null
    pubmed: '15608221'
    title: null
    year: null
  - doi: 10.1093/nar/gkz920
    pmc: null
    pubmed: '31642470'
    title: null
    year: null
  - doi: 10.1186/1471-2105-12-175
    pmc: null
    pubmed: null
    title: 'Toward an interactive article: integrating journals and biological databases.'
    year: null
  - doi: 10.1093/nar/gkq1116
    pmc: null
    pubmed: null
    title: 'The BioGRID Interaction Database: 2011 update.'
    year: null
  - doi: 10.1186/1471-2105-11-550
    pmc: null
    pubmed: null
    title: Localizing triplet periodicity in DNA and cDNA sequences.
    year: null
  - doi: 10.1002/mrd.21130
    pmc: null
    pubmed: null
    title: 'Representing ontogeny through ontology: a developmental biologist''s guide
      to the gene ontology.'
    year: null
  - doi: 10.1093/nar/gkp1018
    pmc: null
    pubmed: null
    title: 'The Gene Ontology in 2010: extensions and refinements.'
    year: null
  - doi: 10.1093/nar/gkp952
    pmc: null
    pubmed: null
    title: 'WormBase: a comprehensive resource for nematode research.'
    year: null
  - doi: 10.1186/1471-2105-10-228
    pmc: null
    pubmed: null
    title: 'Semi-automated curation of protein subcellular localization: a text mining-based
      approach to Gene Ontology (GO) Cellular Component curation.'
    year: null
  - doi: 10.1371/journal.pcbi.1000431
    pmc: null
    pubmed: null
    title: 'The Gene Ontology''s Reference Genome Project: a unified framework for
      functional annotation across species.'
    year: null
  - doi: 10.1186/1471-2105-9-549
    pmc: null
    pubmed: null
    title: nGASP--the nematode genome annotation assessment project.
    year: null
  - doi: 10.1093/nar/gkz920
    pmc: null
    pubmed: null
    title: 'WormBase: a modern Model Organism Information Resource.'
    year: null
  - doi: 10.1093/nar/gkx998
    pmc: null
    pubmed: null
    title: 'WormBase 2017: molting into a new stage.'
    year: null
  - doi: null
    pmc: null
    pubmed: '11125056'
    title: null
    year: null
  - doi: null
    pmc: null
    pubmed: '24194605'
    title: null
    year: null
  - doi: null
    pmc: null
    pubmed: '19910365'
    title: null
    year: null
  - doi: null
    pmc: null
    pubmed: '17991679'
    title: null
    year: null
  - doi: null
    pmc: null
    pubmed: '15608221'
    title: null
    year: null
  - doi: 10.1093/nar/gkz920
    pmc: null
    pubmed: '31642470'
    title: null
    year: null
  - doi: 10.1186/1471-2105-12-175
    pmc: null
    pubmed: null
    title: 'Toward an interactive article: integrating journals and biological databases.'
    year: null
  - doi: 10.1093/nar/gkq1116
    pmc: null
    pubmed: null
    title: 'The BioGRID Interaction Database: 2011 update.'
    year: null
  - doi: 10.1186/1471-2105-11-550
    pmc: null
    pubmed: null
    title: Localizing triplet periodicity in DNA and cDNA sequences.
    year: null
  - doi: 10.1002/mrd.21130
    pmc: null
    pubmed: null
    title: 'Representing ontogeny through ontology: a developmental biologist''s guide
      to the gene ontology.'
    year: null
  - doi: 10.1093/nar/gkp1018
    pmc: null
    pubmed: null
    title: 'The Gene Ontology in 2010: extensions and refinements.'
    year: null
  - doi: 10.1093/nar/gkp952
    pmc: null
    pubmed: null
    title: 'WormBase: a comprehensive resource for nematode research.'
    year: null
  - doi: 10.1186/1471-2105-10-228
    pmc: null
    pubmed: null
    title: 'Semi-automated curation of protein subcellular localization: a text mining-based
      approach to Gene Ontology (GO) Cellular Component curation.'
    year: null
  - doi: 10.1371/journal.pcbi.1000431
    pmc: null
    pubmed: null
    title: 'The Gene Ontology''s Reference Genome Project: a unified framework for
      functional annotation across species.'
    year: null
  - doi: 10.1186/1471-2105-9-549
    pmc: null
    pubmed: null
    title: nGASP--the nematode genome annotation assessment project.
    year: null
  - doi: 10.1093/nar/gkz920
    pmc: null
    pubmed: null
    title: 'WormBase: a modern Model Organism Information Resource.'
    year: null
  - doi: 10.1093/nar/gkx998
    pmc: null
    pubmed: null
    title: 'WormBase 2017: molting into a new stage.'
    year: null
  - doi: null
    pmc: null
    pubmed: '11125056'
    title: null
    year: null
  - doi: null
    pmc: null
    pubmed: '24194605'
    title: null
    year: null
  - doi: null
    pmc: null
    pubmed: '19910365'
    title: null
    year: null
  - doi: null
    pmc: null
    pubmed: '17991679'
    title: null
    year: null
  - doi: null
    pmc: null
    pubmed: '15608221'
    title: null
    year: null
  - doi: 10.1093/nar/gkz920
    pmc: null
    pubmed: '31642470'
    title: null
    year: null
  re3data:
    description: Launched in 2000, WormBase is an international consortium of biologists
      and computer scientists dedicated to providing the research community with accurate,
      current, accessible information concerning the genetics, genomics and biology
      of C. elegans and some related nematodes. In addition to their curation work,
      all sites have ongoing programs in bioinformatics research to develop the next
      generations of WormBase structure, content and accessibility
    doi: 10.17616/R3089Z
    homepage: https://www.wormbase.org/
    name: WormBase
    prefix: r3d100010424
    synonyms:
    - facilitating insights into nematode biology
    xrefs:
      nif: 0000-00053
      omics: '01664'
  rrid:
    abbreviation: WB, WB REF, WP
    homepage: http://www.wormbase.org
    keywords:
    - FASEB list
    - blast
    - c elegans
    - catalog
    - database
    - gene expression
    - gene function
    - gene mapping
    - gene prediction
    - geneotype
    - genomic sequence
    - genomics
    - ortholog
    - orthology assignment
    - phenotype
    - roundworm
    - transposon family
    - wormmart
    name: WormBase
    prefix: WB-STRAIN:WBStrain
    pubmeds:
    - '24194605'
    - '19910365'
    - '17991679'
    - '15608221'
    scr: 003098
  synonyms:
  - WB
  - WB_REF
  - wb
  - wormbase
  uniprot:
    abbreviation: WormBase
    category: Organism-specific databases
    homepage: https://wormbase.org/
    name: WormBase
    prefix: DB-0110
    publications:
    - doi: 10.1093/nar/gkz920
      pubmed: '31642470'
    uri_format: https://wormbase.org/db/seq/protein?name=$1;class=CDS
  wikidata:
    description: Identifier for a genetic element in Wormbase
    example:
    - WBGene00000875
    - WBGene00000898
    - WBGene00000973
    homepage: http://www.wormbase.org
    miriam: wb
    name: Wormbase Gene ID
    prefix: P3860
    uri_format: https://www.wormbase.org/db/gene/gene?name=$1;class=Gene
wormpep:
  biocontext:
    prefix: WORMPEP
  mappings:
    biocontext: WORMPEP
    miriam: wormpep
    n2t: wormpep
    prefixcommons: wormpep
  miriam:
    deprecated: false
    description: Wormpep contains the predicted proteins from the Caenorhabditis elegans
      genome sequencing project.
    homepage: https://www.wormbase.org/db/seq/protein
    id: '00000031'
    name: Wormpep
    namespaceEmbeddedInLui: false
    pattern: ^CE\d{5}$
    prefix: wormpep
    sampleId: CE28239
    uri_format: https://www.wormbase.org/db/seq/protein?name=$1
  n2t:
    description: Wormpep contains the predicted proteins from the Caenorhabditis elegans
      genome sequencing project.
    example: CE28239
    homepage: https://www.wormbase.org/db/seq/protein
    name: Wormpep (Master)
    namespaceEmbeddedInLui: false
    pattern: ^CE\d{5}$
    prefix: wormpep
    uri_format: https://www.wormbase.org/db/seq/protein?name=WP:$1
  prefix: wormpep
  prefixcommons:
    description: Wormpep contains the predicted proteins from the Caenorhabditis elegans
      genome sequencing project.
    example: CE28239
    homepage: http://www.wormbase.org/db/seq/protein
    keywords:
    - protein
    - structure
    name: Caenorhabditis elegans genome sequencing project protein database
    pattern: ^CE\d{5}$
    prefix: wormpep
    uri_format: http://www.wormbase.org/db/seq/protein?name=$1
worms:
  bartoc:
    abbreviation: WoRMS
    description: The aim of a World Register of Marine Species (WoRMS) is to provide
      an authoritative and comprehensive list of names of marine organisms, including
      information on synonymy. While highest priority goes to valid names, other names
      in use are included so that this register can serve as a guide to interpret
      taxonomic literature. The content of WoRMS is controlled by taxonomic experts,
      not by database managers. WoRMS has an editorial management system where each
      taxonomic group is represented by an expert who has the authority over the content,
      and is responsible for controlling the quality of the information. Each of these
      main taxonomic editors can invite several specialists of smaller groups within
      their area of responsibility to join them. This register of marine species grew
      out of the European Register of Marine Species (ERMS), and its combination with
      several other species registers maintained at the Flanders Marine Institute
      (VLIZ). Rather than building separate registers for all projects, and to make
      sure taxonomy used in these different projects is consistent, VLIZ developed
      a consolidated database called ‘Aphia’. A list of marine species registers included
      in Aphia is available below. MarineSpecies.org is the web interface for this
      database. The WoRMS is an idea that is being developed, and will combine information
      from Aphia with other authoritative marine species lists which are maintained
      by others (e.g. AlgaeBase, FishBase, Hexacorallia, NeMys). Resources to build
      MarineSpecies.org and Aphia were provided mainly by the EU Network of Excellence
      ‘Marine Biodiversity and Ecosystem Functioning’ (MarBEF), and also by the EU
      funded Species 2000 Europe and ERMS projects. Intellectual property rights of
      the European part of the register is managed through the Society for the Management
      of Electronic Biodiversity Data (SMEBD). Similar solutions are now being investigated
      for the other parts of the register. Aphia contains valid species names, synonyms
      and vernacular names, and extra information such as literature and biogeographic
      data. Besides species names, Aphia also contains the higher classification in
      which each scientific name is linked to its parent taxon. The classification
      used is a ‘compromise’ between established systems and recent changes. Its aim
      is to aid data management, rather than suggest any taxonomic or phylogenetic
      opinion on species relationships. Keeping WoRMS up-to-date is a continuous process.
      New information is entered daily by the taxonomic editors and by the members
      of our data management team. Often data also come in from contributions of large
      datasets, such as global or regional species lists. No database of this size
      is without errors and omissions. We can’t promise to make no errors, but we
      do promise to follow up and give feedback on any communications pointing out
      errors. Feedback is very welcome!
    homepage: http://www.marinespecies.org/
    license: CC-BY-3.0
    name: World Register of Marine Species
    prefix: '720'
    wikidata_database: Q604063
  biocontext:
    prefix: WORMS
  contributor_extras:
  - email: meghan.balk@gmail.com
    github: megbalk
    name: Meghan Balk
    orcid: 0000-0003-2699-3066
  fairsharing:
    abbreviation: WoRMS
    contact:
      email: leen.vandepitte@vliz.be
      name: Leen Vandepitte
      orcid: 0000-0002-8160-7941
    description: The aim of a World Register of Marine Species (WoRMS) is to provide
      an authoritative and comprehensive list of names of marine organisms, including
      information on synonymy. While highest priority goes to valid names, other names
      in use are included so that this register can serve as a guide to interpret
      taxonomic literature.
    homepage: http://www.marinespecies.org
    license: CC-BY-4.0
    name: World Register of Marine Species
    prefix: FAIRsharing.7g1bzj
    publications:
    - doi: 10.1371/journal.pone.0194599
      pubmed_id: 29624577
      title: 'A decade of the World Register of Marine Species - General insights
        and experiences from the Data Management Team: Where are we, what have we
        learned and how can we continue?'
    subjects:
    - Environmental Science
    - Taxonomy
    - Biodiversity
    twitter: WRMarineSpecies
  mappings:
    bartoc: '720'
    biocontext: WORMS
    fairsharing: FAIRsharing.7g1bzj
    miriam: worms
    n2t: worms
    wikidata: P850
    wikidata.entity: Q604063
  miriam:
    deprecated: false
    description: The World Register of Marine Species (WoRMS) provides an authoritative
      and comprehensive list of names of marine organisms. It includes synonyms for
      valid taxonomic names allowing a more complete interpretation of taxonomic literature.
      The content of WoRMS is administered by taxonomic experts.
    homepage: http://www.marinespecies.org/
    id: 00000581
    name: World Register of Marine Species
    namespaceEmbeddedInLui: false
    pattern: ^\d+$
    prefix: worms
    sampleId: '146421'
    uri_format: http://www.marinespecies.org/aphia.php?p=taxdetails&id=$1
  n2t:
    description: The World Register of Marine Species (WoRMS) provides an authoritative
      and comprehensive list of names of marine organisms. It includes synonyms for
      valid taxonomic names allowing a more complete interpretation of taxonomic literature.
      The content of WoRMS is administered by taxonomic experts.
    example: '146421'
    homepage: http://www.marinespecies.org/
    name: World Register of Marine Species
    namespaceEmbeddedInLui: false
    pattern: ^\d+$
    prefix: worms
    uri_format: http://www.marinespecies.org/aphia.php?p=taxdetails&id=$1
  prefix: worms
  publications:
  - doi: 10.1371/journal.pone.0194599
    pmc: PMC5889062
    pubmed: '29624577'
    title: 'A decade of the World Register of Marine Species - General insights and
      experiences from the Data Management Team: Where are we, what have we learned
      and how can we continue?'
    year: 2018
  - doi: 10.1371/journal.pone.0194599
    pmc: null
    pubmed: null
    title: 'A decade of the World Register of Marine Species - General insights and
      experiences from the Data Management Team: Where are we, what have we learned
      and how can we continue?'
    year: null
  wikidata:
    description: identifier in the World Register of Marine Species
    example:
    - '11'
    - '145548'
    homepage: https://www.marinespecies.org/aphia.php?p=search
    name: WoRMS-ID for taxa
    pattern: ^[1-9]\d{0,6}$
    prefix: P850
    uri_format: https://www.marinespecies.org/aphia.php?p=taxdetails&id=$1
wos.researcher:
  example: B-5720-2018
  mappings:
    wikidata: P1053
  part_of_database: wos
  prefix: wos.researcher
  wikidata:
    database: Q7315186
    description: identifier for a researcher in a system for scientific authors, redirects
      to a Web of Science ID, along with P3829
    example:
    - J-3403-2017
    - K-8011-2013
    homepage: https://access.clarivate.com/login?app=wos
    name: ResearcherID
    pattern: ^[A-Z]{1,3}-\d{4}-(19|20)\d\d$
    prefix: P1053
    uri_format: https://www.webofscience.com/wos/author/record/$1
wos.work:
  homepage: https://www.webofscience.com
  mappings:
    wikidata: P8372
  part_of_database: wos
  prefix: wos.work
  references:
  - https://github.com/biopragmatics/bioregistry/issues/805
  synonyms:
  - wos
  - wosid
  - wosuid
  wikidata:
    description: 'unique academic work identifier assigned in Web of Science bibliographic
      database (Web of Science Core Collection only and do not include WOS: prefix)'
    example:
    - 000177759000002
    - '000271214700001'
    - '000301355700052'
    - 000503382400004
    - A1953UA43400007
    name: Web of Science work ID
    prefix: P8372
    uri_format: https://www.webofscience.com/wos/woscc/full-record/WOS:$1
wot:
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: he WOT, or Web Of Trust, schema is designed to facilitate the use of
    Public Key Cryptography tools such as PGP or GPG to sign RDF documents and document
    these signatures.
  example: EncryptedDocument
  homepage: http://xmlns.com/wot/0.1/
  lov:
    description: Web Of Trust (wot) RDF vocabulary, described using W3C RDF Schema
      and the Web Ontology Language.
    homepage: http://xmlns.com/wot/0.1/
    keywords:
    - Quality
    - Security
    modified: '2004-02-23'
    name: Web Of Trust
    prefix: wot
    uri_prefix: http://xmlns.com/wot/0.1/$1
  mappings:
    lov: wot
  name: XML Web of Trust Ontology
  prefix: wot
  rdf_uri_format: http://xmlns.com/wot/0.1/$1
  uri_format: http://xmlns.com/wot/0.1/$1
wot.hypermedia:
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: an ontology for links and forms, the main hypermedia controls in use
    on the Web. This ontology offers, among others, a means to reify RDF statements
    interpreted as links between Web resources. It also provides a versatile exchange
    format for links and forms in RESTful Web applications. [from homepage]
  example: AdditionalExpectedResponse
  homepage: https://www.w3.org/2019/wot/hypermedia#
  name: Web of Things Hypermedia Controls Ontology
  prefix: wot.hypermedia
  rdf_uri_format: https://www.w3.org/2019/wot/hypermedia#$1
  uri_format: https://www.w3.org/2019/wot/hypermedia#$1
wot.security:
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: an RDF vocabulary for the security metadata definitions
  example: APIKeySecurityScheme
  homepage: https://www.w3.org/2019/wot/security
  name: Web of Things Security Ontology
  prefix: wot.security
  rdf_uri_format: https://www.w3.org/2019/wot/security#$1
  uri_format: https://www.w3.org/2019/wot/security#$1
wot.td:
  example: description
  mappings:
    tib: td
  prefix: wot.td
  tib:
    description: This ontology aims to model the Web of Things domain according to
      the W3C Interest Group (http://w3c.github.io/wot/)
    download_rdf: https://akswnc7.informatik.uni-leipzig.de/dstreitmatter/archivo/w3.org/2019--wot--td/2021.09.22-190316/2019--wot--td_type=parsed.ttl
    homepage: https://akswnc7.informatik.uni-leipzig.de/dstreitmatter/archivo/w3.org/2019--wot--td/2021.09.22-190316/2019--wot--td_type=pyLodeDoc.html
    keywords:
    - NFDI4ING
    - engineering
    name: Thing Description Ontology
    prefix: td
    tracker: https://github.com/w3c/wot-thing-description/issues
    uri_format: https://www.w3.org/2019/wot/td#$1
wot.tm:
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: The Thing Model (TM) ontology is an RDF axiomatization of the TM concepts,
    one of the building blocks of the Web of Things (WoT). Besides providing an alternative
    to the standard JSON representation format for TM documents, the TM ontology can
    also be used to process contextual information on Things and for alignments with
    other WoT-related ontologies. [from homepage]
  example: model
  homepage: https://www.w3.org/2022/wot/tm
  name: Web of Things Thing Model
  prefix: wot.tm
  rdf_uri_format: https://www.w3.org/2022/wot/tm#$1
  uri_format: https://www.w3.org/2022/wot/tm#$1
wwf.ecoregion:
  comment: ENVO includes xrefs to this resource. See EnvironmentOntology/envo#658
  contributor:
    email: cjmungall@lbl.gov
    github: cmungall
    name: Chris Mungall
    orcid: 0000-0002-6601-2165
  description: WWF ecoregions are large unit of land or water containing a geographically
    distinct assemblage of species, natural communities, and environmental conditions.
  example: AT1402
  github_request_issue: 153
  homepage: https://www.worldwildlife.org/biomes
  mappings:
    wikidata: P1294
    wikidata.entity: Q6617741
  name: World Wildlife Fund Ecoregion
  pattern: ^AT\d+$
  prefix: wwf.ecoregion
  reviewer:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  synonyms:
  - WWF
  uri_format: https://www.worldwildlife.org/ecoregions/$1
  wikidata:
    database: Q6617741
    description: identifier for ecoregions
    example:
    - AA1101
    - AT1201
    homepage: https://www.worldwildlife.org/biomes
    name: WWF ecoregion code
    pattern: ^[A-Z]{2}\d{4}$
    prefix: P1294
    uri_format: https://www.worldwildlife.org/ecoregions/$1
xao:
  aberowl:
    description: XAO represents the anatomy and development of the African frogs Xenopus
      laevis and tropicalis.
    download_owl: http://aber-owl.net/media/ontologies/XAO/35/xao.owl
    homepage: http://www.xenbase.org/anatomy/xao.do?method=display
    name: Xenopus Anatomy Ontology
    prefix: XAO
  bartoc:
    abbreviation: XAO
    description: The Xenopus Anatomical Ontology describes Xenopus anatomy and development
      as a controlled vocabulary of terms, organized in a graphical structure. Tissues
      are shown as being part of other tissues and the timing of their development
      is indicated by start and end stages. The lineage of tissues is represented
      by develops from relationships between different tissues at different developmental
      stages. Many items have been classified according to the Common Anatomy Reference
      Ontology. The ontology is listed at the Open Biomedical Ontologies (OBO Foundry).
    homepage: http://xenbase.org/anatomy/xao.do?method=display
    name: Xenopus Anatomical Ontology
    prefix: '581'
  biocontext:
    prefix: XAO
  bioportal:
    contact:
      email: Virgilio.Ponferrada@cchmc.org
      name: VG Ponferrada
    description: A structured, controlled vocabulary of the anatomy and development
      of the African clawed frogs (Xenopus laevis and tropicalis).
    homepage: http://www.xenbase.org/anatomy/xao.do?method=display
    name: Xenopus Anatomy Ontology
    prefix: XAO
    publications:
    - http://www.jbiomedsem.com/content/4/1/31/abstract
    version: releases/2024-09-03
  example: 0004486
  fairsharing:
    abbreviation: XAO
    contact:
      email: segerdel@ohsu.edu
      name: Erik Segerdell
      orcid: 0000-0002-9611-1279
    description: The Xenopus Anatomical Ontology (XAO) describes Xenopus anatomy and
      embryological development using a 'controlled vocabulary' of anatomy terms that
      are organized in an hierarchy with a graphical structure. XAO terms describe
      gene expression, and the XAO is constantly being updated in response to the
      latest published Xenopus research.
    domains:
    - morphology
    - structure
    - life cycle
    - life cycle stage
    homepage: http://www.xenbase.org/anatomy/xao.do?method=display
    license: CC-BY-3.0
    name: Xenopus Anatomy Ontology
    prefix: FAIRsharing.17zapb
    publications:
    - doi: 10.1186/2041-1480-4-31
      pubmed: '24139024'
      title: 'Enhanced XAO: the ontology of Xenopus anatomy and development underpins
        more accurate annotation of gene expression and queries on Xenbase'
      year: 2013
    - doi: 10.1186/1471-213x-8-92
      pubmed: '18817563'
      title: An ontology for Xenopus anatomy and development
      year: 2008
    repository: https://github.com/xenopus-anatomy
    subjects:
    - Life Science
    - Anatomy
    - Developmental Biology
  mappings:
    aberowl: XAO
    bartoc: '581'
    biocontext: XAO
    bioportal: XAO
    fairsharing: FAIRsharing.17zapb
    obofoundry: xao
    ols: xao
    ontobee: XAO
    wikidata: P4495
    wikidata.entity: Q42400040
  obofoundry:
    appears_in:
    - xpo
    contact: Erik.Segerdell@cchmc.org
    contact.github: seger
    contact.label: Erik Segerdell
    contact.orcid: 0000-0002-9611-1279
    deprecated: false
    description: XAO represents the anatomy and development of the African frogs Xenopus
      laevis and tropicalis.
    domain: anatomy and development
    download.obo: http://purl.obolibrary.org/obo/xao.obo
    download.owl: http://purl.obolibrary.org/obo/xao.owl
    homepage: http://www.xenbase.org/anatomy/xao.do?method=display
    license: CC BY 3.0
    license.url: http://creativecommons.org/licenses/by/3.0/
    name: Xenopus Anatomy Ontology
    preferredPrefix: XAO
    prefix: xao
    publications:
    - id: https://www.ncbi.nlm.nih.gov/pubmed/18817563
      title: An ontology for Xenopus anatomy and development.
    - id: https://www.ncbi.nlm.nih.gov/pubmed/24139024
      title: 'Enhanced XAO: the ontology of Xenopus anatomy and development underpins
        more accurate annotation of gene expression and queries on Xenbase.'
    repository: https://github.com/xenopus-anatomy/xao
  ols:
    description: XAO represents the anatomy and development of the African frogs Xenopus
      laevis and tropicalis.
    download_owl: http://purl.obolibrary.org/obo/xao.owl
    homepage: http://www.xenbase.org/anatomy/xao.do?method=display
    name: Xenopus Anatomy Ontology
    prefix: xao
    tracker: https://github.com/xenopus-anatomy/xao/issues
    version: '2024-09-03'
    version.iri: http://purl.obolibrary.org/obo/xao/releases/2024-09-03/xao.owl
  ontobee:
    library: Foundry
    name: Xenopus Anatomy Ontology
    prefix: XAO
  pattern: ^\d{7}$
  prefix: xao
  publications:
  - doi: 10.1186/2041-1480-4-31
    pmc: PMC3816597
    pubmed: '24139024'
    title: 'Enhanced XAO: the ontology of Xenopus anatomy and development underpins
      more accurate annotation of gene expression and queries on Xenbase'
    year: 2013
  - doi: 10.1186/1471-213x-8-92
    pmc: PMC2561031
    pubmed: '18817563'
    title: An ontology for Xenopus anatomy and development
    year: 2008
  - doi: null
    pmc: null
    pubmed: '18817563'
    title: An ontology for Xenopus anatomy and development
    year: null
  - doi: null
    pmc: null
    pubmed: '24139024'
    title: 'Enhanced XAO: the ontology of Xenopus anatomy and development underpins
      more accurate annotation of gene expression and queries on Xenbase'
    year: null
  - doi: 10.1186/2041-1480-4-31
    pmc: null
    pubmed: '24139024'
    title: 'Enhanced XAO: the ontology of Xenopus anatomy and development underpins
      more accurate annotation of gene expression and queries on Xenbase'
    year: 2013
  - doi: 10.1186/1471-213x-8-92
    pmc: null
    pubmed: '18817563'
    title: An ontology for Xenopus anatomy and development
    year: 2008
  - doi: null
    pmc: null
    pubmed: '18817563'
    title: An ontology for Xenopus anatomy and development
    year: null
  - doi: null
    pmc: null
    pubmed: '24139024'
    title: 'Enhanced XAO: the ontology of Xenopus anatomy and development underpins
      more accurate annotation of gene expression and queries on Xenbase'
    year: null
  - doi: 10.1186/2041-1480-4-31
    pmc: null
    pubmed: '24139024'
    title: 'Enhanced XAO: the ontology of Xenopus anatomy and development underpins
      more accurate annotation of gene expression and queries on Xenbase'
    year: 2013
  - doi: 10.1186/1471-213x-8-92
    pmc: null
    pubmed: '18817563'
    title: An ontology for Xenopus anatomy and development
    year: 2008
  uri_format: http://purl.obolibrary.org/obo/XAO_$1
  wikidata:
    description: identifier for an anatomical structure in the Xenopus Anatomical
      Ontology, a controlled vocubulary for describing Xenopus anatomy and embryological
      development
    example:
    - XAO_0000010
    - XAO_0000168
    - XAO_0000388
    name: Xenopus Anatomical Ontology ID
    pattern: ^XAO_\d{7}$
    prefix: P4495
xco:
  aberowl:
    description: Conditions under which physiological and morphological measurements
      are made both in the clinic and in studies involving humans or model organisms.
    download_owl: http://aber-owl.net/media/ontologies/XCO/154/xco.owl
    homepage: https://rgd.mcw.edu/rgdweb/ontology/view.html?acc_id=XCO:0000000
    name: Experimental condition ontology
    prefix: XCO
  biocontext:
    prefix: XCO
  bioportal:
    contact:
      email: akwitek@mcw.edu
      name: Anne Kwitek
    description: The Experimental Conditions Ontology is designed to represent the
      conditions under which physiological and morphological measurements are made
      both in the clinic and in studies involving humans or model organisms.
    homepage: https://rgd.mcw.edu/rgdweb/ontology/view.html?acc_id=XCO:0000000
    name: Experimental Conditions Ontology
    prefix: XCO
    publications:
    - http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3361058/
    version: '4.205'
  example: 0000780
  fairsharing:
    abbreviation: XCO
    contact:
      email: shimoyama@mcw.edu
      name: Mary Shimoyama
      orcid: 0000-0003-1176-0796
    description: The Experimental Conditions Ontology is designed to represent the
      conditions under which physiological and morphological measurements are made
      both in the clinic and in studies involving humans or model organisms.
    domains:
    - Experimental measurement
    - assay
    - study design
    - experimentally determined
    homepage: https://rgd.mcw.edu/rgdweb/ontology/view.html?acc_id=XCO:0000000
    license: CC-BY-4.0
    name: Experimental Conditions Ontology
    prefix: FAIRsharing.x39h5y
    publications:
    - doi: 10.3389/fgene.2012.00087
      pubmed: '22654893'
      title: Three ontologies to define phenotype measurement data
      year: 2012
    subjects:
    - Life Science
    - Biomedical Science
    twitter: ratgenome
    user_defined_tags:
    - Experimental condition
  mappings:
    aberowl: XCO
    biocontext: XCO
    bioportal: XCO
    fairsharing: FAIRsharing.x39h5y
    obofoundry: xco
    ols: xco
    ontobee: XCO
    prefixcommons: xco
    wikidata.entity: Q81661839
  obofoundry:
    appears_in:
    - agro
    - ecto
    contact: jrsmith@mcw.edu
    contact.github: jrsjrs
    contact.label: Jennifer Smith
    contact.orcid: 0000-0002-6443-9376
    deprecated: false
    description: Conditions under which physiological and morphological measurements
      are made both in the clinic and in studies involving humans or model organisms.
    domain: health
    download.obo: http://purl.obolibrary.org/obo/xco.obo
    download.owl: http://purl.obolibrary.org/obo/xco.owl
    homepage: https://rgd.mcw.edu/rgdweb/ontology/view.html?acc_id=XCO:0000000
    license: CC0 1.0
    license.url: https://creativecommons.org/publicdomain/zero/1.0/
    logo: http://rgd.mcw.edu/common/images/rgd_LOGO_blue_rgd.gif
    name: Experimental condition ontology
    preferredPrefix: XCO
    prefix: xco
    publications:
    - id: https://www.ncbi.nlm.nih.gov/pubmed/22654893
      title: Three ontologies to define phenotype measurement data.
    - id: https://www.ncbi.nlm.nih.gov/pubmed/24103152
      title: 'The clinical measurement, measurement method and experimental condition
        ontologies: expansion, improvements and new applications.'
    repository: https://github.com/rat-genome-database/XCO-experimental-condition-ontology
  ols:
    description: Conditions under which physiological and morphological measurements
      are made both in the clinic and in studies involving humans or model organisms.
    download_owl: http://purl.obolibrary.org/obo/xco.owl
    homepage: https://rgd.mcw.edu/rgdweb/ontology/view.html?acc_id=XCO:0000000
    name: Experimental condition ontology
    prefix: xco
    tracker: https://github.com/rat-genome-database/XCO-experimental-condition-ontology/issues
    version: '4.221'
    version.iri: http://purl.obolibrary.org/obo/xco/4.221/xco.owl
  ontobee:
    library: Library
    name: Experimental condition ontology
    prefix: XCO
  pattern: ^\d{7}$
  prefix: xco
  prefixcommons:
    bioportal: '1585'
    description: The Experimental Conditions Ontology is designed to represent the
      conditions under which physiological and morphological measurements are made
      both in the clinic and in studies involving humans or model organisms.
    example: XCO_0000001
    homepage: http://sourceforge.net/projects/phenoonto/
    keywords:
    - obo
    - measurement
    name: Experimental Conditions Ontology
    pattern: ^XCO_\d{7}$
    prefix: xco
  publications:
  - doi: 10.1186/2041-1480-4-26
    pmc: PMC3882879
    pubmed: '24103152'
    title: 'The clinical measurement, measurement method and experimental condition
      ontologies: expansion, improvements and new applications'
    year: 2013
  - doi: 10.3389/fgene.2012.00087
    pmc: PMC3361058
    pubmed: '22654893'
    title: Three ontologies to define phenotype measurement data
    year: 2012
  - doi: null
    pmc: null
    pubmed: '22654893'
    title: Three ontologies to define phenotype measurement data
    year: null
  - doi: null
    pmc: null
    pubmed: '24103152'
    title: 'The clinical measurement, measurement method and experimental condition
      ontologies: expansion, improvements and new applications'
    year: null
  - doi: 10.3389/fgene.2012.00087
    pmc: null
    pubmed: '22654893'
    title: Three ontologies to define phenotype measurement data
    year: 2012
  - doi: null
    pmc: null
    pubmed: '22654893'
    title: Three ontologies to define phenotype measurement data
    year: null
  - doi: null
    pmc: null
    pubmed: '24103152'
    title: 'The clinical measurement, measurement method and experimental condition
      ontologies: expansion, improvements and new applications'
    year: null
  - doi: 10.3389/fgene.2012.00087
    pmc: null
    pubmed: '22654893'
    title: Three ontologies to define phenotype measurement data
    year: 2012
  - doi: null
    pmc: null
    pubmed: '22654893'
    title: Three ontologies to define phenotype measurement data
    year: null
  - doi: null
    pmc: null
    pubmed: '24103152'
    title: 'The clinical measurement, measurement method and experimental condition
      ontologies: expansion, improvements and new applications'
    year: null
  - doi: 10.3389/fgene.2012.00087
    pmc: null
    pubmed: '22654893'
    title: Three ontologies to define phenotype measurement data
    year: 2012
  - doi: null
    pmc: null
    pubmed: '22654893'
    title: Three ontologies to define phenotype measurement data
    year: null
  - doi: null
    pmc: null
    pubmed: '24103152'
    title: 'The clinical measurement, measurement method and experimental condition
      ontologies: expansion, improvements and new applications'
    year: null
  - doi: 10.3389/fgene.2012.00087
    pmc: null
    pubmed: '22654893'
    title: Three ontologies to define phenotype measurement data
    year: 2012
  twitter: ratgenome
  uri_format: http://purl.obolibrary.org/obo/XCO_$1
xenbase:
  biocontext:
    prefix: Xenbase
    uri_format: http://www.xenbase.org/gene/showgene.do?method=display&geneId=$1
  biolink:
    is_identifiers: false
    is_obo: false
    prefix: Xenbase
    uri_format: http://www.xenbase.org/gene/showgene.do?method=display&geneId=$1
  contact:
    email: troy_pells@yahoo.ca
    github: pellst
    name: Troy Pells
    orcid: 0000-0002-2340-5356
  edam:
    description: A unique identifier of gene in the Xenbase database.
    name: Gene ID (Xenbase)
    obsolete: false
    prefix: '2738'
  fairsharing:
    abbreviation: Xenbase
    contact:
      email: xenbase@cchmc.org
      name: Aaron Zorn
      orcid: 0000-0003-3217-3590
    description: Xenbase is the model organism database for Xenopus laevis and X.
      (Silurana) tropicalis which was created to improve knowledge of developmental
      and disease processes. Through curation and automated data provisioning from
      various sources, Xenbase aims to integrate the body of knowledge on Xenopus
      genomics and biology together with the visualization of biologically-significant
      interactions.
    homepage: http://www.xenbase.org
    license: CC-BY-3.0
    name: Xenopus laevis and tropicalis biology and genomics resource
    prefix: FAIRsharing.jrv6wj
    providers:
    - code: agr
      description: Xenbase through the Alliance of Genome Resources
      homepage: https://www.alliancegenome.org
      name: Xenbase through the Alliance of Genome Resources
      uri_format: https://www.alliancegenome.org/gene/Xenbase:$1
    publications:
    - doi: 10.1093/database/bau108
      pubmed_id: 25380782
      title: 'The Virtual Xenbase: transitioning an online bioinformatics resource
        to a private cloud'
    - doi: 10.1186/2041-1480-4-31
      pubmed_id: 24139024
      title: 'Enhanced XAO: the ontology of Xenopus anatomy and development underpins
        more accurate annotation of gene expression and queries on Xenbase.'
    - doi: 10.1093/nar/gkp953
      pubmed_id: 19884130
      title: 'Xenbase: gene expression and improved integration.'
    - doi: 10.1016/j.ydbio.2016.03.030
      pubmed_id: 27039265
      title: Xenopus genomic data and browser resources.
    - doi: 10.1093/nar/gku956
      pubmed_id: 25313157
      title: Xenbase, the Xenopus model organism database; new virtualized system,
        data types and genomes
    - doi: doi:10.3389/fphys.2019.00154
      pubmed_id: 30863320
      title: 'Xenbase: Facilitating the Use of Xenopus to Model Human Disease.'
    - doi: 10.1093/nar/gkz933
      pubmed_id: 31733057
      title: 'Xenbase: deep integration of GEO & SRA RNA-seq and ChIP-seq data in
        a model organism database.'
    - doi: doi:10.1007/978-1-4939-7737-6_10.
      pubmed_id: 29761462
      title: 'Navigating Xenbase: An Integrated Xenopus Genomics and Gene Expression
        Database.'
    - doi: 10.1186/s12859-022-04636-8
      pubmed_id: 35317743
      title: 'The Xenopus phenotype ontology: bridging model organism phenotype data
        to human health and development.'
    subjects:
    - Functional Genomics
    - Anatomy
    - Genomics
    - Genetics
    - Proteomics
    - Developmental Biology
    - Cell Biology
    twitter: Xenbase
  go:
    homepage: http://www.xenbase.org/
    name: Xenbase
    prefix: Xenbase
  logo: https://www.xenbase.org/xenbase/img/Xenbase-Logo-Small.png
  mappings:
    biocontext: Xenbase
    biolink: Xenbase
    edam: '2738'
    fairsharing: FAIRsharing.jrv6wj
    go: Xenbase
    miriam: xenbase
    n2t: xenbase
    ncbi: Xenbase
    prefixcommons: xenbase
    re3data: r3d100011331
    uniprot: DB-0129
  miriam:
    deprecated: false
    description: Xenbase is the model organism database for Xenopus laevis and X.
      (Silurana) tropicalis. It contains genomic, development data and community information
      for Xenopus research. it includes gene expression patterns that incorporates
      image data from the literature, large scale screens and community submissions.
    homepage: https://www.xenbase.org/
    id: 00000186
    name: Xenbase
    namespaceEmbeddedInLui: false
    pattern: ^XB\-\w+\-\d+$
    prefix: xenbase
    sampleId: XB-GENE-922462
    uri_format: https://www.xenbase.org/entry/$1
  n2t:
    description: Xenbase is the model organism database for Xenopus laevis and X.
      (Silurana) tropicalis. It contains genomic, development data and community information
      for Xenopus research. it includes gene expression patterns that incorporates
      image data from the literature, large scale screens and community submissions.
    example: '922462'
    homepage: http://www.xenbase.org/
    name: Xenbase at University of Calgary
    namespaceEmbeddedInLui: false
    pattern: ^(XB-GENE-)?\d+$
    prefix: xenbase
    uri_format: http://www.xenbase.org/gene/showgene.do?method=displayGeneSummary&geneId=$1
  ncbi:
    example: XB-GENE-1019547
    homepage: http://www.xenbase.org/common/
    name: Xenopus laevis and tropicalis biology and genomics resource
    prefix: Xenbase
  prefix: xenbase
  prefixcommons:
    description: Xenbase is the model organism database for Xenopus laevis and X.
      (Silurana) tropicalis. It contains genomic, development data and community information
      for Xenopus research. it includes gene expression patterns that incorporates
      image data from the literature, large scale screens and community submissions.
    example: '6453898'
    homepage: http://www.xenbase.org
    keywords:
    - expression
    - genome
    name: Xenopus laevis and tropicalis biology and genomics resource
    pattern: ^\d+$
    prefix: xenbase
    pubmed_ids:
    - '19884130'
    uri_format: http://www.xenbase.org/gene/showgene.do?method=display&geneId=$1
  publications:
  - doi: 10.1186/s12859-022-04636-8
    pmc: PMC8939077
    pubmed: '35317743'
    title: 'The Xenopus phenotype ontology: bridging model organism phenotype data
      to human health and development'
    year: 2022
  - doi: 10.1093/nar/gkz933
    pmc: PMC7145613
    pubmed: '31733057'
    title: 'Xenbase: deep integration of GEO & SRA RNA-seq and ChIP-seq data in a
      model organism database'
    year: 2020
  - doi: 10.3389/fphys.2019.00154
    pmc: PMC6399412
    pubmed: '30863320'
    title: 'Xenbase: Facilitating the Use of'
    year: 2019
  - doi: 10.1007/978-1-4939-7737-6_10
    pmc: PMC6853059
    pubmed: '29761462'
    title: 'Navigating Xenbase: An Integrated Xenopus Genomics and Gene Expression
      Database'
    year: 2018
  - doi: 10.1093/nar/gkx936
    pmc: PMC5753396
    pubmed: '29059324'
    title: 'Xenbase: a genomic, epigenomic and transcriptomic model organism database'
    year: 2018
  - doi: 10.1016/j.ydbio.2016.03.030
    pmc: PMC5045824
    pubmed: '27039265'
    title: Xenopus genomic data and browser resources
    year: 2016
  - doi: 10.1093/database/bau108
    pmc: PMC4224262
    pubmed: '25380782'
    title: 'The Virtual Xenbase: transitioning an online bioinformatics resource to
      a private cloud'
    year: 2014
  - doi: 10.1093/nar/gku956
    pmc: PMC4384024
    pubmed: '25313157'
    title: Xenbase, the Xenopus model organism database; new virtualized system, data
      types and genomes
    year: 2014
  - doi: 10.1186/2041-1480-4-31
    pmc: PMC3816597
    pubmed: '24139024'
    title: 'Enhanced XAO: the ontology of Xenopus anatomy and development underpins
      more accurate annotation of gene expression and queries on Xenbase'
    year: 2013
  - doi: 10.1093/nar/gkp953
    pmc: PMC2808955
    pubmed: '19884130'
    title: 'Xenbase: gene expression and improved integration'
    year: 2009
  - doi: 10.1093/database/bau108
    pmc: null
    pubmed: null
    title: 'The Virtual Xenbase: transitioning an online bioinformatics resource to
      a private cloud'
    year: null
  - doi: 10.1186/2041-1480-4-31
    pmc: null
    pubmed: null
    title: 'Enhanced XAO: the ontology of Xenopus anatomy and development underpins
      more accurate annotation of gene expression and queries on Xenbase.'
    year: null
  - doi: 10.1093/nar/gkp953
    pmc: null
    pubmed: null
    title: 'Xenbase: gene expression and improved integration.'
    year: null
  - doi: 10.1016/j.ydbio.2016.03.030
    pmc: null
    pubmed: null
    title: Xenopus genomic data and browser resources.
    year: null
  - doi: 10.1093/nar/gku956
    pmc: null
    pubmed: null
    title: Xenbase, the Xenopus model organism database; new virtualized system, data
      types and genomes
    year: null
  - doi: doi:10.3389/fphys.2019.00154
    pmc: null
    pubmed: null
    title: 'Xenbase: Facilitating the Use of Xenopus to Model Human Disease.'
    year: null
  - doi: 10.1093/nar/gkz933
    pmc: null
    pubmed: null
    title: 'Xenbase: deep integration of GEO & SRA RNA-seq and ChIP-seq data in a
      model organism database.'
    year: null
  - doi: doi:10.1007/978-1-4939-7737-6_10.
    pmc: null
    pubmed: null
    title: 'Navigating Xenbase: An Integrated Xenopus Genomics and Gene Expression
      Database.'
    year: null
  - doi: 10.1186/s12859-022-04636-8
    pmc: null
    pubmed: null
    title: 'The Xenopus phenotype ontology: bridging model organism phenotype data
      to human health and development.'
    year: null
  - doi: null
    pmc: null
    pubmed: '19884130'
    title: null
    year: null
  - doi: 10.1093/genetics/iyad018
    pmc: null
    pubmed: '36755307'
    title: null
    year: null
  re3data:
    description: Xenbase's mission is to provide the international research community
      with a comprehensive, integrated and easy to use web based resource that gives
      access the diverse and rich genomic, expression and functional data available
      from Xenopus research. Xenbase also provides a critical data sharing infrastructure
      for many other NIH-funded projects, and is a focal point for the Xenopus community.
      In addition to our primary goal of supporting Xenopus researchers, Xenbase enhances
      the availability and visibility of Xenopus data to the broader biomedical research
      community.
    doi: 10.17616/R3JH0X
    homepage: https://www.xenbase.org/xenbase/
    name: Xenbase
    prefix: r3d100011331
    synonyms:
    - Xenopus Genomics Database
    xrefs:
      nif: 0000-01286
  synonyms:
  - Xenbase
  uniprot:
    abbreviation: Xenbase
    category: Organism-specific databases
    homepage: https://www.xenbase.org/xenbase/
    name: Xenopus laevis and tropicalis biology and genomics resource
    prefix: DB-0129
    publications:
    - doi: 10.1093/genetics/iyad018
      pubmed: '36755307'
    uri_format: https://www.xenbase.org/gene/showgene.do?method=display&geneId=$1
  uri_format: https://www.xenbase.org/entry/$1
xhv:
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: This is a vocabulary collection utilized by XHTML Family modules and
    document types using XHTML Modularization, including XHTML Role and XHTML + RDFa
    as defined in rdfa-syntax. The XHTML specifications are developed by the W3C XHTML
    2 Working Group as part of the W3C HTML Activity. [from homepage]
  example: alternate
  homepage: https://www.w3.org/1999/xhtml/vocab
  lov:
    description: This is a vocabulary collection utilized by XHTML Family modules
      and document types using XHTML Modularization, including XHTML Role and XHTML
      + RDFa as defined in rdfa-syntax.
    homepage: http://www.w3.org/1999/xhtml/vocab
    keywords:
    - API
    modified: '2010-01-27'
    name: XHTML Vocabulary
    prefix: xhv
    uri_prefix: http://www.w3.org/1999/xhtml/vocab#$1
  mappings:
    lov: xhv
    zazuko: xhv
  name: XHTML Vocabulary
  prefix: xhv
  uri_format: http://www.w3.org/1999/xhtml/vocab#$1
  zazuko:
    prefix: xhv
    uri_format: http://www.w3.org/1999/xhtml/vocab#$1
ximbio:
  cellosaurus:
    category: Cell line collections (Providers)
    homepage: https://ximbio.com
    name: Ximbio reagents online portal
    prefix: Ximbio
    uri_format: https://ximbio.com/reagent/$1
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  example: '151022'
  homepage: https://ximbio.com
  mappings:
    cellosaurus: Ximbio
  name: Ximbio
  pattern: ^\d+$
  prefix: ximbio
  uri_format: https://ximbio.com/reagent/$1
xkos:
  example: belongsTo
  homepage: http://rdf-vocabulary.ddialliance.org/xkos
  lov:
    description: An extension of SKOS for representaion of nomenclatures
    homepage: http://rdf-vocabulary.ddialliance.org/xkos
    keywords:
    - Vocabularies
    modified: '2016-03-20'
    name: XKOS
    prefix: xkos
    uri_prefix: http://rdf-vocabulary.ddialliance.org/xkos#$1
  mappings:
    lov: xkos
    zazuko: xkos
  name: An SKOS extension for representing statistical classifications
  prefix: xkos
  zazuko:
    prefix: xkos
    uri_format: http://rdf-vocabulary.ddialliance.org/xkos#$1
xl:
  aberowl:
    name: Cross-linker reagents ontology
    prefix: XL
  biocontext:
    prefix: XL
  deprecated: true
  mappings:
    aberowl: XL
    biocontext: XL
    ols: xl
    ontobee: XL
  ols:
    contact: psidev-ms-vocab@lists.sourceforge.net
    description: A structured controlled vocabulary for cross-linking reagents used
      with proteomics mass spectrometry.
    download: http://purl.obolibrary.org/obo/xl.owl
    homepage: http://www.psidev.info/groups/controlled-vocabularies
    name: Cross-linker reagents ontology
    prefix: xl
  ontobee:
    library: Library
    name: Cross-linker reagents ontology
    prefix: XL
  prefix: xl
xlmod:
  aberowl:
    description: A structured controlled vocabulary for cross-linking reagents used
      with proteomics mass spectrometry.
    download_owl: http://aber-owl.net/media/ontologies/XLMOD/4/xlmod.owl
    homepage: http://www.psidev.info/groups/controlled-vocabularies
    name: HUPO-PSI cross-linking and derivatization reagents controlled vocabulary
    prefix: XLMOD
  bioportal:
    contact:
      email: gerhard.mayer@rub.de
      name: Gerhard Mayer
    description: XLMOD is an ontology for cross-linking mass spectrometry reagents
      and GC-MS derivatization reagents.
    homepage: https://github.com/HUPO-PSI/mzIdentML/tree/master/cv
    name: mass spectrometry cross-linking and derivatization reagents
    prefix: XLMOD
    version: release/2019-10-28
  contact:
    email: gerhard.mayer@rub.de
    github: germa
    name: Gerhard Mayer
    orcid: 0000-0002-1767-2343
  example: '00050'
  fairsharing:
    abbreviation: XLMOD
    contact:
      email: lutz.fischer@tu-berlin.de
      name: Lutz Fischer
      orcid: 0000-0003-4978-0864
    description: The XLMOD ontology is a structured, controlled vocabulary for cross-linking
      reagents and cross-linker related post-translational modifications used in cross-linking
      mass spectrometry experiments and derivatization reagents for GC-MS. Developed
      by the HUPO Proteomics Standards Initiative (PSI).
    domains:
    - Mass spectrum
    - Experimental measurement
    - reagent
    - gas chromatography
    - mass spectrometry assay
    homepage: https://github.com/HUPO-PSI/xlmod-CV
    license: CC-BY-3.0
    name: HUPO-PSI cross-linking and derivatization reagents controlled vocabulary
    prefix: FAIRsharing.6ccbe6
    repository: https://github.com/HUPO-PSI/xlmod-CV
    subjects:
    - Metabolomics
    - Chemical Biology
    - Omics
  mappings:
    aberowl: XLMOD
    bioportal: XLMOD
    fairsharing: FAIRsharing.6ccbe6
    obofoundry: xlmod
    ols: xlmod
    ontobee: XLMOD
    wikidata.entity: Q81661841
  obofoundry:
    contact: lutz.fischer@tu-berlin.de
    contact.github: lutzfischer
    contact.label: Lutz Fischer
    contact.orcid: 0000-0003-4978-0864
    deprecated: false
    description: A structured controlled vocabulary for cross-linking reagents used
      with proteomics mass spectrometry.
    domain: chemistry and biochemistry
    download.obo: http://purl.obolibrary.org/obo/xlmod.obo
    download.owl: http://purl.obolibrary.org/obo/xlmod.owl
    homepage: http://www.psidev.info/groups/controlled-vocabularies
    license: CC BY 3.0
    license.url: https://creativecommons.org/licenses/by/3.0/
    name: HUPO-PSI cross-linking and derivatization reagents controlled vocabulary
    preferredPrefix: XLMOD
    prefix: xlmod
    repository: https://github.com/HUPO-PSI/xlmod-CV
  ols:
    contact: psidev-ms-vocab@lists.sourceforge.net
    description: A structured controlled vocabulary for cross-linking reagents used
      with proteomics mass spectrometry.
    download_owl: http://purl.obolibrary.org/obo/xlmod.owl
    homepage: http://www.psidev.info/groups/controlled-vocabularies
    name: HUPO-PSI cross-linking and derivatization reagents controlled vocabulary
    prefix: xlmod
    tracker: https://github.com/HUPO-PSI/xlmod-CV/issues
    version: 1.5.1
    version.iri: http://purl.obolibrary.org/obo/xlmod/1.5.1/xlmod.owl
  ontobee:
    library: Library
    name: HUPO-PSI cross-linking and derivatization reagents controlled vocabulary
    prefix: XLMOD
  pattern: ^\d{5}$
  prefix: xlmod
  uri_format: http://purl.obolibrary.org/obo/XLMOD_$1
xmetdb:
  banana: XMETDB
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  deprecated: true
  description: Metabolites in the Xenobiotics Metabolism Database.
  example: '171'
  homepage: https://xmetdb.org
  name: Xenobiotics Metabolism Database
  pattern: ^\d+$
  prefix: xmetdb
  uri_format: http://www.xmetdb.org/xmetdb/protocol/$1
xml:
  biocontext:
    prefix: xml
    uri_format: http://www.w3.org/XML/1998/namespace$1
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: The Extensible Markup Language (XML) is a subset of SGML that is completely
    described in this document. Its goal is to enable generic SGML to be served, received,
    and processed on the Web in the way that is now possible with HTML. XML has been
    designed for ease of implementation and for interoperability with both SGML and
    HTML.
  example: lang
  fairsharing:
    abbreviation: XML
    description: The Extensible Markup Language (XML) describes a class of data objects
      called XML documents and partially describes the behavior of computer programs
      which process them. XML is an application profile or restricted form of SGML,
      the Standard Generalized Markup Language [ISO 8879]. By construction, XML documents
      are conforming SGML documents. XML documents are made up of storage units called
      entities, which contain either parsed or unparsed data. Parsed data is made
      up of characters, some of which form character data, and some of which form
      markup. Markup encodes a description of the document's storage layout and logical
      structure. XML provides a mechanism to impose constraints on the storage layout
      and logical structure.
    homepage: https://www.w3.org/TR/xml/
    name: Extensible Markup Language
    prefix: FAIRsharing.b5cc91
    publications: []
    subjects:
    - Subject Agnostic
  homepage: https://www.w3.org/TR/xml/
  mappings:
    biocontext: xml
    fairsharing: FAIRsharing.b5cc91
  name: Extensible Markup Language
  prefix: xml
  uri_format: http://www.w3.org/XML/1998/namespace#$1
xpo:
  aberowl:
    description: XPO represents anatomical, cellular, and gene function phenotypes
      occurring throughout the development of the African frogs Xenopus laevis and
      tropicalis.
    download_owl: http://aber-owl.net/media/ontologies/XPO/17/xpo.owl
    homepage: https://github.com/obophenotype/xenopus-phenotype-ontology
    name: Xenopus Phenotype Ontology
    prefix: XPO
  biolink:
    is_identifiers: false
    is_obo: true
    prefix: XPO
    uri_format: http://purl.obolibrary.org/obo/XPO_$1
  bioportal:
    contact:
      email: esegerd3@gmail.com
      name: Erik Segerdell
    description: An ontology of anatomical, cellular, and gene function phenotypes
      in Xenopus, the African clawed frogs. The Xenopus Phenotype Ontology represents
      and standardizes anatomical, the African clawed frogs. The XPO is being designed
      primarily to support phenotype curation in Xenbase, the model organism database
      for Xenopus, and to facilitate mappings between frog phenotypes and human disease.,
      XPO represents anatomical, and gene function phenotypes occurring throughout
      the development of the African frogs Xenopus laevis and tropicalis.
    homepage: https://github.com/obophenotype/xenopus-phenotype-ontology
    license: CC-BY-3.0
    name: Xenopus Phenotype Ontology
    prefix: XPO
    version: '2025-07-25'
  example: '0100002'
  mappings:
    aberowl: XPO
    biolink: XPO
    bioportal: XPO
    obofoundry: xpo
    ols: xpo
    ontobee: XPO
    wikidata.entity: Q81661843
  obofoundry:
    contact: Erik.Segerdell@cchmc.org
    contact.github: seger
    contact.label: Erik Segerdell
    contact.orcid: 0000-0002-9611-1279
    depends_on:
    - bfo
    - chebi
    - cl
    - go
    - iao
    - pato
    - ro
    - xao
    deprecated: false
    description: XPO represents anatomical, cellular, and gene function phenotypes
      occurring throughout the development of the African frogs Xenopus laevis and
      tropicalis.
    domain: phenotype
    download.obo: http://purl.obolibrary.org/obo/xpo.obo
    download.owl: http://purl.obolibrary.org/obo/xpo.owl
    homepage: https://github.com/obophenotype/xenopus-phenotype-ontology
    license: CC BY 3.0
    license.url: http://creativecommons.org/licenses/by/3.0/
    name: Xenopus Phenotype Ontology
    preferredPrefix: XPO
    prefix: xpo
    publications:
    - id: https://www.ncbi.nlm.nih.gov/pubmed/35317743
      title: 'The Xenopus phenotype ontology: bridging model organism phenotype data
        to human health and development.'
    repository: https://github.com/obophenotype/xenopus-phenotype-ontology
  ols:
    description: XPO represents anatomical, cellular, and gene function phenotypes
      occurring throughout the development of the African frogs Xenopus laevis and
      tropicalis.
    download_owl: http://purl.obolibrary.org/obo/xpo.owl
    homepage: https://github.com/obophenotype/xenopus-phenotype-ontology
    name: Xenopus Phenotype Ontology
    prefix: xpo
    tracker: https://github.com/obophenotype/xenopus-phenotype-ontology/issues
    version: '2025-07-25'
    version.iri: http://purl.obolibrary.org/obo/xpo/releases/2025-07-25/xpo.owl
  ontobee:
    library: Library
    name: Xenopus Phenotype Ontology
    prefix: XPO
  pattern: ^\d+$
  prefix: xpo
  publications:
  - doi: 10.1186/s12859-022-04636-8
    pmc: PMC8939077
    pubmed: '35317743'
    title: 'The Xenopus phenotype ontology: bridging model organism phenotype data
      to human health and development'
    year: 2022
  uri_format: http://purl.obolibrary.org/obo/XPO_$1
xsd:
  biocontext:
    prefix: xsd
    uri_format: http://www.w3.org/2001/XMLSchema#$1
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: This document describes the XML Schema namespace. It also contains
    a directory of links to these related resources, using Resource Directory Description
    Language.
  example: decimal
  homepage: http://www.w3.org/2001/XMLSchema
  lov:
    description: The XML Schema representation
    homepage: http://www.w3.org/2001/XMLSchema
    keywords:
    - W3C Rec
    name: XML Schema
    prefix: xsd
    uri_prefix: http://www.w3.org/2001/XMLSchema#$1
  mappings:
    biocontext: xsd
    lov: xsd
    zazuko: xsd
  name: XML Schema Definition
  preferred_prefix: xsd
  prefix: xsd
  uri_format: http://www.w3.org/2001/XMLSchema#$1
  zazuko:
    prefix: xsd
    uri_format: http://www.w3.org/2001/XMLSchema#$1
xuo:
  appears_in:
  - hsapdv
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  deprecated: true
  name: XUO
  prefix: xuo
ydpm:
  biocontext:
    prefix: YDPM
  mappings:
    biocontext: YDPM
    miriam: ydpm
    n2t: ydpm
    prefixcommons: ydpm
  miriam:
    deprecated: true
    description: The YDPM database serves to support the Yeast Deletion and the Mitochondrial
      Proteomics Project. The project aims to increase the understanding of mitochondrial
      function and biogenesis in the context of the cell. In the Deletion Project,
      strains from the deletion collection were monitored under 9 different media
      conditions selected for the study of mitochondrial function. The YDPM database
      contains both the raw data and growth rates calculated for each strain in each
      media condition.
    homepage: http://www-deletion.stanford.edu/YDPM/
    id: '00000465'
    name: YDPM
    namespaceEmbeddedInLui: false
    pattern: ^Y[A-Z]{2}\d+[CW]$
    prefix: ydpm
    sampleId: YAL001C
    uri_format: http://www-deletion.stanford.edu/cgi-bin/YDPM/YDPM_search.cgi?thelist=$1
  n2t:
    description: The YDPM database serves to support the Yeast Deletion and the Mitochondrial
      Proteomics Project. The project aims to increase the understanding of mitochondrial
      function and biogenesis in the context of the cell. In the Deletion Project,
      strains from the deletion collection were monitored under 9 different media
      conditions selected for the study of mitochondrial function. The YDPM database
      contains both the raw data and growth rates calculated for each strain in each
      media condition.
    example: YAL001C
    homepage: http://www-deletion.stanford.edu/YDPM/
    name: YDPM at Stanford University School of Medicine
    namespaceEmbeddedInLui: false
    pattern: ^Y[A-Z]{2}\d+[CW]$
    prefix: ydpm
    uri_format: http://www-deletion.stanford.edu/cgi-bin/YDPM/YDPM_search.cgi?thelist=$1
  name: Yeast Deletion and the Mitochondrial Proteomics Project
  prefix: ydpm
  prefixcommons:
    description: The YDPM database serves to support the Yeast Deletion and the Mitochondrial
      Proteomics Project. The database is hyperlinked with other public databases.
      The project aims to increase the understanding of mitochondrial function and
      biogenesis in the context of the cell
    example: YBL031W
    homepage: http://www-deletion.stanford.edu/YDPM/YDPM_index.html
    keywords:
    - protein
    name: Yeast Deletion Project and Proteomics of Mitochondria Database
    pattern: ^[A-Z,0-9]+$
    prefix: ydpm
yeastintron:
  biocontext:
    prefix: YEASTINTRON
  mappings:
    biocontext: YEASTINTRON
    miriam: yeastintron
    n2t: yeastintron
  miriam:
    deprecated: false
    description: The YEast Intron Database (version 4.3) contains information on the
      spliceosomal introns of the yeast Saccharomyces cerevisiae. It includes expression
      data that relates to the efficiency of splicing relative to other processes
      in strains of yeast lacking nonessential splicing factors. The data are displayed
      on each intron page. This is an updated version of the previous dataset, which
      can be accessed through [MIR:00000460].
    homepage: http://intron.ucsc.edu/yeast4.3/
    id: '00000521'
    name: Yeast Intron Database v4.3
    namespaceEmbeddedInLui: false
    pattern: ^[A-Z0-9]+$
    prefix: yeastintron
    sampleId: SNR17A
    uri_format: http://intron.ucsc.edu/cgi-bin/yeast4.3/intronreports.pl?outputformat=full&amp;orfName=$1
  n2t:
    description: The YEast Intron Database (version 4.3) contains information on the
      spliceosomal introns of the yeast Saccharomyces cerevisiae. It includes expression
      data that relates to the efficiency of splicing relative to other processes
      in strains of yeast lacking nonessential splicing factors. The data are displayed
      on each intron page. This is an updated version of the previous dataset, which
      can be accessed through [MIR:00000460].
    example: SNR17A
    homepage: http://intron.ucsc.edu/yeast4.3/
    name: Yeast Intron Database version 4.3 at Baskin School of Engineering
    namespaceEmbeddedInLui: false
    pattern: ^[A-Z0-9]+$
    prefix: yeastintron
    uri_format: http://intron.ucsc.edu/cgi-bin/yeast4.3/intronreports.pl?outputformat=full&amp;orfName=$1
  prefix: yeastintron
yeastract:
  contact:
    email: isacorreia@tecnico.ulisboa.pt
    github: null
    name: Isabel Sá-Correia
    orcid: 0000-0003-2208-5183
  fairsharing:
    abbreviation: YEASTRACT
    description: YEASTRACT (Yeast Search for Transcriptional Regulators And Consensus
      Tracking) is a curated repository of more than 48333 regulatory associations
      between transcription factors (TF) and target genes in Saccharomyces cerevisiae,
      based on more than 1200 bibliographic references.
    homepage: http://www.yeastract.com
    name: Yeast Searching for Transcriptional Regulators and Consensus Tracking
    prefix: FAIRsharing.mphj4z
    publications:
    - doi: 10.1093/nar/gkt1015
      pubmed_id: 24170807
      title: 'The YEASTRACT database: an upgraded information system for the analysis
        of gene and genomic transcription regulation in Saccharomyces cerevisiae.'
    - doi: 10.1093/nar/gkj013
      pubmed_id: 16381908
      title: 'The YEASTRACT database: a tool for the analysis of transcription regulatory
        associations in Saccharomyces cerevisiae.'
    - doi: 10.1093/nar/gkq964
      pubmed_id: 20972212
      title: 'YEASTRACT: providing a programmatic access to curated transcriptional
        regulatory associations in Saccharomyces cerevisiae through a web services
        interface.'
    - doi: 10.1093/nar/gkm976
      pubmed_id: 18032429
      title: 'YEASTRACT-DISCOVERER: new tools to improve the analysis of transcriptional
        regulatory associations in Saccharomyces cerevisiae.'
    subjects:
    - Life Science
  mappings:
    fairsharing: FAIRsharing.mphj4z
    pathguide: '205'
    prefixcommons: yeastract
  pathguide:
    abbreviation: YEASTRACT
    homepage: http://www.yeastract.com/
    name: YEAst Search for Transcriptional Regulators And Consensus Tracking
    prefix: '205'
  prefix: yeastract
  prefixcommons:
    description: YEASTRACT (Yeast Search for Transcriptional Regulators And Consensus
      Tracking) is a curated repository of more than 48333 regulatory associations
      between transcription factors (TF) and target genes in Saccharomyces cerevisiae,
      based on more than 1200 bibliographic references.
    example: YBR125c
    homepage: http://www.yeastract.com
    keywords:
    - regulation
    - DNA
    - small molecule
    - gene
    name: Yeast Searching for Transcriptional Regulators and Consensus Tracking
    pattern: ^[A-Z,0-9]+$
    prefix: yeastract
    uri_format: http://www.yeastract.com/view.php?existing=locus&orfname=$1
  publications:
  - doi: 10.1093/nar/gkt1015
    pmc: PMC3965121
    pubmed: '24170807'
    title: 'The YEASTRACT database: an upgraded information system for the analysis
      of gene and genomic transcription regulation in Saccharomyces cerevisiae'
    year: 2013
  - doi: 10.1093/nar/gkq964
    pmc: PMC3013800
    pubmed: '20972212'
    title: 'YEASTRACT: providing a programmatic access to curated transcriptional
      regulatory associations in Saccharomyces cerevisiae through a web services interface'
    year: 2010
  - doi: 10.1093/nar/gkm976
    pmc: PMC2238916
    pubmed: '18032429'
    title: 'YEASTRACT-DISCOVERER: new tools to improve the analysis of transcriptional
      regulatory associations in Saccharomyces cerevisiae'
    year: 2007
  - doi: 10.1093/nar/gkj013
    pmc: PMC1347376
    pubmed: '16381908'
    title: 'The YEASTRACT database: a tool for the analysis of transcription regulatory
      associations in Saccharomyces cerevisiae'
    year: 2006
  reviewer:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
yetfasco:
  biocontext:
    prefix: YETFASCO
  mappings:
    biocontext: YETFASCO
    miriam: yetfasco
    n2t: yetfasco
  miriam:
    deprecated: false
    description: The Yeast Transcription Factor Specificity Compendium (YeTFasCO)
      is a database of transcription factor specificities for the yeast Saccharomyces
      cerevisiae in Position Frequency Matrix (PFM) or Position Weight Matrix (PWM)
      formats.
    homepage: http://yetfasco.ccbr.utoronto.ca/
    id: 00000339
    name: YeTFasCo
    namespaceEmbeddedInLui: false
    pattern: ^\w+\_\d+(\.\d+)?$
    prefix: yetfasco
    sampleId: YOR172W_571.0
    uri_format: http://yetfasco.ccbr.utoronto.ca/showPFM.php?mot=$1
  n2t:
    description: The Yeast Transcription Factor Specificity Compendium (YeTFasCO)
      is a database of transcription factor specificities for the yeast Saccharomyces
      cerevisiae in Position Frequency Matrix (PFM) or Position Weight Matrix (PWM)
      formats.
    example: YOR172W_571.0
    homepage: http://yetfasco.ccbr.utoronto.ca/
    name: YeTFasCo at University of Toronto
    namespaceEmbeddedInLui: false
    pattern: ^\w+\_\d+(\.\d+)?$
    prefix: yetfasco
    uri_format: http://yetfasco.ccbr.utoronto.ca/showPFM.php?mot=$1
  prefix: yetfasco
ygob:
  comment: This resource doesn't exist on the web anymore
  deprecated: true
  mappings:
    prefixcommons: ygob
  prefix: ygob
  prefixcommons:
    description: YGOB is an online tool for visualising the syntenic context of any
      gene from several yeast genomes.
    example: ADH1
    homepage: http://wolfe.gen.tcd.ie/ygob
    keywords:
    - gene
    - genome
    name: Yeast Genome Order Browser
    pattern: ^[A-Z,0-9]+$
    prefix: ygob
    uri_format: http://wolfe.gen.tcd.ie/cgi/browser/ygob.pl?gene=$1
  provides: hgnc.symbol
  reviewer:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
yid:
  biocontext:
    prefix: YID
  mappings:
    biocontext: YID
    miriam: yid
    n2t: yid
  miriam:
    deprecated: true
    description: The YEast Intron Database (version 3) contains information on the
      spliceosomal introns of the yeast Saccharomyces cerevisiae. It includes expression
      data that relates to the efficiency of splicing relative to other processes
      in strains of yeast lacking nonessential splicing factors.  The data are displayed
      on each intron page. An updated version of the database is available through
      [MIR:00000521].
    homepage: http://compbio.soe.ucsc.edu/yeast_introns.html
    id: '00000460'
    name: Yeast Intron Database v3
    namespaceEmbeddedInLui: false
    pattern: ^[A-Z0-9]+$
    prefix: yid
    sampleId: SNR17A
    uri_format: http://metarray.ucsc.edu/cgi-bin/intron/yirIntrondb?orfName=$1
  n2t:
    description: The YEast Intron Database (version 3) contains information on the
      spliceosomal introns of the yeast Saccharomyces cerevisiae. It includes expression
      data that relates to the efficiency of splicing relative to other processes
      in strains of yeast lacking nonessential splicing factors.  The data are displayed
      on each intron page. An updated version of the database is available through
      [MIR:00000521].
    example: SNR17A
    homepage: http://compbio.soe.ucsc.edu/yeast_introns.html
    name: Yeast Intron Database version 3 at Baskin School of Engineering
    namespaceEmbeddedInLui: false
    pattern: ^[A-Z0-9]+$
    prefix: yid
    uri_format: http://metarray.ucsc.edu/cgi-bin/intron/yirIntrondb?orfName=$1
  prefix: yid
ymdb:
  contact:
    email: david.wishart@ualberta.ca
    github: DavidWishartLab
    name: David S. Wishart
    orcid: 0000-0002-3207-2434
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: The Yeast Metabolome Database (YMDB) is a manually curated database
    of small molecule metabolites found in or produced by Saccharomyces cerevisiae
    (also known as Baker’s yeast and Brewer’s yeast).
  example: YMDB00001
  fairsharing:
    abbreviation: YMDB
    description: The Yeast Metabolome Database (YMDB) is a manually curated database
      of small molecule metabolites found in or produced by Saccharomyces cerevisiae
      (also known as Baker’s yeast and Brewer’s yeast). This database covers metabolites
      described in textbooks, scientific journals, metabolic reconstructions and other
      electronic databases.
    homepage: http://www.ymdb.ca
    name: The Yeast Metabolome Database
    prefix: FAIRsharing.tawpg2
    publications:
    - doi: 10.1093/nar/gkr916
      pubmed_id: 22064855
      title: 'YMDB: the Yeast Metabolome Database.'
    subjects:
    - Life Science
    - Metabolomics
    twitter: WishartLab
  homepage: http://www.ymdb.ca
  mappings:
    fairsharing: FAIRsharing.tawpg2
    pathguide: '388'
    re3data: r3d100012733
  name: Yeast Metabolome Database
  pathguide:
    abbreviation: YMDB
    homepage: http://www.ymdb.ca/
    name: The Yeast Metabolome Database
    prefix: '388'
  pattern: ^YMDB\d+$
  prefix: ymdb
  publications:
  - doi: 10.1093/nar/gkr916
    pmc: PMC3245085
    pubmed: '22064855'
    title: 'YMDB: the Yeast Metabolome Database'
    year: 2011
  re3data:
    description: The Yeast Metabolome Database (YMDB) is a manually curated database
      of small molecule metabolites found in or produced by Saccharomyces cerevisiae
      (also known as Baker’s yeast and Brewer’s yeast). This database covers metabolites
      described in textbooks, scientific journals, metabolic reconstructions and other
      electronic databases.
    doi: 10.17616/R3Z51K
    homepage: https://www.ymdb.ca/
    name: The Yeast Metabolome Database
    prefix: r3d100012733
    synonyms:
    - YMDB
  uri_format: http://www.ymdb.ca/compounds/$1
ypo:
  biocontext:
    prefix: YPO
  mappings:
    biocontext: YPO
    obofoundry: ypo
  name: Yeast Phenotype Ontology
  obofoundry:
    contact: cherry@genome.stanford.edu
    contact.label: Mike Cherry
    contact.orcid: 0000-0001-9163-5180
    deprecated: true
    domain: phenotype
    homepage: http://www.yeastgenome.org/
    name: Yeast phenotypes
    prefix: ypo
  prefix: ypo
  uri_format: http://purl.obolibrary.org/obo/YPO_$1
yrcpdr:
  biocontext:
    prefix: YRCPDR
  fairsharing:
    abbreviation: YRC PDR
    contact:
      email: mriffle@u.washington.edu
      name: Michael Riffle
      orcid: 0000-0003-1633-8607
    description: The National Center for Research Resources' Yeast Resource Center
      is located at the University of Washington in Seattle, Washington. The mission
      of the center is to facilitate the identification and characterization of protein
      complexes in the yeast Saccharomyces cerevisiae.
    homepage: http://www.yeastrc.org/pdr/
    name: Yeast Resource Center Public Data Repository
    prefix: FAIRsharing.karvzj
    publications: []
    subjects:
    - Computational Biology
    - Life Science
  mappings:
    biocontext: YRCPDR
    fairsharing: FAIRsharing.karvzj
    miriam: yrcpdr
    n2t: yrcpdr
    prefixcommons: yrc
    re3data: r3d100010975
  miriam:
    deprecated: false
    description: The Yeast Resource Center Public Data Repository (YRC PDR) serves
      as a single point of access for the experimental data produced from many collaborations
      typically studying Saccharomyces cerevisiae (baker's yeast). The experimental
      data include large amounts of mass spectrometry results from protein co-purification
      experiments, yeast two-hybrid interaction experiments, fluorescence microscopy
      images and protein structure predictions.
    homepage: http://www.yeastrc.org/pdr/
    id: 00000459
    name: YRC PDR
    namespaceEmbeddedInLui: false
    pattern: ^\d+$
    prefix: yrcpdr
    sampleId: '2673500'
    uri_format: http://yeastrc.org/pdr/viewProtein.do?id=$1
  n2t:
    description: The Yeast Resource Center Public Data Repository (YRC PDR) serves
      as a single point of access for the experimental data produced from many collaborations
      typically studying Saccharomyces cerevisiae (baker's yeast). The experimental
      data include large amounts of mass spectrometry results from protein co-purification
      experiments, yeast two-hybrid interaction experiments, fluorescence microscopy
      images and protein structure predictions.
    example: '2673500'
    homepage: http://www.yeastrc.org/pdr/
    name: YRC PDR at University of Washington
    namespaceEmbeddedInLui: false
    pattern: ^\d+$
    prefix: yrcpdr
    uri_format: http://yeastrc.org/pdr/viewProtein.do?id=$1
  prefix: yrcpdr
  prefixcommons:
    description: The National Center for Research Resources' Yeast Resource Center
      is located at the University of Washington in Seattle, Washington. The mission
      of the center is to facilitate the identification and characterization of protein
      complexes in the yeast Saccharomyces cerevisiae.
    example: '846763'
    homepage: http://www.yeastrc.org/pdr/
    keywords:
    - protein
    name: Yeast Resource Center Public Data Repository
    pattern: ^\d+$
    prefix: yrc
    uri_format: http://www.yeastrc.org/pdr/viewProtein.do?id=$1
  re3data:
    description: The Yeast Resource Center provides access to data about mass spectrometry,
      yeast two-hybrid arrays, deconvolution florescence microscopy, protein structure
      prediction and computational biology. These services are provided to further
      the goal of a complete understanding of the chemical interactions required for
      the maintenance and faithful reproduction of a living cell. The observation
      that the fundamental biological processes of yeast are conserved among all eukaryotes
      ensures that this knowledge will shape and advance our understanding of living
      systems.
    doi: 10.17616/R30W5N
    homepage: http://depts.washington.edu/yeastrc/
    license: other
    name: Yeast Resource Center
    prefix: r3d100010975
    synonyms:
    - Yeast Resource Center Public Data Repository
    xrefs:
      nif: 0000-03650
zazuko:
  contact:
    email: ktk@netlabs.org
    github: ktk
    name: Adrian Gschwend
    orcid: 0000-0002-2079-9636
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: This service fills a gap between services like prefix.cc and LOV or
    looking up the original vocabulary specification. Not all vocabularies (or schema
    or ontology, whatever you want to call them) provide an HTML view. If you resolve
    some of the common prefixes all you get back is some RDF serialization which is
    not ideal. (from <https://prefix.zazuko.com/about>)
  example: frbr
  homepage: https://prefix.zazuko.com/
  license: MIT
  name: Zazuko Prefix Server
  prefix: zazuko
  uri_format: 'https://prefix.zazuko.com/prefix/$1:'
zbw.stw:
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: 'Der Thesaurus enthält Vokabular zu allen ökonomischen Themenstellungen:
    über 6.000 Schlagwörter und über 28.000 zusätzliche Synonyme als Zugangshilfe,
    um individuelle Formulierungen bei der Suche aufzufangen. Auch Fachbegriffe aus
    benachbarten Bereichen wie z.B. Recht, Soziologie oder Politik sowie Geobegriffe
    sind dort zu finden. Wenn Sie Schlagwörter aus diesem Vokabular auswählen, können
    Sie sicher sein Treffer zu erhalten, die zu dem gewünschten Sachgebiet passen.
    [from homepage]'
  example: n
  example_extras:
  - '70060'
  github_request_issue: 1614
  homepage: https://zbw.eu/stw/
  mappings:
    tib: stw
  name: Standard-Thesaurus Wirtschaft
  prefix: zbw.stw
  tib:
    description: 'The thesaurus provides vocabulary on any economic subject: almost
      6,000 standardized subject headings and about 20,000 additional entry terms
      to support individual keywords. You can also find technical terms used in law,
      sociology, or politics, and geographic names. When selecting terms from this
      vocabulary, you can be sure to get results matching your search query.'
    homepage: https://www.zbw.eu/stw/version/latest/about.en.html
    keywords:
    - Educational Resources
    - NFDI4Energy
    - economics
    name: STW Thesaurus for Economics
    prefix: stw
    uri_format: http://zbw.eu/stw/$1
  uri_format: http://zbw.eu/stw/thsys/$1
zea:
  aberowl:
    download_obo: http://aber-owl.net/media/ontologies/ZEA/2/zea.obo
    homepage: http://www.maizemap.org/
    name: Maize Gross Anatomy Ontology
    prefix: ZEA
    version: '1.2'
  biocontext:
    prefix: ZEA
  bioportal:
    contact:
      email: Leszek@missouri.edu
      name: Leszek Vincent
    homepage: http://www.maizemap.org/
    name: Maize Gross Anatomy Ontology
    prefix: ZEA
    version: '1.2'
  example: '0015177'
  mappings:
    aberowl: ZEA
    biocontext: ZEA
    bioportal: ZEA
    obofoundry: zea
    prefixcommons: zea
    wikidata.entity: Q114677917
  obofoundry:
    contact: Leszek@missouri.edu
    contact.label: Leszek Vincent
    contact.orcid: 0000-0002-9316-2919
    deprecated: true
    domain: anatomy and development
    homepage: http://www.maizemap.org/
    name: Maize gross anatomy
    prefix: zea
  pattern: ^\d{7}$
  prefix: zea
  prefixcommons:
    bioportal: '1050'
    description: Maize gross anatomy
    example: ZEA_0015177
    homepage: http://www.maizemap.org/
    keywords:
    - obo
    - anatomy
    - maize
    name: Maize gross anatomy
    pattern: ^ZEA_\d{7}$
    prefix: zea
zeco:
  aberowl:
    description: Experimental conditions applied to zebrafish, developed to facilitate
      experiment condition annotation at ZFIN
    download_owl: http://aber-owl.net/media/ontologies/ZECO/10/zeco.owl
    homepage: https://github.com/ybradford/zebrafish-experimental-conditions-ontology
    name: Zebrafish Experimental Conditions Ontology
    prefix: ZECO
  biocontext:
    prefix: ZECO
  bioportal:
    contact:
      email: ybradford@zfin.org
      name: Yvonne Bradford
    description: This ontology is designed to represent the experimental conditions
      applied to zebrafish and has been developed to facilitate experiment condition
      annotation at ZFIN.
    homepage: https://github.com/ybradford/zebrafish-experimental-conditions-ontology
    name: Zebrafish Experimental Conditions Ontology
    prefix: ZECO
    version: '2022-02-14'
  example: '0000171'
  fairsharing:
    abbreviation: ZECO
    description: This ontology is designed to represent the experimental conditions
      applied to zebrafish and has been developed to facilitate experiment condition
      annotation at ZFIN.
    domains:
    - Expression data
    - Model organisms
    - mutation
    - phenotype
    - disease course
    - gene
    - allele
    - genome
    homepage: https://github.com/ybradford/zebrafish-experimental-conditions-ontology
    name: Zebrafish Experimental Conditions Ontology
    prefix: FAIRsharing.np2wfz
    subjects:
    - Animal Physiology
    - Developmental Biology
    - Genetics
    - Genomics
  mappings:
    aberowl: ZECO
    biocontext: ZECO
    bioportal: ZECO
    fairsharing: FAIRsharing.np2wfz
    obofoundry: zeco
    ols: zeco
    ontobee: ZECO
    wikidata.entity: Q81661845
  obofoundry:
    appears_in:
    - mco
    contact: ybradford@zfin.org
    contact.github: ybradford
    contact.label: Yvonne Bradford
    contact.orcid: 0000-0002-9900-7880
    deprecated: false
    description: Experimental conditions applied to zebrafish, developed to facilitate
      experiment condition annotation at ZFIN
    domain: environment
    download.json: http://purl.obolibrary.org/obo/zeco.json
    download.obo: http://purl.obolibrary.org/obo/zeco.obo
    download.owl: http://purl.obolibrary.org/obo/zeco.owl
    homepage: https://github.com/ybradford/zebrafish-experimental-conditions-ontology
    license: CC BY 3.0
    license.url: http://creativecommons.org/licenses/by/3.0/
    name: Zebrafish Experimental Conditions Ontology
    preferredPrefix: ZECO
    prefix: zeco
    repository: https://github.com/ybradford/zebrafish-experimental-conditions-ontology
  ols:
    description: Ontology of Zebrafish Experimental Conditions
    download_owl: http://purl.obolibrary.org/obo/zeco.owl
    homepage: https://github.com/ybradford/zebrafish-experimental-conditions-ontology
    name: Zebrafish Experimental Conditions Ontology
    prefix: zeco
    tracker: https://github.com/ybradford/zebrafish-experimental-conditions-ontology/issues
    version: '2022-02-14'
    version.iri: http://purl.obolibrary.org/obo/zeco/releases/2022-02-14/zeco.owl
  ontobee:
    library: Library
    name: Zebrafish Experimental Conditions Ontology
    prefix: ZECO
  pattern: ^\d{7}$
  prefix: zeco
  uri_format: http://purl.obolibrary.org/obo/ZECO_$1
zenodo.record:
  contributor:
    email: benjamin_gyori@hms.harvard.edu
    github: bgyori
    name: Benjamin M. Gyori
    orcid: 0000-0001-9439-5346
  description: Zenodo is an open repository that allows researchers to deposit research
    papers, data sets, research software, reports, and any other research related
    digital artefacts.
  example: '4390079'
  fairsharing:
    abbreviation: Zenodo
    contact:
      email: lars.holm.nielsen@cern.ch
      name: Lars Holm Nielsen
      orcid: 0000-0001-8135-3489
    description: Zenodo is a generalist research data repository built and developed
      by OpenAIRE and CERN. It was developed to aid Open Science and is built on open
      source code. Zenodo helps researchers receive credit by making the research
      results citable and through OpenAIRE integrates them into existing reporting
      lines to funding agencies like the European Commission. Citation information
      is also passed to DataCite and onto the scholarly aggregators. Content is available
      publicly under any one of 400 open licences (from opendefinition.org and spdx.org).
      Restricted and Closed content is also supported. Free for researchers below
      50 GB/dataset. Content is both online on disk and offline on tape as part of
      a long-term preservation policy. Zenodo supports managed access (with an access
      request workflow) as well as embargoing generally and during peer review. The
      base infrastructure of Zenodo is provided by CERN, a non-profit IGO. Projects
      are funded through grants.
    homepage: https://www.zenodo.org
    license: http://about.zenodo.org/policies
    name: Zenodo
    prefix: FAIRsharing.wy4egf
    publications: []
    subjects:
    - Data Management
    - Subject Agnostic
    twitter: zenodo_org
  github_request_issue: 454
  homepage: https://zenodo.org
  integbio:
    description: Generalist research data repository built and developed by OpenAIRE
      and CERN, to ensure that everyone can join in Open Science.
    fairsharing: FAIRsharing.wy4egf
    homepage: https://www.zenodo.org
    information_keywords:
    - Bibliography/Documents
    - Repository
    maintainer: CERN (European Organisation for Nuclear Research)
    name: Zenodo
    prefix: nbdc02187
    status: Active
    target_keywords:
    - Health/Disease
  mappings:
    fairsharing: FAIRsharing.wy4egf
    integbio: nbdc02187
    re3data: r3d100010468
    wikidata: P4901
  name: Zenodo
  pattern: ^\d+$
  prefix: zenodo.record
  re3data:
    description: 'ZENODO builds and operates a simple and innovative service that
      enables researchers, scientists, EU projects and institutions to share and showcase
      multidisciplinary research results (data and publications) that are not part
      of the existing institutional or subject-based repositories of the research
      communities.

      ZENODO enables researchers, scientists, EU projects and institutions to:

      easily share the long tail of small research results in a wide variety of formats
      including text, spreadsheets, audio, video, and images across all fields of
      science.

      display their research results and get credited by making the research results
      citable and integrate them into existing reporting lines to funding agencies
      like the European Commission.

      easily access and reuse shared research results.'
    doi: 10.17616/R3QP53
    homepage: https://zenodo.org/
    license: CC0
    name: Zenodo
    prefix: r3d100010468
  reviewer:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  synonyms:
  - zenodo
  uri_format: https://zenodo.org/record/$1
  wikidata:
    description: ID of a work in Zenodo repository
    example:
    - '1038611'
    - '1481308'
    name: Zenodo ID
    pattern: ^[1-9]\d+$
    prefix: P4901
    uri_format: https://zenodo.org/record/$1
zfa:
  aberowl:
    description: A structured controlled vocabulary of the anatomy and development
      of the Zebrafish
    download_owl: http://aber-owl.net/media/ontologies/ZFA/89/zfa.owl
    homepage: https://wiki.zfin.org/display/general/Anatomy+Atlases+and+Resources
    name: Zebrafish anatomy and development ontology
    prefix: ZFA
  biocontext:
    prefix: ZFA
  bioportal:
    contact:
      email: zfinadmin@zfin.org
      name: ZFIN administrators
    description: A structured controlled vocabulary of the anatomy and development
      of the Zebrafish (<i>Danio rerio</i>).
    homepage: http://zfin.org/zf_info/anatomy/dict/sum.html
    name: Zebrafish Anatomy and Development Ontology
    prefix: ZFA
    publications:
    - http://www.jbiomedsem.com/content/5/1/12
    version: releases/2025-01-28
  download_json: http://purl.obolibrary.org/obo/zfa.json
  example: 0005926
  fairsharing:
    abbreviation: ZFA
    description: A structured controlled vocabulary of the anatomy and development
      of the Zebrafish. If you work on the project responsible for "Zebrafish anatomy
      and development" then please consider helping us by claiming this record and
      updating it appropriately.
    domains:
    - morphology
    - structure
    - life cycle
    - life cycle stage
    homepage: https://wiki.zfin.org/display/general/Anatomy+Atlases+and+Resources
    name: Zebrafish anatomy and development
    prefix: FAIRsharing.s3r6sk
    publications:
    - doi: 10.1186/2041-1480-5-12
      pubmed: '24568621'
      title: 'The zebrafish anatomy and stage ontologies: representing the anatomy
        and development of Danio rerio'
      year: 2014
    subjects:
    - Life Science
    - Anatomy
    - Developmental Biology
  mappings:
    aberowl: ZFA
    biocontext: ZFA
    bioportal: ZFA
    fairsharing: FAIRsharing.s3r6sk
    obofoundry: zfa
    ols: zfa
    ontobee: ZFA
    prefixcommons: zfa
    wikidata.entity: Q81661530
  obofoundry:
    appears_in:
    - zp
    contact: van_slyke@zfin.org
    contact.github: cerivs
    contact.label: Ceri Van Slyke
    contact.orcid: 0000-0002-2244-7917
    deprecated: false
    description: A structured controlled vocabulary of the anatomy and development
      of the Zebrafish
    domain: anatomy and development
    download.obo: http://purl.obolibrary.org/obo/zfa.obo
    download.owl: http://purl.obolibrary.org/obo/zfa.owl
    homepage: https://wiki.zfin.org/display/general/Anatomy+Atlases+and+Resources
    license: CC BY 3.0
    license.url: http://creativecommons.org/licenses/by/3.0/
    name: Zebrafish anatomy and development ontology
    preferredPrefix: ZFA
    prefix: zfa
    publications:
    - id: https://www.ncbi.nlm.nih.gov/pubmed/24568621
      title: 'The zebrafish anatomy and stage ontologies: representing the anatomy
        and development of Danio rerio.'
    repository: https://github.com/cerivs/zebrafish-anatomical-ontology
  ols:
    description: ZFA description.
    download_owl: http://purl.obolibrary.org/obo/zfa.owl
    homepage: https://wiki.zfin.org/display/general/Anatomy+Atlases+and+Resources
    name: Zebrafish Anatomy Ontology (ZFA)
    prefix: zfa
    tracker: https://github.com/cerivs/zebrafish-anatomical-ontology/issues
    version: '2025-09-05'
    version.iri: http://purl.obolibrary.org/obo/zfa/releases/2025-09-05/zfa.owl
  ontobee:
    library: Foundry
    name: Zebrafish anatomy and development ontology
    prefix: ZFA
  pattern: ^\d{7}$
  prefix: zfa
  prefixcommons:
    bioportal: '1051'
    description: A structured controlled vocabulary of the anatomy and development
      of the Zebrafish (<i>Danio rerio</i>).
    example: ZFS_0000011
    homepage: http://zfin.org/zf_info/anatomy/dict/sum.html
    keywords:
    - obo
    - anatomy
    - zebrafish
    name: Zebrafish anatomy and development Ontology
    pattern: ^ZFS_\d{7}$
    prefix: zfa
  publications:
  - doi: 10.1186/2041-1480-5-12
    pmc: PMC3944782
    pubmed: '24568621'
    title: 'The zebrafish anatomy and stage ontologies: representing the anatomy and
      development of Danio rerio'
    year: 2014
  repository: https://github.com/ZFIN/zebrafish-anatomical-ontology
  synonyms:
  - ZFA_RETIRED
  uri_format: http://purl.obolibrary.org/obo/ZFA_$1
zfin:
  biocontext:
    prefix: ZFIN
    uri_format: http://zfin.org/$1
  domain: gene
  fairsharing:
    abbreviation: ZFIN
    contact:
      email: dhowe@zfin.org
      name: Doug Howe
      orcid: 0000-0001-5831-7439
    description: The Zebrafish Information Network, ZFIN, serves as the primary community
      database resource for the laboratory use of zebrafish. We develop and support
      integrated zebrafish genetic, genomic, developmental and physiological information
      and link this information extensively to corresponding data in other model organism
      and human databases.
    homepage: https://zfin.org/
    name: The Zebrafish Information Network
    prefix: FAIRsharing.ybxnhg
    publications:
    - doi: 10.1093/nar/gkj086
      pubmed_id: 16381936
      title: 'The Zebrafish Information Network: the zebrafish model organism database.'
    - doi: 10.1093/nar/gkq1077
      pubmed_id: 21036866
      title: 'ZFIN: enhancements and updates to the Zebrafish Model Organism Database.'
    - doi: 10.1093/nar/gkg027
      pubmed_id: 12519991
      title: 'The Zebrafish Information Network (ZFIN): the zebrafish model organism
        database.'
    - doi: 10.1016/s0168-9525(99)01741-2
      pubmed_id: 10354586
      title: Zebrafish in the Net.
    - doi: 10.1002/0471250953.bi0118s31.
      pubmed_id: 20836073
      title: Exploring zebrafish genomic, functional and phenotypic data using ZFIN.
    - doi: 10.1016/B978-0-12-374814-0.00017-3
      pubmed_id: 21924170
      title: Data extraction, transformation, and dissemination through ZFIN.
    - doi: 10.1093/nar/gky1090
      pubmed_id: 30407545
      title: 'The Zebrafish Information Network: new support for non-coding genes,
        richer Gene Ontology annotations and the Alliance of Genome Resources.'
    - doi: 10.1093/nar/gks938
      pubmed_id: 23074187
      title: 'ZFIN, the Zebrafish Model Organism Database: increased support for mutants
        and transgenics.'
    - doi: 10.1093/nar/gkm956
      pubmed_id: 17991680
      title: 'The Zebrafish Information Network: the zebrafish model organism database
        provides expanded support for genotypes and phenotypes.'
    subjects:
    - Genomics
    - Animal Physiology
    - Genetics
    - Developmental Biology
    twitter: zfinmod
  go:
    homepage: http://zfin.org/
    name: Zebrafish Information Network
    prefix: ZFIN
  integbio:
    alt_name: The Zebrafish Model Organism Database
    description: 'ZFIN is a central repository and web-based resource for zebrafish
      genetics and development. This database contains manually curated data for zebrafish
      genes, phenotypes, genotypes, gene expression, antibodies, anatomical structures
      and publications from three primary sources: curation of zebrafish publications,
      individual research laboratories and collaborations with bioinformatics organizations.
      The database also contains a wide-ranging collection of web-based search forms
      and tools facilitates access to integrated views of these data promoting analysis
      and scientific discovery. ZFIN works closely with ZIRC to connect their genetic
      data with available probes and fish lines.'
    fairsharing: biodbcore-000575
    homepage: http://zfin.org/
    information_keywords:
    - Bioresource
    - Ontology/Terminology/Nomenclature
    - Sequence
    - Expression
    - Bibliography/Documents
    - Repository
    maintainer: University of Oregon/Zebrafish Information Network
    name: ZFIN
    prefix: nbdc00746
    pubmeds:
    - '21036866'
    - '17991680'
    - '11125057'
    - '10354586'
    - '9891346'
    - '9441953'
    status: Active
    target_keywords:
    - Genome/Gene
    - cDNA/EST
    - Genetic variation
    - Protein
    - Organism
  license: CC-BY-4.0
  logo: https://zfin.org/images/zfinlogo_lg.gif
  mappings:
    biocontext: ZFIN
    fairsharing: FAIRsharing.ybxnhg
    go: ZFIN
    integbio: nbdc00746
    miriam: zfin
    n2t: zfin
    ncbi: ZFIN
    prefixcommons: zfin
    re3data: r3d100010421
    rrid: ZIRC
    uniprot: DB-0113
    wikidata: P3870
  miriam:
    deprecated: false
    description: ZFIN serves as the zebrafish model organism database. This collection
      references all zebrafish biological entities in ZFIN.
    homepage: http://zfin.org
    id: 00000079
    name: ZFIN Bioentity
    namespaceEmbeddedInLui: false
    pattern: ^ZDB\-\w+\-\d+\-\d+$
    prefix: zfin
    providers:
    - code: agr
      description: ZFIN through the Alliance of Genome Resources
      homepage: https://www.alliancegenome.org
      name: ZFIN through the Alliance of Genome Resources
      uri_format: https://test.alliancegenome.org/gene/ZFIN:$1
    sampleId: ZDB-GENE-041118-11
    uri_format: http://zfin.org/$1
  n2t:
    description: ZFIN serves as the zebrafish model organism database. This collection
      references all zebrafish biological entities in ZFIN.
    example: ZDB-GENE-041118-11
    homepage: http://zfin.org
    name: ZFIN at University of Oregon
    namespaceEmbeddedInLui: false
    pattern: ^ZDB\-\w+\-\d+\-\d+$
    prefix: zfin
    uri_format: http://zfin.org/$1
  name: Zebrafish Information Network Gene
  ncbi:
    example: ZDB-GENE-011205-17
    homepage: http://zfin.org
    name: Zebrafish Information Network
    prefix: ZFIN
  prefix: zfin
  prefixcommons:
    description: ZFIN serves as the zebrafish model organism database.
    example: ZDB-GENE-041118-11
    homepage: http://zfin.org/
    keywords:
    - zebrafish
    - gene
    - genome
    name: Zebrafish Information Network genome database
    pattern: ^ZDB\-GENE\-\d+\-\d+$
    prefix: zfin
    pubmed_ids:
    - '17991680'
    uri_format: http://zfin.org/cgi-bin/webdriver?MIval=aa-markerview.apg&OID=$1
  publications:
  - doi: 10.1093/nar/gky1090
    pmc: PMC6323962
    pubmed: '30407545'
    title: 'The Zebrafish Information Network: new support for non-coding genes, richer
      Gene Ontology annotations and the Alliance of Genome Resources'
    year: 2019
  - doi: 10.1093/nar/gkm956
    pmc: PMC2238839
    pubmed: '17991680'
    title: 'The Zebrafish Information Network: the zebrafish model organism database
      provides expanded support for genotypes and phenotypes'
    year: 2007
  - doi: 10.1016/b978-0-12-374814-0.00017-3
    pmc: null
    pubmed: '21924170'
    title: Data extraction, transformation, and dissemination through ZFIN
    year: null
  - doi: 10.1002/0471250953.bi0118s31.
    pmc: null
    pubmed: '20836073'
    title: Exploring zebrafish genomic, functional and phenotypic data using ZFIN
    year: null
  - doi: 10.1093/nar/gkg027
    pmc: null
    pubmed: '12519991'
    title: 'The Zebrafish Information Network (ZFIN): the zebrafish model organism
      database'
    year: null
  - doi: 10.1093/nar/gkj086
    pmc: null
    pubmed: '16381936'
    title: 'The Zebrafish Information Network: the zebrafish model organism database'
    year: null
  - doi: 10.1016/s0168-9525(99)01741-2
    pmc: null
    pubmed: '10354586'
    title: Zebrafish in the Net
    year: null
  - doi: 10.1093/nar/gks938
    pmc: null
    pubmed: '23074187'
    title: 'ZFIN, the Zebrafish Model Organism Database: increased support for mutants
      and transgenics'
    year: null
  - doi: 10.1093/nar/gkq1077
    pmc: null
    pubmed: '21036866'
    title: 'ZFIN: enhancements and updates to the Zebrafish Model Organism Database'
    year: null
  - doi: 10.1093/nar/gkj086
    pmc: null
    pubmed: null
    title: 'The Zebrafish Information Network: the zebrafish model organism database.'
    year: null
  - doi: 10.1093/nar/gkq1077
    pmc: null
    pubmed: null
    title: 'ZFIN: enhancements and updates to the Zebrafish Model Organism Database.'
    year: null
  - doi: 10.1093/nar/gkg027
    pmc: null
    pubmed: null
    title: 'The Zebrafish Information Network (ZFIN): the zebrafish model organism
      database.'
    year: null
  - doi: 10.1016/s0168-9525(99)01741-2
    pmc: null
    pubmed: null
    title: Zebrafish in the Net.
    year: null
  - doi: 10.1002/0471250953.bi0118s31.
    pmc: null
    pubmed: null
    title: Exploring zebrafish genomic, functional and phenotypic data using ZFIN.
    year: null
  - doi: 10.1016/B978-0-12-374814-0.00017-3
    pmc: null
    pubmed: null
    title: Data extraction, transformation, and dissemination through ZFIN.
    year: null
  - doi: 10.1093/nar/gky1090
    pmc: null
    pubmed: null
    title: 'The Zebrafish Information Network: new support for non-coding genes, richer
      Gene Ontology annotations and the Alliance of Genome Resources.'
    year: null
  - doi: 10.1093/nar/gks938
    pmc: null
    pubmed: null
    title: 'ZFIN, the Zebrafish Model Organism Database: increased support for mutants
      and transgenics.'
    year: null
  - doi: 10.1093/nar/gkm956
    pmc: null
    pubmed: null
    title: 'The Zebrafish Information Network: the zebrafish model organism database
      provides expanded support for genotypes and phenotypes.'
    year: null
  - doi: null
    pmc: null
    pubmed: '17991680'
    title: null
    year: null
  - doi: 10.1093/genetics/iyac016
    pmc: null
    pubmed: '35166825'
    title: null
    year: null
  - doi: 10.1093/nar/gkj086
    pmc: null
    pubmed: null
    title: 'The Zebrafish Information Network: the zebrafish model organism database.'
    year: null
  - doi: 10.1093/nar/gkq1077
    pmc: null
    pubmed: null
    title: 'ZFIN: enhancements and updates to the Zebrafish Model Organism Database.'
    year: null
  - doi: 10.1093/nar/gkg027
    pmc: null
    pubmed: null
    title: 'The Zebrafish Information Network (ZFIN): the zebrafish model organism
      database.'
    year: null
  - doi: 10.1016/s0168-9525(99)01741-2
    pmc: null
    pubmed: null
    title: Zebrafish in the Net.
    year: null
  - doi: 10.1002/0471250953.bi0118s31.
    pmc: null
    pubmed: null
    title: Exploring zebrafish genomic, functional and phenotypic data using ZFIN.
    year: null
  - doi: 10.1016/B978-0-12-374814-0.00017-3
    pmc: null
    pubmed: null
    title: Data extraction, transformation, and dissemination through ZFIN.
    year: null
  - doi: 10.1093/nar/gky1090
    pmc: null
    pubmed: null
    title: 'The Zebrafish Information Network: new support for non-coding genes, richer
      Gene Ontology annotations and the Alliance of Genome Resources.'
    year: null
  - doi: 10.1093/nar/gks938
    pmc: null
    pubmed: null
    title: 'ZFIN, the Zebrafish Model Organism Database: increased support for mutants
      and transgenics.'
    year: null
  - doi: 10.1093/nar/gkm956
    pmc: null
    pubmed: null
    title: 'The Zebrafish Information Network: the zebrafish model organism database
      provides expanded support for genotypes and phenotypes.'
    year: null
  - doi: null
    pmc: null
    pubmed: '17991680'
    title: null
    year: null
  - doi: 10.1093/genetics/iyac016
    pmc: null
    pubmed: '35166825'
    title: null
    year: null
  re3data:
    description: 'ZFIN serves as the zebrafish model organism database. The long term
      goals for ZFIN are a) to be the community database resource for the laboratory
      use of zebrafish, b) to develop and support integrated zebrafish genetic, genomic
      and developmental information, c) to maintain the definitive reference data
      sets of zebrafish research information, d) to link this information extensively
      to corresponding data in other model organism and human databases, e) to facilitate
      the use of zebrafish as a model for human biology and f) to serve the needs
      of the research community.

      ZIRC is the Zebrafish International Resource Center, an independent NIH-funded
      facility providing a wide range of zebrafish lines, probes and health services.
      ZFIN works closely with ZIRC to connect our genetic data with available probes
      and fish lines.'
    doi: 10.17616/R3CK5Z
    homepage: https://zfin.org/
    name: The Zebrafish Information Network
    prefix: r3d100010421
    synonyms:
    - The zebrafish model organism database (formerly)
    - ZFIN
    xrefs:
      nif: 0000-21427
      omics: '01666'
  rrid:
    homepage: http://zebrafish.org
    keywords:
    - adult
    - antibody
    - cdna
    - embryo
    - expressed sequence tag
    - fish
    - pathology
    - research
    - zebrafish line
    name: Zebrafish International Resource Center
    prefix: ZIRC
    scr: '005065'
    twitter: ZFINmod
  synonyms:
  - ZFIN
  uniprot:
    abbreviation: ZFIN
    category: Organism-specific databases
    homepage: https://zfin.org/
    name: Zebrafish Information Network genome database
    prefix: DB-0113
    publications:
    - doi: 10.1093/genetics/iyac016
      pubmed: '35166825'
    uri_format: https://zfin.org/$1
  wikidata:
    description: identifier for a genetic element in the Zebrafish Model Organism
      Database
    example:
    - ZDB-GENE-030131-1564
    - ZDB-GENE-080416-2
    - ZDB-GENE-980526-388
    homepage: http://zfin.org
    name: ZFIN Gene ID
    prefix: P3870
    uri_format: https://zfin.org/$1
zfs:
  aberowl:
    description: Developmental stages of the Zebrafish
    download_owl: http://aber-owl.net/media/ontologies/ZFS/9/zfs.owl
    homepage: https://wiki.zfin.org/display/general/Anatomy+Atlases+and+Resources
    name: Zebrafish developmental stages ontology
    prefix: ZFS
  biocontext:
    prefix: ZFS
  bioportal:
    contact:
      email: zfinadmin@zfin.org
      name: ZFIN administrators
    description: An ontology of developmental stages of the Zebrafish (Danio rerio).
      Note that ZFA includes the leaf nodes of this ontology.
    name: Zebrafish Developmental Stages
    prefix: ZFS
  example: '0000050'
  fairsharing:
    abbreviation: ZFS
    description: An ontology of developmental stages of the Zebrafish (Danio rerio).
      Note that ZFA includes the leaf nodes of this ontology.
    domains:
    - life cycle
    - aging
    homepage: http://bioportal.bioontology.org/ontologies/ZFS
    name: Zebrafish Developmental Stages
    prefix: FAIRsharing.bc8ayj
    subjects:
    - Anatomy
    - Marine Biology
    - Developmental Biology
    - Zoology
  mappings:
    aberowl: ZFS
    biocontext: ZFS
    bioportal: ZFS
    fairsharing: FAIRsharing.bc8ayj
    obofoundry: zfs
    ols: zfs
    ontobee: ZFS
    wikidata.entity: Q81661847
  obofoundry:
    contact: van_slyke@zfin.org
    contact.github: cerivs
    contact.label: Ceri Van Slyke
    contact.orcid: 0000-0002-2244-7917
    deprecated: false
    description: Developmental stages of the Zebrafish
    domain: anatomy and development
    download.obo: http://purl.obolibrary.org/obo/zfs.obo
    download.owl: http://purl.obolibrary.org/obo/zfs.owl
    homepage: https://wiki.zfin.org/display/general/Anatomy+Atlases+and+Resources
    license: CC BY 3.0
    license.url: http://creativecommons.org/licenses/by/3.0/
    name: Zebrafish developmental stages ontology
    preferredPrefix: ZFS
    prefix: zfs
    repository: https://github.com/cerivs/zebrafish-anatomical-ontology
  ols:
    description: Developmental stages of the Zebrafish
    download_owl: http://purl.obolibrary.org/obo/zfs.owl
    homepage: https://wiki.zfin.org/display/general/Anatomy+Atlases+and+Resources
    name: Zebrafish developmental stages ontology
    prefix: zfs
    tracker: https://github.com/cerivs/zebrafish-anatomical-ontology/issues
  ontobee:
    library: Library
    name: Zebrafish developmental stages ontology
    prefix: ZFS
  pattern: ^\d{7}$
  prefix: zfs
  uri_format: http://purl.obolibrary.org/obo/ZFS_$1
zinc:
  biocontext:
    prefix: ZINC
  mappings:
    biocontext: ZINC
    miriam: zinc
    n2t: zinc
    re3data: r3d100010372
    wikidata: P2084
  miriam:
    deprecated: false
    description: ZINC is a free public resource for ligand discovery. The database
      contains over twenty million commercially available molecules in biologically
      relevant representations that may be downloaded in popular ready-to-dock formats
      and subsets. The Web site enables searches by structure, biological activity,
      physical property, vendor, catalog number, name, and CAS number.
    homepage: http://zinc15.docking.org/
    id: 00000529
    name: ZINC
    namespaceEmbeddedInLui: false
    pattern: ^(ZINC)?\d+$
    prefix: zinc
    sampleId: ZINC1084
    uri_format: http://zinc15.docking.org/substances/$1
  n2t:
    description: ZINC is a free public resource for ligand discovery. The database
      contains over twenty million commercially available molecules in biologically
      relevant representations that may be downloaded in popular ready-to-dock formats
      and subsets. The Web site enables searches by structure, biological activity,
      physical property, vendor, catalog number, name, and CAS number.
    example: ZINC1084
    homepage: http://zinc15.docking.org/
    name: ZINC at University of California (San Francisco)
    namespaceEmbeddedInLui: false
    pattern: ^(ZINC)?\d+$
    prefix: zinc
    uri_format: http://zinc15.docking.org/substances/$1
  name: ZINC is not Commercial
  prefix: zinc
  re3data:
    description: The ZINC Database contains commercially available compounds for structure
      based virtual screening. It currently has compounds that can simply be purchased.
      It is provided in ready-to-dock, 3D formats with molecules represented in biologically
      relevant forms. It is available in subsets for general screening as well as
      target-, chemotype- and vendor-focused subsets. ZINC is free for everyone to
      use and download at the website zinc.docking.org.
    doi: 10.17616/R3JG77
    homepage: https://cartblanche22.docking.org/
    name: ZINC
    prefix: r3d100010372
    synonyms:
    - CartBlanche
    xrefs:
      nif: 0000-31930
  wikidata:
    description: identifier for a chemical compound in the ZINC database
    example:
    - '13476531'
    - '1562396'
    - '6032158'
    homepage: http://zinc.docking.org/
    name: ZINC ID
    pattern: ^\d{4,10}$
    prefix: P2084
    uri_format: https://zinc.docking.org/substances/ZINC$1
zp:
  aberowl:
    description: The Zebrafish Phenotype Ontology formally defines all phenotypes
      of the Zebrafish model organism.
    download_owl: http://aber-owl.net/media/ontologies/ZP/10/zp.owl
    homepage: https://github.com/obophenotype/zebrafish-phenotype-ontology
    name: Zebrafish Phenotype Ontology
    prefix: ZP
  biocontext:
    prefix: ZP
  bioportal:
    contact:
      email: ybradford@zfin.org
      name: Yvonne Bradford
    description: The Zebrafish Phenotype Ontology formally defines all phenotypes
      of the Zebrafish model organism.
    homepage: https://github.com/obophenotype/zebrafish-phenotype-ontology
    name: Zebrafish Phenotype Ontology
    prefix: ZP
    version: '2024-04-18'
  example: 0019030
  mappings:
    aberowl: ZP
    biocontext: ZP
    bioportal: ZP
    obofoundry: zp
    ols: zp
    ontobee: ZP
    wikidata.entity: Q81661852
  obofoundry:
    contact: ybradford@zfin.org
    contact.github: ybradford
    contact.label: Yvonne Bradford
    contact.orcid: 0000-0002-9900-7880
    depends_on:
    - bfo
    - bspo
    - go
    - pato
    - ro
    - uberon
    - zfa
    deprecated: false
    description: The Zebrafish Phenotype Ontology formally defines all phenotypes
      of the Zebrafish model organism.
    domain: phenotype
    download.obo: http://purl.obolibrary.org/obo/zp.obo
    download.owl: http://purl.obolibrary.org/obo/zp.owl
    homepage: https://github.com/obophenotype/zebrafish-phenotype-ontology
    license: CC BY 3.0
    license.url: http://creativecommons.org/licenses/by/3.0/
    name: Zebrafish Phenotype Ontology
    preferredPrefix: ZP
    prefix: zp
    repository: https://github.com/obophenotype/zebrafish-phenotype-ontology
  ols:
    description: The Zebrafish Phenotype Ontology formally defines all phenotypes
      of the Zebrafish model organism.
    download_owl: http://purl.obolibrary.org/obo/zp.owl
    homepage: https://github.com/obophenotype/zebrafish-phenotype-ontology
    name: Zebrafish Phenotype Ontology (ZP)
    prefix: zp
    tracker: https://github.com/obophenotype/zebrafish-phenotype-ontology/issues
    version: '2024-04-18'
    version.iri: http://purl.obolibrary.org/obo/zp/releases/2024-04-18/zp.owl
  ontobee:
    library: Library
    name: Zebrafish Phenotype Ontology
    prefix: ZP
  pattern: ^\d+$
  prefix: zp
  uri_format: http://purl.obolibrary.org/obo/ZP_$1
