3dmet:
  biocontext:
    is_identifiers: true
    is_obo: false
    prefix: 3DMET
    uri_format: http://identifiers.org/3dmet/$1
  edam:
    description: Identifier of a metabolite from the 3DMET database.
    name: Compound ID (3DMET)
    obsolete: false
    prefix: '2635'
  fairsharing:
    abbreviation: 3DMET
    description: 3DMET is a database of three-dimensional structures of natural metabolites.
    id: '1999'
    name: Three-Dimensional Structure Database of Natural Metabolites
    prefix: FAIRsharing.5ab0n7
    subjects:
    - Life Science
    - Metabolomics
  mappings:
    biocontext: 3DMET
    edam: '2635'
    fairsharing: FAIRsharing.5ab0n7
    miriam: 3dmet
    n2t: 3dmet
    prefixcommons: 3dmet
    wikidata: P2796
  miriam:
    deprecated: false
    description: 3DMET is a database collecting three-dimensional structures of natural
      metabolites.
    homepage: http://www.3dmet.dna.affrc.go.jp/
    id: '00000066'
    name: 3DMET
    namespaceEmbeddedInLui: false
    pattern: ^B\d{5}$
    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=$1
  name: 3D Metabolites
  prefixcommons:
    description: 3DMET is a database of three-dimensional structures of natural metabolites.
    example: B00162
    homepage: http://www.3dmet.dna.affrc.go.jp
    keywords:
    - chemical
    - metabolite
    - structure
    miriam: 3dmet
    name: Three-Dimensional Structure Database of Natural Metabolites
    pattern: ^B\d{5}$
    prefix: 3dmet
    pubmed_ids:
    - '23293959'
    - '29892514'
  publications:
  - doi: 10.1021/ci300309k
    pmc: null
    pubmed: '23293959'
    title: 'Three-dimensional structure database of natural metabolites (3DMET): a
      novel database of curated 3D structures.'
    year: 2013
  - 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
  wikidata:
    database: Q23948774
    prefix: P2796
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/$1
  example: 4DNSR73BT2A2
  fairsharing:
    abbreviation: 4DN
    description: The 4D Nucleome Data Portal (4DN) hosts data generated by the 4DN
      Network and other reference nucleomics data sets, and an expanding tool set
      for open data processing and visualization. It is a platform to search, visualize,
      and download nucleomics data.
    id: '2771'
    name: 4DNucleome Data Portal
    prefix: FAIRsharing.CugtbQ
    subjects:
    - Life Science
  homepage: https://data.4dnucleome.org/biosources
  mappings:
    cellosaurus: 4DN
    fairsharing: FAIRsharing.CugtbQ
    miriam: 4dn
    prefixcommons: 4dn
  miriam:
    deprecated: false
    description: The 4D Nucleome Data Portal hosts data generated by the 4DN Network
      and other reference nucleomics data sets. The 4D Nucleome Network aims to understand
      the principles underlying nuclear organization in space and time, the role nuclear
      organization plays in gene expression and cellular function, and how changes
      in nuclear organization affect normal development as well as various diseases.
    homepage: https://data.4dnucleome.org/
    id: 00000833
    name: 4D Nucleome
    namespaceEmbeddedInLui: false
    pattern: ^4DN[A-Z]{2}[A-Z0-9]{7}$
    prefix: 4dn
    sampleId: 4DNES265ETYQ
    uri_format: https://data.4dnucleome.org/$1
  name: 4D Nucleome Data Portal Biosource
  prefixcommons:
    description: The 4D Nucleome Data Portal hosts data generated by the 4DN Network
      and other reference nucleomics data sets. The 4D Nucleome Network aims to understand
      the principles underlying nuclear organization in space and time, the role nuclear
      organization plays in gene expression and cellular function, and how changes
      in nuclear organization affect normal development as well as various diseases.
    example: 4DNESBOY2QLJ
    homepage: https://data.4dnucleome.org/
    keywords:
    - DNA
    - protein
    miriam: 4dn
    name: 4D Nucleome
    pattern: ^4DN[A-Z]{2}[A-Z0-9]{7}$
    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
  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 Mich\xE1n Aguirre"
    orcid: 0000-0002-5798-662X
  - email: mineromero2901@ciencias.unam.mx
    github: MinRo60
    name: "Minerva Mar\xEDa Romero P\xE9rez"
    orcid: 0000-0002-6240-9325
  - email: victorinolavida@ciencias.unam.mx
    github: Victorinolavida
    name: "Jos\xE9 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/
  name: 4D Nucleome Data Portal Experiment Replicate
  uri_format: https://data.4dnucleome.org/experiment-set-replicates/$1
  wikidata:
    database: Q110613797
aao:
  biocontext:
    is_identifiers: false
    is_obo: true
    prefix: AAO
    uri_format: http://purl.obolibrary.org/obo/AAO_$1
  description: A structured controlled vocabulary of the anatomy of Amphibians. Note
    that AAO is currently being integrated into Uberon.
  fairsharing:
    abbreviation: AAO
    description: A structured controlled vocabulary of the anatomy of Amphibians.
      Note that AAO has been integrated into Uberon.
    id: '876'
    name: Amphibian gross Anatomy Ontology
    prefix: FAIRsharing.mxx5rp
    publications:
    - doi: 10.1186/2041-1480-5-21
      pubmed_id: 25009735
      title: Unification of multi-species vertebrate anatomy ontologies for comparative
        biology in Uberon
    - doi: 10.1142/9789812772435_0035
      pubmed_id: null
      title: AN ANATOMICAL ONTOLOGY FOR AMPHIBIANS
    subjects:
    - Anatomy
  mappings:
    biocontext: AAO
    fairsharing: FAIRsharing.mxx5rp
    obofoundry: aao
    prefixcommons: aao
  no_own_terms: true
  obofoundry:
    contact: david.c.blackburn@gmail.com
    contact.label: David Blackburn
    deprecated: true
    homepage: http://github.com/seger/aao
    name: Amphibian gross anatomy
    prefix: aao
  prefixcommons:
    bioportal: '1090'
    description: The Amphibian Anatomical Ontology (AmphibAnat) is an NSF-sponsored
      project dedicated to constructing semi-automatically a draft ontology of amphibian
      anatomy. In this project, small, subset ontologies are constructed manually,
      and data-mining software (that we develop) is used to mine electronic media
      for instances of concepts and properties to be added to the ontologies.
    example: ASD:0000138
    homepage: http://www.amphibanat.org
    keywords:
    - obo
    - anatomy
    name: Amphibian Anatomical Ontology
    pattern: ^[A-Z]+:\d+$
    prefix: aao
    pubmed_ids:
    - '17992749'
  publications:
  - doi: 10.1142/9789812772435_0035
    pmc: null
    pubmed: '17992749'
    title: An anatomical ontology for amphibians.
    year: 2007
  - 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
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
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  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.
    id: '2969'
    name: ABCD database
    prefix: FAIRsharing.Z8OKi5
    subjects:
    - Molecular biology
    - Immunology
  homepage: https://web.expasy.org/abcd/
  mappings:
    cellosaurus: ABCD
    fairsharing: FAIRsharing.Z8OKi5
    uniprot: ABCD
  name: AntiBodies Chemically Defined database
  uniprot:
    category: Protocols and materials databases
    identifier: '236'
    link_is_explicit: 'true'
    name: ABCD curated depository of sequenced antibodies
    prefix: ABCD
    uri_format: https://web.expasy.org/cgi-bin/abcd/search_abcd.pl?input=$1
  uri_format: https://web.expasy.org/abcd/ABCD_$1
abm:
  cellosaurus:
    category: Cell line collections
    homepage: https://www.abmgood.com/Cell-Biology.html
    name: Applied Biological Materials cell line products
    prefix: ABM
    uri_format: https://www.abmgood.com/catalogsearch/result/?cat=&q=$1
  example: T0599
  mappings:
    cellosaurus: ABM
abs:
  biocontext:
    is_identifiers: true
    is_obo: false
    prefix: ABS
    uri_format: http://identifiers.org/abs/$1
  edam:
    description: Identifier of an entry (promoter) from the ABS database.
    name: ABS
    obsolete: false
    prefix: '2741'
  fairsharing:
    abbreviation: ABS
    description: ABS is a database of Annotated regulatory Binding Sites from known
      binding sites identified in promoters of orthologous vertebrate genes.
    id: '1899'
    name: Annotated regulatory Binding Sites from Orthologous Promoters
    prefix: FAIRsharing.7mnebr
    subjects:
    - Biology
  mappings:
    biocontext: ABS
    edam: '2741'
    fairsharing: FAIRsharing.7mnebr
    miriam: abs
    n2t: abs
    prefixcommons: abs
  miriam:
    deprecated: false
    description: The database of Annotated regulatory Binding Sites (from orthologous
      promoters), ABS, is a public database of known binding sites identified in promoters
      of orthologous vertebrate genes that have been manually curated from bibliography.
    homepage: http://genome.crg.es/datasets/abs2005/
    id: '00000277'
    name: ABS
    namespaceEmbeddedInLui: false
    pattern: ^A\d+$
    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/$1.html
  name: Annotated Regulatory Binding Sites
  prefixcommons:
    description: 'ABS: A database of Annotated regulatory Binding Sites from known
      binding sites identified in promoters of orthologous vertebrate genes.'
    example: A0014
    homepage: http://genome.imim.es/datasets/abs2005/
    keywords:
    - interaction
    - gene
    - regulation
    miriam: abs
    name: 'ABS: a database of Annotated regulatory Binding Sites from Orthologous
      Promoters'
    pattern: ^A\d+$
    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: null
    pmc: null
    pubmed: '16381947'
    title: null
    year: null
  wikidata:
    database: Q111134507
ac:
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  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
  name: Activity Streams
  uri_format: http://www.w3.org/ns/activitystreams#$1
aceview.worm:
  biocontext:
    is_identifiers: true
    is_obo: false
    prefix: ACEVIEW.WORM
    uri_format: http://identifiers.org/aceview.worm/$1
  mappings:
    biocontext: ACEVIEW.WORM
    miriam: aceview.worm
    n2t: aceview.worm
    prefixcommons: aceview.worm
  miriam:
    deprecated: false
    description: AceView provides a curated sequence representation of all public
      mRNA sequences (mRNAs from GenBank or RefSeq, and single pass cDNA sequences
      from dbEST and Trace). These are aligned on the genome and clustered into a
      minimal number of alternative transcript variants and grouped into genes. In
      addition, alternative features such as promoters, and expression in tissues
      is recorded. This collection references C. elegans genes and expression.
    homepage: https://www.ncbi.nlm.nih.gov/IEB/Research/Acembly/index.html?worm
    id: 00000282
    name: Aceview Worm
    namespaceEmbeddedInLui: false
    pattern: ^[a-z0-9-]+$
    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=$1
  prefixcommons:
    description: AceView provides a curated, comprehensive and non-redundant sequence
      representation of all public mRNA sequences (mRNAs from GenBank or RefSeq, and
      single pass cDNA sequences from dbEST and Trace). These experimental cDNA sequences
      are first co-aligned on the genome then clustered into a minimal number of alternative
      transcript variants and grouped into genes.
    example: AP2B1
    homepage: http://www.ncbi.nlm.nih.gov/IEB/Research/Acembly/
    keywords:
    - RNA
    - DNA
    - gene
    miriam: aceview.worm
    name: AceView Worm Genome
    pattern: ^[a-z0-9-]+$
    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
addexbio:
  cellosaurus:
    category: Cell line collections
    homepage: https://www.addexbio.com/productshow?id=4
    name: AddexBio cell line products
    prefix: AddexBio
    uri_format: https://www.addexbio.com/productdetail?pid=$1
  example: C0020004/4992
  mappings:
    cellosaurus: AddexBio
addgene:
  fairsharing:
    abbreviation: Addgene
    description: Addgene is a non-profit plasmid repository dedicated to helping scientists
      around the world share high-quality plasmids. Addgene are working with thousands
      of laboratories to assemble a high-quality library of published plasmids for
      use in research and discovery. By linking plasmids with articles, scientists
      can always find data related to the materials they request.
    id: '1738'
    name: Addgene
    prefix: FAIRsharing.8hcczk
    subjects:
    - Life Science
  mappings:
    fairsharing: FAIRsharing.8hcczk
    miriam: addgene
    n2t: addgene
    prefixcommons: addgene
    re3data: r3d100010741
  miriam:
    deprecated: false
    description: Addgene is a non-profit plasmid repository. Addgene facilitates the
      exchange of genetic material between laboratories by offering plasmids and their
      associated cloning data to not-for-profit laboratories around the world.
    homepage: http://addgene.org/
    id: '00000675'
    name: Addgene Plasmid Repository
    namespaceEmbeddedInLui: false
    pattern: ^[0-9]{5}(-[a-zA-Z0-9-]{0,7})?$|^[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/$1
  prefixcommons:
    description: Addgene is a global, nonprofit repository that was created to help
      scientists share plasmids.
    example: '41816'
    homepage: http://www.addgene.org
    keywords:
    - plasmid
    miriam: addgene
    name: Addgene
    pattern: ^\d+$
    prefix: addgene
    pubmed_ids:
    - '25392412'
    uri_format: http://www.addgene.org/$1
  publications:
  - doi: 10.1093/nar/gku893
    pmc: PMC4384007
    pubmed: '25392412'
    title: 'The Addgene repository: an international nonprofit plasmid and data resource.'
    year: 2014
  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.
    homepage: https://www.addgene.org/
    name: Addgene
    prefix: r3d100010741
    xrefs:
      fairsharing: FAIRsharing.8hcczk
      miriam: '00000675'
      nif: 0000-11872
      omics: '04712'
      scr: '002037'
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/4/ado.owl
    homepage: https://github.com/Fraunhofer-SCAI-Applied-Semantics/ADO
    name: Alzheimer's Disease Ontology
    prefix: ADO
  bioportal:
    contact:
      email: ashutosh.malhotra@scai.fraunhofer.de
      name: Ashutosh Malhotra
    description: "ADO is a first attempt to develop an open, public ontology representing\
      \ relevant knowledge on Alzheimer\u2019s disease."
    homepage: http://www.scai.fraunhofer.de/en/business-research-areas/bioinformatics.html
    name: Alzheimer's disease ontology
    prefix: ADO
    publication: http://www.ncbi.nlm.nih.gov/pubmed/?term=ADO%3A+A+disease+ontology+representing+the+domain+knowledge+specific+to+Alzheimer's+disease
    version: 1.1.1
  example: '0000001'
  fairsharing:
    abbreviation: ADO
    description: "The Alzheimer's Disease Ontology (ADO) is an ontology representing\
      \ relevant knowledge on Alzheimer\u2019s disease. ADO was developed with the\
      \ purpose of containing information relevant to four main biological views\u2014\
      preclinical, clinical, etiological, and molecular/cellular mechanisms\u2014\
      and contains synonyms and references."
    id: '437'
    name: Alzheimer's Disease Ontology
    prefix: FAIRsharing.ckd4rf
    publications:
    - doi: 10.1016/j.jalz.2013.02.009
      pubmed_id: 23830913
      title: 'ADO: a disease ontology representing the domain knowledge specific to
        Alzheimer''s disease.'
    subjects:
    - Health Science
  mappings:
    aberowl: ADO
    bioportal: ADO
    fairsharing: FAIRsharing.ckd4rf
    obofoundry: ado
    ols: ado
  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.
    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: http://purl.obolibrary.org/obo/ado.owl
    homepage: https://github.com/Fraunhofer-SCAI-Applied-Semantics/ADO
    name: Alzheimer's Disease Ontology (ADO)
    prefix: ado
    version: 2.0.0
    version.iri: http://purl.obolibrary.org/obo/ado/releases/2022-06-11/ado.owl
  pattern: ^\d{7}$
  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
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
  biocontext:
    is_identifiers: false
    is_obo: true
    prefix: ADW
    uri_format: http://purl.obolibrary.org/obo/ADW_$1
  bioportal:
    contact:
      email: adw.staff@umich.edu
      name: Animal Diversity Web technical staff
    description: An ontology for animal life history and natural history characteristics
      suitable for populations and higher taxonomic entities.
    homepage: http://www.animaldiversity.org
    name: Animal Natural History and Life History Ontology
    prefix: ADW
    version: 10/11/04
  fairsharing:
    abbreviation: ADW
    description: An ontology for animal life history and natural history characteristics
      suitable for populations and higher taxonomic entities.
    id: '1038'
    name: Animal natural history and life history
    prefix: FAIRsharing.t9fvdn
    publications: []
    subjects:
    - Anatomy
    - Life Science
  mappings:
    aberowl: ADW
    biocontext: ADW
    bioportal: ADW
    fairsharing: FAIRsharing.t9fvdn
    miriam: adw
    n2t: adw
    obofoundry: adw
  miriam:
    deprecated: false
    description: Animal Diversity Web (ADW) is an online database of animal natural
      history, distribution, classification, and conservation biology.
    homepage: https://animaldiversity.org/
    id: 00000492
    name: Animal Diversity Web
    namespaceEmbeddedInLui: false
    pattern: ^[A-Z_a-z]+$
    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
    homepage: http://www.animaldiversity.org
    name: Animal natural history and life history
    prefix: adw
  uri_format: https://animaldiversity.org/accounts/$1
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
  biocontext:
    is_identifiers: false
    is_obo: true
    prefix: AEO
    uri_format: http://purl.obolibrary.org/obo/AEO_$1
  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
  download_obo: https://raw.githubusercontent.com/obophenotype/human-developmental-anatomy-ontology/master/src/ontology/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.
    id: '1175'
    name: Anatomical Entity Ontology
    prefix: FAIRsharing.93ee19
    publications:
    - doi: 10.3389/fgene.2012.00018
      pubmed_id: 22347883
      title: The AEO, an Ontology of Anatomical Entities for Classifying Animal Tissues
        and Organs.
    subjects:
    - Anatomy
    - Life Science
  mappings:
    aberowl: AEO
    biocontext: AEO
    bioportal: AEO
    fairsharing: FAIRsharing.93ee19
    obofoundry: aeo
    ols: aeo
    ontobee: AEO
  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
    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: http://purl.obolibrary.org/obo/aeo.owl
    homepage: https://github.com/obophenotype/human-developmental-anatomy-ontology/
    name: Anatomical Entity Ontology
    prefix: aeo
    version: '2014-12-05'
    version.iri: http://purl.obolibrary.org/obo/aeo/releases/2014-12-05/aeo.owl
  ontobee:
    library: Library
    name: Anatomical Entity Ontology
    prefix: AEO
  pattern: ^\d{7}$
  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
  synonyms:
  - AEO_RETIRED
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:
    is_identifiers: false
    is_obo: true
    prefix: AERO
    uri_format: http://purl.obolibrary.org/obo/AERO_$1
  bioportal:
    contact:
      email: mcourtot@gmail.com
      name: Melanie Courtot
    description: The Adverse Event Reporting Ontology (AERO) is an ontology aimed
      at supporting clinicians at the time of data entry, increasing quality and accuracy
      of reported adverse events.
    homepage: http://purl.obolibrary.org/obo/aero
    name: Adverse Event Reporting Ontology
    prefix: AERO
    version: unknown
  example: '0000125'
  fairsharing:
    abbreviation: AERO
    description: The Adverse Event Reporting Ontology (AERO) is an ontology aimed
      at supporting clinicians at the time of data entry, increasing quality and accuracy
      of reported adverse events.
    id: '221'
    name: Adverse Event Reporting ontology
    prefix: FAIRsharing.rycy2x
    publications: []
    subjects:
    - Medicine
    - Health Science
    - Biomedical Science
    - Preclinical Studies
  mappings:
    aberowl: AERO
    biocontext: AERO
    bioportal: AERO
    fairsharing: FAIRsharing.rycy2x
    obofoundry: aero
  obofoundry:
    contact: mcourtot@gmail.com
    contact.label: Melanie Courtot
    contact.orcid: 0000-0002-9551-6370
    deprecated: true
    description: The Adverse Event Reporting Ontology (AERO) is an ontology aimed
      at supporting clinicians at the time of data entry, increasing quality and accuracy
      of reported adverse events
    download.owl: http://purl.obolibrary.org/obo/aero.owl
    homepage: http://purl.obolibrary.org/obo/aero
    license: CC BY 3.0
    license.url: http://creativecommons.org/licenses/by/3.0/
    name: Adverse Event Reporting Ontology
    prefix: aero
  pattern: ^\d{7}$
affy.probeset:
  biocontext:
    is_identifiers: true
    is_obo: false
    prefix: AFFY.PROBESET
    uri_format: http://identifiers.org/affy.probeset/$1
  mappings:
    biocontext: AFFY.PROBESET
    miriam: affy.probeset
    n2t: affy.probeset
  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://www.affymetrix.com/
    id: 00000394
    name: Affymetrix Probeset
    namespaceEmbeddedInLui: false
    pattern: \d{4,}((_[asx])?_at)?
    prefix: affy.probeset
    providers:
    - code: CURATOR_REVIEW
      description: Bio2RDF
      homepage: http://cu.affymetrix.bio2rdf.org/fct/
      name: Bio2RDF
      uri_format: http://cu.affymetrix.bio2rdf.org/describe/?url=http://bio2rdf.org/affymetrix:$1
    sampleId: 243002_at
    uri_format: https://www.affymetrix.com/LinkServlet?probeset=$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
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>This version
      of Allotrope Foundation Ontology (AFO) has been prepared specifically for publication
      on the NCBO platform.</p> <p>license: http://purl.allotrope.org/voc/creative-commons-attribution-license<br/>
      rights: http://purl.allotrope.org/voc/copyright<br/></p>  <p>Please get the
      latest version of AFO from http://purl.allotrope.org</p>'
    download_owl: http://aber-owl.net/media/ontologies/AFO/30/afo.owl
    homepage: http://purl.allotrope.org
    name: Allotrope Merged Ontology Suite
    prefix: AFO
    version: REC/2022/09
  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>This version
      of Allotrope Foundation Ontology (AFO) has been prepared specifically for publication
      on the NCBO platform.</p> <p>license: http://purl.allotrope.org/voc/creative-commons-attribution-license<br/>
      rights: http://purl.allotrope.org/voc/copyright<br/></p> <p>Please get the latest
      version of AFO from http://purl.allotrope.org</p>'
    homepage: http://purl.allotrope.org
    name: Allotrope Merged Ontology Suite
    prefix: AFO
    publication: http://www.allotrope.org
    version: REC/2022/09
  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.
    id: '924'
    name: Agriculture and Forestry Ontology
    prefix: FAIRsharing.595710
    publications: []
    subjects:
    - Environmental Science
    - Forest Management
    - Agricultural Engineering
    - Agriculture
    - Veterinary Medicine
    - Food Chemistry
    - Biology
  homepage: https://www.allotrope.org/
  mappings:
    aberowl: AFO
    bioportal: AFO
    fairsharing: FAIRsharing.595710
    ols: afo
  no_own_terms: true
  ols:
    description: Allotrope Merged Ontology Suite
    download: http://afo-ols.semanticsfirst.com/ontologies/afo
    name: Allotrope Merged Ontology Suite
    prefix: afo
    version: '2019-05-10'
    version.iri: http://purl.allotrope.org/voc/afo/merged-OLS/REC/2019/05/10
aftol.taxonomy:
  biocontext:
    is_identifiers: true
    is_obo: false
    prefix: AFTOL.TAXONOMY
    uri_format: http://identifiers.org/aftol.taxonomy/$1
  contributor_extras:
  - email: laylamichan@ciencias.unam.mx
    github: lmichan
    name: "Layla Mich\xE1n Aguirre"
    orcid: 0000-0002-5798-662X
  homepage: https://aftol.umn.edu
  mappings:
    biocontext: AFTOL.TAXONOMY
    miriam: aftol.taxonomy
    n2t: aftol.taxonomy
  miriam:
    deprecated: false
    description: The Assembling the Fungal Tree of Life (AFTOL) project is dedicated
      to significantly enhancing our understanding of the evolution of the Kingdom
      Fungi, which represents one of the major clades of life. There are roughly 80,000
      described species of Fungi, but the actual diversity in the group has been estimated
      to be about 1.5 million species.
    homepage: http://aftol.org/data.php
    id: '00000411'
    name: AFTOL
    namespaceEmbeddedInLui: false
    pattern: ^\d+$
    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=$1
  name: Assembling the Fungal Tree of Life - Taxonomy
agilent.probe:
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: 'This is the Agilent SurePrint G3 Human GE v2 8x60k Microarray, Agilent
    design ID 039494, GridName 039494_D_F_20120628. Probe layout is 1 x 1 x 384 rows
    x 164 cols, which is different from a similar ADF A-GEOD-16699 (1 x 1 x 328 rows
    x 192 cols). Version 2 of this array  contains long intergenic non-coding RNA
    (lincRNA) probes designed to the human catalog of lincRNAs from the Broad Institute,
    along with an update of mRNA content when compared to version 1. Probes were designed
    using GRCh37 assembly of the human genome. Annotation of probes came from the
    following database: RefSeq Build 50, Ensembl Release 52, Unigene Build 216, GenBank
    (April 2009), Broad Institute Human lincRNA catalog (Nov 2011), Broad Institute
    TUCP transcripts catalog (Nov 2011).  Probe annotation was taken from A-GEOD-16699.'
  example: A_24_P98555
  homepage: https://www.ebi.ac.uk/arrayexpress/files/A-MEXP-2320/A-MEXP-2320.adf.txt
  name: Agilent Probe
  pattern: ^A_\d+_.+$
  references:
  - http://www.cs.tau.ac.il/cgi-bin/cgiwrap/click/get.cgi/conversionFiles/conversion_human_14850_agilent2entrez.txt
agricola:
  biocontext:
    is_identifiers: true
    is_obo: false
    prefix: AGRICOLA
    uri_format: http://identifiers.org/agricola/$1
  contributor_extras:
  - email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  - email: cjmungall@lbl.gov
    github: cmungall
    name: Chris Mungall
    orcid: 0000-0002-6601-2165
  go:
    homepage: http://agricola.nal.usda.gov/
    name: AGRICultural OnLine Access
    prefix: AGRICOLA_ID
  mappings:
    biocontext: AGRICOLA
    go: AGRICOLA_ID
    miriam: agricola
    n2t: agricola
  miriam:
    deprecated: false
    description: AGRICOLA (AGRICultural OnLine Access) serves as the catalog and index
      to the collections of the National Agricultural Library, as well as a primary
      public source for world-wide access to agricultural information. The database
      covers materials in all formats and periods, including printed works from as
      far back as the 15th century.
    homepage: http://agricola.nal.usda.gov/
    id: 00000589
    name: AGRICOLA
    namespaceEmbeddedInLui: false
    pattern: ^\d+$
    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
  synonyms:
  - AGR
  - AGRICOLA_ID
  uri_format: https://agricola.nal.usda.gov/vwebv/holdingsInfo?bibId=$1
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: null
    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
  mappings:
    biolink: AGRKB
  name: Alliance of Genome Resources Knowledge Base
  pattern: ^[1-9][0-9]{14}$
  reviewer:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  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/6/agro.owl
    homepage: https://github.com/AgriculturalSemantics/agro
    name: Agronomy Ontology
    prefix: AGRO
  agroportal:
    contact:
      email: c.aubert@cgiar.org
      name: "C\xE9line Aubert"
    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
    publication: http://ceur-ws.org/Vol-1747/IT205_ICBO2016.pdf
    repository: https://github.com/AgriculturalSemantics/agro
    version: '1.0'
  biocontext:
    is_identifiers: false
    is_obo: true
    prefix: AGRO
    uri_format: http://purl.obolibrary.org/obo/AGRO_$1
  bioportal:
    contact:
      email: m.a.laporte@cgiar.org
      name: "Marie-Ang\xE9lique 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
  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.
    id: '714'
    name: Agronomy Ontology
    prefix: FAIRsharing.m40bhw
    publications: []
    subjects:
    - Farming Systems Research
    - Plant Breeding
    - Agronomy
    - Agriculture
  mappings:
    aberowl: AGRO
    agroportal: AGRO
    biocontext: AGRO
    bioportal: AGRO
    fairsharing: FAIRsharing.m40bhw
    obofoundry: agro
    ols: agro
    ontobee: AGRO
  obofoundry:
    contact: m.a.laporte@cgiar.org
    contact.github: marieALaporte
    contact.label: "Marie-Ang\xE9lique 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
    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: http://purl.obolibrary.org/obo/agro.owl
    homepage: https://github.com/AgriculturalSemantics/agro
    name: Agronomy Ontology
    prefix: agro
    version: '2021-11-05'
    version.iri: http://purl.obolibrary.org/obo/agro/releases/2021-11-05/agro.owl
  ontobee:
    library: Library
    name: Agronomy Ontology
    prefix: AGRO
  pattern: ^\d{8}$
agrovoc:
  agroportal:
    contact:
      email: AGROVOC@fao.org
      name: AGROVOC
    description: Since the early 1980's, the Food and Agriculture Organization of
      the United Nations (FAO) has coordinated AGROVOC, a valuable tool for data to
      be classified homogeneously, facilitating interoperability and reuse. AGROVOC
      is a multilingual and controlled vocabulary designed to cover concepts and terminology
      under FAO's areas of interest.
    example_uri: http://aims.fao.org/aos/agrovoc/c_38445
    homepage: http://www.fao.org/agrovoc/
    license: CC-BY IGO 3.0
    name: AGROVOC
    prefix: AGROVOC
    publication: https://www.fao.org/agrovoc/publications
    version: 2022-07
  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.
  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 December
      2021, AGROVOC consists of +39 600 concepts and +926 000 terms in up to 41 languages.
    homepage: https://agrovoc.fao.org/browse/agrovoc/en/
    name: AGROVOC
    prefix: AGROVOC
    publication: https://data.apps.fao.org/catalog/organization/agrovoc?q=&sort=title_string+desc
  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 40,100
      concepts available in up to 41 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.
    id: '399'
    name: AGROVOC
    prefix: FAIRsharing.anpj91
    publications:
    - doi: https://doi.org/10.3390/engproc2021009017
      pubmed_id: null
      title: 'How Agricultural Digital Innovation Can Benefit from Semantics: The
        Case of the AGROVOC Multilingual Thesaurus'
    - doi: https://doi.org/10.4060/cb2838en
      pubmed_id: null
      title: "AGROVOC \u2013 Semantic data interoperability on food and agriculture"
    - doi: 10.1016/j.compag.2020.105965
      pubmed_id: null
      title: 'AGROVOC: The linked data concept hub for food and agriculture'
    subjects:
    - Botany
    - Fisheries Science
    - Environmental Science
    - Forest Management
    - Data Management
    - Agriculture
    - Nutritional Science
  homepage: https://data.apps.fao.org/catalog/organization/agrovoc
  mappings:
    agroportal: AGROVOC
    ecoportal: AGROVOC
    fairsharing: FAIRsharing.anpj91
  name: Agronomy Vocabulary
  pattern: ^[a-z0-9]+$
  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
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/9/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. Gir\xF3n"
    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
    version: '2021-11-19'
  example: '0000027'
  mappings:
    aberowl: AISM
    bioportal: AISM
    obofoundry: aism
    ols: aism
    ontobee: AISM
  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. Gir\xF3n"
    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.
    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: 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
    version: '2022-06-27'
    version.iri: http://purl.obolibrary.org/obo/aism/releases/2022-06-27/aism.owl
  ontobee:
    library: Library
    name: Ontology for the Anatomy of the Insect SkeletoMuscular system (AISM)
    prefix: AISM
  pattern: ^\d{7}$
allergome:
  biocontext:
    is_identifiers: true
    is_obo: false
    prefix: ALLERGOME
    uri_format: http://identifiers.org/allergome/$1
  fairsharing:
    abbreviation: Allergome
    description: Allergome aims to supply information on Allergenic Molecules (Allergens)
      causing an IgE-mediated (allergic, atopic) disease (anaphylaxis, asthma, atopic
      dermatitis, conjunctivitis, rhinitis, urticaria). The resource is funded through
      the Allergen Data Laboratories via unrestricted grants from companies and institutions.
    id: '1746'
    name: Allergome
    prefix: FAIRsharing.w6cxgb
    subjects:
    - Medicine
    - Health Science
    - Life Science
    - Biomedical Science
  mappings:
    biocontext: ALLERGOME
    fairsharing: FAIRsharing.w6cxgb
    miriam: allergome
    n2t: allergome
    prefixcommons: allergome
    uniprot: Allergome
  miriam:
    deprecated: false
    description: Allergome is a repository of data related to all IgE-binding compounds.
      Its purpose is to collect a list of allergenic sources and molecules by using
      the widest selection criteria and sources.
    homepage: http://www.allergome.org/
    id: '00000334'
    name: Allergome
    namespaceEmbeddedInLui: false
    pattern: ^\d+$
    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=$1
  prefixcommons:
    description: Allergome aims to supply information on Allergenic Molecules (Allergens)
      causing an IgE-mediated (allergic, atopic) disease (anaphylaxis, asthma, atopic
      dermatitis, conjunctivitis, rhinitis, urticaria).
    example: '1948'
    homepage: http://www.allergome.org
    keywords:
    - allergen
    miriam: allergome
    name: 'Allergome: a platform for allergen knowledge'
    pattern: ^\d+$
    prefix: allergome
    pubmed_ids:
    - '17393720'
    - '17434469'
    uri_format: http://www.allergome.org/script/refArray_view.php?idMol=$1
  publications:
  - doi: null
    pmc: null
    pubmed: '17393720'
    title: 'Allergome: a unifying platform.'
    year: 2006
  - 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
  uniprot:
    category: Protein family/group databases
    identifier: '160'
    link_is_explicit: 'true'
    name: Allergome; a platform for allergen knowledge
    prefix: Allergome
    uri_format: http://www.allergome.org/script/dettaglio.php?id_molecule=$1
alzforum.mutation:
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  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
  name: Alzforum Mutations
  synonyms:
  - Alzforum_mut
  uri_format: https://www.alzforum.org/mutations/$1
amoebadb:
  biocontext:
    is_identifiers: true
    is_obo: false
    prefix: AMOEBADB
    uri_format: http://identifiers.org/amoebadb/$1
  fairsharing:
    abbreviation: AmoebaDB
    description: AmoebaDB belongs to the EuPathDB family of databases and is an integrated
      genomic and functional genomic database for Entamoeba and Acanthamoeba parasites.
      In its first released, AmoebaDB contained the genomes of three Entamoeba species.
      AmoebaDB integrates whole genome sequence and annotation and will rapidly expand
      to include experimental data and environmental isolate sequences provided by
      community researchers . The database includes supplemental bioinformatics analyses
      and a web interface for data-mining.
    id: '2095'
    name: AmoebaDB
    prefix: FAIRsharing.swbypy
    subjects:
    - Genomics
    - Life Science
  mappings:
    biocontext: AMOEBADB
    fairsharing: FAIRsharing.swbypy
    miriam: amoebadb
    n2t: amoebadb
    prefixcommons: amoebadb
    re3data: r3d100012457
  miriam:
    deprecated: false
    description: AmoebaDB is one of the databases that can be accessed through the
      EuPathDB (http://EuPathDB.org; formerly ApiDB) portal, covering eukaryotic pathogens
      of the genera Cryptosporidium, Giardia, Leishmania, Neospora, Plasmodium, Toxoplasma,
      Trichomonas and Trypanosoma. While each of these groups is supported by a taxon-specific
      database built upon the same infrastructure, the EuPathDB portal offers an entry
      point to all these resources, and the opportunity to leverage orthology for
      searches across genera.
    homepage: http://amoebadb.org/amoeba/
    id: 00000148
    name: AmoebaDB
    namespaceEmbeddedInLui: false
    pattern: ^EDI_\d+$
    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/$1
  prefixcommons:
    description: AmoebaDB is one of the databases that can be accessed through the
      EuPathDB (http://EuPathDB.org; formerly ApiDB) portal, covering eukaryotic pathogens
      of the genera Cryptosporidium, Giardia, Leishmania, Neospora, Plasmodium, Toxoplasma,
      Trichomonas and Trypanosoma. While each of these groups is supported by a taxon-specific
      database built upon the same infrastructure, the EuPathDB portal offers an entry
      point to all these resources, and the opportunity to leverage orthology for
      searches across genera.
    example: EDI_244000
    homepage: http://amoebadb.org
    keywords:
    - model organism
    miriam: amoebadb
    name: AmoebaDB
    pattern: ^EDI_\d+$
    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.
    homepage: https://amoebadb.org/amoeba/app
    name: AmoebaDB
    prefix: r3d100012457
    xrefs:
      fairsharing: FAIRsharing.swbypy
      miriam: 00000148
      omics: '03152'
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
  example: '1000160'
  mappings:
    aberowl: AMPHX
    bioportal: AMPHX
    obofoundry: amphx
    ols: amphx
    ontobee: AMPHX
  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).
    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: https://raw.githubusercontent.com/EBISPOT/amphx_ontology/master/amphx.owl
    name: Amphioxus Development and Anatomy Ontology (AMPHX)
    prefix: amphx
    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+$
antibodyregistry:
  biocontext:
    is_identifiers: true
    is_obo: false
    prefix: ANTIBODYREGISTRY
    uri_format: http://identifiers.org/antibodyregistry/$1
  mappings:
    biocontext: ANTIBODYREGISTRY
    miriam: antibodyregistry
    n2t: antibodyregistry
  miriam:
    deprecated: false
    description: The Antibody Registry provides identifiers for antibodies used in
      publications. It lists commercial antibodies from numerous vendors, each assigned
      with a unique identifier. Unlisted antibodies can be submitted by providing
      the catalog number and vendor information.
    homepage: http://antibodyregistry.org/
    id: '00000516'
    name: Antibody Registry
    namespaceEmbeddedInLui: false
    pattern: ^\d{6}$
    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
antweb:
  biocontext:
    is_identifiers: true
    is_obo: false
    prefix: ANTWEB
    uri_format: http://identifiers.org/antweb/$1
  fairsharing:
    abbreviation: AntWeb
    description: AntWeb is a website documenting the known species of ants, with records
      for each species linked to their geographical distribution, life history, and
      includes pictures.
    id: '1749'
    name: AntWeb
    prefix: FAIRsharing.yk38tw
    subjects:
    - Anatomy
    - Life Science
  mappings:
    biocontext: ANTWEB
    fairsharing: FAIRsharing.yk38tw
    miriam: antweb
    n2t: antweb
    ncbi: AntWeb
    prefixcommons: antweb
    wikidata: P5299
  miriam:
    deprecated: false
    description: AntWeb is a website documenting the known species of ants, with records
      for each species linked to their geographical distribution, life history, and
      includes pictures.
    homepage: http://www.antweb.org/
    id: '00000146'
    name: AntWeb
    namespaceEmbeddedInLui: false
    pattern: ^casent\d+(\-D\d+)?$
    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=$1
  name: AntWeb
  ncbi:
    example: CASENT0058943-D01
    homepage: http://www.antweb.org
    name: Ant Database
    prefix: AntWeb
  prefixcommons:
    description: AntWeb is a website documenting the known species of ants, with records
      for each species linked to their geographical distribution, life history, and
      includes pictures.
    example: casent0106247
    homepage: https://www.antweb.org
    keywords:
    - classification
    - anatomy
    miriam: antweb
    name: 'AntWeb: Ant of the World'
    pattern: ^casent\d+(\-\w+\d+)?$
    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:
    database: Q2507304
    database.homepage: http://www.antweb.org/
    database.label: AntWeb
    description: identifier for a taxon in the AntWeb database
    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
aop:
  biocontext:
    is_identifiers: true
    is_obo: false
    prefix: AOP
    uri_format: http://identifiers.org/aop/$1
  mappings:
    biocontext: AOP
    miriam: aop
    n2t: aop
  miriam:
    deprecated: false
    description: International repository of Adverse Outcome Pathways.
    homepage: https://aopwiki.org/
    id: '00000617'
    name: AOPWiki
    namespaceEmbeddedInLui: false
    pattern: ^\d+$
    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
aop.events:
  biocontext:
    is_identifiers: true
    is_obo: false
    prefix: AOP.EVENTS
    uri_format: http://identifiers.org/aop.events/$1
  mappings:
    biocontext: AOP.EVENTS
    miriam: aop.events
    n2t: aop.events
  miriam:
    deprecated: false
    description: International repository of Adverse Outcome Pathways.
    homepage: https://aopwiki.org/
    id: '00000652'
    name: AOPWiki (Key Event)
    namespaceEmbeddedInLui: false
    pattern: ^\d+$
    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
aop.relationships:
  biocontext:
    is_identifiers: true
    is_obo: false
    prefix: AOP.RELATIONSHIPS
    uri_format: http://identifiers.org/aop.relationships/$1
  mappings:
    biocontext: AOP.RELATIONSHIPS
    miriam: aop.relationships
    n2t: aop.relationships
  miriam:
    deprecated: false
    description: International repository of Adverse Outcome Pathways.
    homepage: https://aopwiki.org/
    id: '00000653'
    name: AOPWiki (Key Event Relationship)
    namespaceEmbeddedInLui: false
    pattern: ^\d+$
    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
aop.stressor:
  biocontext:
    is_identifiers: true
    is_obo: false
    prefix: AOP.STRESSOR
    uri_format: http://identifiers.org/aop.stressor/$1
  mappings:
    biocontext: AOP.STRESSOR
    miriam: aop.stressor
    n2t: aop.stressor
  miriam:
    deprecated: false
    description: International repository of Adverse Outcome Pathways.
    homepage: https://aopwiki.org/
    id: '00000654'
    name: AOPWiki (Stressor)
    namespaceEmbeddedInLui: false
    pattern: ^\d+$
    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
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: awalker@apa.org
      name: Alvin Walker
    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
  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: APA thesaurus . Flat ontology file
    id: '567'
    name: Psychology Ontology
    prefix: FAIRsharing.gkw1w8
    publications: []
    subjects: []
  homepage: https://bioportal.bioontology.org/ontologies/APAONTO
  mappings:
    aberowl: APAONTO
    bioportal: APAONTO
    fairsharing: FAIRsharing.gkw1w8
  references:
  - https://github.com/biopragmatics/bioregistry/issues/528
  uri_format: http://ontology.apa.org/apaonto/termsonlyOUT%20(5).owl#$1
apd:
  biocontext:
    is_identifiers: true
    is_obo: false
    prefix: APD
    uri_format: http://identifiers.org/apd/$1
  fairsharing:
    abbreviation: APD
    description: The Antimicrobial Peptide Database (APD) contains information on
      antimicrobial peptides from across a wide taxonomic range. It includes a glossary,
      nomenclature, classification, information search, prediction, design, and statistics
      of AMPs. The antimicrobial peptides in this database contain less than 100 amino
      acid residues, are in the mature and active form, and primarily from natural
      sources, ranging from bacteria, fungi, plants, to animals.
    id: '2105'
    name: Antimicrobial Peptide Database
    prefix: FAIRsharing.ctwd7b
    subjects:
    - Biology
  mappings:
    biocontext: APD
    fairsharing: FAIRsharing.ctwd7b
    miriam: apd
    n2t: apd
    prefixcommons: apd
  miriam:
    deprecated: false
    description: The antimicrobial peptide database (APD) provides information on
      anticancer, antiviral, antifungal and antibacterial peptides.
    homepage: http://aps.unmc.edu/AP/
    id: 00000278
    name: APD
    namespaceEmbeddedInLui: false
    pattern: ^\d{5}$
    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=$1
  name: Antimicrobial Peptide Database
  prefixcommons:
    description: The Antimicrobial Peptide Database (APD) contains data from the Protein
      Data Bank (PDB), Swiss-Prot Protein Knowledgebase and PubMed National Library
      of Medicine. The antimicrobial peptides in this database contain less than 100
      amino acid residues, are in the mature and active form, and primarily from natural
      sources, ranging from bacteria, fungi, plants, to animals.
    example: '1228'
    homepage: http://aps.unmc.edu/AP/
    keywords:
    - protein
    miriam: apd
    name: Antimicrobial Peptide Database
    pattern: ^\d+$
    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
aphidbase.transcript:
  biocontext:
    is_identifiers: true
    is_obo: false
    prefix: APHIDBASE.TRANSCRIPT
    uri_format: http://identifiers.org/aphidbase.transcript/$1
  mappings:
    biocontext: APHIDBASE.TRANSCRIPT
    miriam: aphidbase.transcript
    n2t: aphidbase.transcript
  miriam:
    deprecated: false
    description: AphidBase is a centralized bioinformatic resource that was developed
      to facilitate community annotation of the pea aphid genome by the International
      Aphid Genomics Consortium (IAGC). The AphidBase Information System was designed
      to organize and distribute genomic data and annotations for a large international
      community. This collection references the transcript report, which describes
      genomic location, sequence and exon information.
    homepage: http://www.aphidbase.com/aphidbase
    id: 00000393
    name: AphidBase Transcript
    namespaceEmbeddedInLui: false
    pattern: ^ACYPI\d{6}(-RA)?$
    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
apid.interactions:
  biocontext:
    is_identifiers: true
    is_obo: false
    prefix: APID.INTERACTIONS
    uri_format: http://identifiers.org/apid.interactions/$1
  mappings:
    biocontext: APID.INTERACTIONS
    miriam: apid.interactions
    n2t: apid.interactions
  miriam:
    deprecated: false
    description: APID (Agile Protein Interactomes DataServer) provides information
      on the protein interactomes of numerous  organisms, based on the integration
      of known experimentally validated protein-protein physical interactions (PPIs).
      Interactome data includes a report on  quality levels and coverage over the
      proteomes for each organism included. APID integrates PPIs from primary databases
      of molecular interactions (BIND, BioGRID, DIP, HPRD, IntAct, MINT) and also
      from experimentally resolved 3D structures (PDB) where more than two distinct
      proteins have been identified. This collection references protein interactors,
      through a UniProt identifier.
    homepage: http://cicblade.dep.usal.es:8080/APID/
    id: '00000576'
    name: APID Interactomes
    namespaceEmbeddedInLui: false
    pattern: ^([A-N,R-Z][0-9]([A-Z][A-Z, 0-9][A-Z, 0-9][0-9]){1,2})|([O,P,Q][0-9][A-Z,
      0-9][A-Z, 0-9][A-Z, 0-9][0-9])(\.\d+)?$
    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
  provides: uniprot
apo:
  aberowl:
    description: A structured controlled vocabulary for the phenotypes of Ascomycete
      fungi
    download_owl: http://aber-owl.net/media/ontologies/APO/40/apo.owl
    homepage: http://www.yeastgenome.org/
    name: Ascomycete phenotype ontology
    prefix: APO
  biocontext:
    is_identifiers: false
    is_obo: true
    prefix: YPO
    uri_format: http://purl.obolibrary.org/obo/YPO_$1
  bioportal:
    contact:
      email: sgd-helpdesk@lists.stanford.edu
      name: Saccharomyces Genome Database
    description: A structured controlled vocabulary for the phenotypes of Ascomycete
      fungi
    homepage: http://www.yeastgenome.org/
    name: Ascomycete Phenotype Ontology
    prefix: APO
    version: releases/2018-03-24
  example: 0000184
  fairsharing:
    abbreviation: APO
    description: Ascomycete Phenotype Ontology is a structured controlled vocabulary
      for the phenotypes of Ascomycete fungi.
    id: '113'
    name: Ascomycete Phenotype Ontology
    prefix: FAIRsharing.dyqz3y
    publications: []
    subjects:
    - Life Science
    - Cell Biology
  mappings:
    aberowl: APO
    biocontext: YPO
    bioportal: APO
    fairsharing: FAIRsharing.dyqz3y
    obofoundry: apo
    ols: apo
    ontobee: APO
  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
    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: http://purl.obolibrary.org/obo/apo.owl
    homepage: http://www.yeastgenome.org/
    name: Ascomycete Phenotype Ontology (APO)
    prefix: apo
    version: '2022-07-06'
    version.iri: http://purl.obolibrary.org/obo/apo/releases/2022-07-06/apo.owl
  ontobee:
    library: Library
    name: Ascomycete phenotype ontology
    prefix: APO
  pattern: ^\d{7}$
  preferred_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
  uri_format: https://www.yeastgenome.org/observable/APO:$1
apollosv:
  aberowl:
    description: Defines terms and relations necessary for interoperation between
      epidemic models and public health application software that interface with these
      models
    download_owl: http://aber-owl.net/media/ontologies/APOLLO_SV/17/apollo_sv.owl
    homepage: https://github.com/ApolloDev/apollo-sv
    name: Apollo Structured Vocabulary
    prefix: APOLLO_SV
  bioportal:
    name: Apollo Structured Vocabulary
    prefix: APOLLO-SV
  example: '00000443'
  fairsharing:
    abbreviation: Apollo-SV
    description: An ontology of infectious disease epidemiology and ecology (a.k.a.
      population biology).
    id: '88'
    name: Apollo-SV
    prefix: FAIRsharing.ngv2xx
    publications:
    - doi: null
      pubmed_id: 24551417
      title: 'Apollo: giving application developers a single point of access to public
        health models using structured vocabularies and Web services.'
    - doi: 10.1186/s13326-016-0092-y
      pubmed_id: 27538448
      title: 'The Apollo Structured Vocabulary: an OWL2 ontology of phenomena in infectious
        disease epidemiology and population biology for use in epidemic simulation.'
    subjects:
    - Ecology
    - Biomedical Science
    - Epidemiology
    - Population Genetics
  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@ufl.edu
    contact.github: hoganwr
    contact.label: William Hogan
    contact.orcid: 0000-0002-9881-1017
    deprecated: false
    description: Defines terms and relations necessary for interoperation between
      epidemic models and public health application software that interface with these
      models
    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: Defines terms and relations necessary for interoperation between
      epidemic models and public health application software that interface with these
      models
    download: http://purl.obolibrary.org/obo/apollo_sv.owl
    homepage: https://github.com/ApolloDev/apollo-sv
    name: Apollo Structured Vocabulary (Apollo-SV)
    prefix: apollo_sv
    version: 4.1.1
    version.iri: http://purl.obolibrary.org/obo/apollo_sv/v4.1.1./apollo_sv.owl
  ontobee:
    library: Library
    name: Apollo Structured Vocabulary
    prefix: APOLLO_SV
  pattern: ^\d{8}$
  publications:
  - 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
  - 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
arachnoserver:
  biocontext:
    is_identifiers: true
    is_obo: false
    prefix: ARACHNOSERVER
    uri_format: http://identifiers.org/arachnoserver/$1
  edam:
    description: Unique identifier of a toxin from the ArachnoServer database.
    name: ArachnoServer
    obsolete: false
    prefix: '2578'
  fairsharing:
    abbreviation: ArachnoServer
    description: ArachnoServer is a manually curated database containing information
      on the sequence, three-dimensional structure, and biological activity of protein
      toxins derived from spider venom.
    id: '2037'
    name: 'ArachnoServer: Spider toxin database'
    prefix: FAIRsharing.c54ywe
    subjects:
    - Life Science
  mappings:
    biocontext: ARACHNOSERVER
    edam: '2578'
    fairsharing: FAIRsharing.c54ywe
    miriam: arachnoserver
    n2t: arachnoserver
    prefixcommons: arachnoserver
    re3data: r3d100012902
    uniprot: ArachnoServer
  miriam:
    deprecated: false
    description: ArachnoServer (www.arachnoserver.org) is a manually curated database
      providing information on the sequence, structure and biological activity of
      protein toxins from spider venoms. It include a molecular target ontology designed
      specifically for venom toxins, as well as current and historic taxonomic information.
    homepage: http://www.arachnoserver.org/
    id: 00000193
    name: ArachnoServer
    namespaceEmbeddedInLui: false
    pattern: ^AS\d{6}$
    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=$1
  prefixcommons:
    description: ArachnoServer is a manually curated database containing information
      on the sequence, three-dimensional structure, and biological activity of protein
      toxins derived from spider venom.
    example: AS000060
    homepage: http://www.arachnoserver.org
    keywords:
    - drug
    - protein
    miriam: arachnoserver
    name: 'ArachnoServer: Spider toxin database'
    pattern: ^AS\d{6}$
    prefix: arachnoserver
    pubmed_ids:
    - '21036864'
    - '29069336'
    uri_format: http://www.arachnoserver.org/toxincard.html?id=$1
  publications:
  - doi: 10.1093/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/bioinformatics/btx661
    pmc: null
    pubmed: '29069336'
    title: 'ArachnoServer 3.0: an online resource for automated discovery, analysis
      and annotation of spider toxins.'
    year: 2018
  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.
    homepage: http://www.arachnoserver.org/mainMenu.html
    name: ArachnoServer
    prefix: r3d100012902
    xrefs:
      fairsharing: FAIRsharing.c54ywe
      miriam: 00000193
      omics: '03117'
  uniprot:
    category: Organism-specific databases
    identifier: '145'
    link_is_explicit: 'true'
    name: 'ArachnoServer: Spider toxin database'
    prefix: ArachnoServer
    uri_format: http://www.arachnoserver.org
araport:
  description: Website with general information about Arabidopsis and functionalities
    such as a genomic viewer
  homepage: https://www.araport.org/
  mappings:
    ncbi: Araport
    uniprot: Araport
  name: Arabidopsis Information Portal
  ncbi:
    example: AT1G01010
    homepage: https://www.araport.org/
    name: Arabidopsis Information Portal
    prefix: Araport
  uniprot:
    category: Organism-specific databases
    identifier: '221'
    link_is_explicit: 'true'
    name: Arabidopsis Information Portal
    prefix: Araport
    uri_format: https://bar.utoronto.ca/thalemine/portal.do?externalids=$1
  uri_format: https://www.arabidopsis.org/servlets/TairObject?type=locus&name=$1
ardb:
  biocontext:
    is_identifiers: true
    is_obo: false
    prefix: ARDB
    uri_format: http://identifiers.org/ardb/$1
  mappings:
    biocontext: ARDB
    miriam: ardb
    n2t: ardb
  miriam:
    deprecated: false
    description: The Antibiotic Resistance Genes Database (ARDB) is a manually curated
      database which characterises genes involved in antibiotic resistance. Each gene
      and resistance type is annotated with information, including resistance profile,
      mechanism of action, ontology, COG and CDD annotations, as well as external
      links to sequence and protein databases. This collection references resistance
      genes.
    homepage: http://ardb.cbcb.umd.edu/
    id: '00000522'
    name: Antibiotic Resistance Genes Database
    namespaceEmbeddedInLui: false
    pattern: ^[A-Z_]{3}[0-9]{4,}$
    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
ark:
  banana: ark
  biocontext:
    is_identifiers: true
    is_obo: false
    prefix: ARK
    uri_format: http://identifiers.org/ark/$1
  mappings:
    biocontext: ARK
    miriam: ark
    n2t: ark
  miriam:
    deprecated: false
    description: An Archival Resource Key (ARK) is a Uniform Resource Locator (URL)
      that is a multi-purpose persistent identifier for information objects of any
      type.
    homepage: http://n2t.net/
    id: 00000592
    name: ARK
    namespaceEmbeddedInLui: true
    pattern: ^(ark\:)/*[0-9A-Za-z]+(?:/[\w/.=*+@\$-]*)?(?:\?.*)?$
    prefix: ark
    sampleId: /12345/fk1234
    uri_format: http://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:$1
  name: Archival Resource Key
  pattern: ^/*[0-9A-Za-z]+(?:/[\w/.=*+@\$-]*)?(?:\?.*)?$
  uri_format: http://n2t.net/ark:$1
aro:
  aberowl:
    description: Antibiotic resistance genes and mutations
    download_owl: http://aber-owl.net/media/ontologies/ARO/24/aro.owl
    homepage: https://github.com/arpcard/aro
    name: Antibiotic Resistance Ontology
    prefix: ARO
  biocontext:
    is_identifiers: false
    is_obo: true
    prefix: ARO
    uri_format: http://purl.obolibrary.org/obo/ARO_$1
  bioportal:
    contact:
      email: mcarthua@mcmaster.ca
      name: Andrew G. McArthur
    description: The Antibiotic Resistance Ontology describes antibiotic resistance
      genes and mutations, their products, mechanisms, and associated phenotypes,
      as well as antibiotics and their molecular targets. It is integrated with the
      Comprehensive Antibiotic Resistance Database, a curated resource containing
      high quality reference data on the molecular basis of antimicrobial resistance.
    homepage: https://github.com/arpcard/aro
    name: Antibiotic Resistance Ontology
    prefix: ARO
  download_obo: http://purl.obolibrary.org/obo/aro.obo
  example: '1000001'
  mappings:
    aberowl: ARO
    biocontext: ARO
    bioportal: ARO
    obofoundry: aro
    ols: aro
    ontobee: ARO
  obofoundry:
    appears_in:
    - scdo
    contact: mcarthua@mcmaster.ca
    contact.github: agmcarthur
    contact.label: Andrew G. McArthur
    contact.orcid: 0000-0002-1142-3063
    deprecated: false
    description: Antibiotic resistance genes and mutations
    download.owl: http://purl.obolibrary.org/obo/aro.owl
    homepage: https://github.com/arpcard/aro
    license: CC BY 4.0
    license.url: https://creativecommons.org/licenses/by/4.0/
    name: Antibiotic Resistance Ontology
    preferredPrefix: ARO
    prefix: aro
    publications:
    - id: https://www.ncbi.nlm.nih.gov/pubmed/31665441
      title: 'CARD 2020: antibiotic resistome surveillance with the comprehensive
        antibiotic resistance database.'
    repository: https://github.com/arpcard/aro
  ols:
    description: Antibiotic resistance genes and mutations
    download: http://purl.obolibrary.org/obo/aro.owl
    homepage: https://github.com/arpcard/aro
    name: Antibiotic Resistance Ontology
    prefix: aro
  ontobee:
    library: Library
    name: Antibiotic Resistance Ontology
    prefix: ARO
  pattern: ^\d{7}$
  publications:
  - doi: 10.1093/nar/gkz935
    pmc: PMC7145624
    pubmed: '31665441'
    title: 'CARD 2020: antibiotic resistome surveillance with the comprehensive antibiotic
      resistance database.'
    year: 2020
arrayexpress:
  biocontext:
    is_identifiers: true
    is_obo: false
    prefix: ARRAYEXPRESS
    uri_format: http://identifiers.org/arrayexpress/$1
  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/$1
  fairsharing:
    abbreviation: ArrayExpress
    description: ArrayExpress is a database of functional genomics experiments that
      can be queried and the data downloaded. It includes gene expression data from
      microarray and high throughput sequencing studies. Data is collected to MIAME
      and MINSEQE standards. Experiments are submitted directly to ArrayExpress or
      are imported from the NCBI GEO database.
    id: '1845'
    name: ArrayExpress
    prefix: FAIRsharing.6k0kwd
    subjects:
    - Functional Genomics
  mappings:
    biocontext: ARRAYEXPRESS
    cellosaurus: ArrayExpress
    fairsharing: FAIRsharing.6k0kwd
    miriam: arrayexpress
    n2t: arrayexpress
    prefixcommons: arrayexpress
    re3data: r3d100010222
  miriam:
    deprecated: false
    description: ArrayExpress is a public repository for microarray data, which is
      aimed at storing MIAME-compliant data in accordance with Microarray Gene Expression
      Data (MGED) recommendations.
    homepage: https://www.ebi.ac.uk/arrayexpress/
    id: '00000036'
    name: ArrayExpress
    namespaceEmbeddedInLui: false
    pattern: ^[AEP]-\w{4}-\d+$
    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/$1
  prefixcommons:
    description: ArrayExpress is a public repository for microarray data, which is
      aimed at storing MIAME-compliant data in accordance with Microarray Gene Expression
      Data (MGED) recommendations.
    example: E-MEXP-1712
    homepage: http://www.ebi.ac.uk/arrayexpress
    keywords:
    - expression
    - microarray
    - nucleotide
    miriam: arrayexpress
    name: ArrayExpress
    pattern: ^[AEP]-\w{4}-\d+$
    prefix: arrayexpress
    pubmed_ids:
    - '12519949'
    uri_format: http://www.ebi.ac.uk/arrayexpress/experiments/$1
  publications:
  - doi: 10.1093/nar/gkg091
    pmc: PMC165538
    pubmed: '12519949'
    title: ArrayExpress--a public repository for microarray gene expression data at
      the EBI.
    year: 2003
  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.
    homepage: https://www.ebi.ac.uk/arrayexpress/
    name: ArrayExpress
    prefix: r3d100010222
    synonyms:
    - functional genomics data
    xrefs:
      fairsharing: FAIRsharing.6k0kwd
      miriam: '00000036'
      nif: 0000-30123
      omics: '01023'
      scr: 002964
arrayexpress.platform:
  biocontext:
    is_identifiers: true
    is_obo: false
    prefix: ARRAYEXPRESS.PLATFORM
    uri_format: http://identifiers.org/arrayexpress.platform/$1
  mappings:
    biocontext: ARRAYEXPRESS.PLATFORM
    miriam: arrayexpress.platform
    n2t: arrayexpress.platform
  miriam:
    deprecated: false
    description: ArrayExpress is a public repository for microarray data, which is
      aimed at storing MIAME-compliant data in accordance with Microarray Gene Expression
      Data (MGED) recommendations.This collection references the specific platforms
      used in the generation of experimental results.
    homepage: https://www.ebi.ac.uk/arrayexpress/
    id: 00000294
    name: ArrayExpress Platform
    namespaceEmbeddedInLui: false
    pattern: ^[AEP]-\w{4}-\d+$
    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
arraymap:
  biocontext:
    is_identifiers: true
    is_obo: false
    prefix: ARRAYMAP
    uri_format: http://identifiers.org/arraymap/$1
  fairsharing:
    abbreviation: arrayMap
    description: Part of the Progenetix project, the arrayMap database facilitates
      the study of the genetics of human cancer. The Progenetix project provides the
      data customisation and visualization tools to mine the available data. The arrayMap
      database is developed by the group "Theoretical Cytogenetics and Oncogenomics"
      at the Department of Molecular Life Sciences of the University of Zurich.
    id: '2135'
    name: arrayMap - Genomic Array Data for Cancer CNV Profiles
    prefix: FAIRsharing.1fbc5y
    subjects:
    - Genomics
    - Bioinformatics
    - Life Science
    - Biomedical Science
  mappings:
    biocontext: ARRAYMAP
    fairsharing: FAIRsharing.1fbc5y
    miriam: arraymap
    n2t: arraymap
    re3data: r3d100012630
  miriam:
    deprecated: false
    description: arrayMap is a collection of pre-processed oncogenomic array data
      sets and CNA (somatic copy number aberrations) profiles. CNA are a type of mutation
      commonly found in cancer genomes. arrayMap data is assembled from public repositories
      and supplemented with additional sources, using custom curation pipelines. This
      information has been mapped to multiple editions of the reference human genome.
    homepage: https://www.arraymap.org
    id: '00000621'
    name: ArrayMap
    namespaceEmbeddedInLui: false
    pattern: ^[\w\-:,]{3,64}$
    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
  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.
    homepage: https://arraymap.progenetix.org/
    name: arrayMap
    prefix: r3d100012630
    xrefs:
      fairsharing: FAIRsharing.1fbc5y
      omics: 02596
arxiv:
  biocontext:
    is_identifiers: true
    is_obo: false
    prefix: ARXIV
    uri_format: http://identifiers.org/arxiv/$1
  mappings:
    biocontext: ARXIV
    miriam: arxiv
    n2t: arxiv
    prefixcommons: arxiv
  miriam:
    deprecated: false
    description: arXiv is an e-print service in the fields of physics, mathematics,
      non-linear science, computer science, and quantitative biology.
    homepage: https://arxiv.org/
    id: '00000035'
    name: arXiv
    namespaceEmbeddedInLui: false
    pattern: ^(\w+(\-\w+)?(\.\w+)?)?\d{4,7}(\.\d+(v\d+)?)?$
    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/$1
  prefixcommons:
    description: arXiv is an e-print service in the fields of physics, mathematics,
      non-linear science, computer science, and quantitative biology.
    example: 0807.4956v1
    homepage: http://arxiv.org
    keywords:
    - bibliography
    name: arXiv
    pattern: ^(\w+(\-\w+)?(\.\w+)?/)?\d{4,7}(\.\d{4}(v\d+)?)?$
    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.
    homepage: https://scholia.toolforge.org/
    name: Scholia
    uri_format: https://scholia.toolforge.org/arxiv/$1
  - code: ar5iv
    description: Articles from arXiv.org as responsive HTML5 web pages.
    homepage: https://ar5iv.labs.arxiv.org/
    name: ar5iv
    uri_format: https://ar5iv.org/abs/$1
asap:
  biocontext:
    is_identifiers: true
    is_obo: false
    prefix: ASAP
    uri_format: http://identifiers.org/asap/$1
  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.
    id: '2115'
    name: A Systematic Annotation Package
    prefix: FAIRsharing.anpa6
    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=$1
  mappings:
    biocontext: ASAP
    fairsharing: FAIRsharing.anpa6
    go: ASAP
    miriam: asap
    n2t: asap
    ncbi: ASAP
    prefixcommons: asap
    re3data: r3d100010666
  miriam:
    deprecated: false
    description: ASAP (a systematic annotation package for community analysis of genomes)
      stores bacterial genome sequence and functional characterization data. It includes
      multiple genome sequences at various stages of analysis, corresponding experimental
      data and access to collections of related genome resources.
    homepage: http://asap.ahabs.wisc.edu/asap/home.php
    id: 00000283
    name: ASAP
    namespaceEmbeddedInLui: false
    pattern: ^[A-Za-z0-9-]+$
    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=$1
  name: A Systematic Annotation Package for Community Analysis of Genomes
  ncbi:
    example: ABE-0000006
    homepage: https://asap.genetics.wisc.edu/asap/logon.php
    name: A Systematic Annotation Package for Community Analysis of Genomes
    prefix: ASAP
  prefixcommons:
    description: ASAP is a relational database and web interface developed to store,
      update and distribute genome sequence data and gene expression data.  It was
      designed to facilitate ongoing community annotation of genomes and to grow with
      genome projects as they move from the preliminary data stage through post-sequencing
      functional analysis.
    example: ABZ-0129277
    homepage: https://asap.ahabs.wisc.edu/annotation/php/ASAP1.htm
    keywords:
    - genome
    - gene expression
    name: A Systematic Annotation Package
    pattern: ^ABZ-\d+$
    prefix: asap
    pubmed_ids:
    - '12519969'
    - '16381899'
    uri_format: https://asap.ahabs.wisc.edu/asap/feature_info.php?FeatureID=$1
  publications:
  - doi: 10.1093/nar/gkg125
    pmc: PMC165572
    pubmed: '12519969'
    title: ASAP, a systematic annotation package for community analysis of genomes.
    year: 2003
  - doi: 10.1093/nar/gkj164
    pmc: PMC1347526
    pubmed: '16381899'
    title: 'ASAP: a resource for annotating, curating, comparing, and disseminating
      genomic data.'
    year: 2006
  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.'
    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
      scr: 001849
ascl:
  biocontext:
    is_identifiers: true
    is_obo: false
    prefix: ASCL
    uri_format: http://identifiers.org/ascl/$1
  fairsharing:
    abbreviation: ASCL
    description: The Astrophysics Source Code Library (ASCL) is a free online registry
      for source code of interest to astronomers and astrophysicists. It provides
      code that has been used in research that has appeared in, or been submitted
      to, peer-reviewed publications.Peer-reviewed papers that describe methods or
      experiments involving the development or use of source code are added by the
      ASCL team.
    id: '2546'
    name: Astrophysics Source Code Library
    prefix: FAIRsharing.wb0txg
    subjects:
    - Astrophysics and Astronomy
  mappings:
    biocontext: ASCL
    fairsharing: FAIRsharing.wb0txg
    miriam: ascl
    n2t: ascl
  miriam:
    deprecated: false
    description: The Astrophysics Source Code Library (ASCL) is a free online registry
      for software that have been used in research that has appeared in, or been submitted
      to, peer-reviewed publications. The ASCL is indexed by the SAO/NASA Astrophysics
      Data System (ADS) and Web of Science's Data Citation Index (WoS DCI), and is
      citable by using the unique ascl ID assigned to each code. The ascl ID can be
      used to link to the code entry by prefacing the number with ascl.net (i.e.,
      ascl.net/1201.001).
    homepage: http://ascl.net/
    id: '00000641'
    name: Astrophysics Source Code Library
    namespaceEmbeddedInLui: false
    pattern: ^[0-9\.]+$
    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
asin:
  biocontext:
    is_identifiers: true
    is_obo: false
    prefix: ASIN
    uri_format: http://identifiers.org/asin/$1
  mappings:
    biocontext: ASIN
    miriam: asin
    n2t: asin
  miriam:
    deprecated: false
    description: Almost every product on our site has its own ASIN, a unique code
      we use to identify it. For books, the ASIN is the same as the ISBN number, but
      for all other products a new ASIN is created when the item is uploaded to our
      catalogue.
    homepage: https://www.amazon.co.uk/gp/help/customer/display.html/277-3416785-8259466?ie=UTF8&nodeId=898182
    id: '00000670'
    name: Amazon Standard Identification Number (ASIN)
    namespaceEmbeddedInLui: false
    pattern: ^[0-9]{10}$
    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
aspgd.locus:
  biocontext:
    is_identifiers: true
    is_obo: false
    prefix: ASPGD.LOCUS
    uri_format: http://identifiers.org/aspgd.locus/$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=$1
  mappings:
    biocontext: ASPGD.LOCUS
    go: AspGD_LOCUS
    miriam: aspgd.locus
    n2t: aspgd.locus
  miriam:
    deprecated: false
    description: The Aspergillus Genome Database (AspGD) is a repository for information
      relating to fungi of the genus Aspergillus, which includes organisms of clinical,
      agricultural and industrial importance. AspGD facilitates comparative genomics
      by providing a full-featured genomics viewer, as well as matched and standardized
      sets of genomic information for the sequenced aspergilli. This collection references
      gene information.
    homepage: http://www.aspgd.org/
    id: '00000412'
    name: AspGD Locus
    namespaceEmbeddedInLui: false
    pattern: ^[A-Za-z_0-9]+$
    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
aspgd.protein:
  biocontext:
    is_identifiers: true
    is_obo: false
    prefix: ASPGD.PROTEIN
    uri_format: http://identifiers.org/aspgd.protein/$1
  mappings:
    biocontext: ASPGD.PROTEIN
    miriam: aspgd.protein
    n2t: aspgd.protein
  miriam:
    deprecated: false
    description: The Aspergillus Genome Database (AspGD) is a repository for information
      relating to fungi of the genus Aspergillus, which includes organisms of clinical,
      agricultural and industrial importance. AspGD facilitates comparative genomics
      by providing a full-featured genomics viewer, as well as matched and standardized
      sets of genomic information for the sequenced aspergilli. This collection references
      protein information.
    homepage: http://www.aspgd.org/
    id: '00000413'
    name: AspGD Protein
    namespaceEmbeddedInLui: false
    pattern: ^[A-Za-z_0-9]+$
    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=$1
asrp:
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: Arabidopsis Small RNA Project is a repository of data on Arabidopsis
    small RNA genes.
  example: ASRP1423
  homepage: https://asrp.danforthcenter.org/
  mappings:
    prefixcommons: asrp
  name: Arabidopsis Small RNA Project
  prefixcommons:
    description: This project focuses on small RNAs. It involves function analysis,
      regulation, and the evolution of RNA silencing pathways at a genome-wide level.
      Technologies are being used in the sequence-based profiling of the genome of
      A. thaliana small RNAs and their classification associated with silencing effector
      proteins.
    example: '365115'
    homepage: http://asrp.cgrb.oregonstate.edu
    keywords:
    - RNA
    - genome
    - regulation
    name: Arabidopsis Small RNA Project
    pattern: ^\d+$
    prefix: asrp
    pubmed_ids:
    - '15608278'
    - '17999994'
    uri_format: http://asrp.cgrb.oregonstate.edu/db/sRNAdisplay.html?ASRP_id=$1
  publications:
  - doi: 10.1093/nar/gki127
    pmc: PMC540081
    pubmed: '15608278'
    title: 'ASRP: the Arabidopsis Small RNA Project Database.'
    year: 2005
  - doi: 10.1093/nar/gkm997
    pmc: PMC2238918
    pubmed: '17999994'
    title: 'Update of ASRP: the Arabidopsis Small RNA Project database.'
    year: 2007
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
  biocontext:
    is_identifiers: true
    is_obo: false
    prefix: ATC
    uri_format: http://identifiers.org/atc/$1
  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
    publication: http://en.wikipedia.org/wiki/Anatomical_Therapeutic_Chemical_Classification_System
    version: 2022AA
  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.
    id: '1152'
    name: Anatomical Therapeutic Chemical Classification
    prefix: FAIRsharing.1a27h8
    publications:
    - doi: 10.1007/s002280000200
      pubmed_id: 11214783
      title: Different versions of the anatomical therapeutic chemical classification
        system and the defined daily dose--are drug utilisation data comparable?
    - doi: null
      pubmed_id: 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].'
    subjects:
    - Chemical Biology
    - Pharmacology
    - Biomedical Science
  mappings:
    aberowl: ATC
    biocontext: ATC
    bioportal: ATC
    edam: '3103'
    fairsharing: FAIRsharing.1a27h8
    hl7: whoATC
    miriam: atc
    n2t: atc
    prefixcommons: atc
    wikidata: P267
  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=$1
  name: Anatomical Therapeutic Chemical Classification System
  prefixcommons:
    bioportal: '3021'
    description: The Anatomical Therapeutic Chemical (ATC) classification system,
      divides active substances into different groups according to the organ or system
      on which they act and their therapeutic, pharmacological and chemical properties.
      Drugs are classified in groups at five different levels; Drugs are divided into
      fourteen main groups (1st level), with pharmacological/therapeutic subgroups
      (2nd level). The 3rd and 4th levels are chemical/pharmacological/therapeutic
      subgroups and the 5th level is the chemical substance. The Anatomical Therapeutic
      Chemical (ATC) classification system and the Defined Daily Dose (DDD) is a tool
      for exchanging and comparing data on drug use at international, national or
      local levels.
    example: A10BA02
    homepage: http://www.whocc.no/atc_ddd_index/
    keywords:
    - chemical
    name: Anatomical Therapeutic Chemical
    pattern: ^\w(\d+)?(\w{1,2})?(\d+)?$
    prefix: atc
    synonyms:
    - atc
    - uatc
    uri_format: http://www.whocc.no/atc_ddd_index/?code=$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
  synonyms:
  - ATC_code
  - ATTC
  wikidata:
    prefix: P267
atcc:
  biocontext:
    is_identifiers: true
    is_obo: false
    prefix: ATCC
    uri_format: http://identifiers.org/atcc/$1
  cellosaurus:
    category: Cell line collections
    homepage: https://www.atcc.org/
    name: American Type Culture Collection
    prefix: ATCC
    uri_format: https://www.atcc.org/Products/$1
  fairsharing:
    abbreviation: ATCC
    description: ATCC authenticates microorganisms and cell lines and manages logistics
      of long-term preservation and distribution of cultures for the scientific community.
      ATCC supports the cultures it acquires and authenticates with expert technical
      support, intellectual property management and characterization data.
    id: '1752'
    name: American Type Culture Collection database
    prefix: FAIRsharing.j0ezpm
    subjects:
    - Virology
    - Life Science
    - Epidemiology
  hl7:
    description: American Type Culture Collection
    name: ATC
    preferred_prefix: ATC
    prefix: 2.16.840.1.113883.6.77
    status: Pending
  homepage: https://www.lgcstandards-atcc.org
  mappings:
    biocontext: ATCC
    cellosaurus: ATCC
    fairsharing: FAIRsharing.j0ezpm
    hl7: 2.16.840.1.113883.6.77
    miriam: atcc
    n2t: atcc
    ncbi: ATCC
  miriam:
    deprecated: false
    description: The American Type Culture Collection (ATCC) is a private, nonprofit
      biological resource center whose mission focuses on the acquisition, authentication,
      production, preservation, development and distribution of standard reference
      microorganisms, cell lines and other materials for research in the life sciences.
    homepage: http://www.atcc.org/
    id: 00000284
    name: ATCC
    namespaceEmbeddedInLui: false
    pattern: ^\d+$
    prefix: atcc
    sampleId: '11303'
    uri_format: http://www.lgcstandards-atcc.org/Products/All/$1.aspx
  n2t:
    description: The American Type Culture Collection (ATCC) is a private, nonprofit
      biological resource center whose mission focuses on the acquisition, authentication,
      production, preservation, development and distribution of standard reference
      microorganisms, cell lines and other materials for research in the life sciences.
    example: '11303'
    homepage: http://www.atcc.org/
    name: ATCC in Virginia
    namespaceEmbeddedInLui: false
    pattern: ^\d+$
    prefix: atcc
    uri_format: http://www.lgcstandards-atcc.org/Products/All/$1.aspx
  name: American Type Culture Collection
  ncbi:
    example: '123456'
    homepage: http://www.atcc.org/
    name: American Type Culture Collection database
    prefix: ATCC
  pattern: ^([A-Z]+-)?\d+$
  synonyms:
  - ATCC
  - ATCC number
  - ATCC(dna)
  - ATCC(in host)
  uri_format: https://www.atcc.org/products/$1
atcvet:
  biocontext:
    is_identifiers: true
    is_obo: false
    prefix: ATCVET
    uri_format: http://identifiers.org/atcvet/$1
  mappings:
    biocontext: ATCVET
    miriam: atcvet
    n2t: atcvet
  miriam:
    deprecated: false
    description: The ATCvet system for the classification of veterinary medicines
      is based on the same overall principles as the ATC system for substances used
      in human medicine. In ATCvet systems, preparations are divided into groups,
      according to their therapeutic use. First, they are divided into 15 anatomical
      groups (1st level), classified as QA-QV in the ATCvet system, on the basis of
      their main therapeutic use.
    homepage: http://www.whocc.no/atcvet/atcvet_index/
    id: '00000267'
    name: Anatomical Therapeutic Chemical Vetinary
    namespaceEmbeddedInLui: false
    pattern: ^Q[A-Z0-9]+$
    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
atfdb.family:
  biocontext:
    is_identifiers: true
    is_obo: false
    prefix: ATFDB.FAMILY
    uri_format: http://identifiers.org/atfdb.family/$1
  mappings:
    biocontext: ATFDB.FAMILY
    miriam: atfdb.family
    n2t: atfdb.family
  miriam:
    deprecated: false
    description: The Animal Transcription Factor DataBase (AnimalTFDB) classifies
      TFs in sequenced animal genomes, as well as collecting the transcription co-factors
      and chromatin remodeling factors of those genomes. This collections refers to
      transcription factor families, and the species in which they are found.
    homepage: http://www.bioguo.org/AnimalTFDB/family_index.php
    id: '00000316'
    name: Animal TFDB Family
    namespaceEmbeddedInLui: false
    pattern: ^\w+$
    prefix: atfdb.family
    sampleId: CUT
    uri_format: http://www.bioguo.org/AnimalTFDB/family.php?fam=$1
  n2t:
    description: The Animal Transcription Factor DataBase (AnimalTFDB) classifies
      TFs in sequenced animal genomes, as well as collecting the transcription co-factors
      and chromatin remodeling factors of those genomes. This collections refers to
      transcription factor families, and the species in which they are found.
    example: CUT
    homepage: http://www.bioguo.org/AnimalTFDB/family_index.php
    name: Animal TFDB at Hubei Bioinformatics & Molecular Imaging Key Laboratory
    namespaceEmbeddedInLui: false
    pattern: ^\w+$
    prefix: atfdb.family
    uri_format: http://www.bioguo.org/AnimalTFDB/family.php?fam=$1
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:
    is_identifiers: false
    is_obo: true
    prefix: ATO
    uri_format: http://purl.obolibrary.org/obo/ATO_$1
  bioportal:
    contact:
      email: sbhdbe@mst.edu
      name: AmphiAnat list
    description: A taxonomy of Amphibia
    homepage: http://www.amphibanat.org
    name: Amphibian Taxonomy Ontology
    prefix: ATO
    version: See Remote Site
  example: '0000000'
  fairsharing:
    abbreviation: ATO
    description: Amphibian Taxonomy Ontology is an ontology of Amphibian species and
      genres. It is being integrated into UBERON resource
    id: '583'
    name: Amphibian Taxonomy Ontology
    prefix: FAIRsharing.ayjdsm
    publications: []
    subjects: []
  mappings:
    aberowl: ATO
    biocontext: ATO
    bioportal: ATO
    fairsharing: FAIRsharing.ayjdsm
    obofoundry: ato
  obofoundry:
    contact: david.c.blackburn@gmail.com
    contact.label: David Blackburn
    deprecated: true
    homepage: http://www.amphibanat.org
    name: Amphibian taxonomy
    prefix: ato
  pattern: ^\d{7}$
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: pierre-yves.le-bail@inrae.fr
      name: Pierre-yves Le-Bail
    description: "ATOL d\xE9finit et organise les caract\xE8res ph\xE9notypiques des\
      \ animaux d\u2019\xE9levage, en prenant en compte les pr\xE9occupations soci\xE9\
      tales et les grands types de production (lait, \u0153uf, viande, fertilit\xE9\
      , 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
    publication: http://www.atol-ontology.com/rb/fr/6
    version: '6.0'
  bioportal:
    contact:
      email: pylebail@rennes.inra.fr
      name: LeBail Pierre-Yves
    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: www.atol-ontology.com
    name: Animal Trait Ontology for Livestock
    prefix: ATOL
    version: '6.0'
  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.'
    id: '1535'
    name: Animal Trait Ontology for Livestock
    prefix: FAIRsharing.wsfk5z
    publications: []
    subjects:
    - Animal Husbandry
    - Agriculture
    - Life Science
  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}$
  uri_format: http://opendata.inra.fr/ATOL/ATOL_$1
autdb:
  biocontext:
    is_identifiers: true
    is_obo: false
    prefix: AUTDB
    uri_format: http://identifiers.org/autdb/$1
  mappings:
    biocontext: AUTDB
    miriam: autdb
    n2t: autdb
  miriam:
    deprecated: false
    description: AutDB is a curated database for autism research. It is built on information
      extracted from the studies on molecular genetics and biology of Autism Spectrum
      Disorders (ASD). The four modules of AutDB include information on Human Genes,
      Animal models, Protein Interactions (PIN) and Copy Number Variants (CNV) respectively.
      It provides an annotated list of ASD candidate genes in the form of reference
      dataset for interrogating molecular mechanisms underlying the disorder.
    homepage: http://autism.mindspec.org/autdb/
    id: '00000415'
    name: AutDB
    namespaceEmbeddedInLui: false
    pattern: ^[A-Z]+[A-Z-0-9]{2,}$
    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/$1
bacdive:
  fairsharing:
    abbreviation: BacDive
    description: "BacDive\u2014the Bacterial Diversity Metadatabase merges detailed\
      \ strain-linked information on the different aspects of bacterial and archaeal\
      \ biodiversity. BacDive contains entries for over 63,000 strains and provides\
      \ information on their taxonomy, morphology, physiology, sampling and concomitant\
      \ environmental conditions as well as molecular biology."
    id: '2674'
    name: Bacterial Diversity Metadatabase
    prefix: FAIRsharing.aSszvY
    subjects:
    - Biodiversity
    - Life Science
    - Microbiology
  mappings:
    fairsharing: FAIRsharing.aSszvY
    miriam: bacdive
    n2t: bacdive
    re3data: r3d100013060
  miriam:
    deprecated: false
    description: "BacDive\u2014the Bacterial Diversity Metadatabase merges detailed\
      \ strain-linked information on the different aspects of bacterial and archaeal\
      \ biodiversity."
    homepage: https://bacdive.dsmz.de/
    id: '00000676'
    name: Bacterial Diversity Metadatabase
    namespaceEmbeddedInLui: false
    pattern: ^[0-9]+$
    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
  re3data:
    description: BacDive is a bacterial metadatabase that provides strain-linked information
      about bacterial and archaeal biodiversity. The database is a resource for different
      kind of phenotypic data like taxonomy, morphology, physiology, environment and
      molecular-biology. The majority of data is manually annotated and curated. With
      the release in April 2019 BacDive offers information for 80,584 strains. The
      database is hosted by the Leibniz Institute DSMZ - German Collection of Microorganisms
      and Cell Cultures GmbH and is part of de.NBI the German Network for Bioinformatics
      Infrastructure.
    homepage: https://bacdive.dsmz.de/
    name: BacDive
    prefix: r3d100013060
    synonyms:
    - Bacterial Diversity Metadatabase
    xrefs:
      fairsharing: FAIRsharing.aSszvY
      miriam: '00000676'
      omics: '10161'
bacmap.biog:
  biocontext:
    is_identifiers: true
    is_obo: false
    prefix: BACMAP.BIOG
    uri_format: http://identifiers.org/bacmap.biog/$1
  mappings:
    biocontext: BACMAP.BIOG
    miriam: bacmap.biog
    n2t: bacmap.biog
  miriam:
    deprecated: false
    description: BacMap is an electronic, interactive atlas of fully sequenced bacterial
      genomes. It contains labeled, zoomable and searchable chromosome maps for sequenced
      prokaryotic (archaebacterial and eubacterial) species. Each map can be zoomed
      to the level of individual genes and each gene is hyperlinked to a richly annotated
      gene card. All bacterial genome maps are supplemented with separate prophage
      genome maps as well as separate tRNA and rRNA maps. Each bacterial chromosome
      entry in BacMap contains graphs and tables on a variety of gene and protein
      statistics. Likewise, every bacterial species entry contains a bacterial 'biography'
      card, with taxonomic details, phenotypic details, textual descriptions and images.
      This collection references 'biography' information.
    homepage: http://bacmap.wishartlab.com/
    id: '00000361'
    name: BacMap Biography
    namespaceEmbeddedInLui: false
    pattern: ^\d+$
    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
bacmap.map:
  biocontext:
    is_identifiers: true
    is_obo: false
    prefix: BACMAP.MAP
    uri_format: http://identifiers.org/bacmap.map/$1
  mappings:
    biocontext: BACMAP.MAP
    miriam: bacmap.map
    n2t: bacmap.map
  miriam:
    deprecated: false
    description: BacMap is an electronic, interactive atlas of fully sequenced bacterial
      genomes. It contains labeled, zoomable and searchable chromosome maps for sequenced
      prokaryotic (archaebacterial and eubacterial) species. Each map can be zoomed
      to the level of individual genes and each gene is hyperlinked to a richly annotated
      gene card. All bacterial genome maps are supplemented with separate prophage
      genome maps as well as separate tRNA and rRNA maps. Each bacterial chromosome
      entry in BacMap contains graphs and tables on a variety of gene and protein
      statistics. Likewise, every bacterial species entry contains a bacterial 'biography'
      card, with taxonomic details, phenotypic details, textual descriptions and images.
      This collection references genome map information.
    homepage: http://bacmap.wishartlab.com/
    id: '00000416'
    name: BacMap Map
    namespaceEmbeddedInLui: false
    pattern: ^\w+(\_)?\d+(\.\d+)?$
    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/$1/index.html
bactibase:
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: Bactibase is a database describing the physical and chemical properties
    of bacteriocins from gram-negative and gram-positive bacteria.
  example: BAC045
  fairsharing:
    abbreviation: BACTIBASE
    description: BACTIBASE contains calculated or predicted physicochemical properties
      of bacteriocins produced by both Gram-positive and Gram-negative bacteria. The
      information in this database is very easy to extract and allows rapid prediction
      of relationships structure/function and target organisms of these peptides and
      therefore better exploitation of their biological activity in both the medical
      and food sectors.
    id: '1928'
    name: 'Bactibase: database dedicated to bacteriocins'
    prefix: FAIRsharing.5f5mfm
    subjects:
    - Life Science
  homepage: http://bactibase.hammamilab.org
  mappings:
    fairsharing: FAIRsharing.5f5mfm
    prefixcommons: bactibase
    re3data: r3d100012755
  name: Bactibase
  prefixcommons:
    description: BACTIBASE contains calculated or predicted physicochemical properties
      of 177 bacteriocins produced by both Gram-positive and Gram-negative bacteria.
      The information in this database is very easy to extract and allows rapid prediction
      of relationships structure/function and target organisms of these peptides and
      therefore better exploitation of their biological activity in both the medical
      and food sectors.
    example: BAC152
    homepage: http://bactibase.pfba-lab-tun.org/main.php
    keywords:
    - protein
    name: 'Bactibase: database dedicated to bacteriocins'
    pattern: ^BA\d+$
    prefix: bactibase
    uri_format: http://bactibase.pfba-lab-tun.org/$1
  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.
    homepage: http://bactibase.hammamilab.org/main.php
    name: BACTIBASE
    prefix: r3d100012755
    synonyms:
    - a database dedicated to bacteriocins
    xrefs:
      fairsharing: FAIRsharing.5f5mfm
      nlx: '54530'
      omics: '05726'
      scr: 006694
  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
  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:
    is_identifiers: true
    is_obo: false
    prefix: BAO
    uri_format: http://identifiers.org/bao/$1
  bioportal:
    name: BioAssay Ontology
    prefix: BAO
  fairsharing:
    abbreviation: BAO
    description: The BioAssay Ontology (BAO) describes chemical biology screening
      assays and their results including high-throughput screening (HTS) data for
      the purpose of categorizing assays and data analysis.
    id: '874'
    name: BioAssay Ontology
    prefix: FAIRsharing.mye76w
    publications:
    - doi: 10.1186/2041-1480-5-S1-S5
      pubmed_id: 25093074
      title: 'Evolving BioAssay Ontology (BAO): modularization, integration and applications.'
    - doi: 10:1371/journal.pone.0049198
      pubmed_id: 10
      title: Digitoxin metabolism by rat liver microsomes.
    - doi: 10.1371/journal.pone.0049198
      pubmed_id: 23155465
      title: Formalization, annotation and analysis of diverse drug and probe screening
        assay datasets using the BioAssay Ontology (BAO).
    - doi: 10.1186/1471-2105-12-257
      pubmed_id: 21702939
      title: 'BioAssay Ontology (BAO): a semantic description of bioassays and high-throughput
        screening results.'
    subjects:
    - Biochemistry
    - Life Science
    - Biomedical Science
  mappings:
    aberowl: BAO
    biocontext: BAO
    bioportal: BAO
    fairsharing: FAIRsharing.mye76w
    miriam: bao
    n2t: bao
    ols: bao
    ontobee: BAO
  miriam:
    deprecated: false
    description: The BioAssay Ontology (BAO) describes chemical biology screening
      assays and their results including high-throughput screening (HTS) data for
      the purpose of categorizing assays and data analysis.
    homepage: http://bioportal.bioontology.org/ontologies/BAO/
    id: 00000597
    name: BioAssay Ontology
    namespaceEmbeddedInLui: false
    pattern: ^\d{7}$
    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:
    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.
    download: http://www.bioassayontology.org/bao/
    homepage: http://bioassayontology.org
    name: BioAssay Ontology
    prefix: bao
    version: 2.7.2
    version.iri: http://www.bioassayontology.org/bao/bao_complete.owl
  ontobee:
    library: Not Specified/No
    name: BioAssay Ontology
    prefix: BAO
  publications:
  - doi: 10:1371/journal.pone.0049198
    pmc: null
    pubmed: '10'
    title: Digitoxin metabolism by rat liver microsomes.
    year: 1975
  - 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: PMC3498356
    pubmed: '23155465'
    title: Formalization, annotation and analysis of diverse drug and probe screening
      assay datasets using the BioAssay Ontology (BAO).
    year: 2012
  - doi: 10.1186/2041-1480-5-s1-s5
    pmc: PMC4108877
    pubmed: '25093074'
    title: 'Evolving BioAssay Ontology (BAO): modularization, integration and applications.'
    year: 2014
  synonyms:
  - BAO
bbkg:
  mappings:
    miriam: bbkg
  miriam:
    deprecated: false
    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
bbtp:
  mappings:
    miriam: bbtp
  miriam:
    deprecated: false
    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
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:
    is_identifiers: false
    is_obo: true
    prefix: BCGO
    uri_format: http://purl.obolibrary.org/obo/BCGO_$1
  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
    uri_format: http://www.ontobee.org/ontology/BCGO?iri=http://purl.obolibrary.org/obo/$1
  download_owl: https://github.com/obi-bcgo/bcgo/raw/master/ontology/bcgo.owl
  example: '0000015'
  mappings:
    aberowl: BCGO
    biocontext: BCGO
    bioportal: BCGO
    cellosaurus: BCGO
    obofoundry: bcgo
    ontobee: BCGO
  obofoundry:
    contact: jiezheng@pennmedicine.upenn.edu
    contact.github: zhengj2007
    contact.label: Jie Zheng
    contact.orcid: 0000-0002-2999-0103
    deprecated: true
    description: An application ontology built for beta cell genomics studies.
    download.owl: http://purl.obolibrary.org/obo/bcgo.owl
    homepage: https://github.com/obi-bcgo/bcgo
    license: CC BY 3.0
    license.url: http://creativecommons.org/licenses/by/3.0/
    name: Beta Cell Genomics Ontology
    prefix: bcgo
    repository: https://github.com/obi-bcgo/bcgo
  ontobee:
    library: Library
    name: Beta Cell Genomics Ontology
    prefix: BCGO
  pattern: ^\d{7}$
bcio:
  aberowl:
    description: 'The BCI ontology specifies a foundational metadata model set for
      real-world multimodal Brain-Computer Interaction (BCI) data capture activities.
      Its structure depicts a conceptual framework that BCI applications can extend
      and use in their implementations, to define core concepts that capture a relevant
      and interoperable metadata vocabulary. This ontology is aligned to the Semantic
      Sensor Network Ontology (SSN): a domain-independent and end-to-end model for
      sensor/actuator applications. Hence, its structure has been normalized to assist
      its use in conjunction with other ontologies or linked data resources to specify
      any particular definitions (such as units of measurement, time and time series,
      and location and mobility), that specialized applications in the BCI domain
      might need. Its spec provides general alignment data modeling guidelines for
      core concepts, to help BCI applications in their design.'
    download_owl: http://aber-owl.net/media/ontologies/BCI-O/6/bci-o.owl
    homepage: http://lov.okfn.org/dataset/lov/vocabs/bci
    name: Brain-Computer Interaction (BCI) Ontology
    prefix: BCI-O
    version: 0.9.6
  bioportal:
    contact:
      email: srodriguez@pet.cs.nctu.edu.tw
      name: "Sergio Jos\xE9 Rodr\xEDguez M\xE9ndez"
    description: 'The BCI ontology specifies a foundational metadata model set for
      real-world multimodal Brain-Computer Interaction (BCI) data capture activities.
      Its structure depicts a conceptual framework that BCI applications can extend
      and use in their implementations, to define core concepts that capture a relevant
      and interoperable metadata vocabulary. This ontology is aligned to the Semantic
      Sensor Network Ontology (SSN): a domain-independent and end-to-end model for
      sensor/actuator applications. Hence, its structure has been normalized to assist
      its use in conjunction with other ontologies or linked data resources to specify
      any particular definitions (such as units of measurement, time and time series,
      and location and mobility), that specialized applications in the BCI domain
      might need. Its spec provides general alignment data modeling guidelines for
      core concepts, to help BCI applications in their design.'
    homepage: http://lov.okfn.org/dataset/lov/vocabs/bci
    name: Brain-Computer Interaction (BCI) Ontology
    prefix: BCI-O
    publication: https://github.com/perma-id/w3id.org/tree/master/BCI-ontology
    version: 0.9.6
  download_owl: http://humanbehaviourchange.org/ontology/bcio.owl
  example: '040000'
  mappings:
    aberowl: BCI-O
    bioportal: BCI-O
    ols: bcio
  ols:
    description: The Behaviour Change Intervention Ontology is an ontology for all
      aspects of human behaviour change interventions and their evaluation.
    download: http://humanbehaviourchange.org/ontology/bcio.owl
    homepage: https://www.humanbehaviourchange.org/
    name: The Behaviour Change Intervention Ontology
    prefix: bcio
    version.iri: http://humanbehaviourchange.org/ontology/bcio.owl/2022-04-30
  pattern: ^\d{6}$
  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.
    example_uri: http://purl.obolibrary.org/obo/bco_0000036
    homepage: https://github.com/BiodiversityOntologies
    license: CC0 1.0
    name: Biological Collections Ontology
    prefix: BCO
    publication: https://doi.org/10.1371/journal.pone.0089606
    repository: https://github.com/BiodiversityOntologies/bco
  biocontext:
    is_identifiers: false
    is_obo: true
    prefix: BCO
    uri_format: http://purl.obolibrary.org/obo/BCO_$1
  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 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.
    homepage: https://github.com/BiodiversityOntologies/bco
    name: BioCollections Ontology
    prefix: BCO
    publication: 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.
    id: '1080'
    name: Biological Collections Ontology
    prefix: FAIRsharing.8ktkqy
    publications:
    - doi: 10.1371/journal.pone.0089606
      pubmed_id: 24595056
      title: 'Semantics in support of biodiversity knowledge discovery: an introduction
        to the biological collections ontology and related ontologies.'
    subjects:
    - Metagenomics
    - Taxonomy
    - Ecology
    - Biodiversity
  mappings:
    aberowl: BCO
    agroportal: BCO
    biocontext: BCO
    bioportal: BCO
    ecoportal: BCO
    fairsharing: FAIRsharing.8ktkqy
    obofoundry: bco
    ols: bco
    ontobee: BCO
  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.
    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
    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: http://purl.obolibrary.org/obo/bco.owl
    homepage: https://github.com/BiodiversityOntologies/bco
    name: Biological Collections Ontology
    prefix: bco
    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}$
  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
bcrc:
  cellosaurus:
    category: Cell line collections
    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=$1
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  example: '60316'
  homepage: https://catalog.bcrc.firdi.org.tw
  mappings:
    cellosaurus: BCRC
  name: BCRC Strain Collection Catalog
  pattern: ^\d+$
  uri_format: https://catalog.bcrc.firdi.org.tw/BcrcContent?bid=$1
bcrj:
  cellosaurus:
    category: Cell line collections
    homepage: http://bcrj.org.br/celula/bcrj
    name: Banco de Celulas do Rio de Janeiro
    prefix: BCRJ
    uri_format: http://bcrj.org.br/celula/$1
  example: 0278
  mappings:
    cellosaurus: BCRJ
  pattern: ^\d{4}$
bdgp.est:
  biocontext:
    is_identifiers: true
    is_obo: false
    prefix: BDGP.EST
    uri_format: http://identifiers.org/bdgp.est/$1
  has_canonical: dbest
  mappings:
    biocontext: BDGP.EST
    miriam: bdgp.est
    n2t: bdgp.est
    ncbi: BDGP_EST
    prefixcommons: flybase.est
  miriam:
    deprecated: false
    description: The BDGP EST database collects the expressed sequence tags (ESTs)
      derived from a variety of tissues and developmental stages for Drosophila melanogaster.
      All BDGP ESTs are available at dbEST (NCBI).
    homepage: https://www.ncbi.nlm.nih.gov/dbEST/index.html
    id: 00000285
    name: BDGP EST
    namespaceEmbeddedInLui: false
    pattern: ^\w+(\.)?(\d+)?$
    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/$1
  ncbi:
    example: '123456'
    homepage: http://www.fruitfly.org/EST/index.shtml
    name: Berkeley Drosophila Genome Project EST database
    prefix: BDGP_EST
  prefixcommons:
    description: The goals of the Drosophila Genome Center are to finish the sequence
      of the euchromatic genome of Drosophila melanogaster to high quality and to
      generate and maintain biological annotations of this sequence.
    example: '123456'
    homepage: http://www.fruitfly.org/EST/index.shtml
    keywords:
    - genome
    name: Berkeley Drosophila Genome Project EST database
    pattern: ^\d+$
    prefix: flybase.est
    synonyms:
    - bdgp_est
bdgp.insertion:
  biocontext:
    is_identifiers: true
    is_obo: false
    prefix: BDGP.INSERTION
    uri_format: http://identifiers.org/bdgp.insertion/$1
  mappings:
    biocontext: BDGP.INSERTION
    miriam: bdgp.insertion
    n2t: bdgp.insertion
    prefixcommons: bdgp
  miriam:
    deprecated: false
    description: BDGP gene disruption collection provides a public resource of gene
      disruptions of Drosophila genes using a single transposable element.
    homepage: http://flypush.imgen.bcm.tmc.edu/pscreen/
    id: '00000156'
    name: BDGP insertion DB
    namespaceEmbeddedInLui: false
    pattern: ^\w+$
    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=$1
  prefixcommons:
    description: BDGP gene disruption collection provides a public resource of gene
      disruptions of Drosophila genes using a single transposable element.
    example: KG09531
    keywords:
    - gene
    - sequence
    name: Drosphila Gene Disruption Database
    pattern: ^\w+$
    prefix: bdgp
    pubmed_ids:
    - '15238527'
    synonyms:
    - BDGP.insertion
    uri_format: http://flypush.imgen.bcm.tmc.edu/pscreen/details.php?line=$1
  publications:
  - doi: 10.1534/genetics.104.026427
    pmc: PMC1470905
    pubmed: '15238527'
    title: 'The BDGP gene disruption project: single transposon insertions associated
      with 40% of Drosophila genes.'
    year: 2004
bdsc:
  mappings:
    miriam: bdsc
    n2t: bdsc
  miriam:
    deprecated: false
    description: The Bloomington Drosophila Stock Center collects, maintains and distributes
      Drosophila melanogaster strains for research.
    homepage: https://bdsc.indiana.edu/about/mission.html
    id: '00000332'
    name: Bloomington Drosophila Stock Center
    namespaceEmbeddedInLui: false
    pattern: ^\d+$
    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
beetlebase:
  biocontext:
    is_identifiers: true
    is_obo: false
    prefix: BEETLEBASE
    uri_format: http://identifiers.org/beetlebase/$1
  fairsharing:
    abbreviation: BeetleBase
    description: BeetleBase is a community resource for Tribolium genetics, genomics
      and developmental biology. The database is built on the Chado generic data model,
      and is able to store various types of data, ranging from genome sequences to
      mutant phenotypes.
    id: '1940'
    name: BeetleBase
    prefix: FAIRsharing.h5f091
    subjects:
    - Computational Biology
    - Life Science
  mappings:
    biocontext: BEETLEBASE
    fairsharing: FAIRsharing.h5f091
    miriam: beetlebase
    n2t: beetlebase
    ncbi: BEETLEBASE
    prefixcommons: beetlebase
    re3data: r3d100010921
  miriam:
    deprecated: false
    description: BeetleBase is a comprehensive sequence database and community resource
      for Tribolium genetics, genomics and developmental biology. It incorporates
      information about genes, mutants, genetic markers, expressed sequence tags and
      publications.
    homepage: http://beetlebase.org/
    id: '00000157'
    name: BeetleBase
    namespaceEmbeddedInLui: false
    pattern: ^TC\d+$
    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=$1
  ncbi:
    example: TC030551
    homepage: http://www.beetlebase.org/
    name: Tribolium Genome Database -- Insertion
    prefix: BEETLEBASE
  prefixcommons:
    description: BeetleBase is being developed as an important community resource
      for Tribolium genetics, genomics and developmental biology.The database is built
      on the Chado generic data model, and is able to store various types of data,
      ranging from genome sequences to mutant phenotypes.
    example: TC010103
    homepage: http://www.beetlebase.org/
    keywords:
    - genome
    name: BeetleBase
    pattern: ^TC\d+$
    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   !!!!!BeetleBase
      is a comprehensive sequence database and important community resource for Tribolium
      genetics, genomics and developmental biology. It provides genetic data on the
      Tribolium Castaneum, Red Flour Beetle, as gene maps, official gene set, reference
      sequences, predicted models, and whole-genome tiling array representing developmental
      stages.'
    homepage: http://beetlebase.org/
    name: BeetleBase
    prefix: r3d100010921
    xrefs:
      fairsharing: FAIRsharing.h5f091
      nif: 0000-02599
      omics: 03118
begdb:
  biocontext:
    is_identifiers: true
    is_obo: false
    prefix: BEGDB
    uri_format: http://identifiers.org/begdb/$1
  fairsharing:
    abbreviation: BEGDB
    description: The Benchmark Energy & Geometry Database (BEGDB) collects results
      of highly accurate QM calculations of molecular structures, energies and properties.
      These data can serve as benchmarks for testing and parameterization of other
      computational methods.
    id: '2365'
    name: The Benchmark Energy & Geometry Database
    prefix: FAIRsharing.nbe4fq
    subjects:
    - Life Science
  mappings:
    biocontext: BEGDB
    fairsharing: FAIRsharing.nbe4fq
    miriam: begdb
    n2t: begdb
  miriam:
    deprecated: false
    description: The Benchmark Energy & Geometry Database (BEGDB) collects results
      of highly accurate quantum mechanics (QM) calculations of molecular structures,
      energies and properties. These data can serve as benchmarks for testing and
      parameterization of other computational methods.
    homepage: http://www.begdb.com
    id: '00000622'
    name: Benchmark Energy & Geometry Database
    namespaceEmbeddedInLui: false
    pattern: ^[0-9]+$
    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
beiresources:
  cellosaurus:
    category: Cell line collections
    homepage: https://www.beiresources.org/Home.aspx
    name: BEI Resources
    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
  mappings:
    cellosaurus: BEI_Resources
  name: BEI Resources
  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
  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
    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.
    id: '1243'
    name: Biological Expression Language
    prefix: FAIRsharing.dp0jvd
    subjects:
    - Biology
  homepage: https://biological-expression-language.github.io/
  mappings:
    fairsharing: FAIRsharing.dp0jvd
  name: Biological Expression Language
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
    publication: http://ifomis.uni-saarland.de/bfo/publications
    repository: https://github.com/BFO-ontology/BFO
    version: '1.1'
  biocontext:
    is_identifiers: false
    is_obo: true
    prefix: BFO
    uri_format: http://purl.obolibrary.org/obo/BFO_$1
  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'
  example: '0000001'
  fairsharing:
    abbreviation: ISO/IEC 21838-2:2021 BFO
    description: "ISO/IEC 21838-2:2021 describes Basic Formal Ontology (BFO), which\
      \ is an ontology that is conformant to the requirements specified for top-level\
      \ ontologies in ISO/IEC 21838\u20111."
    id: '1248'
    name: "ISO/IEC 21838-2:2021 Information technology \u2014 Top-level ontologies\
      \ (TLO) \u2014 Part 2: Basic Formal Ontology (BFO)"
    prefix: FAIRsharing.wcpd6f
    publications: []
    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
  obofoundry:
    appears_in:
    - ado
    - agro
    - aism
    - cdno
    - colao
    - duo
    - ecocore
    - epio
    - foodon
    - fovt
    - hso
    - lepao
    - mco
    - ons
    - pcl
    - pco
    - psdo
    - rbo
    - 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.
    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/
    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: http://purl.obolibrary.org/obo/bfo.owl
    homepage: https://github.com/BFO-ontology/BFO
    name: Basic Formal Ontology
    prefix: bfo
    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}$
bgee.family:
  biocontext:
    is_identifiers: true
    is_obo: false
    prefix: BGEE.FAMILY
    uri_format: http://identifiers.org/bgee.family/$1
  mappings:
    biocontext: BGEE.FAMILY
    miriam: bgee.family
    n2t: bgee.family
  miriam:
    deprecated: false
    description: Bgee is a database of gene expression patterns within particular
      anatomical structures within a species, and between different animal species.
      This collection refers to expression across species.
    homepage: http://bgee.unil.ch/bgee/bgee
    id: '00000417'
    name: Bgee family
    namespaceEmbeddedInLui: false
    pattern: ^(ENSFM|ENSGTV:)\d+$
    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
bgee.gene:
  biocontext:
    is_identifiers: true
    is_obo: false
    prefix: BGEE.GENE
    uri_format: http://identifiers.org/bgee.gene/$1
  mappings:
    biocontext: BGEE.GENE
    miriam: bgee.gene
    n2t: bgee.gene
  miriam:
    deprecated: false
    description: Bgee is a database to retrieve and compare gene expression patterns
      in multiple species, produced from multiple data types (RNA-Seq, Affymetrix,
      in situ hybridization, and EST data). This collection references genes in Bgee.
    homepage: https://bgee.org/
    id: 00000418
    name: Bgee gene
    namespaceEmbeddedInLui: false
    pattern: ^[A-Za-z]+\d+$
    prefix: bgee.gene
    sampleId: FBgn0000015
    uri_format: https://bgee.org/?page=gene&gene_id=$1
  n2t:
    description: Bgee is a database to retrieve and compare gene expression patterns
      in multiple species, produced from multiple data types (RNA-Seq, Affymetrix,
      in situ hybridization, and EST data). This collection references genes in Bgee.
    example: FBgn0000015
    homepage: https://bgee.org/
    name: Bgee gene
    namespaceEmbeddedInLui: false
    pattern: ^[A-Za-z]+\d+$
    prefix: bgee.gene
    uri_format: https://bgee.org/?page=gene&gene_id=$1
bgee.organ:
  biocontext:
    is_identifiers: true
    is_obo: false
    prefix: BGEE.ORGAN
    uri_format: http://identifiers.org/bgee.organ/$1
  mappings:
    biocontext: BGEE.ORGAN
    miriam: bgee.organ
    n2t: bgee.organ
  miriam:
    deprecated: false
    description: Bgee is a database of gene expression patterns within particular
      anatomical structures within a species, and between different animal species.
      This collection refers to anatomical structures.
    homepage: http://bgee.unil.ch/bgee/bgee
    id: '00000420'
    name: Bgee organ
    namespaceEmbeddedInLui: false
    pattern: ^(XAO|ZFA|EHDAA|EMAPA|EV|MA)\:\d+$
    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
  uri_format: http://bgee.unil.ch/bgee/bgee?page=anatomy&action=organ_details&organ_children=on&organ_id=$1
bgee.stage:
  biocontext:
    is_identifiers: true
    is_obo: false
    prefix: BGEE.STAGE
    uri_format: http://identifiers.org/bgee.stage/$1
  mappings:
    biocontext: BGEE.STAGE
    miriam: bgee.stage
    n2t: bgee.stage
  miriam:
    deprecated: false
    description: Bgee is a database of gene expression patterns within particular
      anatomical structures within a species, and between different animal species.
      This collection refers to developmental stages.
    homepage: http://bgee.unil.ch/bgee/bgee
    id: 00000419
    name: Bgee stage
    namespaceEmbeddedInLui: false
    pattern: ^(FBvd|XtroDO|HsapDO|MmusDO)\:\d+$
    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
  uri_format: http://bgee.unil.ch/bgee/bgee?page=anatomy&action=organs&stage_children=on&stage_id=$1
bibo:
  contact:
    email: fred@fgiasson.com
    github: fgiasson
    name: "Fr\xE9d\xE9rick 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.
  example: authorList
  homepage: https://bibliontology.com/
  name: The Bibliographic Ontology
  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
    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.
    id: '3737'
    name: 'Bibliometric Data Ontology '
    prefix: FAIRsharing.d7f0a9
    publications: []
    subjects:
    - Subject Agnostic
  homepage: http://www.sparontologies.net/ontologies/bido
  mappings:
    fairsharing: FAIRsharing.d7f0a9
  name: Bibliometric Data Ontology
  preferred_prefix: BiDO
  repository: https://github.com/sparontologies/bido
  uri_format: http://purl.org/spar/bido/$1
bigg.compartment:
  biocontext:
    is_identifiers: true
    is_obo: false
    prefix: BIGG.COMPARTMENT
    uri_format: http://identifiers.org/bigg.compartment/$1
  mappings:
    biocontext: BIGG.COMPARTMENT
    miriam: bigg.compartment
    n2t: bigg.compartment
  miriam:
    deprecated: false
    description: BiGG is a knowledgebase of Biochemically, Genetically and Genomically
      structured genome-scale metabolic network reconstructions. It more published
      genome-scale metabolic networks into a single database with a set of stardized
      identifiers called BiGG IDs. Genes in the BiGG models are mapped to NCBI genome
      annotations, and metabolites are linked to many external databases (KEGG, PubChem,
      and many more). This collection references model compartments.
    homepage: http://bigg.ucsd.edu/compartments/
    id: '00000555'
    name: BiGG Compartment
    namespaceEmbeddedInLui: false
    pattern: ^[a-z_A-Z]+$
    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
bigg.metabolite:
  biocontext:
    is_identifiers: true
    is_obo: false
    prefix: BIGG.METABOLITE
    uri_format: http://identifiers.org/bigg.metabolite/$1
  mappings:
    biocontext: BIGG.METABOLITE
    miriam: bigg.metabolite
    n2t: bigg.metabolite
  miriam:
    deprecated: false
    description: BiGG is a knowledgebase of Biochemically, Genetically and Genomically
      structured genome-scale metabolic network reconstructions. It more published
      genome-scale metabolic networks into a single database with a set of stardized
      identifiers called BiGG IDs. Genes in the BiGG models are mapped to NCBI genome
      annotations, and metabolites are linked to many external databases (KEGG, PubChem,
      and many more). This collection references individual metabolotes.
    homepage: http://bigg.ucsd.edu/universal/metabolites
    id: '00000556'
    name: BiGG Metabolite
    namespaceEmbeddedInLui: false
    pattern: ^[a-z_A-Z0-9]+$
    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
bigg.model:
  biocontext:
    is_identifiers: true
    is_obo: false
    prefix: BIGG.MODEL
    uri_format: http://identifiers.org/bigg.model/$1
  mappings:
    biocontext: BIGG.MODEL
    miriam: bigg.model
    n2t: bigg.model
  miriam:
    deprecated: false
    description: BiGG is a knowledgebase of Biochemically, Genetically and Genomically
      structured genome-scale metabolic network reconstructions. It more published
      genome-scale metabolic networks into a single database with a set of stardized
      identifiers called BiGG IDs. Genes in the BiGG models are mapped to NCBI genome
      annotations, and metabolites are linked to many external databases (KEGG, PubChem,
      and many more). This collection references individual models.
    homepage: http://bigg.ucsd.edu/models
    id: '00000554'
    name: BiGG Model
    namespaceEmbeddedInLui: false
    pattern: ^[a-z_A-Z0-9]+$
    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
bigg.reaction:
  biocontext:
    is_identifiers: true
    is_obo: false
    prefix: BIGG.REACTION
    uri_format: http://identifiers.org/bigg.reaction/$1
  mappings:
    biocontext: BIGG.REACTION
    miriam: bigg.reaction
    n2t: bigg.reaction
  miriam:
    deprecated: false
    description: BiGG is a knowledgebase of Biochemically, Genetically and Genomically
      structured genome-scale metabolic network reconstructions. It more published
      genome-scale metabolic networks into a single database with a set of stardized
      identifiers called BiGG IDs. Genes in the BiGG models are mapped to NCBI genome
      annotations, and metabolites are linked to many external databases (KEGG, PubChem,
      and many more). This collection references reactions.
    homepage: http://bigg.ucsd.edu/universal/reactions
    id: '00000557'
    name: BiGG Reaction
    namespaceEmbeddedInLui: false
    pattern: ^[a-z_A-Z0-9]+$
    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
bila:
  biocontext:
    is_identifiers: false
    is_obo: true
    prefix: BILA
    uri_format: http://purl.obolibrary.org/obo/BILA_$1
  deprecated: true
  example: '0000000'
  fairsharing:
    abbreviation: BILA
    description: This is a record of the Bilateria anatomy terminology and ontology.
      We have been unable to find any further information about this resource.
    id: '1035'
    name: Bilateria anatomy
    prefix: FAIRsharing.eqgjeq
    publications: []
    subjects:
    - Anatomy
  mappings:
    biocontext: BILA
    fairsharing: FAIRsharing.eqgjeq
    obofoundry: bila
  obofoundry:
    contact: henrich@embl.de
    contact.label: Thorsten Heinrich
    deprecated: true
    download.owl: http://purl.obolibrary.org/obo/bila.owl
    homepage: http://4dx.embl.de/4DXpress
    name: Bilateria anatomy
    prefix: bila
  pattern: ^\d{7}$
bind:
  biocontext:
    is_identifiers: true
    is_obo: false
    prefix: BIND
    uri_format: http://identifiers.org/bind/$1
  deprecated: true
  edam:
    description: Accession number of an entry from the BIND database.
    name: BIND accession number
    obsolete: false
    prefix: '1129'
  homepage: http://bind.ca
  mappings:
    biocontext: BIND
    edam: '1129'
    prefixcommons: bind
  prefixcommons:
    description: BIND is a database designed to store full descriptions of interactions,
      molecular complexes and pathways.
    example: '98346'
    homepage: http://bond.unleashedinformatics.com/
    keywords:
    - interaction
    - small molecule
    - pathway
    name: Biomolecular Interaction Network Databank
    pattern: ^\d+$
    prefix: bind
    synonyms:
    - bind_translation (irefindex)
    uri_format: http://www.bind.ca/Action?identifier=bindid&idsearch=$1
  publications:
  - doi: null
    pmc: null
    pubmed: '12519993'
    title: 'BIND: the Biomolecular Interaction Network Database'
    year: null
  - doi: null
    pmc: null
    pubmed: '10871269'
    title: BIND--a data specification for storing and describing biomolecular interactions,
      molecular complexes and pathways
    year: null
  uri_format: http://www.bind.ca/Action?identifier=bindid&idsearch=$1
bindingdb:
  biocontext:
    is_identifiers: true
    is_obo: false
    prefix: BINDINGDB
    uri_format: http://identifiers.org/bindingDB/$1
  fairsharing:
    abbreviation: BindingDB
    description: BindingDB enables research by making a growing collection of high-quality,
      quantitative, protein-ligand binding data findable and usable. Funded by NIGMS/NIH.
    id: '1772'
    name: BindingDB database of measured binding affinities
    prefix: FAIRsharing.3b36hk
    subjects:
    - Drug Discovery
    - Chemistry
    - Life Science
    - Computational Chemistry
    - Medicinal Chemistry
  mappings:
    biocontext: BINDINGDB
    fairsharing: FAIRsharing.3b36hk
    miriam: bindingdb
    n2t: bindingdb
    prefixcommons: bindingdb
    re3data: r3d100012074
    uniprot: BindingDB
  miriam:
    deprecated: false
    description: BindingDB is the first public database of protein-small molecule
      affinity data.
    homepage: https://www.bindingdb.org
    id: '00000264'
    name: BindingDB
    namespaceEmbeddedInLui: false
    pattern: ^\w\d+$
    prefix: bindingdb
    sampleId: e999
    uri_format: http://www.bindingdb.org/compact/$1
  n2t:
    description: BindingDB is the first public database of protein-small molecule
      affinity data.
    example: e999
    homepage: https://www.bindingdb.org
    name: BindingDB
    namespaceEmbeddedInLui: false
    pattern: ^\w\d+$
    prefix: bindingdb
    uri_format: http://www.bindingdb.org/compact/$1
  prefixcommons:
    description: BindingDB is a public, web-accessible database of measured binding
      affinities, focusing chiefly on the interactions of protein considered to be
      drug-targets with small, drug-like molecules.
    example: '22360'
    homepage: http://www.bindingdb.org
    keywords:
    - protein
    - interaction
    name: BindingDB database of measured binding affinities
    pattern: ^\d+$
    prefix: bindingdb
    pubmed_ids:
    - '17145705'
    uri_format: http://www.bindingdb.org/bind/chemsearch/marvin/MolStructure.jsp?monomerid=$1
  publications:
  - doi: 10.1093/nar/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.'
    homepage: http://bindingdb.org/bind/index.jsp
    name: BindingDB
    prefix: r3d100012074
    synonyms:
    - BDB
    - The Binding Database
    xrefs:
      fairsharing: FAIRsharing.3b36hk
      nif: 0000-02603
      scr: 000390
  uniprot:
    category: Chemistry databases
    identifier: '127'
    link_is_explicit: 'true'
    name: BindingDB database of measured binding affinities
    prefix: BindingDB
    uri_format: https://www.bindingdb.org/uniprot/$1
biocarta.pathway:
  biocontext:
    is_identifiers: true
    is_obo: false
    prefix: BIOCARTA.PATHWAY
    uri_format: http://identifiers.org/biocarta.pathway/$1
  mappings:
    biocontext: BIOCARTA.PATHWAY
    miriam: biocarta.pathway
    n2t: biocarta.pathway
  miriam:
    deprecated: false
    description: BioCarta is a supplier and distributor of characterized reagents
      and assays for biopharmaceutical and academic research. It catalogs community
      produced online maps depicting molecular relationships from areas of active
      research, generating classical pathways as well as suggestions for new pathways.
      This collections references pathway maps.
    homepage: https://www.biocarta.com/
    id: '00000421'
    name: BioCarta Pathway
    namespaceEmbeddedInLui: false
    pattern: ^([hm]\_)?\w+Pathway$
    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
biocatalogue.service:
  biocontext:
    is_identifiers: true
    is_obo: false
    prefix: BIOCATALOGUE.SERVICE
    uri_format: http://identifiers.org/biocatalogue.service/$1
  mappings:
    biocontext: BIOCATALOGUE.SERVICE
    miriam: biocatalogue.service
    n2t: biocatalogue.service
  miriam:
    deprecated: false
    description: The BioCatalogue provides a common interface for registering, browsing
      and annotating Web Services to the Life Science community. Registered services
      are monitored, allowing the identification of service problems and changes and
      the filtering-out of unavailable or unreliable resources. BioCatalogue is free
      to use, for all.
    homepage: https://www.biocatalogue.org/
    id: '00000140'
    name: BioCatalogue
    namespaceEmbeddedInLui: false
    pattern: ^\d+$
    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
biocyc:
  biocontext:
    is_identifiers: true
    is_obo: false
    prefix: BIOCYC
    uri_format: http://identifiers.org/biocyc/$1
  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=$1
  mappings:
    biocontext: BIOCYC
    edam: '2104'
    go: BioCyc
    miriam: biocyc
    n2t: biocyc
    prefixcommons: biocyc
    uniprot: BioCyc
  miriam:
    deprecated: false
    description: BioCyc is a collection of Pathway/Genome Databases (PGDBs) which
      provides an electronic reference source on the genomes and metabolic pathways
      of sequenced organisms.
    homepage: http://biocyc.org
    id: 00000194
    name: BioCyc
    namespaceEmbeddedInLui: false
    pattern: ^[A-Z-0-9]+(\:)?[A-Za-z0-9+_.%-:]+$
    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=$1
  prefixcommons:
    description: The BioCyc collection of Pathway/Genome Databases (PGDBs) provides
      electronic reference sources on the pathways and genomes of different organisms.
    example: ECOLI:CYT-D-UBIOX-CPLX
    homepage: http://www.biocyc.org/
    keywords:
    - genome
    - pathway
    - sequence
    name: BioCyc Database Collection
    pattern: ^\w+\:[A-Za-z0-9-]+$
    prefix: biocyc
    pubmed_ids:
    - '16246909'
    uri_format: http://biocyc.org/ECOLI/NEW-IMAGE?object=$1
  publications:
  - doi: 10.1093/nar/gki892
    pmc: PMC1266070
    pubmed: '16246909'
    title: Expansion of the BioCyc collection of pathway/genome databases to 160 genomes.
    year: 2005
  uniprot:
    category: Enzyme and pathway databases
    identifier: '5'
    link_is_explicit: 'true'
    name: BioCyc Collection of Pathway/Genome Databases
    prefix: BioCyc
    uri_format: https://biocyc.org/getid?id=$1
biogrid:
  biocontext:
    is_identifiers: false
    is_obo: false
    prefix: BIOGRID
    uri_format: http://thebiogrid.org/$1
  fairsharing:
    abbreviation: BioGRID
    description: "The Biological General Repository for Interaction Datasets (BioGRID)\
      \ is a public database that archives and disseminates genetic and protein interaction\
      \ data from model organisms and humans. BioGRID currently holds over\_1,740,000\
      \ interactions\_curated from both high-throughput datasets and individual focused\
      \ studies, as derived from over 70,000+ publications in the primary literature.\
      \ Complete coverage of the entire literature is maintained for budding yeast\
      \ (S. cerevisiae), fission yeast (S. pombe) and thale cress (A. thaliana), and\
      \ efforts to expand curation across multiple metazoan species are underway.\
      \ All data are freely provided via our search index and available for download\
      \ in many standardized formats."
    id: '2028'
    name: Biological General Repository for Interaction Datasets
    prefix: FAIRsharing.9d5f5r
    subjects:
    - Cheminformatics
    - Biochemistry
    - Bioinformatics
    - Chemical Biology
    - Proteomics
    - Life Science
    - Systems Biology
  mappings:
    biocontext: BIOGRID
    fairsharing: FAIRsharing.9d5f5r
    miriam: biogrid
    n2t: biogrid
    prefixcommons: biogrid
    re3data: r3d100010350
    uniprot: BioGRID
  miriam:
    deprecated: false
    description: BioGRID is a database of physical and genetic interactions in Saccharomyces
      cerevisiae, Caenorhabditis elegans, Drosophila melanogaster, Homo sapiens, and
      Schizosaccharomyces pombe.
    homepage: http://thebiogrid.org/
    id: 00000058
    name: BioGRID
    namespaceEmbeddedInLui: false
    pattern: ^\d+$
    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/$1
  prefixcommons:
    description: BioGRID is a database of physical and genetic interactions in Saccharomyces
      cerevisiae, Caenorhabditis elegans, Drosophila melanogaster, Homo sapiens, and
      Schizosaccharomyces pombe.
    example: '31623'
    homepage: http://www.thebiogrid.org
    keywords:
    - protein
    - gene
    - interaction
    name: Biological General Repository for Interaction Datasets
    pattern: ^\d+$
    prefix: biogrid
    pubmed_ids:
    - '16381927'
    synonyms:
    - grid
    uri_format: http://thebiogrid.org/$1
  publications:
  - doi: 10.1093/nar/gkj109
    pmc: PMC1347471
    pubmed: '16381927'
    title: 'BioGRID: a general repository for interaction datasets.'
    year: 2006
  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.
    homepage: https://thebiogrid.org/
    name: BioGRID
    prefix: r3d100010350
    synonyms:
    - Biological General Repository for Interaction Datasets
    xrefs:
      fairsharing: fairsharing.9d5f5r
      miriam: 00000058
      nif: 0000-00432
      omics: 01901
      scr: 007393
  twitter: biogrid
  uniprot:
    category: Protein-protein interaction databases
    identifier: '184'
    link_is_explicit: 'true'
    name: The Biological General Repository for Interaction Datasets (BioGRID)
    prefix: BioGRID
    uri_format: https://thebiogrid.org/$1
biogrid.interaction:
  contact:
    email: md.tyers@umontreal.ca
    github: null
    name: Mike Tyers
    orcid: 0000-0002-9713-9994
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: BioGRID is a database of physical and genetic interactions in Saccharomyces
    cerevisiae, Caenorhabditis elegans, Drosophila melanogaster, Homo sapiens, and
    Schizosaccharomyces pombe.
  edam:
    description: A unique identifier of an interaction from the BioGRID database.
    name: BioGRID interaction
    obsolete: false
    prefix: '2628'
  example: '2649230'
  homepage: https://thebiogrid.org/
  mappings:
    edam: '2628'
  name: BioGRID Interactions
  part_of: biogrid
  pattern: ^\d+$
  twitter: biogrid
  uri_format: https://thebiogrid.org/interaction/$1
biolegend:
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: BioLegend is a life sciences supply vendor.
  example: '3403'
  homepage: https://www.biolegend.com
  name: BioLegend
  pattern: ^\d+$
  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/41/biolink.owl
    homepage: https://biolink.github.io/biolink-model/
    name: Biolink Model
    prefix: BIOLINK
    version: 2.2.13
  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/
    name: Biolink Model
    prefix: BIOLINK
    version: 2.2.13
  fairsharing:
    abbreviation: biolink
    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).'
    id: '3649'
    name: Biolink Model
    prefix: FAIRsharing.ad9d85
    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
  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
biominder:
  biocontext:
    is_identifiers: true
    is_obo: false
    prefix: BIOMINDER
    uri_format: http://identifiers.org/biominder/$1
  mappings:
    biocontext: BIOMINDER
    miriam: biominder
    n2t: biominder
  miriam:
    deprecated: false
    description: Database of the dielectric properties of biological tissues.
    homepage: https://datalab.rwth-aachen.de/MINDER
    id: '00000634'
    name: Bio-MINDER Tissue Database
    namespaceEmbeddedInLui: false
    pattern: ^[a-z0-9\-]+$
    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
biomodels.db:
  biocontext:
    is_identifiers: true
    is_obo: false
    prefix: BIOMODELS.DB
    uri_format: http://identifiers.org/biomodels.db/$1
  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: CURATOR_REVIEW
      description: Caltech mirror
      homepage: http://biomodels.caltech.edu/
      name: Caltech mirror
      uri_format: http://biomodels.caltech.edu/$1
    - 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/$1
  prefixcommons:
    bioportal: '3022'
    description: BioModels Database is a data resource that allows biologists to store,
      search and retrieve published mathematical models of biological interests.
    example: BIOMD0000000048
    homepage: http://www.ebi.ac.uk/biomodels/
    keywords:
    - model
    name: A Database of Annotated Published Models
    pattern: ^((BIOMD|MODEL)\d{10})|(BMID\d{12})$
    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
  synonyms:
  - BIOMD
biomodels.kisao:
  aberowl:
    description: A classification of algorithms for simulating biology and their outputs
    download_owl: http://aber-owl.net/media/ontologies/KISAO/36/kisao.owl
    homepage: http://co.mbine.org/standards/kisao
    name: Kinetic Simulation Algorithm Ontology
    prefix: KISAO
  banana: KISAO
  banana_peel: _
  biocontext:
    is_identifiers: false
    is_obo: true
    prefix: KISAO
    uri_format: http://purl.obolibrary.org/obo/KISAO_$1
  bioportal:
    name: Kinetic Simulation Algorithm Ontology
    prefix: KISAO
  example: '0000057'
  fairsharing:
    abbreviation: KiSAO
    description: The Kinetic Simulation Algorithm Ontology aims at providing support
      in unambiguously referring to simulation algorithms when describing a simulation
      experiment. It describes and classifies existing algorithms and their inter-relationships
      through the algorithm characteristics and parameters.
    id: '974'
    name: Kinetic Simulation Algorithm Ontology
    prefix: FAIRsharing.jcg19w
    publications:
    - doi: 10.1038/msb.2011.77
      pubmed_id: 22027554
      title: Controlled vocabularies and semantics in systems biology.
    subjects:
    - Bioinformatics
    - Computer Science
  mappings:
    aberowl: KISAO
    biocontext: KISAO
    bioportal: KISAO
    fairsharing: FAIRsharing.jcg19w
    miriam: biomodels.kisao
    n2t: biomodels.kisao
    obofoundry: kisao
    ols: kisao
    ontobee: KISAO
    prefixcommons: kisao
  miriam:
    deprecated: false
    description: The Kinetic Simulation Algorithm Ontology (KiSAO) is an ontology
      that describes simulation algorithms and methods used for biological kinetic
      models, and the relationships between them. This provides a means to unambiguously
      refer to simulation algorithms when describing a simulation experiment.
    homepage: http://bioportal.bioontology.org/ontologies/KISAO
    id: 00000108
    name: KiSAO
    namespaceEmbeddedInLui: false
    pattern: ^KISAO_\d+$
    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:$1
  namespace_in_lui: true
  obofoundry:
    contact: jonrkarr@gmail.com
    contact.github: jonrkarr
    contact.label: Jonathan Karr
    contact.orcid: 0000-0002-2605-5080
    deprecated: false
    description: A classification of algorithms for simulating biology, their parameters,
      and their outputs
    download.owl: http://purl.obolibrary.org/obo/kisao.owl
    homepage: https://github.com/SED-ML/KiSAO
    license: Artistic License 2.0
    license.url: http://opensource.org/licenses/Artistic-2.0
    name: Kinetic Simulation Algorithm Ontology
    preferredPrefix: KISAO
    prefix: kisao
    publications:
    - id: https://www.ncbi.nlm.nih.gov/pubmed/22027554
      title: Controlled vocabularies and semantics in systems biology
    repository: https://github.com/SED-ML/KiSAO
  ols:
    description: A classification of algorithms for simulating biology, their parameters,
      and their outputs
    download: http://purl.obolibrary.org/obo/kisao.owl
    homepage: https://github.com/SED-ML/KiSAO
    name: Kinetic Simulation Algorithm Ontology
    prefix: kisao
    version: '2.30'
  ontobee:
    library: Library
    name: Kinetic Simulation Algorithm Ontology
    prefix: KISAO
  pattern: ^\d+$
  preferred_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
    synonyms:
    - biomodels.kisao
  providers:
  - code: legacy
    description: This is the URI scheme used in the ontology but it does not resolve.
    homepage: https://www.biomodels.net
    name: Legacy Biomodels URL
    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:
  - kisao
  uri_format: https://bioportal.bioontology.org/ontologies/KISAO?p=classes&conceptid=kisao: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:
    is_identifiers: true
    is_obo: false
    prefix: BIOMODELS.TEDDY
    uri_format: http://identifiers.org/biomodels.teddy/$1
  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
    publication: http://www.nature.com/msb/journal/v7/n1/full/msb201177.html
    version: rel-2014-04-24 (inferred)
  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.
    id: '923'
    name: TErminology for the Description of DYnamics
    prefix: FAIRsharing.w9jvbt
    publications:
    - doi: 10.1038/msb.2011.77
      pubmed_id: 22027554
      title: Controlled vocabularies and semantics in systems biology.
    subjects:
    - Neurophysiology
    - Synthetic Biology
    - Systems 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/$1
  ols:
    description: TEDDY is an ontology for dynamical behaviours, observable dynamical
      phenomena, and control elements of bio-models and biological systems in Systems
      and Synthetic Biology.
    download: http://www.biomodels.net/teddy/TEDDY
    name: Terminology for Description of Dynamics
    prefix: teddy
    version: '2014-04-24'
    version.iri: http://identifiers.org/combine.specifications/teddy.rel-2014-04-24
  pattern: ^\d+$
  prefixcommons:
    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
    name: Terminology for the Description of Dynamics
    pattern: ^TEDDY_\d{7}$
    prefix: teddy
    synonyms:
    - biomodels.teddy
  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:
    is_identifiers: true
    is_obo: false
    prefix: BIOMODELS.VOCABULARY
    uri_format: http://identifiers.org/biomodels.vocabulary/$1
  mappings:
    biocontext: BIOMODELS.VOCABULARY
    miriam: biomodels.vocabulary
    n2t: biomodels.vocabulary
  miriam:
    deprecated: false
    description: Vocabulary used in the RDF representation of SBML models.
    homepage: http://biomodels.net/rdf/vocabulary.rdf
    id: '00000514'
    name: SBML RDF Vocabulary
    namespaceEmbeddedInLui: false
    pattern: ^[A-Za-z]+$
    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
bionumbers:
  biocontext:
    is_identifiers: true
    is_obo: false
    prefix: BIONUMBERS
    uri_format: http://identifiers.org/bionumbers/$1
  edam:
    description: Identifier of an entry from the BioNumbers database of key numbers
      and associated data in molecular biology.
    name: BioNumbers
    obsolete: false
    prefix: '2660'
  mappings:
    biocontext: BIONUMBERS
    edam: '2660'
    miriam: bionumbers
    n2t: bionumbers
    prefixcommons: bionumbers
  miriam:
    deprecated: false
    description: BioNumbers is a database of key numberical information that may be
      used in molecular biology. Along with the numbers, it contains references to
      the original literature, useful comments, and related numeric data.
    homepage: https://bionumbers.hms.harvard.edu
    id: '00000101'
    name: BioNumbers
    namespaceEmbeddedInLui: false
    pattern: ^\d+$
    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=$1
  prefixcommons:
    description: BioNumbers is a database of key numberical information that may be
      used in molecular biology. Along with the numbers, it contains references to
      the original literature, useful comments, and related numeric data.
    example: '104674'
    homepage: http://www.bionumbers.hms.harvard.edu/search.aspx
    name: The Database of Useful Biological Numbers
    pattern: ^\d+$
    prefix: bionumbers
    uri_format: http://www.bionumbers.hms.harvard.edu/bionumber.aspx?s=y&id=$1&ver=1
bioportal:
  biocontext:
    is_identifiers: true
    is_obo: false
    prefix: BIOPORTAL
    uri_format: http://identifiers.org/bioportal/$1
  fairsharing:
    abbreviation: BioPortal
    description: "BioPortal is a library of biomedical ontologies and terminologies\
      \ developed in Web Ontology Language (OWL), Resource Description Framework (RDF)(S),\
      \ Open Biological and Biomedical Ontologies (OBO) format, and Prot\xE9g\xE9\
      \ frames and Rich Release Format. BioPortal groups ontologies by domain to aid\
      \ discoverability and allows users to browse, search and visualize the content\
      \ of ontologies. BioPortal also provides ontology recommendation, text annotation,\
      \ ontology mapping, and a reference index to resources like PubMed."
    id: '2290'
    name: BioPortal
    prefix: FAIRsharing.4m97ah
    subjects:
    - Life Science
    - Ontology and Terminology
  mappings:
    biocontext: BIOPORTAL
    fairsharing: FAIRsharing.4m97ah
    miriam: bioportal
    n2t: bioportal
    prefixcommons: bioportal
    re3data: r3d100012344
  miriam:
    deprecated: false
    description: "BioPortal is an open repository of biomedical ontologies that provides\
      \ access via Web services and Web browsers to ontologies developed in OWL, RDF,\
      \ OBO format and Prot\xE9g\xE9 frames. BioPortal functionality includes the\
      \ ability to browse, search and visualize ontologies."
    homepage: http://bioportal.bioontology.org/
    id: 00000187
    name: BioPortal
    namespaceEmbeddedInLui: false
    pattern: ^\d+$
    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/$1
  prefixcommons:
    description: BioPortal is an open repository of biomedical ontologies that provides
      access via Web services and Web browsers to ontologies developed in OWL, RDF,
      OBO format and Protege frames. BioPortal functionality includes the ability
      to browse, search and visualize ontologies.
    example: '1046'
    homepage: http://bioportal.bioontology.org/
    keywords:
    - ontology
    name: BioPortal
    pattern: ^\d+$
    prefix: bioportal
    pubmed_ids:
    - '19483092'
    uri_format: http://bioportal.bioontology.org/ontologies/$1
  publications:
  - doi: 10.1093/nar/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.'
    homepage: https://bioportal.bioontology.org/
    name: BioPortal
    prefix: r3d100012344
    xrefs:
      fairsharing: FAIRsharing.4m97ah
      miriam: 00000187
      nif: 0000-23346
      scr: '002713'
bioproject:
  biocontext:
    is_identifiers: true
    is_obo: false
    prefix: BIOPROJECT
    uri_format: http://identifiers.org/bioproject/$1
  fairsharing:
    abbreviation: BioProject
    description: A BioProject is a collection of biological data related to a single
      initiative, originating from a single organization or from a consortium. A BioProject
      record provides users a single place to find links to the diverse data types
      generated for that project. The BioProject database is a searchable collection
      of complete and incomplete (in-progress) large-scale sequencing, assembly, annotation,
      and mapping projects for cellular organisms.
    id: '2210'
    name: NCBI BioProject
    prefix: FAIRsharing.aqhv1y
    subjects:
    - Life Science
  has_canonical: ena.embl
  mappings:
    biocontext: BIOPROJECT
    fairsharing: FAIRsharing.aqhv1y
    miriam: bioproject
    n2t: bioproject
    re3data: r3d100013330
  miriam:
    deprecated: false
    description: "BioProject provides an organizational framework to access metadata\
      \ about research projects and the data from the projects that are deposited\
      \ into different databases. It provides information about a project\u2019s scope,\
      \ material, objectives, funding source and general relevance categories."
    homepage: http://trace.ddbj.nig.ac.jp/bioproject/
    id: 00000349
    name: BioProject
    namespaceEmbeddedInLui: false
    pattern: ^PRJ[DEN][A-Z]\d+$
    prefix: bioproject
    providers:
    - code: ncbi
      description: BioProject at NCBI
      homepage: https://www.ncbi.nlm.nih.gov/bioproject
      name: BioProject at NCBI
      uri_format: https://www.ncbi.nlm.nih.gov/bioproject?term=$1
    - code: ebi
      description: BioProject at European Nucleotide Archive (ENA)
      homepage: https://www.ebi.ac.uk/ena/
      name: BioProject at European Nucleotide Archive (ENA)
      uri_format: https://www.ebi.ac.uk/ena/browser/view/$1
    sampleId: PRJDB3
    uri_format: http://trace.ddbj.nig.ac.jp/BPSearch/bioproject?acc=$1
  n2t:
    description: BioProject provides an organizational framework to access metadata
      about research projects and the data from the projects that are deposited into
      different databases. It provides information about a project&#x2019;s scope,
      material, objectives, funding source and general relevance categories.
    example: PRJDB3
    homepage: https://www.ncbi.nlm.nih.gov/bioproject
    name: BioProject at NCBI
    namespaceEmbeddedInLui: false
    pattern: ^PRJ[DEN][A-Z]\d+$
    prefix: bioproject
    uri_format: https://www.ncbi.nlm.nih.gov/bioproject?term=$1
  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.
    homepage: https://www.ncbi.nlm.nih.gov/bioproject/
    name: BioProject
    prefix: r3d100013330
    xrefs:
      fairsharing: FAIRsharing.aqhv1y
      nlx: '143909'
      omics: 05338
      scr: 004801
  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
  homepage: https://bioregistry.io
  name: Bioregistry
  publications:
  - 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/$1
bioregistry.collection:
  contact:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: Manually curated collections of resources stored in the bioregistry
  example: '0000001'
  homepage: https://bioregistry.io/collection
  name: Bioregistry Collections
  pattern: ^\d{7}$
  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/
  name: Bioregistry Metaregistry
  uri_format: https://bioregistry.io/metaregistry/$1
bioregistry.schema:
  contact:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: Schema for the export of the Bioregistry as RDF
  example: '0000001'
  homepage: https://bioregistry.io/schema
  name: Bioregistry Schema
  pattern: ^\d{7}$
  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/$1
  homepage: https://biorxiv.org
  mappings:
    go: bioRxiv
  name: bioRxiv
  pattern: ^(\d{4}\.\d{2}\.\d{2}\.)?\d{6,8}(v\d{1,3})?$
  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/biorxiv/$1
  uri_format: https://www.biorxiv.org/content/10.1101/$1
biosample:
  biocontext:
    is_identifiers: true
    is_obo: false
    prefix: BIOSAMPLE
    uri_format: http://identifiers.org/biosample/$1
  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/$1
  fairsharing:
    abbreviation: BioSample
    description: "The NCBI BioSample database stores submitter-supplied descriptive\
      \ information, or metadata, about the biological materials from which data stored\
      \ in NCBI\u2019s primary data archives are derived. NCBI\u2019s archives host\
      \ data from diverse types of samples from any species, so the BioSample database\
      \ is similarly diverse; typical examples of a BioSample include a cell line,\
      \ a primary tissue biopsy, an individual organism or an environmental isolate.\
      \ The BioSample database promotes the use of structured and consistent attribute\
      \ names and values that describe what the samples are as well as information\
      \ about their provenance, where appropriate."
    id: '2211'
    name: NCBI BioSample
    prefix: FAIRsharing.qr6pqk
    subjects:
    - Biology
  mappings:
    biocontext: BIOSAMPLE
    cellosaurus: BioSamples
    fairsharing: FAIRsharing.qr6pqk
    miriam: biosample
    n2t: biosample
    re3data: r3d100012828
  miriam:
    deprecated: false
    description: The BioSample Database stores information about biological samples
      used in molecular experiments, such as sequencing, gene expression or proteomics.
      It includes reference samples, such as cell lines, which are repeatedly used
      in experiments. Accession numbers for the reference samples will be exchanged
      with a similar database at NCBI, and DDBJ (Japan). Record access may be affected
      due to different release cycles and inter-institutional synchronisation.
    homepage: https://www.ebi.ac.uk/biosamples/
    id: '00000350'
    name: BioSample
    namespaceEmbeddedInLui: false
    pattern: ^SAM[NED](\w)?\d+$
    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: CURATOR_REVIEW
      description: BioSample at DNA Data Bank of Japan
      homepage: http://trace.ddbj.nig.ac.jp/biosample/
      name: BioSample at DNA Data Bank of Japan
      uri_format: http://trace.ddbj.nig.ac.jp/BSSearch/biosample?acc=$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/$1
  re3data:
    description: The BioSample database contains descriptions of biological source
      materials used in experimental assays.
    homepage: https://www.ncbi.nlm.nih.gov/biosample/
    name: BioSample
    prefix: r3d100012828
    synonyms:
    - BioSample at the NCBI
    xrefs:
      fairsharing: FAIRsharing.qr6pqk
      nlx: '143929'
      omics: '01024'
      scr: 004854
  synonyms:
  - biosamples
biosimulations:
  mappings:
    miriam: biosimulations
    re3data: r3d100013361
  miriam:
    deprecated: false
    description: BioSimulations is an open repository of simulation projects, including
      simulation experiments, their results, and data visualizations of their results.
      BioSimulations supports a broad range of model languages, modeling frameworks,
      simulation algorithms, and simulation software tools.
    homepage: https://icahn.mssm.edu/
    id: 00000880
    name: biosimulations
    namespaceEmbeddedInLui: false
    pattern: ^[a-zA-Z0-9_-]{3,}$
    prefix: biosimulations
    sampleId: Yeast-cell-cycle-Irons-J-Theor-Biol-2009
    uri_format: https://biosimulations.org/projects/$1
  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.
    homepage: https://www.biosimulations.org
    name: BioSimulations
    prefix: r3d100013361
    xrefs:
      scr: 018733
biosimulators:
  fairsharing:
    abbreviation: BioSimulators
    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.
    id: '3207'
    name: BioSimulators
    prefix: FAIRsharing.pwEima
    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/$1
  re3data:
    description: BioSimulators is a registry of containerized biosimulation tools
      that provide consistent command-line interfaces. The BioSimulations web application
      helps investigators browse this registry to find simulation tools that have
      the capabilities (supported modeling frameworks, simulation algorithms, and
      modeling formats) needed for specific modeling projects.
    homepage: https://biosimulators.org
    name: BioSimulators
    prefix: r3d100013432
    xrefs:
      fairsharing: FAIRsharing.pwEima
biostudies:
  fairsharing:
    abbreviation: BioStudies
    description: The BioStudies database holds descriptions of biological studies,
      links to data from these studies in other databases at EMBL-EBI or outside,
      as well as data that do not fit in the structured archives at EMBL-EBI. The
      database can accept a wide range of types of studies described via a simple
      format. It also enables manuscript authors to submit supplementary information
      and link to it from the publication.
    id: '2507'
    name: BioStudies
    prefix: FAIRsharing.mtjvme
    subjects:
    - Life Science
    - Biomedical Science
  mappings:
    fairsharing: FAIRsharing.mtjvme
    miriam: biostudies
    n2t: biostudies
    re3data: r3d100012627
  miriam:
    deprecated: false
    description: The BioStudies database holds descriptions of biological studies,
      links to data from these studies in other databases at EMBL-EBI or outside,
      as well as data that do not fit in the structured archives at EMBL-EBI. The
      database can accept a wide range of types of studies described via a simple
      format. It also enables manuscript authors to submit supplementary information
      and link to it from the publication.
    homepage: https://www.ebi.ac.uk/biostudies/
    id: 00000694
    name: BioStudies database
    namespaceEmbeddedInLui: false
    pattern: ^S-[A-Z]{4}[A-Z\d\-]+$
    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
  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.
    homepage: https://www.ebi.ac.uk/biostudies/
    name: BioStudies
    prefix: r3d100012627
    xrefs:
      fairsharing: FAIRsharing.mtjvme
      omics: '23022'
biosystems:
  biocontext:
    is_identifiers: true
    is_obo: false
    prefix: BIOSYSTEMS
    uri_format: http://identifiers.org/biosystems/$1
  fairsharing:
    abbreviation: BioSystems
    description: The NCBI BioSystems database centralizes and cross-links existing
      biological systems databases, increasing their utility and target audience by
      integrating their pathways and systems into NCBI resources. The resource provides
      categorical information on genes, proteins and small molecules of biosystems.
    id: '1964'
    name: NCBI BioSystems Database
    prefix: FAIRsharing.w2eeqr
    subjects:
    - Biology
    - Systems Biology
  mappings:
    biocontext: BIOSYSTEMS
    fairsharing: FAIRsharing.w2eeqr
    miriam: biosystems
    n2t: biosystems
    prefixcommons: biosystems
  miriam:
    deprecated: false
    description: The NCBI BioSystems database centralizes and cross-links existing
      biological systems databases, increasing their utility and target audience by
      integrating their pathways and systems into NCBI resources.
    homepage: https://www.ncbi.nlm.nih.gov/biosystems/
    id: 00000097
    name: BioSystems
    namespaceEmbeddedInLui: false
    pattern: ^\d+$
    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/$1
  prefixcommons:
    description: The NCBI BioSystems database centralizes and cross-links existing
      biological systems databases, increasing their utility and target audience by
      integrating their pathways and systems into NCBI resources.
    example: '1'
    homepage: http://www.ncbi.nlm.nih.gov/biosystems/
    keywords:
    - molecules
    - pathways
    name: BioSystems
    pattern: ^\d+$
    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
biotools:
  biocontext:
    is_identifiers: true
    is_obo: false
    prefix: BIOTOOLS
    uri_format: http://identifiers.org/biotools/$1
  description: BioTools is a registry of databases and software with tools, services,
    and workflows for biological and biomedical research.
  example: bioregistry
  fairsharing:
    abbreviation: bio.tools
    description: bio.tools is a registry of information about bioinformatics software
      and data services. It was created to help researchers in biological and biomedical
      science to find and use such resources.
    id: '3300'
    name: bio.tools
    prefix: FAIRsharing.63520c
    subjects:
    - Bioinformatics
    - Biomedical Science
    - Biology
  mappings:
    biocontext: BIOTOOLS
    fairsharing: FAIRsharing.63520c
    miriam: biotools
    n2t: biotools
    re3data: r3d100013668
  miriam:
    deprecated: false
    description: Tool and data services registry.
    homepage: https://bio.tools/
    id: '00000616'
    name: BioTools
    namespaceEmbeddedInLui: false
    pattern: ^[A-Za-z0-9\_]*$
    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/$1
  pattern: ^[-A-Za-z0-9\_]*$
  re3data:
    description: bio.tools is a software registry for bioinformatics and the life
      sciences.
    homepage: https://bio.tools
    name: bio.tools
    prefix: r3d100013668
    xrefs:
      biodbcore: 001815
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
  name: 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: 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.
    id: '522'
    name: Biomedical Informatics Research Network Project Lexicon
    prefix: FAIRsharing.jedbbt
    publications: []
    subjects: []
  homepage: https://bioportal.bioontology.org/ontologies/BIRNLEX
  mappings:
    aberowl: BIRNLEX
    bioportal: BIRNLEX
    fairsharing: FAIRsharing.jedbbt
  name: Biomedical Informatics Research Network Lexicon
  pattern: ^\d+$
  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
    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.


      '
    id: '3726'
    name: 'Bibliographic Reference Ontology '
    prefix: FAIRsharing.99da5f
    publications: []
    subjects:
    - Subject Agnostic
  homepage: http://www.sparontologies.net/ontologies/biro
  mappings:
    fairsharing: FAIRsharing.99da5f
  name: Bibliographic Reference Ontology
  preferred_prefix: BiRO
  repository: https://github.com/sparontologies/biro
  uri_format: http://purl.org/spar/biro/$1
bitbucket:
  fairsharing:
    abbreviation: Bitbucket
    description: Bitbucket is a Git-based source code repository hosting service owned
      by Atlassian. It provides a number of different access levels, from free through
      to premium paid services. Users can create public or private repositories, the
      latter of which is restricted to 5 users under the free plan.
    id: '3275'
    name: Bitbucket
    prefix: FAIRsharing.fc3431
    subjects:
    - Knowledge and Information Systems
    - Subject Agnostic
    - Software Engineering
  mappings:
    fairsharing: FAIRsharing.fc3431
    miriam: bitbucket
    re3data: r3d100013478
  miriam:
    deprecated: false
    description: Bitbucket is a Git-based source code repository hosting service owned
      by Atlassian.
    homepage: https://www.atlassian.com/
    id: 00000899
    name: Bitbucket
    namespaceEmbeddedInLui: false
    pattern: ^[0-9A-Za-z-_\.]+/[0-9A-Za-z-_\.]+$
    prefix: bitbucket
    sampleId: andreadega/systems-biology-compiler
    uri_format: https://bitbucket.org/$1
  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.
    homepage: https://bitbucket.org/
    name: Bitbucket
    prefix: r3d100013478
    synonyms:
    - Atlassian Bitbucket
    xrefs:
      biodbcore: 001790
      nlx: '158615'
      scr: '000502'
bitterdb.cpd:
  biocontext:
    is_identifiers: true
    is_obo: false
    prefix: BITTERDB.CPD
    uri_format: http://identifiers.org/bitterdb.cpd/$1
  mappings:
    biocontext: BITTERDB.CPD
    miriam: bitterdb.cpd
    n2t: bitterdb.cpd
  miriam:
    deprecated: false
    description: BitterDB is a database of compounds reported to taste bitter to humans.
      The compounds can be searched by name, chemical structure, similarity to other
      bitter compounds, association with a particular human bitter taste receptor,
      and so on. The database also contains information on mutations in bitter taste
      receptors that were shown to influence receptor activation by bitter compounds.
      The aim of BitterDB is to facilitate studying the chemical features associated
      with bitterness. This collection references compounds.
    homepage: http://bitterdb.agri.huji.ac.il/dbbitter.php
    id: 00000348
    name: BitterDB Compound
    namespaceEmbeddedInLui: false
    pattern: ^\d+$
    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
bitterdb.rec:
  biocontext:
    is_identifiers: true
    is_obo: false
    prefix: BITTERDB.REC
    uri_format: http://identifiers.org/bitterdb.rec/$1
  mappings:
    biocontext: BITTERDB.REC
    miriam: bitterdb.rec
    n2t: bitterdb.rec
  miriam:
    deprecated: false
    description: BitterDB is a database of compounds reported to taste bitter to humans.
      The compounds can be searched by name, chemical structure, similarity to other
      bitter compounds, association with a particular human bitter taste receptor,
      and so on. The database also contains information on mutations in bitter taste
      receptors that were shown to influence receptor activation by bitter compounds.
      The aim of BitterDB is to facilitate studying the chemical features associated
      with bitterness. This collection references receptors.
    homepage: http://bitterdb.agri.huji.ac.il/dbbitter.php
    id: '00000347'
    name: BitterDB Receptor
    namespaceEmbeddedInLui: false
    pattern: ^\d+$
    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
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+$
  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:$1
bmrb:
  fairsharing:
    abbreviation: BMRB
    description: BMRB collects, annotates, archives, and disseminates (worldwide in
      the public domain) the important spectral and quantitative data derived from
      NMR spectroscopic investigations of biological macromolecules and metabolites.
      The goal is to empower scientists in their analysis of the structure, dynamics,
      and chemistry of biological systems and to support further development of the
      field of biomolecular NMR spectroscopy.
    id: '2114'
    name: Biological Magnetic Resonance Data Bank
    prefix: FAIRsharing.p06nme
    subjects:
    - Structural Biology
  mappings:
    fairsharing: FAIRsharing.p06nme
    miriam: bmrb
    uniprot: BMRB
  miriam:
    deprecated: false
    description: BMRB collects, annotates, archives, and disseminates (worldwide in
      the public domain) the important spectral and quantitative data derived from
      NMR spectroscopic investigations of biological macromolecules and metabolites.
      The goal is to empower scientists in their analysis of the structure, dynamics,
      and chemistry of biological systems and to support further development of the
      field of biomolecular NMR spectroscopy.
    homepage: http://www.bmrb.wisc.edu/
    id: '00000716'
    name: Biological Magnetic Resonance Data Bank
    namespaceEmbeddedInLui: false
    pattern: ^(bmr|bmse|bmst)?[0-9]{1,6}$
    prefix: bmrb
    sampleId: '15000'
    uri_format: http://rest.bmrb.wisc.edu/bmrb/$1/html
  uniprot:
    category: 3D structure databases
    identifier: '256'
    link_is_explicit: 'true'
    name: Biological Magnetic Resonance Data Bank
    prefix: BMRB
    uri_format: https://bmrb.io/data_library/summary/protein.php?uniprot=$1
bmrb.restraint:
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: The NMR Restraints Grid contains the original NMR data as collected
    for over 2500 protein and nucleic acid structures with corresponding PDB entries.
    In addition to the original restraints, most of the distance, dihedral angle and
    RDC restraint data (>85%) were parsed, and those in over 500 entries were converted
    and filtered. The converted and filtered data sets constitute the DOCR and FRED
    databases respectively.
  example: '28789'
  homepage: https://restraintsgrid.bmrb.io/NRG/MRGridServlet
  name: NMR Restraints Grid
  pattern: ^\d+$
  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
bold.taxonomy:
  biocontext:
    is_identifiers: true
    is_obo: false
    prefix: BOLD.TAXONOMY
    uri_format: http://identifiers.org/bold.taxonomy/$1
  mappings:
    biocontext: BOLD.TAXONOMY
    miriam: bold.taxonomy
    n2t: bold.taxonomy
    ncbi: BOLD
    prefixcommons: bold
  miriam:
    deprecated: false
    description: The Barcode of Life Data System (BOLD) is an informatics workbench
      aiding the acquisition, storage, analysis and publication of DNA barcode records.
      The associated taxonomy browser shows the progress of DNA barcoding and provides
      sample collection site distribution, and taxon occurence information.
    homepage: http://www.boldsystems.org/
    id: 00000158
    name: BOLD Taxonomy
    namespaceEmbeddedInLui: false
    pattern: ^\d+$
    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=$1
  ncbi:
    example: EPAF263
    homepage: http://www.barcodinglife.com
    name: Barcode of Life database
    prefix: BOLD
  prefixcommons:
    description: The Barcode of Life Data Systems (BOLD) is an online workbench that
      aids collection, management, analysis, and use of DNA barcodes. It consists
      of 3 components (MAS, IDS, and ECS) that each address the needs of various groups
      in the barcoding community.
    example: '27267'
    homepage: http://www.barcodinglife.com
    keywords:
    - DNA
    name: The Barcode of Life Data Systems
    pattern: ^\d+$
    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
bootstrep:
  biocontext:
    is_identifiers: false
    is_obo: true
    prefix: BOOTSTREP
    uri_format: http://purl.obolibrary.org/obo/BOOTSTREP_$1
  mappings:
    biocontext: BOOTSTREP
    obofoundry: bootstrep
  obofoundry:
    contact: vlee@ebi.ac.uk
    contact.label: Vivian Lee
    deprecated: true
    homepage: http://www.ebi.ac.uk/Rebholz-srv/GRO/GRO.html
    name: Gene Regulation Ontology
    prefix: bootstrep
bpdb:
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: 'Database of biopesticides maintained by the University of Hertfordshire '
  example: '2404'
  homepage: https://sitem.herts.ac.uk/aeru/bpdb/index.htm
  name: Bio-Pesticides DataBase
  pattern: ^\d+$
  uri_format: https://sitem.herts.ac.uk/aeru/bpdb/Reports/$1.htm
brenda:
  biocontext:
    is_identifiers: true
    is_obo: false
    prefix: BRENDA
    uri_format: http://identifiers.org/brenda/$1
  fairsharing:
    abbreviation: BRENDA
    description: BRENDA is the main collection of enzyme functional data available
      to the scientific community.
    id: '1789'
    name: BRENDA Enzyme Database
    prefix: FAIRsharing.etp533
    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=$1
  mappings:
    biocontext: BRENDA
    fairsharing: FAIRsharing.etp533
    go: BRENDA
    miriam: brenda
    n2t: brenda
    prefixcommons: brenda
    re3data: r3d100010616
    uniprot: BRENDA
  miriam:
    deprecated: false
    description: BRENDA is a collection of enzyme functional data available to the
      scientific community. Data on enzyme function are extracted directly from the
      primary literature The database covers information on classification and nomenclature,
      reaction and specificity, functional parameters, occurrence, enzyme structure
      and stability, mutants and enzyme engineering, preparation and isolation, the
      application of enzymes, and ligand-related data.
    homepage: https://www.brenda-enzymes.org/
    id: '00000071'
    name: BRENDA
    namespaceEmbeddedInLui: false
    pattern: ^((\d+\.-\.-\.-)|(\d+\.\d+\.-\.-)|(\d+\.\d+\.\d+\.-)|(\d+\.\d+\.\d+\.\d+))$
    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=$1
  prefixcommons:
    description: BRENDA is the main collection of enzyme functional data available
      to the scientific community.
    example: 1.1.1.1
    homepage: http://www.brenda-enzymes.org
    keywords:
    - enzyme
    name: The Comprehensive Enzyme Information System
    pattern: ^((\d+\.-\.-\.-)|(\d+\.\d+\.-\.-)|(\d+\.\d+\.\d+\.-)|(\d+\.\d+\.\d+\.\d+))$
    prefix: brenda
    pubmed_ids:
    - '18984617'
    uri_format: http://www.brenda-enzymes.org/php/result_flat.php4?ecno=$1
  publications:
  - 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
  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.
    homepage: https://www.brenda-enzymes.info/
    name: BRENDA
    prefix: r3d100010616
    synonyms:
    - BRaunschweig ENzyme DAtabase
    - the comprehensive enzyme information system
    xrefs:
      fairsharing: FAIRsharing.etp533
      nif: 0000-30222
      omics: 02681
      scr: 002997
  uniprot:
    category: Enzyme and pathway databases
    identifier: '131'
    link_is_explicit: 'true'
    name: BRENDA Comprehensive Enzyme Information System
    prefix: BRENDA
    uri_format: https://www.brenda-enzymes.org/enzyme.php?ecno=%s&UniProtAcc=%u&OrganismID=%d
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
  name: BRENDA Ligand
  pattern: ^\d+$
  uri_format: https://www.brenda-enzymes.de/ligand.php?brenda_ligand_id=$1
brenda.ligandgroup:
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: Information for ligand groups (chemical classes).
  example: '18030'
  homepage: https://www.brenda-enzymes.de/ligand.php
  name: BRENDA Ligand Group
  pattern: ^\d+$
  uri_format: https://www.brenda-enzymes.de/ligand.php?brenda_group_id=$1
broad:
  biocontext:
    is_identifiers: true
    is_obo: false
    prefix: BROAD
    uri_format: http://identifiers.org/broad/$1
  mappings:
    biocontext: BROAD
    miriam: broad
    n2t: broad
  miriam:
    deprecated: false
    description: Magnaporthe grisea, the causal agent of rice blast disease, is one
      of the most devasting threats to food security worldwide and is a model organism
      for studying fungal phytopathogenicity and host-parasite interactions. The Magnaporthe
      comparative genomics database provides accesses to multiple fungal genomes from
      the Magnaporthaceae family to facilitate the comparative analysis. As part of
      the Broad Fungal Genome Initiative, the Magnaporthe comparative project includes
      the finished M. oryzae (formerly M. grisea) genome, as well as the draft assemblies
      of Gaeumannomyces graminis var. tritici and M. poae.
    homepage: https://www.broadinstitute.org/annotation/genome/magnaporthe_grisea/
    id: 00000438
    name: Broad Fungal Genome Initiative
    namespaceEmbeddedInLui: false
    pattern: ^S\d+$
    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=$1
bs:
  comment: An alernative vocabulary that has been aligned and integrated in Sequence
    Ontology (SO).
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: SO is a collaborative ontology project for the definition of sequence
    features used in biological sequence annotation. It is part of the Open Biomedical
    Ontologies library.
  download_obo: https://raw.githubusercontent.com/The-Sequence-Ontology/SO-Ontologies/master/Ontology_Files/subsets/biosapiens.obo
  example: '00042'
  homepage: https://github.com/The-Sequence-Ontology/SO-Ontologies
  name: Biosapiens Protein Feature Ontology
  pattern: ^\d+$
  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/28/bspo.owl
    homepage: https://github.com/obophenotype/biological-spatial-ontology
    name: Biological Spatial Ontology
    prefix: BSPO
  biocontext:
    is_identifiers: false
    is_obo: true
    prefix: BSPO
    uri_format: http://purl.obolibrary.org/obo/BSPO_$1
  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: '2022-06-28'
  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
    description: This ontology represents 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.
    id: '1034'
    name: Biological SPatial Ontology
    prefix: FAIRsharing.newa3z
    publications:
    - doi: 10.1186/2041-1480-5-34
      pubmed_id: 25140222
      title: 'Nose to tail, roots to shoots: spatial descriptors for phenotypic diversity
        in the Biological Spatial Ontology.'
    subjects:
    - Anatomy
    - Life Science
  mappings:
    aberowl: BSPO
    biocontext: BSPO
    bioportal: BSPO
    fairsharing: FAIRsharing.newa3z
    obofoundry: bspo
    ols: bspo
    ontobee: BSPO
  obofoundry:
    appears_in:
    - aism
    - colao
    - fovt
    - lepao
    - 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
    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: http://purl.obolibrary.org/obo/bspo.owl
    homepage: https://github.com/obophenotype/biological-spatial-ontology
    name: Biological Spatial Ontology
    prefix: bspo
    version: '2022-06-28'
    version.iri: http://purl.obolibrary.org/obo/bspo/releases/2022-06-28/bspo.owl
  ontobee:
    library: Library
    name: Biological Spatial Ontology
    prefix: BSPO
  pattern: ^\d{7}$
  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
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:
    is_identifiers: false
    is_obo: true
    prefix: BTO
    uri_format: http://purl.obolibrary.org/obo/BTO_$1
  bioportal:
    contact:
      email: a.chang@tu-bs.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
    uri_format: https://bioportal.bioontology.org/ontologies/BTO?p=classes&conceptid=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FBTO_$1
  example: 0000590
  fairsharing:
    abbreviation: BTO
    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.
    id: '1'
    name: BRENDA tissue / enzyme source
    prefix: FAIRsharing.1414v8
    publications:
    - doi: 10.1093/nar/gkq968
      pubmed_id: 21030441
      title: 'The BRENDA Tissue Ontology (BTO): the first all-integrating ontology
        of all organisms for enzyme sources.'
    - doi: 10.1093/nar/gky1048
      pubmed_id: 30395242
      title: 'BRENDA in 2019: a European ELIXIR core data resource.'
    - doi: 10.1093/nar/gkh081
      pubmed_id: 14681450
      title: 'BRENDA, the enzyme database: updates and major new developments.'
    - doi: 10.1093/nar/gku1068
      pubmed_id: 25378310
      title: 'BRENDA in 2015: exciting developments in its 25th year of existence.'
    - 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.'
    subjects:
    - Enzymology
    - Life Science
  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
  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
    wikidata: P5501
  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: https://www.ebi.ac.uk/ols/ontologies/bto
    id: '00000111'
    name: Brenda Tissue Ontology
    namespaceEmbeddedInLui: true
    pattern: ^BTO:\d{7}$
    prefix: bto
    sampleId: '0000146'
    uri_format: https://www.ebi.ac.uk/ols/ontologies/bto/terms?obo_id=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:$1
  obofoundry:
    contact: c.dudek@tu-braunschweig.de
    contact.github: chdudek
    contact.label: Christian-Alexander Dudek
    contact.orcid: 0000-0001-9117-7909
    deprecated: false
    description: A structured controlled vocabulary for the source of an enzyme comprising
      tissues, cell lines, cell types and cell cultures.
    download.json: http://purl.obolibrary.org/obo/bto.json
    download.obo: http://purl.obolibrary.org/obo/bto.obo
    download.owl: http://purl.obolibrary.org/obo/bto.owl
    homepage: http://www.brenda-enzymes.org
    license: CC BY 4.0
    license.url: https://creativecommons.org/licenses/by/4.0/
    name: BRENDA tissue / enzyme source
    preferredPrefix: BTO
    prefix: bto
    publications:
    - id: https://www.ncbi.nlm.nih.gov/pubmed/21030441
      title: 'The BRENDA Tissue Ontology (BTO): the first all-integrating ontology
        of all organisms for enzyme sources'
    repository: https://github.com/BRENDA-Enzymes/BTO
  ols:
    description: A structured controlled vocabulary for the source of an enzyme comprising
      tissues, cell lines, cell types and cell cultures.
    download: http://purl.obolibrary.org/obo/bto.owl
    name: The BRENDA Tissue Ontology (BTO)
    prefix: bto
    version: '2021-10-26'
    version.iri: http://purl.obolibrary.org/obo/bto/releases/2021-10-26/bto.owl
  ontobee:
    library: Library
    name: BRENDA tissue / enzyme source
    prefix: BTO
  pattern: ^\d{7}$
  prefixcommons:
    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
  publications:
  - doi: 10.1093/nar/gkh081
    pmc: PMC308815
    pubmed: '14681450'
    title: 'BRENDA, the enzyme database: updates and major new developments.'
    year: 2004
  - 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/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/gku1068
    pmc: PMC4383907
    pubmed: '25378310'
    title: 'BRENDA in 2015: exciting developments in its 25th year of existence.'
    year: 2014
  - doi: 10.1093/nar/gky1048
    pmc: PMC6323942
    pubmed: '30395242'
    title: 'BRENDA in 2019: a European ELIXIR core data resource.'
    year: 2019
  synonyms:
  - BTO
  wikidata:
    database: Q4836352
    database.homepage: https://www.brenda-enzymes.org
    database.label: BRENDA Tissue Ontology
    description: identifier in the Brenda Tissue Ontology
    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:
    is_identifiers: true
    is_obo: false
    prefix: BUGBASE.EXPT
    uri_format: http://identifiers.org/bugbase.expt/$1
  mappings:
    biocontext: BUGBASE.EXPT
    miriam: bugbase.expt
    n2t: bugbase.expt
  miriam:
    deprecated: false
    description: BugBase is a MIAME-compliant microbial gene expression and comparative
      genomic database. It stores experimental annotation and multiple raw and analysed
      data formats, as well as protocols for bacterial microarray designs. This collection
      references microarray experiments.
    homepage: http://bugs.sgul.ac.uk/E-BUGS
    id: '00000404'
    name: BugBase Expt
    namespaceEmbeddedInLui: false
    pattern: ^\d+$
    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
bugbase.protocol:
  biocontext:
    is_identifiers: true
    is_obo: false
    prefix: BUGBASE.PROTOCOL
    uri_format: http://identifiers.org/bugbase.protocol/$1
  mappings:
    biocontext: BUGBASE.PROTOCOL
    miriam: bugbase.protocol
    n2t: bugbase.protocol
  miriam:
    deprecated: false
    description: BugBase is a MIAME-compliant microbial gene expression and comparative
      genomic database. It stores experimental annotation and multiple raw and analysed
      data formats, as well as protocols for bacterial microarray designs. This collection
      references design protocols.
    homepage: http://bugs.sgul.ac.uk/E-BUGS
    id: '00000403'
    name: BugBase Protocol
    namespaceEmbeddedInLui: false
    pattern: ^\d+$
    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
bykdb:
  biocontext:
    is_identifiers: true
    is_obo: false
    prefix: BYKDB
    uri_format: http://identifiers.org/bykdb/$1
  fairsharing:
    abbreviation: BYKdb
    description: The Bacterial protein tYrosine Kinase database (BYKdb) contains computer-annotated
      BY-kinase sequences. The database web interface allows static and dynamic queries
      and provides integrated analysis tools including sequence annotation.
    id: '1557'
    name: Bacterial protein tYrosine Kinase database
    prefix: FAIRsharing.jr30xc
    subjects:
    - Life Science
  mappings:
    biocontext: BYKDB
    fairsharing: FAIRsharing.jr30xc
    miriam: bykdb
    n2t: bykdb
    prefixcommons: bykdb
  miriam:
    deprecated: false
    description: The bacterial tyrosine kinase database (BYKdb) that collects sequences
      of putative and authentic bacterial tyrosine kinases,  providing structural
      and functional information.
    homepage: https://bykdb.ibcp.fr/BYKdb/
    id: '00000253'
    name: BYKdb
    namespaceEmbeddedInLui: false
    pattern: ^[A-Z0-9]+$
    prefix: bykdb
    sampleId: A0A009E7X8
    uri_format: https://bykdb.ibcp.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/$1.html
  name: Bacterial Tyrosine Kinase Database
  prefixcommons:
    description: The bacterial tyrosine kinase database (BYKdb) that collects sequences
      of putative and authentic bacterial tyrosine kinases,  providing structural
      and functional information.
    example: A0AYT5
    homepage: http://bykdb.ibcp.fr/BYKdb/
    keywords:
    - domain
    - microbial
    - sequence
    name: Bacterial Tyrosine Kinase Database
    pattern: ^\w+$
    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
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
    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;
    id: '3727'
    name: 'Citation Counting and Context Characterization Ontology '
    prefix: FAIRsharing.beb855
    publications: []
    subjects:
    - Subject Agnostic
  homepage: http://www.sparontologies.net/ontologies/c4o
  mappings:
    fairsharing: FAIRsharing.beb855
  name: Citation Counting and Context Characterisation Ontology
  preferred_prefix: C4O
  repository: https://github.com/sparontologies/c4o
  uri_format: http://purl.org/spar/c4o/$1
cabri:
  biocontext:
    is_identifiers: true
    is_obo: false
    prefix: CABRI
    uri_format: http://identifiers.org/cabri/$1
  edam:
    description: A unique identifier of an item from the CABRI database.
    name: CABRI
    obsolete: false
    prefix: '2380'
  fairsharing:
    abbreviation: CABRI
    description: CABRI provides an integrated resource including catalogues of strains
      of different organism types, genetic materials and other biologicals resources
      of European culture collections so that the user world-wide can access these
      relevant data during one searching session through a common entry point and
      get in touch with collections for ordering products to be delivered to their
      place of work.
    id: '1815'
    name: Common Access to Biological Resources and Information
    prefix: FAIRsharing.qx2rvz
    subjects:
    - Molecular biology
    - Medical Microbiology
    - Applied Microbiology
    - Virology
    - Molecular Microbiology
    - Microbiology
  mappings:
    biocontext: CABRI
    edam: '2380'
    fairsharing: FAIRsharing.qx2rvz
    miriam: cabri
    n2t: cabri
    ncbi: CABRI
  miriam:
    deprecated: false
    description: CABRI (Common Access to Biotechnological Resources and Information)
      is an online service where users can search a number of European Biological
      Resource Centre catalogues. It lists the availability of a particular organism
      or genetic resource and defines the set of technical specifications and procedures
      which should be used to handle it.
    homepage: http://www.cabri.org/
    id: '00000261'
    name: CABRI
    namespaceEmbeddedInLui: false
    pattern: ^([A-Za-z]+)?(\_)?([A-Za-z-]+)\:([A-Za-z0-9 ]+)$
    prefix: cabri
    providers:
    - code: CURATOR_REVIEW
      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+[$1]
  ncbi:
    example: ACC 424
    name: Common Access to Biological Resources and Information Project
    prefix: CABRI
cadsr:
  mappings:
    miriam: cadsr
    n2t: cadsr
  miriam:
    deprecated: false
    description: The US National Cancer Institute (NCI) maintains and administers
      data elements, forms, models, and components of these items in a metadata registry
      referred to as the Cancer Data Standards Registry and Repository, or caDSR.
    homepage: https://wiki.nci.nih.gov/display/caDSR/caDSR+Wiki
    id: 00000695
    name: Cancer Data Standards Registry and Repository
    namespaceEmbeddedInLui: false
    pattern: ^[0-9]*$
    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=$1]
caloha:
  banana: TS
  banana_peel: '-'
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: This is a code repository for the SIB - Swiss Institute of Bioinformatics
    CALIPHO group neXtProt project, which is a comprehensive human-centric discovery
    platform, that offers a integration of and navigation through protein-related
    data. CALIPHO is an interdisciplinary team which aims to use a variety of methodologies
    to help uncover the function of uncharacterized human proteins.
  download_obo: https://download.nextprot.org/pub/current_release/controlled_vocabularies/caloha.obo
  example: '0001'
  homepage: https://github.com/calipho-sib/controlled-vocabulary
  name: CALIPHO Group Ontology of Human Anatomy
  pattern: ^\d+$
  references:
  - https://twitter.com/neXtProt_news/status/1350105997633867781
  repository: https://github.com/calipho-sib/controlled-vocabulary
  twitter: neXtProt_news
  uri_format: https://biopragmatics.github.io/providers/caloha/$1
cameo:
  biocontext:
    is_identifiers: true
    is_obo: false
    prefix: CAMEO
    uri_format: http://identifiers.org/cameo/$1
  fairsharing:
    abbreviation: CAMEO
    description: Continuous automated benchmarking of computational protein structure
      prediction methods (and model quality estimation techniques). CAMEO assessment
      is based on blind predictions for weekly pre-released targets from PDB. Benchmarking
      results are made available as reference data for methods development.
    id: '2382'
    name: Continuously Automated Model Evaluation
    prefix: FAIRsharing.dq34p2
    subjects:
    - Life Science
  mappings:
    biocontext: CAMEO
    fairsharing: FAIRsharing.dq34p2
    miriam: cameo
    n2t: cameo
  miriam:
    deprecated: false
    description: The goal of the CAMEO (Continuous Automated Model EvaluatiOn) community
      project is to continuously evaluate the accuracy and reliability of protein
      structure prediction servers, offering scores on  tertiary and quaternary structure
      prediction, model quality estimation, accessible surface area prediction, ligand
      binding site residue prediction and contact prediction services in a fully automated
      manner. These predictions are regularly compared against reference structures
      from PDB.
    homepage: https://cameo3d.org
    id: '00000623'
    name: CAMEO
    namespaceEmbeddedInLui: false
    pattern: ^[0-9\-_]+$
    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
caps:
  biocontext:
    is_identifiers: true
    is_obo: false
    prefix: CAPS
    uri_format: http://identifiers.org/caps/$1
  mappings:
    biocontext: CAPS
    miriam: caps
    n2t: caps
  miriam:
    deprecated: false
    description: CAPS-DB is a structural classification of helix-cappings or caps
      compiled from protein structures. The regions of the polypeptide chain immediately
      preceding or following an alpha-helix are known as Nt- and Ct cappings, respectively.
      Caps extracted from protein structures have been structurally classified based
      on geometry and conformation and organized in a tree-like hierarchical classification
      where the different levels correspond to different properties of the caps.
    homepage: http://www.bioinsilico.org/cgi-bin/CAPSDB/staticHTML/home
    id: 00000396
    name: CAPS-DB
    namespaceEmbeddedInLui: false
    pattern: ^\d+$
    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
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/16/caro.owl
    homepage: https://github.com/obophenotype/caro/
    name: Common Anatomy Reference Ontology
    prefix: CARO
  biocontext:
    is_identifiers: false
    is_obo: true
    prefix: CARO
    uri_format: http://purl.obolibrary.org/obo/CARO_$1
  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: '2022-02-18'
  download_json: http://purl.obolibrary.org/obo/caro.json
  download_obo: http://purl.obolibrary.org/obo/caro.obo
  example: '0000000'
  fairsharing:
    abbreviation: CARO
    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.
    id: '551'
    name: Common Anatomy Reference Ontology
    prefix: FAIRsharing.3kcgmr
    publications:
    - doi: 10.1007/978-1-84628-885-2_16
      pubmed_id: null
      title: "CARO \u2013 The Common Anatomy Reference Ontology"
    subjects:
    - Anatomy
    - Life Science
  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
  obofoundry:
    appears_in:
    - aism
    - colao
    - lepao
    - pco
    - ehdaa2
    contact: haendel@ohsu.edu
    contact.github: mellybelly
    contact.label: Melissa Haendel
    contact.orcid: 0000-0001-9114-8737
    deprecated: false
    description: An upper level ontology to facilitate interoperability between existing
      anatomy ontologies for different species
    download.owl: http://purl.obolibrary.org/obo/caro.owl
    homepage: https://github.com/obophenotype/caro/
    license: CC BY 3.0
    license.url: https://creativecommons.org/licenses/by/3.0/
    name: Common Anatomy Reference Ontology
    preferredPrefix: CARO
    prefix: caro
    repository: https://github.com/obophenotype/caro
  ols:
    description: None
    download: http://purl.obolibrary.org/obo/caro.owl
    homepage: https://github.com/obophenotype/caro/
    name: Common Anatomy Reference Ontology
    prefix: caro
    version: '2022-02-18'
    version.iri: http://purl.obolibrary.org/obo/caro/releases/2022-02-18/caro.owl
  ontobee:
    library: Library
    name: Common Anatomy Reference Ontology
    prefix: CARO
  pattern: ^\d{7}$
cas:
  biocontext:
    is_identifiers: true
    is_obo: false
    prefix: CAS
    uri_format: http://identifiers.org/cas/$1
  cheminf:
    description: Identifier used by the Chemical Abstracts Service database.
    name: CAS registry number
    obsolete: false
    prefix: '000446'
  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.
    id: '381'
    name: CAS Registry Number
    prefix: FAIRsharing.r7Kwy7
    subjects:
    - Cheminformatics
  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
  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?ref=$1
  n2t:
    description: CAS (Chemical Abstracts Service) is a division of the American Chemical
      Society and is the producer of comprehensive databases of chemical information.
    example: 50-00-0
    homepage: http://commonchemistry.org
    name: CAS through Common Chemistry
    namespaceEmbeddedInLui: false
    pattern: ^\d{1,7}\-\d{2}\-\d$
    prefix: cas
    uri_format: http://commonchemistry.org/ChemicalDetail.aspx?ref=$1
  prefixcommons:
    description: CAS (Chemical Abstracts Service) is a division of the American Chemical
      Society and is the producer of comprehensive databases of chemical information.
    example: 50-00-0
    homepage: http://www.cas.org/
    keywords:
    - chemical
    - structure
    name: 'CAS: A Divison of the American Chemical Society'
    pattern: ^\d{1,7}\-\d{2}\-\d$
    prefix: cas
    synonyms:
    - chemicalabstractscas
    uri_format: http://commonchemistry.org/ChemicalDetail.aspx?ref=$1
  synonyms:
  - CASID
  - CAS_RN
  - SECONDARY_CAS_RN
  - cas_id
  wikidata:
    prefix: P231
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.
  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'
  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=$1
  homepage: https://researcharchive.calacademy.org/research/ichthyology/catalog/fishcatmain.asp
  mappings:
    go: CASSPC
  name: Eschmeyer's Catalog of Fishes
  pattern: ^\d+$
cath:
  biocontext:
    is_identifiers: true
    is_obo: false
    prefix: CATH
    uri_format: http://identifiers.org/cath/$1
  edam:
    description: Identifier of a protein domain (or other node) from the CATH database.
    name: CATH
    obsolete: false
    prefix: '2700'
  fairsharing:
    abbreviation: CATH
    description: The CATH database is a free, publicly available online resource that
      provides information on the evolutionary relationships of protein domains. It
      provides a hierarchical domain classification of protein structures in the Protein
      Data Bank. Protein structures are classified using a combination of automated
      and manual procedures. There are four major levels in this hierarchy; Class
      (secondary structure classification, e.g. mostly alpha), Architecture (classification
      based on overall shape), Topology (fold family) and Homologous superfamily (protein
      domains which are thought to share a common ancestor).
    id: '2082'
    name: CATH
    prefix: FAIRsharing.xgcyyn
    subjects:
    - Evolutionary Biology
    - Biology
  mappings:
    biocontext: CATH
    edam: '2700'
    fairsharing: FAIRsharing.xgcyyn
    miriam: cath
    n2t: cath
    prefixcommons: cath
    re3data: r3d100012629
  miriam:
    deprecated: false
    description: CATH is a classification of protein structural domains. We group
      protein domains into superfamilies when there is sufficient evidence they have
      diverged from a common ancestor. CATH can be used to predict structural and
      functional information directly from protein sequence.
    homepage: http://www.cathdb.info
    id: '00000612'
    name: CATH Protein Structural Domain Superfamily
    namespaceEmbeddedInLui: false
    pattern: ^[1-6]\.[0-9]+\.[0-9]+\.[0-9]+$
    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/$1
  prefixcommons:
    description: The CATH database is a hierarchical domain classification of protein
      structures in the Protein Data Bank. Protein structures are classified using
      a combination of automated and manual procedures. There are four major levels
      in this hierarchy; Class (secondary structure classification, e.g. mostly alpha),
      Architecture (classification based on overall shape), Topology (fold family)
      and  Homologous superfamily (protein domains which are thought to share a common
      ancestor). This collection is concerned with superfamily classification.
    example: '3.15'
    homepage: http://www.cathdb.info/
    keywords:
    - classification
    - protein
    - structure
    name: CATH Protein Structure Classification
    pattern: ^\d+(\.\d+(\.\d+(\.\d+)?)?)?$
    prefix: cath
    pubmed_ids:
    - '9309224'
    synonyms:
    - cath.domain
    - cath.superfamily
    uri_format: http://www.cathdb.info/cathnode/$1
  publications:
  - doi: 10.1016/s0969-2126(97)00260-8
    pmc: null
    pubmed: '9309224'
    title: CATH--a hierarchic classification of protein domain structures.
    year: 1997
  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.
    homepage: http://www.cathdb.info/
    name: CATH
    prefix: r3d100012629
    synonyms:
    - CATH-Gene3D
    - Class  Architecture Topology  Homologous superfamily
    xrefs:
      fairsharing: FAIRsharing.xgcyyn
      miriam: '00000210'
      nif: 0000-02640
      scr: 007583
cath.domain:
  biocontext:
    is_identifiers: true
    is_obo: false
    prefix: CATH.DOMAIN
    uri_format: http://identifiers.org/cath.domain/$1
  edam:
    description: Identifier of a protein domain from CATH.
    name: CATH domain
    obsolete: false
    prefix: '1040'
  mappings:
    biocontext: CATH.DOMAIN
    edam: '1040'
    miriam: cath.domain
    n2t: cath.domain
  miriam:
    deprecated: false
    description: The CATH database is a hierarchical domain classification of protein
      structures in the Protein Data Bank. Protein structures are classified using
      a combination of automated and manual procedures. There are four major levels
      in this hierarchy; Class (secondary structure classification, e.g. mostly alpha),
      Architecture (classification based on overall shape), Topology (fold family)
      and Homologous superfamily (protein domains which are thought to share a common
      ancestor). This colelction is concerned with CATH domains.
    homepage: http://www.cathdb.info/
    id: '00000210'
    name: CATH domain
    namespaceEmbeddedInLui: false
    pattern: ^\w+$
    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
cath.superfamily:
  biocontext:
    is_identifiers: true
    is_obo: false
    prefix: CATH.SUPERFAMILY
    uri_format: http://identifiers.org/cath.superfamily/$1
  mappings:
    biocontext: CATH.SUPERFAMILY
    miriam: cath.superfamily
    n2t: cath.superfamily
  miriam:
    deprecated: false
    description: The CATH database is a hierarchical domain classification of protein
      structures in the Protein Data Bank. Protein structures are classified using
      a combination of automated and manual procedures. There are four major levels
      in this hierarchy; Class (secondary structure classification, e.g. mostly alpha),
      Architecture (classification based on overall shape), Topology (fold family)
      and  Homologous superfamily (protein domains which are thought to share a common
      ancestor). This colelction is concerned with superfamily classification.
    homepage: http://www.cathdb.info/
    id: 00000209
    name: CATH superfamily
    namespaceEmbeddedInLui: false
    pattern: ^\d+(\.\d+(\.\d+(\.\d+)?)?)?$
    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
cattleqtldb:
  biocontext:
    is_identifiers: true
    is_obo: false
    prefix: CATTLEQTLDB
    uri_format: http://identifiers.org/cattleqtldb/$1
  mappings:
    biocontext: CATTLEQTLDB
    miriam: cattleqtldb
    n2t: cattleqtldb
    prefixcommons: cattleqtldb
  miriam:
    deprecated: false
    description: The Animal Quantitative Trait Loci (QTL) database (Animal QTLdb)
      is designed to house publicly all available QTL and single-nucleotide polymorphism/gene
      association data on livestock animal species. This collection references cattle
      QTLs.
    homepage: https://www.animalgenome.org/QTLdb
    id: '00000504'
    name: Animal Genome Cattle QTL
    namespaceEmbeddedInLui: false
    pattern: ^\d+$
    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=$1
  part_of: qtldb
  prefixcommons:
    description: This Cattle Quantitative Trait Locus (QTL) database (Cattle QTLdb)
      has gathered all cattle QTL data published during the past 10+ years. The database
      and its peripheral tools make it possible to compare, confirm and locate on
      cattle chromosomes the most feasible location for genes responsible for quantitative
      trait important to cattle production.
    example: '66'
    homepage: http://www.animalgenome.org/cgi-bin/QTLdb/BT/index
    keywords:
    - DNA
    - genome
    name: Cattle Quantitative Trait Locus database
    pattern: ^\d+$
    prefix: cattleqtldb
    uri_format: http://www.animalgenome.org/cgi-bin/QTLdb/BT/qdetails?QTL_ID=$1
cazy:
  biocontext:
    is_identifiers: true
    is_obo: false
    prefix: CAZY
    uri_format: http://identifiers.org/cazy/$1
  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.
    id: '1834'
    name: The Carbohydrate-Active enZYmes Database
    prefix: FAIRsharing.ntyq70
    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/$1.html
  mappings:
    biocontext: CAZY
    fairsharing: FAIRsharing.ntyq70
    go: CAZY
    miriam: cazy
    n2t: cazy
    prefixcommons: cazy
    uniprot: CAZy
  miriam:
    deprecated: false
    description: The Carbohydrate-Active Enzyme (CAZy) database is a resource specialized
      in enzymes that build and breakdown complex carbohydrates and glycoconjugates.
      These enzymes are classified into families based on structural features.
    homepage: http://www.cazy.org/
    id: 00000195
    name: CAZy
    namespaceEmbeddedInLui: false
    pattern: ^(GT|GH|PL|CE|CBM)\d+(\_\d+)?$
    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/$1.html
  prefixcommons:
    description: The CAZy database describes the families of structurally-related
      catalytic and carbohydrate-binding modules (or functional domains) of enzymes
      that degrade, modify, or create glycosidic bonds.
    example: GT10
    homepage: http://www.cazy.org/
    keywords:
    - classification
    - polysaccharide
    name: The Carbohydrate-Active enZYmes Database
    pattern: ^GT\d+$
    prefix: cazy
    pubmed_ids:
    - '18838391'
    uri_format: http://www.cazy.org/$1.html
  publications:
  - doi: 10.1093/nar/gkn663
    pmc: PMC2686590
    pubmed: '18838391'
    title: 'The Carbohydrate-Active EnZymes database (CAZy): an expert resource for
      Glycogenomics.'
    year: 2008
  uniprot:
    category: Protein family/group databases
    identifier: '136'
    link_is_explicit: 'true'
    name: Carbohydrate-Active enZymes
    prefix: CAZy
    uri_format: http://www.cazy.org/fam/$1.html
cba:
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: 'CBA: http://www.cba.ac.cn/ and the Shanghai Institutes for Biological
    Sciences (SIBS at http://www.sibs.ac.cn/) provide EBI with citation data not available
    in MEDLINE.'
  example: '375364'
  homepage: http://www.cba.ac.cn
  name: Chinese Biological Abstracts
  pattern: ^\d+$
  uri_format: https://europepmc.org/article/CBA/$1
cbioportal:
  fairsharing:
    abbreviation: cBioPortal
    description: The cBioPortal for Cancer Genomics provides visualization, analysis
      and download of large-scale cancer genomics data sets.
    id: '2605'
    name: cBioPortal for Cancer Genomics
    prefix: FAIRsharing.6L6MjA
    subjects:
    - Genomics
    - Proteomics
    - Biomedical Science
    - Preclinical Studies
  mappings:
    fairsharing: FAIRsharing.6L6MjA
    miriam: cbioportal
    n2t: cbioportal
  miriam:
    deprecated: false
    description: The cBioPortal for Cancer Genomics provides visualization, analysis
      and download of large-scale cancer genomics data sets.
    homepage: http://www.cbioportal.org
    id: 00000679
    name: The cBioPortal for Cancer Genomics
    namespaceEmbeddedInLui: false
    pattern: ^[a-z0-9\_]+$
    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
  uri_format: https://www.cbioportal.org/study/summary?id=$1
ccdc:
  mappings:
    miriam: ccdc
  miriam:
    deprecated: false
    description: The Cambridge Crystallographic Data Centre (CCDC) develops and maintains
      the Cambridge Stuctural Database, the world's most comprehensive archive of
      small-molecule crystal structure data. A CCDC Number is a unique identifier
      assigned to a dataset deposited with the CCDC.
    homepage: https://www.ccdc.cam.ac.uk/
    id: 00000818
    name: CCDC Number
    namespaceEmbeddedInLui: false
    pattern: ^\d{6,7}$
    prefix: ccdc
    sampleId: '1829126'
    uri_format: https://www.ccdc.cam.ac.uk/services/structures?pid=ccdc:$1&sid=IDORG
ccds:
  biocontext:
    is_identifiers: false
    is_obo: false
    prefix: CCDS
    uri_format: http://www.ncbi.nlm.nih.gov/CCDS/CcdsBrowse.cgi?REQUEST=CCDS&DATA=$1
  fairsharing:
    abbreviation: CCDS
    description: The Consensus CDS (CCDS) project is a collaborative effort to identify
      a core set of human and mouse protein coding regions that are consistently annotated
      and of high quality. The long term goal is to support convergence towards a
      standard set of gene annotations.
    id: '1966'
    name: The Consensus CDS
    prefix: FAIRsharing.46s4nt
    subjects:
    - Life Science
  mappings:
    biocontext: CCDS
    fairsharing: FAIRsharing.46s4nt
    miriam: ccds
    n2t: ccds
    prefixcommons: ccds
    uniprot: CCDS
  miriam:
    deprecated: false
    description: The Consensus CDS (CCDS) project is a collaborative effort to identify
      a core set of human and mouse protein coding regions that are consistently annotated
      and of high quality. The CCDS set is calculated following coordinated whole
      genome annotation updates carried out by the NCBI, WTSI, and Ensembl. The long
      term goal is to support convergence towards a standard set of gene annotations.
    homepage: http://www.ncbi.nlm.nih.gov/CCDS/
    id: '00000375'
    name: Consensus CDS
    namespaceEmbeddedInLui: false
    pattern: ^CCDS\d+\.\d+$
    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=$1
  prefixcommons:
    description: The Consensus CDS (CCDS) project is a collaborative effort to identify
      a core set of human and mouse protein coding regions that are consistently annotated
      and of high quality. The long term goal is to support convergence towards a
      standard set of gene annotations.
    example: '4824'
    homepage: http://www.ncbi.nlm.nih.gov/CCDS/
    keywords:
    - protein
    - gene
    name: The Consensus CDS
    pattern: ^\d+$
    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
  uniprot:
    category: Sequence databases
    identifier: '187'
    link_is_explicit: 'true'
    name: The Consensus CDS (CCDS) project
    prefix: CCDS
    uri_format: https://www.ncbi.nlm.nih.gov/CCDS/CcdsBrowse.cgi?REQUEST=CCDS&GO=MainBrowse&DATA=$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
  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
  example: BT20_BREAST
  homepage: https://www.cbioportal.org/study/summary?id=ccle_broad_2019
  mappings:
    cellosaurus: CCLE
  name: Cancer Cell Line Encyclopedia Cells
  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
  biocontext:
    is_identifiers: true
    is_obo: false
    prefix: CCO
    uri_format: http://identifiers.org/cco/$1
  bioportal:
    contact:
      email: mironov@bio.ntnu.no
      name: Vladimir Mironov
    description: An application ontology integrating knowledge about the eukaryotic
      cell cycle.
    homepage: http://www.semantic-systems-biology.org/cco/
    name: Cell Cycle Ontology
    prefix: CCO
    publication: http://genomebiology.com/2009/10/5/R58
    version: '2.10'
  download_obo: https://www.bio.ntnu.no/ontology/CCO/cco.obo
  download_owl: https://www.bio.ntnu.no/ontology/CCO/cco.owl
  fairsharing:
    abbreviation: CCO
    description: CCO contains genes, proteins, interactions (comprising genes or proteins
      that participate in them), processes from the cell cycle subtree of GO, molecular
      functions (GO), taxa, and ontological constructs (like an upper level ontology
      and relationships) to stick everything together.
    id: '1237'
    name: Cell Cycle Ontology
    prefix: FAIRsharing.xhwrnr
    publications:
    - doi: 10.1186/gb-2009-10-5-r58
      pubmed_id: 19480664
      title: 'The Cell Cycle Ontology: an application ontology for the representation
        and integrated analysis of the cell cycle process.'
    subjects:
    - Functional Genomics
    - Genomics
    - Proteomics
    - Life Science
  mappings:
    aberowl: CCO
    biocontext: CCO
    bioportal: CCO
    fairsharing: FAIRsharing.xhwrnr
    miriam: cco
    n2t: cco
    ols: cco
    prefixcommons: cco
  miriam:
    deprecated: false
    description: The Cell Cycle Ontology is an application ontology that captures
      and integrates detailed knowledge on the cell cycle process.
    homepage: https://www.ebi.ac.uk/ontology-lookup/browse.do?ontName=CCO
    id: '00000234'
    name: Cell Cycle Ontology
    namespaceEmbeddedInLui: true
    pattern: ^CCO\:\w+$
    prefix: cco
    sampleId: '0000003'
    uri_format: https://www.ebi.ac.uk/ols/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:$1
  ols:
    contact: vladimir.n.mironov@gmail.com
    description: The Cell Cycle Ontology extends existing ontologies for cell cycle
      knowledge building a resource that integrates and manages knowledge about the
      cell cycle components and regulatory aspects.
    download: http://www.bio.ntnu.no/ontology/CCO/cco.owl
    homepage: http://www.semantic-systems-biology.org/apo
    name: Cell Cycle Ontology
    prefix: cco
    version: '2016-03-23'
  pattern: ^\w+$
  prefixcommons:
    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'
    synonyms:
    - cell cycle ontology
  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
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
  uri_format: http://www.cellresource.cn/cellsearch.aspx?sc=1&where=$1
cdao:
  aberowl:
    description: a formalization of concepts and relations relevant to evolutionary
      comparative analysis
    download_owl: http://aber-owl.net/media/ontologies/CDAO/9/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
    publication: http://www.evolutionaryontology.org
    repository: https://sourceforge.net/projects/cdao/
    version: '2013-02-01'
  biocontext:
    is_identifiers: false
    is_obo: true
    prefix: CDAO
    uri_format: http://purl.obolibrary.org/obo/CDAO_$1
  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
    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).
    id: '1155'
    name: Comparative Data Analysis Ontology
    prefix: FAIRsharing.kay31r
    publications:
    - doi: 10.4137/ebo.s2320
      pubmed_id: 19812726
      title: Initial implementation of a comparative data analysis ontology.
    subjects:
    - Molecular biology
    - Bioinformatics
    - Taxonomy
    - Phylogenetics
    - Evolutionary Biology
    - Life Science
    - Biomedical Science
  mappings:
    aberowl: CDAO
    agroportal: CDAO
    biocontext: CDAO
    bioportal: CDAO
    fairsharing: FAIRsharing.kay31r
    obofoundry: cdao
    ols: cdao
    ontobee: CDAO
  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
    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: 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.
    download: http://purl.obolibrary.org/obo/cdao.owl
    homepage: https://github.com/evoinfo/cdao
    name: Comparative Data Analysis Ontology
    prefix: cdao
    version: '2019-06-26'
    version.iri: http://purl.obolibrary.org/obo/cdao/2019-06-26/cdao.owl
  ontobee:
    library: Library
    name: Comparative Data Analysis Ontology
    prefix: CDAO
  pattern: ^\d{7}$
  publications:
  - doi: 10.4137/ebo.s2320
    pmc: PMC2747124
    pubmed: '19812726'
    title: Initial implementation of a comparative data analysis ontology.
    year: 2009
cdd:
  biocontext:
    is_identifiers: true
    is_obo: false
    prefix: CDD
    uri_format: http://identifiers.org/cdd/$1
  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.
    id: '2804'
    name: Canadian Disaster Database
    prefix: FAIRsharing.ea287c
    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=$1
  mappings:
    biocontext: CDD
    edam: '2666'
    fairsharing: FAIRsharing.ea287c
    go: CDD
    miriam: cdd
    n2t: cdd
    ncbi: CDD
    prefixcommons: cdd
    uniprot: CDD
  miriam:
    deprecated: false
    description: The Conserved Domain Database (CDD) is a collection of multiple sequence
      alignments and derived database search models, which represent protein domains
      conserved in molecular evolution.
    homepage: https://www.ncbi.nlm.nih.gov/sites/entrez?db=cdd
    id: 00000119
    name: Conserved Domain Database
    namespaceEmbeddedInLui: false
    pattern: ^(cd)?\d{5}$
    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=$1
  ncbi:
    example: 02194
    homepage: https://www.ncbi.nlm.nih.gov/Structure/cdd/cdd.shtml
    name: Conserved Domain Database
    prefix: CDD
  prefixcommons:
    description: The Conserved Domain Database (CDD) brings together several collections
      of multiple sequence alignments representing conserved domains, including NCBI-curated
      domains, which use 3D-structure information to explicitly to define domain boundaries
      and provide insights into sequence/structure/function relationships, as well
      as domain models imported from a number of external source databases (Pfam,
      SMART, COG, PRK, TIGRFAM).
    example: cd00400
    homepage: http://www.ncbi.nlm.nih.gov/Structure/cdd/cdd.shtml
    keywords:
    - protein
    - structure
    name: Conserved Domain Database
    pattern: ^cd\d{5}$
    prefix: cdd
    pubmed_ids:
    - '18984618'
    uri_format: http://www.ncbi.nlm.nih.gov/Structure/cdd/cddsrv.cgi?uid=$1
  publications:
  - doi: 10.1093/nar/gkn845
    pmc: PMC2686570
    pubmed: '18984618'
    title: 'CDD: specific functional annotation with the Conserved Domain Database.'
    year: 2008
  uniprot:
    category: Family and domain databases
    identifier: '214'
    link_is_explicit: 'true'
    name: Conserved Domains Database
    prefix: CDD
    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/7/cdno.owl
    homepage: https://cdno.info/
    name: Compositional Dietary Nutrition Ontology
    prefix: 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
    bioportal: CDNO
    obofoundry: cdno
    ols: cdno
    ontobee: CDNO
  obofoundry:
    contact: l.andres.hernandez.18@student.scu.edu.au
    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.
    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/10.1002/csc2.20092
      title: Knowledge representation and data sharing to unlock crop variation for
        nutritional food security
    repository: https://github.com/Southern-Cross-Plant-Science/cdno
  ols:
    description: None
    download: http://purl.obolibrary.org/obo/cdno.owl
    homepage: https://cdno.info/
    name: Compositional Dietary Nutrition Ontology
    prefix: cdno
    version: '2022-06-23'
    version.iri: http://purl.obolibrary.org/obo/cdno/releases/2022-06-23/cdno.owl
  ontobee:
    library: Library
    name: Compositional Dietary Nutrition Ontology
    prefix: CDNO
  pattern: ^\d{7}$
cdpd:
  biocontext:
    is_identifiers: true
    is_obo: false
    prefix: CDPD
    uri_format: http://identifiers.org/cdpd/$1
  mappings:
    biocontext: CDPD
    miriam: cdpd
    n2t: cdpd
  miriam:
    deprecated: false
    description: The Canadian Drug Product Database (DPD) contains product specific
      information on drugs approved for use in Canada, and includes human pharmaceutical
      and biological drugs, veterinary drugs and disinfectant products. This information
      includes 'brand name', 'route of administration' and a Canadian 'Drug Identification
      Number' (DIN).
    homepage: http://webprod3.hc-sc.gc.ca/dpd-bdpp/index-eng.jsp
    id: '00000272'
    name: Canadian Drug Product Database
    namespaceEmbeddedInLui: false
    pattern: ^\d+$
    prefix: cdpd
    sampleId: '63250'
    uri_format: http://webprod3.hc-sc.gc.ca/dpd-bdpp/info.do?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=$1
cdt:
  appears_in:
  - ohd
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: The Code on Dental Procedures and Nomenclature (the CDT Code) assures
    consistency in documenting dental treatment.
  download_owl: https://github.com/oral-health-and-disease-ontologies/ohd-ontology/blob/master/src/ontology/older/CDTCodes%20as%20Classes_pruned.owl
  example: '1000001'
  hl7:
    description: Version of Current Dental Terminology (CDT) version 4, included in
      the Healthcare Common Procedure Coding System (HCPCS).Request rejected.  This
      is a duplicate of OID 2.16.840.1.113883.6.13
    name: Current Dental Terminology
    preferred_prefix: CDT
    prefix: 2.16.840.1.113883.6.116
    status: Rejected
  homepage: https://www.ada.org/publications/CDT
  mappings:
    hl7: 2.16.840.1.113883.6.116
  name: Current Dental Terminology
  pattern: ^\d{7}$
cell_biolabs:
  cellosaurus:
    category: Cell line collections
    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
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
cellbank.australia:
  cellosaurus:
    category: Cell line collections
    homepage: http://www.cellbankaustralia.com/cellbank-australia-exclusive-lines/
    name: CellBank Australia
    prefix: CBA
    uri_format: http://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
  uri_format: https://www.cellbankaustralia.com/$1.html
cellimage:
  biocontext:
    is_identifiers: true
    is_obo: false
    prefix: CELLIMAGE
    uri_format: http://identifiers.org/cellimage/$1
  fairsharing:
    abbreviation: null
    description: This library is a public and easily accessible resource database
      of images, videos, and animations of cells, capturing a wide diversity of organisms,
      cell types, and cellular processes. The purpose of this database is to advance
      research on cellular activity, with the ultimate goal of improving human health.
      It is a repository for images, movies, and animations of cells from a variety
      of organisms that demonstrate cellular architecture and functions. This comprehensive
      library is designed as a public resource first and foremost for research, and
      secondarily as a tool for education. The long-term goal is the construction
      of a library of images that will serve as primary data for research.
    id: '1723'
    name: Cell Image Library
    prefix: FAIRsharing.8t18te
    subjects:
    - Life Science
    - Cell Biology
  mappings:
    biocontext: CELLIMAGE
    fairsharing: FAIRsharing.8t18te
    miriam: cellimage
    n2t: cellimage
    prefixcommons: cellimage
  miriam:
    deprecated: false
    description: "The Cell: An Image Library\u2122 is a freely accessible, public\
      \ repository of reviewed and annotated images, videos, and animations of cells\
      \ from a variety of organisms, showcasing cell architecture, intracellular functionalities,\
      \ and both normal and abnormal processes."
    homepage: http://cellimagelibrary.org/
    id: '00000257'
    name: Cell Image Library
    namespaceEmbeddedInLui: false
    pattern: ^\d+$
    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/$1
  prefixcommons:
    description: "The Cell: An Image Library\u2122 is a freely accessible, public\
      \ repository of reviewed and annotated images, videos, and animations of cells\
      \ from a variety of organisms, showcasing cell architecture, intracellular functionalities,\
      \ and both normal and abnormal processes."
    example: '24801'
    keywords:
    - image
    name: 'The Cell: An Image Library'
    pattern: ^\d+$
    prefix: cellimage
    synonyms:
    - cellimage
    uri_format: http://cellimagelibrary.org/images/$1
cellopub:
  cellosaurus:
    category: Reference resources
    homepage: https://www.cellosaurus.org/
    name: Cellosaurus Publication
    prefix: CelloPub
    uri_format: https://www.cellosaurus.org/cellopub/$1
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: Cellosaurus identifeirs for publications, like Pubmed
  example: CLPUB00496
  homepage: https://web.expasy.org/cellosaurus/
  mappings:
    cellosaurus: CelloPub
  name: Cellosaurus Publication
  pattern: ^CLPUB\d+$
  uri_format: https://web.expasy.org/cellosaurus/cellopub/$1
cellosaurus:
  banana: CVCL
  banana_peel: _
  biocontext:
    is_identifiers: true
    is_obo: false
    prefix: CELLOSAURUS
    uri_format: http://identifiers.org/cellosaurus/$1
  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
    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.'
    id: '2348'
    name: Cellosaurus
    prefix: FAIRsharing.hkk309
    subjects:
    - Life Science
  homepage: https://cellosaurus.org
  mappings:
    biocontext: CELLOSAURUS
    cellosaurus: Cellosaurus
    fairsharing: FAIRsharing.hkk309
    miriam: cellosaurus
    n2t: cellosaurus
    re3data: r3d100013293
    wikidata: P3289
  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://web.expasy.org/cellosaurus/
    id: 00000598
    name: Cellosaurus
    namespaceEmbeddedInLui: false
    pattern: ^CVCL_[A-Z0-9]{4}$
    prefix: cellosaurus
    sampleId: CVCL_0030
    uri_format: https://web.expasy.org/cellosaurus/$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/$1
  name: Cellosaurus
  pattern: ^[A-Z0-9]{4}$
  providers:
  - code: legacy
    description: The legacy URI for the Cellosaurus website, updated on August 30,
      2022 [ref](https://twitter.com/Cellosaurus/status/1564658792691810305).
    homepage: https://web.expasy.org/cellosaurus
    name: Legacy Endpoint
    uri_format: https://web.expasy.org/cellosaurus/CVCL_$1
  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).'
    homepage: https://web.expasy.org/cellosaurus/
    name: Cellosaurus
    prefix: r3d100013293
    synonyms:
    - The Cellosaurus On ExPASy
    xrefs:
      fairsharing: FAIRsharing.hkk309
      scr: 013869
  synonyms:
  - CVCL
  twitter: cellosaurus
  uri_format: https://www.cellosaurus.org/CVCL_$1
  wikidata:
    database: Q24691710
    database.homepage: https://www.cellosaurus.org/
    database.label: Cellosaurus
    description: Cellosaurus cell line identifier
    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/
  name: Cellosaurus Registry
  uri_format: https://bioregistry.io/metaregistry/cellosaurus/$1
cellrepo:
  mappings:
    miriam: cellrepo
  miriam:
    deprecated: false
    description: The Cell Version Control Repository is the single worldwide version
      control repository for engineered and natural cell lines
    homepage: https://cellrepo.ico2s.org/
    id: 00000829
    name: Cell Version Control Repository
    namespaceEmbeddedInLui: false
    pattern: ^[0-9]+$
    prefix: cellrepo
    sampleId: '82'
    uri_format: https://cellrepo.ico2s.org/repositories/$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:
    is_identifiers: false
    is_obo: true
    prefix: CEPH
    uri_format: http://purl.obolibrary.org/obo/CEPH_$1
  bioportal:
    contact:
      email: cjmungall@lbl.gov
      name: Chris Mungall
    description: An anatomical and developmental ontology for cephalopods
    homepage: https://github.com/obophenotype/cephalopod-ontology
    name: Cephalopod Ontology
    prefix: CEPH
  download_obo: https://raw.githubusercontent.com/obophenotype/cephalopod-ontology/master/ceph.obo
  example: 0000109
  fairsharing:
    abbreviation: CEPH
    description: An anatomical and developmental ontology for cephalopods
    id: '668'
    name: Cephalopod Ontology
    prefix: FAIRsharing.p58bm4
    publications: []
    subjects: []
  mappings:
    aberowl: CEPH
    biocontext: CEPH
    bioportal: CEPH
    fairsharing: FAIRsharing.p58bm4
    obofoundry: ceph
    ols: ceph
    ontobee: CEPH
  obofoundry:
    contact: cjmungall@lbl.gov
    contact.github: cmungall
    contact.label: Chris Mungall
    contact.orcid: 0000-0002-6601-2165
    deprecated: true
    description: An anatomical and developmental ontology for cephalopods
    download.obo: http://purl.obolibrary.org/obo/ceph.obo
    download.owl: http://purl.obolibrary.org/obo/ceph.owl
    homepage: https://github.com/obophenotype/cephalopod-ontology
    license: CC BY 3.0
    license.url: http://creativecommons.org/licenses/by/3.0/
    name: Cephalopod Ontology
    prefix: ceph
    repository: https://github.com/obophenotype/cephalopod-ontology
  ols:
    description: An anatomical and developmental ontology for cephalopods
    download: http://purl.obolibrary.org/obo/ceph.owl
    homepage: https://github.com/obophenotype/cephalopod-ontology
    name: Cephalopod Ontology
    prefix: ceph
    version: '2016-01-12'
    version.iri: http://purl.obolibrary.org/obo/ceph/releases/2016-01-12/ceph.owl
  ontobee:
    library: Library
    name: Cephalopod Ontology
    prefix: CEPH
  pattern: ^\d{7}$
cgd:
  biocontext:
    is_identifiers: true
    is_obo: false
    prefix: CGD
    uri_format: http://identifiers.org/cgd/$1
  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.
    id: '1816'
    name: Candida Genome Database
    prefix: FAIRsharing.j7j53
    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=$1
  mappings:
    biocontext: CGD
    fairsharing: FAIRsharing.j7j53
    go: CGD
    miriam: cgd
    n2t: cgd
    ncbi: CGD
    prefixcommons: cgd
    uniprot: CGD
  miriam:
    deprecated: false
    description: The Candida Genome Database (CGD) provides access to genomic sequence
      data and manually curated functional information about genes and proteins of
      the human pathogen Candida albicans. It collects gene names and aliases, and
      assigns gene ontology terms to describe the molecular function, biological process,
      and subcellular localization of gene products.
    homepage: http://www.candidagenome.org/
    id: '00000145'
    name: Candida Genome Database
    namespaceEmbeddedInLui: false
    pattern: ^CAL\d{7}$
    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=$1
  ncbi:
    example: CAL0005934
    homepage: http://www.candidagenome.org/
    name: Candida Genome Database
    prefix: CGD
  prefixcommons:
    description: The Candida Genome Database (CGD) provides access to genomic sequence
      data and manually curated functional information about genes and proteins of
      the human pathogen Candida albicans. It collects gene names and aliases, and
      assigns gene ontology terms to describe the molecular function, biological process,
      and subcellular localization of gene products.
    example: CAL0003079
    homepage: http://www.candidagenome.org/
    keywords:
    - eukaryotic
    - genome
    - nucleotide
    name: Candida Genome Database
    pattern: ^CAL\d{7}$
    prefix: cgd
    pubmed_ids:
    - '15608216'
    uri_format: http://www.candidagenome.org/cgi-bin/locus.pl?dbid=$1
  publications:
  - doi: 10.1093/nar/gki003
    pmc: PMC539957
    pubmed: '15608216'
    title: The Candida Genome Database (CGD), a community resource for Candida albicans
      gene and protein information.
    year: 2005
  uniprot:
    category: Organism-specific databases
    identifier: '126'
    link_is_explicit: 'true'
    name: Candida Genome Database
    prefix: CGD
    uri_format: http://www.candidagenome.org/cgi-bin/locus.pl?dbid=$1
cghdb:
  cellosaurus:
    category: Cell line databases/resources
    homepage: http://www.cghtmd.jp/CGHDatabase/index_e.jsp
    name: CGH Data Base
    prefix: CGH-DB
    uri_format: http://www.cghtmd.jp/CGHDatabase/mapViewer?hid=$1&aid=%t&lang=en
  example: 300165/p13898_2106T
  mappings:
    cellosaurus: CGH-DB
cgnc:
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: Nomenclature Consortium around Chicken genes (analogous to the HGNC
    for humans)
  example: '10087'
  homepage: http://birdgenenames.org/cgnc/
  mappings:
    prefixcommons: cgnc
    re3data: r3d100012429
  name: Chicken Gene Nomenclature Consortium
  pattern: ^\d+$
  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
    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: '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.'
    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:
    is_identifiers: true
    is_obo: false
    prefix: CGSC
    uri_format: http://identifiers.org/cgsc/$1
  fairsharing:
    abbreviation: CGSC
    description: The CGSC Database of E. coli genetic information includes genotypes
      and reference information for the strains in the CGSC collection, the names,
      synonyms, properties, and map position for genes, gene product information,
      and information on specific mutations and references to primary literature.
    id: '1818'
    name: Coli Genetic Stock Center
    prefix: FAIRsharing.1tbrdz
    subjects:
    - Life Science
  go:
    homepage: http://cgsc.biology.yale.edu/
    name: CGSC
    prefix: CGSC
  mappings:
    biocontext: CGSC
    fairsharing: FAIRsharing.1tbrdz
    go: CGSC
    miriam: cgsc
    n2t: cgsc
    prefixcommons: cgsc
  miriam:
    deprecated: false
    description: The CGSC Database of E. coli genetic information includes genotypes
      and reference information for the strains in the CGSC collection, the names,
      synonyms, properties, and map position for genes, gene product information,
      and information on specific mutations and references to primary literature.
    homepage: http://cgsc.biology.yale.edu/index.php
    id: 00000295
    name: CGSC Strain
    namespaceEmbeddedInLui: false
    pattern: ^\d+$
    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=$1
  name: Coli Genetic Stock Center
  prefixcommons:
    description: The CGSC Database of E. coli genetic information includes genotypes
      and reference information for the strains in the CGSC collection, the names,
      synonyms, properties, and map position for genes, gene product information,
      and information on specific mutations and references to primary literature.
    example: '96846'
    homepage: http://cgsc.biology.yale.edu/
    keywords:
    - gene
    name: The Coli Genetic Stock Center
    pattern: ^\d+$
    prefix: cgsc
    uri_format: http://cgsc.biology.yale.edu/Site.php?ID=$1
charprot:
  biocontext:
    is_identifiers: true
    is_obo: false
    prefix: CHARPROT
    uri_format: http://identifiers.org/charprot/$1
  mappings:
    biocontext: CHARPROT
    miriam: charprot
    n2t: charprot
  miriam:
    deprecated: false
    description: CharProt is a database of biochemically characterized proteins designed
      to support automated annotation pipelines. Entries are annotated with gene name,
      symbol and various controlled vocabulary terms, including Gene Ontology terms,
      Enzyme Commission number and TransportDB accession.
    homepage: http://www.jcvi.org/charprotdb
    id: '00000341'
    name: CharProt
    namespaceEmbeddedInLui: false
    pattern: ^CH_\d+$
    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
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/174/chebi.owl
    homepage: http://www.ebi.ac.uk/chebi
    name: Chemical Entities of Biological Interest
    prefix: CHEBI
  biocontext:
    is_identifiers: false
    is_obo: true
    prefix: CHEBI
    uri_format: http://purl.obolibrary.org/obo/CHEBI_$1
  bioportal:
    contact:
      email: gowen@ebi.ac.uk
      name: Gareth Owen
    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
    version: '213'
  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/searchId.do?chebiId=$1
  cheminf:
    description: Database identifier used by ChEBI.
    name: ChEBI
    obsolete: false
    prefix: '000407'
  edam:
    description: Identifier of an entry from the ChEBI database.
    name: ChEBI
    obsolete: false
    prefix: '1174'
  example: '24867'
  fairsharing:
    abbreviation: ChEBI
    description: "Chemical Entities of Biological Interest (ChEBI) is a free dictionary\
      \ that describes 'small\u2019 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."
    id: '1036'
    name: Chemical Entities of Biological Interest
    prefix: FAIRsharing.62qk8w
    publications:
    - doi: 10.1002/0471250953.bi1409s26
      pubmed_id: 19496059
      title: 'ChEBI: an open bioinformatics and cheminformatics resource.'
    - doi: 10.1093/nar/gkm791
      pubmed_id: 17932057
      title: 'ChEBI: a database and ontology for chemical entities of biological interest.'
    - doi: 10.1093/nar/gkv1031
      pubmed_id: 26467479
      title: 'ChEBI in 2016: Improved services and an expanding collection of metabolites.'
    - doi: 10.1093/nar/gkp886
      pubmed_id: 19854951
      title: 'Chemical Entities of Biological Interest: an update.'
    - doi: 10.1093/nar/gks1146
      pubmed_id: 23180789
      title: 'The ChEBI reference database and ontology for biologically relevant
        chemistry: enhancements for 2013.'
    subjects:
    - Biochemistry
    - Chemistry
  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:$1
  mappings:
    aberowl: CHEBI
    biocontext: CHEBI
    bioportal: CHEBI
    cellosaurus: ChEBI
    cheminf: '000407'
    edam: '1174'
    fairsharing: FAIRsharing.62qk8w
    go: CHEBI
    miriam: chebi
    n2t: chebi
    obofoundry: chebi
    ols: chebi
    ontobee: CHEBI
    prefixcommons: chebi
    re3data: r3d100012626
    wikidata: P683
  miriam:
    deprecated: false
    description: Chemical Entities of Biological Interest (ChEBI) is a freely available
      dictionary of molecular entities focused on 'small' chemical compounds.
    homepage: https://www.ebi.ac.uk/chebi/
    id: '00000002'
    name: ChEBI
    namespaceEmbeddedInLui: true
    pattern: ^CHEBI:\d+$
    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:$1
  name: Chemical Entities of Biological Interest
  obofoundry:
    appears_in:
    - cdno
    - chiro
    - cl
    - ecocore
    - ecto
    - envo
    - fobi
    - foodon
    - genepio
    - maxo
    - mco
    - ons
    - pcl
    - proco
    - xpo
    - uberon
    - scdo
    contact: amalik@ebi.ac.uk
    contact.github: amalik01
    contact.label: Adnan Malik
    contact.orcid: 0000-0001-8123-5351
    deprecated: false
    description: A structured classification of molecular entities of biological interest
      focusing on 'small' chemical compounds.
    download.obo: http://purl.obolibrary.org/obo/chebi.obo
    download.owl: http://purl.obolibrary.org/obo/chebi.owl
    homepage: http://www.ebi.ac.uk/chebi
    license: CC BY 4.0
    license.url: https://creativecommons.org/licenses/by/4.0/
    name: Chemical Entities of Biological Interest
    preferredPrefix: CHEBI
    prefix: chebi
    publications:
    - id: https://www.ncbi.nlm.nih.gov/pubmed/26467479
      title: 'ChEBI in 2016: Improved services and an expanding collection of metabolites.'
    repository: https://github.com/ebi-chebi/ChEBI
    twitter: chebit
  ols:
    description: A structured classification of molecular entities of biological interest
      focusing on 'small' chemical compounds.
    download: http://purl.obolibrary.org/obo/chebi.owl
    homepage: http://www.ebi.ac.uk/chebi
    name: Chemical Entities of Biological Interest
    prefix: chebi
    version: '211'
    version.iri: http://purl.obolibrary.org/obo/chebi/211/chebi.owl
  ontobee:
    library: Foundry
    name: Chemical Entities of Biological Interest
    prefix: CHEBI
  pattern: ^\d+$
  prefixcommons:
    bioportal: '1007'
    description: A structured classification of chemical compounds of biological relevance.
    example: '17234'
    homepage: http://www.ebi.ac.uk/chebi/
    keywords:
    - obo
    - chemical
    name: Chemical Entities of Biological Interest
    pattern: ^\d+$
    prefix: chebi
    pubmed_ids:
    - '23180789'
    synonyms:
    - obo.chebi (miriam)
    - atp_chebi
    uri_format: http://www.ebi.ac.uk/chebi/searchId.do?chebiId=$1
  providers:
  - code: chebi-img
    description: Image server from chebi
    homepage: https://www.ebi.ac.uk/chebi/
    name: ChEBI
    uri_format: https://www.ebi.ac.uk/chebi/displayImage.do?defaultImage=true&imageIndex=0&chebiId=$1
  publications:
  - doi: 10.1093/nar/gkm791
    pmc: PMC2238832
    pubmed: '17932057'
    title: 'ChEBI: a database and ontology for chemical entities of biological interest.'
    year: 2007
  - doi: 10.1002/0471250953.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/gks1146
    pmc: PMC3531142
    pubmed: '23180789'
    title: 'The ChEBI reference database and ontology for biologically relevant chemistry:
      enhancements for 2013.'
    year: 2012
  - doi: 10.1093/nar/gkv1031
    pmc: PMC4702775
    pubmed: '26467479'
    title: 'ChEBI in 2016: Improved services and an expanding collection of metabolites.'
    year: 2015
  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.
    homepage: https://www.ebi.ac.uk/chebi/
    name: ChEBI
    prefix: r3d100012626
    synonyms:
    - Chemical Entities of Biological Interest
    xrefs:
      fairsharing: FAIRsharing.62qk8w
      miriam: '00000002'
      nif: 0000-02655
      omics: '02752'
      scr: 002088
  synonyms:
  - CHEBI
  - CHEBIID
  - ChEBI
  uri_format: https://www.ebi.ac.uk/chebi/searchId.do?chebiId=CHEBI:$1
  wikidata:
    database: Q902623
    database.homepage: http://www.ebi.ac.uk/chebi
    database.label: ChEBI
    description: "identifier from\_database and ontology of molecular entities focused\
      \ on 'small' chemical compounds"
    format.rdf: http://purl.obolibrary.org/obo/CHEBI_$1
    homepage: https://www.ebi.ac.uk/chebi
    name: ChEBI ID
    pattern: \d+
    prefix: P683
    uri_format: https://www.ebi.ac.uk/chebi/searchId.do?chebiId=CHEBI:$1
chembl:
  cheminf:
    description: Identifier used by the ChEMBL database for compounds, assays, target,
      etc.
    name: ChEMBL
    obsolete: false
    prefix: '000412'
  fairsharing:
    abbreviation: ChEMBL
    description: ChEMBL is an open, manually-curated, large-scale bioactivity database
      containing information from medicinal chemistry literature. It brings together
      chemical, bioactivity and genomic data to aid the translation of genomic information
      into effective new drugs. Information regarding the compounds tested (including
      their structures), the biological or physicochemical assays performed on these
      and the targets of these assays are recorded in a structured form, allowing
      users to address a broad range of drug discovery questions.
    id: '1561'
    name: ChEMBL
    prefix: FAIRsharing.m3jtpg
    subjects:
    - Drug Discovery
    - Biochemistry
    - Genomics
    - Medicinal Chemistry
  homepage: https://www.ebi.ac.uk/chembl
  mappings:
    cheminf: '000412'
    fairsharing: FAIRsharing.m3jtpg
    miriam: chembl
    prefixcommons: chembl
    re3data: r3d100010539
    uniprot: ChEMBL
  miriam:
    deprecated: false
    description: ChEMBL is a database of bioactive compounds, their quantitative properties
      and bioactivities (binding constants, pharmacology and ADMET, etc). The data
      is abstracted and curated from the primary scientific literature.
    homepage: https://www.ebi.ac.uk/chembl
    id: 00000799
    name: ChEMBL
    namespaceEmbeddedInLui: false
    pattern: ^CHEMBL\d+$
    prefix: chembl
    sampleId: CHEMBL4303805
    uri_format: https://www.ebi.ac.uk/chembl/entity/$1
  prefixcommons:
    description: ChEMBL is a database of bioactive compounds, their quantitative properties
      and bioactivities (binding constants, pharmacology and ADMET, etc). The data
      is abstracted and curated from the primary scientific literature.
    example: '210313'
    homepage: https://www.ebi.ac.uk/chembldb/
    keywords:
    - molecules
    name: chEMBL
    pattern: ^\d+$
    prefix: chembl
    synonyms:
    - chembldb
    uri_format: https://www.ebi.ac.uk/chembldb/index.php/compound/inspect/$1
  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.'
    homepage: https://www.ebi.ac.uk/chembl/
    name: ChEMBL
    prefix: r3d100010539
    xrefs:
      fairsharing: fairsharing.m3jtpg
      omics: '02731'
      scr: '014042'
  synonyms:
  - ChEMBL
  - ChEMBL_ID
  - chembl
  uniprot:
    category: Chemistry databases
    identifier: '174'
    link_is_explicit: 'true'
    name: ChEMBL database of bioactive drug-like small molecules
    prefix: ChEMBL
    uri_format: https://www.ebi.ac.uk/chembldb/target/inspect/$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
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  example: CHEMBL3307800
  mappings:
    cellosaurus: ChEMBL-Cells
  part_of: chembl
  synonyms:
  - ChEMBL-Cells
  uri_format: https://www.ebi.ac.uk/chembl/cell_line_report_card/$1
chembl.compound:
  biocontext:
    is_identifiers: true
    is_obo: false
    prefix: CHEMBL.COMPOUND
    uri_format: http://identifiers.org/chembl.compound/$1
  edam:
    description: Identifier of a small molecular from the ChEMBL database.
    name: Compound ID (ChEMBL)
    obsolete: false
    prefix: '2646'
  example: CHEMBL465070
  mappings:
    biocontext: CHEMBL.COMPOUND
    edam: '2646'
    miriam: chembl.compound
    n2t: chembl.compound
    wikidata: P592
  miriam:
    deprecated: false
    description: ChEMBL is a database of bioactive compounds, their quantitative properties
      and bioactivities (binding constants, pharmacology and ADMET, etc). The data
      is abstracted and curated from the primary scientific literature.
    homepage: https://www.ebi.ac.uk/chembldb/
    id: 00000084
    name: ChEMBL compound
    namespaceEmbeddedInLui: false
    pattern: ^CHEMBL\d+$
    prefix: chembl.compound
    providers:
    - code: CURATOR_REVIEW
      description: ChEMBL compound RDF
      homepage: https://github.com/egonw/chembl.rdf
      name: ChEMBL compound RDF
      uri_format: http://linkedchemistry.info/chembl/chemblid/$1
    - code: CURATOR_REVIEW
      description: ChEMBL compound RDF through EBI RDF Platform
      homepage: https://www.ebi.ac.uk/rdf/services/chembl/
      name: ChEMBL compound RDF through EBI RDF Platform
      uri_format: https://rdf.ebi.ac.uk/resource/chembl/molecule/$1
    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/$1
  name: ChEMBL
  part_of: chembl
  pattern: ^CHEMBL\d+$
  wikidata:
    database: Q6120337
    database.homepage: http://www.ebi.ac.uk/chembl
    database.label: ChEMBL
    description: identifier from a chemical database of bioactive molecules with drug-like
      properties
    format.rdf: http://rdf.ebi.ac.uk/resource/chembl/molecule/$1
    homepage: https://www.ebi.ac.uk/chembl
    name: ChEMBL ID
    pattern: CHEMBL\d+
    prefix: P592
    uri_format: https://www.ebi.ac.uk/chembl/compound_report_card/$1/
chembl.target:
  biocontext:
    is_identifiers: true
    is_obo: false
    prefix: CHEMBL.TARGET
    uri_format: http://identifiers.org/chembl.target/$1
  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/$1
  mappings:
    biocontext: CHEMBL.TARGET
    cellosaurus: ChEMBL-Targets
    miriam: chembl.target
    n2t: chembl.target
  miriam:
    deprecated: false
    description: ChEMBL is a database of bioactive compounds, their quantitative properties
      and bioactivities (binding constants, pharmacology and ADMET, etc). The data
      is abstracted and curated from the primary scientific literature.
    homepage: https://www.ebi.ac.uk/chembldb/
    id: 00000085
    name: ChEMBL target
    namespaceEmbeddedInLui: false
    pattern: ^CHEMBL\d+$
    prefix: chembl.target
    providers:
    - code: CURATOR_REVIEW
      description: ChEMBL target RDF
      homepage: https://github.com/egonw/chembl.rdf
      name: ChEMBL target RDF
      uri_format: http://linkedchemistry.info/chembl/chemblid/$1
    - code: CURATOR_REVIEW
      description: ChEMBL target RDF through EBI RDF Platform
      homepage: https://rdf.ebi.ac.uk/resource/chembl/
      name: ChEMBL target RDF through EBI RDF Platform
      uri_format: https://rdf.ebi.ac.uk/resource/chembl/target/$1
    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
  part_of: chembl
  synonyms:
  - ChEMBL-Targets
chemdb:
  biocontext:
    is_identifiers: true
    is_obo: false
    prefix: CHEMDB
    uri_format: http://identifiers.org/chemdb/$1
  fairsharing:
    abbreviation: ChemDB
    description: ChemDB is a chemical database containing nearly 5M commercially available
      small molecules, important for use as synthetic building blocks, probes in systems
      biology and as leads for the discovery of drugs and other useful compounds.
    id: '2088'
    name: The UC Irvine ChemDB
    prefix: FAIRsharing.dstf7h
    subjects:
    - Biochemistry
    - Life Science
    - Biomedical Science
    - Systems Biology
    - Preclinical Studies
  mappings:
    biocontext: CHEMDB
    fairsharing: FAIRsharing.dstf7h
    miriam: chemdb
    n2t: chemdb
    prefixcommons: chemdb
  miriam:
    deprecated: false
    description: ChemDB is a chemical database containing commercially available small
      molecules, important for use as synthetic building blocks, probes in systems
      biology and as leads for the discovery of drugs and other useful compounds.
    homepage: http://cdb.ics.uci.edu/
    id: 00000279
    name: ChemDB
    namespaceEmbeddedInLui: false
    pattern: ^\d+$
    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=$1
  prefixcommons:
    description: ChemDB is a chemical database containing nearly 5M commercially available
      small molecules, important for use as synthetic building blocks, probes in systems
      biology and as leads for the discovery of drugs and other useful compounds.
    example: '3965223'
    homepage: http://cdb.ics.uci.edu
    keywords:
    - small molecule
    name: The UC Irvine ChemDB
    pattern: ^\d+$
    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
chemidplus:
  biocontext:
    is_identifiers: true
    is_obo: false
    prefix: CHEMIDPLUS
    uri_format: http://identifiers.org/chemidplus/$1
  edam:
    description: Identifier of a chemical from the ChemIDplus database.
    name: Compound ID (ChemIDplus)
    obsolete: false
    prefix: '2658'
  fairsharing:
    abbreviation: ChemIDplus
    description: ChemIDplus is a web-based search system that provides access to structure
      and nomenclature authority files used for the identification of chemical substances
      cited in National Library of Medicine (NLM) databases. It also provides structure
      searching and direct links to many biomedical resources at NLM and on the Internet
      for chemicals of interest.
    id: '2003'
    name: ChemIDplus
    prefix: FAIRsharing.5949vn
    subjects:
    - Chemistry
    - Biomedical Science
  mappings:
    biocontext: CHEMIDPLUS
    edam: '2658'
    fairsharing: FAIRsharing.5949vn
    miriam: chemidplus
    n2t: chemidplus
    prefixcommons: chemidplus
  miriam:
    deprecated: false
    description: ChemIDplus is a web-based search system that provides access to structure
      and nomenclature authority files used for the identification of chemical substances
      cited in National Library of Medicine (NLM) databases. It also provides structure
      searching and direct links to many biomedical resources at NLM and on the Internet
      for chemicals of interest.
    homepage: https://chem.nlm.nih.gov/chemidplus/chemidheavy.jsp
    id: 00000096
    name: ChemIDplus
    namespaceEmbeddedInLui: false
    pattern: ^\d+\-\d+\-\d+$
    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/$1
  prefixcommons:
    description: ChemIDplus is a web-based search system that provides access to structure
      and nomenclature authority files used for the identification of chemical substances
      cited in National Library of Medicine (NLM) databases. It also provides structure
      searching and direct links to many biomedical resources at NLM and on the Internet
      for chemicals of interest.
    example: '000057272'
    homepage: http://chem.sis.nlm.nih.gov/chemidplus/chemidheavy.jsp
    keywords:
    - structure
    - molecules
    name: ChemIDplus
    pattern: ^\d+$
    prefix: chemidplus
    uri_format: http://chem.sis.nlm.nih.gov/chemidplus/direct.jsp?regno=$1
  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/47/cheminf.owl
    homepage: https://github.com/semanticchemistry/semanticchemistry
    name: Chemical Information Ontology
    prefix: CHEMINF
  biocontext:
    is_identifiers: false
    is_obo: true
    prefix: CHEMINF
    uri_format: http://purl.obolibrary.org/obo/CHEMINF_$1
  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
    publication: 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
    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.
    id: '1056'
    name: CHEMical INFormation Ontology
    prefix: FAIRsharing.sjhvyy
    publications:
    - doi: 10.1371/journal.pone.0025513
      pubmed_id: 21991315
      title: 'The chemical information ontology: provenance and disambiguation for
        chemical data on the biological semantic web.'
    subjects:
    - Biochemistry
    - Chemistry
    - Life Science
  mappings:
    aberowl: CHEMINF
    biocontext: CHEMINF
    bioportal: CHEMINF
    fairsharing: FAIRsharing.sjhvyy
    obofoundry: cheminf
    ols: cheminf
    ontobee: CHEMINF
  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.
    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:
    download: http://purl.obolibrary.org/obo/cheminf.owl
    name: chemical information ontology (cheminf) - information entities about chemical
      entities
    prefix: cheminf
    version: '2.0'
  ontobee:
    library: Library
    name: Chemical Information Ontology
    prefix: CHEMINF
  pattern: ^\d{6}$
  providers:
  - code: semanticscience
    description: Legacy URLs before conversion of CHEMINF to OBO PURLs
    homepage: http://semanticscience.org
    name: Semantic Science
    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
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/2/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
    name: CHEMROF
    prefix: CHEMROF
  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
  example: FullySpecifiedAtom
  homepage: https://chemkg.github.io/chemrof/
  mappings:
    aberowl: CHEMROF
    bioportal: CHEMROF
  name: Chemical Entity Materials and Reactions Ontological Framework
  preferred_prefix: ChEMROF
  uri_format: https://chemkg.github.io/chemrof/$1
chemspider:
  biocontext:
    is_identifiers: true
    is_obo: false
    prefix: CHEMSPIDER
    uri_format: http://identifiers.org/chemspider/$1
  cheminf:
    description: Database identifier used by ChemSpider.
    name: ChemSpider
    obsolete: false
    prefix: '000405'
  edam:
    description: Identifier of an entry from the ChemSpider database.
    name: ChemSpider
    obsolete: false
    prefix: '1173'
  fairsharing:
    abbreviation: ChemSpider
    description: ChemSpider is a freely available collection of compound data from
      across the web, which aggregates chemical structures and their associated information
      into a single searchable repository entry. These entries are supplemented with
      additional properties, related information and links back to original data sources.
    id: '2042'
    name: ChemSpider
    prefix: FAIRsharing.96f3gm
    subjects:
    - Chemistry
    - Life Science
  mappings:
    biocontext: CHEMSPIDER
    cheminf: '000405'
    edam: '1173'
    fairsharing: FAIRsharing.96f3gm
    miriam: chemspider
    n2t: chemspider
    prefixcommons: chemspider
    re3data: r3d100010205
    wikidata: P661
  miriam:
    deprecated: false
    description: ChemSpider is a collection of compound data from across the web,
      which aggregates chemical structures and their associated information into a
      single searchable repository entry. These entries are supplemented with additional
      properties, related information and links back to original data sources.
    homepage: http://www.chemspider.com/
    id: 00000138
    name: ChemSpider
    namespaceEmbeddedInLui: false
    pattern: ^\d+$
    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.$1.html
  name: ChemSpider
  prefixcommons:
    description: ChemSpider is a collection of compound data from across the web,
      which aggregates chemical structures and their associated information into a
      single searchable repository entry. These entries are supplemented with additional
      properties, related information and links back to original data sources.
    example: '56586'
    homepage: http://www.chemspider.com/
    keywords:
    - structure
    - molecules
    name: ChemSpider - Database of Chemical Structures and Property Predictions
    pattern: ^\d+$
    prefix: chemspider
    uri_format: http://www.chemspider.com/Chemical-Structure.$1.html
  re3data:
    description: "ChemSpider is a free chemical structure database providing fast\
      \ access to over 58 million structures, properties and associated information.\
      \ By integrating and linking compounds from more than 400 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.\nChemSpider 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\u2019 applications."
    homepage: http://www.chemspider.com/
    name: ChemSpider
    prefix: r3d100010205
    synonyms:
    - Search and share chemistry
    xrefs:
      nlx: '152101'
      scr: '006360'
  synonyms:
  - ChemSpiderID
  - Chemspider
  wikidata:
    database: Q2311683
    database.homepage: https://www.chemspider.com/
    database.label: ChemSpider
    description: identifier in a free chemical database, owned by the Royal Society
      of Chemistry
    format.rdf: http://rdf.chemspider.com/$1
    homepage: https://www.chemspider.com/
    name: ChemSpider ID
    pattern: '[1-9]\d*'
    prefix: P661
    uri_format: https://www.chemspider.com/Chemical-Structure.$1.html
chickenqtldb:
  biocontext:
    is_identifiers: true
    is_obo: false
    prefix: CHICKENQTLDB
    uri_format: http://identifiers.org/chickenqtldb/$1
  mappings:
    biocontext: CHICKENQTLDB
    miriam: chickenqtldb
    n2t: chickenqtldb
    prefixcommons: chickenqtldb
  miriam:
    deprecated: false
    description: The Animal Quantitative Trait Loci (QTL) database (Animal QTLdb)
      is designed to house publicly all available QTL and single-nucleotide polymorphism/gene
      association data on livestock animal species. This collection references chicken
      QTLs.
    homepage: https://www.animalgenome.org/QTLdb
    id: '00000505'
    name: Animal Genome Chicken QTL
    namespaceEmbeddedInLui: false
    pattern: ^\d+$
    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=$1
  part_of: qtldb
  prefixcommons:
    description: This Chicken Quantitative Trait Locus (QTL) database (Chicken QTLdb)
      has gathered all chicken QTL data published during the past 10+ years. The database
      and its peripheral tools make it possible to compare, confirm and locate on
      chicken chromosomes the most feasible location for genes responsible for quantitative
      trait important to chicken production.
    example: '66'
    homepage: http://www.animalgenome.org/cgi-bin/QTLdb/GG/index
    keywords:
    - DNA
    - genome
    name: Chicken Quantitative Trait Locus database
    pattern: ^\d+$
    prefix: chickenqtldb
    uri_format: http://www.animalgenome.org/cgi-bin/QTLdb/GG/qdetails?QTL_ID=$1
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
  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.
    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: http://purl.obolibrary.org/obo/chiro.owl
    homepage: https://github.com/obophenotype/chiro
    name: CHEBI Integrated Role Ontology
    prefix: chiro
    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
chmo:
  aberowl:
    description: CHMO, the chemical methods ontology, describes methods used to
    download_owl: http://aber-owl.net/media/ontologies/CHMO/30/chmo.owl
    homepage: https://github.com/rsc-ontologies/rsc-cmo
    name: Chemical Methods Ontology
    prefix: CHMO
  biocontext:
    is_identifiers: false
    is_obo: true
    prefix: CHMO
    uri_format: http://purl.obolibrary.org/obo/CHMO_$1
  bioportal:
    name: Chemical Methods Ontology
    prefix: CHMO
  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).
    id: '1424'
    name: Chemical Methods Ontology
    prefix: FAIRsharing.9j4wh2
    publications: []
    subjects:
    - Chemistry
  mappings:
    aberowl: CHMO
    biocontext: CHMO
    bioportal: CHMO
    fairsharing: FAIRsharing.9j4wh2
    obofoundry: chmo
    ols: chmo
    ontobee: CHMO
  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
    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 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: http://purl.obolibrary.org/obo/chmo.owl
    homepage: https://github.com/rsc-ontologies/rsc-cmo
    name: Chemical Methods Ontology
    prefix: chmo
    version: '2022-04-19'
    version.iri: http://purl.obolibrary.org/obo/chmo/releases/2022-04-19/chmo.owl
  ontobee:
    library: Library
    name: Chemical Methods Ontology
    prefix: CHMO
  pattern: ^\d{7}$
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/31/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
    publication: He Y, Yu H, Ong E, Wang Y, Liu Y, Huffman A, Huang H, Beverley J,
      Hur J, Yang X, Chen L, Omenn GS, Athey B, Smith B. CIDO, a community-based ontology
      for coronavirus disease knowledge and data integration, sharing, and analysis.
      Scientific Data. (2020) 7:181 | https://doi.org/10.1038/s41597-020-0523-6.
    version: 1.0.337
  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.
    id: '1401'
    name: Coronavirus Infectious Disease Ontology
    prefix: FAIRsharing.aVmpKl
    publications:
    - doi: 10.1038/s41597-020-0523-6
      pubmed_id: 32533075
      title: CIDO, a community-based ontology for coronavirus disease knowledge and
        data integration, sharing, and analysis.
    subjects:
    - Drug Discovery
    - Bioinformatics
    - Drug Repositioning
    - Virology
    - Epidemiology
  mappings:
    aberowl: CIDO
    bioportal: CIDO
    fairsharing: FAIRsharing.aVmpKl
    obofoundry: cido
    ols: cido
    ontobee: CIDO
  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.
    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
    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: http://purl.obolibrary.org/obo/cido.owl
    homepage: https://github.com/cido-ontology/cido
    name: 'CIDO: Ontology of Coronavirus Infectious Disease'
    prefix: cido
    version: 1.0.326
  ontobee:
    library: Library
    name: Coronavirus Infectious Disease Ontology
    prefix: CIDO
  pattern: ^\d{7}$
  publications:
  - 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
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:
    is_identifiers: false
    is_obo: true
    prefix: CIO
    uri_format: http://purl.obolibrary.org/obo/CIO_$1
  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.
    id: '644'
    name: Confidence Information Ontology
    prefix: FAIRsharing.e3t0yw
    publications:
    - doi: 10.1093/database/bav043
      pubmed_id: null
      title: 'The Confidence Information Ontology: a step towards a standard for asserting
        confidence in annotations'
    subjects:
    - Biology
  mappings:
    aberowl: CIO
    biocontext: CIO
    bioportal: CIO
    fairsharing: FAIRsharing.e3t0yw
    obofoundry: cio
    ols: cio
    ontobee: CIO
  obofoundry:
    contact: frederic.bastian@unil.ch
    contact.github: fbastian
    contact.label: "Fr\xE9d\xE9ric Bastian"
    contact.orcid: 0000-0002-9415-5104
    deprecated: false
    description: An ontology to capture confidence information about annotations.
    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: http://purl.obolibrary.org/obo/cio.owl
    homepage: https://github.com/BgeeDB/confidence-information-ontology
    name: Confidence Information Ontology
    prefix: cio
    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}$
  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
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
    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.
    id: '936'
    name: Cerebrotendinous Xanthomatosis Ontology
    prefix: FAIRsharing.619eqr
    publications:
    - doi: 10.1097/MOL.0b013e328362df13
      pubmed_id: 23759795
      title: Cerebrotendinous xanthomatosis.
    subjects:
    - Genetics
    - Biomedical Science
    - Preclinical Studies
  homepage: https://www.ebi.ac.uk/citexplore/
  mappings:
    fairsharing: FAIRsharing.619eqr
    prefixcommons: citexplore
  name: 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/
    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.
  example: sharesAuthorInstitutionWith
  fairsharing:
    abbreviation: CiTO
    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.

      '
    id: '3629'
    name: 'Citation Typing Ontology '
    prefix: FAIRsharing.b220d4
    publications:
    - doi: 10.1016/j.websem.2012.08.001
      pubmed_id: null
      title: 'FaBiO and CiTO: Ontologies for describing bibliographic resources and
        citations'
    subjects:
    - Knowledge and Information Systems
  homepage: http://www.sparontologies.net/ontologies/cito
  mappings:
    fairsharing: FAIRsharing.b220d4
  name: Citation Typing Ontology
  preferred_prefix: CiTO
  repository: https://github.com/sparontologies/cito
  uri_format: http://purl.org/spar/cito/$1
civic.aid:
  mappings:
    miriam: civic.aid
  miriam:
    deprecated: false
    description: 'A CIViC assertion classifies the clinical significance of a variant-disease
      relationship under recognized guidelines. The CIViC Assertion (AID) summarizes
      a collection of Evidence Items (EIDs) that covers predictive/therapeutic, diagnostic,
      prognostic or predisposing clinical information for a variant in a specific
      cancer context. CIViC currently has two main types of Assertions: those based
      on variants of primarily somatic origin (predictive/therapeutic, prognostic,
      and diagnostic) and those based on variants of primarily germline origin (predisposing).
      When the number and quality of Predictive, Prognostic, Diagnostic or Predisposing
      Evidence Items (EIDs) in CIViC sufficiently cover what is known for a particular
      variant and cancer type, then a corresponding assertion be created in CIViC.'
    homepage: https://civicdb.org/
    id: 00000835
    name: CIViC Assertion
    namespaceEmbeddedInLui: false
    pattern: ^[0-9]+$
    prefix: civic.aid
    sampleId: '3'
    uri_format: https://civicdb.org/links/assertions/$1
civic.did:
  mappings:
    miriam: civic.did
  miriam:
    deprecated: false
    description: Within the CIViC database, the disease should be the cancer or cancer
      subtype that is a result of the described variant. The disease selected should
      be as specific as possible should reflect the disease type used in the source
      that supports the evidence statement.
    homepage: https://civicdb.org/
    id: 00000957
    name: CIViC Disease
    namespaceEmbeddedInLui: false
    pattern: ^[0-9]+$
    prefix: civic.did
    sampleId: '46'
    uri_format: https://civicdb.org/links/diseases/$1
civic.eid:
  mappings:
    miriam: civic.eid
  miriam:
    deprecated: false
    description: "Evidence Items are the central building block of the Clinical Interpretation\
      \ of Variants in Cancer (CIViC) knowledgebase. The clinical Evidence Item is\
      \ a piece of information that has been manually curated from trustable medical\
      \ literature about a Variant or genomic \u2018event\u2019 that has implications\
      \ in cancer Predisposition, Diagnosis (aka molecular classification), Prognosis,\
      \ Predictive response to therapy, Oncogenicity or protein Function. For example,\
      \ an Evidence Item might describe a line of evidence supporting the notion that\
      \ tumors with a somatic BRAF V600 mutation generally respond well to the drug\
      \ dabrafenib. A Variant may be a single nucleotide substitution, a small insertion\
      \ or deletion, an RNA gene fusion, a chromosomal rearrangement, an RNA expression\
      \ pattern (e.g. over-expression), etc. Each clinical Evidence statement corresponds\
      \ to a single citable Source (a publication or conference abstract)."
    homepage: https://civicdb.org/
    id: 00000839
    name: CIViC Evidence
    namespaceEmbeddedInLui: false
    pattern: ^[0-9]+$
    prefix: civic.eid
    sampleId: '1199'
    uri_format: https://civicdb.org/links/evidence/$1
civic.gid:
  mappings:
    miriam: civic.gid
  miriam:
    deprecated: false
    description: "A CIViC Gene Summary is created to provide a high-level overview\
      \ of clinical relevance of cancer variants for the gene. Gene Summaries in CIViC\
      \ focus on emphasizing the clinical relevance from a molecular perspective rather\
      \ than describing the biological function of the gene unless necessary to contextualize\
      \ its clinical relevance in cancer. Gene Summaries include relevant cancer subtypes,\
      \ specific treatments for the gene\u2019s associated variants, pathway interactions,\
      \ functional alterations caused by the variants in the gene, and normal/abnormal\
      \ functions of the gene with associated roles in oncogenesis"
    homepage: https://civicdb.org/
    id: 00000907
    name: CIViC Gene
    namespaceEmbeddedInLui: false
    pattern: ^[0-9]+$
    prefix: civic.gid
    sampleId: '272'
    uri_format: https://civicdb.org/links/gene/$1
civic.sid:
  mappings:
    miriam: civic.sid
  miriam:
    deprecated: false
    description: In CIViC, each Evidence Item must be associated with a Source Type
      and Source ID, which link the Evidence Item to the original source of information
      supporting clinical claims. Currently, CIViC accepts publications indexed on
      PubMed OR abstracts published through the American Society of Clinical Oncology
      (ASCO). Each such source entered into CIViC is assigned a unique identifier
      and expert curators can curate guidance that assists future curators in the
      interpretation of information from this source.
    homepage: https://civicdb.org/
    id: 00000953
    name: CIViC Source
    namespaceEmbeddedInLui: false
    pattern: ^[0-9]+$
    prefix: civic.sid
    sampleId: '62'
    uri_format: https://civicdb.org/links/sources/$1
civic.tid:
  mappings:
    miriam: civic.tid
  miriam:
    deprecated: false
    description: Therapies (often drugs) in CIViC are associated with Predictive Evidence
      Types, which describe sensitivity, resistance or adverse response to therapies
      when a given variant is present. The Therapy field may also be used to describe
      more general treatment types and regimes, such as FOLFOX or Radiation, as long
      as the literature derived Evidence Item makes a scientific association between
      the Therapy (treatment type) and the presence of the variant.
    homepage: https://civicdb.org/
    id: 00000955
    name: CIViC Therapy
    namespaceEmbeddedInLui: false
    pattern: ^[0-9]+$
    prefix: civic.tid
    sampleId: '14'
    uri_format: https://civicdb.org/links/drugs/$1
civic.vid:
  mappings:
    miriam: civic.vid
  miriam:
    deprecated: false
    description: "CIViC variants are usually genomic alterations, including single\
      \ nucleotide variants (SNVs), insertion/deletion events (indels), copy number\
      \ alterations (CNV\u2019s such as amplification or deletion), structural variants\
      \ (SVs such as translocations and inversions), and other events that differ\
      \ from the \u201Cnormal\u201D genome. In some cases a CIViC variant may represent\
      \ events of the transcriptome or proteome. For example, \u2018expression\u2019\
      \ or \u2018over-expression\u2019 is a valid variant. Regardless of the variant,\
      \ it must have a Predictive, Prognostic, Predisposing, Diagnostic, Oncogenic,\
      \ or Functional relevance that is clinical in nature to be entered in CIViC.\
      \ i.e. There must be some rationale for why curation of this variant could ultimately\
      \ aid clinical decision making."
    homepage: https://civicdb.org/
    id: 00000909
    name: CIViC Variant
    namespaceEmbeddedInLui: false
    pattern: ^[0-9]+$
    prefix: civic.vid
    sampleId: '12'
    uri_format: https://civicdb.org/links/variant/$1
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/88/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/PR_000001889
    homepage: https://github.com/obophenotype/cell-ontology
    license: CC BY 4.0
    name: Cell Ontology
    prefix: CL
    publication: http://dx.doi.org/doi:10.1093/database/bav010, http://dx.doi.org/doi:10.1186/s13059-014-0560-6
    repository: https://github.com/obophenotype/cell-ontology
    version: '2022-09-15'
  biocontext:
    is_identifiers: false
    is_obo: true
    prefix: CL
    uri_format: http://purl.obolibrary.org/obo/CL_$1
  bioportal:
    homepage: http://cellontology.org
    name: Cell Ontology
    prefix: CL
    version: '2022-08-16'
  cellosaurus:
    category: Anatomy/cell type resources
    homepage: https://obophenotype.github.io/cell-ontology/
    name: Cell Ontology
    prefix: CL
    uri_format: https://www.ebi.ac.uk/ols/ontologies/cl/terms?iri=http://purl.obolibrary.org/obo/$1
  download_obo: https://raw.githubusercontent.com/obophenotype/cell-ontology/master/cl-full.obo
  example: '0000062'
  fairsharing:
    abbreviation: CL
    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.
    id: '1004'
    name: Cell Ontology
    prefix: FAIRsharing.j9y503
    publications:
    - doi: 10.1186/1471-2105-12-6
      pubmed_id: 21208450
      title: Logical development of the cell ontology.
    - doi: 10.1186/s13326-016-0088-7
      pubmed_id: 27377652
      title: 'The Cell Ontology 2016: enhanced content, modularization, and ontology
        interoperability.'
    subjects:
    - Anatomy
    - Life Science
    - Cell Biology
  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
  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: https://www.ebi.ac.uk/ols/ontologies/cl
    id: '00000110'
    name: Cell Type Ontology
    namespaceEmbeddedInLui: true
    pattern: ^CL:\d{7}$
    prefix: cl
    sampleId: '0000232'
    uri_format: https://www.ebi.ac.uk/ols/ontologies/cl/terms?obo_id=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:$1
  obofoundry:
    appears_in:
    - clo
    - ecao
    - go
    - mco
    - pcl
    - xpo
    - uberon
    - ehdaa2
    contact: addiehl@buffalo.edu
    contact.github: addiehl
    contact.label: Alexander Diehl
    contact.orcid: 0000-0001-9990-8331
    depends_on:
    - chebi
    - go
    - ncbitaxon
    - pato
    - pr
    - ro
    - uberon
    deprecated: false
    description: The Cell Ontology is a structured controlled vocabulary for cell
      types in animals.
    download.obo: http://purl.obolibrary.org/obo/cl.obo
    download.owl: http://purl.obolibrary.org/obo/cl.owl
    homepage: https://obophenotype.github.io/cell-ontology/
    license: CC BY 4.0
    license.url: http://creativecommons.org/licenses/by/4.0/
    name: Cell Ontology
    preferredPrefix: CL
    prefix: cl
    publications:
    - id: https://www.ncbi.nlm.nih.gov/pubmed/27377652
      title: 'The Cell Ontology 2016: enhanced content, modularization, and ontology
        interoperability.'
    repository: https://github.com/obophenotype/cell-ontology
  ols:
    description: An ontology of cell types.
    download: http://purl.obolibrary.org/obo/cl.owl
    name: Cell Ontology
    prefix: cl
    version: '2022-08-16'
    version.iri: http://purl.obolibrary.org/obo/cl/releases/2022-08-16/cl.owl
  ontobee:
    library: Library
    name: Cell Ontology
    prefix: CL
  pattern: ^\d{7}$
  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
  publications:
  - doi: 10.1186/1471-2105-12-6
    pmc: PMC3024222
    pubmed: '21208450'
    title: Logical development of the cell ontology.
    year: 2011
  - doi: 10.1186/s13326-016-0088-7
    pmc: PMC4932724
    pubmed: '27377652'
    title: 'The Cell Ontology 2016: enhanced content, modularization, and ontology
      interoperability.'
    year: 2016
  wikidata:
    database: Q55118285
    database.label: Cell Ontology
    homepage: http://www.ontobee.org/ontology/CL
    name: Cell Ontology ID
    pattern: CL_[0-9]{7}
    prefix: P7963
    uri_format: http://purl.obolibrary.org/obo/$1
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. Gonz\xE1lez-Monta\xF1a"
    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: '2020-16-05'
  example: 0000088
  mappings:
    aberowl: CLAO
    bioportal: CLAO
    obofoundry: clao
    ols: clao
    ontobee: CLAO
  obofoundry:
    contact: lagonzalezmo@unal.edu.co
    contact.github: luis-gonzalez-m
    contact.label: "Luis Gonz\xE1lez-Monta\xF1a"
    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).'
    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: http://purl.obolibrary.org/obo/clao.owl
    homepage: https://github.com/luis-gonzalez-m/Collembola
    name: Collembola Anatomy Ontology
    prefix: clao
    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}$
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/$1
  pattern: ^\d{7}$
  synonyms:
  - CHEMONTID
  uri_format: http://classyfire.wishartlab.com/tax_nodes/C$1
cldb:
  biocontext:
    is_identifiers: true
    is_obo: false
    prefix: CLDB
    uri_format: http://identifiers.org/cldb/$1
  cellosaurus:
    category: Cell line databases/resources
    homepage: http://bioinformatics.hsanmartino.it/cldb/
    name: Cell Line Data Base
    prefix: CLDB
    uri_format: http://bioinformatics.hsanmartino.it/cldb/$1.html
  mappings:
    biocontext: CLDB
    cellosaurus: CLDB
    miriam: cldb
    n2t: cldb
  miriam:
    deprecated: false
    description: The Cell Line Data Base (CLDB) is a reference information source
      for human and animal cell lines. It provides the characteristics of the cell
      lines and their availability through  distributors, allowing cell line requests
      to be made from collections and laboratories.
    homepage: http://bioinformatics.hsanmartino.it/hypercldb/indexes.html
    id: 00000390
    name: CLDB
    namespaceEmbeddedInLui: false
    pattern: ^(cl|tum)\d+$
    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
clingene:
  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
  description: The allele registry provides and maintains identifiers for genetic
    variants
  example: CA981206459
  homepage: https://reg.clinicalgenome.org
  mappings:
    biolink: CAID
  name: ClinGen Allele Registry
  uri_format: https://reg.clinicalgenome.org/redmine/projects/registry/genboree_registry/by_caid?caid=$1
clinicaltrials:
  biocontext:
    is_identifiers: true
    is_obo: false
    prefix: CLINICALTRIALS
    uri_format: http://identifiers.org/clinicaltrials/$1
  mappings:
    biocontext: CLINICALTRIALS
    miriam: clinicaltrials
    n2t: clinicaltrials
    prefixcommons: clinicaltrials
  miriam:
    deprecated: false
    description: ClinicalTrials.gov provides free access to information on clinical
      studies for a wide range of diseases and conditions. Studies listed in the database
      are conducted in 175 countries
    homepage: https://clinicaltrials.gov/
    id: '00000137'
    name: ClinicalTrials.gov
    namespaceEmbeddedInLui: false
    pattern: ^NCT\d{8}$
    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/$1
  prefixcommons:
    description: ClinicalTrials.gov is a registry and results database of publicly
      and privately supported clinical studies of human participants conducted around
      the world.
    example: NCT00050895
    homepage: http://clinicaltrials.gov/
    keywords:
    - disease
    - drug
    - human
    name: ClinicalTrials.gov
    pattern: ^NCT\d{8}$
    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.
    homepage: https://www.smartpatients.com
    name: Smart Patients
    uri_format: https://www.smartpatients.com/trials/$1
clinvar:
  biocontext:
    is_identifiers: false
    is_obo: false
    prefix: ClinVar
    uri_format: http://www.ncbi.nlm.nih.gov/clinvar/$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
  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.
    id: '2265'
    name: ClinVar
    prefix: FAIRsharing.wx5r6f
    subjects:
    - Genomics
    - Clinical Studies
    - Biomedical Science
    - Preclinical Studies
  mappings:
    biocontext: ClinVar
    biolink: CLINVAR
    cellosaurus: ClinVar
    fairsharing: FAIRsharing.wx5r6f
    hl7: clinVar-V
    miriam: clinvar
    n2t: clinvar
    re3data: r3d100013331
    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
  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
    homepage: https://www.ncbi.nlm.nih.gov/clinvar/
    name: ClinVar
    prefix: r3d100013331
    xrefs:
      fairsharing: FAIRsharing.wx5r6f
      nlx: '151671'
      scr: 006169
  wikidata:
    database: Q20023123
    database.homepage: http://www.ncbi.nlm.nih.gov/clinvar/
    database.label: ClinVar
    description: identifier in the ClinVar database for human genomic variation
    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/
clinvar.record:
  biocontext:
    is_identifiers: true
    is_obo: false
    prefix: CLINVAR.RECORD
    uri_format: http://identifiers.org/clinvar.record/$1
  mappings:
    biocontext: CLINVAR.RECORD
    miriam: clinvar.record
    n2t: clinvar.record
  miriam:
    deprecated: false
    description: ClinVar archives reports of relationships among medically important
      variants and phenotypes. It records human variation, interpretations of the
      relationship specific variations to human health, and supporting evidence for
      each interpretation. Each ClinVar record (RCV identifier) represents an aggregated
      view of interpretations of  the same variation and condition from one or more
      submitters. Submissions for individual variation/phenotype combinations (SCV
      identifier) are also collected and made available separately. This collection
      references the Record Report, based on RCV accession.
    homepage: http://www.ncbi.nlm.nih.gov/clinvar/
    id: '00000534'
    name: ClinVar Record
    namespaceEmbeddedInLui: false
    pattern: ^RCV\d+(\.\d+)?$
    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: clinvar
  uri_format: http://www.ncbi.nlm.nih.gov/clinvar/$1
clinvar.submission:
  biocontext:
    is_identifiers: true
    is_obo: false
    prefix: CLINVAR.SUBMISSION
    uri_format: http://identifiers.org/clinvar.submission/$1
  mappings:
    biocontext: CLINVAR.SUBMISSION
    miriam: clinvar.submission
    n2t: clinvar.submission
  miriam:
    deprecated: false
    description: ClinVar archives reports of relationships among medically important
      variants and phenotypes. It records human variation, interpretations of the
      relationship specific variations to human health, and supporting evidence for
      each interpretation. Each ClinVar record (RCV identifier) represents an aggregated
      view of interpretations of the same variation and condition from one or more
      submitters. Submissions for individual variation/phenotype combinations (SCV
      identifier) are also collected and made available separately. This collection
      references submissions, and is based on SCV accession.
    homepage: http://www.ncbi.nlm.nih.gov/clinvar/
    id: 00000595
    name: ClinVar Submission
    namespaceEmbeddedInLui: false
    pattern: ^SCV\d+(\.\d+)?$
    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=$1
clinvar.submitter:
  mappings:
    miriam: clinvar.submitter
  miriam:
    deprecated: false
    description: ClinVar archives reports of relationships among medically important
      variants and phenotypes. It records human variation, interpretations of the
      relationship specific variations to human health, and supporting evidence for
      each interpretation. Each ClinVar record (RCV identifier) represents an aggregated
      view of interpretations of the same variation and condition from one or more
      submitters (Submitter IDs). Submissions for individual variation/phenotype combinations
      (SCV identifier) are also collected and made available separately. This collection
      references submitters (submitter ids) that submit the submissions (SCVs).
    homepage: https://www.ncbi.nlm.nih.gov/clinvar/
    id: 00000769
    name: ClinVar Submitter
    namespaceEmbeddedInLui: false
    pattern: ^\d+$
    prefix: clinvar.submitter
    sampleId: '26957'
    uri_format: https://www.ncbi.nlm.nih.gov/clinvar/submitters/$1
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/6/clo.owl
    homepage: http://www.clo-ontology.org
    name: Cell Line Ontology
    prefix: CLO
  biocontext:
    is_identifiers: false
    is_obo: true
    prefix: CLO
    uri_format: http://purl.obolibrary.org/obo/CLO_$1
  bioportal:
    name: Cell Line Ontology
    prefix: CLO
  cellosaurus:
    category: Cell line databases/resources
    homepage: http://www.clo-ontology.org
    name: Cell Line Ontology
    prefix: CLO
    uri_format: https://www.ebi.ac.uk/ols/ontologies/clo/terms?iri=http://purl.obolibrary.org/obo/$1
  example: 0000091
  fairsharing:
    abbreviation: CLO
    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.
    id: '1012'
    name: Cell Line Ontology
    prefix: FAIRsharing.4dvtcz
    publications:
    - doi: 10.1186/2041-1480-5-37
      pubmed_id: 25852852
      title: 'CLO: The cell line ontology.'
    subjects:
    - Life Science
    - Cell Biology
  mappings:
    aberowl: CLO
    biocontext: CLO
    bioportal: CLO
    cellosaurus: CLO
    fairsharing: FAIRsharing.4dvtcz
    obofoundry: clo
    ols: clo
    ontobee: CLO
    prefixcommons: clo
    wikidata: P2158
  obofoundry:
    appears_in:
    - mco
    contact: siiraa@umich.edu
    contact.github: siiraa
    contact.label: Sirarat Sarntivijai
    contact.orcid: 0000-0002-2548-641X
    depends_on:
    - cl
    - doid
    - ncbitaxon
    - uberon
    deprecated: false
    description: An ontology to standardize and integrate cell line information and
      to support computer-assisted reasoning.
    download.owl: http://purl.obolibrary.org/obo/clo.owl
    homepage: http://www.clo-ontology.org
    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: http://purl.obolibrary.org/obo/clo.owl
    homepage: http://www.clo-ontology.org
    name: 'CLO: Cell Line Ontology'
    prefix: clo
    version: 2.1.178
  ontobee:
    library: Library
    name: Cell Line Ontology
    prefix: CLO
  pattern: ^\d{7}$
  prefixcommons:
    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/gb-2005-6-2-r21
    pmc: PMC551541
    pubmed: '15693950'
    title: An ontology for cell types.
    year: 2005
  - doi: 10.1186/2041-1480-5-37
    pmc: PMC4387853
    pubmed: '25852852'
    title: 'CLO: The cell line ontology.'
    year: 2014
  synonyms:
  - CLO
  wikidata:
    prefix: P2158
cls:
  cellosaurus:
    category: Cell line collections
    homepage: https://cls.shop/
    name: Cell Lines Service
    prefix: CLS
    uri_format: https://cls.shop/$1
  example: 300108/p3934_A-172
  mappings:
    cellosaurus: 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
  obofoundry:
    contact: lucas.leclere@obs-vlfr.fr
    contact.github: L-Leclere
    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.
    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: https://raw.githubusercontent.com/EBISPOT/clyh_ontology/master/clyh.owl
    name: Clytia hemisphaerica Development and Anatomy Ontology (CLYH)
    prefix: clyh
    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+$
cmecs:
  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.
  example: '595'
  homepage: https://cmecscatalog.org/cmecs
  name: Costal and Marine Ecological Classification Standard
  pattern: ^\d+$
  references:
  - http://www.natureserve.org/sites/default/files/publications/files/cmecs_version_06-2012_final.pdf
  uri_format: https://cmecscatalog.org/cmecs/classification/unit/$1.html
cmf:
  aberowl:
    name: CranioMaxilloFacial ontology
    prefix: CMF
  biocontext:
    is_identifiers: false
    is_obo: true
    prefix: CMF
    uri_format: http://purl.obolibrary.org/obo/CMF_$1
  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
  obofoundry:
    contact: engelsta@ohsu.edu
    contact.label: Mark Engelstad
    contact.orcid: 0000-0001-5889-4463
    deprecated: true
    homepage: https://code.google.com/p/craniomaxillofacial-ontology/
    name: CranioMaxilloFacial ontology
    prefix: cmf
  ontobee:
    library: Library
    name: CranioMaxilloFacial ontology
    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/91/cmo.owl
    homepage: http://rgd.mcw.edu/rgdweb/ontology/search.html
    name: Clinical measurement ontology
    prefix: CMO
  biocontext:
    is_identifiers: false
    is_obo: true
    prefix: CMO
    uri_format: http://purl.obolibrary.org/obo/CMO_$1
  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
    publication: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3361058/
    version: '2.170'
  example: '0001350'
  fairsharing:
    abbreviation: CMO
    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.
    id: '885'
    name: Clinical Measurement Ontology
    prefix: FAIRsharing.dq78pn
    publications:
    - doi: 10.3389/fgene.2012.00087
      pubmed_id: 22654893
      title: Three ontologies to define phenotype measurement data.
    - doi: 10.1186/2041-1480-4-26
      pubmed_id: 24103152
      title: 'The clinical measurement, measurement method and experimental condition
        ontologies: expansion, improvements and new applications.'
    subjects:
    - Life Science
    - Biomedical Science
    - Preclinical Studies
  mappings:
    aberowl: CMO
    biocontext: CMO
    bioportal: CMO
    fairsharing: FAIRsharing.dq78pn
    obofoundry: cmo
    ols: cmo
    ontobee: CMO
  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.
    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/
    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: http://purl.obolibrary.org/obo/cmo.owl
    homepage: http://rgd.mcw.edu/rgdweb/ontology/search.html
    name: Clinical measurement ontology
    prefix: cmo
    version: '2019-02-19'
    version.iri: http://purl.obolibrary.org/obo/cmo/releases/2019-02-19/cmo.owl
  ontobee:
    library: Library
    name: Clinical measurement ontology
    prefix: CMO
  pattern: ^\d{7}$
  publications:
  - doi: 10.3389/fgene.2012.00087
    pmc: PMC3361058
    pubmed: '22654893'
    title: Three ontologies to define phenotype measurement data.
    year: 2012
  - 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
  twitter: ratgenome
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'
  example: '0000435'
  fairsharing:
    abbreviation: CMPO
    description: 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
    id: '157'
    name: Cellular Microscopy Phenotype Ontology
    prefix: FAIRsharing.knp11s
    publications:
    - doi: 10.1186/s13326-016-0074-0
      pubmed_id: 27195102
      title: The cellular microscopy phenotype ontology.
    subjects:
    - 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: http://www.ebi.ac.uk/cmpo/cmpo.owl
    homepage: http://www.ebi.ac.uk/cmpo
    name: Cellular Microscopy Phenotype Ontology
    prefix: cmpo
    version: '2017-12-19'
    version.iri: http://www.ebi.ac.uk/cmpo/releases/2017-12-19/cmpo.owl
  pattern: ^\d{7}$
  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
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
    publication: https://doi.org/10.1093/aobpla/plq008
    version: March 2016
  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: https://cropontology.org/ontology/CO_320/Rice/owl
    homepage: https://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\u2019 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."
    id: '832'
    name: Rice Ontology
    prefix: FAIRsharing.2jkxp5
    publications: []
    subjects:
    - Botany
    - Agriculture
    - Life Science
  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}$
  uri_format: https://www.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
    publication: https://doi.org/10.1093/aobpla/plq008
    version: Feb 2016
  cropoct:
    description: July 2018
    download_owl: https://cropontology.org/ontology/CO_321/Wheat/owl
    homepage: https://cropontology.org/term/CO_321:ROOT
    name: Wheat ontology
    prefix: CO_321
  example: 0000449
  fairsharing:
    abbreviation: CO_321
    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.
    id: '728'
    name: Wheat Ontology
    prefix: FAIRsharing.czzmpg
    publications:
    - doi: 10.1093/aobpla/plq008
      pubmed_id: 22476066
      title: 'Multifunctional crop trait ontology for breeders'' data: field book,
        annotation, data discovery and semantic enrichment of the literature.'
    subjects:
    - Agriculture
    - Life Science
  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}$
  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
  uri_format: https://www.cropontology.org/rdf/CO_321:$1
co_322:
  agroportal:
    contact:
      email: helpdesk@cropontology-curationtool.org
      name: Crop Ontology Helpdesk
    description: Maize Trait Dictionary in template 5.
    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
    version: September 2016
  cropoct:
    description: Maize Trait Dictionary in template 5 - CIMMYT- September 2016
    download_owl: https://cropontology.org/ontology/CO_322/Maize/owl
    homepage: https://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.
    id: '925'
    name: Maize Ontology
    prefix: FAIRsharing.eeyne8
    publications: []
    subjects:
    - Botany
    - Agriculture
    - Life Science
  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}$
  uri_format: https://www.cropontology.org/rdf/CO_322:$1
co_323:
  agroportal:
    contact:
      email: r.verma@cgiar.org
      name: Ramesh Verna
    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
    version: '1.2'
  cropoct:
    description: ICARDA - TDv5 - Sept 2018
    download_owl: https://cropontology.org/ontology/CO_323/Barley/owl
    homepage: https://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\u2019 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."
    id: '872'
    name: Barley Ontology
    prefix: FAIRsharing.f69084
    publications: []
    subjects:
    - Botany
    - Agriculture
  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}$
  uri_format: https://www.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
    version: '1.0'
  cropoct:
    description: Sorghum TDv5 - Oct 2019
    download_owl: https://cropontology.org/ontology/CO_324/Sorghum/owl
    homepage: https://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.
    id: '1077'
    name: Sorghum Ontology
    prefix: FAIRsharing.dxx0c
    publications: []
    subjects:
    - Botany
    - Agriculture
  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}$
  uri_format: https://www.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
    version: April 2019
  cropoct:
    description: Banana Trait Dictionary in template 5 - Bioversity & IITA - April
      2019
    download_owl: https://cropontology.org/ontology/CO_325/Banana/owl
    homepage: https://cropontology.org/term/CO_325:ROOT
    name: Banana ontology
    prefix: CO_325
  example: 0000519
  fairsharing:
    abbreviation: CO_325
    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.
    id: '642'
    name: Banana Ontology
    prefix: FAIRsharing.gdszhh
    publications: []
    subjects:
    - Agriculture
    - Life Science
  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}$
  uri_format: https://www.cropontology.org/rdf/CO_325:$1
co_326:
  cropoct:
    download_owl: https://cropontology.org/ontology/CO_326/Coconut/owl
    homepage: https://cropontology.org/term/CO_326:ROOT
    name: Coconut ontology
    prefix: CO_326
  example: '0000254'
  mappings:
    cropoct: CO_326
    ols: co_326
  ols:
    contact: helpdesk@cropontology-curationtool.org
    description: Draft version
    download: https://cropontology.org/ontology/CO_326/Coconut/owl
    homepage: https://cropontology.org/ontology/CO_326/Coconut
    name: Coconut ontology
    prefix: co_326
  pattern: ^\d{7}$
  uri_format: https://www.cropontology.org/rdf/CO_326:$1
co_327:
  agroportal:
    contact:
      email: helpdesk@cropontology-curationtool.org
      name: Crop Ontology Helpdesk
    description: Pearl millet Trait Dictionary in template 5.
    example_uri: http://www.cropontology.org/rdf/CO_327:0000185
    homepage: http://www.cropontology.org/
    license: CC BY 4.0
    name: Pearl Millet Ontology
    prefix: CO_327
    version: April 2016
  cropoct:
    description: Pearl millet Trait Dictionary in template 5 - ICRISAT/INERA - April
      2016
    download_owl: https://cropontology.org/ontology/CO_327/Pearl millet/owl
    homepage: https://cropontology.org/term/CO_327:ROOT
    name: Pearl millet ontology
    prefix: CO_327
  example: 0000095
  fairsharing:
    abbreviation: CO_327
    description: The goal of the CGIAR Pearl Millet Ontology is to help improve food
      security for subsistence smallholder farmers in East and West Africa with productive
      and nutritious pearl millet food and fodder production technologies.
    id: '495'
    name: Pearl Millet Ontology
    prefix: FAIRsharing.4e3qh9
    publications: []
    subjects:
    - Botany
    - Agriculture
  mappings:
    agroportal: CO_327
    cropoct: CO_327
    fairsharing: FAIRsharing.4e3qh9
    ols: co_327
  ols:
    contact: helpdesk@cropontology-curationtool.org
    description: Pearl millet Trait Dictionary in template 5 - ICRISAT/INERA - April
      2016
    download: http://www.cropontology.org/ontology/CO_327/Pearl%20millet/owl
    homepage: http://www.cropontology.org/ontology/CO_327/Pearl%20millet
    name: Pearl millet ontology
    prefix: co_327
  pattern: ^\d{7}$
  uri_format: https://www.cropontology.org/rdf/CO_327:$1
co_330:
  agroportal:
    contact:
      email: helpdesk@cropontology-curationtool.org
      name: Crop Ontology Helpdesk
    description: Potato Ontology
    example_uri: http://www.cropontology.org/rdf/CO_330:0000056/2
    homepage: http://www.cropontology.org/
    license: CC BY 4.0
    name: Potato Ontology
    prefix: CO_330
    version: december 2017
  cropoct:
    description: CIP - potato ontology - december 2018
    download_owl: https://cropontology.org/ontology/CO_330/Potato/owl
    homepage: https://cropontology.org/term/CO_330:ROOT
    name: Potato ontology
    prefix: CO_330
  example: '0000106'
  fairsharing:
    abbreviation: CO_330
    description: "Reference Plant Ontologies are being developed in the context of\
      \ the Planteome project and are being integrated with the Crop Ontology, which\
      \ provides harmonized breeders\u2019 trait names, measurement methods, scales\
      \ and standard variables for many crops. The Potato Ontology is one of these\
      \ reference plant ontologies integrated within the Crop Ontology."
    id: '1307'
    name: Potato Ontology
    prefix: FAIRsharing.4fa657
    publications: []
    subjects:
    - Botany
    - Agriculture
    - Life Science
  mappings:
    agroportal: CO_330
    cropoct: CO_330
    fairsharing: FAIRsharing.4fa657
    ols: co_330
  ols:
    contact: helpdesk@cropontology-curationtool.org
    description: CIP - potato ontology - december 2018
    download: https://cropontology.org/ontology/CO_330/Potato/owl
    homepage: https://cropontology.org/ontology/CO_330/Potato
    name: Potato ontology
    prefix: co_330
    version: '2019-10-09'
  pattern: ^\d{7}$
  uri_format: https://www.cropontology.org/rdf/CO_330:$1
co_331:
  agroportal:
    contact:
      email: helpdesk@cropontology-curationtool.org
      name: Crop Ontology Helpdesk
    description: Sweet Potato Trait Dictionary in template v5
    example_uri: http://www.cropontology.org/rdf/CO_331:0000601/1
    homepage: http://www.cropontology.org/
    license: CC BY 4.0
    name: Sweet Potato Ontology
    prefix: CO_331
    version: June 2016
  cropoct:
    description: Sweetpotato Trait Dictionary in template v5 - CIP - November 2019
    download_owl: https://cropontology.org/ontology/CO_331/Sweet Potato/owl
    homepage: https://cropontology.org/term/CO_331:ROOT
    name: Sweet Potato ontology
    prefix: CO_331
  example: 0000088
  fairsharing:
    abbreviation: CO_331
    description: "Reference Plant Ontologies are being developed in the context of\
      \ the Planteome project and are being integrated with the Crop Ontology, which\
      \ provides harmonized breeders\u2019 trait names, measurement methods, scales\
      \ and standard variables for many crops. The Sweet Potato Ontology is one of\
      \ these reference plant ontologies integrated within the Crop Ontology."
    id: '496'
    name: Sweet Potato Ontology
    prefix: FAIRsharing.4g5qcw
    publications: []
    subjects:
    - Botany
    - Agriculture
    - Life Science
  mappings:
    agroportal: CO_331
    cropoct: CO_331
    fairsharing: FAIRsharing.4g5qcw
    ols: co_331
  ols:
    contact: helpdesk@cropontology-curationtool.org
    description: Sweet Potato Trait Dictionary in template v5 - CIP - November 2019
    download: http://www.cropontology.org/ontology/CO_331/Sweet%20Potato/owl
    homepage: http://www.cropontology.org/ontology/CO_331/Sweet%20Potato
    name: Sweet Potato ontology
    prefix: co_331
  pattern: ^\d{7}$
  uri_format: https://www.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, Unversit\xE9 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
    version: November 2017
  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: https://cropontology.org/ontology/CO_333/Beet Ontology/owl
    homepage: https://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\u2019 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."
    id: '1079'
    name: Beet Ontology
    prefix: FAIRsharing.af5655
    publications: []
    subjects:
    - Botany
    - Plant Breeding
    - Agriculture
    - Life Science
  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+$
  uri_format: https://www.cropontology.org/rdf/CO_333:$1
co_334:
  agroportal:
    contact:
      email: helpdesk@cropontology-curationtool.org
      name: Crop Ontology Helpdesk
    description: Cassava Trait Dictionary in template 5
    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
    publication: http://www.cropontology.org/
    version: February 2016
  cropoct:
    description: Cassava Trait Dictionary in template 5 - IITA - July 2015, updated
      in February 2016
    download_owl: https://cropontology.org/ontology/CO_334/Cassava/owl
    homepage: https://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.
    id: '1099'
    name: IBP Cassava Trait Ontology
    prefix: FAIRsharing.v06c4q
    publications: []
    subjects:
    - Botany
    - Agriculture
    - Nutritional Science
  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}$
  uri_format: https://www.cropontology.org/rdf/CO_334:$1
co_335:
  agroportal:
    contact:
      email: helpdesk@cropontology-curationtool.org
      name: Crop Ontology Helpdesk
    description: Common bean trait dictionary
    example_uri: http://www.cropontology.org/rdf/CO_335:0000475/4
    homepage: http://www.cropontology.org/
    license: CC BY 4.0
    name: Common Bean Ontology
    prefix: CO_335
    version: August 2014
  cropoct:
    description: CIAT Common bean trait dictionary - version Oct 2021
    download_owl: https://cropontology.org/ontology/CO_335/Common Bean/owl
    homepage: https://cropontology.org/term/CO_335:ROOT
    name: Common Bean ontology
    prefix: CO_335
  example: 0000189
  fairsharing:
    abbreviation: CO_335
    description: "Reference Plant Ontologies are being developed in the context of\
      \ the Planteome project and are being integrated with the Crop Ontology, which\
      \ provides harmonized breeders\u2019 trait names, measurement methods, scales\
      \ and standard variables for many crops. The Common Bean Ontology is one of\
      \ these reference plant ontologies integrated within the Crop Ontology."
    id: '1096'
    name: Common Bean Ontology
    prefix: FAIRsharing.a14123
    publications: []
    subjects:
    - Botany
    - Agriculture
  mappings:
    agroportal: CO_335
    cropoct: CO_335
    fairsharing: FAIRsharing.a14123
    ols: co_335
  ols:
    contact: helpdesk@cropontology-curationtool.org
    description: CIAT Common bean trait dictionary - version August 2014
    download: http://www.cropontology.org/ontology/CO_335/Common%20Bean/owl
    homepage: http://www.cropontology.org/ontology/CO_335/Common%20Bean
    name: Common Bean ontology
    prefix: co_335
  pattern: ^\d{7}$
  uri_format: https://www.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
    version: July 2015
  cropoct:
    description: Soybean Trait Dictionary in template v5 - IITA - July 2015
    download_owl: https://cropontology.org/ontology/CO_336/Soybean/owl
    homepage: https://cropontology.org/term/CO_336:ROOT
    name: Soybean ontology
    prefix: CO_336
  example: 0000339
  fairsharing:
    abbreviation: CO_336
    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.
    id: '669'
    name: Soybean Ontology
    prefix: FAIRsharing.j75srj
    publications: []
    subjects:
    - Agriculture
    - Life Science
  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}$
  uri_format: https://www.cropontology.org/rdf/CO_336:$1
co_337:
  agroportal:
    contact:
      email: tm.shah@cgiar.org
      name: Trushar Shah
    description: Groundnut Trait Dictionary in template v5
    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
    version: Sept 2015
  cropoct:
    description: Groundnut Trait Dictionary in template v5 - ICRISAT/ISRA/DARS - Sept
      2015
    download_owl: https://cropontology.org/ontology/CO_337/Groundnut/owl
    homepage: https://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.
    id: '40'
    name: Groundnut Ontology
    prefix: FAIRsharing.ge8y23
    publications: []
    subjects:
    - Botany
    - Agriculture
    - Life Science
  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}$
  uri_format: https://www.cropontology.org/rdf/CO_337:$1
co_338:
  agroportal:
    contact:
      email: tm.shah@cgiar.org
      name: Trushar Shah
    description: Chickpea Trait Dictionary in template v5
    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
    publication: https://doi.org/10.1093/aobpla/plq008
    version: July 2015
  cropoct:
    description: Chickpea Trait Dictionary in template v5 - ICRISAT - July 2015
    download_owl: https://cropontology.org/ontology/CO_338/Chickpea/owl
    homepage: https://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.
    id: '1321'
    name: Chickpea Ontology
    prefix: FAIRsharing.js20q3
    publications: []
    subjects:
    - Botany
    - Agriculture
  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}$
  uri_format: https://www.cropontology.org/rdf/CO_338:$1
co_339:
  agroportal:
    contact:
      email: helpdesk@cropontology-curationtool.org
      name: Crop Ontology Helpdesk
    description: Lentil Trait Dictionary in template v5
    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
    version: July 2015
  cropoct:
    description: Lentil Trait Dictionary in template v5 - ICARDA - July 2015
    download_owl: https://cropontology.org/ontology/CO_339/Lentil/owl
    homepage: https://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.
    id: '1352'
    name: Lentil Ontology
    prefix: FAIRsharing.ry1ezg
    publications: []
    subjects:
    - Botany
    - Agriculture
    - Life Science
  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}$
  uri_format: https://www.cropontology.org/rdf/CO_339:$1
co_340:
  agroportal:
    contact:
      email: helpdesk@cropontology-curationtool.org
      name: Crop Ontology Helpdesk
    description: Cowpea Trait Dictionary in template v5
    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
    publication: http://www.cropontology.org/
    version: August 2015
  cropoct:
    description: Cowpea Trait Dictionary in template v5 - IITA - August 2015
    download_owl: https://cropontology.org/ontology/CO_340/Cowpea/owl
    homepage: https://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.
    id: '1302'
    name: IBP Cowpea Trait Ontology
    prefix: FAIRsharing.31apg2
    publications:
    - doi: 10.3389/fphys.2012.00326
      pubmed_id: 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.
    subjects:
    - Botany
    - Agriculture
  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}$
  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
  uri_format: https://www.cropontology.org/rdf/CO_340:$1
co_341:
  agroportal:
    contact:
      email: helpdesk@cropontology-curationtool.org
      name: Crop Ontology Helpdesk
    description: Pigeonpea Trait Dictionary in template v5
    example_uri: http://www.cropontology.org/rdf/CO_341:0000015
    homepage: http://www.cropontology.org/
    license: CC BY 4.0
    name: Pigeon Pea Ontology
    prefix: CO_341
    version: July 2015
  cropoct:
    description: Pigeonpea Trait Dictionary in template v5 - ICRISAT - July 2015
    download_owl: https://cropontology.org/ontology/CO_341/Pigeonpea/owl
    homepage: https://cropontology.org/term/CO_341:ROOT
    name: Pigeonpea ontology
    prefix: CO_341
  example: '0000140'
  fairsharing:
    abbreviation: CO_341
    description: "Reference Plant Ontologies are being developed in the context of\
      \ the Planteome project and are being integrated with the Crop Ontology, which\
      \ provides harmonized breeders\u2019 trait names, measurement methods, scales\
      \ and standard variables for many crops. The Pigeon Pea Ontology is one of these\
      \ reference plant ontologies integrated within the Crop Ontology."
    id: '1078'
    name: Pigeon Pea Ontology
    prefix: FAIRsharing.ehe3yp
    publications: []
    subjects:
    - Botany
    - Agriculture
    - Life Science
  mappings:
    agroportal: CO_341
    cropoct: CO_341
    fairsharing: FAIRsharing.ehe3yp
    ols: co_341
  ols:
    contact: helpdesk@cropontology-curationtool.org
    description: Pigeonpea Trait Dictionary in template v5 - ICRISAT - July 2015
    download: https://cropontology.org/ontology/CO_341/Pigeonpea/owl
    homepage: https://cropontology.org/ontology/CO_341/Pigeonpea
    name: Pigeonpea ontology
    prefix: co_341
    version: '2019-11-18'
  pattern: ^\d{7}$
  uri_format: https://www.cropontology.org/rdf/CO_341:$1
co_343:
  agroportal:
    contact:
      email: helpdesk@cropontology-curationtool.org
      name: Crop Ontology Helpdesk
    description: Yam trait ontology
    example_uri: http://www.cropontology.org/rdf/CO_343:0000357
    homepage: http://www.cropontology.org/
    license: CC BY 4.0
    name: Yam Ontology
    prefix: CO_343
    version: Feb 2017
  cropoct:
    description: version 2019 - pvs
    download_owl: https://cropontology.org/ontology/CO_343/Yam/owl
    homepage: https://cropontology.org/term/CO_343:ROOT
    name: Yam ontology
    prefix: CO_343
  example: '0100010'
  fairsharing:
    abbreviation: CO_343
    description: "Reference Plant Ontologies are being developed in the context of\
      \ the Planteome project and are being integrated with the Crop Ontology, which\
      \ provides harmonized breeders\u2019 trait names, measurement methods, scales\
      \ and standard variables for many crops. The Yam Ontology is one of these reference\
      \ plant ontologies integrated within the Crop Ontology."
    id: '838'
    name: Yam Ontology
    prefix: FAIRsharing.7e9cff
    publications: []
    subjects:
    - Botany
    - Agriculture
    - Life Science
  mappings:
    agroportal: CO_343
    cropoct: CO_343
    fairsharing: FAIRsharing.7e9cff
    ols: co_343
  ols:
    contact: helpdesk@cropontology-curationtool.org
    description: version 2019 - pvs
    download: https://cropontology.org/ontology/CO_343/Yam/owl
    homepage: https://cropontology.org/ontology/CO_343/Yam
    name: Yam ontology
    prefix: co_343
    version: '2019-10-09'
  pattern: ^\d{7}$
  uri_format: https://www.cropontology.org/rdf/CO_343:$1
co_345:
  agroportal:
    contact:
      email: helpdesk@cropontology-curationtool.org
      name: Crop Ontology Helpdesk
    description: Brachiaria (forages) ontology TD v5
    example_uri: http://www.cropontology.org/rdf/CO_345:0000044
    homepage: http://www.cropontology.org/
    license: CC BY 4.0
    name: Brachiaria Ontology
    prefix: CO_345
    version: Oct 2016
  cropoct:
    description: Brachiaria (forages) ontology TD v5 - Version Oct 2016
    download_owl: https://cropontology.org/ontology/CO_345/Brachiaria/owl
    homepage: https://cropontology.org/term/CO_345:ROOT
    name: Brachiaria ontology
    prefix: CO_345
  example: '0000127'
  fairsharing:
    abbreviation: CO_345
    description: "Reference Plant Ontologies are being developed in the context of\
      \ the Planteome project and are being integrated with the Crop Ontology, which\
      \ provides harmonized breeders\u2019 trait names, measurement methods, scales\
      \ and standard variables for many crops. The Brachiaria Ontology is one of these\
      \ reference plant ontologies integrated within the Crop Ontology."
    id: '494'
    name: Brachiaria Ontology
    prefix: FAIRsharing.9e9683
    publications: []
    subjects:
    - Botany
    - Agriculture
    - Life Science
  mappings:
    agroportal: CO_345
    cropoct: CO_345
    fairsharing: FAIRsharing.9e9683
    ols: co_345
  ols:
    contact: helpdesk@cropontology-curationtool.org
    description: Brachiaria (forages) ontology TD v5 - Version Oct 2016
    download: https://cropontology.org/ontology/CO_345/Brachiaria/owl
    homepage: https://cropontology.org/ontology/CO_345/Brachiaria
    name: Brachiaria ontology
    prefix: co_345
    version: '2019-10-09'
  pattern: ^\d{7}$
  uri_format: https://www.cropontology.org/rdf/CO_345:$1
co_346:
  agroportal:
    contact:
      email: helpdesk@cropontology-curationtool.org
      name: Crop Ontology Helpdesk
    description: Mungbean Ontology
    example_uri: http://www.cropontology.org/rdf/CO_346:0000095
    homepage: http://www.cropontology.org/
    license: CC BY 4.0
    name: Mungbean Ontology
    prefix: CO_346
    version: Oct 2016
  cropoct:
    description: oct 2016
    download_owl: https://cropontology.org/ontology/CO_346/Mungbean/owl
    homepage: https://cropontology.org/term/CO_346:ROOT
    name: Mungbean ontology
    prefix: CO_346
  example: 0000199
  fairsharing:
    abbreviation: CO_346
    description: The Mungbean Ontology is part of the Crop Ontology (CO) project.
      The Crop Ontology has been created to compile validated concepts along with
      their inter-relationships on anatomy, structure and phenotype of Crops, on trait
      measurement and methods as well as on Germplasm with the multi-crop passport
      terms. The concepts of the CO are being used to curate agronomic databases and
      describe data.
    id: '1100'
    name: Mungbean Ontology
    prefix: FAIRsharing.fgd5gq
    publications: []
    subjects:
    - Agriculture
    - Life Science
  mappings:
    agroportal: CO_346
    cropoct: CO_346
    fairsharing: FAIRsharing.fgd5gq
    ols: co_346
  ols:
    contact: helpdesk@cropontology-curationtool.org
    description: oct 2016
    download: https://cropontology.org/ontology/CO_346/Mungbean/owl
    homepage: https://cropontology.org/ontology/CO_346/Mungbean
    name: Mungbean ontology
    prefix: co_346
    version: '2019-10-09'
  pattern: ^\d{7}$
  uri_format: https://www.cropontology.org/rdf/CO_346:$1
co_347:
  agroportal:
    contact:
      email: helpdesk@cropontology-curationtool.org
      name: Crop Ontology Helpdesk
    description: Castor Bean Ontology
    example_uri: http://www.cropontology.org/rdf/CO_347:0000108
    homepage: http://www.cropontology.org/
    license: CC BY 4.0
    name: Castor Bean Ontology
    prefix: CO_347
    version: March 2017
  cropoct:
    description: 'March 2017 version '
    download_owl: https://cropontology.org/ontology/CO_347/Castor bean/owl
    homepage: https://cropontology.org/term/CO_347:ROOT
    name: Castor bean ontology
    prefix: CO_347
  example: 0000108
  fairsharing:
    abbreviation: CO_347
    description: The Castor Bean Ontology is part of the Crop Ontology (CO) project.
      The Crop Ontology has been created to compile validated concepts along with
      their inter-relationships on anatomy, structure and phenotype of Crops, on trait
      measurement and methods as well as on Germplasm with the multi-crop passport
      terms. The concepts of the CO are being used to curate agronomic databases and
      describe data.
    id: '1070'
    name: Castor Bean Ontology
    prefix: FAIRsharing.qrrvyk
    publications: []
    subjects:
    - Botany
    - Agriculture
    - Life Science
  mappings:
    agroportal: CO_347
    cropoct: CO_347
    fairsharing: FAIRsharing.qrrvyk
    ols: co_347
  ols:
    contact: helpdesk@cropontology-curationtool.org
    description: 'March 2017 version '
    download: http://www.cropontology.org/ontology/CO_347/Castor%20bean/owl
    homepage: http://www.cropontology.org/ontology/CO_347/Castor%20bean
    name: Castor bean ontology
    prefix: co_347
  pattern: ^\d{7}$
  uri_format: https://www.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
  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: https://cropontology.org/ontology/CO_348/Brassica/owl
    homepage: https://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\u2019 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."
    id: '1019'
    name: Brassica Ontology
    prefix: FAIRsharing.af7a2d
    publications: []
    subjects:
    - Botany
    - Agriculture
    - Life Science
  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+$
  uri_format: https://www.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
    version: '1.0'
  cropoct:
    description: Oat trait dictionary started by Oat Global (http://oatglobal.org/)
      and improved by NIAB and PepsiCo
    download_owl: https://cropontology.org/ontology/CO_350/Oat/owl
    homepage: https://cropontology.org/term/CO_350:ROOT
    name: Oat ontology
    prefix: CO_350
  example: '0000215'
  fairsharing:
    abbreviation: CO_350
    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\u2019 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/)."
    id: '652'
    name: Oat Trait Ontology
    prefix: FAIRsharing.35e1c3
    publications: []
    subjects:
    - Botany
    - Agriculture
    - Life Science
  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}$
  uri_format: https://www.cropontology.org/rdf/CO_350:$1
co_356:
  agroportal:
    contact:
      email: helpdesk@cropontology-curationtool.org
      name: Crop Ontology Helpdesk
    description: Grape Ontology including OIV and bioversity descriptors. INRA July
      2017
    example_uri: http://www.cropontology.org/rdf/CO_356:1000182
    homepage: http://www.cropontology.org/
    license: CC BY 4.0
    name: Vitis Ontology
    prefix: CO_356
    version: '2019-11-29'
  cropoct:
    description: Grape Ontology including OIV and bioversity descriptors. INRA July
      2017
    download_owl: https://cropontology.org/ontology/CO_356/Vitis/owl
    homepage: https://cropontology.org/term/CO_356:ROOT
    name: Vitis ontology
    prefix: CO_356
  example: '4000027'
  fairsharing:
    abbreviation: CO_356
    description: "Reference Plant Ontologies are being developed in the context of\
      \ the Planteome project and are being integrated with the Crop Ontology, which\
      \ provides harmonized breeders\u2019 trait names, measurement methods, scales\
      \ and standard variables for many crops. The Vitis Ontology is one of these\
      \ reference plant ontologies integrated within the Crop Ontology."
    id: '1092'
    name: Vitis Ontology
    prefix: FAIRsharing.c7f4d7
    publications: []
    subjects:
    - Botany
    - Agriculture
    - Life Science
  mappings:
    agroportal: CO_356
    cropoct: CO_356
    fairsharing: FAIRsharing.c7f4d7
    ols: co_356
  ols:
    contact: helpdesk@cropontology-curationtool.org
    description: Grape Ontology including OIV and bioversity descriptors. INRA July
      2017
    download: https://cropontology.org/ontology/CO_356/Vitis/owl
    homepage: https://cropontology.org/ontology/CO_356/Vitis
    name: Vitis ontology
    prefix: co_356
    version: '2019-11-29'
  pattern: ^\d+$
  uri_format: https://www.cropontology.org/rdf/CO_356:$1
co_357:
  agroportal:
    contact:
      email: celia.michotey@inrae.fr
      name: "C\xE9lia 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
    version: August 2017
  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 (IBET)
      - Version 2 submitted on Jun 2020 by INRAE.'
    download_owl: https://cropontology.org/ontology/CO_357/Woody Plant Ontology/owl
    homepage: https://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 all variables used for woody plant\
      \ observations. Terms are collected from various sources (past and ongoing projects\
      \ at national and international levels). 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\u2019 trait names,\
      \ measurement methods, scales and standard variables for many crops. The Woody\
      \ Plant Ontology is one of these reference plant ontologies integrated within\
      \ the Crop Ontology."
    id: '1103'
    name: Woody Plant Ontology
    prefix: FAIRsharing.2b04ae
    publications: []
    subjects:
    - Botany
    - Life Science
  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+$
  uri_format: https://www.cropontology.org/rdf/CO_357:$1
co_358:
  agroportal:
    contact:
      email: helpdesk@cropontology-curationtool.org
      name: Crop Ontology Helpdesk
    description: Cotton ontology from CottonGen database - June 2019
    example_uri: http://www.cropontology.org/rdf/CO_358:0000215
    homepage: http://www.cropontology.org/
    license: CC BY 4.0
    name: Cotton Ontology
    prefix: CO_358
    version: '2020-01-03'
  cropoct:
    description: Cotton ontology from CottonGen database - June 2019
    download_owl: https://cropontology.org/ontology/CO_358/Cotton/owl
    homepage: https://cropontology.org/term/CO_358:ROOT
    name: Cotton ontology
    prefix: CO_358
  example: 0000139
  mappings:
    agroportal: CO_358
    cropoct: CO_358
    ols: co_358
  ols:
    contact: helpdesk@cropontology-curationtool.org
    description: Cotton ontology from CottonGen database - June 2019
    download: https://cropontology.org/ontology/CO_358/Cotton/owl
    homepage: https://cropontology.org/ontology/CO_358/Cotton
    name: Cotton ontology
    prefix: co_358
    version: '2020-01-03'
  pattern: ^\d{7}$
  uri_format: https://www.cropontology.org/rdf/CO_358:$1
co_359:
  agroportal:
    contact:
      email: helpdesk@cropontology-curationtool.org
      name: Crop Ontology Helpdesk
    description: Created in December 2019.
    example_uri: https://cropontology.org/rdf/CO_359:0000568
    homepage: https://www.cropontology.org/
    license: CC BY 4.0
    name: Sunflower
    prefix: CO_359
    version: '2019-12-16'
  cropoct:
    description: December 2019
    download_owl: https://cropontology.org/ontology/CO_359/Sunflower/owl
    homepage: https://cropontology.org/term/CO_359:ROOT
    name: Sunflower ontology
    prefix: CO_359
  example: 0000947
  mappings:
    agroportal: CO_359
    cropoct: CO_359
    ols: co_359
  ols:
    contact: helpdesk@cropontology-curationtool.org
    description: December 2019
    download: https://cropontology.org/ontology/CO_359/Sunflower/owl
    homepage: https://cropontology.org/ontology/CO_359/Sunflower
    name: Sunflower ontology
    prefix: co_359
  pattern: ^\d{7}$
  uri_format: https://www.cropontology.org/rdf/CO_359:$1
co_360:
  agroportal:
    contact:
      email: helpdesk@cropontology-curationtool.org
      name: Crop Ontology Helpdesk
    description: Sugar Kelp trait ontology
    example_uri: http://www.cropontology.org/rdf/CO_360:0000085
    homepage: http://www.cropontology.org/
    license: CC BY 4.0
    name: Sugar Kelp Ontology
    prefix: CO_360
    version: June 2019
  cropoct:
    description: Sugar Kelp trait ontology
    download_owl: https://cropontology.org/ontology/CO_360/Sugar Kelp trait/owl
    homepage: https://cropontology.org/term/CO_360:ROOT
    name: Sugar Kelp trait ontology
    prefix: CO_360
  example: '0000071'
  fairsharing:
    abbreviation: CO_360
    description: "Reference Plant Ontologies are being developed in the context of\
      \ the Planteome project and are being integrated with the Crop Ontology, which\
      \ provides harmonized breeders\u2019 trait names, measurement methods, scales\
      \ and standard variables for many crops. The Sugar Kelp Trait Ontology is one\
      \ of these reference plant ontologies integrated within the Crop Ontology."
    id: '1093'
    name: Sugar Kelp Trait Ontology
    prefix: FAIRsharing.1c1738
    publications: []
    subjects:
    - Botany
    - Life Science
  mappings:
    agroportal: CO_360
    cropoct: CO_360
    fairsharing: FAIRsharing.1c1738
    ols: co_360
  ols:
    contact: helpdesk@cropontology-curationtool.org
    description: Sugar Kelp trait ontology
    download: http://www.cropontology.org/ontology/CO_360/Sugar%20Kelp%20trait/owl
    homepage: http://www.cropontology.org/ontology/CO_360/Sugar%20Kelp%20trait
    name: Sugar Kelp trait ontology
    prefix: co_360
  pattern: ^\d{7}$
  uri_format: https://www.cropontology.org/rdf/CO_360:$1
co_365:
  agroportal:
    contact:
      email: ICARDA-ethiopia@cgiar.org
      name: ICARDA Ethiopia
    description: developed by ICARDA - Dec 2018
    example_uri: http://www.cropontology.org/rdf/CO_365:0000146
    homepage: http://www.cropontology.org
    license: CC BY 4.0
    name: Fababean Ontology
    prefix: CO_365
    version: '2019-10-15'
  cropoct:
    description: developed by ICARDA - Dec 2018
    download_owl: https://cropontology.org/ontology/CO_365/Fababean/owl
    homepage: https://cropontology.org/term/CO_365:ROOT
    name: Fababean ontology
    prefix: CO_365
  example: '0000205'
  mappings:
    agroportal: CO_365
    cropoct: CO_365
    ols: co_365
  ols:
    contact: helpdesk@cropontology-curationtool.org
    description: developed by ICARDA - Dec 2018
    download: https://cropontology.org/ontology/CO_365/Fababean/owl
    homepage: https://cropontology.org/ontology/CO_365/Fababean
    name: Fababean ontology
    prefix: co_365
    version: '2019-10-15'
  pattern: ^\d{7}$
  uri_format: https://www.cropontology.org/rdf/CO_365:$1
co_366:
  agroportal:
    contact:
      email: helpdesk@cropontology-curationtool.org
      name: Crop Ontology Helpdesk
    description: version Dec 2019
    example_uri: http://www.cropontology.org/rdf/CO_366:0000253/9
    homepage: http://www.cropontology.org
    license: CC BY 4.0
    name: Bambara Groundnut Ontology
    prefix: CO_366
    publication: https://doi.org/10.1093/database/baab028
    version: '2019-12-23'
  cropoct:
    description: version Dec 2019
    download_owl: https://cropontology.org/ontology/CO_366/Bambara groundnut/owl
    homepage: https://cropontology.org/term/CO_366:ROOT
    name: Bambara groundnut ontology
    prefix: CO_366
  example: '0000072'
  mappings:
    agroportal: CO_366
    cropoct: CO_366
    ols: co_366
  ols:
    contact: helpdesk@cropontology-curationtool.org
    description: version Dec 2019
    download: http://www.cropontology.org/ontology/CO_366/Bambara%20groundnut/owl
    homepage: http://www.cropontology.org/ontology/CO_366/Bambara%20groundnut
    name: Bambara groundnut ontology
    prefix: co_366
  pattern: ^\d{7}$
  uri_format: https://www.cropontology.org/rdf/CO_366:$1
co_367:
  cropoct:
    description: 'Curator name: Clara S. Stanschewski; Curator Affiliation: King Abdullah
      University of Science and Technology; Contributing Scientists or Crop expert
      group: The Salt Lab and the Quinoa Phenotyping Consortium Creation Date: 23.05.2021'
    download_owl: https://cropontology.org/ontology/CO_367/Quinoa Ontology/owl
    homepage: https://cropontology.org/term/CO_367:ROOT
    name: Quinoa Ontology ontology
    prefix: CO_367
  example: '0000004'
  mappings:
    cropoct: CO_367
  pattern: ^\d{7}$
co_370:
  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: https://cropontology.org/ontology/CO_370/Apple/owl
    homepage: https://cropontology.org/term/CO_370:ROOT
    name: Apple ontology
    prefix: CO_370
  example: 0000890
  mappings:
    cropoct: CO_370
  pattern: ^\d{7}$
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/7/cob.owl
    homepage: https://github.com/OBOFoundry/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.
    homepage: https://github.com/OBOFoundry/COB
    name: Core Ontology for Biology and Biomedicine
    prefix: COB
    version: '2022-05-02'
  example: 0000080
  mappings:
    aberowl: COB
    bioportal: COB
    obofoundry: cob
    ols: cob
    ontobee: COB
  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.
    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: http://purl.obolibrary.org/obo/cob.owl
    homepage: https://github.com/OBOFoundry/COB
    name: Core Ontology for Biology and Biomedicine
    prefix: cob
    version: '2022-05-02'
    version.iri: http://purl.obolibrary.org/obo/cob/releases/2022-05-02/cob.owl
  ontobee:
    library: Library
    name: Core Ontology for Biology and Biomedicine
    prefix: COB
  pattern: ^\d{7}$
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
  github_request_issue: 221
  homepage: https://coconut.naturalproducts.net
  name: COlleCtion of Open Natural ProdUcTs
  pattern: ^CNP\d{7}$
  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/$1
codelink:
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: 'GE Healthcare/Amersham Biosciences CodeLink? Human Whole Genome Bioarray
    targets most of the known and predictive genes of the human genome as it is described
    today in the public domain. It is comprised of approximately 55,000 30-mer probes
    designed to conserved exons across the transcripts of targeted genes. These 55,000
    probes represent well annotated, full length, and partial human gene sequences
    from major public databases. GE Healthcare/Amersham Biosciences CodeLink? Human
    Whole Genome Bioarray probe sequences were selected from the NCBI UniGene build
    #165, RefSeq database (January 5, 2004 release) and dbEST database (January 8,
    2004 release).'
  example: GE86325
  homepage: https://www.ebi.ac.uk/arrayexpress/files/A-GEHB-1/A-GEHB-1.adf.txt
  name: GE Healthcare/Amersham Biosciences CodeLink Human Whole Genome Bioarray
  pattern: ^GE\d+$
  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
cog:
  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
    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.
    id: '1968'
    name: 'Clusters of Orthologous Groups of Proteins: Phylogenetic classification
      of proteins encoded in complete genomes'
    prefix: FAIRsharing.djsbw2
    subjects:
    - Life Science
  go:
    homepage: http://www.ncbi.nlm.nih.gov/COG/
    name: NCBI COG cluster
    prefix: COG_Cluster
    uri_format: http://www.ncbi.nlm.nih.gov/COG/new/release/cow.cgi?cog=$1
  homepage: https://www.ncbi.nlm.nih.gov/research/cog/
  mappings:
    biolink: COG
    fairsharing: FAIRsharing.djsbw2
    go: COG_Cluster
    prefixcommons: cog
  name: Cluster of orthologous genes
  pattern: ^COG\d+$
  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
  synonyms:
  - COG_Cluster
  uri_format: https://www.ncbi.nlm.nih.gov/research/cog/cog/$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/
  name: COG Categories
  part_of: cog
  uri_format: https://www.ncbi.nlm.nih.gov/research/cog/cogcategory/$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: http://www.ncbi.nlm.nih.gov/COG/new/release/coglist.cgi?pathw=$1
  homepage: https://www.ncbi.nlm.nih.gov/research/cog/pathways
  mappings:
    go: COG_Pathway
  name: COG Pathways
  part_of: cog
  uri_format: https://www.ncbi.nlm.nih.gov/research/cog/pathway/$1
cohd:
  comment: not really sure where the source is. this also links to a system called
    athena. I was not able to figure out what COHD stands for.
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: MIMIC-III is a dataset comprising health-related data associated with
    over 40,000 patients who stayed in critical care units of the Beth Israel Deaconess
    Medical Center between 2001 and 2012
  homepage: https://github.com/MIT-LCP/mimic-omop
  name: MIMIC III Database
  no_own_terms: true
  repository: https://github.com/MIT-LCP/mimic-omop
col.taiwan:
  contributor:
    email: meghan.balk@gmail.com
    github: megbalk
    name: Meghan Balk
    orcid: 0000-0003-2699-3066
  description: Identifier (name code) for a taxon in the catalogue of life in taiwan
  example: '431472'
  github_request_issue: 466
  homepage: http://taibnet.sinica.edu.tw/home.php
  mappings:
    wikidata: P3088
  name: Catalogue of Life in Taiwan
  pattern: ^[1-9]\d{5}$
  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
    database.homepage: https://taibnet.sinica.edu.tw/home.php
    database.label: Catalogue of Life in Taiwan
    description: identifier (name code) for a taxon in the Catalogue of Life in Taiwan
    homepage: http://taibnet.sinica.edu.tw/home.php
    name: Catalogue of Life in Taiwan ID
    pattern: ([1-9]\d{5})
    prefix: P3088
    uri_format: http://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/4/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. Gir\xF3n"
    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: '2021-11-19'
  example: '0000000'
  mappings:
    aberowl: COLAO
    bioportal: COLAO
    obofoundry: colao
    ols: colao
    ontobee: COLAO
  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.
    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: http://purl.obolibrary.org/obo/colao.owl
    homepage: https://github.com/insect-morphology/colao
    name: Coleoptera Anatomy Ontology
    prefix: colao
    version: '2022-06-18'
    version.iri: http://purl.obolibrary.org/obo/colao/releases/2022-06-18/colao.owl
  ontobee:
    library: Library
    name: Coleoptera Anatomy Ontology
    prefix: COLAO
  pattern: ^\d{7}$
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
combine.specifications:
  biocontext:
    is_identifiers: true
    is_obo: false
    prefix: COMBINE.SPECIFICATIONS
    uri_format: http://identifiers.org/combine.specifications/$1
  mappings:
    biocontext: COMBINE.SPECIFICATIONS
    miriam: combine.specifications
    n2t: combine.specifications
  miriam:
    deprecated: false
    description: The 'COmputational Modeling in BIology' NEtwork (COMBINE) is an initiative
      to coordinate the development of the various community standards and formats
      for computational models, initially in Systems Biology and related fields. This
      collection pertains to specifications of the standard formats developed by the
      Computational Modeling in Biology Network.
    homepage: https://co.mbine.org/standards/
    id: 00000258
    name: COMBINE specifications
    namespaceEmbeddedInLui: false
    pattern: ^\w+(\-|\.|\w)*$
    prefix: combine.specifications
    sampleId: sbgn.er.level-1.version-1.2
    uri_format: https://co.mbine.org/specifications/$1
  n2t:
    description: The 'COmputational Modeling in BIology' NEtwork (COMBINE) is an initiative
      to coordinate the development of the various community standards and formats
      for computational models, initially in Systems Biology and related fields. This
      collection pertains to specifications of the standard formats developed by the
      Computational Modeling in Biology Network.
    example: sbgn.er.level-1.version-1.2
    homepage: https://co.mbine.org/standards/
    name: COMBINE at EBI
    namespaceEmbeddedInLui: false
    pattern: ^\w+(\-|\.|\w)*$
    prefix: combine.specifications
    uri_format: https://co.mbine.org/specifications/$1
come:
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: COMe (Co-Ordination of Metals) at the EBI represents an ontology for
    bioinorganic and other small molecule centres in complex proteins, using a classification
    system based on the concept of a bioinorganic motif.
  example: MOL000160
  homepage: https://www.flymine.org/come
  mappings:
    prefixcommons: come
  name: The Bioinorganic Motif Database
  prefixcommons:
    description: COMe is an attempt to classify metalloproteins and some other complex
      proteins using the concept of bioinorganic motif.
    example: BIM000347
    homepage: http://www.flymine.org/come/
    keywords:
    - protein
    name: COMe
    pattern: ^BIM\d+$
    prefix: come
    uri_format: http://www.flymine.org/come/entry?gn=$1
  uri_format: https://www.flymine.org/come/entry?gn=$1
complexportal:
  biocontext:
    is_identifiers: true
    is_obo: false
    prefix: COMPLEXPORTAL
    uri_format: http://identifiers.org/complexportal/$1
  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/$1
  mappings:
    biocontext: COMPLEXPORTAL
    go: ComplexPortal
    miriam: complexportal
    n2t: complexportal
    re3data: r3d100013295
    uniprot: ComplexPortal
    wikidata: P7718
  miriam:
    deprecated: false
    description: A database that describes manually curated macromolecular complexes
      and provides links to details about these complexes in other databases.
    homepage: https://www.ebi.ac.uk/complexportal
    id: '00000657'
    name: Complex Portal
    namespaceEmbeddedInLui: false
    pattern: ^CPX-[0-9]+$
    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
  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.
    homepage: https://www.ebi.ac.uk/complexportal/
    name: Complex Portal
    prefix: r3d100013295
    synonyms:
    - CP
    xrefs:
      fairsharing: FAIRsharing.wP3t2
  synonyms:
  - ComplexPortal
  uniprot:
    category: Protein-protein interaction databases
    identifier: '228'
    link_is_explicit: 'true'
    name: 'ComplexPortal: manually curated resource of macromolecular complexes'
    prefix: ComplexPortal
    uri_format: https://www.ebi.ac.uk/complexportal/complex/$1
  wikidata:
    database: Q47196990
    database.homepage: https://www.ebi.ac.uk/complexportal/home
    database.label: Complex Portal
    description: accession number of protein complex at the Complex Portal
    homepage: https://www.ebi.ac.uk/complexportal/home
    name: Complex Portal accession ID
    pattern: ^CPX-[0-9]+$
    prefix: P7718
    uri_format: https://www.ebi.ac.uk/complexportal/complex/$1
comptox:
  biocontext:
    is_identifiers: true
    is_obo: false
    prefix: COMPTOX
    uri_format: http://identifiers.org/comptox/$1
  mappings:
    biocontext: COMPTOX
    miriam: comptox
    n2t: comptox
    wikidata: P3117
  miriam:
    deprecated: false
    description: The Chemistry Dashboard is a part of a suite of databases and web
      applications developed by the US Environmental Protection Agency's Chemical
      Safety for Sustainability Research Program. These databases and apps support
      EPA's computational toxicology research efforts to develop innovative methods
      to change how chemicals are currently evaluated for potential health risks.
    homepage: https://comptox.epa.gov/dashboard
    id: 00000658
    name: CompTox Chemistry Dashboard
    namespaceEmbeddedInLui: false
    pattern: ^DTXSID\d+$
    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
  wikidata:
    prefix: P3117
compulyeast:
  biocontext:
    is_identifiers: true
    is_obo: false
    prefix: COMPULYEAST
    uri_format: http://identifiers.org/compulyeast/$1
  fairsharing:
    abbreviation: Compulyeast
    description: Compluyeast-2D-DB is a two-dimensional polyacrylamide gel electrophoresis
      federated database. This collection references a subset of Uniprot, and contains
      general information about the protein record.
    id: '2079'
    name: Compulyeast
    prefix: FAIRsharing.rbjs3e
    subjects: []
  mappings:
    biocontext: COMPULYEAST
    fairsharing: FAIRsharing.rbjs3e
    miriam: compulyeast
    n2t: compulyeast
  miriam:
    deprecated: false
    description: Compluyeast-2D-DB is a two-dimensional polyacrylamide gel electrophoresis
      federated database. This collection references a subset of Uniprot, and contains
      general information about the protein record.
    homepage: http://compluyeast2dpage.dacya.ucm.es/
    id: 00000198
    name: Compulyeast
    namespaceEmbeddedInLui: false
    pattern: ^([A-N,R-Z][0-9][A-Z][A-Z, 0-9][A-Z, 0-9][0-9])|([O,P,Q][0-9][A-Z, 0-9][A-Z,
      0-9][A-Z, 0-9][0-9])$
    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=$1
  name: Compluyeast-2D-DB
  provides: uniprot
confident.event:
  contact:
    email: Philip.Stroemert@tib.eu
    github: StroemPhi
    name: "Philip Str\xF6mert"
    orcid: 0000-0002-1595-3213
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: Confident makes descriptive metadata on conferences and other formats
    of scientific events permanently accessible in a high quality through automated
    processes and scientific data curating.
  example: 37af84f2-bfd7-4653-b608-eaff44febba6
  github_request_issue: 519
  homepage: https://www.confident-conference.org/index.php/Category:Event
  name: ConfIDent Event
  pattern: ^[0-9a-f]{8}-[0-9a-f]{4}-[0-9a-f]{4}-[0-9a-f]{4}-[0-9a-f]{12}$
  uri_format: https://www.confident-conference.org/index.php/Event:$1
confident.series:
  contact:
    email: Philip.Stroemert@tib.eu
    github: StroemPhi
    name: "Philip Str\xF6mert"
    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
  name: ConfIDent Event Series
  uri_format: https://www.confident-conference.org/index.php/Event_Series:$1
conoserver:
  biocontext:
    is_identifiers: true
    is_obo: false
    prefix: CONOSERVER
    uri_format: http://identifiers.org/conoserver/$1
  fairsharing:
    abbreviation: ConoServer
    description: ConoServer is a database specializing in sequences and structures
      of peptides expressed by marine cone snails. The database gives access to protein
      sequences, nucleic acid sequences and structural information on conopeptides.
      ConoServer's data are first collected from the peer reviewed literature and
      from publicly available databases, including UniProtKB/Swiss-Prot, NCBI nucleotide
      (nt), and the World Wide Protein Data Bank. The data are then curated manually,
      which include the addition of references, the analysis of sequence regions,
      the identification of cysteine frameworks and gene superfamilies, and the identification
      of mature peptides in the precusor sequences.
    id: '1563'
    name: ConoServer
    prefix: FAIRsharing.y00hz4
    subjects:
    - Neurophysiology
    - Statistics
    - Life Science
    - Synthetic Biology
  mappings:
    biocontext: CONOSERVER
    fairsharing: FAIRsharing.y00hz4
    miriam: conoserver
    n2t: conoserver
    uniprot: ConoServer
  miriam:
    deprecated: false
    description: ConoServer is a database specialized in the sequence and structures
      of conopeptides, which are peptides expressed by carnivorous marine cone snails.
    homepage: http://www.conoserver.org/
    id: '00000254'
    name: Conoserver
    namespaceEmbeddedInLui: false
    pattern: ^\d+$
    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
  uniprot:
    category: Organism-specific databases
    identifier: '156'
    link_is_explicit: 'true'
    name: 'ConoServer: Cone snail toxin database'
    prefix: ConoServer
    uri_format: http://www.conoserver.org/?page=card&table=protein&id=$1
conso:
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: An ontology describing phenomena encountered in the literature surrounding
    neurodegenerative diseases such as Alzheimer's disease, Parkinson's disease, Huntington's
    disease, tauopathies, and related protein aggregation diseases.
  example: CONSO00010
  homepage: https://pharmacome.github.io/conso/
  name: Curation of Neurodegeneration Supporting Ontology
  pattern: ^CONSO\d{5}$
  uri_format: https://pharmacome.github.io/conso/$1
cordis.article:
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: The Community Research and Development Information Service (CORDIS)
    is the European Commission's primary source of results from the projects funded
    by the EU's framework programmes for research and innovation (FP1 to Horizon 2020).
  example: '436605'
  homepage: https://cordis.europa.eu/
  name: CORDIS Article
  pattern: ^\d+$
  uri_format: https://cordis.europa.eu/article/id/$1
cordis.project:
  contributor:
    email: benjamin_gyori@hms.harvard.edu
    github: bgyori
    name: Benjamin M. Gyori
    orcid: 0000-0001-9439-5346
  description: The Community Research and Development Information Service (CORDIS)
    is the European Commission's primary source of results from the projects funded
    by the EU's framework programmes for research and innovation (FP1 to Horizon 2020).
  example: '817732'
  github_request_issue: 450
  homepage: https://cordis.europa.eu/
  name: CORDIS Project
  pattern: ^\d+$
  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:
    is_identifiers: false
    is_obo: false
    prefix: Coriell
    uri_format: https://catalog.coriell.org/0/Sections/Search/Sample_Detail.aspx?Ref=$1
  cellosaurus:
    category: Cell line collections
    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=$1
corrdb:
  fairsharing:
    abbreviation: CorrDB
    description: A genetic correlation is the proportion of shared variance between
      two traits that is due to genetic causes; a phenotypic correlation is the degree
      to which two traits co-vary among individuals in a population. In the genomics
      era, while gene expression, genetic association, and network analysis provide
      unprecedented means to decode the genetic basis of complex phenotypes, it is
      important to recognize the possible effects genetic progress in one trait can
      have on other traits. This database is designed to collect all published livestock
      genetic/phenotypic trait correlation data, aimed at facilitating genetic network
      analysis or systems biology studies
    id: '2591'
    name: Animal Trait Correlation Database
    prefix: FAIRsharing.IziuCK
    subjects:
    - Animal Genetics
    - Genetics
    - Life Science
    - Systems Biology
  mappings:
    fairsharing: FAIRsharing.IziuCK
    miriam: corrdb
    re3data: r3d100011496
  miriam:
    deprecated: false
    description: A genetic correlation is the proportion of shared variance between
      two traits that is due to genetic causes; a phenotypic correlation is the degree
      to which two traits co-vary among individuals in a population. In the genomics
      era, while gene expression, genetic association, and network analysis provide
      unprecedented means to decode the genetic basis of complex phenotypes, it is
      important to recognize the possible effects genetic progress in one trait can
      have on other traits. This database is designed to collect all published livestock
      genetic/phenotypic trait correlation data, aimed at facilitating genetic network
      analysis or systems biology studies.
    homepage: https://www.animalgenome.org
    id: 00000831
    name: CorrDB
    namespaceEmbeddedInLui: false
    pattern: ^[0-9]+$
    prefix: corrdb
    sampleId: '37232'
    uri_format: https://www.animalgenome.org/CorrDB/q/?id=CorrID:$1
  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.
    homepage: https://www.animalgenome.org/cgi-bin/CorrDB/index
    name: CorrDB
    prefix: r3d100011496
    synonyms:
    - Animal Trait Correlation Database
corum:
  biocontext:
    is_identifiers: true
    is_obo: false
    prefix: CORUM
    uri_format: http://identifiers.org/corum/$1
  fairsharing:
    abbreviation: CORUM
    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.
    id: '2839'
    name: ' Comprehensive Resource of Mammalian protein complexes'
    prefix: FAIRsharing.ohbpNw
    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=$1
  mappings:
    biocontext: CORUM
    fairsharing: FAIRsharing.ohbpNw
    go: CORUM
    miriam: corum
    n2t: corum
    prefixcommons: corum
    uniprot: CORUM
  miriam:
    deprecated: false
    description: The CORUM database provides a resource of manually annotated protein
      complexes from mammalian organisms. Annotation includes protein complex function,
      localization, subunit composition, literature references and more. All information
      is obtained from individual experiments published in scientific articles, data
      from high-throughput experiments is excluded.
    homepage: https://mips.helmholtz-muenchen.de/genre/proj/corum/
    id: '00000440'
    name: CORUM
    namespaceEmbeddedInLui: false
    pattern: ^\d+$
    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=$1
  name: Comprehensive Resource of Mammalian protein complexes
  prefixcommons:
    description: The CORUM database provides a resource of manually annotated protein
      complexes from mammalian organisms. Annotation includes protein complex function,
      localization, subunit composition, literature references and more.
    example: '56'
    homepage: http://mips.gsf.de/genre/proj/corum
    keywords:
    - protein
    name: the Comprehensive Resource of Mammalian protein complexes
    pattern: ^\d+$
    prefix: corum
    uri_format: http://mips.helmholtz-muenchen.de/genre/proj/corum/complexdetails.html?id=$1
  uniprot:
    category: Protein-protein interaction databases
    identifier: '224'
    link_is_explicit: 'true'
    name: CORUM comprehensive resource of mammalian protein complexes
    prefix: CORUM
    uri_format: http://mips.helmholtz-muenchen.de/corum/#?uniprotID=$1
cosmic:
  biocontext:
    is_identifiers: false
    is_obo: false
    prefix: COSMIC
    uri_format: http://cancer.sanger.ac.uk/cosmic/mutation/overview?id=$1
  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=$1
  edam:
    description: Identifier of a COSMIC database entry.
    name: COSMIC
    obsolete: false
    prefix: '3264'
  fairsharing:
    abbreviation: COSMIC
    description: The Catalogue of Somatic Mutations in Cancer (COSMIC) is a database
      of manually-curated somatic mutation information relating to human cancers.
      The COSMIC database combines manually-curated data and genome-wide screen data.
    id: '2204'
    name: Catalogue of Somatic Mutations in Cancer
    prefix: FAIRsharing.s5zmbp
    subjects:
    - Genetics
    - Biomedical Science
  mappings:
    biocontext: COSMIC
    cellosaurus: Cosmic
    edam: '3264'
    fairsharing: FAIRsharing.s5zmbp
    miriam: cosmic
    n2t: cosmic
  miriam:
    deprecated: false
    description: COSMIC is a comprehensive global resource for information on somatic
      mutations in human cancer, combining curation of the scientific literature with
      tumor resequencing data from the Cancer Genome Project at the Sanger Institute,
      U.K. This collection references genes.
    homepage: http://cancer.sanger.ac.uk/cosmic/
    id: '00000601'
    name: COSMIC Gene
    namespaceEmbeddedInLui: false
    pattern: ^[A-Z0-9]+$
    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
cosmic.cell:
  cellosaurus:
    category: Cell line databases/resources
    homepage: https://cancer.sanger.ac.uk/cell_lines
    name: COSMIC Cell lines Project
    prefix: Cosmic-CLP
    uri_format: https://cancer.sanger.ac.uk/cell_lines/sample/overview?id=$1
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: COSMIC, the Catalogue Of Somatic Mutations In Cancer, is the world's
    largest and most comprehensive resource for exploring the impact of somatic mutations
    in human cancer
  example: '906801'
  homepage: https://cancer.sanger.ac.uk/cell_lines/
  mappings:
    cellosaurus: Cosmic-CLP
  name: COSMIC Cell Lines
  pattern: ^\d+$
  uri_format: https://cancer.sanger.ac.uk/cell_lines/sample/overview?id=$1
covid19:
  aberowl:
    description: The COVID-19 Surveillance Ontology is an application ontology used
      to support SARS-CoV-2 (severe acute respiratory syndrome coronavirus 2) surveillance
      in primary care. The ontology facilitates monitoring of COVID-19 cases and related
      respiratory conditions using data from multiple brands of computerised medical
      record systems.
    download_owl: http://aber-owl.net/media/ontologies/COVID19/3/covid19.owl
    homepage: https://orchid.phc.ox.ac.uk/index.php/cov-19/
    name: COVID-19 Surveillance Ontology
    prefix: COVID19
    version: V1.0
  bioportal:
    contact:
      email: dylan.mcgagh@magd.ox.ac.uk
      name: Dylan McGagh
    description: The COVID-19 Surveillance Ontology is an application ontology used
      to support SARS-CoV-2 (severe acute respiratory syndrome coronavirus 2) surveillance
      in primary care. The ontology facilitates monitoring of COVID-19 cases and related
      respiratory conditions using data from multiple brands of computerised medical
      record systems.
    homepage: https://orchid.phc.ox.ac.uk/index.php/cov-19/
    name: COVID-19 Surveillance Ontology
    prefix: COVID19
    publication: https://publichealth.jmir.org/2020/4/e21434/
    version: V1.0
  mappings:
    aberowl: COVID19
    bioportal: COVID19
    miriam: covid19
  miriam:
    deprecated: false
    description: Curated contextual database gathering samples related to SARS-CoV-2
      virus and covid-19 disease.
    homepage: https://covid19.sfb.uit.no
    id: 00000789
    name: SARS-CoV-2
    namespaceEmbeddedInLui: false
    pattern: ^\w+_COVID19_[-\w]+$
    prefix: covid19
    sampleId: SFB_COVID19_MW286762
    uri_format: https://covid19.sfb.uit.no/api/records/$1
covoc:
  contact:
    email: zmp@ebi.ac.uk
    github: zoependlington
    name: "Zo\xEB May Pendlington"
    orcid: 0000-0002-4071-8397
  example: '0010034'
  homepage: https://github.com/EBISPOT/covoc
  mappings:
    ols: covoc
  ols:
    description: The COVID-19 Vocabulary (COVoc) is an ontology containing terms related
      to the research of the COVID-19 pandemic. This includes host organisms, pathogenicity,
      gene and gene products, barrier gestures, treatments and more.
    download: https://github.com/EBISPOT/covoc/releases/download/current/covoc.owl
    homepage: https://github.com/EBISPOT/covoc
    name: CoVoc Coronavirus Vocabulary
    prefix: covoc
    version: '2020-08-28'
    version.iri: http://purl.obolibrary.org/obo/covoc/releases/2020-08-28/covoc.owl
  pattern: ^\d{7}$
  repository: https://github.com/EBISPOT/covoc
  uri_format: http://purl.obolibrary.org/obo/COVOC_$1
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
cpc:
  biocontext:
    is_identifiers: true
    is_obo: false
    prefix: CPC
    uri_format: http://identifiers.org/cpc/$1
  fairsharing:
    abbreviation: CPC
    description: The Climate Prediction Center (CPC) produces operational predictions
      of climate variability, real-time monitoring of climate and the required data
      bases, and assessments of the origins of major climate anomalies. These cover
      time scales from a week to seasons, extending into the future as far as technically
      feasible, and cover the land, the ocean, and the atmosphere, extending into
      the stratosphere.
    id: '2998'
    name: Climate Prediction Center
    prefix: FAIRsharing.e08886
    subjects:
    - Hydrogeology
    - Geography
    - Meteorology
    - Geodesy
    - Earth Science
    - Atmospheric Science
  mappings:
    biocontext: CPC
    fairsharing: FAIRsharing.e08886
    miriam: cpc
    n2t: cpc
  miriam:
    deprecated: false
    description: The Cooperative Patent Classification (CPC) is a patent classification
      system, developed jointly by the European Patent Office (EPO) and the United
      States Patent and Trademark Office (USPTO). It is based on the previous European
      classification system (ECLA), which itself was a version of the International
      Patent Classification (IPC) system. The CPC patent classification system has
      been used by EPO and USPTO since 1st January, 2013.
    homepage: https://worldwide.espacenet.com/classification
    id: 00000539
    name: Cooperative Patent Classification
    namespaceEmbeddedInLui: false
    pattern: ^([A-H,Y]|[A-H, Y]\d{2}|[A-H, Y]\d{2}[A-Z]|[A-H, Y]\d{2}[A-Z]\d{1,3}|[A-H,
      Y]\d{2}[A-Z]\d{1,3}(\/)?\d{2,})$
    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
cpga:
  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
    publication: https://planteome.org/pub
    version: unknown
  deprecated: true
  description: A structured controlled vocabulary for the anatomy of Graminae. Please
    note that this ontology has now been superseded by the Plant Ontology.
  mappings:
    biocontext: gro.cpga
    bioportal: GRO-CPGA
    obofoundry: gro
  obofoundry:
    contact: po-discuss@plantontology.org
    contact.label: Plant Ontology Administrators
    deprecated: true
    homepage: http://www.gramene.org/plant_ontology/
    name: Cereal Plant Gross Anatomy
    prefix: gro
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: null
    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\xAE, refers\
    \ to a medical code set created and maintained by the American Medical Association\
    \ \u2014 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\xAE codes. [Description taken from this site](https://www.aapc.com/codes/cpt-codes-range/)]"
  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.
    id: '198'
    name: Current Procedural Terminology
    prefix: FAIRsharing.wpxab1
    publications:
    - doi: 10.1136/neurintsurg-2014-011156
      pubmed_id: 24589819
      title: Current procedural terminology; a primer.
    - doi: 10.1016/j.jacr.2007.10.004
      pubmed_id: 18359442
      title: 'CPT: an open system that describes all that you do.'
    subjects:
    - Medicine
    - Health Science
    - Biomedical Science
  github_request_issue: 357
  homepage: https://www.aapc.com
  mappings:
    aberowl: CPT
    biolink: CPT
    bioportal: CPT
    fairsharing: FAIRsharing.wpxab1
  name: Current Procedural Terminology
  pattern: ^\d+$
  publications:
  - 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
  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
credit:
  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\u2019s specific\
    \ contribution to the scholarly output."
  example: Software
  homepage: https://casrai.org/credit/
  name: CASRAI Contributor Roles Taxonomy
crisprdb:
  biocontext:
    is_identifiers: true
    is_obo: false
    prefix: CRISPRDB
    uri_format: http://identifiers.org/crisprdb/$1
  fairsharing:
    abbreviation: CRISPRdb
    description: CRISPRdb acts as a gateway to a publicly accessible database and
      software. It enables the easy detection of CRISPR sequences in locally-produced
      data and the consultation of CRISPR sequence data present in the database. It
      also gives information on the presence of CRISPR-associated (cas) genes when
      they have been annotated as such.
    id: '2384'
    name: CRISPRdb
    prefix: FAIRsharing.7sfedh
    subjects:
    - Life Science
  mappings:
    biocontext: CRISPRDB
    fairsharing: FAIRsharing.7sfedh
    miriam: crisprdb
    n2t: crisprdb
  miriam:
    deprecated: false
    description: Repeated CRISPR ("clustered regularly interspaced short palindromic
      repeats") elements found in archaebacteria and eubacteria are believed to defend
      against viral infection, potentially targeting invading DNA for degradation.
      CRISPRdb is a database that stores information on CRISPRs that are automatically
      extracted from newly released genome sequence data.
    homepage: http://crispr.i2bc.paris-saclay.fr/
    id: '00000626'
    name: CRISPRdb
    namespaceEmbeddedInLui: false
    pattern: ^[0-9]+$
    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
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:
    is_identifiers: false
    is_obo: true
    prefix: CRO
    uri_format: http://purl.obolibrary.org/obo/CRO_$1
  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
    publication: 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
  mappings:
    aberowl: CRO
    biocontext: CRO
    bioportal: CRO
    obofoundry: cro
    ols: cro
    ontobee: CRO
  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.
    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: http://purl.obolibrary.org/obo/cro.owl
    homepage: https://github.com/data2health/contributor-role-ontology
    name: Contributor Role Ontology
    prefix: cro
    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}$
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/$1
cryoem:
  aberowl:
    description: Ontology that describes data types and image processing operations
      in Cryo Electron Microscopy of Single Particles
    download_owl: http://aber-owl.net/media/ontologies/CRYOEM/4/cryoem.owl
    homepage: http://scipion.i2pc.es/ontology/cryoem
    name: Cryo Electron Microscopy
    prefix: CRYOEM
    version: '2021-03-09'
  bioportal:
    contact:
      email: coss@cnb.csic.es
      name: Carlos Oscar Sorzano
    description: Ontology that describes data types and image processing operations
      in Cryo Electron Microscopy of Single Particles
    homepage: http://scipion.i2pc.es/ontology/cryoem
    name: Cryo Electron Microscopy
    prefix: CRYOEM
    version: '2021-03-09'
  example: '0000052'
  fairsharing:
    abbreviation: CryoEM
    description: The CryoEM Ontology for describing objects and workflows in Single
      Particle Analysis by Cryo Electron Microscopy.
    id: '1415'
    name: CryoEM Ontology
    prefix: FAIRsharing.q47I0t
    publications: []
    subjects:
    - Structural Biology
  mappings:
    aberowl: CRYOEM
    bioportal: CRYOEM
    fairsharing: FAIRsharing.q47I0t
    ols: cryoem
  ols:
    contact: isanchez@cnb.csic.es
    description: Ontology that describes data types and image processing operations
      in Cryo Electron Microscopy of Single Particles
    download: http://scipion.i2pc.es/ontology/cryoem.owl
    homepage: http://scipion.i2pc.es/ontology/cryoem
    name: Cryo Electron Microscopy ontology
    prefix: cryoem
    version: '2021-03-09'
    version.iri: http://scipion.i2pc.es/ontology/cryoem/releases/2021-03-09/cryoem.owl
  pattern: ^\d{7}$
  uri_format: http://scipion.i2pc.es/ontology/CRYOEM_$1
cryptodb:
  biocontext:
    is_identifiers: true
    is_obo: false
    prefix: CRYPTODB
    uri_format: http://identifiers.org/cryptodb/$1
  fairsharing:
    abbreviation: CryptoDB
    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.
    id: '1878'
    name: CryptoDB
    prefix: FAIRsharing.t3nprm
    subjects:
    - Functional Genomics
    - Genomics
    - Parasitology
  mappings:
    biocontext: CRYPTODB
    fairsharing: FAIRsharing.t3nprm
    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/$1
  prefixcommons:
    description: CryptoDB is an integrated genomic and functional genomic database
      for the parasite Cryptosporidium. CryptoDB integrates whole genome sequence
      and annotation along with experimental data and environmental isolate sequences
      provided by community researchers, it also includes supplemental bioinformatics
      analyses and a web interface for data-mining.
    example: cgd7_230
    homepage: http://cryptodb.org/cryptodb/
    keywords:
    - genome
    name: Cryptosporidum Genomics Resource
    pattern: ^\w+$
    prefix: cryptodb
    pubmed_ids:
    - '16381902'
    uri_format: http://cryptodb.org/cryptodb/showRecord.do?name=GeneRecordClasses.GeneRecordClass&source_id=$1
  publications:
  - doi: 10.1093/nar/gkj078
    pmc: PMC1347441
    pubmed: '16381902'
    title: 'CryptoDB: a Cryptosporidium bioinformatics resource update.'
    year: 2006
  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.
    homepage: https://cryptodb.org/cryptodb/app
    name: CryptoDB
    prefix: r3d100012265
    xrefs:
      fairsharing: FAIRsharing.t3nprm
      miriam: 00000149
      scr: '013455'
csa:
  biocontext:
    is_identifiers: true
    is_obo: false
    prefix: CSA
    uri_format: http://identifiers.org/csa/$1
  fairsharing:
    abbreviation: CSA
    description: The Catalytic Site Atlas (CSA) is a database documenting enzyme active
      sites and catalytic residues in enzymes of 3D structure. It uses a defined classification
      for catalytic residues which includes only those residues thought to be directly
      involved in some aspect of the reaction catalysed by an enzyme.
    id: '1849'
    name: Catalytic Site Atlas
    prefix: FAIRsharing.2ajtcf
    subjects:
    - Life Science
  mappings:
    biocontext: CSA
    fairsharing: FAIRsharing.2ajtcf
    miriam: csa
    n2t: csa
    prefixcommons: csa
  miriam:
    deprecated: false
    description: The Catalytic Site Atlas (CSA) is a database documenting enzyme active
      sites and catalytic residues in enzymes of 3D structure. It uses a defined classification
      for catalytic residues which includes only those residues thought to be directly
      involved in some aspect of the reaction catalysed by an enzyme.
    homepage: https://www.ebi.ac.uk/thornton-srv/databases/CSA/
    id: '00000144'
    name: CSA
    namespaceEmbeddedInLui: false
    pattern: ^[0-9][A-Za-z0-9]{3}$
    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=$1
  name: Catalytic Site Atlas
  prefixcommons:
    description: The Catalytic Site Atlas (CSA) is a database documenting enzyme active
      sites and catalytic residues in enzymes of 3D structure. It uses a defined classification
      for catalytic residues which includes only those residues thought to be directly
      involved in some aspect of the reaction catalysed by an enzyme.
    example: 1a05
    homepage: http://www.ebi.ac.uk/thornton-srv/databases/CSA/
    keywords:
    - enzyme
    - structure
    name: Catalytic Site Atlas
    pattern: ^[0-9][A-Za-z0-9]{3}$
    prefix: csa
    pubmed_ids:
    - '14681376'
    uri_format: http://www.ebi.ac.uk/thornton-srv/databases/cgi-bin/CSA/CSA_Site_Wrapper.pl?pdb=$1
  publications:
  - doi: 10.1093/nar/gkh028
    pmc: PMC308762
    pubmed: '14681376'
    title: 'The Catalytic Site Atlas: a resource of catalytic sites and residues identified
      in enzymes using structural data.'
    year: 2004
csd:
  fairsharing:
    abbreviation: CSD
    description: Established in 1965, the Cambridge Structural Database (CSD) is the
      a repository for small-molecule organic and metal-organic crystal 3D structures.
      Database records are automatically checked and manually curated by one of our
      expert in-house scientific editors. Every structure is enriched with chemical
      representations, as well as bibliographic, chemical and physical property information,
      adding further value to the raw structural data.
    id: '1796'
    name: The Cambridge Structural Database
    prefix: FAIRsharing.vs7865
    subjects:
    - Organic Chemistry
    - Biochemistry
    - Organic Molecular Chemistry
    - Chemistry
  mappings:
    fairsharing: FAIRsharing.vs7865
    miriam: csd
  miriam:
    deprecated: false
    description: The Cambridge Stuctural Database (CSD) is the world's most comprehensive
      collection of small-molecule crystal structures. Entries curated into the CSD
      are identified by a CSD Refcode.
    homepage: https://www.ccdc.cam.ac.uk/
    id: 00000820
    name: Cambridge Structural Database
    namespaceEmbeddedInLui: false
    pattern: ^[A-Z]{6}(\d{2})?$
    prefix: csd
    sampleId: PELNAW
    uri_format: https://www.ccdc.cam.ac.uk/services/structures?pid=csd:$1&sid=IDORG
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: Computer Retrieval of Information on Scientific Projects (CRISP)
    name: Computer Retrieval of Information on Scientific Projects Thesaurus
    prefix: CRISP
    version: 2022AA
  deprecated: true
  example: 2004-2820
  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
    hl7: 2.16.840.1.113883.6.120
  name: Computer Retrieval of Information on Science Projects Thesaurus
  synonyms:
  - CRISP
  - CRISP Thesaurus
  - CRISP Thesaurus, 2006
  - CSP2005
  uri_format: http://purl.bioontology.org/ontology/CSP/$1
cst:
  biocontext:
    is_identifiers: true
    is_obo: false
    prefix: CST
    uri_format: http://identifiers.org/cst/$1
  fairsharing:
    abbreviation: CST
    description: A small pathway portal for showcasing Cell Signaling Technology phospho-antibody
      products. Contains pathway diagrams that are clickable and link to more information
      about each protein and the commercial products that are available for that protein.
    id: '1800'
    name: Cell Signaling Technology Pathway Database
    prefix: FAIRsharing.n8pxvx
    subjects:
    - Life Science
    - Biomedical Science
  hl7:
    description: COSTART
    name: CST
    preferred_prefix: CST
    prefix: 2.16.840.1.113883.6.62
    status: Pending
  mappings:
    biocontext: CST
    fairsharing: FAIRsharing.n8pxvx
    hl7: 2.16.840.1.113883.6.62
    miriam: cst
    n2t: cst
  miriam:
    deprecated: false
    description: Cell Signaling Technology is a commercial organisation which provides
      a pathway portal to showcase their phospho-antibody products. This collection
      references pathways.
    homepage: http://www.cellsignal.com/pathways/index.html
    id: 00000429
    name: Cell Signaling Technology Pathways
    namespaceEmbeddedInLui: false
    pattern: ^[A-Za-z0-9_-]+$
    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
cst.ab:
  biocontext:
    is_identifiers: true
    is_obo: false
    prefix: CST.AB
    uri_format: http://identifiers.org/cst.ab/$1
  mappings:
    biocontext: CST.AB
    miriam: cst.ab
    n2t: cst.ab
    prefixcommons: cst
  miriam:
    deprecated: false
    description: Cell Signaling Technology is a commercial organisation which provides
      a pathway portal to showcase their phospho-antibody products. This collection
      references antibody products.
    homepage: http://www.cellsignal.com/catalog/index.html
    id: '00000430'
    name: Cell Signaling Technology Antibody
    namespaceEmbeddedInLui: false
    pattern: ^\d+$
    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/$1.html
  prefixcommons:
    description: A small pathway portal for showcasing Cell Signaling Technology phospho-antibody
      products.  Contains pathway diagrams that are clickable and link to more information
      about each protein and the commercial products that are available for that protein.
    example: '3762'
    homepage: http://www.cellsignal.com/
    keywords:
    - pathway
    name: Cell Signaling Technology Pathway Database
    pattern: ^\d+$
    prefix: cst
    uri_format: http://www.cellsignal.com/products/$1.html
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'
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  deprecated: true
  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
  homepage: https://evs.nci.nih.gov/ftp1/CTCAE/About.html
  mappings:
    aberowl: CTCAE
    bioportal: CTCAE
  name: Common Terminology Criteria for Adverse Events
  pattern: ^E\d+$
  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
  references:
  - https://github.com/OAE-ontology/OAE/issues/8
  - https://en.wikipedia.org/wiki/Common_Terminology_Criteria_for_Adverse_Events
  synonyms:
  - CTCAE
ctd.chemical:
  biocontext:
    is_identifiers: true
    is_obo: false
    prefix: CTD.CHEMICAL
    uri_format: http://identifiers.org/ctd.chemical/$1
  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: ctd
  provides: mesh
ctd.disease:
  biocontext:
    is_identifiers: true
    is_obo: false
    prefix: CTD.DISEASE
    uri_format: http://identifiers.org/ctd.disease/$1
  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: ctd
  provides: mesh
ctd.gene:
  biocontext:
    is_identifiers: true
    is_obo: false
    prefix: CTD.GENE
    uri_format: http://identifiers.org/ctd.gene/$1
  biolink:
    is_identifiers: false
    is_obo: false
    prefix: CTD.GENE
    uri_format: http://ctdbase.org/detail.go?type=gene&acc=$1
  mappings:
    biocontext: CTD.GENE
    biolink: CTD.GENE
    miriam: ctd.gene
    n2t: ctd.gene
  miriam:
    deprecated: false
    description: The Comparative Toxicogenomics Database (CTD) presents scientifically
      reviewed and curated information on chemicals, relevant genes and proteins,
      and their interactions in vertebrates and invertebrates. It integrates sequence,
      reference, species, microarray, and general toxicology information to provide
      a unique centralized resource for toxicogenomic research. The database also
      provides visualization capabilities that enable cross-species comparisons of
      gene and protein sequences.
    homepage: http://ctdbase.org/
    id: '00000100'
    name: CTD Gene
    namespaceEmbeddedInLui: false
    pattern: ^\d+$
    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: ctd
  provides: ncbigene
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:
    is_identifiers: false
    is_obo: true
    prefix: CTENO
    uri_format: http://purl.obolibrary.org/obo/CTENO_$1
  bioportal:
    name: Ctenophore Ontology
    prefix: CTENO
  download_obo: https://raw.githubusercontent.com/obophenotype/ctenophore-ontology/master/cteno.obo
  example: '0000047'
  fairsharing:
    abbreviation: CTENO
    description: An anatomical and developmental ontology for ctenophores (Comb Jellies).
      Please note that, while available, this ontology has not been updated since
      2016.
    id: '529'
    name: Ctenophore Ontology
    prefix: FAIRsharing.mgxgza
    publications: []
    subjects:
    - Anatomy
    - Developmental Biology
  mappings:
    aberowl: CTENO
    biocontext: CTENO
    bioportal: CTENO
    fairsharing: FAIRsharing.mgxgza
    obofoundry: cteno
    ols: cteno
    ontobee: CTENO
  obofoundry:
    contact: cjmungall@lbl.gov
    contact.github: cmungall
    contact.label: Chris Mungall
    contact.orcid: 0000-0002-6601-2165
    depends_on:
    - ro
    - uberon
    deprecated: false
    description: An anatomical and developmental ontology for ctenophores (Comb Jellies)
    download.owl: http://purl.obolibrary.org/obo/cteno.owl
    homepage: https://github.com/obophenotype/ctenophore-ontology
    license: CC BY 3.0
    license.url: http://creativecommons.org/licenses/by/3.0/
    name: Ctenophore Ontology
    preferredPrefix: CTENO
    prefix: cteno
    repository: https://github.com/obophenotype/ctenophore-ontology
  ols:
    description: An anatomical and developmental ontology for ctenophores (Comb Jellies)
    download: http://purl.obolibrary.org/obo/cteno.owl
    homepage: https://github.com/obophenotype/ctenophore-ontology
    name: Ctenophore Ontology
    prefix: cteno
    version: '2016-10-19'
    version.iri: http://purl.obolibrary.org/obo/cteno/releases/2016-10-19/cteno.owl
  ontobee:
    library: Library
    name: Ctenophore Ontology
    prefix: CTENO
  pattern: ^\d{7}$
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: Dr. 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\u2019s 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\u2013Peking 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
    description: The Clinical Trials Ontology (CTO) is also known as the Clinical
      Trial Ontology-Neurodegenerative Diseases (CTO-NDD), and describes clinical
      trials in the field of neurodegeneration. This resource has been created for
      use in the IMI-funded AETIONOMY project (www.aetionomy.org).
    id: '421'
    name: Clinical Trials Ontology
    prefix: FAIRsharing.qp211a
    publications: []
    subjects:
    - Neurobiology
    - Biomedical Science
    - Preclinical Studies
  mappings:
    aberowl: CTO
    bioportal: CTO
    fairsharing: FAIRsharing.qp211a
    obofoundry: cto
    ols: cto
    ontobee: CTO
  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.
    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}$
cubedb:
  biocontext:
    is_identifiers: true
    is_obo: false
    prefix: CUBEDB
    uri_format: http://identifiers.org/cubedb/$1
  comment: website down as of 2021-10-04
  deprecated: true
  mappings:
    biocontext: CUBEDB
    miriam: cubedb
    n2t: cubedb
  miriam:
    deprecated: false
    description: Cube-DB is a database of pre-evaluated results for detection of functional
      divergence in human/vertebrate protein families. It analyzes comparable taxonomical
      samples for all paralogues under consideration, storing functional specialisation
      at the level of residues. The data are presented as a table of per-residue scores,
      and mapped onto related structures where available.
    homepage: http://epsf.bmad.bii.a-star.edu.sg/cube/db/html/home.html
    id: 00000397
    name: Cube db
    namespaceEmbeddedInLui: false
    pattern: ^[A-Za-z_0-9]+$
    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/
cvdo:
  aberowl:
    description: An ontology to describe entities related to cardiovascular diseases
    download_owl: http://aber-owl.net/media/ontologies/CVDO/3/cvdo.owl
    homepage: https://github.com/OpenLHS/CVDO
    name: Cardiovascular Disease Ontology
    prefix: CVDO
  biocontext:
    is_identifiers: false
    is_obo: true
    prefix: CVDO
    uri_format: http://purl.obolibrary.org/obo/CVDO_$1
  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 Sant\xE9 et de la Recherche M\xE9dicale)."
    homepage: https://github.com/OpenLHS/CVDO
    name: Cardiovascular Disease Ontology
    prefix: CVDO
  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).
    id: '371'
    name: Cardiovascular Disease Ontology
    prefix: FAIRsharing.2basyz
    publications: []
    subjects:
    - Cardiology
  mappings:
    aberowl: CVDO
    biocontext: CVDO
    bioportal: CVDO
    fairsharing: FAIRsharing.2basyz
    obofoundry: cvdo
    ols: cvdo
    ontobee: CVDO
  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
    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: http://purl.obolibrary.org/obo/cvdo.owl
    homepage: https://github.com/OpenLHS/CVDO
    name: Cardiovascular Disease Ontology
    prefix: cvdo
    version: '2020-03-05'
    version.iri: http://purl.obolibrary.org/obo/2020-03-05/cvdo.owl
  ontobee:
    library: Library
    name: Cardiovascular Disease Ontology
    prefix: CVDO
  pattern: ^\d{7}$
cvx:
  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.
  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
  mappings:
    hl7: 2.16.840.1.113883.6.59
  name: Vaccine administered code set
  pattern: ^\d+$
d1id:
  biocontext:
    is_identifiers: true
    is_obo: false
    prefix: D1ID
    uri_format: http://identifiers.org/d1id/$1
  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/{$1}
  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}
dailymed:
  biocontext:
    is_identifiers: true
    is_obo: false
    prefix: DAILYMED
    uri_format: http://identifiers.org/dailymed/$1
  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=$1
  prefixcommons:
    description: DailyMed provides high quality information about marketed drugs including
      FDA labels (package inserts).
    example: 3be94523-f6d6-4b25-82b0-3e0d021594c5
    homepage: http://dailymed.nlm.nih.gov/dailymed/
    name: Dailymed
    pattern: ^[A-Za-z0-9]{8}-[A-Za-z0-9]{4}-[A-Za-z0-9]{4}-[A-Za-z0-9]{4}-[A-Za-z0-9]{12}$
    prefix: dailymed
    uri_format: http://dailymed.nlm.nih.gov/dailymed/lookup.cfm?setid=$1
dandi:
  mappings:
    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
  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.
    homepage: https://dandiarchive.org/
    name: DANDI
    prefix: r3d100013638
    synonyms:
    - DANDI Archive
    - Distributed Archives for Neurophysiology Data Integration
    xrefs:
      biodbcore: 001838
      fairsharing.legacy: '3322'
      scr: '017571'
darc:
  biocontext:
    is_identifiers: true
    is_obo: false
    prefix: DARC
    uri_format: http://identifiers.org/darc/$1
  fairsharing:
    abbreviation: DARC
    description: The Database for Aligned Ribosomal Complexes (DARC) site provides
      a resource for directly comparing the structures of available ribosomal complexes.
    id: '1566'
    name: Database of Aligned Ribosomal Complexes
    prefix: FAIRsharing.evfe2s
    subjects:
    - Life Science
  mappings:
    biocontext: DARC
    fairsharing: FAIRsharing.evfe2s
    miriam: darc
    n2t: darc
  miriam:
    deprecated: false
    description: DARC (Database of Aligned Ribosomal Complexes) stores available cryo-EM
      (electron microscopy) data and atomic coordinates of ribosomal particles from
      the PDB, which are aligned within a common coordinate system. The aligned coordinate
      system simplifies direct visualization of conformational changes in the ribosome,
      such as subunit rotation and head-swiveling, as well as direct comparison of
      bound ligands, such as antibiotics or translation factors.
    homepage: http://darcsite.genzentrum.lmu.de/darc/index.php
    id: '00000366'
    name: DARC
    namespaceEmbeddedInLui: false
    pattern: ^\d+$
    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
dashr:
  biocontext:
    is_identifiers: true
    is_obo: false
    prefix: DASHR
    uri_format: http://identifiers.org/dashr/$1
  fairsharing:
    abbreviation: DASHR
    description: Integrated annotation and sequencing-based expression data for all
      major classes of human small non-coding RNAs (sncRNAs) for both full sncRNA
      transcripts and mature sncRNA products derived from these larger RNAs.
    id: '2248'
    name: Database of small human non-coding RNAs
    prefix: FAIRsharing.ztvs34
    subjects:
    - Life Science
  mappings:
    biocontext: DASHR
    fairsharing: FAIRsharing.ztvs34
    miriam: dashr
    n2t: dashr
  miriam:
    deprecated: false
    description: DASHR reports the annotation, expression and evidence for specific
      RNA processing (cleavage specificity scores/entropy) of human sncRNA genes,
      precursor and mature sncRNA products across different human tissues and cell
      types. DASHR integrates information from multiple existing annotation resources
      for small non-coding RNAs, including microRNAs (miRNAs), Piwi-interacting (piRNAs),
      small nuclear (snRNAs), nucleolar (snoRNAs), cytoplasmic (scRNAs), transfer
      (tRNAs), tRNA fragments (tRFs), and ribosomal RNAs (rRNAs). These datasets were
      obtained from non-diseased human tissues and cell types and were generated for
      studying or profiling small non-coding RNAs. This collection references RNA
      records.
    homepage: http://lisanwanglab.org/DASHR/
    id: '00000564'
    name: DASHR
    namespaceEmbeddedInLui: false
    pattern: ^(hsa-(let|mir)-\w+(-\w+)?)|(piR-\d+)|(chr\w+.tRNA\d+-\w+)|(chr\w+.tRNA\d+-\w+-tRF\d)|((SNORD|SNORA|ACA|HBII|HBI|U)(-)?\w+)|(HY\d\+(-L\d+)?)|((LSU|SSU|5S)(-rRNA_Hsa)?(-L\d+)?)$
    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
dashr.expression:
  biocontext:
    is_identifiers: true
    is_obo: false
    prefix: DASHR.EXPRESSION
    uri_format: http://identifiers.org/dashr.expression/$1
  mappings:
    biocontext: DASHR.EXPRESSION
    miriam: dashr.expression
    n2t: dashr.expression
  miriam:
    deprecated: false
    description: DASHR reports the annotation, expression and evidence for specific
      RNA processing (cleavage specificity scores/entropy) of human sncRNA genes,
      precursor and mature sncRNA products across different human tissues and cell
      types. DASHR integrates information from multiple existing annotation resources
      for small non-coding RNAs, including microRNAs (miRNAs), Piwi-interacting (piRNAs),
      small nuclear (snRNAs), nucleolar (snoRNAs), cytoplasmic (scRNAs), transfer
      (tRNAs), tRNA fragments (tRFs), and ribosomal RNAs (rRNAs). These datasets were
      obtained from non-diseased human tissues and cell types and were generated for
      studying or profiling small non-coding RNAs. This collection references RNA
      expression.
    homepage: https://dashr1.lisanwanglab.org/show-expression-table.php?start=0
    id: '00000565'
    name: DASHR expression
    namespaceEmbeddedInLui: false
    pattern: ^(hsa-(let|mir)-\w+(-\w+)?)|(piR-\d+)|(chr\w+.tRNA\d+-\w+)|(chr\w+.tRNA\d+-\w+-tRF\d)|((SNORD|SNORA|ACA|HBII|HBI|U)(-)?\w+)|(HY\d\+(-L\d+)?)|((LSU|SSU|5S)(-rRNA_Hsa)?(-L\d+)?)$
    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
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.
    download_owl: http://aber-owl.net/media/ontologies/DATACITE/2/datacite.owl
    homepage: http://www.sparontologies.net/ontologies/datacite
    name: SPAR DataCite Ontology
    prefix: DATACITE
    version: '1.2'
  bioportal:
    contact:
      email: p.vanschayck@maastrichtuniversity.nl
      name: Paul van Schayck
    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
    name: SPAR DataCite Ontology
    prefix: DATACITE
    publication: http://dx.doi.org/10.6084/m9.figshare.2075356
    version: '1.2'
  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
    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.
    id: '3736'
    name: 'DataCite Ontology '
    prefix: FAIRsharing.c06f1e
    publications: []
    subjects:
    - Subject Agnostic
  homepage: http://www.sparontologies.net/ontologies/datacite
  mappings:
    aberowl: DATACITE
    bioportal: DATACITE
    fairsharing: FAIRsharing.c06f1e
  name: DataCite Ontology
  preferred_prefix: DataCite
  repository: https://github.com/sparontologies/datacite
  uri_format: http://purl.org/spar/datacite/$1
datanator.gene:
  mappings:
    miriam: datanator.gene
  miriam:
    deprecated: false
    description: Datanator is an integrated database of genomic and biochemical data
      designed to help investigators find data about specific molecules and reactions
      in specific organisms and specific environments for meta-analyses and mechanistic
      models. Datanator currently includes metabolite concentrations, RNA modifications
      and half-lives, protein abundances and modifications, and reaction kinetics
      integrated from several databases and numerous publications. The Datanator website
      and REST API provide tools for extracting clouds of data about specific molecules
      and reactions in specific organisms and specific environments, as well as data
      about similar molecules and reactions in taxonomically similar organisms.
    homepage: https://datanator.info/
    id: '00000720'
    name: Datanator Gene
    namespaceEmbeddedInLui: false
    pattern: ^K[0-9]+$
    prefix: datanator.gene
    sampleId: K00973
    uri_format: https://www.datanator.info/gene/$1
  part_of: datanator
datanator.metabolite:
  mappings:
    miriam: datanator.metabolite
  miriam:
    deprecated: false
    description: Datanator is an integrated database of genomic and biochemical data
      designed to help investigators find data about specific molecules and reactions
      in specific organisms and specific environments for meta-analyses and mechanistic
      models. Datanator currently includes metabolite concentrations, RNA modifications
      and half-lives, protein abundances and modifications, and reaction kinetics
      integrated from several databases and numerous publications. The Datanator website
      and REST API provide tools for extracting clouds of data about specific molecules
      and reactions in specific organisms and specific environments, as well as data
      about similar molecules and reactions in taxonomically similar organisms.
    homepage: https://datanator.info/
    id: 00000718
    name: Datanator Metabolite
    namespaceEmbeddedInLui: false
    pattern: ^[A-Z\-]+$
    prefix: datanator.metabolite
    sampleId: OUYCCCASQSFEME-MRVPVSSYSA-N
    uri_format: https://www.datanator.info/metabolite/$1
  part_of: datanator
datanator.reaction:
  mappings:
    miriam: datanator.reaction
  miriam:
    deprecated: false
    description: "\tDatanator is an integrated database of genomic and biochemical\
      \ data designed to help investigators find data about specific molecules and\
      \ reactions in specific organisms and specific environments for meta-analyses\
      \ and mechanistic models. Datanator currently includes metabolite concentrations,\
      \ RNA modifications and half-lives, protein abundances and modifications, and\
      \ reaction kinetics integrated from several databases and numerous publications.\
      \ The Datanator website and REST API provide tools for extracting clouds of\
      \ data about specific molecules and reactions in specific organisms and specific\
      \ environments, as well as data about similar molecules and reactions in taxonomically\
      \ similar organisms."
    homepage: https://icahn.mssm.edu/
    id: 00000855
    name: Datanator Reaction
    namespaceEmbeddedInLui: false
    pattern: ^.*?--%3E.*?$
    prefix: datanator.reaction
    sampleId: XLYOFNOQVPJJNP-UHFFFAOYSA-N,NBSCHQHZLSJFNQ-GASJEMHNSA-N--%3ENBIIXXVUZAFLBC-UHFFFAOYSA-N,WQZGKKKJIJFFOK-GASJEMHNSA-N
    uri_format: https://datanator.info/reaction/$1
datf:
  biocontext:
    is_identifiers: true
    is_obo: false
    prefix: DATF
    uri_format: http://identifiers.org/datf/$1
  deprecated: true
  mappings:
    biocontext: DATF
    miriam: datf
    n2t: datf
    prefixcommons: datf
  miriam:
    deprecated: false
    description: DATF contains known and predicted Arabidopsis transcription factors
      (1827 genes in 56 families) with the unique information of 1177 cloned sequences
      and many other features including 3D structure templates, EST expression information,
      transcription factor binding sites and nuclear location signals.
    homepage: http://datf.cbi.pku.edu.cn/
    id: '00000456'
    name: DATF
    namespaceEmbeddedInLui: false
    pattern: ^AT[1-5]G\d{5}(\.\d+)?$
    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=$1
  name: Database of Arabidopsis Transcription Factors
  prefixcommons:
    description: The Database of Arabidopsis Transcription Factors (DATF) collects
      all Arabidopsis transcription factors (totally 1922 Loci; 2290 Gene Models)
      and classifies them into 64 families.The Version 2 of DATF was updated at July
      2006. It is based on the Arabidopsis Sequence of TAIR http://www.pdb.org, predicted
      Nuclear Location Signals, UniGene information, as well as links to literature
      reference.
    example: AT1G08970.3
    homepage: http://datf.cbi.pku.edu.cn
    keywords:
    - regulation
    name: Database of Arabidopsis Transcription Factors
    pattern: ^AT\d[A-Z]\d+$
    prefix: datf
    uri_format: http://datf.cbi.pku.edu.cn/entry-display.php?id=$1
dbd:
  biocontext:
    is_identifiers: true
    is_obo: false
    prefix: DBD
    uri_format: http://identifiers.org/dbd/$1
  edam:
    description: Identifier of a predicted transcription factor from the DBD database.
    name: DBD
    obsolete: false
    prefix: '2716'
  mappings:
    biocontext: DBD
    edam: '2716'
    miriam: dbd
    n2t: dbd
    prefixcommons: dbd
  miriam:
    deprecated: false
    description: The DBD (transcription factor database) provides genome-wide transcription
      factor predictions for organisms across the tree of life. The prediction method
      identifies sequence-specific DNA-binding transcription factors through homology
      using profile hidden Markov models (HMMs) of domains from Pfam and SUPERFAMILY.
      It does not include basal transcription factors or chromatin-associated proteins.
    homepage: http://www.transcriptionfactor.org/
    id: '00000455'
    name: DBD
    namespaceEmbeddedInLui: false
    pattern: ^\d+$
    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:$1+cat:DBD
  name: Transcription Factor Database
  prefixcommons:
    description: DBD provides transcription factor predictions for more than 150 completely
      sequenced genomes available for browsing and download. Predictions are based
      on presence of sequence specific DNA binding domain assignments using hidden
      Markov models from the SUPERFAMILY and PFAM databases
    example: '0035306'
    homepage: http://www.transcriptionfactor.org
    keywords:
    - regulation
    - genome
    name: DBD
    pattern: ^\d+$
    prefix: dbd
    uri_format: http://dbd.mrc-lmb.cam.ac.uk/DBD/index.cgi?Search/Domain+domain:$1
dbest:
  biocontext:
    is_identifiers: true
    is_obo: false
    prefix: DBEST
    uri_format: http://identifiers.org/dbest/$1
  edam:
    description: Identifier of a dbEST database entry.
    name: dbEST
    obsolete: false
    prefix: '1105'
  fairsharing:
    abbreviation: dbEST
    description: The dbEST contains sequence data and other information on "single-pass"
      cDNA sequences, or "Expressed Sequence Tags", from a number of organisms. NCBI
      is in the process of merging EST and GSS records into the Nucleotide database,
      and the process is expected to be completed 2019. Accession.version and GI identifiers
      will not change during this process. For more information please see https://ncbiinsights.ncbi.nlm.nih.gov/2018/07/30/upcoming-changes-est-gss-databases/
    id: '1969'
    name: Expressed Sequence Tags database
    prefix: FAIRsharing.v9fya8
    subjects:
    - Bioinformatics
    - Life Science
  mappings:
    biocontext: DBEST
    edam: '1105'
    fairsharing: FAIRsharing.v9fya8
    miriam: dbest
    n2t: dbest
    ncbi: dbEST
    prefixcommons: dbest
  miriam:
    deprecated: false
    description: The dbEST contains sequence data and other information on "single-pass"
      cDNA sequences, or "Expressed Sequence Tags", from a number of organisms.
    homepage: https://www.ncbi.nlm.nih.gov/nucest
    id: 00000159
    name: dbEST
    namespaceEmbeddedInLui: false
    pattern: ^([A-Z]+)?\d+(\.\d+)?$
    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: CURATOR_REVIEW
      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: http://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/$1
  ncbi:
    example: '123456'
    homepage: https://www.ncbi.nlm.nih.gov/genbank/dbest
    name: EST database maintained at the NCBI.
    prefix: dbEST
  prefixcommons:
    description: The dbEST contains sequence data and other information on "single-pass"
      cDNA sequences, or "Expressed Sequence Tags", from a number of organisms.
    example: BP100000.1
    homepage: http://www.ncbi.nlm.nih.gov/dbEST/index.html
    keywords:
    - DNA
    name: EST database maintained at the NCBI.
    pattern: ^BP\d+(\.\d+)?$
    prefix: dbest
    uri_format: http://www.ncbi.nlm.nih.gov/nucest/$1
dbg2introns:
  biocontext:
    is_identifiers: true
    is_obo: false
    prefix: DBG2INTRONS
    uri_format: http://identifiers.org/dbg2introns/$1
  mappings:
    biocontext: DBG2INTRONS
    miriam: dbg2introns
    n2t: dbg2introns
    prefixcommons: mgiid
  miriam:
    deprecated: false
    description: The Database for Bacterial Group II Introns  provides a catalogue
      of full-length, non-redundant group II introns present in bacterial DNA sequences
      in GenBank.
    homepage: http://webapps2.ucalgary.ca/~groupii/
    id: 00000318
    name: DBG2 Introns
    namespaceEmbeddedInLui: false
    pattern: ^\w{1,2}\.(\w{1,2}\.)?[A-Za-z0-9]+$
    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=$1
  prefixcommons:
    description: Many newly sequenced bacterial group II introns are incorrectly identified
      or annotated. A major goal of this database is to be a resource in helping to
      identify and catalog group II introns in the databases.
    example: Cu.me.I1
    homepage: http://www.fp.ucalgary.ca/group2introns/
    keywords:
    - DNA
    name: Mobile group II introns database
    pattern: ^\w{1,2}\.(\w{1,2}\.)?[A-Za-z0-9]+$
    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
dbgap:
  biocontext:
    is_identifiers: true
    is_obo: false
    prefix: DBGAP
    uri_format: http://identifiers.org/dbgap/$1
  fairsharing:
    abbreviation: dbGaP
    description: The Database of Genotypes and Phenotypes (dbGaP) archives and distributes
      the results of studies that have investigated the interaction of genotype and
      phenotype. Such studies include genome-wide association studies, medical sequencing,
      molecular diagnostic assays, as well as association between genotype and non-clinical
      traits.
    id: '1996'
    name: Database of Genotypes and Phenotypes
    prefix: FAIRsharing.88v2k0
    subjects:
    - Epigenetics
    - Genetics
    - Biomedical Science
  mappings:
    biocontext: DBGAP
    fairsharing: FAIRsharing.88v2k0
    miriam: dbgap
    n2t: dbgap
  miriam:
    deprecated: false
    description: The database of Genotypes and Phenotypes (dbGaP) archives and distributes
      the results of studies that have investigated the interaction of genotype and
      phenotype.
    homepage: https://www.ncbi.nlm.nih.gov/projects/gap
    id: '00000602'
    name: dbGaP
    namespaceEmbeddedInLui: false
    pattern: ^phs[0-9]{6}(.v\d+.p\d+)?$
    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=$1
  name: Database of Genotypes and Phenotypes
dbmhc:
  appears_in:
  - cellosaurus
  cellosaurus:
    category: Cell line databases/resources
    homepage: https://www.ncbi.nlm.nih.gov/gv/mhc/
    name: dbMHC database
    prefix: dbMHC
  deprecated: true
  example: '48439'
  mappings:
    cellosaurus: dbMHC
  name: Database of human Major Histocompatibility Complex
  pattern: ^\d+$
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
  name: DBPedia Ontology
  uri_format: https://dbpedia.org/ontology/$1
dbprobe:
  biocontext:
    is_identifiers: true
    is_obo: false
    prefix: DBPROBE
    uri_format: http://identifiers.org/dbprobe/$1
  edam:
    description: Identifier of an oligonucleotide probe from the dbProbe database.
    name: dbProbe
    obsolete: false
    prefix: '2719'
  mappings:
    biocontext: DBPROBE
    edam: '2719'
    miriam: dbprobe
    n2t: dbprobe
    ncbi: dbProbe
    prefixcommons: dbprobe
  miriam:
    deprecated: false
    description: The NCBI Probe Database is a public registry of nucleic acid reagents
      designed for use in a wide variety of biomedical research applications, together
      with information on reagent distributors, probe effectiveness, and computed
      sequence similarities.
    homepage: https://www.ncbi.nlm.nih.gov/sites/entrez?db=probe
    id: '00000160'
    name: dbProbe
    namespaceEmbeddedInLui: false
    pattern: ^\d+$
    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=$1
  ncbi:
    example: '38'
    homepage: https://www.ncbi.nlm.nih.gov/sites/entrez?db=probe
    name: NCBI Probe database Public registry of nucleic acid reagents
    prefix: dbProbe
  prefixcommons:
    description: The NCBI Probe Database is a public registry of nucleic acid reagents
      designed for use in a wide variety of biomedical research applications, together
      with information on reagent distributors, probe effectiveness, and computed
      sequence similarities.
    example: '1000000'
    homepage: http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=probe
    keywords:
    - nucleotide
    name: NCBI Probe database Public registry of nucleic acid reagents
    pattern: ^\d+$
    prefix: dbprobe
    uri_format: http://www.ncbi.nlm.nih.gov/genome/probe/reports/probereport.cgi?uid=$1
dbsnp:
  biocontext:
    is_identifiers: false
    is_obo: false
    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
  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.
    id: '1972'
    name: Database of Single Nucleotide Polymorphism
    prefix: FAIRsharing.edxb58
    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
  mappings:
    biocontext: dbSNP
    cellosaurus: dbSNP
    edam: '1106'
    fairsharing: FAIRsharing.edxb58
    go: dbSNP
    hl7: 2.16.840.1.113883.6.284
    miriam: dbsnp
    n2t: dbsnp
    ncbi: dbSNP
    prefixcommons: dbsnp
    re3data: r3d100010652
    uniprot: dbSNP
  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://ccg.epfl.ch/snp2tfbs/
      name: SNP2TFBS
      uri_format: https://ccg.epfl.ch/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/$1
  ncbi:
    example: '4647'
    homepage: https://www.ncbi.nlm.nih.gov/snp
    name: Variation database maintained at the NCBI.
    prefix: dbSNP
  prefixcommons:
    description: The dbSNP database is a repository for both single base nucleotide
      subsitutions and short deletion and insertion polymorphisms.
    example: rs199422184
    homepage: http://www.ncbi.nlm.nih.gov/SNP/
    keywords:
    - genome
    name: Database of single nucleotide polymorphism
    pattern: ^rs\d+$
    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/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***'
    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'
      scr: 002338
  uniprot:
    category: Genetic variation databases
    identifier: '13'
    link_is_explicit: 'true'
    name: Database of single nucleotide polymorphism
    prefix: dbSNP
    uri_format: https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=$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
  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
  synonyms:
  - dbvar.variants
  uri_format: https://www.ncbi.nlm.nih.gov/dbvar/variants/$1
dc:
  aberowl:
    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.
    download_owl: http://aber-owl.net/media/ontologies/DC/3/dc.owl
    homepage: http://dublincore.org
    name: Dublin Core
    prefix: DC
  biocontext:
    is_identifiers: false
    is_obo: false
    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
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: Metadata terms maintained by the Dublin Core Metadata Initiative, including
    properties, vocabulary encoding schemes, syntax encoding schemes, and classes.
  example: contributor
  fairsharing:
    abbreviation: DC
    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.
    id: '1245'
    name: Dublin Core Metadata Element Set
    prefix: FAIRsharing.3nx7t
    publications: []
    subjects:
    - Life Science
    - Subject Agnostic
    - Biomedical Science
  homepage: https://www.dublincore.org/specifications/dublin-core/dcmi-terms/
  mappings:
    aberowl: DC
    biocontext: dc
    bioportal: DC
    fairsharing: FAIRsharing.3nx7t
  name: Dublin Core
  synonyms:
  - dc11
  uri_format: http://purl.org/dc/elements/1.1/$1
dc_cl:
  biocontext:
    is_identifiers: false
    is_obo: true
    prefix: DC_CL
    uri_format: http://purl.obolibrary.org/obo/DC_CL_$1
  example: '0000003'
  mappings:
    biocontext: DC_CL
    obofoundry: dc_cl
  obofoundry:
    contact: Lindsay.Cowell@utsouthwestern.edu
    contact.label: Lindsay Cowell
    contact.orcid: 0000-0003-1617-8244
    deprecated: true
    homepage: http://www.dukeontologygroup.org/Projects.html
    name: Dendritic cell
    prefix: dc_cl
  pattern: ^\d{7}$
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:
    is_identifiers: false
    is_obo: false
    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
  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
    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.
    id: '747'
    name: Data Catalog Vocabulary
    prefix: FAIRsharing.h4j3qm
    subjects:
    - Data Management
    - Subject Agnostic
  homepage: https://www.w3.org/ns/dcat
  mappings:
    aberowl: DCAT
    biocontext: dcat
    biolink: dcat
    bioportal: DCAT
    fairsharing: FAIRsharing.h4j3qm
  name: Data Catalog
  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:
    is_identifiers: false
    is_obo: false
    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.
  example: title
  fairsharing:
    abbreviation: DCTERMS
    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.
    id: '905'
    name: Dublin Core Metadata Initiative (DCMI) Metadata Terms
    prefix: FAIRsharing.9vtwjs
    publications: []
    subjects:
    - Subject Agnostic
  homepage: https://www.dublincore.org/specifications/dublin-core/dcmi-terms/
  mappings:
    aberowl: dcterms
    biocontext: dcterms
    biolink: dct
    bioportal: DCTERMS
    fairsharing: FAIRsharing.9vtwjs
  name: Dublin Core Metadata Vocabulary
  synonyms:
  - dc.terms
  - dct
  uri_format: http://purl.org/dc/terms/$1
dctypes:
  biocontext:
    is_identifiers: false
    is_obo: false
    prefix: dctypes
    uri_format: http://purl.org/dc/dcmitype/$1
  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:
    biocontext: dctypes
  name: Dublin Core Types
  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/133/ddanat.owl
    homepage: http://dictybase.org/
    name: Dictyostelium discoideum anatomy
    prefix: DDANAT
  biocontext:
    is_identifiers: false
    is_obo: true
    prefix: DDANAT
    uri_format: http://purl.obolibrary.org/obo/DDANAT_$1
  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
    publication: http://www.biomedcentral.com/1471-2164/9/130
    version: '1.19'
  example: '0000006'
  fairsharing:
    abbreviation: DDANAT
    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.'
    id: '928'
    name: Dictyostelium Anatomy Ontology
    prefix: FAIRsharing.z656ab
    publications:
    - doi: 10.1186/1471-2164-9-130
      pubmed_id: 18366659
      title: An anatomy ontology to represent biological knowledge in Dictyostelium
        discoideum.
    subjects:
    - Anatomy
    - Life Science
  go:
    homepage: http://dictybase.org/Dicty_Info/dicty_anatomy_ontology.html
    name: Dictyostelium discoideum anatomy
    prefix: DDANAT
  mappings:
    aberowl: DDANAT
    biocontext: DDANAT
    bioportal: DDANAT
    fairsharing: FAIRsharing.z656ab
    go: DDANAT
    obofoundry: ddanat
    ols: ddanat
    ontobee: DDANAT
    prefixcommons: ddanat
  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
    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 the anatomy of the slime-mold
      Dictyostelium discoideum
    download: http://purl.obolibrary.org/obo/ddanat.owl
    homepage: http://dictybase.org/
    name: Dictyostelium discoideum anatomy
    prefix: ddanat
    version: '2020-04-13'
    version.iri: http://purl.obolibrary.org/obo/ddanat/releases/2020-04-13/ddanat.owl
  ontobee:
    library: Library
    name: Dictyostelium discoideum anatomy
    prefix: DDANAT
  pattern: ^\d{7}$
  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
ddinter.drug:
  contact:
    email: oriental-cds@163.com
    github: null
    name: Dongsheng Cao
    orcid: 0000-0003-3604-3785
  contributor:
    email: null
    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
  license: CC-BY-NC-SA-4.0
  name: Curated Drug-Drug Interactions Database - Drug
  pattern: ^DDInter\d+$
  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/$1
ddinter.interaction:
  contact:
    email: oriental-cds@163.com
    github: null
    name: Dongsheng Cao
    orcid: 0000-0003-3604-3785
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: Ddinter is a comprehensive, professional, and open-access database
    specific to drug-drug interactions. it provides abundant annotations for each
    ddi association including mechanism description, risk levels, management strategies,
    alternative medications, etc. to improve clinical decision-making and patient
    safety.
  example: '1122888'
  github_request_issue: 492
  homepage: http://ddinter.scbdd.com
  license: CC-BY-NC-SA-4.0
  name: Curated Drug-Drug Interactions Database - Interaction
  pattern: ^\d+$
  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/163/ddpheno.owl
    homepage: http://dictybase.org/
    name: Dictyostelium discoideum phenotype ontology
    prefix: DDPHENO
  biocontext:
    is_identifiers: false
    is_obo: true
    prefix: DDPHENO
    uri_format: http://purl.obolibrary.org/obo/DDPHENO_$1
  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
    description: "A structured controlled vocabulary of phenotypes of the social amoeba\
      \ Dictyostelium discoideum. The Dicty Phenotype Ontology is a hierarchical controlled\
      \ vocabulary used for annotating strains with phenotypes. Terms from the Dicty\
      \ Phenotype Ontology are required when annotating phenotypes within 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 \u2018delayed aggregation\u2019 phenotype\
      \ qualifies the \u2018aggregation\u2019 (biological process) as being \u2018\
      delayed\u2019, or the \u2018decreased spore size\u2019 qualifies the \u2018\
      spore\u2019 to be of \u2018decreased size\u2019."
    id: '867'
    name: Dictyostelium Phenotype Ontology
    prefix: FAIRsharing.9c1p18
    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.'
    subjects:
    - Life Science
  mappings:
    aberowl: DDPHENO
    biocontext: DDPHENO
    bioportal: DDPHENO
    fairsharing: FAIRsharing.9c1p18
    obofoundry: ddpheno
    ols: ddpheno
    ontobee: DDPHENO
  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>.
    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: http://purl.obolibrary.org/obo/ddpheno.owl
    homepage: http://dictybase.org/
    name: Dicty Phenotype Ontology (DDPHENO)
    prefix: ddpheno
    version: '2020-06-19'
    version.iri: http://purl.obolibrary.org/obo/ddpheno/releases/2020-06-19/ddpheno.owl
  ontobee:
    library: Library
    name: Dictyostelium discoideum phenotype ontology
    prefix: DDPHENO
  pattern: ^\d{7}$
  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: 10.1387/ijdb.190226pf
    pmc: PMC7409682
    pubmed: '31840793'
    title: dictyBase and the Dicty Stock Center (version 2.0) - a progress report.
    year: 2019
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}$
  preferred_prefix: DeBiO
  uri_format: https://biopragmatics.github.io/debio/$1
decipher:
  biocontext:
    is_identifiers: false
    is_obo: true
    prefix: DECIPHER
    uri_format: http://purl.obolibrary.org/obo/DECIPHER_$1
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: CNV syndromes in the DECIPHER genomics database that are linked to
    Human Phenotype Ontology terms
  example: '1'
  fairsharing:
    abbreviation: DECIPHER
    description: DECIPHER (Database of Chromosomal Imbalance and Phenotype in Humans
      Using Ensembl Resources) is an interactive web-based resource that incorporates
      a suite of tools designed to aid the interpretation of submicroscopic chromosomal
      imbalance, inversions, and translocations.
    id: '2636'
    name: DatabasE of genomiC varIation and Phenotype in Humans using Ensembl Resources
    prefix: FAIRsharing.l8Sf5x
    subjects:
    - Life Science
    - Biomedical Science
  homepage: https://www.deciphergenomics.org/
  mappings:
    biocontext: DECIPHER
    fairsharing: FAIRsharing.l8Sf5x
  name: DECIPHER CNV Syndromes
  pattern: ^\d+$
  publications:
  - 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:
    is_identifiers: true
    is_obo: false
    prefix: DEGRADOME
    uri_format: http://identifiers.org/degradome/$1
  mappings:
    biocontext: DEGRADOME
    miriam: degradome
    n2t: degradome
  miriam:
    deprecated: false
    description: The Degradome Database contains information on the complete set of
      predicted proteases present in a a variety of mammalian species that have been
      subjected to whole genome sequencing. Each protease sequence is curated and,
      when necessary, cloned and sequenced.
    homepage: http://degradome.uniovi.es/
    id: '00000454'
    name: Degradome Database
    namespaceEmbeddedInLui: false
    pattern: ^[AMCST][0-9x][0-9]$
    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
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
    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.
    id: '3733'
    name: Discourse Elements Ontology
    prefix: FAIRsharing.39fd58
    publications:
    - doi: https://doi.org/10.3233/SW-150177
      pubmed_id: null
      title: The Document Components Ontology (DoCO)
    subjects:
    - Subject Agnostic
  homepage: http://www.sparontologies.net/ontologies/deo
  mappings:
    fairsharing: FAIRsharing.39fd58
  name: Discourse Elements Ontology
  preferred_prefix: DEO
  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/$1
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: Cell lines used in the Dependency Map (DepMap). Highly related to CCLE
    Cells.
  example: ACH-000001
  homepage: https://depmap.org/portal
  mappings:
    cellosaurus: DepMap
  name: DepMap Cell Lines
  pattern: ^ACH-\d+$
  uri_format: https://depmap.org/portal/cell_line/$1
depod:
  biocontext:
    is_identifiers: true
    is_obo: false
    prefix: DEPOD
    uri_format: http://identifiers.org/depod/$1
  fairsharing:
    abbreviation: DEPOD
    description: DEPOD - the human DEPhOsphorylation Database is a manually curated
      database collecting human active and inactive phosphatases, their experimentally
      verified protein and non-protein substrates, and dephosphorylation site information,
      and pathways in which they are involved. It also provides links to popular kinase
      databases and protein-protein interaction databases for these phosphatases and
      substrates.
    id: '2178'
    name: The human DEPhOsphorylation Database
    prefix: FAIRsharing.q9j2e3
    subjects:
    - Life Science
  mappings:
    biocontext: DEPOD
    fairsharing: FAIRsharing.q9j2e3
    miriam: depod
    n2t: depod
    re3data: r3d100011936
    uniprot: DEPOD
  miriam:
    deprecated: false
    description: The human DEPhOsphorylation Database (DEPOD) contains information
      on known human active phosphatases and their experimentally verified protein
      and nonprotein substrates. Reliability scores are provided for dephosphorylation
      interactions, according to the type of assay used, as well as the number of
      laboratories that have confirmed such interaction. Phosphatase and substrate
      entries are listed along with the dephosphorylation site, bioassay type, and
      original literature, and contain links to other resources.
    homepage: http://www.depod.bioss.uni-freiburg.de
    id: 00000428
    name: DEPOD
    namespaceEmbeddedInLui: false
    pattern: ^[A-Z0-9]+$
    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
  provides: hgnc.symbol
  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.
    homepage: http://depod.bioss.uni-freiburg.de/
    name: DEPOD
    prefix: r3d100011936
    synonyms:
    - DEPhOsphorylation Database
    xrefs:
      fairsharing: FAIRsharing.q9j2e3
      miriam: 00000428
  uniprot:
    category: PTM databases
    identifier: '190'
    link_is_explicit: 'true'
    name: DEPOD human dephosphorylation database
    prefix: DEPOD
    uri_format: http://depod.bioss.uni-freiburg.de/showp.php?name=$1
dermo:
  aberowl:
    description: Ontology of human dermatologic disease
    download_obo: http://aber-owl.net/media/ontologies/DERMO/10/dermo.obo
    name: Human Dermatological Disease Ontology
    prefix: DERMO
    version: '1.19'
  bioportal:
    contact:
      email: pns12@cam.ac.uk
      name: Paul Schofield
    description: Ontology of human dermatologic disease
    name: Human Dermatological Disease Ontology
    prefix: DERMO
    version: '1.19'
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: DermO is an ontology with broad coverage of the domain of dermatologic
    disease and we demonstrate here its utility for text mining and investigation
    of phenotypic relationships between dermatologic disorders
  example: '0000000'
  fairsharing:
    abbreviation: DERMO
    description: Ontology of human dermatologic disease
    id: '808'
    name: Human Dermatological Disease Ontology
    prefix: FAIRsharing.k008w7
    publications: []
    subjects: []
  homepage: https://jbiomedsem.biomedcentral.com/articles/10.1186/s13326-016-0085-x
  mappings:
    aberowl: DERMO
    bioportal: DERMO
    fairsharing: FAIRsharing.k008w7
  name: Human Dermatological Disease Ontology
  pattern: ^\d{7}$
  uri_format: http://purl.obolibrary.org/obo/DERMO_$1
dev.ga4ghdos:
  biocontext:
    is_identifiers: true
    is_obo: false
    prefix: DEV.GA4GHDOS
    uri_format: http://identifiers.org/dev.ga4ghdos/$1
  mappings:
    biocontext: DEV.GA4GHDOS
    miriam: dev.ga4ghdos
    n2t: dev.ga4ghdos
  miriam:
    deprecated: false
    description: Assists in resolving data across cloud resources.
    homepage: http://github.com/ga4gh/data-object-service-schemas
    id: '00000656'
    name: Development Data Object Service
    namespaceEmbeddedInLui: false
    pattern: ^[a-zA-Z0-9\-:#\.]+$
    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
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
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
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
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
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
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
dgrc:
  cellosaurus:
    category: Cell line collections
    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=$1
  example: '215'
  mappings:
    cellosaurus: DGRC
  pattern: ^\d+$
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/
  name: Developing Human Brain Atlas
  pattern: ^\d+$
  preferred_prefix: DHBA
  uri_format: https://biopragmatics.github.io/providers/dhba/$1
dicom:
  bioportal:
    contact:
      email: dclunie@dclunie.com
      name: David Clunie
    description: DICOM Controlled Terminology (PS3.16 2022c Annex D)
    homepage: http://dicom.nema.org/medical/dicom/current/output/chtml/part16/chapter_D.html
    name: DICOM Controlled Terminology
    prefix: DCM
    version: 2022c_20220720
  example: '109082'
  fairsharing:
    abbreviation: DICOM
    description: "DICOM \u2014 Digital Imaging and Communications in Medicine \u2014\
      \ 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 \u201Cchanged the face of clinical medicine\u201D. From the emergency\
      \ department, to cardiac stress testing, to breast cancer detection, DICOM is\
      \ the standard that makes medical imaging work \u2014 for doctors and for patients."
    id: '84'
    name: Digital Imaging and COmmunications in Medicine
    prefix: FAIRsharing.b7z8by
    subjects:
    - Anatomy
    - Medicine
    - Biomedical Science
  mappings:
    bioportal: DCM
    fairsharing: FAIRsharing.b7z8by
    hl7: DCM
    ols: dicom
  ols:
    contact: dclunie@dclunie.com
    description: DICOM Controlled Terminology
    download: 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: 2021e_20211122
  pattern: ^\d+$
  uri_format: http://dicom.nema.org/resources/ontology/DCM/$1
dictybase:
  biocontext:
    is_identifiers: false
    is_obo: false
    prefix: dictyBase
    uri_format: http://dictybase.org/gene/$1
  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.
    id: '2293'
    name: dictyBase
    prefix: FAIRsharing.4shj9c
    subjects:
    - Anatomy
    - Life Science
    - Comparative Genomics
  go:
    homepage: http://dictybase.org
    name: dictyBase
    prefix: dictyBase
    synonyms:
    - DDB
    - DictyBase
    uri_format: http://dictybase.org/gene/$1
  mappings:
    biocontext: dictyBase
    fairsharing: FAIRsharing.4shj9c
    go: dictyBase
    ncbi: dictyBase
    prefixcommons: dictybase
    re3data: r3d100010586
    uniprot: dictyBase
  name: dictyBase
  ncbi:
    example: DDB0191090
    homepage: http://dictybase.org/
    name: Dictyostelium genome database
    prefix: dictyBase
  prefixcommons:
    description: Genome information, literature and experimental resources for Dictyostelium
      discoideum
    example: DBS0237308
    homepage: http://dictybase.org/
    keywords:
    - genome
    name: Dictyostelium discoideum online informatics resource
    pattern: ^DBS\d{7}$
    prefix: dictybase
  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.
    homepage: http://dictybase.org/
    name: dictybase
    prefix: r3d100010586
    synonyms:
    - Dictyostelium discoideum
    xrefs:
      fairsharing: FAIRsharing.4shj9c
      miriam: '00100367'
      nif: 0000-02751
      omics: 03158
      scr: '006643'
  synonyms:
  - dictyBase
  uniprot:
    category: Organism-specific databases
    comment: Replacement for DictyBase
    identifier: '15'
    link_is_explicit: 'true'
    name: Dictyostelium discoideum online informatics resource
    prefix: dictyBase
    uri_format: http://dictybase.org/db/cgi-bin/gene_page.pl?primary_id=$1
dictybase.est:
  biocontext:
    is_identifiers: true
    is_obo: false
    prefix: DICTYBASE.EST
    uri_format: http://identifiers.org/dictybase.est/$1
  mappings:
    biocontext: DICTYBASE.EST
    miriam: dictybase.est
    n2t: dictybase.est
  miriam:
    deprecated: false
    description: The dictyBase database provides data on the model organism Dictyostelium
      discoideum and related species. It contains the complete genome sequence, ESTs,
      gene models and functional annotations. This collection references expressed
      sequence tag (EST) information.
    homepage: http://dictybase.org/
    id: '00000330'
    name: Dictybase EST
    namespaceEmbeddedInLui: false
    pattern: ^DDB\d+$
    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: dictybase
dictybase.gene:
  biocontext:
    is_identifiers: true
    is_obo: false
    prefix: DICTYBASE.GENE
    uri_format: http://identifiers.org/dictybase.gene/$1
  mappings:
    biocontext: DICTYBASE.GENE
    miriam: dictybase.gene
    n2t: dictybase.gene
  miriam:
    deprecated: false
    description: The dictyBase database provides data on the model organism Dictyostelium
      discoideum and related species. It contains the complete genome sequence, ESTs,
      gene models and functional annotations. This collection references gene information.
    homepage: http://dictybase.org/
    id: 00000286
    name: Dictybase Gene
    namespaceEmbeddedInLui: false
    pattern: ^DDB_G\d+$
    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/$1
  part_of: dictybase
did:
  banana: did
  mappings:
    miriam: did
    n2t: did
  miriam:
    deprecated: false
    description: DIDs are an effort by the W3C Credentials Community Group and the
      wider Internet identity community to define identifiers that can be registered,
      updated, resolved, and revoked without any dependency on a central authority
      or intermediary.
    homepage: https://w3c-ccg.github.io/did-spec/
    id: 00000691
    name: Decentralized Identifiers (DIDs)
    namespaceEmbeddedInLui: true
    pattern: ^did:[a-z0-9]+:[A-Za-z0-9.\-:]+$
    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:$1
  name: Decentralized Identifier
  pattern: ^[a-z0-9]+:[A-Za-z0-9.\-:]+$
dideo:
  aberowl:
    description: The Potential Drug-drug Interaction and Potential Drug-drug Interaction
      Evidence Ontology
    download_owl: http://aber-owl.net/media/ontologies/DIDEO/53/dideo.owl
    homepage: https://github.com/DIDEO/DIDEO
    name: Drug-drug Interaction and Drug-drug Interaction Evidence Ontology
    prefix: DIDEO
  biocontext:
    is_identifiers: false
    is_obo: true
    prefix: DIDEO
    uri_format: http://purl.obolibrary.org/obo/DIDEO_$1
  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
    publication: https://dikb.org
    version: release version 2017-11-17
  example: 00000180
  fairsharing:
    abbreviation: DIDEO
    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.'
    id: '295'
    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
      pubmed_id: null
      title: 'Conceptual models of drug-drug interactions : A summary of recent efforts'
    - 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.
    - doi: null
      pubmed_id: 29295242
      title: Formalizing Evidence Type Definitions for Drug-Drug Interaction Studies
        to Improve Evidence Base Curation.
    subjects: []
  mappings:
    aberowl: DIDEO
    biocontext: DIDEO
    bioportal: DIDEO
    fairsharing: FAIRsharing.9y8f0n
    obofoundry: dideo
    ols: dideo
    ontobee: DIDEO
  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
    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: 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
    version: '2022-06-14'
    version.iri: http://purl.obolibrary.org/obo/dideo/release/2021-06-11/dideo.owl
  ontobee:
    library: Library
    name: Drug-drug Interaction and Drug-drug Interaction Evidence Ontology
    prefix: DIDEO
  pattern: ^\d{8}$
  publications:
  - 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: null
  - doi: null
    pmc: PMC5765984
    pubmed: '29295242'
    title: Formalizing Evidence Type Definitions for Drug-Drug Interaction Studies
      to Improve Evidence Base Curation.
    year: 2017
  - doi: 10.1186/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: 10.1016/j.knosys.2016.10.006
    pmc: null
    pubmed: null
    title: 'Conceptual models of drug-drug interactions : A summary of recent efforts'
    year: null
  - doi: 10.1186/s13326-018-0183-z
    pmc: null
    pubmed: '29743102'
    title: Extending the DIDEO ontology to include entities from the natural product
      drug interaction domain of discourse.
    year: null
  - doi: null
    pmc: null
    pubmed: '29295242'
    title: Formalizing Evidence Type Definitions for Drug-Drug Interaction Studies
      to Improve Evidence Base Curation.
    year: null
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:
    is_identifiers: false
    is_obo: true
    prefix: DINTO
    uri_format: http://purl.obolibrary.org/obo/DINTO_$1
  bioportal:
    name: The Drug-Drug Interactions Ontology
    prefix: DINTO
  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.
    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\u2013Drug Interactions\
        \ and Their Mechanisms."
    repository: https://github.com/labda/DINTO
  ontobee:
    library: Library
    name: The Drug-Drug Interactions Ontology
    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:
    is_identifiers: true
    is_obo: false
    prefix: DIP
    uri_format: http://identifiers.org/dip/$1
  edam:
    description: Unique identifier of an entry from the DIP database of protein-protein
      interactions.
    name: DIP
    obsolete: false
    prefix: '2616'
  fairsharing:
    abbreviation: DIP
    description: The database of interacting protein (DIP) database stores experimentally
      determined interactions between proteins. It combines information from a variety
      of sources to create a single, consistent set of protein-protein interactions.
      The data stored within the DIP database were curated, both manually by expert
      curators and automatically using computational approaches that utilize the the
      knowledge about the protein-protein interaction networks extracted from the
      core DIP data.
    id: '2089'
    name: Database of Interacting Proteins
    prefix: FAIRsharing.qje0v8
    subjects:
    - Biology
  mappings:
    biocontext: DIP
    edam: '2616'
    fairsharing: FAIRsharing.qje0v8
    miriam: dip
    n2t: dip
    prefixcommons: dip
    uniprot: DIP
  miriam:
    deprecated: false
    description: The database of interacting protein (DIP) database stores experimentally
      determined interactions between proteins. It combines information from a variety
      of sources to create a single, consistent set of protein-protein interactions
    homepage: https://dip.doe-mbi.ucla.edu/
    id: '00000044'
    name: Database of Interacting Proteins
    namespaceEmbeddedInLui: false
    pattern: ^DIP(\:)?\-\d{1,}[ENXS]$
    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=$1
  prefixcommons:
    description: The database of interacting protein (DIP) database stores experimentally
      determined interactions between proteins. It combines information from a variety
      of sources to create a single, consistent set of protein-protein interactions
    example: DIP-743N
    homepage: http://dip.doe-mbi.ucla.edu
    keywords:
    - interaction
    - protein
    name: Database of Interacting Proteins
    pattern: ^DIP[\:\-]\d{3}[EN]$
    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
  uniprot:
    category: Protein-protein interaction databases
    identifier: '16'
    link_is_explicit: 'true'
    name: Database of interacting proteins
    prefix: DIP
    uri_format: https://dip.doe-mbi.ucla.edu/dip/Browse.cgi?ID=$1
discoverx:
  cellosaurus:
    category: Cell line collections
    homepage: https://www.discoverx.com/products-applications/cell-lines
    name: DiscoverX cell line products
    prefix: DiscoverX
    uri_format: https://www.discoverx.com/searchproduct?searchtext=$1&searchmode=exact
  example: 95-0166C6
  mappings:
    cellosaurus: 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/1/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
  example: '0000000'
  mappings:
    aberowl: DISDRIV
    bioportal: DISDRIV
    obofoundry: disdriv
    ols: disdriv
  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.
    download.owl: http://purl.obolibrary.org/obo/disdriv.owl
    homepage: http://www.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: http://purl.obolibrary.org/obo/disdriv.owl
    homepage: http://www.disease-ontology.org
    name: Disease Drivers
    prefix: disdriv
  pattern: ^\d+$
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}$
  uri_format: https://biopragmatics.github.io/providers/diseaseclass/$1
diseasesdb:
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: 'The Diseases Database is a cross-referenced index of human disease,
    medications, symptoms, signs, abnormal investigation findings etc. This site provides
    a medical textbook-like index and search portal covering areas including: internal
    medical disorders, symptoms and signs, congenital and inherited disorders, infectious
    diseases and organisms, drugs and medications, common haematology and biochemistry
    investigation abnormalities.'
  example: '1784'
  homepage: http://www.diseasesdatabase.com/
  mappings:
    wikidata: P557
  name: Diseases Database
  pattern: ^\d+$
  uri_format: https://www.diseasesdatabase.com/ddb$1.htm
  wikidata:
    database: Q213103
    prefix: P557
disprot:
  biocontext:
    is_identifiers: true
    is_obo: false
    prefix: DISPROT
    uri_format: http://identifiers.org/disprot/$1
  edam:
    description: Unique identifier for a protein from the DisProt database.
    name: Protein ID (DisProt)
    obsolete: false
    prefix: '2723'
  fairsharing:
    abbreviation: DisProt
    description: The Database of Protein Disorder (DisProt) is a curated database
      that provides information about intrinsically disordered proteins that lack
      fixed 3D structure in their putatively native states, either in their entirety
      or in part. Disordered regions are manually curated from literature. DisProt
      annotations cover both structural and functional aspects of disorder detected
      by specific experimental methods.
    id: '1904'
    name: Database of Protein Disorder
    prefix: FAIRsharing.dt9z89
    subjects:
    - Biomedical Science
  mappings:
    biocontext: DISPROT
    edam: '2723'
    fairsharing: FAIRsharing.dt9z89
    miriam: disprot
    n2t: disprot
    prefixcommons: disprot
    re3data: r3d100010561
    uniprot: DisProt
  miriam:
    deprecated: false
    description: DisProt is a database of intrinsically disordered proteins and protein
      disordered regions, manually curated from literature.
    homepage: https://disprot.org/
    id: 00000199
    name: DisProt
    namespaceEmbeddedInLui: false
    pattern: ^DP\d{5}$
    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/$1
  prefixcommons:
    description: The Database of Protein Disorder (DisProt) is a curated database
      that provides information about proteins that lack fixed 3D structure in their
      putatively native states, either in their entirety or in part.
    example: DP00001
    homepage: http://www.disprot.org/
    keywords:
    - protein
    - structure
    name: Database of protein disorder
    pattern: ^DP\d{5}$
    prefix: disprot
    pubmed_ids:
    - '17145717'
    uri_format: http://www.disprot.org/protein.php?id=$1
  publications:
  - doi: 10.1093/nar/gkl893
    pmc: PMC1751543
    pubmed: '17145717'
    title: 'DisProt: the Database of Disordered Proteins.'
    year: 2006
  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.'
    homepage: http://www.disprot.org/
    name: DisProt
    prefix: r3d100010561
    synonyms:
    - Database of Protein Disorder
    xrefs:
      nif: 0000-02754
      scr: 007097
  uniprot:
    category: Family and domain databases
    identifier: '17'
    link_is_explicit: 'true'
    name: Database of protein disorder
    prefix: DisProt
    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/$1
dlxb:
  mappings:
    miriam: dlxb
  miriam:
    deprecated: false
    description: DOULIX lab-tested standard biological parts, in this case linear
      double stranded DNA sequences.
    homepage: https://doulix.com
    id: '00000747'
    name: Linear double stranded DNA sequences
    namespaceEmbeddedInLui: false
    pattern: ^[A-Z0-9]{6,7}$
    prefix: dlxb
    sampleId: 6VDC956
    uri_format: https://doulix.com/biomodules/$1/
  part_of: dlx
  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: dlx
  uri_format: https://doulix.com/constructs/$1
dmba:
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: A controlled vocabulary to support the study of transcription in the
    developing mouse brain
  download_obo: https://raw.githubusercontent.com/obophenotype/uberon/master/source-ontologies/allen-dmba.obo
  example: '15567'
  homepage: https://developingmouse.brain-map.org/
  name: Developing Mouse Brain Atlas
  pattern: ^\d+$
  preferred_prefix: DMBA
  uri_format: https://biopragmatics.github.io/providers/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
  name: Description of a Project
  references:
  - https://en.wikipedia.org/wiki/DOAP
  repository: https://github.com/ewilderj/doap
  uri_format: http://usefulinc.com/ns/doap#$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
    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).
    id: '3728'
    name: 'Document Components Ontology '
    prefix: FAIRsharing.162003
    publications:
    - doi: 10.3233/SW-150177
      pubmed_id: null
      title: The Document Components Ontology (DoCO)
    subjects:
    - Subject Agnostic
  homepage: http://www.sparontologies.net/ontologies/doco
  mappings:
    fairsharing: FAIRsharing.162003
  name: Document Components Ontology
  preferred_prefix: DoCO
  repository: https://github.com/sparontologies/doco
  uri_format: http://purl.org/spar/doco/$1
doi:
  banana: doi
  biocontext:
    is_identifiers: false
    is_obo: false
    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://dx.doi.org
    name: Digital Object Identifier
    prefix: DOI
    uri_format: https://dx.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: 10.1101/2022.07.08.499378
  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
    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\xAE 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."
    id: '1332'
    name: Digital Object Identifier
    prefix: FAIRsharing.hFLKCn
    subjects:
    - Knowledge and Information Systems
  go:
    homepage: http://dx.doi.org/
    name: Digital Object Identifier
    prefix: DOI
    uri_format: http://dx.doi.org/$1
  mappings:
    biocontext: DOI
    biolink: doi
    cellosaurus: DOI
    edam: '1188'
    fairsharing: FAIRsharing.hFLKCn
    go: DOI
    miriam: doi
    n2t: doi
    prefixcommons: doi
  miriam:
    deprecated: false
    description: The Digital Object Identifier System is for identifying content objects
      in the digital environment.
    homepage: https://www.doi.org/
    id: 00000019
    name: DOI
    namespaceEmbeddedInLui: false
    pattern: ^(doi\:)?\d{2}\.\d{4}.*$
    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/$1
  pattern: ^10.\d{2,9}/.*$
  prefixcommons:
    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
    homepage: https://www.doi.org
    name: Digital Object Identifier
    uri_format: http://dx.doi.org/$1
  - code: dx_doi_https
    description: An alternate provider from the DOI website using HTTPS
    homepage: https://www.doi.org
    name: Digital Object Identifier
    uri_format: https://dx.doi.org/$1
  - code: doi_http
    description: An alternate provider from the DOI website using HTTP
    homepage: https://www.doi.org
    name: Digital Object Identifier
    uri_format: http://doi.org/$1
  references:
  - https://github.com/biopragmatics/bioregistry/issues/287
  - https://github.com/biopragmatics/bioregistry/pull/316
  uri_format: https://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/661/doid.owl
    homepage: http://www.disease-ontology.org
    name: Human Disease Ontology
    prefix: DOID
  biocontext:
    is_identifiers: false
    is_obo: true
    prefix: DOID
    uri_format: http://purl.obolibrary.org/obo/DOID_$1
  bioportal:
    contact:
      email: lynn.schriml@gmail.com
      name: Lynn Schriml
    description: Creating a comprehensive hierarchical controlled vocabulary for human
      disease representation.
    homepage: https://disease-ontology.org/
    name: Human Disease Ontology
    prefix: DOID
    publication: https://disease-ontology.org/community/publications
    version: releases/2021-12-15
  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
    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.
    id: '870'
    name: Disease Ontology
    prefix: FAIRsharing.8b6wfq
    publications:
    - doi: 10.1093/nar/gkr972
      pubmed_id: 22080554
      title: 'Disease Ontology: a backbone for disease semantic integration.'
    - doi: 10.1093/database/baw015
      pubmed_id: 26989148
      title: Wikidata as a semantic framework for the Gene Wiki initiative.
    - doi: 10.1093/nar/gku1011
      pubmed_id: 25348409
      title: 'Disease Ontology 2015 update: an expanded and updated database of human
        diseases for linking biomedical knowledge through disease data.'
    - doi: 10.1093/bioinformatics/btp193
      pubmed_id: 19478018
      title: 'From disease ontology to disease-ontology lite: statistical methods
        to adapt a general-purpose ontology for the test of gene-ontology associations.'
    - doi: 10.1093/nar/gkab1063
      pubmed_id: 34755882
      title: The Human Disease Ontology 2022 update.
    - doi: 10.1093/nar/gky1032
      pubmed_id: 30407550
      title: 'Human Disease Ontology 2018 update: classification, content and workflow
        expansion.'
    - doi: 10.1242/dmm.032839
      pubmed_id: 29590633
      title: 'Disease Ontology: improving and unifying disease annotations across
        species.'
    - doi: 10.1007/s00335-015-9576-9
      pubmed_id: 26093607
      title: 'The Disease Ontology: fostering interoperability between biological
        and clinical human disease-related data.'
    - doi: 10.1093/database/bav032
      pubmed_id: 25841438
      title: Generating a focused view of disease ontology cancer terms for pan-cancer
        data integration and analysis.
    - doi: 10.1186/1471-2164-10-S1-S6
      pubmed_id: 19594883
      title: Annotating the human genome with Disease Ontology.
    - doi: 10.1093/bib/bbab191
      pubmed_id: 34015823
      title: COVID-19 biomarkers and their overlap with comorbidities in a disease
        biomarker data model.
    - doi: 10.7554/eLife.52614
      pubmed_id: 32180547
      title: Wikidata as a knowledge graph for the life sciences.
    - doi: 10.1093/nar/gky1036
      pubmed_id: 30407590
      title: 'ECO, the Evidence &amp; Conclusion Ontology: community standard for
        evidence information.'
    - doi: 10.1016/j.ajhg.2015.05.020
      pubmed_id: 26119816
      title: 'The Human Phenotype Ontology: Semantic Unification of Common and Rare
        Disease.'
    subjects:
    - Life Science
    - Biomedical Science
  mappings:
    aberowl: DOID
    biocontext: DOID
    bioportal: DOID
    fairsharing: FAIRsharing.8b6wfq
    miriam: doid
    n2t: doid
    obofoundry: doid
    ols: doid
    ontobee: DOID
    prefixcommons: do
    wikidata: P699
  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/ols/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/ols/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:$1
  obofoundry:
    appears_in:
    - clo
    - scdo
    contact: lynn.schriml@gmail.com
    contact.github: lschriml
    contact.label: Lynn Schriml
    contact.orcid: 0000-0001-8910-9851
    deprecated: false
    description: An ontology for describing the classification of human diseases organized
      by etiology.
    download.obo: http://purl.obolibrary.org/obo/doid.obo
    download.owl: http://purl.obolibrary.org/obo/doid.owl
    homepage: http://www.disease-ontology.org
    license: CC0 1.0
    license.url: https://creativecommons.org/publicdomain/zero/1.0/
    name: Human Disease Ontology
    preferredPrefix: DOID
    prefix: doid
    publications:
    - id: https://www.ncbi.nlm.nih.gov/pubmed/25348409
      title: 'Disease Ontology 2015 update: an expanded and updated database of human
        diseases for linking biomedical knowledge through disease data'
    - id: https://www.ncbi.nlm.nih.gov/pubmed/34755882
      title: The Human Disease Ontology 2022 update
    repository: https://github.com/DiseaseOntology/HumanDiseaseOntology
    twitter: diseaseontology
  ols:
    description: The Disease Ontology has been developed as a standardized ontology
      for human disease with the purpose of providing the biomedical community with
      consistent, reusable and sustainable descriptions of human disease terms, phenotype
      characteristics and related medical vocabulary disease concepts.
    download: http://purl.obolibrary.org/obo/doid.owl
    name: Human Disease Ontology
    prefix: doid
    version: '2022-06-07'
    version.iri: http://purl.obolibrary.org/obo/doid/releases/2022-06-07/doid.owl
  ontobee:
    library: Foundry
    name: Human Disease Ontology
    prefix: DOID
  pattern: ^\d+$
  prefixcommons:
    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
    - human disease ontology
    uri_format: http://disease-ontology.org/term/$1
  providers:
  - code: purl
    description: Legacy PURLs found in OAE
    homepage: http://purl.org/obo/owl/
    name: Legacy PURL
    uri_format: http://purl.org/obo/owl/DOID#DOID_$1
  publications:
  - 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: 10.1186/1471-2164-10-s1-s6
    pmc: PMC2709267
    pubmed: '19594883'
    title: Annotating the human genome with Disease Ontology.
    year: 2009
  - doi: 10.1093/nar/gkr972
    pmc: PMC3245088
    pubmed: '22080554'
    title: 'Disease Ontology: a backbone for disease semantic integration.'
    year: 2011
  - 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/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/database/baw015
    pmc: PMC4795929
    pubmed: '26989148'
    title: Wikidata as a semantic framework for the Gene Wiki initiative.
    year: 2016
  - doi: 10.1242/dmm.032839
    pmc: PMC5897730
    pubmed: '29590633'
    title: 'Disease Ontology: improving and unifying disease annotations across species.'
    year: 2018
  - doi: 10.1093/nar/gky1032
    pmc: PMC6323977
    pubmed: '30407550'
    title: 'Human Disease Ontology 2018 update: classification, content and workflow
      expansion.'
    year: 2019
  - doi: 10.1093/nar/gky1036
    pmc: PMC6323956
    pubmed: '30407590'
    title: 'ECO, the Evidence & Conclusion Ontology: community standard for evidence
      information.'
    year: 2019
  - doi: 10.7554/elife.52614
    pmc: PMC7077981
    pubmed: '32180547'
    title: Wikidata as a knowledge graph for the life sciences.
    year: 2020
  - 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: 10.1093/nar/gkab1063
    pmc: PMC8728220
    pubmed: '34755882'
    title: The Human Disease Ontology 2022 update.
    year: 2022
  synonyms:
  - do
  wikidata:
    database: Q5282129
    database.homepage: http://disease-ontology.org/
    database.label: Disease Ontology
    description: identifier in the Disease Ontology database
    homepage: http://disease-ontology.org
    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
dommino:
  biocontext:
    is_identifiers: true
    is_obo: false
    prefix: DOMMINO
    uri_format: http://identifiers.org/dommino/$1
  homepage: http://korkinlab.org/dommino
  mappings:
    biocontext: DOMMINO
    miriam: dommino
    n2t: dommino
  miriam:
    deprecated: false
    description: DOMMINO is a database of macromolecular interactions that includes
      the interactions between protein domains, interdomain linkers, N- and C-terminal
      regions and protein peptides.
    homepage: http://dommino.org/
    id: '00000373'
    name: DOMMINO
    namespaceEmbeddedInLui: false
    pattern: ^[0-9][A-Za-z0-9]{3}$
    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
door:
  biocontext:
    is_identifiers: true
    is_obo: false
    prefix: DOOR
    uri_format: http://identifiers.org/door/$1
  mappings:
    biocontext: DOOR
    miriam: door
    n2t: door
    prefixcommons: door
  miriam:
    deprecated: false
    description: DOOR (Database for prOkaryotic OpeRons) contains computationally
      predicted operons of all the sequenced prokaryotic genomes. It includes operons
      for RNA genes.
    homepage: http://csbl.bmb.uga.edu/DOOR/operon.php
    id: '00000453'
    name: DOOR
    namespaceEmbeddedInLui: false
    pattern: ^\d+$
    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=$1
  name: Database for Prokaryotic Operons
  prefixcommons:
    description: DOOR (Database of prOkaryotic OpeRons) is an operon database developed
      by Computational Systems Biology Lab (CSBL) at University of Georgia. The operons
      in the database are based on prediction.
    example: '607986'
    homepage: http://csbl1.bmb.uga.edu/OperonDB/
    keywords:
    - DNA
    name: Database of prOkaryotic OpeRons
    pattern: ^\d+$
    prefix: door
    uri_format: http://csbl1.bmb.uga.edu/OperonDB/genedetail.php?id=$1
doqcs.model:
  biocontext:
    is_identifiers: true
    is_obo: false
    prefix: DOQCS.MODEL
    uri_format: http://identifiers.org/doqcs.model/$1
  mappings:
    biocontext: DOQCS.MODEL
    miriam: doqcs.model
    n2t: doqcs.model
    prefixcommons: doqcs.model
  miriam:
    deprecated: false
    description: The Database of Quantitative Cellular Signaling is a repository of
      models of signaling pathways. It includes reaction schemes, concentrations,
      rate constants, as well as annotations on the models. The database provides
      a range of search, navigation, and comparison functions. This datatype provides
      access to specific models.
    homepage: http://doqcs.ncbs.res.in/
    id: '00000134'
    name: 'Database of Quantitative Cellular Signaling: Model'
    namespaceEmbeddedInLui: false
    pattern: ^\d+$
    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=$1
  part_of: doqcs
  prefixcommons:
    description: The Database of Quantitative Cellular Signaling is a repository of
      models of signaling pathways. It includes reaction schemes, concentrations,
      rate constants, as well as annotations on the models. The database provides
      a range of search, navigation, and comparison functions. This datatype provides
      access to specific models.
    example: '57'
    homepage: http://doqcs.ncbs.res.in/
    keywords:
    - model
    name: 'Database of Quantitative Cellular Signaling: Model'
    pattern: ^\d+$
    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:
    is_identifiers: true
    is_obo: false
    prefix: DOQCS.PATHWAY
    uri_format: http://identifiers.org/doqcs.pathway/$1
  mappings:
    biocontext: DOQCS.PATHWAY
    miriam: doqcs.pathway
    n2t: doqcs.pathway
    prefixcommons: doqcs.pathway
  miriam:
    deprecated: false
    description: The Database of Quantitative Cellular Signaling is a repository of
      models of signaling pathways. It includes reaction schemes, concentrations,
      rate constants, as well as annotations on the models. The database provides
      a range of search, navigation, and comparison functions. This datatype provides
      access to pathways.
    homepage: http://doqcs.ncbs.res.in/
    id: '00000135'
    name: 'Database of Quantitative Cellular Signaling: Pathway'
    namespaceEmbeddedInLui: false
    pattern: ^\d+$
    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=$1
  part_of: doqcs
  prefixcommons:
    description: The Database of Quantitative Cellular Signaling is a repository of
      models of signaling pathways. It includes reaction schemes, concentrations,
      rate constants, as well as annotations on the models. The database provides
      a range of search, navigation, and comparison functions.
    example: '38'
    homepage: http://doqcs.ncbs.res.in/
    keywords:
    - pathway
    name: 'Database of Quantitative Cellular Signaling: Pathway'
    pattern: ^\d+$
    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
dpo:
  aberowl:
    description: An ontology of commonly encountered and/or high level Drosophila
      phenotypes.
    download_owl: http://aber-owl.net/media/ontologies/DPO/22/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.
    homepage: http://purl.obolibrary.org/obo/fbcv
    name: Drosophila Phenotype Ontology
    prefix: DPO
    version: '2022-08-11'
  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.
    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 for the description of Drosophila melanogaster phenotypes.
    download: http://purl.obolibrary.org/obo/dpo.owl
    homepage: http://purl.obolibrary.org/obo/fbcv
    name: Drosophila Phenotype Ontology (DPO)
    prefix: dpo
    version: '2022-08-11'
    version.iri: http://purl.obolibrary.org/obo/dpo/releases/2022-08-11/dpo.owl
  ontobee:
    library: Library
    name: Drosophila Phenotype Ontology
    prefix: DPO
  part_of: fbcv
  preferred_prefix: DPO
  publications:
  - doi: 10.1186/2041-1480-4-30
    pmc: PMC3816596
    pubmed: '24138933'
    title: The Drosophila phenotype ontology.
    year: 2013
  - doi: null
    pmc: null
    pubmed: '24138933'
    title: The Drosophila phenotype ontology.
    year: null
dpv:
  biocontext:
    is_identifiers: true
    is_obo: false
    prefix: DPV
    uri_format: http://identifiers.org/dpv/$1
  mappings:
    biocontext: DPV
    miriam: dpv
    n2t: dpv
  miriam:
    deprecated: false
    description: Description of Plant Viruses (DPV) provides information about viruses,
      viroids and satellites of plants, fungi and protozoa. It provides taxonomic
      information, including brief descriptions of each family and genus, and classified
      lists of virus sequences. The database also holds detailed information for all
      sequences of viruses, viroids and satellites of plants, fungi and protozoa that
      are complete or that contain at least one complete gene.
    homepage: http://www.dpvweb.net/
    id: 00000280
    name: DPV
    namespaceEmbeddedInLui: false
    pattern: ^\d+$
    prefix: dpv
    sampleId: '100'
    uri_format: http://www.dpvweb.net/dpv/showdpv.php?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
dragondb.allele:
  biocontext:
    is_identifiers: true
    is_obo: false
    prefix: DRAGONDB.ALLELE
    uri_format: http://identifiers.org/dragondb.allele/$1
  comment: Deprecated because the website is dead
  deprecated: true
  mappings:
    biocontext: DRAGONDB.ALLELE
    miriam: dragondb.allele
    n2t: dragondb.allele
  miriam:
    deprecated: false
    description: DragonDB is a genetic and genomic database for Antirrhinum majus
      (Snapdragon). This collection refers to allele information.
    homepage: http://www.antirrhinum.net/
    id: '00000300'
    name: DragonDB Allele
    namespaceEmbeddedInLui: false
    pattern: ^\w+$
    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: dragondb
dragondb.dna:
  biocontext:
    is_identifiers: true
    is_obo: false
    prefix: DRAGONDB.DNA
    uri_format: http://identifiers.org/dragondb.dna/$1
  comment: Deprecated because the website is dead
  deprecated: true
  mappings:
    biocontext: DRAGONDB.DNA
    miriam: dragondb.dna
    n2t: dragondb.dna
  miriam:
    deprecated: false
    description: DragonDB is a genetic and genomic database for Antirrhinum majus
      (Snapdragon). This collection refers to DNA sequence information.
    homepage: http://www.antirrhinum.net/
    id: 00000297
    name: DragonDB DNA
    namespaceEmbeddedInLui: false
    pattern: ^\d\w+$
    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: dragondb
dragondb.locus:
  biocontext:
    is_identifiers: true
    is_obo: false
    prefix: DRAGONDB.LOCUS
    uri_format: http://identifiers.org/dragondb.locus/$1
  comment: Deprecated because the website is dead
  deprecated: true
  mappings:
    biocontext: DRAGONDB.LOCUS
    miriam: dragondb.locus
    n2t: dragondb.locus
  miriam:
    deprecated: false
    description: DragonDB is a genetic and genomic database for Antirrhinum majus
      (Snapdragon). This collection refers to Locus information.
    homepage: http://www.antirrhinum.net/
    id: 00000299
    name: DragonDB Locus
    namespaceEmbeddedInLui: false
    pattern: ^\w+$
    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: dragondb
dragondb.protein:
  biocontext:
    is_identifiers: true
    is_obo: false
    prefix: DRAGONDB.PROTEIN
    uri_format: http://identifiers.org/dragondb.protein/$1
  comment: Deprecated because the website is dead
  deprecated: true
  mappings:
    biocontext: DRAGONDB.PROTEIN
    miriam: dragondb.protein
    n2t: dragondb.protein
  miriam:
    deprecated: false
    description: DragonDB is a genetic and genomic database for Antirrhinum majus
      (Snapdragon). This collection refers to protein sequence information.
    homepage: http://www.antirrhinum.net/
    id: 00000298
    name: DragonDB Protein
    namespaceEmbeddedInLui: false
    pattern: ^\w+$
    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: dragondb
dron:
  aberowl:
    description: An ontology to support comparative effectiveness researchers studying
      claims data.
    download_owl: http://aber-owl.net/media/ontologies/DRON/16/dron.owl
    homepage: https://github.com/ufbmi/dron
    name: The Drug Ontology
    prefix: DRON
  biocontext:
    is_identifiers: false
    is_obo: true
    prefix: DRON
    uri_format: http://purl.obolibrary.org/obo/DRON_$1
  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
    name: The Drug Ontology
    prefix: DRON
    version: '2022-04-22'
  download_json: http://purl.obolibrary.org/obo/dron.json
  download_obo: http://purl.obolibrary.org/obo/dron.obo
  example: '00023232'
  fairsharing:
    abbreviation: DrOn
    description: An ontology of drug products and packaged drug products.
    id: '641'
    name: The Drug Ontology
    prefix: FAIRsharing.w5ntfd
    publications:
    - doi: 10.1186/s13326-016-0048-2
      pubmed_id: 27096073
      title: An accurate and precise representation of drug ingredients
    - doi: 10.1186/s13326-017-0121-5
      pubmed_id: 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'
    - doi: 10.1186/2041-1480-4-44
      pubmed_id: 24345026
      title: Building a drug ontology based on RxNorm and other sources.
    subjects:
    - Biomedical Science
  mappings:
    aberowl: DRON
    biocontext: DRON
    bioportal: DRON
    fairsharing: FAIRsharing.w5ntfd
    obofoundry: dron
    ols: dron
    ontobee: DRON
  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.
    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: 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).
    download: http://purl.obolibrary.org/obo/dron.owl
    homepage: https://github.com/ufbmi/dron
    name: The Drug Ontology
    prefix: dron
    version: '2022-04-22'
    version.iri: http://purl.obolibrary.org/obo/dron/releases/2022-04-22/dron.owl
  ontobee:
    library: Library
    name: The Drug Ontology
    prefix: DRON
  pattern: ^\d{8}$
  publications:
  - doi: 10.1186/2041-1480-4-44
    pmc: PMC3931349
    pubmed: '24345026'
    title: Building a drug ontology based on RxNorm and other sources.
    year: 2013
  - 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/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
drsc:
  biocontext:
    is_identifiers: true
    is_obo: false
    prefix: DRSC
    uri_format: http://identifiers.org/drsc/$1
  mappings:
    biocontext: DRSC
    miriam: drsc
    n2t: drsc
  miriam:
    deprecated: false
    description: The DRSC (Drosophila RNAi Screening Cente) tracks both production
      of reagents for RNA interference (RNAi) screening in Drosophila cells and RNAi
      screen results. It maintains a list of Drosophila gene names, identifiers, symbols
      and synonyms and provides  information for cell-based or in vivo RNAi reagents,
      other types of reagents, screen results, etc. corresponding for a given gene.
    homepage: http://flyrnai.org/
    id: '00000367'
    name: DRSC
    namespaceEmbeddedInLui: false
    pattern: ^DRSC\d+$
    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
drugbank:
  biocontext:
    is_identifiers: false
    is_obo: false
    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/$1
  cheminf:
    description: Database identifier used by DrugBank.
    name: DrugBank
    obsolete: false
    prefix: '000406'
  edam:
    description: Unique identifier of a drug from the DrugBank database.
    name: DrugBank
    obsolete: false
    prefix: '2326'
  example: DB14938
  fairsharing:
    abbreviation: DrugBank
    description: The DrugBank database is a freely available bioinformatics and chemoinformatics
      resource that combines detailed drug (i.e. chemical, pharmacological and pharmaceutical)
      data with comprehensive drug target (i.e. sequence, structure, and pathway)
      information.
    id: '1844'
    name: DrugBank
    prefix: FAIRsharing.353yat
    subjects:
    - Life Science
    - Biomedical Science
  homepage: http://www.drugbank.ca
  mappings:
    biocontext: DrugBank
    cellosaurus: DrugBank
    cheminf: '000406'
    edam: '2326'
    fairsharing: FAIRsharing.353yat
    miriam: drugbank
    n2t: drugbank
    prefixcommons: drugbank
    re3data: r3d100010544
    uniprot: DrugBank
    wikidata: P715
  miriam:
    deprecated: false
    description: The DrugBank database is a bioinformatics and chemoinformatics resource
      that combines detailed drug (i.e. chemical, pharmacological and pharmaceutical)
      data with comprehensive drug target (i.e. sequence, structure, and pathway)
      information. This collection references drug information.
    homepage: http://www.drugbank.ca/
    id: '00000102'
    name: DrugBank
    namespaceEmbeddedInLui: false
    pattern: ^DB\d{5}$
    prefix: drugbank
    sampleId: DB00001
    uri_format: http://www.drugbank.ca/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/$1
  name: DrugBank
  prefixcommons:
    description: The DrugBank database is a bioinformatics and chemoinformatics resource
      that combines detailed drug (i.e. chemical, pharmacological and pharmaceutical)
      data with comprehensive drug target (i.e. sequence, structure, and pathway)
      information.
    example: DB00001
    homepage: http://www.drugbank.ca/
    keywords:
    - drug
    - protein
    name: DrugBank
    pattern: ^DB\d{5}$
    prefix: drugbank
    pubmed_ids:
    - '24203711'
    - '21059682'
    - '18048412'
    - '16381955'
    uri_format: http://www.drugbank.ca/drugs/$1
  publications:
  - doi: 10.1093/nar/gkj067
    pmc: PMC1347430
    pubmed: '16381955'
    title: 'DrugBank: a comprehensive resource for in silico drug discovery and exploration.'
    year: 2006
  - 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/gkq1126
    pmc: PMC3013709
    pubmed: '21059682'
    title: 'DrugBank 3.0: a comprehensive resource for ''omics'' research on drugs.'
    year: 2010
  - doi: 10.1093/nar/gkt1068
    pmc: PMC3965102
    pubmed: '24203711'
    title: 'DrugBank 4.0: shedding new light on drug metabolism.'
    year: 2013
  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 (version 5.1.1, released 2018-07-03)
      contains 11,881 drug entries including 2,526 approved small molecule drugs,
      1,184 approved biotech (protein/peptide) drugs, 129 nutraceuticals and over
      5,751 experimental drugs. Additionally, 5,132 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: https://go.drugbank.com/
    name: DrugBank
    prefix: r3d100010544
    synonyms:
    - DrugBank Online
    - Open Data Drug & Drug Target Database
    xrefs:
      fairsharing: fairsharing.353yat
      miriam: '00000102'
      nif: 0000-00417
      scr: '002700'
  synonyms:
  - DRUGBANK_ID
  - DrugBank
  uniprot:
    category: Chemistry databases
    identifier: '19'
    link_is_explicit: 'true'
    name: Drug and drug target database
    prefix: DrugBank
    uri_format: https://www.drugbank.ca/drugs/$1
  wikidata:
    database: Q1122544
    database.homepage: http://www.drugbank.ca/
    database.label: DrugBank
    description: identifier in the bioinformatics and cheminformatics database from
      the University of Alberta
    homepage: https://www.drugbank.ca
    name: DrugBank ID
    pattern: (SALT\d{1}|CAT\d{1})?\d{5}
    prefix: P715
    uri_format: https://go.drugbank.com/drugs/DB$1
drugbank.category:
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: Close to 5K Categorizations for drugs, similar to ATCC.
  example: DBCAT000600
  homepage: https://go.drugbank.com/categories
  name: DrugBank Drug Category
  part_of: drugbank
  pattern: ^DBCAT\d+$
  uri_format: https://www.drugbank.ca/categories/$1
drugbank.salt:
  biocontext:
    is_identifiers: true
    is_obo: false
    prefix: DRUGBANK.TARGET
    uri_format: http://identifiers.org/drugbank.target/$1
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: DrugBank is a web-enabled database containing comprehensive molecular
    information about drugs, their mechanisms, their interactions and their targets.
  example: DBSALT001211
  homepage: http://www.drugbank.ca
  mappings:
    biocontext: DRUGBANK.TARGET
  name: DrugBank Salts
  part_of: drugbank
  pattern: ^DBSALT\d{6}$
  synonyms:
  - drugbank.target
  uri_format: https://go.drugbank.com/salts/$1
drugbankv4.target:
  biocontext:
    is_identifiers: true
    is_obo: false
    prefix: DRUGBANKV4.TARGET
    uri_format: http://identifiers.org/drugbankv4.target/$1
  mappings:
    biocontext: DRUGBANKV4.TARGET
    miriam: drugbankv4.target
    n2t: drugbankv4.target
  miriam:
    deprecated: false
    description: The DrugBank database is a bioinformatics and chemoinformatics resource
      that combines detailed drug (i.e. chemical, pharmacological and pharmaceutical)
      data with comprehensive drug target (i.e. sequence, structure, and pathway)
      information. This collection references target information from version 4 of
      the database.
    homepage: http://www.drugbank.ca/targets
    id: 00000528
    name: DrugBank Target v4
    namespaceEmbeddedInLui: false
    pattern: ^BE\d{7}$
    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: drugbank
drugcentral:
  biolink:
    is_identifiers: false
    is_obo: false
    prefix: DrugCentral
    uri_format: http://drugcentral.org/drugcard/$1
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: DrugCentral  provides information on active ingredients chemical entities,
    pharmaceutical products, drug mode of action, indications, pharmacologic action.
  example: '307'
  fairsharing:
    abbreviation: DrugCentral
    description: DrugCentral is online drug information that provides information
      on active ingredients, chemical entities, pharmaceutical products, drug mode
      of action, indications, and pharmacologic mode of action. DrugCentral monitors
      FDA, EMA, and PMDA for new drug approval on regular basis to ensure currency
      of the resource. This resource was created and is maintained by the Division
      of Translational Informatics at the University of New Mexico School of Medicine.
    id: '2363'
    name: DrugCentral
    prefix: FAIRsharing.3me82d
    subjects:
    - Drug Discovery
    - Drug Repositioning
    - Drug Development
    - Pharmacy
    - Pharmacology
    - Biomedical Science
  homepage: http://drugcentral.org
  mappings:
    biolink: DrugCentral
    fairsharing: FAIRsharing.3me82d
    uniprot: DrugCentral
  name: Drug Central
  pattern: ^\d+$
  synonyms:
  - Drug_Central
  uniprot:
    category: Chemistry databases
    identifier: '239'
    link_is_explicit: 'true'
    name: DrugCentral
    prefix: DrugCentral
    uri_format: https://drugcentral.org/target/$1
  uri_format: http://drugcentral.org/drugcard/$1
dsm4:
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: A terminology published by the American Psychiatric Association (APA)
    for the classification of mental disorders using a common language and standard
    criteria. [wikipedia]
  example: '315.1'
  example_extras:
  - '291.89'
  hl7:
    description: 'Diagnostic and Statistical Manual of Mental Disorders (DSM-IV).
      4th ed. Washington (DC): American Psychiatric Association, 1994.'
    homepage: http://www.psych.org
    name: DSM-IV
    organization: American Psychiatric Association
    preferred_prefix: dsm4
    prefix: 2.16.840.1.113883.6.126
    status: Complete
  homepage: https://en.wikipedia.org/wiki/Diagnostic_and_Statistical_Manual_of_Mental_Disorders#DSM-IV-TR_(2000)
  mappings:
    hl7: 2.16.840.1.113883.6.126
    wikidata: P663
  name: Diagnostic and Statistical Manual of Mental Disorders (4th Edition)
  pattern: ^\d+\.\d+$
  synonyms:
  - dsm-iv
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}$
  references:
  - https://archive.org/details/diagnosticstatis0005unse
  synonyms:
  - dsm-v
dsmz:
  cellosaurus:
    category: Cell line collections
    homepage: https://www.dsmz.de/collection/catalogue/human-and-animal-cell-lines/catalogue
    name: Deutsche Sammlung von Mikroorganismen und Zellkulturen
    prefix: DSMZ
    uri_format: https://www.dsmz.de/collection/catalogue/details/culture/$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).
  example: ACC-1
  homepage: https://www.dsmz.de
  mappings:
    cellosaurus: DSMZ
    re3data: r3d100010219
  name: Deutsche Sammlung von Mikroorganismen und Zellkulturen
  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.
    homepage: https://www.dsmz.de/
    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
      scr: '001711'
  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/
  name: Data Science Ontology
  repository: https://github.com/IBM/datascienceontology
  uri_format: https://www.datascienceontology.org/concept/$1
dto:
  aberowl:
    description: "Drug Target Ontology (DTO) is being developed at the University\
      \ of Miami in the research group of Stephan Sch\xFCrer. 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 Sch\xFCrer. 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
    publication: 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).
    id: '1469'
    name: Drug Target Ontology
    prefix: FAIRsharing.tke3y2
    publications:
    - doi: 10.1186/s13326-017-0161-x
      pubmed_id: 29122012
      title: Drug target ontology to classify and integrate drug discovery data.
    subjects:
    - Drug Discovery
    - Biomedical Science
  homepage: https://github.com/DrugTargetOntology/DTO
  mappings:
    aberowl: DTO
    bioportal: DTO
    fairsharing: FAIRsharing.tke3y2
  name: Drug Target Ontology
  pattern: ^\d+$
  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: null
  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:
    is_identifiers: false
    is_obo: true
    prefix: DUO
    uri_format: http://purl.obolibrary.org/obo/DUO_$1
  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).
    id: '256'
    name: The Data Use Ontology
    prefix: FAIRsharing.5dnjs2
    publications: []
    subjects:
    - Data Management
    - Subject Agnostic
  mappings:
    aberowl: DUO
    biocontext: DUO
    bioportal: DUO
    fairsharing: FAIRsharing.5dnjs2
    obofoundry: duo
    ols: duo
    ontobee: DUO
  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.
    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:
    download: http://purl.obolibrary.org/obo/duo.owl
    name: duo
    prefix: duo
    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}$
  repository: https://github.com/EBISPOT/DUO
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
  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
  re3data:
    description: Groundbreaking biomedical research requires access to cutting edge
      scientific resources; however such resources are often invisible beyond the
      laboratories or universities where they were developed. eagle-i is a discovery
      platform that helps biomedical scientists find previously invisible, but highly
      valuable, resources.
    homepage: https://www.eagle-i.net/
    name: eagle-i
    prefix: r3d100011564
    xrefs:
      nlx: '143592'
      scr: '013153'
  uri_format: http://hawaii.eagle-i.net/i/$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/
  name: EasyChair Call for Paper
  uri_format: https://easychair.org/cfp/$1
easychair.topic:
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: Call for paper topics in EasyChair
  example: '27106865'
  homepage: https://easychair.org/cfp/
  name: EasyChair Topic
  pattern: ^\d+$
  uri_format: https://easychair.org/cfp/topic.cgi?tid=$1
ebisc:
  cellosaurus:
    category: Cell line collections
    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
  mappings:
    cellosaurus: EBiSC
ecacc:
  cellosaurus:
    category: Cell line collections
    homepage: https://www.phe-culturecollections.org.uk/products/celllines/index.aspx
    name: European Collection of Cell Cultures
    prefix: ECACC
    uri_format: https://www.phe-culturecollections.org.uk/products/celllines/generalcell/detail.jsp?refId=$1&collection=ecacc_gc
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: The European Collection of Authenticated Cell Cultures (ECACC) is one
    of four Culture Collections of Public Health England. We supply authenticated
    and quality controlled cell lines, nucleic acids and induced Pluripotent Stem
    Cells (iPSCs).
  example: '90062901'
  homepage: https://www.phe-culturecollections.org.uk/collections/ecacc.aspx
  mappings:
    cellosaurus: ECACC
  name: European Collection of Authenticated Cell Culture
  pattern: ^\d+$
  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/1/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
  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).
    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: http://purl.obolibrary.org/obo/ecao.owl
    homepage: https://github.com/echinoderm-ontology/ecao_ontology
    name: Echinoderm Anatomy and Development Ontology
    prefix: ecao
    version: '2020-05-22'
    version.iri: http://purl.obolibrary.org/obo/ecao/releases/2020-05-22/ecao.owl
  ontobee:
    library: Library
    name: The Echinoderm Anatomy and Development Ontology
    prefix: ECAO
  pattern: ^\d{7}$
eccode:
  biocontext:
    is_identifiers: true
    is_obo: false
    prefix: EC-CODE
    uri_format: http://identifiers.org/ec-code/$1
  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.
  example_extras:
  - '2'
  - '2.3'
  - 2.3.1
  - 2.3.1.n12
  - 3.1.26.n2
  fairsharing:
    abbreviation: IntEnz
    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.
    id: '1853'
    name: Integrated relational Enzyme database
    prefix: FAIRsharing.q1fdkc
    subjects:
    - Bioinformatics
    - Enzymology
  go:
    homepage: http://enzyme.expasy.org/
    name: Enzyme Commission
    prefix: EC
    uri_format: https://enzyme.expasy.org/EC/$1
  mappings:
    biocontext: EC-CODE
    edam: '1011'
    fairsharing: FAIRsharing.q1fdkc
    go: EC
    miriam: ec-code
    n2t: ec-code
    prefixcommons: intenz
    wikidata: P591
  miriam:
    deprecated: false
    description: The Enzyme Classification contains the recommendations of the Nomenclature
      Committee of the International Union of Biochemistry and Molecular Biology on
      the nomenclature and classification of enzyme-catalysed reactions.
    homepage: https://www.ebi.ac.uk/intenz/
    id: '00000004'
    name: Enzyme Nomenclature
    namespaceEmbeddedInLui: false
    pattern: ^\d+\.-\.-\.-|\d+\.\d+\.-\.-|\d+\.\d+\.\d+\.-|\d+\.\d+\.\d+\.(n)?\d+$
    prefix: ec-code
    providers:
    - code: CURATOR_REVIEW
      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
    - code: expenz
      description: ExploreEnz at Trinity College
      homepage: http://www.enzyme-database.org/
      name: ExploreEnz at Trinity College
      uri_format: http://www.enzyme-database.org/query.php?ec=$1
    - code: enzymeportal
      description: Enzyme Portal through EMBL-EBI
      homepage: https://www.ebi.ac.uk/enzymeportal
      name: Enzyme Portal through EMBL-EBI
      uri_format: https://www.ebi.ac.uk/enzymeportal/ec/$1
    - 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
    sampleId: 1.1.1.1
    uri_format: https://www.ebi.ac.uk/intenz/query?cmd=SearchEC&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=$1
  name: Enzyme Commission Code
  pattern: ^\d{1,2}(((\.\d{1,3}){1,3})|(\.\d+){2}\.n\d{1,3})?$
  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
    name: Integrated relational Enzyme database
    pattern: ^\d+$
    prefix: intenz
    uri_format: http://www.ebi.ac.uk/intenz/query?cmd=SearchID&id=$1
  synonyms:
  - EC
  - EC number
  - EC-CODE
  - ECCODE
  - EC_CODE
  - ec-code
  - intenz
  uri_format: https://www.ebi.ac.uk/intenz/query?cmd=SearchEC&ec=$1
  wikidata:
    prefix: P591
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
    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).
    id: '19'
    name: ElectroCardioGraphy Ontology
    prefix: FAIRsharing.azr389
    publications:
    - doi: 10.1016/j.jbi.2010.08.007
      pubmed_id: 20800107
      title: Using an ECG reference ontology for semantic interoperability of ECG
        data.
    subjects:
    - Biomedical Science
  homepage: https://bioportal.bioontology.org/ontologies/ECG
  mappings:
    aberowl: ECG
    bioportal: ECG
    fairsharing: FAIRsharing.azr389
  name: Electrocardiogram Ontology
  pattern: ^\d+$
  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
echobase:
  biocontext:
    is_identifiers: true
    is_obo: false
    prefix: ECHOBASE
    uri_format: http://identifiers.org/echobase/$1
  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=$1
  mappings:
    biocontext: ECHOBASE
    go: EchoBASE
    miriam: echobase
    n2t: echobase
    prefixcommons: echobase
    re3data: r3d100011646
    uniprot: EchoBASE
  miriam:
    deprecated: false
    description: EchoBASE is a database designed to contain and manipulate information
      from post-genomic experiments using the model bacterium Escherichia coli K-12.
      The database is built on an enhanced annotation of the updated genome sequence
      of strain MG1655 and the association of experimental data with the E.coli genes
      and their products.
    homepage: http://www.york.ac.uk/
    id: '00000200'
    name: EchoBASE
    namespaceEmbeddedInLui: false
    pattern: ^EB\d+$
    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=$1
  prefixcommons:
    description: EchoBase is a database that curates new experimental and bioinformatic
      information about the genes and gene products of the model bacterium Escherichia
      coli K-12 strain MG1655.
    example: EB0170
    homepage: http://www.ecoli-york.org/
    keywords:
    - gene
    - gene expression
    name: EchoBASE - an integrated post-genomic database for E. coli
    pattern: ^EB\d+$
    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
  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.
    homepage: https://www.york.ac.uk/res/thomas/index.cfm
    name: EchoBase
    prefix: r3d100011646
    synonyms:
    - an integrated post-genomic database for E.coli
    xrefs:
      miriam: '00000200'
      nif: 0000-02781
      scr: '002430'
  uniprot:
    category: Organism-specific databases
    identifier: '20'
    link_is_explicit: 'true'
    name: EchoBASE - an integrated post-genomic database for E. coli
    prefix: EchoBASE
    uri_format: https://www.york.ac.uk/res/thomas/Gene.cfm?recordID=$1
ecmdb:
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: "The ECMDB is an expertly curated database containing extensive metabolomic\
    \ data and metabolic pathway diagrams about Escherichia coli (strain K12, MG1655).\
    \ This database includes significant quantities of \u201Coriginal\u201D data compiled\
    \ by members of the Wishart laboratory as well as additional material derived\
    \ from hundreds of textbooks, scientific journals, metabolic reconstructions and\
    \ other electronic databases. Each metabolite is linked to more than 100 data\
    \ fields describing the compound, its ontology, physical properties, reactions,\
    \ pathways, references, external links and associated proteins or enzymes."
  example: ECMDB00005
  homepage: https://ecmdb.ca
  name: E. coli Metabolite Database
  pattern: ^ECMDB\d+$
  synonyms:
  - ECMDB
  uri_format: http://ecmdb.ca/compounds/$1
  wikidata:
    database: Q17052437
ecn:
  cheminf:
    description: A seven-digit identifier for chemical substances for regulatory purposes
      within the European Union.
    name: European Community number
    obsolete: false
    prefix: '000447'
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  example: 200-003-9
  homepage: https://echa.europa.eu/information-on-chemicals
  mappings:
    cheminf: '000447'
  pattern: ^\d{3}-\d{3}-\d$
  references:
  - https://github.com/biopragmatics/bioregistry/issues/257
  - https://en.wikipedia.org/wiki/European_Community_number
eco:
  aberowl:
    description: An ontology for experimental and other evidence statements.
    download_owl: http://aber-owl.net/media/ontologies/ECO/105/eco.owl
    homepage: https://github.com/evidenceontology/evidenceontology/
    name: Evidence ontology
    prefix: ECO
  biocontext:
    is_identifiers: false
    is_obo: true
    prefix: ECO
    uri_format: http://purl.obolibrary.org/obo/ECO_$1
  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
    publication: https://github.com/evidenceontology/evidenceontology
    version: releases/2022-08-05
  example: 0007807
  fairsharing:
    abbreviation: ECO
    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
    id: '1483'
    name: Evidence and Conclusion Ontology
    prefix: FAIRsharing.wvpgwn
    publications:
    - doi: 10.1142/9789812704856_0019
      pubmed_id: 14992503
      title: An evidence ontology for use in pathway/genome databases.
    - doi: 10.1093/nar/gky1036
      pubmed_id: 30407590
      title: 'ECO, the Evidence & Conclusion Ontology: community standard for evidence
        information.'
    - doi: 10.1007/978-1-4939-3743-1_18
      pubmed_id: 27812948
      title: 'The Evidence and Conclusion Ontology (ECO): Supporting GO Annotations.'
    subjects:
    - Computational Biology
    - Life Science
  go:
    homepage: http://www.evidenceontology.org/
    name: Evidence Code Ontology
    prefix: ECO
    uri_format: http://www.evidenceontology.org/browse/#ECO_$1
  mappings:
    aberowl: ECO
    biocontext: ECO
    bioportal: ECO
    fairsharing: FAIRsharing.wvpgwn
    go: ECO
    miriam: eco
    n2t: eco
    obofoundry: eco
    ols: eco
    ontobee: ECO
    prefixcommons: eco
  miriam:
    deprecated: false
    description: Evidence codes can be used to specify the type of supporting evidence
      for a piece of knowledge. This allows inference of a 'level of support' between
      an entity and an annotation made to an entity.
    homepage: https://www.ebi.ac.uk/ols/ontologies/eco
    id: '00000055'
    name: Evidence Code Ontology
    namespaceEmbeddedInLui: true
    pattern: ECO:\d{7}$
    prefix: eco
    sampleId: '0000006'
    uri_format: https://www.ebi.ac.uk/ols/ontologies/eco/terms?obo_id=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:$1
  obofoundry:
    contact: mgiglio@som.umaryland.edu
    contact.github: mgiglio99
    contact.label: Michelle Giglio
    contact.orcid: 0000-0001-7628-5565
    deprecated: false
    description: An ontology for experimental and other evidence statements.
    download.obo: http://purl.obolibrary.org/obo/eco.obo
    download.owl: http://purl.obolibrary.org/obo/eco.owl
    homepage: https://www.evidenceontology.org
    license: CC0 1.0
    license.url: https://creativecommons.org/publicdomain/zero/1.0/
    name: Evidence ontology
    preferredPrefix: ECO
    prefix: eco
    publications:
    - id: https://www.ncbi.nlm.nih.gov/pubmed/30407590
      preferred: true
      title: 'ECO, the Evidence & Conclusion Ontology: community standard for evidence
        information.'
    - id: https://www.ncbi.nlm.nih.gov/pubmed/25052702
      title: Standardized description of scientific evidence using the Evidence Ontology
        (ECO)
    repository: https://github.com/evidenceontology/evidenceontology
  ols:
    description: The Evidence & Conclusion Ontology (ECO) describes types of scientific
      evidence within the biological research domain that arise from laboratory experiments,
      computational methods, literature curation, or other means.
    download: http://purl.obolibrary.org/obo/eco.owl
    homepage: https://www.evidenceontology.org
    name: Evidence & Conclusion Ontology (ECO)
    prefix: eco
    version: '2022-08-05'
    version.iri: http://purl.obolibrary.org/obo/eco/releases/2022-08-05/eco.owl
  ontobee:
    library: Library
    name: Evidence ontology
    prefix: ECO
  pattern: ^\d{7}$
  prefixcommons:
    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
    name: Evidence Code Ontology
    pattern: ^ECO:\d{7}$
    prefix: eco
    synonyms:
    - evidence codes ontologyobo.eco
    uri_format: http://www.ebi.ac.uk/ontology-lookup/?termId=$1
  publications:
  - doi: 10.1142/9789812704856_0019
    pmc: null
    pubmed: '14992503'
    title: An evidence ontology for use in pathway/genome databases.
    year: 2004
  - doi: 10.1093/database/bau075
    pmc: PMC4105709
    pubmed: '25052702'
    title: Standardized description of scientific evidence using the Evidence Ontology
      (ECO).
    year: 2014
  - 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/nar/gky1036
    pmc: PMC6323956
    pubmed: '30407590'
    title: 'ECO, the Evidence & Conclusion Ontology: community standard for evidence
      information.'
    year: 2019
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:
    is_identifiers: false
    is_obo: true
    prefix: ECOCORE
    uri_format: http://purl.obolibrary.org/obo/ECOCORE_$1
  bioportal:
    homepage: https://github.com/EcologicalSemantics/ecocore
    name: An ontology of core ecological entities
    prefix: ECOCORE
    version: '2022-03-09'
  example: '00000001'
  mappings:
    aberowl: ECOCORE
    biocontext: ECOCORE
    bioportal: ECOCORE
    obofoundry: ecocore
    ols: ecocore
    ontobee: ECOCORE
  obofoundry:
    contact: p.buttigieg@gmail.com
    contact.github: pbuttigieg
    contact.label: Pier Luigi Buttigieg
    contact.orcid: 0000-0002-4366-3088
    depends_on:
    - bfo
    - chebi
    - envo
    - go
    - iao
    - pato
    - pco
    - po
    - ro
    - uberon
    deprecated: false
    description: Ecocore is a community ontology for the concise and controlled description
      of ecological traits of organisms.
    download.obo: http://purl.obolibrary.org/obo/ecocore.obo
    download.owl: http://purl.obolibrary.org/obo/ecocore.owl
    homepage: https://github.com/EcologicalSemantics/ecocore
    license: CC BY 3.0
    license.url: http://creativecommons.org/licenses/by/3.0/
    name: An ontology of core ecological entities
    preferredPrefix: ECOCORE
    prefix: ecocore
    repository: https://github.com/EcologicalSemantics/ecocore
  ols:
    description: Ecocore is a community ontology for the concise and controlled description
      of ecological traits of organisms.
    download: http://purl.obolibrary.org/obo/ecocore.owl
    homepage: https://github.com/EcologicalSemantics/ecocore
    name: An ontology of core ecological entities
    prefix: ecocore
    version: '2022-03-09'
    version.iri: http://purl.obolibrary.org/obo/ecocore/releases/2022-03-09/ecocore.owl
  ontobee:
    library: Library
    name: An ontology of core ecological entities
    prefix: ECOCORE
  pattern: ^\d+$
ecocyc:
  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 37,000 publications as of 2019. Updates to EcoCyc
      content continue to improve the 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.
    id: '2054'
    name: EcoCyc E. coli Database
    prefix: FAIRsharing.65dmtr
    subjects:
    - Biology
  go:
    homepage: http://ecocyc.org/
    name: Encyclopedia of E. coli metabolism
    prefix: EcoCyc
    uri_format: http://biocyc.org/ECOLI/NEW-IMAGE?type=PATHWAY&object=$1
  mappings:
    fairsharing: FAIRsharing.65dmtr
    go: EcoCyc
    ncbi: ECOCYC
  name: EcoCyc
  ncbi:
    example: sroC
    homepage: https://ecocyc.org/
    name: E. coli database
    prefix: ECOCYC
  uri_format: https://biocyc.org/gene?id=$1
ecogene:
  biocontext:
    is_identifiers: false
    is_obo: false
    prefix: EcoGene
    uri_format: http://ecogene.org/gene/$1
  fairsharing:
    abbreviation: EcoGene
    description: The EcoGene database contains updated information about the E. coli
      K-12 genome and proteome sequences, including extensive gene bibliographies.
      A major EcoGene focus has been the re-evaluation of translation start sites.
    id: '1869'
    name: Escherichia coli strain K12 genome database
    prefix: FAIRsharing.3q3kvn
    subjects: []
  mappings:
    biocontext: EcoGene
    fairsharing: FAIRsharing.3q3kvn
    miriam: ecogene
    n2t: ecogene
    ncbi: EcoGene
    prefixcommons: ecogene
    re3data: r3d100010546
  miriam:
    deprecated: false
    description: The EcoGene database contains updated information about the E. coli
      K-12 genome and proteome sequences, including extensive gene bibliographies.
      A major EcoGene focus has been the re-evaluation of translation start sites.
    homepage: http://ecogene.org/
    id: '00000163'
    name: EcoGene
    namespaceEmbeddedInLui: false
    pattern: ^EG\d+$
    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/$1
  ncbi:
    example: EG11277
    homepage: http://ecogene.org
    name: Database of Escherichia coli Sequence and Function
    prefix: EcoGene
  prefixcommons:
    description: The EcoGene database contains updated information about the E. coli
      K-12 genome and proteome sequences, including extensive gene bibliographies.
      A major EcoGene focus has been the re-evaluation of translation start sites.
    example: EG10173
    homepage: http://ecogene.org/
    keywords:
    - genome
    - protein
    name: Escherichia coli strain K12 genome database
    pattern: ^EG\d+$
    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 >>>!!!<<<'
    homepage: http://ecogene.org/
    name: EcoGene
    prefix: r3d100010546
    synonyms:
    - Escherichia coli strain K12 genome database
    xrefs:
      fairsharing: FAIRsharing.3q3kvn
      miriam: '00000163'
      nif: 0000-02784
      omics: 03184
      scr: '002437'
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
  name: EcoLexicon
ecoliwiki:
  biocontext:
    is_identifiers: true
    is_obo: false
    prefix: ECOLIWIKI
    uri_format: http://identifiers.org/ecoliwiki/$1
  fairsharing:
    abbreviation: EcoliWiki
    description: EcoliWiki is a community-based resource for the annotation of all
      non-pathogenic E. coli, its phages, plasmids, and mobile genetic elements.
    id: '1576'
    name: EcoliWiki
    prefix: FAIRsharing.tx95wa
    subjects:
    - Genomics
    - Bioinformatics
    - Life Science
    - Ontology and Terminology
  go:
    description: EcoliHub\'s subsystem for community annotation of E. coli K-12
    homepage: http://ecoliwiki.net/
    name: EcoliWiki from EcoliHub
    prefix: EcoliWiki
  mappings:
    biocontext: ECOLIWIKI
    fairsharing: FAIRsharing.tx95wa
    go: EcoliWiki
    miriam: ecoliwiki
    n2t: ecoliwiki
  miriam:
    deprecated: false
    description: EcoliWiki is a wiki-based resource to store information related to
      non-pathogenic E. coli, its phages, plasmids, and mobile genetic elements. This
      collection references genes.
    homepage: http://ecoliwiki.net/colipedia/
    id: '00000442'
    name: EcoliWiki
    namespaceEmbeddedInLui: false
    pattern: ^[A-Za-z0-9-]+$
    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
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/10/ecto.owl
    homepage: https://github.com/EnvironmentOntology/environmental-exposure-ontology
    name: Environmental conditions, treatments and exposures ontology
    prefix: ECTO
  biolink:
    is_identifiers: false
    is_obo: true
    prefix: ECTO
    uri_format: http://purl.obolibrary.org/obo/ECTO_$1
  bioportal:
    name: Environmental conditions, treatments and exposures ontology
    prefix: ECTO
  example: '0000001'
  mappings:
    aberowl: ECTO
    biolink: ECTO
    bioportal: ECTO
    obofoundry: ecto
    ols: ecto
    ontobee: ECTO
  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).
    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/
    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: http://purl.obolibrary.org/obo/ecto.owl
    homepage: https://github.com/EnvironmentOntology/environmental-exposure-ontology
    name: Environment Exposure Ontology
    prefix: ecto
    version: '2022-08-12'
    version.iri: http://purl.obolibrary.org/obo/ecto/releases/2022-08-12/ecto.owl
  ontobee:
    library: Library
    name: Environmental conditions, treatments and exposures ontology
    prefix: ECTO
  pattern: ^\d{7}$
ecyano.entity:
  biocontext:
    is_identifiers: true
    is_obo: false
    prefix: ECYANO.ENTITY
    uri_format: http://identifiers.org/ecyano.entity/$1
  mappings:
    biocontext: ECYANO.ENTITY
    miriam: ecyano.entity
    n2t: ecyano.entity
  miriam:
    deprecated: false
    description: "E-cyanobacterium.org is a web-based platform for public sharing,\
      \ annotation, analysis, and visualisation of dynamical models and wet-lab experiments\
      \ related to cyanobacteria. It allows models to be represented at different\
      \ levels of abstraction \u2014 as biochemical reaction networks or ordinary\
      \ differential equations.It provides concise mappings of mathematical models\
      \ to a formalised consortium-agreed biochemical description, with the aim of\
      \ connecting the world of biological knowledge with benefits of mathematical\
      \ description of dynamic processes. This collection references entities."
    homepage: http://www.e-cyanobacterium.org/bcs/entity/
    id: 00000585
    name: E-cyanobacterium entity
    namespaceEmbeddedInLui: false
    pattern: ^\d+$
    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: ecyano
  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: ecyano
ecyano.model:
  biocontext:
    is_identifiers: true
    is_obo: false
    prefix: ECYANO.MODEL
    uri_format: http://identifiers.org/ecyano.model/$1
  mappings:
    biocontext: ECYANO.MODEL
    miriam: ecyano.model
    n2t: ecyano.model
  miriam:
    deprecated: false
    description: "E-cyanobacterium.org is a web-based platform for public sharing,\
      \ annotation, analysis, and visualisation of dynamical models and wet-lab experiments\
      \ related to cyanobacteria. It allows models to be represented at different\
      \ levels of abstraction \u2014 as biochemical reaction networks or ordinary\
      \ differential equations.It provides concise mappings of mathematical models\
      \ to a formalised consortium-agreed biochemical description, with the aim of\
      \ connecting the world of biological knowledge with benefits of mathematical\
      \ description of dynamic processes. This collection references models."
    homepage: http://e-cyanobacterium.org/models/
    id: 00000586
    name: E-cyanobacterium model
    namespaceEmbeddedInLui: false
    pattern: ^\d+$
    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/
  uri_format: https://e-cyanobacterium.org/models/model/$1
ecyano.rule:
  biocontext:
    is_identifiers: true
    is_obo: false
    prefix: ECYANO.RULE
    uri_format: http://identifiers.org/ecyano.rule/$1
  mappings:
    biocontext: ECYANO.RULE
    miriam: ecyano.rule
    n2t: ecyano.rule
  miriam:
    deprecated: false
    description: "E-cyanobacterium.org is a web-based platform for public sharing,\
      \ annotation, analysis, and visualisation of dynamical models and wet-lab experiments\
      \ related to cyanobacteria. It allows models to be represented at different\
      \ levels of abstraction \u2014 as biochemical reaction networks or ordinary\
      \ differential equations.It provides concise mappings of mathematical models\
      \ to a formalised consortium-agreed biochemical description, with the aim of\
      \ connecting the world of biological knowledge with benefits of mathematical\
      \ description of dynamic processes. This collection references rules."
    homepage: http://www.e-cyanobacterium.org/bcs/rule/
    id: 00000587
    name: E-cyanobacterium rule
    namespaceEmbeddedInLui: false
    pattern: ^\d+$
    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: ecyano
  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.
    example_uri: http://edamontology.org/topic_3519
    homepage: http://edamontology.org/page
    license: CC BY 4.0
    name: EDAM bioinformatics operations, data types, formats, identifiers and topics
    prefix: EDAM
    publication: http://dx.doi.org/10.1093/bioinformatics/btt113
    repository: https://github.com/edamontology/edamontology
    version: '1.25'
  biocontext:
    is_identifiers: true
    is_obo: false
    prefix: EDAM
    uri_format: http://identifiers.org/edam/$1
  bioportal:
    contact:
      email: matus.kalas@uib.no
      name: "Mat\xFA\u0161 Kala\u0161"
    description: 'EDAM is a comprehensive ontology of well-established, familiar concepts
      that are prevalent within bioscientific data analysis and data management. EDAM
      includes topics, operations, types of data and data identifiers, and data formats,
      relevant in data analysis and 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.'
    homepage: http://edamontology.org
    name: EDAM - Bioscientific data analysis ontology
    prefix: EDAM
    publication: https://doi.org/10.7490/f1000research.1118900.1
    version: unstable(1.26_dev)
  contact:
    email: matus.kalas@uib.no
    github: matuskalas
    name: "Mat\xFA\u0161 Kala\u0161"
    orcid: 0000-0002-1509-4981
  download_obo: https://github.com/edamontology/edamontology/raw/main/releases/EDAM.obo
  fairsharing:
    abbreviation: EDAM
    description: "EDAM (originally from \u201CEMBRACE Data and Methods\u201D) is an\
      \ ontology of well established, familiar concepts that are prevalent within\
      \ bioinformatics, including types of data and data identifiers, data formats,\
      \ operations and topics."
    id: '1205'
    name: EMBRACE Data and Methods Ontology
    prefix: FAIRsharing.a6r7zs
    publications:
    - doi: 10.1093/bioinformatics/btt113
      pubmed_id: 23479348
      title: 'EDAM: an ontology of bioinformatics operations, types of data and identifiers,
        topics and formats.'
    subjects:
    - Bioinformatics
    - Life Science
  mappings:
    aberowl: EDAM
    agroportal: EDAM
    biocontext: EDAM
    bioportal: EDAM
    fairsharing: FAIRsharing.a6r7zs
    miriam: edam
    n2t: edam
    ols: edam
    ontobee: EDAM
    prefixcommons: 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/$1
  ols:
    contact: edam@elixir-dk.org
    description: EDAM is a simple ontology of well established, familiar concepts
      that are prevalent within bioinformatics, including types of data and data identifiers,
      data formats, operations and topics. EDAM provides a set of terms with synonyms
      and definitions - organised into an intuitive hierarchy for convenient use.
    download: https://raw.githubusercontent.com/edamontology/edamontology/master/releases/EDAM.owl
    homepage: http://edamontology.org
    name: Bioinformatics operations, data types, formats, identifiers and topics
    prefix: edam
    version: '2019-07-17'
  ontobee:
    library: Not Specified/No
    name: EMBRACE Data and Methods
    prefix: EDAM
  prefixcommons:
    bioportal: '1498'
    description: EDAM (EMBRACE Data And Methods) is an ontology of bioinformatics
      operations (tool, application, or workflow functions), types of data, topics
      (application domains), and data formats. The applications of EDAM are within
      organising tools and data, finding suitable tools in catalogues, and integrating
      them into complex applications or workflows. Semantic annotations with EDAM
      are applicable to diverse entities such as for example Web services, databases,
      programmatic libraries, standalone tools and toolkits, interactive applications,
      data schemas, data sets, or publications within bioinformatics. Annotation with
      EDAM may also contribute to data provenance, and EDAM terms and synonyms can
      be used in text mining. EDAM - and in particular the EDAM Data sub-ontology
      - serves also as a markup vocabulary for bioinformatics data on the Semantic
      Web.
    example: EDAM_data:1664
    homepage: https://sourceforge.net/projects/edamontology/
    keywords:
    - obo
    - ontology
    name: Bioinformatics operations, types of data, data formats and topics
    pattern: ^EDAM_(data|topic)\:\d{4}$
    prefix: edam
    synonyms:
    - edam
    uri_format: http://www.ebi.ac.uk/ontology-lookup/?termId=$1
  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
  repository: https://github.com/edamontology/edamontology
  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_$1
  contact:
    email: matus.kalas@uib.no
    github: matuskalas
    name: "Mat\xFA\u0161 Kala\u0161"
    orcid: 0000-0002-1509-4981
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: Information, represented in an information artefact (data record) that
    is 'understandable' by dedicated computational tools that can use the data as
    input or produce it as output.
  download_obo: https://github.com/edamontology/edamontology/raw/main/releases/EDAM.obo
  example: '1664'
  homepage: http://edamontology.org
  mappings:
    biolink: EDAM-DATA
  name: EDAM Data
  part_of: edam
  pattern: ^\d+$
  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_$1
  contact:
    email: matus.kalas@uib.no
    github: matuskalas
    name: "Mat\xFA\u0161 Kala\u0161"
    orcid: 0000-0002-1509-4981
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: A defined way or layout of representing and structuring data in a computer
    file, blob, string, message, or elsewhere. The main focus in EDAM lies on formats
    as means of structuring data exchanged between different tools or resources. The
    serialisation, compression, or encoding of concrete data formats/models is not
    in scope of EDAM. Format 'is format of' Data.
  download_obo: https://github.com/edamontology/edamontology/raw/main/releases/EDAM.obo
  example: '1915'
  homepage: http://edamontology.org
  mappings:
    biolink: EDAM-FORMAT
  name: EDAM Format
  part_of: edam
  pattern: ^\d+$
  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_$1
  contact:
    email: matus.kalas@uib.no
    github: matuskalas
    name: "Mat\xFA\u0161 Kala\u0161"
    orcid: 0000-0002-1509-4981
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: 'A function that processes a set of inputs and results in a set of
    outputs, or associates arguments (inputs) with values (outputs). Special cases
    are: a) An operation that consumes no input (has no input arguments). Such operation
    is either a constant function, or an operation depending only on the underlying
    state. b) An operation that may modify the underlying state but has no output.
    c) The singular-case operation with no input or output, that still may modify
    the underlying state.'
  download_obo: https://github.com/edamontology/edamontology/raw/main/releases/EDAM.obo
  example: '0004'
  homepage: http://edamontology.org
  mappings:
    biolink: EDAM-OPERATION
  name: EDAM Operation
  part_of: edam
  pattern: ^\d+$
  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_$1
  contact:
    email: matus.kalas@uib.no
    github: matuskalas
    name: "Mat\xFA\u0161 Kala\u0161"
    orcid: 0000-0002-1509-4981
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: A category denoting a rather broad domain or field of interest, of
    study, application, work, data, or technology. Topics have no clearly defined
    borders between each other.
  download_obo: https://github.com/edamontology/edamontology/raw/main/releases/EDAM.obo
  example: '0003'
  homepage: http://edamontology.org
  mappings:
    biolink: EDAM-TOPIC
  name: EDAM Topic
  part_of: edam
  pattern: ^\d+$
  repository: https://github.com/edamontology/edamontology
  twitter: edamontology
  uri_format: http://edamontology.org/topic_$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\u2013NonCommercial\u2013ShareAlike 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\u2013NonCommercial\u2013ShareAlike 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'
  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.'
    id: '1289'
    name: EDDA Study Designs Taxonomy
    prefix: FAIRsharing.2ffmsb
    publications: []
    subjects: []
  homepage: https://bioportal.bioontology.org/ontologies/EDDA
  mappings:
    aberowl: EDDA
    bioportal: EDDA
    fairsharing: FAIRsharing.2ffmsb
  uri_format: http://ontologies.dbmi.pitt.edu/edda/StudyDesigns.owl#$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.
    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
    publication: https://doi.org/10.1093/bioinformatics/btq099
    repository: https://github.com/EBISPOT/efo
    version: 3.46.0
  biocontext:
    is_identifiers: false
    is_obo: true
    prefix: EFO
    uri_format: http://purl.obolibrary.org/obo/EFO_$1
  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: 3.46.0
  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
  example: '0005147'
  fairsharing:
    abbreviation: EFO
    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.
    id: '1498'
    name: Experimental Factor Ontology
    prefix: FAIRsharing.1gr4tz
    publications:
    - doi: 10.1093/bioinformatics/btq099
      pubmed_id: 20200009
      title: Modeling sample variables with an Experimental Factor Ontology.
    subjects:
    - Functional Genomics
  mappings:
    aberowl: EFO
    agroportal: EFO
    biocontext: EFO
    biolink: EFO
    bioportal: EFO
    cellosaurus: EFO
    fairsharing: FAIRsharing.1gr4tz
    miriam: efo
    n2t: efo
    ols: efo
    ontobee: EFO
  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: https://www.ebi.ac.uk/ols/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: https://www.ebi.ac.uk/ols/ontologies/efo/terms?obo_id=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 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: http://www.ebi.ac.uk/efo/efo.owl
    homepage: http://www.ebi.ac.uk/efo
    name: Experimental Factor Ontology
    prefix: efo
    version: 3.45.0
    version.iri: http://www.ebi.ac.uk/efo/releases/v3.45.0/efo.owl
  ontobee:
    library: Not Specified/No
    name: Experimental Factor Ontology
    prefix: EFO
  preferred_prefix: EFO
  publications:
  - doi: 10.1093/bioinformatics/btq099
    pmc: PMC2853691
    pubmed: '20200009'
    title: Modeling sample variables with an Experimental Factor Ontology.
    year: 2010
  repository: https://github.com/EBISPOT/efo/
  uri_format: http://www.ebi.ac.uk/efo/EFO_$1
ega.dataset:
  biocontext:
    is_identifiers: true
    is_obo: false
    prefix: EGA.DATASET
    uri_format: http://identifiers.org/ega.dataset/$1
  fairsharing:
    abbreviation: EGA
    description: The European Genome-phenome Archive (EGA) is a service for permanent
      archiving and sharing of all types of personally identifiable genetic and phenotypic
      data resulting from biomedical research projects. Access to data must be approved
      by the specified Data Access Committee (DAC).
    id: '1865'
    name: The European Genome-phenome Archive
    prefix: FAIRsharing.mya1ff
    subjects:
    - Genomics
    - Phenomics
    - Biomedical Science
    - Biology
  homepage: https://ega-archive.org/
  mappings:
    biocontext: EGA.DATASET
    fairsharing: FAIRsharing.mya1ff
    miriam: ega.dataset
    n2t: ega.dataset
  miriam:
    deprecated: false
    description: The EGA is a service for permanent archiving and sharing of all types
      of personally identifiable genetic and phenotypic data resulting from biomedical
      research projects. The EGA contains exclusive data collected from individuals
      whose consent agreements authorize data release only for specific research use
      or to bona fide researchers. Strict protocols govern how information is managed,
      stored and distributed by the EGA project. This collection references 'Datasets'.
    homepage: https://www.ebi.ac.uk/ega/dataset
    id: '00000512'
    name: European Genome-phenome Archive Dataset
    namespaceEmbeddedInLui: false
    pattern: ^EGAD\d{11}$
    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
ega.study:
  biocontext:
    is_identifiers: true
    is_obo: false
    prefix: EGA.STUDY
    uri_format: http://identifiers.org/ega.study/$1
  mappings:
    biocontext: EGA.STUDY
    miriam: ega.study
    n2t: ega.study
  miriam:
    deprecated: false
    description: The EGA is a service for permanent archiving and sharing of all types
      of personally identifiable genetic and phenotypic data resulting from biomedical
      research projects. The EGA contains exclusive data collected from individuals
      whose consent agreements authorize data release only for specific research use
      or to bona fide researchers. Strict protocols govern how information is managed,
      stored and distributed by the EGA project. This collection references 'Studies'
      which are experimental investigations of a particular phenomenon, often drawn
      from different datasets.
    homepage: https://www.ebi.ac.uk/ega/studies
    id: '00000511'
    name: European Genome-phenome Archive Study
    namespaceEmbeddedInLui: false
    pattern: ^EGAS\d{11}$
    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
eggnog:
  biocontext:
    is_identifiers: true
    is_obo: false
    prefix: EGGNOG
    uri_format: http://identifiers.org/eggnog/$1
  fairsharing:
    abbreviation: eggNOG
    description: 'eggNOG (evolutionary genealogy of genes: Non-supervised Orthologous
      Groups) is a database of orthologous groups of genes. The orthologous groups
      are annotated with functional description lines (derived by identifying a common
      denominator for the genes based on their various annotations), with functional
      categories (i.e derived from the original COG/KOG categories).'
    id: '1577'
    name: 'Evolutionary Genealogy of Genes: Non-supervised Orthologous Groups'
    prefix: FAIRsharing.j1wj7d
    subjects:
    - Life Science
  mappings:
    biocontext: EGGNOG
    fairsharing: FAIRsharing.j1wj7d
    miriam: eggnog
    n2t: eggnog
    prefixcommons: eggnog
    uniprot: eggNOG
  miriam:
    deprecated: false
    description: 'eggNOG (evolutionary genealogy of genes: Non-supervised Orthologous
      Groups) is a database of orthologous groups of genes. The orthologous groups
      are annotated with functional description lines (derived by identifying a common
      denominator for the genes based on their various annotations), with functional
      categories (i.e derived from the original COG/KOG categories).'
    homepage: http://eggnog.embl.de/version_3.0/
    id: '00000201'
    name: eggNOG
    namespaceEmbeddedInLui: false
    pattern: ^\w+$
    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=$1
  prefixcommons:
    description: 'eggNOG (evolutionary genealogy of genes: Non-supervised Orthologous
      Groups) is a database of orthologous groups of genes. The orthologous groups
      are annotated with functional description lines (derived by identifying a common
      denominator for the genes based on their various annotations), with functional
      categories (i.e derived from the original COG/KOG categories).'
    example: NOG80852
    homepage: http://eggnog.embl.de
    keywords:
    - gene
    name: 'Evolutionary Genealogy of Genes: Non-supervised Orthologous Groups'
    pattern: ^\w+$
    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
  uniprot:
    category: Phylogenomic databases
    identifier: '152'
    link_is_explicit: 'true'
    name: 'evolutionary genealogy of genes: Non-supervised Orthologous Groups'
    prefix: eggNOG
    uri_format: http://eggnogdb.embl.de/#/app/results?seqid=%u&target_nogs=%s
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:
    is_identifiers: false
    is_obo: true
    prefix: EHDA
    uri_format: http://purl.obolibrary.org/obo/EHDA_$1
  bioportal:
    contact:
      email: J.Bard@ed.ac.uk
      name: Jonathan Bard
    description: A structured controlled vocabulary of stage-specific anatomical structures
      of the human. It has been designed to mesh with the mouse anatomy and incorporates
      each Carnegie stage of development (CS1-20). The timed version of the human
      developmental anatomy ontology gives all the tissues present at each Carnegie
      Stage (CS) of human development (1-20) linked by a part-of rule. Each term is
      mentioned only once so that the embryo at each stage can be seen as the simple
      sum of its parts. Users should note that tissues that are symmetric (e.g. eyes,
      ears, limbs) are only mentioned once.
    homepage: http://obofoundry.org/ontology/ehda.html
    name: Human Developmental Anatomy Ontology, timed version
    prefix: EHDA
    version: unknown
  example: '1'
  mappings:
    aberowl: EHDA
    biocontext: EHDA
    bioportal: EHDA
    obofoundry: ehda
    prefixcommons: ehda
  obofoundry:
    contact: J.Bard@ed.ac.uk
    contact.label: Jonathan Bard
    deprecated: true
    homepage: http://genex.hgu.mrc.ac.uk/
    name: Human developmental anatomy, timed version
    prefix: ehda
  pattern: ^\d+$
  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:
    is_identifiers: false
    is_obo: true
    prefix: EHDAA
    uri_format: http://purl.obolibrary.org/obo/EHDAA_$1
  bioportal:
    contact:
      email: J.Bard@ed.ac.uk
      name: Jonathan Bard
    description: A structured controlled vocabulary of stage-specific anatomical structures
      of the human. It has been designed to mesh with the mouse anatomy and incorporates
      each Carnegie stage of development (CS1-20). The abstract version of the human
      developmental anatomy ontology compresses all the tissues present over Carnegie
      stages 1-20 into a single hierarchy. The heart, for example, is present from
      Carnegie Stage 9 onwards and is thus represented by 12 EHDA IDs (one for each
      stage). In the abstract mouse, it has a single ID so that the abstract term
      given as just <i>heart</i> really means <i>heart (CS 9-20)</i>. Timing details
      will be added to the abstract version of the ontology in a future release.
    homepage: http://obofoundry.org/ontology/ehdaa.html
    name: Human Developmental Anatomy Ontology, abstract version 1
    prefix: EHDAA
    version: unknown
  example: '1'
  mappings:
    aberowl: EHDAA
    biocontext: EHDAA
    bioportal: EHDAA
    obofoundry: ehdaa
    prefixcommons: ehdaa
  obofoundry:
    contact: J.Bard@ed.ac.uk
    contact.label: Jonathan Bard
    deprecated: true
    name: Human developmental anatomy, abstract version
    prefix: ehdaa
  pattern: ^\d+$
  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:
    is_identifiers: false
    is_obo: true
    prefix: EHDAA2
    uri_format: http://purl.obolibrary.org/obo/EHDAA2_$1
  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/2022-09-13
  example: '0000000'
  fairsharing:
    abbreviation: EHDAA2
    description: "The EHDAA2 ontology is a human developmental anatomy covering the\
      \ first 49 days [Carnegie stages (CS)1\u201320], 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.\
      \ The intention has been to include as much information about human developmental\
      \ anatomy as is practical and as is available in the literature."
    id: '199'
    name: Edinburgh human developmental anatomy abstract version 2
    prefix: FAIRsharing.7zxrs6
    publications:
    - doi: 10.1111/j.1469-7580.2012.01566.x
      pubmed_id: 22973865
      title: A new ontology (structured hierarchy) of human developmental anatomy
        for the first 7 weeks (Carnegie stages 1-20).
    subjects:
    - Anatomy
    - Life Science
    - Biomedical Science
  mappings:
    aberowl: EHDAA2
    biocontext: EHDAA2
    bioportal: EHDAA2
    fairsharing: FAIRsharing.7zxrs6
    obofoundry: ehdaa2
    ols: ehdaa2
    ontobee: EHDAA2
  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.
    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: http://purl.obolibrary.org/obo/ehdaa2.owl
    homepage: https://github.com/obophenotype/human-developmental-anatomy-ontology
    name: Human developmental anatomy, abstract
    prefix: ehdaa2
    version: '2013-07-04'
    version.iri: http://purl.obolibrary.org/obo/ehdaa2/releases/2013-07-04/ehdaa2.owl
  ontobee:
    library: Library
    name: Human developmental anatomy, abstract
    prefix: EHDAA2
  pattern: ^\d{7}$
  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
  synonyms:
  - EHDAA2_RETIRED
  - HDAA2
  - RETIRED_EHDAA2
elm:
  biocontext:
    is_identifiers: true
    is_obo: false
    prefix: ELM
    uri_format: http://identifiers.org/elm/$1
  fairsharing:
    abbreviation: ELM
    description: This computational biology resource mainly focuses on annotation
      and detection of eukaryotic linear motifs (ELMs) by providing both a repository
      of annotated motif data and an exploratory tool for motif prediction. ELMs,
      or short linear motifs (SLiMs), are compact protein interaction sites composed
      of short stretches of adjacent amino acids.
    id: '1578'
    name: Eukaryotic Linear Motifs
    prefix: FAIRsharing.rj3kj5
    subjects:
    - Life Science
  mappings:
    biocontext: ELM
    fairsharing: FAIRsharing.rj3kj5
    miriam: elm
    n2t: elm
    uniprot: ELM
  miriam:
    deprecated: false
    description: Linear motifs are short, evolutionarily plastic components of regulatory
      proteins. Mainly focused on the eukaryotic sequences,the Eukaryotic Linear Motif
      resource (ELM) is a database of curated motif classes and instances.
    homepage: http://elm.eu.org/
    id: '00000250'
    name: ELM
    namespaceEmbeddedInLui: false
    pattern: ^[A-Za-z_0-9]+$
    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
  uniprot:
    category: Protein-protein interaction databases
    identifier: '223'
    link_is_explicit: 'true'
    name: The Eukaryotic Linear Motif resource for Functional Sites in Proteins
    prefix: ELM
    uri_format: http://elm.eu.org/instances.html?q=$1
emap:
  biocontext:
    is_identifiers: false
    is_obo: true
    prefix: EMAP
    uri_format: http://purl.obolibrary.org/obo/EMAP_$1
  bioportal:
    name: Mouse Gross Anatomy and Development Ontology
    prefix: EMAP
  example: '1'
  mappings:
    biocontext: EMAP
    bioportal: EMAP
    obofoundry: emap
  obofoundry:
    contact: Terry.Hayamizu@jax.org
    contact.github: tfhayamizu
    contact.label: Terry Hayamizu
    contact.orcid: 0000-0002-0956-8634
    deprecated: true
    description: A structured controlled vocabulary of stage-specific anatomical structures
      of the mouse (Mus).
    download.owl: http://purl.obolibrary.org/obo/emap.owl
    homepage: http://emouseatlas.org
    name: Mouse gross anatomy and development, timed
    prefix: emap
  pattern: ^\d+$
emapa:
  aberowl:
    description: An ontology for mouse anatomy covering embryonic development and
      postnatal stages.
    download_owl: http://aber-owl.net/media/ontologies/EMAPA/21/emapa.owl
    homepage: http://www.informatics.jax.org/expression.shtml
    name: Mouse Developmental Anatomy Ontology
    prefix: EMAPA
  biocontext:
    is_identifiers: false
    is_obo: true
    prefix: EMAPA
    uri_format: http://purl.obolibrary.org/obo/EMAPA_$1
  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: Abstract (i.e. non-stage specific) stage-specific anatomical structures
      of the mouse.
    id: '513'
    name: Mouse gross anatomy and development, timed
    prefix: FAIRsharing.j0fa1d
    publications: []
    subjects: []
  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:$1
  mappings:
    aberowl: EMAPA
    biocontext: EMAPA
    bioportal: EMAPA
    fairsharing: FAIRsharing.j0fa1d
    go: EMAPA
    obofoundry: emapa
    ols: emapa
    ontobee: EMAPA
  obofoundry:
    contact: Terry.Hayamizu@jax.org
    contact.github: tfhayamizu
    contact.label: Terry Hayamizu
    contact.orcid: 0000-0002-0956-8634
    deprecated: false
    description: An ontology for mouse anatomy covering embryonic development and
      postnatal stages.
    download.obo: http://purl.obolibrary.org/obo/emapa.obo
    download.owl: http://purl.obolibrary.org/obo/emapa.owl
    homepage: http://www.informatics.jax.org/expression.shtml
    license: CC BY 4.0
    license.url: https://creativecommons.org/licenses/by/4.0/
    name: Mouse Developmental Anatomy Ontology
    preferredPrefix: EMAPA
    prefix: emapa
    repository: https://github.com/obophenotype/mouse-anatomy-ontology
  ols:
    description: An ontology for mouse anatomy covering embryonic development and
      postnatal stages.
    download: http://purl.obolibrary.org/obo/emapa.owl
    homepage: http://www.informatics.jax.org/expression.shtml
    name: Mouse Developmental Anatomy Ontology
    prefix: emapa
    version: '2022-07-14'
    version.iri: http://purl.obolibrary.org/obo/emapa/releases/2022-07-14/emapa.owl
  ontobee:
    library: Library
    name: Mouse Developmental Anatomy Ontology
    prefix: EMAPA
  pattern: ^\d+$
  synonyms:
  - EMAPA_RETIRED
emdb:
  biocontext:
    is_identifiers: true
    is_obo: false
    prefix: EMDB
    uri_format: http://identifiers.org/emdb/$1
  edam:
    description: Identifier of an entry from the EMDB electron microscopy database.
    name: EMDB
    obsolete: false
    prefix: '1146'
  fairsharing:
    abbreviation: EMDB
    description: Cryo-electron microscopy reconstruction methods are uniquely able
      to reveal structures of many important macromolecules and macromolecular complexes.
      The Electron Microscopy Data Bank (EMDB) is a public repository for electron
      microscopy density maps of macromolecular complexes and subcellular structures.
      It covers a variety of techniques, including single-particle analysis, electron
      tomography, and electron (2D) crystallography. The EMDB was founded at EBI in
      2002, under the leadership of Kim Henrick. Since 2007 it has been operated jointly
      by the PDBe, and the Research Collaboratory for Structural Bioinformatics (RCSB
      PDB) as a part of EMDataBank which is funded by a joint NIH grant to PDBe, the
      RCSB and the National Center for Macromolecular Imaging (NCMI).
    id: '2126'
    name: Electron Microscopy Data Bank
    prefix: FAIRsharing.651n9j
    subjects:
    - Virology
    - Biology
    - Epidemiology
  mappings:
    biocontext: EMDB
    edam: '1146'
    fairsharing: FAIRsharing.651n9j
    miriam: emdb
    n2t: emdb
  miriam:
    deprecated: false
    description: The Electron Microscopy Data Bank (EMDB) is a public repository for
      electron microscopy density maps of macromolecular complexes and subcellular
      structures. It covers a variety of techniques, including single-particle analysis,
      electron tomography, and electron (2D) crystallography. The EMDB map distribution
      format follows the CCP4 definition, which is widely recognized by software packages
      used by the structural biology community.
    homepage: https://www.ebi.ac.uk/pdbe/emdb/
    id: '00000561'
    name: Electron Microscopy Data Bank
    namespaceEmbeddedInLui: false
    pattern: ^EMD-\d{4}$
    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/$1
emolecules:
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: Catalog of purchasable reagents and building blocks
  example: '491187'
  homepage: https://reaxys.emolecules.com
  name: Reaxys eMolecules
  pattern: ^\d+$
  uri_format: https://reaxys.emolecules.com/cgi-bin/more?vid=$1
empiar:
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: EMPIAR, the Electron Microscopy Public Image Archive, is a public resource
    for raw, 2D electron microscopy images. Here, you can browse, upload and download
    the raw images used to build a 3D structure
  example: '10595'
  fairsharing:
    abbreviation: EMPIAR
    description: EMPIAR, the Electron Microscopy Public Image Archive, is a public
      resource for raw electron microscopy images. Here, you can browse, upload and
      download the raw images used to build a 3D structure. The purpose of EMPIAR
      is to provide easy access to state-of-the-art raw data to facilitate methods
      development and validation, which will lead to better 3D structures. It complements
      the Electron Microscopy Data Bank (EMDB), where 3D volumes are stored.
    id: '2649'
    name: Electron Microscopy Public Image Archive
    prefix: FAIRsharing.dff3ef
    subjects:
    - Bioinformatics
    - Biology
  homepage: https://www.ebi.ac.uk/pdbe/emdb
  mappings:
    fairsharing: FAIRsharing.dff3ef
  name: Electron Microscopy Public Image Archive
  pattern: ^\d+$
  uri_format: https://www.ebi.ac.uk/pdbe/emdb/empiar/entry/$1
ena.embl:
  biocontext:
    is_identifiers: true
    is_obo: false
    prefix: ENA.EMBL
    uri_format: http://identifiers.org/ena.embl/$1
  fairsharing:
    abbreviation: ENA
    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.
    id: '1850'
    name: European Nucleotide Archive
    prefix: FAIRsharing.dj8nt8
    subjects:
    - Functional Genomics
    - Metagenomics
    - Genomics
    - Bioinformatics
    - Data Management
    - Biodiversity
    - Transcriptomics
  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/$1
  mappings:
    biocontext: ENA.EMBL
    fairsharing: FAIRsharing.dj8nt8
    go: ENA
    miriam: ena.embl
    n2t: ena.embl
    prefixcommons: ena
  miriam:
    deprecated: false
    description: The European Nucleotide Archive (ENA) captures and presents information
      relating to experimental workflows that are based around nucleotide sequencing.
      ENA is made up of a number of distinct databases that includes EMBL-Bank, the
      Sequence Read Archive (SRA) and the Trace Archive each with their own data formats
      and standards. This collection references Embl-Bank identifiers.
    homepage: https://www.ebi.ac.uk/ena/
    id: '00000372'
    name: ENA
    namespaceEmbeddedInLui: false
    pattern: ^[A-Z]+[0-9]+(\.\d+)?$
    prefix: ena.embl
    providers:
    - code: CURATOR_REVIEW
      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/$1
  prefixcommons:
    description: The European Nucleotide Archive (ENA) captures and presents information
      relating to experimental workflows that are based around nucleotide sequencing.
      A typical workflow includes the isolation and preparation of material for sequencing,
      a run of a sequencing machine in which sequencing data are produced and a subsequent
      bioinformatic analysis pipeline.
    example: BN000065
    homepage: http://www.ebi.ac.uk/ena/
    keywords:
    - DNA
    name: European Nucleotide Archive
    pattern: ^[A-Z]+[0-9]+$
    prefix: ena
    uri_format: http://www.ebi.ac.uk/ena/data/view/$1
  synonyms:
  - ena
  uri_format: https://www.ebi.ac.uk/ena/browser/view/$1
encode:
  biocontext:
    is_identifiers: true
    is_obo: false
    prefix: ENCODE
    uri_format: http://identifiers.org/encode/$1
  cellosaurus:
    category: Biological sample resources
    homepage: https://www.encodeproject.org
    name: Encyclopedia of DNA Elements
    prefix: ENCODE
    uri_format: https://www.encodeproject.org/biosamples/$1
  fairsharing:
    abbreviation: ENCODE
    description: Encyclopedia of DNA Elements (ENCODE) has created a comprehensive
      parts list of functional elements in the human genome, including elements that
      act at the protein and RNA levels, and regulatory elements that control cells
      and circumstances in which a gene is active. UCSC coordinated data for the ENCODE
      Consortium from its inception in 2003 (Pilot phase) to the end of the first
      5 year phase of whole-genome data production in 2012. All data produced by ENCODE
      investigators and the results of ENCODE analysis projects from this period are
      hosted in the UCSC Genome browser and database.
    id: '1579'
    name: Encyclopedia of DNA Elements at UCSC
    prefix: FAIRsharing.v0hbjs
    subjects:
    - Life Science
  homepage: https://www.encodeproject.org
  mappings:
    biocontext: ENCODE
    cellosaurus: ENCODE
    fairsharing: FAIRsharing.v0hbjs
    miriam: encode
    n2t: encode
    re3data: r3d100013051
  miriam:
    deprecated: false
    description: The ENCODE Consortium is integrating multiple technologies and approaches
      in a collective effort to discover and define the functional elements encoded
      in the human genome, including genes, transcripts, and transcriptional regulatory
      regions, together with their attendant chromatin states and DNA methylation
      patterns.
    homepage: www.encodeproject.org
    id: '00000662'
    name: 'ENCODE: Encyclopedia of DNA Elements'
    namespaceEmbeddedInLui: false
    pattern: ^ENC[A-Za-z]{2}[0-9]{3}[A-Za-z]{3}$
    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
  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."
    homepage: https://www.encodeproject.org/
    name: ENCODE
    prefix: r3d100013051
    synonyms:
    - ENCODE  Encyclopedia
    - Encyclopedia of DNA Elements
    xrefs:
      fairsharing: FAIRsharing.7ykpy5
      miriam: '00000662'
      omics: '00532'
      scr: 015482
enm:
  aberowl:
    download_owl: http://aber-owl.net/media/ontologies/ENM/17/enm.owl
    name: eNanoMapper
    prefix: ENM
    version: '6.0'
  bioportal:
    contact:
      email: hsarimv@central.ntua.gr
      name: Haralambos Sarimveis
    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
    publication: http://enanomapper.net/library
    version: '8.0'
  example: '8000221'
  fairsharing:
    abbreviation: ENM
    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.
    id: '493'
    name: eNanoMapper Ontology
    prefix: FAIRsharing.2gpf81
    publications:
    - doi: 10.1186/s13326-015-0005-5
      pubmed_id: 25815161
      title: 'eNanoMapper: harnessing ontologies to enable data integration for nanomaterial
        risk assessment.'
    subjects:
    - Health Science
  mappings:
    aberowl: ENM
    bioportal: ENM
    fairsharing: FAIRsharing.2gpf81
    ols: enm
  ols:
    description: 'The eNanoMapper project (www.enanomapper.net) is 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: http://enanomapper.github.io/ontologies/enanomapper.owl
    homepage: http://www.enanomapper.net/
    name: eNanoMapper Ontology
    prefix: enm
    version: '7.4'
  pattern: ^\d+$
  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
  uri_format: http://purl.enanomapper.org/onto/ENM_$1
ensembl:
  biocontext:
    is_identifiers: false
    is_obo: false
    prefix: ENSEMBL
    uri_format: http://ensembl.org/id/$1
  edam:
    description: Identifier of an entry (exon, gene, transcript or protein) from the
      Ensembl database.
    name: Ensembl
    obsolete: false
    prefix: '2610'
  example_extras:
  - ENSG00000049246.14
  - ENSG00000109819.9
  - ENSG00000132326.12
  - ENSG00000179094.16
  - ENST00000264867.7
  fairsharing:
    abbreviation: Ensembl
    description: Ensembl creates, integrates and distributes reference datasets and
      analysis tools that enable genomics. Ensembl is a genome browser that supports
      research in comparative genomics, evolution, sequence variation and transcriptional
      regulation. Ensembl annotate genes, computes multiple alignments, predicts regulatory
      function and collects disease data.
    id: '1867'
    name: Ensembl
    prefix: FAIRsharing.fx0mw7
    subjects:
    - Genomics
    - Biomedical Science
    - Comparative Genomics
  go:
    homepage: http://www.ensembl.org/
    name: Ensembl database of automatically annotated genomic data
    prefix: ENSEMBL
    synonyms:
    - Ensembl
    - ensembl
  mappings:
    biocontext: ENSEMBL
    edam: '2610'
    fairsharing: FAIRsharing.fx0mw7
    go: ENSEMBL
    miriam: ensembl
    n2t: ensembl
    ncbi: ENSEMBL
    prefixcommons: ensembl
    re3data: r3d100010228
    uniprot: Ensembl
    wikidata: P594
  miriam:
    deprecated: false
    description: Ensembl is a joint project between EMBL - EBI and the Sanger Institute  to
      develop a software system which produces and maintains automatic annotation
      on selected eukaryotic genomes. This collections also references outgroup organisms.
    homepage: https://www.ensembl.org/
    id: '00000003'
    name: Ensembl
    namespaceEmbeddedInLui: false
    pattern: ^((ENS[FPTG]\\d{11}(\\.\\d+)?)|(FB\\w{2}\\d{7})|(Y[A-Z]{2}\\d{3}[a-zA-Z](\\-[A-Z])?)|([A-Z_a-z0-9]+(\\.)?(t)?(\\d+)?([a-z])?))$
    prefix: ensembl
    providers:
    - code: CURATOR_REVIEW
      description: Ensembl US West mirror
      homepage: http://uswest.ensembl.org/
      name: Ensembl US West mirror
      uri_format: http://uswest.ensembl.org/id/$1
    - code: CURATOR_REVIEW
      description: Ensembl US East mirror
      homepage: http://useast.ensembl.org/
      name: Ensembl US East mirror
      uri_format: http://useast.ensembl.org/id/$1
    - code: CURATOR_REVIEW
      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/$1
  name: Ensembl Gene
  ncbi:
    example: HUMAN-Clone-AC005612
    homepage: http://useast.ensembl.org/index.html
    name: Database of automatically annotated genomic data
    prefix: ENSEMBL
  pattern: ^((ENS[FPTG]\d{11}(\.\d+)?)|(FB\w{2}\d{7})|(Y[A-Z]{2}\d{3}[a-zA-Z](\-[A-Z])?)|([A-Z_a-z0-9]+(\.)?(t)?(\d+)?([a-z])?))$
  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
    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
    homepage: https://bgee.org
    name: Bgee
    uri_format: https://bgee.org/?page=gene&gene_id=$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.
    homepage: https://gnomad.broadinstitute.org
    name: Genome Aggregation database
    uri_format: https://gnomad.broadinstitute.org/gene/$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.
    homepage: https://genetics.opentargets.org
    name: OpenTargets Genetics
    uri_format: https://genetics.opentargets.org/gene/$1
  publications:
  - doi: 10.1093/nar/gkj133
    pmc: PMC1347495
    pubmed: '16381931'
    title: Ensembl 2006.
    year: 2006
  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.
    homepage: https://www.ensembl.org/index.html
    name: Ensembl
    prefix: r3d100010228
    synonyms:
    - e!
    xrefs:
      fairsharing: FAIRsharing.fx0mw7
      miriam: '00100011'
      nif: 0000-21145
      omics: '01647'
      scr: '002344'
  synonyms:
  - Ensembl
  uniprot:
    category: Genome annotation databases
    identifier: '23'
    link_is_explicit: 'true'
    name: Ensembl eukaryotic genome annotation project
    prefix: Ensembl
    uri_format: https://www.ensembl.org/id/$1
  wikidata:
    database: Q1344256
    database.homepage: http://www.ensembl.org/
    database.label: Ensembl genome database project
    description: identifier for a gene as per the Ensembl (European Bioinformatics
      Institute and the Wellcome Trust Sanger Institute) database
    format.rdf: http://rdf.ebi.ac.uk/resource/ensembl/$1
    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
ensembl.bacteria:
  biocontext:
    is_identifiers: true
    is_obo: false
    prefix: ENSEMBL.BACTERIA
    uri_format: http://identifiers.org/ensembl.bacteria/$1
  fairsharing:
    abbreviation: Ensembl Bacteria
    description: Ensembl Bacteria is a browser for bacterial and archaeal genomes.
      These are taken from the databases of the International Nucleotide Sequence
      Database Collaboration (the European Nucleotide Archive at the EBI, GenBank
      at the NCBI, and the DNA Database of Japan).
    id: '2402'
    name: Ensembl Bacteria
    prefix: FAIRsharing.zsgmvd
    subjects:
    - Genomics
    - Comparative Genomics
  mappings:
    biocontext: ENSEMBL.BACTERIA
    fairsharing: FAIRsharing.zsgmvd
    miriam: ensembl.bacteria
    n2t: ensembl.bacteria
    prefixcommons: ensembl.bacteria
    re3data: r3d100011195
    uniprot: EnsemblBacteria
  miriam:
    deprecated: false
    description: Ensembl Genomes consists of five sub-portals (for bacteria, protists,
      fungi, plants and invertebrate metazoa) designed to complement the availability
      of vertebrate genomes in Ensembl. This collection is concerned with bacterial
      genomes.
    homepage: https://bacteria.ensembl.org/
    id: '00000202'
    name: Ensembl Bacteria
    namespaceEmbeddedInLui: false
    pattern: ^((EB\w+)|([A-Z0-9]+\_[A-Z0-9]+))$
    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/$1
  prefixcommons:
    description: Ensembl Genomes consists of five sub-portals (for bacteria, protists,
      fungi, plants and invertebrate metazoa) designed to complement the availability
      of vertebrate genomes in Ensembl. This collection is concerned with bacterial
      genomes.
    example: EBESCT00000015660
    homepage: http://bacteria.ensembl.org/
    keywords:
    - genome
    name: Ensembl Bacteria
    pattern: ^EB\w+$
    prefix: ensembl.bacteria
    pubmed_ids:
    - '19884133'
    uri_format: http://bacteria.ensembl.org/[?species_name]/Gene/Summary?g=$1
  publications:
  - doi: 10.1093/nar/gkp871
    pmc: PMC2808935
    pubmed: '19884133'
    title: 'Ensembl Genomes: extending Ensembl across the taxonomic space.'
    year: 2009
  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.
    homepage: http://bacteria.ensembl.org/index.html
    name: Ensembl Bacteria
    prefix: r3d100011195
    synonyms:
    - e!EnsemblBacteria
    xrefs:
      fairsharing: FAIRsharing.zsgmvd
      miriam: '00000202'
      nif: 0000-33711
      scr: 008679
  uniprot:
    category: Genome annotation databases
    identifier: '147'
    link_is_explicit: 'true'
    name: Ensembl bacterial and archaeal genome annotation project
    prefix: EnsemblBacteria
    uri_format: http://www.ensemblgenomes.org/id/$1
ensembl.fungi:
  biocontext:
    is_identifiers: true
    is_obo: false
    prefix: ENSEMBL.FUNGI
    uri_format: http://identifiers.org/ensembl.fungi/$1
  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.
    id: '2405'
    name: Ensembl Fungi
    prefix: FAIRsharing.bg5xqs
    subjects:
    - Genomics
    - Comparative Genomics
  go:
    homepage: http://fungi.ensembl.org/
    name: Ensembl Fungi, the Ensembl database for accessing genome-scale data from
      fungi.
    prefix: EnsemblFungi
    uri_format: http://www.ensemblgenomes.org/id/$1
  mappings:
    biocontext: ENSEMBL.FUNGI
    fairsharing: FAIRsharing.bg5xqs
    go: EnsemblFungi
    miriam: ensembl.fungi
    n2t: ensembl.fungi
    prefixcommons: ensembl.fungi
    re3data: r3d100011196
    uniprot: EnsemblFungi
  miriam:
    deprecated: false
    description: Ensembl Genomes consists of five sub-portals (for bacteria, protists,
      fungi, plants and invertebrate metazoa) designed to complement the availability
      of vertebrate genomes in Ensembl. This collection is concerned with fungal genomes.
    homepage: https://fungi.ensembl.org/
    id: '00000206'
    name: Ensembl Fungi
    namespaceEmbeddedInLui: false
    pattern: ^[A-Z-a-z0-9]+$
    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/$1
  prefixcommons:
    description: Ensembl Genomes consists of five sub-portals (for bacteria, protists,
      fungi, plants and invertebrate metazoa) designed to complement the availability
      of vertebrate genomes in Ensembl. This collection is concerned with bacterial
      genomes.
    example: CADAFLAT00006211
    homepage: http://fungi.ensembl.org/
    keywords:
    - genome
    name: Ensembl Fungi
    pattern: ^\w+$
    prefix: ensembl.fungi
    uri_format: http://fungi.ensembl.org/[?species_name]/Gene/Summary?g=$1
  re3data:
    description: EnsemblFungi is a genome-centric portal for fungal species. It is
      a project to maintain annotation on selected genomes.
    homepage: http://fungi.ensembl.org/index.html
    name: Ensembl Fungi
    prefix: r3d100011196
    synonyms:
    - e!EnsemblFungi
    xrefs:
      fairsharing: FAIRsharing.bg5xqs
      miriam: '00000206'
      nif: 0000-33718
      scr: 008681
  uniprot:
    category: Genome annotation databases
    identifier: '148'
    link_is_explicit: 'true'
    name: Ensembl fungal genome annotation project
    prefix: EnsemblFungi
    uri_format: http://www.ensemblgenomes.org/id/$1
ensembl.metazoa:
  biocontext:
    is_identifiers: true
    is_obo: false
    prefix: ENSEMBL.METAZOA
    uri_format: http://identifiers.org/ensembl.metazoa/$1
  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.
    id: '2406'
    name: Ensembl Metazoa
    prefix: FAIRsharing.c23cqq
    subjects:
    - Genomics
    - Comparative Genomics
  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/$1
  mappings:
    biocontext: ENSEMBL.METAZOA
    fairsharing: FAIRsharing.c23cqq
    go: EnsemblMetazoa
    miriam: ensembl.metazoa
    n2t: ensembl.metazoa
    prefixcommons: ensembl.metazoa
    re3data: r3d100011198
    uniprot: EnsemblMetazoa
  miriam:
    deprecated: false
    description: Ensembl Genomes consists of five sub-portals (for bacteria, protists,
      fungi, plants and invertebrate metazoa) designed to complement the availability
      of vertebrate genomes in Ensembl. This collection is concerned with metazoa
      genomes.
    homepage: https://metazoa.ensembl.org/
    id: '00000204'
    name: Ensembl Metazoa
    namespaceEmbeddedInLui: false
    pattern: ^\w+(\.)?\d+$
    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/$1
  prefixcommons:
    description: Ensembl Genomes consists of five sub-portals (for bacteria, protists,
      fungi, plants and invertebrate metazoa) designed to complement the availability
      of vertebrate genomes in Ensembl. This collection is concerned with bacterial
      genomes.
    example: AGAP006864
    homepage: http://metazoa.ensembl.org/
    keywords:
    - genome
    name: Ensembl Metazoa
    pattern: ^\w+(\.)?\d+$
    prefix: ensembl.metazoa
    uri_format: http://metazoa.ensembl.org/[?species_name]/Gene/Summary?g=$1
  re3data:
    description: Ensembl Metazoa is a genome-centric portal for metazoan species of
      scientific interest.
    homepage: http://metazoa.ensembl.org/index.html
    name: Ensembl Metazoa
    prefix: r3d100011198
    synonyms:
    - e!EnsemblMetazoa
    xrefs:
      fairsharing: FAIRsharing.c23cqq
      miriam: '00000204'
      nif: 0000-33714
      scr: 000800
  uniprot:
    category: Genome annotation databases
    identifier: '149'
    link_is_explicit: 'true'
    name: Ensembl metazoan genome annotation project
    prefix: EnsemblMetazoa
    uri_format: http://www.ensemblgenomes.org/id/$1
ensembl.plant:
  biocontext:
    is_identifiers: true
    is_obo: false
    prefix: ENSEMBL.PLANT
    uri_format: http://identifiers.org/ensembl.plant/$1
  mappings:
    biocontext: ENSEMBL.PLANT
    miriam: ensembl.plant
    n2t: ensembl.plant
    prefixcommons: ensembl.plant
  miriam:
    deprecated: false
    description: Ensembl Genomes consists of five sub-portals (for bacteria, protists,
      fungi, plants and invertebrate metazoa) designed to complement the availability
      of vertebrate genomes in Ensembl. This collection is concerned with plant genomes.
    homepage: https://plants.ensembl.org/
    id: '00000205'
    name: Ensembl Plants
    namespaceEmbeddedInLui: false
    pattern: ^\w+(\.\d+)?(\.\d+)?$
    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/$1
  prefixcommons:
    description: Ensembl Genomes consists of five sub-portals (for bacteria, protists,
      fungi, plants and invertebrate metazoa) designed to complement the availability
      of vertebrate genomes in Ensembl. This collection is concerned with bacterial
      genomes.
    example: LOC_Os12g44300
    homepage: http://plants.ensembl.org/
    keywords:
    - genome
    name: Ensembl Plants
    pattern: ^\w+$
    prefix: ensembl.plant
    synonyms:
    - ensembl_plants
    uri_format: http://plants.ensembl.org/[?species_name]/Gene/Summary?g=$1
ensembl.protist:
  biocontext:
    is_identifiers: true
    is_obo: false
    prefix: ENSEMBL.PROTIST
    uri_format: http://identifiers.org/ensembl.protist/$1
  mappings:
    biocontext: ENSEMBL.PROTIST
    miriam: ensembl.protist
    n2t: ensembl.protist
    prefixcommons: ensembl.protist
  miriam:
    deprecated: false
    description: Ensembl Genomes consists of five sub-portals (for bacteria, protists,
      fungi, plants and invertebrate metazoa) designed to complement the availability
      of vertebrate genomes in Ensembl. This collection is concerned with protist
      genomes.
    homepage: https://protists.ensembl.org
    id: '00000203'
    name: Ensembl Protists
    namespaceEmbeddedInLui: false
    pattern: ^\w+$
    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/$1
  prefixcommons:
    description: Ensembl Genomes consists of five sub-portals (for bacteria, protists,
      fungi, plants and invertebrate metazoa) designed to complement the availability
      of vertebrate genomes in Ensembl. This collection is concerned with bacterial
      genomes.
    example: PFC0120w
    homepage: http://protists.ensembl.org/
    keywords:
    - genome
    name: Ensembl Protists
    pattern: ^\w+$
    prefix: ensembl.protist
    synonyms:
    - ensembl_protists
    uri_format: http://protists.ensembl.org/[?species_name]/Gene/Summary?g=$1
ensemblglossary:
  example: 0000198
  mappings:
    ols: ensemblglossary
  ols:
    description: The Ensembl glossary lists the terms, data types and file types that
      are used in Ensembl and describes how they are used.
    download: https://raw.githubusercontent.com/Ensembl/ensembl-glossary/master/ensembl-glossary.owl
    homepage: http://ensembl.org/glossary
    name: Ensembl Glossary
    prefix: ensemblglossary
    version: '2021-07-14'
    version.iri: http://ensembl.org/glossary/ensembl-glossary/releases/2021-07-14/ensembl-glossary.owl
  pattern: ^\d{7}$
  uri_format: http://ensembl.org/glossary/ENSGLOSSARY_$1
envipath:
  fairsharing:
    abbreviation: enviPath
    description: enviPath is both a database and a prediction system, for the microbial
      biotransformation of organic environmental contaminants. The database provides
      the possibility to store and view experimentally observed biotransformation
      pathways, and supports the annotation of pathways with experimental and environmental
      conditions. The pathway prediction system provides different relative reasoning
      models to predict likely biotransformation pathways and products.
    id: '2242'
    name: enviPath
    prefix: FAIRsharing.g0c5qn
    subjects:
    - Environmental Science
  mappings:
    fairsharing: FAIRsharing.g0c5qn
    miriam: envipath
    re3data: r3d100012715
  miriam:
    deprecated: false
    description: enviPath is a database and prediction system for the microbial biotransformation
      of organic environmental contaminants. The database provides the possibility
      to store and view experimentally observed biotransformation pathways. The pathway
      prediction system provides different relative reasoning models to predict likely
      biotransformation pathways and products.
    homepage: https://envipath.org/
    id: '00000727'
    name: enviPath
    namespaceEmbeddedInLui: false
    pattern: ^[\w^_]{8}-[\w^_]{4}-[\w^_]{4}-[\w^_]{4}-[\w^_]{12}\/[\w-]+\/[\w^_]{8}-[\w^_]{4}-[\w^_]{4}-[\w^_]{4}-[\w^_]{12}$
    prefix: envipath
    sampleId: 32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/compound/b545cabc-8c9e-4b20-8848-efa015b481ea
    uri_format: https://envipath.org/package/$1
  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.
    homepage: https://envipath.org/
    name: enviPath
    prefix: r3d100012715
    synonyms:
    - The enironmental contaminant biotransormation pathway resource
    - 'including: Biocatalysis/Biodegradation Database EAWAG PPS Rules'
    xrefs:
      fairsharing: FAIRsharing.g0c5qn
      omics: '11129'
envo:
  aberowl:
    description: Ontology of environmental features and habitats
    download_owl: http://aber-owl.net/media/ontologies/ENVO/56/envo.owl
    homepage: http://environmentontology.org/
    name: Environment Ontology
    prefix: ENVO
  agroportal:
    contact:
      email: pier.buttigieg@awi.de
      name: 'Pier Luigi Buttigieg (ORCID: orcid.org/0000-0002-4366-3088)'
    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
    publication: https://doi.org/10.1186/s13326-016-0097-6
    repository: https://github.com/EnvironmentOntology/envo
    version: '2021-05-14'
  biocontext:
    is_identifiers: false
    is_obo: true
    prefix: ENVO
    uri_format: http://purl.obolibrary.org/obo/ENVO_$1
  bioportal:
    contact:
      email: http://orcid.org/0000-0002-4366-3088
      name: Pier Luigi Buttigieg
    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.'
    homepage: http://environmentontology.org/
    name: Environment Ontology
    prefix: ENVO
    publication: http://environmentontology.org/
    version: '2021-05-14'
  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.
    id: '919'
    name: Environment Ontology
    prefix: FAIRsharing.azqskx
    publications:
    - doi: 10.1186/s13326-016-0097-6
      pubmed_id: 27664130
      title: 'The environment ontology in 2016: bridging domains with increased scope,
        semantic density, and interoperation.'
    - doi: 10.1186/2041-1480-4-43
      pubmed_id: 24330602
      title: 'The environment ontology: contextualising biological and biomedical
        entities.'
    - doi: 10.1093/database/baw005
      pubmed_id: 26896844
      title: 'EXTRACT: interactive extraction of environment metadata and term suggestion
        for metagenomic sample annotation.'
    - doi: 10.7717/peerj.1470
      pubmed_id: 26713234
      title: Emerging semantics to link phenotype and environment.
    subjects:
    - Environmental Science
    - Ecology
    - Life Science
    - Nutritional Science
    - Epidemiology
  mappings:
    aberowl: ENVO
    agroportal: ENVO
    biocontext: ENVO
    bioportal: ENVO
    fairsharing: FAIRsharing.azqskx
    miriam: envo
    n2t: envo
    obofoundry: envo
    ols: envo
    ontobee: ENVO
  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: https://www.ebi.ac.uk/ols/ontologies/envo
    id: 00000591
    name: Environment Ontology
    namespaceEmbeddedInLui: true
    pattern: ^ENVO:\d{7,8}$
    prefix: envo
    sampleId: 09200010
    uri_format: https://www.ebi.ac.uk/ols/ontologies/envo/terms?obo_id=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:$1
  obofoundry:
    appears_in:
    - agro
    - cdno
    - ecocore
    - ecto
    - foodon
    - ons
    - pco
    - rbo
    - scdo
    contact: pier.buttigieg@awi.de
    contact.github: pbuttigieg
    contact.label: Pier Luigi Buttigieg
    contact.orcid: 0000-0002-4366-3088
    depends_on:
    - chebi
    - foodon
    - go
    - ncbitaxon
    - pco
    - po
    - ro
    - uberon
    deprecated: false
    description: An ontology of environmental systems, components, and processes.
    download.json: http://purl.obolibrary.org/obo/envo.json
    download.obo: http://purl.obolibrary.org/obo/envo.obo
    download.owl: http://purl.obolibrary.org/obo/envo.owl
    homepage: http://environmentontology.org/
    license: CC0 1.0
    license.url: http://creativecommons.org/publicdomain/zero/1.0/
    name: Environment Ontology
    preferredPrefix: ENVO
    prefix: envo
    publications:
    - id: https://doi.org/10.1186/2041-1480-4-43
      preferred: true
      title: 'The environment ontology: contextualising biological and biomedical
        entities'
    - id: https://doi.org/10.1186/s13326-016-0097-6
      title: 'The environment ontology in 2016: bridging domains with increased scope,
        semantic density, and interoperation'
    repository: https://github.com/EnvironmentOntology/envo
  ols:
    description: ENVO is an ontology which represents knowledge about environments,environmental
      processes, ecosystems, habitats, and related entities
    download: http://purl.obolibrary.org/obo/envo.owl
    homepage: http://environmentontology.org/
    name: The Environment Ontology
    prefix: envo
    version: '2021-05-14'
    version.iri: http://purl.obolibrary.org/obo/envo/releases/2021-05-14/envo.owl
  ontobee:
    library: Library
    name: Environment Ontology
    prefix: ENVO
  pattern: ^\d{7,8}$
  publications:
  - doi: 10.1186/2041-1480-4-43
    pmc: PMC3904460
    pubmed: '24330602'
    title: 'The environment ontology: contextualising biological and biomedical entities.'
    year: 2013
  - doi: 10.7717/peerj.1470
    pmc: PMC4690371
    pubmed: '26713234'
    title: Emerging semantics to link phenotype and environment.
    year: 2015
  - 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
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.
  example: ALX-210-175
  homepage: https://www.enzolifesciences.com
  name: Enzo Life Sciences
  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: cooperl@science.oregonstate.edu
      name: Laurel Cooper
    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
    publication: http://wiki.plantontology.org/index.php/Category:Publications
    version: releases/2020-08-21
  banana: EO
  biocontext:
    is_identifiers: false
    is_obo: true
    prefix: EO
    uri_format: http://purl.obolibrary.org/obo/EO_$1
  mappings:
    aberowl: EO
    agroportal: EO
    biocontext: EO
    miriam: eo
    n2t: eo
    obofoundry: eo
    prefixcommons: eo
  miriam:
    deprecated: false
    description: The Plant Environment Ontology is a set of standardized controlled
      vocabularies to describe various types of treatments given to an individual
      plant / a population or a cultured tissue and/or cell type sample to evaluate
      the response on its exposure. It also includes the study types, where the terms
      can be used to identify the growth study facility. Each growth facility such
      as field study, growth chamber, green house etc is a environment on its own
      it may also involve instances of biotic and abiotic environments as supplemental
      treatments used in these studies.
    homepage: http://archive.gramene.org/db/ontology/search_term?id=EO:0007359
    id: 00000518
    name: Plant Environment Ontology
    namespaceEmbeddedInLui: true
    pattern: ^(P)?EO\:\d{7}$
    prefix: eo
    sampleId: '0007404'
    uri_format: http://archive.gramene.org/db/ontology/search?query=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:$1
  obofoundry:
    appears_in:
    - foodon
    contact: jaiswalp@science.oregonstate.edu
    contact.github: jaiswalp
    contact.label: Pankaj Jaiswal
    contact.orcid: 0000-0002-1005-8383
    deprecated: true
    description: A structured, controlled vocabulary which describes the treatments,
      growing conditions, and/or study types used in plant biology experiments.
    download.obo: http://purl.obolibrary.org/obo/eo.obo
    download.owl: http://purl.obolibrary.org/obo/eo.owl
    homepage: http://planteome.org/
    license: CC BY 4.0
    license.url: https://creativecommons.org/licenses/by/4.0/
    name: Plant Environment Ontology
    prefix: eo
    publications:
    - id: https://www.ncbi.nlm.nih.gov/pubmed/22847540
      title: Ontologies as integrative tools for plant science.
    repository: https://github.com/Planteome/plant-environment-ontology
  pattern: ^\d{7}$
  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 d\xE9crit les conditions d'environnement des \xE9\
      levages d'animaux domestiques. Elle d\xE9crit plus particuli\xE8rement les modalit\xE9\
      s de l'alimentation, de l'environnement, de la structure des \xE9levages et\
      \ des syst\xE8mes d'\xE9levage"
    download_owl: http://aber-owl.net/media/ontologies/EOL/1/eol.owl
    name: Environment Ontology for Livestock
    prefix: EOL
  agroportal:
    contact:
      email: matthieu.reichstadt@inra.fr
      name: Matthieu Reichstadt
    description: "L'ontologie EOL d\xE9crit les conditions d'environnement des \xE9\
      levages d'animaux domestiques. Elle d\xE9crit plus particuli\xE8rement les modalit\xE9\
      s de l'alimentation, de l'environnement, de la structure des \xE9levages et\
      \ des syst\xE8mes d'\xE9levage., The EOL ontology describes environmental conditions\
      \ of livestock breeding. It includes feeding modalities, 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
    publication: http://www.atol-ontology.com/rb/fr/6
  bioportal:
    contact:
      email: pylebail@rennes.inra.fr
      name: LeBail Pierre-Yves
    description: "L'ontologie EOL d\xE9crit les conditions d'environnement des \xE9\
      levages d'animaux domestiques. Elle d\xE9crit plus particuli\xE8rement les modalit\xE9\
      s de l'alimentation, de l'environnement, de la structure des \xE9levages et\
      \ des syst\xE8mes d'\xE9levage"
    name: Environment Ontology for Livestock
    prefix: EOL
  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.
    id: '743'
    name: Environment Ontology for Livestock
    prefix: FAIRsharing.w7bw2y
    publications: []
    subjects:
    - Environmental Science
    - Animal Husbandry
    - Agriculture
  mappings:
    aberowl: EOL
    agroportal: EOL
    bioportal: EOL
    fairsharing: FAIRsharing.w7bw2y
    ols: eol
    re3data: r3d100011663
  ols:
    contact: pylebail@rennes.inra.fr
    description: "L'ontologie EOL d\xE9crit les conditions d'environnement des \xE9\
      levages d'animaux domestiques. Elle d\xE9crit plus particuli\xE8rement les modalit\xE9\
      s de l'alimentation, de l'environnement, de la structure des \xE9levages et\
      \ des syst\xE8mes d'\xE9levage"
    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}$
  re3data:
    description: "EOL\u2019s 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\u2019s data services are\
      \ committed to the highest standard of data stewardship from collection to validation\
      \ to archival."
    homepage: http://www.eol.ucar.edu/
    name: EOL
    prefix: r3d100011663
    synonyms:
    - Earth Observing Laboratory
  uri_format: http://purl.org/obo/owlEOL_$1
eolife:
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: A collaborative project intended to create an encyclopedia documenting
    all living species known to science
  example: '1044544'
  fairsharing:
    abbreviation: EOL
    description: The Encyclopedia of Life (EOL) is a collaborative encyclopedia to
      describe all known living species. It identifies sources of biodiversity knowledge
      that are legally and practically shareable; integrates them with other sources
      and adds metadata; provides searching and other services; and collaborates with
      other projects to support data sharing.
    id: '2888'
    name: Encyclopedia of Life
    prefix: FAIRsharing.3J6NYn
    subjects:
    - Taxonomy
    - Ecology
    - Biodiversity
    - Biology
  homepage: https://eol.org
  mappings:
    fairsharing: FAIRsharing.3J6NYn
    wikidata: P830
  name: Encyclopedia of Life
  pattern: ^\d+$
  uri_format: https://eol.org/pages/$1
  wikidata:
    database: Q82486
    database.homepage: https://eol.org
    database.label: Encyclopedia of Life
    description: eol.org item reference number
    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/ar/pages/$1
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
  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:
    is_identifiers: true
    is_obo: false
    prefix: EPD
    uri_format: http://identifiers.org/epd/$1
  edam:
    description: Identifier of an entry (promoter) from the EPD database.
    name: EPD
    obsolete: false
    prefix: '2386'
  fairsharing:
    abbreviation: EPD
    description: The EPD has been created and is maintained by the Lamond group in
      the University of Dundee. It combines a polyglot persistent database and web-application
      that provides open access to integrated proteomics data for >30 000 proteins
      from published studies on human cells and model organisms. It is designed to
      provide a user-friendly interface, featuring graphical navigation with interactive
      visualizations that facilitate powerful data exploration in an intuitive manner.
      The EPD offers a flexible and scalable ecosystem to integrate proteomics data
      with genomics information, RNA expression and other related, large-scale datasets.
    id: '2515'
    name: The Encyclopedia of Proteome Dynamics
    prefix: FAIRsharing.sym4ne
    subjects:
    - Proteomics
    - Life Science
    - Data Visualization
  mappings:
    biocontext: EPD
    edam: '2386'
    fairsharing: FAIRsharing.sym4ne
    miriam: epd
    n2t: epd
    ncbi: EPD
    uniprot: EPD
  miriam:
    deprecated: false
    description: The Eukaryotic Promoter Database (EPD) is an annotated non-redundant
      collection of eukaryotic POL II promoters, for which the transcription start
      site has been determined experimentally. Access to promoter sequences is provided
      by pointers to positions in nucleotide sequence entries. The annotation part
      of an entry includes description of the initiation site mapping data, cross-references
      to other databases, and bibliographic references. EPD is structured in a way
      that facilitates dynamic extraction of biologically meaningful promoter subsets
      for comparative sequence analysis.
    homepage: http://epd.vital-it.ch/
    id: 00000408
    name: EPD
    namespaceEmbeddedInLui: false
    pattern: ^[A-Z-_0-9]+$
    prefix: epd
    sampleId: TA_H3
    uri_format: http://epd.vital-it.ch/cgi-bin/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
  uniprot:
    category: Proteomic databases
    identifier: '205'
    link_is_explicit: 'true'
    name: Encyclopedia of Proteome Dynamics
    prefix: EPD
    uri_format: https://www.peptracker.com/epd/analytics/?protein_id=$1
epio:
  aberowl:
    description: A application driven Epilepsy Ontology with official terms from the
      ILAE.
    download_owl: http://aber-owl.net/media/ontologies/EPIO/2/epio.owl
    name: Epilepsy Ontology
    prefix: EPIO
  bioportal:
    name: EpilepsyOntology
    prefix: EPIO
  example: '0000011'
  mappings:
    aberowl: EPIO
    bioportal: EPIO
    obofoundry: epio
    ontobee: EPIO
  obofoundry:
    contact: alpha.tom.kodamullil@scai.fraunhofer.de
    contact.github: akodamullil
    contact.label: Alpha Tom Kodamullil
    contact.orcid: 0000-0001-9896-3531
    depends_on:
    - bfo
    deprecated: false
    description: A application driven Epilepsy Ontology with official terms from the
      ILAE.
    download.owl: http://purl.obolibrary.org/obo/epio.owl
    homepage: https://github.com/SCAI-BIO/EpilepsyOntology
    license: CC BY 4.0
    license.url: http://creativecommons.org/licenses/by/4.0/
    name: Epilepsy Ontology
    preferredPrefix: EPIO
    prefix: epio
    repository: https://github.com/SCAI-BIO/EpilepsyOntology
  ontobee:
    library: Library
    name: Epilepsy Ontology
    prefix: EPIO
  pattern: ^\d{7}$
epo:
  aberowl:
    description: The early pregnancy ontology contains the concepts to describe ectopic
      pregnancy ultrasound images, organized into several subsumption hierarchies
      for types of ectopic pregnancies and the signs, anatomical structures and technical
      elements of imaging associated with ectopic pregnancy. Version 1.1 was used
      for ultrasound image annotations (Dhombres et al. Developing a knowledge base
      to support the annotation of ultrasound images of ectopic pregnancy. J Biomed
      Semantics, 2017)
    download_owl: http://aber-owl.net/media/ontologies/EPO/1/epo.owl
    name: Early Pregnancy Ontology
    prefix: EPO
    version: '1.1'
  biocontext:
    is_identifiers: false
    is_obo: true
    prefix: EPO
    uri_format: http://purl.obolibrary.org/obo/EPO_$1
  bioportal:
    contact:
      email: ferdinand.dhombres@inserm.fr
      name: Ferdinand Dhombres
    description: The early pregnancy ontology contains the concepts to describe ectopic
      pregnancy ultrasound images, organized into several subsumption hierarchies
      for types of ectopic pregnancies and the signs, anatomical structures and technical
      elements of imaging associated with ectopic pregnancy. Version 1.1 was used
      for ultrasound image annotations (Dhombres et al. Developing a knowledge base
      to support the annotation of ultrasound images of ectopic pregnancy. J Biomed
      Semantics, 2017)
    name: Early Pregnancy Ontology
    prefix: EPO
    version: '1.1'
  download_owl: https://storage.googleapis.com/google-code-archive-downloads/v2/code.google.com/epidemiology-ontology/epo.owl
  mappings:
    aberowl: EPO
    biocontext: EPO
    bioportal: EPO
    obofoundry: epo
    ontobee: EPO
  obofoundry:
    deprecated: true
    description: An ontology designed to support the semantic annotation of epidemiology
      resources
    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
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 (BioPortal ID: EpSO) is an application ontology
      developed to support epilepsy research, patient care, and health system management.
      The updated version of the Epilepsy Ontology adds neuropathology terms, including
      immunohistochemistry, microscopy, anatomical description, and referential mappings
      to the ILAE 2017 classification of seizure types. This work is co-funded by
      the International League Against Epilepsy (ILAE), which also retains intellectual
      ownership of the ontology, together with the Case Western Reserve University
      and collaborating institutions. Contact: satya.sahoo@case.edu'
    homepage: https://bmhinformatics.case.edu/
    name: Epilepsy and Seizure Ontology
    prefix: EPSO
    publication: https://bmhinformatics.case.edu/
    version: '2.1'
  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. '
    id: '265'
    name: Epilepsy and Seizure Ontology
    prefix: FAIRsharing.ttprgy
    publications:
    - doi: 10.1136/amiajnl-2013-001696
      pubmed_id: null
      title: 'Epilepsy and seizure ontology: towards an epilepsy informatics infrastructure
        for clinical research and patient care'
    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}$
  uri_format: http://www.case.edu/EpilepsyOntology.owl#$1
erm:
  cheminf:
    description: Identifier used by the European Registry of Materials (https://nanocommons.github.io/identifiers/).
    name: European Registry of Materials
    obsolete: false
    prefix: 000569
  contact:
    email: egon.willighagen@gmail.com
    github: egonw
    name: Egon Willighagen
    orcid: 0000-0001-7542-0286
  download_rdf: https://nanocommons.github.io/identifiers/registry
  mappings:
    cheminf: 000569
    miriam: erm
    n2t: erm
  miriam:
    deprecated: false
    description: The European Registry of Materials is a simple registry with the
      sole purpose to mint material identifiers to be used by research projects throughout
      the life cycle of their project.
    homepage: https://nanocommons.github.io/identifiers/
    id: '00000763'
    name: European Registry of Materials
    namespaceEmbeddedInLui: false
    pattern: ^ERM[0-9]{8}$
    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
  publications:
  - doi: 10.1186/s13321-022-00614-7
    pmc: null
    pubmed: null
    title: 'European Registry of Materials: global, unique identifiers for (undisclosed)
      nanomaterials'
    year: null
  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:
    is_identifiers: false
    is_obo: true
    prefix: ERO
    uri_format: http://purl.obolibrary.org/obo/ERO_$1
  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
    publication: http://code.google.com/p/eagle-i/wiki/Publications
    version: '2013-08-02'
  example: '0001655'
  fairsharing:
    abbreviation: ERO
    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 Prot\xE9g\xE9. 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."
    id: '1166'
    name: eagle-i Research Resource Ontology
    prefix: FAIRsharing.nwgynk
    publications:
    - doi: 10.1109/JCDL.2017.7991571
      pubmed_id: 29599662
      title: 'Automating data citation: the eagle-i experience.'
    - doi: 10.1093/database/bar067
      pubmed_id: 22434835
      title: 'Research resources: curating the new eagle-i discovery system.'
    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.
    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}$
  publications:
  - 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: PMC5868434
    pubmed: '29599662'
    title: 'Automating data citation: the eagle-i experience.'
    year: 2017
erv:
  biocontext:
    is_identifiers: true
    is_obo: false
    prefix: ERV
    uri_format: http://identifiers.org/erv/$1
  mappings:
    biocontext: ERV
    miriam: erv
    n2t: erv
  miriam:
    deprecated: false
    description: Endogenous retroviruses (ERVs) are common in vertebrate genomes;
      a typical mammalian genome contains tens to hundreds of thousands of ERV elements.
      Most ERVs are evolutionarily old and have accumulated multiple mutations, playing
      important roles in physiology and disease processes. The Human Endogenous Retrovirus
      Database (hERV) is compiled from the human genome nucleotide sequences obtained
      from Human Genome Projects, and screens those sequences for hERVs, whilst continuously
      improving classification and characterization of retroviral families. It provides
      access to individual reconstructed HERV elements, their sequence, structure
      and features.
    homepage: https://herv.img.cas.cz/
    id: 00000619
    name: Human Endogenous Retrovirus Database
    namespaceEmbeddedInLui: false
    pattern: ^[A-Za-z0-9\-\_]+$
    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
estdab:
  cellosaurus:
    category: Cell line databases/resources
    homepage: https://www.ebi.ac.uk/ipd/estdab/
    name: European Searchable Tumour Line Database
    prefix: ESTDAB
    uri_format: https://www.ebi.ac.uk/cgi-bin/ipd/estdab/print_cell.cgi?$1
  comment: Website is dead
  deprecated: true
  example: '046'
  mappings:
    cellosaurus: ESTDAB
  pattern: ^\d{3}$
  uri_format: https://www.ebi.ac.uk/cgi-bin/ipd/estdab/print_cell.cgi?ESTDAB-$1
eu89h:
  biocontext:
    is_identifiers: true
    is_obo: false
    prefix: EU89H
    uri_format: http://identifiers.org/eu89h/$1
  mappings:
    biocontext: EU89H
    miriam: eu89h
    n2t: eu89h
  miriam:
    deprecated: false
    description: The JRC Data Catalogue gives access to the multidisciplinary data
      produced and maintained by the Joint Research Centre, the European Commission's
      in-house science service providing independent scientific advice and support
      to policies of the European Union.
    homepage: http://data.jrc.ec.europa.eu/
    id: '00000644'
    name: JRC Data Catalogue
    namespaceEmbeddedInLui: false
    pattern: ^[a-z0-9\-_]+$
    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
euclinicaltrials:
  biocontext:
    is_identifiers: true
    is_obo: false
    prefix: EUCLINICALTRIALS
    uri_format: http://identifiers.org/euclinicaltrials/$1
  mappings:
    biocontext: EUCLINICALTRIALS
    miriam: euclinicaltrials
    n2t: euclinicaltrials
  miriam:
    deprecated: false
    description: "The EU Clinical Trials Register contains information on clinical\
      \ trials conducted in the European Union (EU), or the European Economic Area\
      \ (EEA) which started after 1 May 2004.\r\nIt also includes trials conducted\
      \ outside these areas if they form part of a paediatric investigation plan (PIP),\
      \ or are sponsored by a marketing authorisation holder, and involve the use\
      \ of a medicine in the paediatric population."
    homepage: https://www.clinicaltrialsregister.eu/
    id: '00000536'
    name: EU Clinical Trials
    namespaceEmbeddedInLui: false
    pattern: ^\d{4}\-\d{6}\-\d{2}$
    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
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/16/eupath.owl
    homepage: https://github.com/VEuPathDB-ontology/VEuPathDB-ontology
    name: VEuPathDB ontology
    prefix: EUPATH
  biocontext:
    is_identifiers: false
    is_obo: true
    prefix: EUPATH
    uri_format: http://purl.obolibrary.org/obo/EUPATH_$1
  bioportal:
    contact:
      email: jiezheng@pennmedicine.upenn.edu
      name: Jie Zheng
    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
    publication: https://pdfs.semanticscholar.org/888e/a51dbb138122d39c42f863f2a1ada7976db4.pdf
    version: '2022-08-12'
  example: '0010316'
  fairsharing:
    abbreviation: VEuPathDB
    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
      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.
    id: '1484'
    name: Eukaryotic Pathogen, Host & Vector Genomics Resource Ontology
    prefix: FAIRsharing.9rhr9j
    publications: []
    subjects:
    - Functional Genomics
    - Biomedical Science
    - Epidemiology
    - Population Genetics
  mappings:
    aberowl: EUPATH
    biocontext: EUPATH
    bioportal: EUPATH
    fairsharing: FAIRsharing.9rhr9j
    obofoundry: eupath
    ols: eupath
    ontobee: EUPATH
  obofoundry:
    appears_in:
    - scdo
    contact: jiezheng@pennmedicine.upenn.edu
    contact.github: zhengj2007
    contact.label: Jie Zheng
    contact.orcid: 0000-0002-2999-0103
    deprecated: false
    description: An ontology is developed to support Eukaryotic Pathogen, Host & Vector
      Genomics Resource (VEuPathDB; https://veupathdb.org).
    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/
    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: http://purl.obolibrary.org/obo/eupath.owl
    homepage: https://github.com/VEuPathDB-ontology/VEuPathDB-ontology
    name: VEuPathDB Ontology
    prefix: eupath
    version: '2022-06-08'
    version.iri: http://purl.obolibrary.org/obo/eupath/2022-06-08/eupath.owl
  ontobee:
    library: Library
    name: VEuPathDB ontology
    prefix: EUPATH
  pattern: ^\d{7}$
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
  proprietary: true
ev:
  appears_in:
  - cl
  biocontext:
    is_identifiers: false
    is_obo: true
    prefix: EV
    uri_format: http://purl.obolibrary.org/obo/EV_$1
  mappings:
    biocontext: EV
    obofoundry: ev
    prefixcommons: evoc
  obofoundry:
    contact: evoc@sanbi.ac.za
    contact.label: eVOC mailing list
    deprecated: true
    homepage: http://www.evocontology.org/
    name: eVOC (Expressed Sequence Annotation for Humans)
    prefix: ev
  prefixcommons:
    bioportal: '1013'
    description: Provides structured controlled vocabularies for the annotation of
      expressed sequences with respect to anatomical system, cell type, developmental
      stage, experimental technique, microarray platform, pathology, pooling, tissue
      preparation and treatment.
    example: EV_0100011
    homepage: http://www.evocontology.org/
    keywords:
    - obo
    - anatomy
    - cell
    - development
    - experiment
    name: eVOC (Expressed Sequence Annotation for Humans)
    pattern: ^EV_\d+$
    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
  references:
  - https://genomebiology.biomedcentral.com/articles/10.1186/gb-2007-8-10-r229
exac.gene:
  biocontext:
    is_identifiers: true
    is_obo: false
    prefix: EXAC.GENE
    uri_format: http://identifiers.org/exac.gene/$1
  mappings:
    biocontext: EXAC.GENE
    miriam: exac.gene
    n2t: exac.gene
  miriam:
    deprecated: false
    description: The Exome Aggregation Consortium (ExAC) is a coalition of investigators
      seeking to aggregate and harmonize exome sequencing data from a variety of large-scale
      sequencing projects, and to make summary data available for the wider scientific
      community. The data pertains to unrelated individuals sequenced as part of various
      disease-specific and population genetic studies and serves as a reference set
      of allele frequencies for severe disease studies. This collection references
      gene information.
    homepage: http://exac.broadinstitute.org/
    id: 00000548
    name: ExAC Gene
    namespaceEmbeddedInLui: false
    pattern: ^ENSG\d{11}$
    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
exac.transcript:
  biocontext:
    is_identifiers: true
    is_obo: false
    prefix: EXAC.TRANSCRIPT
    uri_format: http://identifiers.org/exac.transcript/$1
  mappings:
    biocontext: EXAC.TRANSCRIPT
    miriam: exac.transcript
    n2t: exac.transcript
  miriam:
    deprecated: false
    description: The Exome Aggregation Consortium (ExAC) is a coalition of investigators
      seeking to aggregate and harmonize exome sequencing data from a variety of large-scale
      sequencing projects, and to make summary data available for the wider scientific
      community. The data pertains to unrelated individuals sequenced as part of various
      disease-specific and population genetic studies and serves as a reference set
      of allele frequencies for severe disease studies. This collection references
      transcript information.
    homepage: http://exac.broadinstitute.org/
    id: '00000547'
    name: ExAC Transcript
    namespaceEmbeddedInLui: false
    pattern: ^ENST\d{11}$
    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
exac.variant:
  biocontext:
    is_identifiers: true
    is_obo: false
    prefix: EXAC.VARIANT
    uri_format: http://identifiers.org/exac.variant/$1
  mappings:
    biocontext: EXAC.VARIANT
    miriam: exac.variant
    n2t: exac.variant
  miriam:
    deprecated: false
    description: The Exome Aggregation Consortium (ExAC) is a coalition of investigators
      seeking to aggregate and harmonize exome sequencing data from a variety of large-scale
      sequencing projects, and to make summary data available for the wider scientific
      community. The data pertains to unrelated individuals sequenced as part of various
      disease-specific and population genetic studies and serves as a reference set
      of allele frequencies for severe disease studies. This collection references
      variant information.
    homepage: http://exac.broadinstitute.org/
    id: '00000541'
    name: ExAC Variant
    namespaceEmbeddedInLui: false
    pattern: ^\d{1,2}\-\d+\-[GATC]\-[GATC]$
    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
exo:
  aberowl:
    description: Vocabularies for describing exposure data to inform understanding
      of environmental health.
    download_owl: http://aber-owl.net/media/ontologies/EXO/15/exo.owl
    homepage: https://github.com/CTDbase/exposure-ontology
    name: Exposure ontology
    prefix: EXO
  biocontext:
    is_identifiers: false
    is_obo: true
    prefix: EXO
    uri_format: http://purl.obolibrary.org/obo/EXO_$1
  biolink:
    is_identifiers: false
    is_obo: true
    prefix: ExO
    uri_format: http://purl.obolibrary.org/obo/ExO_$1
  bioportal:
    contact:
      email: cjmattin@ncsu.edu
      name: Carolyn Mattingly
    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
    name: Exposure Ontology
    prefix: EXO
  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.
    id: '512'
    name: Exposure Ontology
    prefix: FAIRsharing.6hna78
    publications:
    - doi: 10.1021/es2033857
      pubmed_id: 22324457
      title: 'Providing the missing link: the exposure science ontology ExO.'
    subjects:
    - Environmental Science
    - Epigenetics
    - Toxicology
  mappings:
    aberowl: EXO
    biocontext: EXO
    biolink: ExO
    bioportal: EXO
    fairsharing: FAIRsharing.6hna78
    obofoundry: exo
    ols: exo
    ontobee: ExO
  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.
    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: http://purl.obolibrary.org/obo/exo.owl
    homepage: https://github.com/CTDbase/exposure-ontology
    name: Exposure ontology (ExO)
    prefix: exo
    version: '2022-06-29'
    version.iri: http://purl.obolibrary.org/obo/exo/releases/2022-06-29/exo.owl
  ontobee:
    library: Library
    name: Exposure ontology
    prefix: ExO
  pattern: ^\d{7}$
  publications:
  - doi: 10.1021/es2033857
    pmc: PMC3314380
    pubmed: '22324457'
    title: 'Providing the missing link: the exposure science ontology ExO.'
    year: 2012
  synonyms:
  - ExO
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.
  example: d4e2515
  fairsharing:
    abbreviation: FaBiO
    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.
    id: '3628'
    name: FRBR-aligned Bibliographic Ontology
    prefix: FAIRsharing.2f3180
    publications:
    - doi: 10.1016/j.websem.2012.08.001
      pubmed_id: null
      title: 'FaBiO and CiTO: Ontologies for describing bibliographic resources and
        citations'
    subjects:
    - Subject Agnostic
  homepage: https://github.com/sparontologies/fabio
  mappings:
    aberowl: FaBiO
    biolink: fabio
    fairsharing: FAIRsharing.2f3180
  name: FaBiO, the FRBR-aligned Bibliographic Ontology
  providers:
  - code: rdf
    description: A persistent URL for FaBiO
    homepage: https://github.com/sparontologies/fabio
    name: FABIO PURL
    uri_format: http://purl.org/spar/fabio/$1
  repository: https://github.com/sparontologies/fabio
  uri_format: https://sparontologies.github.io/fabio/current/fabio.html#$1
facebase:
  biocontext:
    is_identifiers: true
    is_obo: false
    prefix: FACEBASE
    uri_format: http://identifiers.org/facebase/$1
  fairsharing:
    abbreviation: FaceBase
    description: FaceBase is a collaborative NIDCR-funded consortium to generate data
      in support of advancing research into craniofacial development and malformation.
      It serves as a community resource by generating large datasets of a variety
      of types and making them available to the wider research community via this
      website. Practices emphasize a comprehensive and multidisciplinary approach
      to understanding the developmental processes that create the face. The data
      offered spotlights high-throughput genetic, molecular, biological, imaging and
      computational techniques. One of the missions of this consortium is to facilitate
      cooperation and collaboration between projects.
    id: '2254'
    name: FaceBase
    prefix: FAIRsharing.mqvqde
    subjects:
    - Anatomy
    - Medicine
    - Epigenetics
    - Genetics
    - Developmental Biology
  mappings:
    biocontext: FACEBASE
    fairsharing: FAIRsharing.mqvqde
    miriam: facebase
    n2t: facebase
    re3data: r3d100013263
  miriam:
    deprecated: false
    description: FaceBase is a collaborative NIDCR-funded consortium to generate data
      in support of advancing research into craniofacial development and malformation.
      It serves as a community resource by generating large datasets of a variety
      of types and making them available to the wider research community via this
      website. Practices emphasize a comprehensive and multidisciplinary approach
      to understanding the developmental processes that create the face. The data
      offered spotlights high-throughput genetic, molecular, biological, imaging and
      computational techniques. One of the missions of this consortium is to facilitate
      cooperation and collaboration between projects.
    homepage: https://www.facebase.org
    id: '00000642'
    name: FaceBase Data Repository
    namespaceEmbeddedInLui: false
    pattern: ^FB\d{8}$
    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
  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.
    homepage: https://www.facebase.org
    name: FaceBase
    prefix: r3d100013263
    xrefs:
      fairsharing: FAIRsharing.mqvqde
      nlx: '151372'
      scr: 005998
fairsharing:
  biocontext:
    is_identifiers: true
    is_obo: false
    prefix: FAIRSHARING
    uri_format: http://identifiers.org/fairsharing/$1
  fairsharing:
    abbreviation: FAIRsharing
    description: FAIRsharing is a FAIR-supporting resource that provides an informative
      and educational registry on data standards, databases, repositories and policy,
      alongside search and visualization tools and services that interoperate with
      other FAIR-enabling resources. FAIRsharing guides consumers to discover, select
      and use standards, databases, repositories and policy with confidence, and producers
      to make their resources more discoverable, more widely adopted and cited. Each
      record in FAIRsharing is curated in collaboration with the maintainers of the
      resource themselves, ensuring that the metadata in the FAIRsharing registry
      is accurate and timely. Every record is manually reviewed at least once a year.
      Records can be collated into collections, based on a project, society or organisation,
      or Recommendations, where they are collated around a policy, such as a journal
      or funder data policy.
    id: '2521'
    name: FAIRsharing
    prefix: FAIRsharing.2abjs5
    subjects:
    - Environmental Science
    - Humanities
    - Natural Science
    - Earth Science
    - Agriculture
    - Life Science
    - Biomedical Science
  mappings:
    biocontext: FAIRSHARING
    fairsharing: FAIRsharing.2abjs5
    miriam: fairsharing
    n2t: fairsharing
    re3data: r3d100010142
  miriam:
    deprecated: false
    description: The web-based FAIRSharing catalogues aim to centralize bioscience
      data policies, reporting standards and links to other related portals. This
      collection references bioinformatics data exchange standards, which includes
      'Reporting Guidelines', Format Specifications and Terminologies.
    homepage: https://fairsharing.org/
    id: '00000364'
    name: FAIRsharing
    namespaceEmbeddedInLui: false
    pattern: ^bsg-[dscp]?\d{6}$
    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
  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.
    homepage: https://fairsharing.org/
    name: FAIRsharing
    prefix: r3d100010142
    synonyms:
    - 'formerly: biosharing'
    xrefs:
      fairsharing: FAIRsharing.2abjs5
      miriam: '00100463'
      nlx: '143602'
      omics: '17902'
      scr: '004177'
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: https://github.com/JervenBolleman/FALDO
    license: CC0 1.0
    name: Feature Annotation Location Description Ontology
    prefix: FALDO
    publication: doi.org/10.1186/s13326-016-0067-z
    version: Created at the Biohackathon 2012 and 2013
  biocontext:
    is_identifiers: false
    is_obo: false
    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
    publication: 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 \u201C\
      omics\u201D 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."
    id: '478'
    name: Feature Annotation Location Description Ontology
    prefix: FAIRsharing.haxp7g
    publications:
    - doi: 10.1186/s13326-016-0067-z
      pubmed_id: 27296299
      title: 'FALDO: a semantic standard for describing the location of nucleotide
        and protein feature annotation.'
    subjects:
    - Genetics
  homepage: http://biohackathon.org/resource/faldo
  mappings:
    aberowl: FALDO
    agroportal: FALDO
    biocontext: faldo
    bioportal: FALDO
    fairsharing: FAIRsharing.haxp7g
  name: 'Feature Annotation Location Description Ontology '
  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
fao:
  aberowl:
    description: A structured controlled vocabulary for the anatomy of fungi.
    download_owl: http://aber-owl.net/media/ontologies/FAO/28/fao.owl
    homepage: https://github.com/obophenotype/fungal-anatomy-ontology/
    name: Fungal gross anatomy
    prefix: FAO
  biocontext:
    is_identifiers: false
    is_obo: true
    prefix: FAO
    uri_format: http://purl.obolibrary.org/obo/FAO_$1
  bioportal:
    contact:
      email: dinglis@stanford.edu
      name: Diane Inglis
    description: A structured controlled vocabulary for the anatomy of fungi.
    homepage: https://github.com/obophenotype/fungal-anatomy-ontology
    name: Fungal Gross Anatomy Ontology
    prefix: FAO
  example: '0000001'
  fairsharing:
    abbreviation: FAO
    description: A structured controlled vocabulary for the anatomy of fungi.
    id: '168'
    name: Fungal Gross Anatomy Ontology
    prefix: FAIRsharing.xs6t67
    publications: []
    subjects:
    - Anatomy
    - Life Science
    - Microbiology
  mappings:
    aberowl: FAO
    biocontext: FAO
    bioportal: FAO
    fairsharing: FAIRsharing.xs6t67
    obofoundry: fao
    ols: fao
    ontobee: FAO
    prefixcommons: fao
  obofoundry:
    contact: vw253@cam.ac.uk
    contact.github: ValWood
    contact.label: Val Wood
    contact.orcid: 0000-0001-6330-7526
    deprecated: false
    description: A structured controlled vocabulary for the anatomy of fungi.
    download.obo: http://purl.obolibrary.org/obo/fao.obo
    download.owl: http://purl.obolibrary.org/obo/fao.owl
    homepage: https://github.com/obophenotype/fungal-anatomy-ontology/
    license: CC0 1.0
    license.url: http://creativecommons.org/publicdomain/zero/1.0/
    name: Fungal gross anatomy
    preferredPrefix: FAO
    prefix: fao
    repository: https://github.com/obophenotype/fungal-anatomy-ontology
  ols:
    description: A structured controlled vocabulary for the anatomy of fungi.
    download: http://purl.obolibrary.org/obo/fao.owl
    homepage: https://github.com/obophenotype/fungal-anatomy-ontology/
    name: Fungal gross anatomy
    prefix: fao
    version: '2020-05-07'
    version.iri: http://purl.obolibrary.org/obo/fao/releases/2020-05-07/fao.owl
  ontobee:
    library: Library
    name: Fungal gross anatomy
    prefix: FAO
  pattern: ^\d{7}$
  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
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:
    is_identifiers: false
    is_obo: true
    prefix: FBbi
    uri_format: http://purl.obolibrary.org/obo/FBbi_$1
  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.
    id: '33'
    name: Biological Imaging methods Ontology
    prefix: FAIRsharing.ny3z9j
    publications: []
    subjects:
    - Life Science
    - Biomedical Science
  mappings:
    aberowl: FBbi
    biocontext: FBbi
    bioportal: FBbi
    fairsharing: FAIRsharing.ny3z9j
    obofoundry: fbbi
    ols: fbbi
    ontobee: FBBI
    prefixcommons: fbbi
  obofoundry:
    contact: wawong@gmail.com
    contact.github: wawong
    contact.label: Willy Wong
    contact.orcid: 0000-0002-8841-5870
    deprecated: false
    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/
    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: http://purl.obolibrary.org/obo/fbbi.owl
    homepage: http://cellimagelibrary.org/
    name: Biological Imaging Methods Ontology
    prefix: fbbi
    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+$
  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
fbbt:
  aberowl:
    description: An ontology representing the gross anatomy of Drosophila melanogaster.
    download_owl: http://aber-owl.net/media/ontologies/FBBT/30/fbbt.owl
    homepage: http://purl.obolibrary.org/obo/fbbt
    name: Drosophila gross anatomy
    prefix: FBBT
  biocontext:
    is_identifiers: false
    is_obo: true
    prefix: FBbt
    uri_format: http://purl.obolibrary.org/obo/FBbt_$1
  bioportal:
    name: Drosophila Gross Anatomy Ontology
    prefix: FB-BT
  example: 00007294
  fairsharing:
    abbreviation: FBbt
    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.
    id: '28'
    name: Drosophila anatomy ontology
    prefix: FAIRsharing.y2qkst
    publications:
    - doi: 10.1093/nar/gkj068
      pubmed_id: 16381917
      title: 'FlyBase: anatomical data, images and queries.'
    - doi: 10.1186/2041-1480-4-32
      pubmed_id: 24139062
      title: The Drosophila anatomy ontology
    - 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
    subjects:
    - Anatomy
    - Developmental Biology
    - Life Science
  go:
    homepage: http://flybase.org/
    name: Drosophila gross anatomy
    prefix: FBbt
    uri_format: http://flybase.org/cgi-bin/fbcvq.html?query=FBbt:$1
  mappings:
    aberowl: FBBT
    biocontext: FBbt
    bioportal: FB-BT
    fairsharing: FAIRsharing.y2qkst
    go: FBbt
    obofoundry: fbbt
    ols: fbbt
    ontobee: FBBT
    prefixcommons: fbbt
  obofoundry:
    contact: cp390@cam.ac.uk
    contact.github: Clare72
    contact.label: Clare Pilgrim
    contact.orcid: 0000-0002-1373-1705
    deprecated: false
    description: An ontology representing the gross anatomy of Drosophila melanogaster.
    download.json: http://purl.obolibrary.org/obo/fbbt.json
    download.obo: http://purl.obolibrary.org/obo/fbbt.obo
    download.owl: http://purl.obolibrary.org/obo/fbbt.owl
    homepage: http://purl.obolibrary.org/obo/fbbt
    license: CC BY 4.0
    license.url: http://creativecommons.org/licenses/by/4.0/
    name: Drosophila gross anatomy
    preferredPrefix: FBbt
    prefix: fbbt
    publications:
    - id: https://www.ncbi.nlm.nih.gov/pubmed/24139062
      preferred: true
      title: The Drosophila anatomy ontology
    - id: https://www.ncbi.nlm.nih.gov/pubmed/22402613
      title: A strategy for building neuroanatomy ontologies
    - id: https://www.ncbi.nlm.nih.gov/pubmed/22180411
      title: The Virtual Fly Brain Browser and Query Interface
    - id: https://www.ncbi.nlm.nih.gov/pubmed/16381917
      title: 'FlyBase: anatomical data, images and queries'
    repository: https://github.com/FlyBase/drosophila-anatomy-developmental-ontology
  ols:
    description: An ontology of Drosophila melanogaster anatomy.
    download: http://purl.obolibrary.org/obo/fbbt.owl
    homepage: http://purl.obolibrary.org/obo/fbbt
    name: Drosophila Anatomy Ontology (DAO)
    prefix: fbbt
    version: '2022-06-09'
    version.iri: http://purl.obolibrary.org/obo/fbbt/releases/2022-06-09/fbbt.owl
  ontobee:
    library: Library
    name: Drosophila gross anatomy
    prefix: FBBT
  part_of: flybase
  pattern: ^\d{8}$
  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: 10.1093/nar/gkj068
    pmc: PMC1347431
    pubmed: '16381917'
    title: 'FlyBase: anatomical data, images and queries.'
    year: 2006
  - 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: '22402613'
    title: A strategy for building neuroanatomy ontologies.
    year: 2012
  - doi: 10.1186/2041-1480-4-32
    pmc: PMC4015547
    pubmed: '24139062'
    title: The Drosophila anatomy ontology.
    year: 2013
  synonyms:
  - FBbt
  - FBbt_root
  uri_format: https://flybase.org/cgi-bin/cvreport.pl?id=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/23/fbcv.owl
    homepage: http://purl.obolibrary.org/obo/fbcv
    name: FlyBase Controlled Vocabulary
    prefix: FBCV
  biocontext:
    is_identifiers: false
    is_obo: true
    prefix: FBcv
    uri_format: http://purl.obolibrary.org/obo/FBcv_$1
  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.
    homepage: http://purl.obolibrary.org/obo/fbcv
    name: FlyBase Controlled Vocabulary
    prefix: FB-CV
    version: '2022-08-11'
  download_obo: https://raw.githubusercontent.com/FlyBase/flybase-controlled-vocabulary/master/fbcv.obo
  example: 0000586
  fairsharing:
    abbreviation: FBcv
    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.
    id: '147'
    name: FlyBase Controlled Vocabulary
    prefix: FAIRsharing.6tgyxf
    publications:
    - doi: 10.1186/2041-1480-4-30
      pubmed_id: 24138933
      title: The Drosophila phenotype ontology
    subjects:
    - Life Science
  mappings:
    aberowl: FBCV
    biocontext: FBcv
    bioportal: FB-CV
    fairsharing: FAIRsharing.6tgyxf
    obofoundry: fbcv
    ols: fbcv
    ontobee: FBCV
    prefixcommons: fbcv
  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.
    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 miscellaneous ontology of terms used for curation in FlyBase, including
      the DPO.
    download: http://purl.obolibrary.org/obo/fbcv.owl
    homepage: http://purl.obolibrary.org/obo/fbcv
    name: FlyBase Controlled Vocabulary (FBcv)
    prefix: fbcv
    version: '2022-06-09'
    version.iri: http://purl.obolibrary.org/obo/fbcv/releases/2022-06-09/fbcv.owl
  ontobee:
    library: Library
    name: FlyBase Controlled Vocabulary
    prefix: FBCV
  part_of: flybase
  pattern: ^\d{7}$
  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
  synonyms:
  - FBcv
fbdv:
  aberowl:
    description: A structured controlled vocabulary of the development of Drosophila
      melanogaster.
    download_owl: http://aber-owl.net/media/ontologies/FBDV/25/fbdv.owl
    homepage: http://purl.obolibrary.org/obo/fbdv
    name: Drosophila development
    prefix: FBDV
  biocontext:
    is_identifiers: false